A photochemical crosslinking technology for tissue engineering: enhancement of the physico-chemical properties of collagen-based scaffolds

NASA Astrophysics Data System (ADS)

Chan, Barbara P.

2005-04-01

Collagen gel is a natural biomaterial commonly used in tissue engineering because of its close resemblance to nature, negligible immunogenecity and excellent biocompatibility. However, unprocessed collagen gel is mechanically weak, highly water binding and vulnerable to chemical and enzymatic attacks that limits its use in tissue engineering in particular tissues for weight-bearing purposes. The current project aimed to strengthen and stabilize collagen scaffolds using a photochemical crosslinking technique. Photochemical crosslinking is rapid, efficient, non-thermal and does not involve toxic chemicals, comparing with other crosslinking methods such as glutaraldehyde and gamma irradiation. Collagen scaffolds were fabricated using rat-tail tendon collagen. An argon laser was used to process the collagen gel after equilibrating with a photosensitizing reagent. Scanning electronic microscope was used to characterize the surface and cross-sectional morphology of the membranes. Physico-chemical properties of the collagen scaffolds such as water-binding capacity, mechanical properties and thermostability were studied. Photochemical crosslinking significantly reduced the water-binding capacity, a parameter inversely proportional to the extent of crosslinking, of collagen scaffolds. Photochemical crosslinking also significantly increased the ultimate stress and tangent modulus at 90% of the rupture strain of the collagen scaffolds. Differential scanning calorimetry analysis showed a significantly higher shrinkage temperature and absence of the denaturation peak during the thermoscan comparing with the controls. This means greater thermostability in the photochemically crosslinked collagen scaffolds. This study demonstrates that the photochemical crosslinking technology is able to enhance the physicochemical propterties of collagen scaffolds by strengthening, stabilizing and controlling the swelling ratio of the collagen scaffolds so as to enable their use for tissue engineering.

Physicochemical and biological characterization of SB2, a biosimilar of Remicade® (infliximab)

PubMed Central

Hong, Juyong; Lee, Yuhwa; Lee, Changsoo; Eo, Suhyeon; Kim, Soyeon; Park, Seungkyu; Seo, Donghyuck; Lee, Youngji; Yeon, Soojeong; Bou-Assaf, George; Sosic, Zoran; Zhang, Wei

2017-01-01

ABSTRACT A biosimilar is a biological medicinal product that contains a version of the active substance of an already authorized original biological medicinal product. Biosimilarity to the reference product (RP) in terms of quality characteristics, such as physicochemical and biological properties, safety, and efficacy, based on a comprehensive comparability exercise needs to be established. SB2 (Flixabi® and Renflexis®) is a biosimilar to Remicade® (infliximab). The development of SB2 was performed in accordance with relevant guidelines of the International Conference on Harmonisation, the European Medicines Agency, and the United States Food and Drug Administration. To determine whether critical quality attributes meet quality standards, an extensive characterization test was performed with more than 80 lots of EU- and US-sourced RP. The physicochemical characterization study results revealed that SB2 was similar to the RP. Although a few differences in physicochemical attributes were observed, the evidence from the related literature, structure-activity relationship studies, and comparative biological assays showed that these differences were unlikely to be clinically meaningful. The biological characterization results showed that SB2 was similar to the RP in terms of tumor necrosis factor–α (TNF-α) binding and TNF-α neutralization activities as a main mode of action. SB2 was also similar in Fc-related biological activities including antibody-dependent cell-mediated cytotoxicity, complement-dependent cytotoxicity, neonatal Fc receptor binding, C1q binding, and Fc gamma receptor binding activities. These analytical findings support that SB2 is similar to the RP and also provide confidence of biosimilarity in terms of clinical safety and efficacy. PMID:28005456

Synthesis of mouse centromere-targeted polyamides and physico-chemical studies of their interaction with the target double-stranded DNA.

PubMed

Nozeret, Karine; Bonan, Marc; Yarmoluk, Serguiy M; Novopashina, Darya S; Boutorine, Alexandre S

2015-09-01

Synthetic minor groove-binding pyrrole-imidazole polyamides labeled by fluorophores are promising candidates for fluorescence imaging of double-stranded DNA in isolated chromosomes or fixed and living cells. We synthesized nine hairpin and two head-to-head tandem polyamides targeting repeated sequences from mouse major satellites. Their interaction with synthetic target dsDNA has been studied by physico-chemical methods in vitro before and after coupling to various fluorophores. Great variability in affinities and fluorescence properties reveals a conclusion that these properties do not only rely on recognition rules, but also on other known and unknown structural factors. Individual testing of each probe is needed before cellular applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Exploring high-affinity binding properties of octamer peptides by principal component analysis of tetramer peptides.

PubMed

Kume, Akiko; Kawai, Shun; Kato, Ryuji; Iwata, Shinmei; Shimizu, Kazunori; Honda, Hiroyuki

2017-02-01

To investigate the binding properties of a peptide sequence, we conducted principal component analysis (PCA) of the physicochemical features of a tetramer peptide library comprised of 512 peptides, and the variables were reduced to two principal components. We selected IL-2 and IgG as model proteins and the binding affinity to these proteins was assayed using the 512 peptides mentioned above. PCA of binding affinity data showed that 16 and 18 variables were suitable for localizing IL-2 and IgG high-affinity binding peptides, respectively, into a restricted region of the PCA plot. We then investigated whether the binding affinity of octamer peptide libraries could be predicted using the identified region in the tetramer PCA. The results show that octamer high-affinity binding peptides were also concentrated in the tetramer high-affinity binding region of both IL-2 and IgG. The average fluorescence intensity of high-affinity binding peptides was 3.3- and 2.1-fold higher than that of low-affinity binding peptides for IL-2 and IgG, respectively. We conclude that PCA may be used to identify octamer peptides with high- or low-affinity binding properties from data from a tetramer peptide library. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Physicochemical and tablet properties of Cyperus alulatus rhizomes starch granules.

PubMed

Paramakrishnan, N; Jha, S; Kumar, K Jayaram

2015-05-01

The starch extracted from rhizomes of Cyperus alulatus (CA) was characterized for its physicochemical, morphological and tableting properties. Rhizomes of CA yield a significant quantity of starch granules (CASG) i.e., 11.93%. CASG was characterized in terms of moisture, ash and amylose contents, solubility and swelling power, paste clarity and water retention capacity. The swelling power was found to be significantly improved with the increase in temperature. Scanning electron micrographs revealed that the granule's surface was smooth, the granules were spherical, mostly round, disc like, and the size range was 6.65-12.13 μm. Finger print region in FTIR spectra confirmed its carbohydrate nature. The evaluated micromeritic properties of extracted granule's bulk density, tapped density, Carr's index, Hausner ratio, true density and porosity render unique practicability of CASG being used as an adjuvant in pharmaceutical solid dosage forms. Tablets prepared by using CASG showed higher mechanical strength and more disintegration time, which depicted the characteristic binding nature of the starch granules. As CASG is imparting better binding properties in less concentration and also it can be used in combination with the established starches to get the synergistic effect; this starch can be used commercially in the tablet preparation. Copyright © 2015 Elsevier B.V. All rights reserved.

Large scale analysis of protein-binding cavities using self-organizing maps and wavelet-based surface patches to describe functional properties, selectivity discrimination, and putative cross-reactivity.

PubMed

Kupas, Katrin; Ultsch, Alfred; Klebe, Gerhard

2008-05-15

A new method to discover similar substructures in protein binding pockets, independently of sequence and folding patterns or secondary structure elements, is introduced. The solvent-accessible surface of a binding pocket, automatically detected as a depression on the protein surface, is divided into a set of surface patches. Each surface patch is characterized by its shape as well as by its physicochemical characteristics. Wavelets defined on surfaces are used for the description of the shape, as they have the great advantage of allowing a comparison at different resolutions. The number of coefficients to describe the wavelets can be chosen with respect to the size of the considered data set. The physicochemical characteristics of the patches are described by the assignment of the exposed amino acid residues to one or more of five different properties determinant for molecular recognition. A self-organizing neural network is used to project the high-dimensional feature vectors onto a two-dimensional layer of neurons, called a map. To find similarities between the binding pockets, in both geometrical and physicochemical features, a clustering of the projected feature vector is performed using an automatic distance- and density-based clustering algorithm. The method was validated with a small training data set of 109 binding cavities originating from a set of enzymes covering 12 different EC numbers. A second test data set of 1378 binding cavities, extracted from enzymes of 13 different EC numbers, was then used to prove the discriminating power of the algorithm and to demonstrate its applicability to large scale analyses. In all cases, members of the data set with the same EC number were placed into coherent regions on the map, with small distances between them. Different EC numbers are separated by large distances between the feature vectors. A third data set comprising three subfamilies of endopeptidases is used to demonstrate the ability of the algorithm to detect similar substructures between functionally related active sites. The algorithm can also be used to predict the function of novel proteins not considered in training data set. 2007 Wiley-Liss, Inc.

Effect of mineral elements on physicochemical properties of oxidised starches and generation of free radicals.

PubMed

Pietrzyk, Sławomir; Fortuna, Teresa; Królikowska, Karolina; Rogozińska, Ewelina; Labanowska, Maria; Kurdziel, Magdalena

2013-09-12

The objective of this study was to determine the effect of enrichment of oxidised starches with mineral compounds on their physicochemical properties and capability for free radical generation. Potato and spelt wheat starches were oxidised with sodium hypochlorite and, afterwards, modified with ions of potassium, magnesium and iron. The modified starches were analysed for: content of mineral elements, colour parameters (L*a*b*), water binding capacity solubility in water at temperature of 50 and 80 °C, and susceptibility to enzymatic hydrolysis with α-amylase. In addition, thermodynamic characteristics of gelatinisation was determined by differential scanning calorimetry (DSC), and the number and character of thermally generated free radicals was assayed using electron paramagnetic resonance (EPR). Based on the results achieved, it was concluded that the quantity of incorporated minerals and changes in the assayed physicochemical parameters depended not only on the botanical type of starch but also on the type of the incorporated mineral element. Copyright © 2013 Elsevier Ltd. All rights reserved.

Polymer sorbent with the properties of an artificial cholesterol receptor

NASA Astrophysics Data System (ADS)

Polyakova, I. V.; Ezhova, N. M.; Osipenko, A. A.; Pisarev, O. A.

2015-02-01

A cholesterol-imprinted polymer sorbent and the corresponding reticular control copolymer were synthesized from hydroxyethyl methacrylate and ethyleneglycol dimethacrylate. The sorption isotherms of cholesterol were analyzed using the generalized Langmuir and Freundlich equations. In the case of the imprinted reticular polymer, cholesterol sorption occurred on the energetically homogeneous binding centers, forming one monolayer, while the nonspecific sorption of cholesterol on the control copolymer occurred with energetically nonhomogeneous binding of the sorbate and depended on the physicochemical conditions of sorption.

Physicochemical properties of low sodium frankfurter with added walnut: effect of transglutaminase combined with caseinate, KCl and dietary fibre as salt replacers.

PubMed

Colmenero, F Jiménez; Ayo, M J; Carballo, J

2005-04-01

This study compares the effects of combinations of microbial transglutaminase (TGase) and various non-meat ingredients (caseinate, KCl and wheat fibre) used as salt replacers, with the effects of NaCl on the physicochemical properties (cooking loss, emulsion stability, texture and colour) of frankfurters with added walnuts. The combination of TGase with caseinate, KCl or fibre led to harder, springier and chewier (P<0.05) frankfurters with better water- and fat-binding properties (emulsion stability and cooking loss) (P<0.05) than those made with TGase only. Ranking of ingredient efficiency in combination with TGase showed that caseinate>KCl>fibre. Frankfurters with caseinate presented the highest lightness and the lowest redness values. Frankfurter with NaCl had a harder, springier and chewier gel/emulsion network with lower cooking loss than those NaCl free.

Binding of pyrene to aquatic and commercial humic substances: The role of molecular weight and aromaticity

USGS Publications Warehouse

Chin, Y.-P.; Aiken, G.R.; Danielsen, K.M.

1997-01-01

The binding of pyrene to a number of humic substances isolated from various aquatic sources and a commercial humic acid was measured using the solubility enhancement method. The humic materials used in this study were characterized by various spectroscopic and liquid chromatography methods. A strong correlation was observed between the pyrene binding coefficient, K(doc), and the molecular weights, molar absorptivities at 280 nm, and aromaticity of the aquatic humic substances. Binding of pyrene to the commercial humic acid, however, was significantly stronger and did not obey the relationships observed between K(doc) and the chemical properties of the aquatic humic substrates. These results suggest that the molecular weight and the aromatic content of the humic substrates exert influences on the binding of nonpolar and planar aromatic molecules and that the physicochemical properties of both humic materials and organic solutes are important in controlling the speciation of nonpolar organic contaminants in natural waters.

Effect of micronization on the physicochemical properties of insoluble dietary fiber from citrus (Citrus junos Sieb. ex Tanaka) pomace.

PubMed

Ye, Fayin; Tao, Bingbing; Liu, Jia; Zou, Yan; Zhao, Guohua

2016-04-01

The aim of this work was to study the effect of micronization (mechanical and jet grindings) on the physicochemical properties of the insoluble dietary fiber from citrus pomace in comparison with ordinary grinding. The results showed that micronization treatment effectively pulverized the IDF-CP powders to micron scale and significantly increased the soluble dietary fiber content (p < 0.05). Compared with mechanical grinding, jet grinding was more effective in size reduction and resulted in IDF-CP powders with narrower particle size distributions. Micronized IDF-CP powders had smaller particle size, smoother surface, higher fluidity, cation-exchange capacity, and metal cation binding capacity values, but lower water holding capacity, oil holding capacity, and swelling capacity values. These functional properties were significantly dependent on surface area and particle size (D0.5). The present study suggested that micronization treatments could modify functional properties of IDF-CP powders, which promotes their use in food applications. © The Author(s) 2015.

Physicochemical and immunologic characterization of low-molecular-weight allergoids of Dactylis glomerata pollen proteins.

PubMed

Cirković, T D; Bukilica, M N; Gavrović, M D; Vujcić, Z M; Petrović, S; Jankov, R M

1999-02-01

Orchard grass (Dactylis glomerata) pollen proteins were chemically modified by means of acid anhydrides (maleic and succinic anhydride) to obtain low-molecular-weight allergoids. Chemical modification in both cases led to the replacement of one positive charge (epsilon amino group of Lys) by one negative charge, yielding proteins with changed physicochemical properties in comparison to the native orchard grass-pollen proteins. Physicochemical characterization of derivatives was done by gel chromatography, SDS-PAGE, and isoelectric focusing. To examine the IgE-binding properties of these derivatives, we carried out immunoblotting. To examine the ability of derivatives to induce IgG production, we immunized rabbits. Skin prick testing with the allergoids was performed on 15 individuals allergic to orchard grass pollens and on two healthy subjects. It was shown that the modified proteins retain their original molecular weights, but change pI to more acidic values. In the case of allergoids, a strong reduction in IgE binding was found. Immunization of rabbits with allergoids showed that the derivatives retain the ability to induce IgG production, and that the antisera obtained in such a way react to native (unmodified) extract. The ability of derivatives to induce allergic reaction was significantly reduced. The patients (86.6%) included in our study exhibited less than 50% of native extract response. Among them, 53.3% had no response to one or both allergoids. These modification procedures yield allergoids with a reduced allergenic activity and preserved immunogenic potential suitable for use in immunotherapy.

Structural Prediction and In Silico Physicochemical Characterization for Mouse Caltrin I and Bovine Caltrin Proteins

PubMed Central

Grasso, Ernesto J.; Sottile, Adolfo E.; Coronel, Carlos E.

2016-01-01

It is known that caltrin (calcium transport inhibitor) protein binds to sperm cells during ejaculation and inhibits extracellular Ca2+ uptake. Although the sequence and some biological features of mouse caltrin I and bovine caltrin are known, their physicochemical properties and tertiary structure are mainly unknown. We predicted the 3D structures of mouse caltrin I and bovine caltrin by molecular homology modeling and threading. Surface electrostatic potentials and electric fields were calculated using the Poisson–Boltzmann equation. Several different bioinformatics tools and available web servers were used to thoroughly analyze the physicochemical characteristics of both proteins, such as their Kyte and Doolittle hydropathy scores and helical wheel projections. The results presented in this work significantly aid further understanding of the molecular mechanisms of caltrin proteins modulating physiological processes associated with fertilization. PMID:27812283

3-Methoxylphenylpropyl amides as novel receptor subtype-selective melatoninergic ligands: characterization of physicochemical and pharmacokinetic properties.

PubMed

Zhu, Jing; Hu, Yueqing; Ho, Maurice K C; Wong, Yung H

2011-01-01

Developing subtype-selective melatoninergic ligands has been a subject of considerable interest in drug discovery. A series of 3-methoxyphenylpropyl amide derivatives showing selective binding capacity to type 2 melatonin receptor with subnanomolar range of affinities has been identified recently by our laboratory. In the present study, their physicochemical properties, Caco-2 cell and mdr1-MDCK cell permeability, plasma protein binding, and metabolic stability were investigated. The selected compounds are lipophilic in nature, exhibiting aqueous solubility ranging from 40 to 200 microg/mL. Cell permeability studies on Caco-2 and mdr1-MDCK model revealed that they were readily transported through intestinal epithelium and possessed high penetration potential through blood-brain barrier, implying good oral absorption and central nervous system (CNS) distribution potential. They also showed substantial binding to human plasma protein ranging from 78.5% to 92.3%. These compounds were, however, subjected to rapid cytochrome P450-mediated degradation in rat and human liver microsomes with in vitro half-life of 9.5-31.9 min in rat and 5.5-66.7 min in human, which were much shorter than that of melatonin (approximately 73 min). Metabolite profiling unveiled that C6-ether linkage and methoxy substituents were likely the major metabolic soft spots in their structures, which provided important information for further improvement of their structural stability.

Binding thermodynamics discriminates fragments from druglike compounds: a thermodynamic description of fragment-based drug discovery.

PubMed

Williams, Glyn; Ferenczy, György G; Ulander, Johan; Keserű, György M

2017-04-01

Small is beautiful - reducing the size and complexity of chemical starting points for drug design allows better sampling of chemical space, reveals the most energetically important interactions within protein-binding sites and can lead to improvements in the physicochemical properties of the final drug. The impact of fragment-based drug discovery (FBDD) on recent drug discovery projects and our improved knowledge of the structural and thermodynamic details of ligand binding has prompted us to explore the relationships between ligand-binding thermodynamics and FBDD. Information on binding thermodynamics can give insights into the contributions to protein-ligand interactions and could therefore be used to prioritise compounds with a high degree of specificity in forming key interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Protein and Lipid Binding Parameters in Rainbow Trout (Oncorhynchus mykiss) Blood and Liver Fractions to Extrapolate from an in Vitro metabolic Degradation Assay to in Vivo Bioaccumulation Potential of Hydrophobic Organic Chemicals

EPA Science Inventory

Biotransformation reduces the extent to which environmental contaminants accumulate in fish and other aquatic biota. Unfortunately, the tendency for compounds to be metabolized is not easily predicted from physico-chemical properties (e.g., octanol:water partitioning) or an exam...

Interrogating the relationship between rat in vivo tissue distribution and drug property data for >200 structurally unrelated molecules

PubMed Central

Harrell, Andrew W; Sychterz, Caroline; Ho, May Y; Weber, Andrew; Valko, Klara; Negash, Kitaw

2015-01-01

The ability to explain distribution patterns from drug physicochemical properties and binding characteristics has been explored for more than 200 compounds by interrogating data from quantitative whole body autoradiography studies (QWBA). These in vivo outcomes have been compared to in silico and in vitro drug property data to determine the most influential properties governing drug distribution. Consistent with current knowledge, in vivo distribution was most influenced by ionization state and lipophilicity which in turn affected phospholipid and plasma protein binding. Basic and neutral molecules were generally better distributed than acidic counterparts demonstrating weaker plasma protein and stronger phospholipid binding. The influence of phospholipid binding was particularly evident in tissues with high phospholipid content like spleen and lung. Conversely, poorer distribution of acidic drugs was associated with stronger plasma protein and weaker phospholipid binding. The distribution of a proportion of acidic drugs was enhanced, however, in tissues known to express anionic uptake transporters such as the liver and kidney. Greatest distribution was observed into melanin containing tissues of the eye, most likely due to melanin binding. Basic molecules were consistently better distributed into parts of the eye and skin containing melanin than those without. The data, therefore, suggest that drug binding to macromolecules strongly influences the distribution of total drug for a large proportion of molecules in most tissues. Reducing lipophilicity, a strategy often used in discovery to optimize pharmacokinetic properties such as absorption and clearance, also decreased the influence of nonspecific binding on drug distribution. PMID:26516585

Statistical Profiling of One Promiscuous Protein Binding Site: Illustrated by Urokinase Catalytic Domain.

PubMed

Cerisier, Natacha; Regad, Leslie; Triki, Dhoha; Petitjean, Michel; Flatters, Delphine; Camproux, Anne-Claude

2017-10-01

While recent literature focuses on drug promiscuity, the characterization of promiscuous binding sites (ability to bind several ligands) remains to be explored. Here, we present a proteochemometric modeling approach to analyze diverse ligands and corresponding multiple binding sub-pockets associated with one promiscuous binding site to characterize protein-ligand recognition. We analyze both geometrical and physicochemical profile correspondences. This approach was applied to examine the well-studied druggable urokinase catalytic domain inhibitor binding site, which results in a large number of complex structures bound to various ligands. This approach emphasizes the importance of jointly characterizing pocket and ligand spaces to explore the impact of ligand diversity on sub-pocket properties and to establish their main profile correspondences. This work supports an interest in mining available 3D holo structures associated with a promiscuous binding site to explore its main protein-ligand recognition tendency. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Physicochemical and Pharmacokinetic Characterization of Amorphous Solid Dispersion of Meloxicam with Enhanced Dissolution Property and Storage Stability.

PubMed

Ochi, Masanori; Kimura, Keisuke; Kanda, Atsushi; Kawachi, Takaki; Matsuda, Akitoshi; Yuminoki, Kayo; Hashimoto, Naofumi

2016-08-01

The aim of the present study was to develop amorphous solid dispersion (ASD) of meloxicam (MEL) for providing rapid onset of action. ASDs of MEL with polyvinylpyrrolidone (PVP) K-30 (MEL/PVP), HPC-SSL (MEL/HPC), and Eudragit EPO (MEL/EPO) were prepared. The physicochemical properties were characterized by focusing on morphology, crystallinity, dissolution properties, stability, and the interaction of MEL with coexisting polymers. MEL/EPO was physicochemically stable after storage at 40°C/75% RH for 30 days. In contrast, recrystallization of MEL was observed in MEL/PVP and MEL/HPC at 40°C/50% RH for 30 days. Infrared spectroscopic studies and (1)H NMR analyses of MEL/EPO revealed that Eudragit EPO interacted with MEL and reduced intermolecular binding between MEL molecules. Intermolecular interaction of drug molecules is necessary for the formation of crystalline. Thus, the interaction of MEL with Eudragit EPO and interruption of the formation of supramolecular interaction between MEL molecules might lead to the inhibition of crystal growth of MEL. Of all the MEL solid dispersions prepared, MEL/EPO showed the largest improvement in dissolution behavior. Oral administration of MEL/EPO to rats showed rapid and enhanced MEL exposure with a 2.4-fold increase in bioavailability compared with crystalline MEL. Based on these findings, MEL/EPO was physicochemically stable and provided a rapid onset of action and enhanced bioavailability after oral administration.

Comparison of specific binding sites for Escherichia coli RNA polymerase with naturally occurring hairpin regions in single-stranded DNA of coliphage M13. [Aspergillus oryzae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niyogi, S.K.; Mitra, S.

Escherichia coli RNA polymerase binds specifically to the single-stranded circular DNA of coliphage M13 in the presence of a saturating concentration of the bacterial DNA binding protein presumably as an essential step in the synthesis of the RNA primer required for synthesizing the complementary DNA strand in parental replicative-form DNA. The RNA polymerase-protected DNA regions were isolated after extensive digestion with pancreatic DNase, S1 endonuclease of Aspergillus oryzae, and exonuclease I of E. coli. The physicochemical properties of the RNA polymerase-protected segments (called PI and PII) were compared with those of the naturally occurring hairpin regions.

Effect of resveratrol or ascorbic acid on the stability of α-tocopherol in O/W emulsions stabilized by whey protein isolate: Simultaneous encapsulation of the vitamin and the protective antioxidant.

PubMed

Wang, Lei; Gao, Yahui; Li, Juan; Subirade, Muriel; Song, Yuanda; Liang, Li

2016-04-01

Food proteins have been widely used as carrier materials due to their multiple functional properties. Hydrophobic bioactives are generally dissolved in the oil phase of O/W emulsions. Ligand-binding properties provide the possibility of binding bioactives to the protein membrane of oil droplets. In this study, the influence of whey protein isolate (WPI) concentration and amphiphilic resveratrol or hydrophilic ascorbic acid on the decomposition of α-tocopherol in the oil phase of WPI emulsions is considered. Impact of ascorbic acid, in the continuous phase, on the decomposition depended on the vitamin concentration. Resveratrol partitioned into the oil-water interface and the cis-isomer contributed most of the protective effect of this polyphenol. About 94% of α-tocopherol and 50% of resveratrol were found in the oil droplets stabilized by 0.01% WPI. These results suggest the feasibility of using the emulsifying and ligand-binding properties of WPI to produce carriers for simultaneous encapsulation of bioactives with different physicochemical properties. Copyright © 2015 Elsevier Ltd. All rights reserved.

Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0

PubMed Central

Zhu, Xiaolei; Xiong, Yi; Kihara, Daisuke

2015-01-01

Motivation: Ligand binding is a key aspect of the function of many proteins. Thus, binding ligand prediction provides important insight in understanding the biological function of proteins. Binding ligand prediction is also useful for drug design and examining potential drug side effects. Results: We present a computational method named Patch-Surfer2.0, which predicts binding ligands for a protein pocket. By representing and comparing pockets at the level of small local surface patches that characterize physicochemical properties of the local regions, the method can identify binding pockets of the same ligand even if they do not share globally similar shapes. Properties of local patches are represented by an efficient mathematical representation, 3D Zernike Descriptor. Patch-Surfer2.0 has significant technical improvements over our previous prototype, which includes a new feature that captures approximate patch position with a geodesic distance histogram. Moreover, we constructed a large comprehensive database of ligand binding pockets that will be searched against by a query. The benchmark shows better performance of Patch-Surfer2.0 over existing methods. Availability and implementation: http://kiharalab.org/patchsurfer2.0/ Contact: dkihara@purdue.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25359888

Binding of ring-substituted indole-3-acetic acids to human serum albumin.

PubMed

Soskić, Milan; Magnus, Volker

2007-07-01

The plant hormone, indole-3-acetic acid (IAA), and its ring-substituted derivatives have recently attracted attention as promising pro-drugs in cancer therapy. Here we present relative binding constants to human serum albumin for IAA and 34 of its derivatives, as obtained using the immobilized protein bound to a support suitable for high-performance liquid chromatography. We also report their octanol-water partition coefficients (logK(ow)) computed from retention data on a C(18) coated silica gel column. A four-parameter QSPR (quantitative structure-property relationships) model, based on physico-chemical properties, is put forward, which accounts for more than 96% of the variations in the binding affinities of these compounds. The model confirms the importance of lipophilicity as a global parameter governing interaction with serum albumin, but also assigns significant roles to parameters specifically related to the molecular topology of ring-substituted IAAs. Bulky substituents at ring-position 6 increase affinity, those at position 2 obstruct binding, while no steric effects were noted at other ring-positions. Electron-withdrawing substituents at position 5 enhance binding, but have no obvious effect at other ring positions.

Profiling the Serum Protein Corona of Fibrillar Human Islet Amyloid Polypeptide.

PubMed

Pilkington, Emily H; Gustafsson, Ove J R; Xing, Yanting; Hernandez-Fernaud, Juan; Zampronio, Cleidi; Kakinen, Aleksandr; Faridi, Ava; Ding, Feng; Wilson, Paul; Ke, Pu Chun; Davis, Thomas P

2018-05-16

Amyloids may be regarded as native nanomaterials that form in the presence of complex protein mixtures. By drawing an analogy with the physicochemical properties of nanoparticles in biological fluids, we hypothesized that amyloids should form a protein corona in vivo that would imbue the underlying amyloid with a modified biological identity. To explore this hypothesis, we characterized the protein corona of human islet amyloid polypeptide (IAPP) fibrils in fetal bovine serum using two complementary methodologies developed herein: quartz crystal microbalance and "centrifugal capture", coupled with nanoliquid chromatography tandem mass spectroscopy. Clear evidence for a significant protein corona was obtained. No trends were identified for amyloid corona proteins based on their physicochemical properties, whereas strong binding with IAPP fibrils occurred for linear proteins or multidomain proteins with structural plasticity. Proteomic analysis identified amyloid-enriched proteins that are known to play significant roles in mediating cellular machinery and processing, potentially leading to pathological outcomes and therapeutic targets.

Computational investigations of physicochemical, pharmacokinetic, toxicological properties and molecular docking of betulinic acid, a constituent of Corypha taliera (Roxb.) with Phospholipase A2 (PLA2).

PubMed

Khan, Mohammad Firoz; Nahar, Nusrat; Rashid, Ridwan Bin; Chowdhury, Akhtaruzzaman; Rashid, Mohammad A

2018-02-02

Betulinic acid (BA) is a natural triterpenoid compound and exhibits a wide range of biological and medicinal properties including anti-inflammatory activity. Therefore, this theoretical investigation is performed to evaluate (a) physicochemical properties such as acid dissociation constant (pKa), distribution coefficient (logD), partition coefficient (logP), aqueous solubility (logS), solvation free energy, dipole moment, polarizability, hyperpolarizability and different reactivity descriptors, (b) pharmacokinetic properties like human intestinal absorption (HIA), cellular permeability, skin permeability (P Skin ), plasma protein binding (PPB), penetration of the blood brain barrier (BBB), (c) toxicological properties including mutagenicity, carcinogenicity, risk of inhibition of hERG gene and (d) molecular mechanism of anti-inflammatory action which will aid the development of analytical method and the synthesis of BA derivatives. The physicochemical properties were calculated using MarvinSketch 15.6.29 and Gaussian 09 software package. The pharmacokinetic and toxicological properties were calculated on online server PreADMET. Further, the molecular docking study was conducted on AutoDock vina in PyRx 0.8. The aqueous solubility increased with increasing pH due to the ionization of BA leading to decrease in distribution coefficient. The solvation energies in water, dimethyl sulfoxide (DMSO), acetonitrile, n-octanol, chloroform and carbon tetrachloride were - 41.74 kJ/mol, - 53.80 kJ/mol, - 66.27 kJ/mol, - 69.64 kJ/mol, - 65.96 kJ/mol and - 60.13 kJ/mol, respectively. From the results of polarizability and softness, it was clear that BA is less stable and hence, kinetically more reactive in water. BA demonstrated good human intestinal absorption (HIA) and moderate cellular permeability. Further, BA also exhibited positive CNS activity due to high permeability through BBB. The toxicological study revealed that BA was a mutagenic compound but noncarcinogenic in mice model. Moreover, molecular docking study of BA with PLA2 revealed that BA interacts with GLY22 & GLY29 through hydrogen bond formation and LEU2, PHE5, HIS6, ALA17, ALA18, HIS47 and TYR51 through different types of hydrophobic interactions. The binding affinity of BA was - 41.00 kJ/mol which is comparable to the binding affinity of potent inhibitor 6-Phenyl-4(R)-(7-Phenyl-heptanoylamino)-hexanoic acid (BR4) (- 33.89 kJ/mol). Our computed properties may assist the development of analytical method to assay BA or to develop BA derivatives with better pharmacokinetic and toxicological profile.

Physicochemical properties and characterization of chitosan synthesized from fish scales, crab and shrimp shells.

PubMed

Kumari, Suneeta; Kumar Annamareddy, Sri Hari; Abanti, Sahoo; Kumar Rath, Pradip

2017-11-01

Chitosan is derived from different starting materials such as fish scales, shrimp and crab shells by the process of deacetylation of chitin, which is carried out using 40% KOH at 90°C for 6h. Prepared chitosan was characterized by Fourier transforms infrared spectroscopy, X-ray powder diffraction, Scanning electron microscope and Thermogravimetric analysis. Futher the physicochemical properties of chitosan like Fat binding capacity (FBC), water binding capacity (WBC), solubility, average molecular weight, ash content, moisture and degree of deacetylation of chitosan were also studied. Crystalline index (%) values of commercial, shrimp, crab and fish chitosan were found to be 96, 82, 88 and 84% respectively. The presence of amino group was confirmed from the FTIR spectra of chitosan synthesized. TGA results demonstrated the lower thermal stability of chitosan. Relatively smother surface and nano-fiber structures were observed from SEM analysis. The degree of deacetylation of chitosan from different sources such as shells of fish, shrimp and crab were found to be 75%, 78%, and 70% respectively. In a similar way the WBC and FBC of fish, shrimp and crab shells were found to be 492, 358 and 138% and 226, 246 and 138% respectively. Copyright © 2017 Elsevier B.V. All rights reserved.

Pharmaceutical differences between block copolymer self-assembled and cross-linked nanoassemblies as carriers for tunable drug release.

PubMed

Lee, Hyun Jin; Bae, Younsoo

2013-02-01

To identify the effects of cross-linkers and drug-binding linkers on physicochemical and biological properties of polymer nanoassembly drug carriers. Four types of polymer nanoassemblies were synthesized from poly(ethylene glycol)-poly(aspartate) [PEG-p(Asp)] block copolymers: self-assembled nanoassemblies (SNAs) and cross-linked nanoassemblies (CNAs) to each of which an anticancer drug doxorubicin (DOX) was loaded by either physical entrapment or chemical conjugation (through acid-sensitive hydrazone linkers). Drug loading in nanoassemblies was 27 ~ 56% by weight. The particle size of SNA changed after drug and drug-binding linker entrapment (20 ~ 100 nm), whereas CNAs remained 30 ~ 40 nm. Drug release rates were fine-tunable by using amide cross-linkers and hydrazone drug-binding linkers in combination. In vitro cytotoxicity assays using a human lung cancer A549 cell line revealed that DOX-loaded nanoassemblies were equally potent as free DOX with a wide range of drug release half-life (t(1/2) = 3.24 ~ 18.48 h, at pH 5.0), but 5 times less effective when t(1/2) = 44.52 h. Nanoassemblies that incorporate cross-linkers and drug-binding linkers in combination have pharmaceutical advantages such as uniform particle size, physicochemical stability, fine-tunable drug release rates, and maximum cytotoxicity of entrapped drug payloads.

Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0.

PubMed

Zhu, Xiaolei; Xiong, Yi; Kihara, Daisuke

2015-03-01

Ligand binding is a key aspect of the function of many proteins. Thus, binding ligand prediction provides important insight in understanding the biological function of proteins. Binding ligand prediction is also useful for drug design and examining potential drug side effects. We present a computational method named Patch-Surfer2.0, which predicts binding ligands for a protein pocket. By representing and comparing pockets at the level of small local surface patches that characterize physicochemical properties of the local regions, the method can identify binding pockets of the same ligand even if they do not share globally similar shapes. Properties of local patches are represented by an efficient mathematical representation, 3D Zernike Descriptor. Patch-Surfer2.0 has significant technical improvements over our previous prototype, which includes a new feature that captures approximate patch position with a geodesic distance histogram. Moreover, we constructed a large comprehensive database of ligand binding pockets that will be searched against by a query. The benchmark shows better performance of Patch-Surfer2.0 over existing methods. http://kiharalab.org/patchsurfer2.0/ CONTACT: dkihara@purdue.edu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The relationship between target-class and the physicochemical properties of antibacterial drugs

PubMed Central

Mugumbate, Grace; Overington, John P.

2015-01-01

The discovery of novel mechanism of action (MOA) antibacterials has been associated with the concept that antibacterial drugs occupy a differentiated region of physicochemical space compared to human-targeted drugs. With, in broad terms, antibacterials having higher molecular weight, lower log P and higher polar surface area (PSA). By analysing the physicochemical properties of about 1700 approved drugs listed in the ChEMBL database, we show, that antibacterials for whose targets are riboproteins (i.e., composed of a complex of RNA and protein) fall outside the conventional human ‘drug-like’ chemical space; whereas antibacterials that modulate bacterial protein targets, generally comply with the ‘rule-of-five’ guidelines for classical oral human drugs. Our analysis suggests a strong target-class association for antibacterials—either protein-targeted or riboprotein-targeted. There is much discussion in the literature on the failure of screening approaches to deliver novel antibacterial lead series, and linkage of this poor success rate for antibacterials with the chemical space properties of screening collections. Our analysis suggests that consideration of target-class may be an underappreciated factor in antibacterial lead discovery, and that in fact bacterial protein-targets may well have similar binding site characteristics to human protein targets, and questions the assumption that larger, more polar compounds are a key part of successful future antibacterial discovery. PMID:25975639

Dietary fibers from mushroom sclerotia: 1. Preparation and physicochemical and functional properties.

PubMed

Wong, Ka-Hing; Cheung, Peter C K

2005-11-30

Preparation of three novel dietary fibers (DFs) from mushroom sclerotia, namely, Pleurotus tuberregium, Polyporous rhinocerus, and Wolfiporia cocos, by a scale-up modified AOAC procedure using industrial enzymes was investigated. A remarkably high level of total dietary fiber (TDF) ranging from 81.7 to 96.3% sample dry matter (DM), in which a content of nonstarch polysaccharide (NSP) ranging from 86.6 to 94.3% sclerotial TDF DM, was obtained from the three sclerotia. All sclerotial DFs were rich in beta-glucan (the glucose residue ranged from 89.7 to 94.5% NSP DM) with a very low level of resistant glycogen (ranged from 3.77 to 3.94% sclerotial TDF DM). All three novel sclerotial DFs also exhibited similar, if not better, physicochemical and functional properties (pH, color, water binding capacity, oil holding capacity, and emulsifying properties) as those of barely DF control and commercial DF-rich ingredients. The potential use of the three mushroom sclerotial DFs as a new beta-glucan type DF-rich ingredient in the food industry was discussed.

Physicochemical functionality of 4-α-glucanotransferase-treated rice flour in food application.

PubMed

Kim, Young-Lim; Mun, Saehun; Park, Kwan-Hwa; Shim, Jae-Yong; Kim, Yong-Ro

2013-09-01

The physicochemical properties of 4-α-glucanotransferase (4αGTase)-modified rice flours were examined by measuring the molecular weight distribution, moisture sorption isotherm, and melting enthalpy of ice crystals. The results obtained by measuring the moisture sorption isotherm and melting enthalpy of ice crystals revealed that 4αGTase-modified rice flours had high water binding capacity than that of control rice flour. When the textural properties of noodles containing 4αGTase-treated rice flours after freeze-thaw cycling were measured by texture profile analysis, the textural properties of control noodle deteriorated. However, those of noodle with 4αGTase-modified rice flours were retained. For the melting enthalpy of ice crystals formed within cooked noodles, 4αGTase-treated rice flour showed similar effect to sucrose for reducing the melting enthalpy of ice crystals, however, the texture and taste of noodle with sucrose was undesirable for consuming. 4αGTase-treated rice flour appeared to have good potential as a non-sweet cryoprotectant of frozen product. Copyright © 2013 Elsevier B.V. All rights reserved.

Formulation, physicochemical characterization and stability study of lithium-loaded microemulsion system.

PubMed

Mouri, Abdelkader; Legrand, Philippe; El Ghzaoui, Abdeslam; Dorandeu, Christophe; Maurel, Jean Claude; Devoisselle, Jean-Marie

2016-04-11

Lithium biocompatible microemulsion based on Peceol(®), lecithin, ethanol and water was studied in attempt to identify the optimal compositions in term of drug content, physicochemical properties and stability. Lithium solubilization in microemulsion was found to be compatible with a drug-surfactant binding model. Lithium ions were predominantly solubilized within lecithin head group altering significantly the interfacial properties of the system. Pseudo-ternary phase diagrams of drug free and drug loaded microemulsions were built at constant ethanol/lecithin weight ratio (40/60). Lithium loaded microemulsion has totally disappeared in the Peceol(®) rich part of phase diagram; critical fractions of lecithin and ethanol were required for the formation of stable microemulsion. The effect of lithium concentration on the properties and physical stability of microemulsions were studied using microscopy, Karl Fischer titrations, rheology analyses, conductivity measurements and centrifugation tests. The investigated microemulsions were found to be stable under accelerated storage conditions. The systems exhibited low viscosity and behaved as Newtonian fluid and no structural transition was shown. Copyright © 2016 Elsevier B.V. All rights reserved.

S2RSLDB: a comprehensive manually curated, internet-accessible database of the sigma-2 receptor selective ligands.

PubMed

Nastasi, Giovanni; Miceli, Carla; Pittalà, Valeria; Modica, Maria N; Prezzavento, Orazio; Romeo, Giuseppe; Rescifina, Antonio; Marrazzo, Agostino; Amata, Emanuele

2017-01-01

Sigma (σ) receptors are accepted as a particular receptor class consisting of two subtypes: sigma-1 (σ 1 ) and sigma-2 (σ 2 ). The two receptor subtypes have specific drug actions, pharmacological profiles and molecular characteristics. The σ 2 receptor is overexpressed in several tumor cell lines, and its ligands are currently under investigation for their role in tumor diagnosis and treatment. The σ 2 receptor structure has not been disclosed, and researchers rely on σ 2 receptor radioligand binding assay to understand the receptor's pharmacological behavior and design new lead compounds. Here we present the sigma-2 Receptor Selective Ligands Database (S2RSLDB) a manually curated database of the σ 2 receptor selective ligands containing more than 650 compounds. The database is built with chemical structure information, radioligand binding affinity data, computed physicochemical properties, and experimental radioligand binding procedures. The S2RSLDB is freely available online without account login and having a powerful search engine the user may build complex queries, sort tabulated results, generate color coded 2D and 3D graphs and download the data for additional screening. The collection here reported is extremely useful for the development of new ligands endowed of σ 2 receptor affinity, selectivity, and appropriate physicochemical properties. The database will be updated yearly and in the near future, an online submission form will be available to help with keeping the database widely spread in the research community and continually updated. The database is available at http://www.researchdsf.unict.it/S2RSLDB.

Novel benzanthrone probes for membrane and protein studies

NASA Astrophysics Data System (ADS)

Ryzhova, Olga; Vus, Kateryna; Trusova, Valeriya; Kirilova, Elena; Kirilov, Georgiy; Gorbenko, Galyna; Kinnunen, Paavo

2016-09-01

The applicability of a series of novel benzanthrone dyes to monitoring the changes in physicochemical properties of lipid bilayer and to differentiating between the native and aggregated protein states has been evaluated. Based on the quantitative parameters of the dye-membrane and dye-protein binding derived from the fluorimetric titration data, the most prospective membrane probes and amyloid tracers have been selected from the group of examined compounds. Analysis of the red edge excitation shifts of the membrane- and amyloid-bound dyes provided information on the properties of benzanthrone binding sites within the lipid and protein matrixes. To understand how amyloid specificity of benzanthrones correlates with their structure, quantitative structure activity relationship (QSAR) analysis was performed involving a range of quantum chemical molecular descriptors. A statistically significant model was obtained for predicting the sensitivity of novel benzanthrone dyes to amyloid fibrils.

Enhanced spectrophotometric determination of Losartan potassium based on its physicochemical interaction with cationic surfactant

NASA Astrophysics Data System (ADS)

Abdel-Fattah, Laila; Abdel-Aziz, Lobna; Gaied, Mariam

2015-02-01

In this study, a simple and sensitive spectrophotometric method was developed for determination of Losartan potassium (LST K), an angiotensin-II receptor (type AT1) antagonist, in presence of cationic surfactant cetyltrimethylammonium bromide (CTAB). The physicochemical interaction of LST K with CTAB was investigated. The effect of cationic micelles on the spectroscopic and acid-base properties of LST K was studied at pH 7.4. The binding constant (Kb) and the partition coefficient (Kx) of LST K-CTAB were 1.62 × 105 M-1 and 1.38 × 105; respectively. The binding of LST K to CTAB micelles implied a shift in drug acidity constant (ΔpKa = 0.422). The developed method is linear over the range 0.5-28 μg mL-1. The accuracy was evaluated and was found to be 99.79 ± 0.509% and the relative standard deviation for intraday and interday precision was 0.821 and 0.963; respectively. The method was successfully applied to determine LST K in pharmaceutical formulations.

Enhanced spectrophotometric determination of Losartan potassium based on its physicochemical interaction with cationic surfactant.

PubMed

Abdel-Fattah, Laila; Abdel-Aziz, Lobna; Gaied, Mariam

2015-02-05

In this study, a simple and sensitive spectrophotometric method was developed for determination of Losartan potassium (LST K), an angiotensin-II receptor (type AT1) antagonist, in presence of cationic surfactant cetyltrimethylammonium bromide (CTAB). The physicochemical interaction of LST K with CTAB was investigated. The effect of cationic micelles on the spectroscopic and acid-base properties of LST K was studied at pH 7.4. The binding constant (Kb) and the partition coefficient (Kx) of LST K-CTAB were 1.62×10(5) M(-1) and 1.38×10(5); respectively. The binding of LST K to CTAB micelles implied a shift in drug acidity constant (ΔpKa=0.422). The developed method is linear over the range 0.5-28 μg mL(-1). The accuracy was evaluated and was found to be 99.79±0.509% and the relative standard deviation for intraday and interday precision was 0.821 and 0.963; respectively. The method was successfully applied to determine LST K in pharmaceutical formulations. Copyright © 2014 Elsevier B.V. All rights reserved.

Coelenterazine-binding protein of Renilla muelleri: cDNA cloning, overexpression, and characterization as a substrate of luciferase.

PubMed

Titushin, Maxim S; Markova, Svetlana V; Frank, Ludmila A; Malikova, Natalia P; Stepanyuk, Galina A; Lee, John; Vysotski, Eugene S

2008-02-01

The Renilla bioluminescent system in vivo is comprised of three proteins--the luciferase, green-fluorescent protein, and coelenterazine-binding protein (CBP), previously called luciferin-binding protein (LBP). This work reports the cloning of the full-size cDNA encoding CBP from soft coral Renilla muelleri, its overexpression and properties of the recombinant protein. The apo-CBP was quantitatively converted to CBP by simple incubation with coelenterazine. The physicochemical properties of this recombinant CBP are determined to be practically the same as those reported for the CBP (LBP) of R. reniformis. CBP is a member of the four-EF-hand Ca(2+)-binding superfamily of proteins with only three of the EF-hand loops having the Ca(2+)-binding consensus sequences. There is weak sequence homology with the Ca(2+)-regulated photoproteins but only as a result of the necessary Ca(2+)-binding loop structure. In combination with Renilla luciferase, addition of only one Ca(2+) is sufficient to release the coelenterazine as a substrate for the luciferase for bioluminescence. This combination of the two proteins generates bioluminescence with higher reaction efficiency than using free coelenterazine alone as the substrate for luciferase. This increased quantum yield, a difference of bioluminescence spectra, and markedly different kinetics, implicate that a CBP-luciferase complex might be involved.

Computational analysis of protein-protein interfaces involving an alpha helix: insights for terphenyl-like molecules binding.

PubMed

Isvoran, Adriana; Craciun, Dana; Martiny, Virginie; Sperandio, Olivier; Miteva, Maria A

2013-06-14

Protein-Protein Interactions (PPIs) are key for many cellular processes. The characterization of PPI interfaces and the prediction of putative ligand binding sites and hot spot residues are essential to design efficient small-molecule modulators of PPI. Terphenyl and its derivatives are small organic molecules known to mimic one face of protein-binding alpha-helical peptides. In this work we focus on several PPIs mediated by alpha-helical peptides. We performed computational sequence- and structure-based analyses in order to evaluate several key physicochemical and surface properties of proteins known to interact with alpha-helical peptides and/or terphenyl and its derivatives. Sequence-based analysis revealed low sequence identity between some of the analyzed proteins binding alpha-helical peptides. Structure-based analysis was performed to calculate the volume, the fractal dimension roughness and the hydrophobicity of the binding regions. Besides the overall hydrophobic character of the binding pockets, some specificities were detected. We showed that the hydrophobicity is not uniformly distributed in different alpha-helix binding pockets that can help to identify key hydrophobic hot spots. The presence of hydrophobic cavities at the protein surface with a more complex shape than the entire protein surface seems to be an important property related to the ability of proteins to bind alpha-helical peptides and low molecular weight mimetics. Characterization of similarities and specificities of PPI binding sites can be helpful for further development of small molecules targeting alpha-helix binding proteins.

Design of Stomach Acid-Stable and Mucin-Binding Enzyme Polymer Conjugates.

PubMed

Cummings, Chad S; Campbell, Alan S; Baker, Stefanie L; Carmali, Sheiliza; Murata, Hironobu; Russell, Alan J

2017-02-13

The reduced immunogenicity and increased stability of protein-polymer conjugates has made their use in therapeutic applications particularly attractive. However, the physicochemical interactions between polymer and protein, as well as the effect of this interaction on protein activity and stability, are still not fully understood. In this work, polymer-based protein engineering was used to examine the role of polymer physicochemical properties on the activity and stability of the chymotrypsin-polymer conjugates and their degree of binding to intestinal mucin. Four different chymotrypsin-polymer conjugates, each with the same polymer density, were synthesized using "grafting-from" atom transfer radical polymerization. The influence of polymer charge on chymotrypsin-polymer conjugate mucin binding, bioactivity, and stability in stomach acid was determined. Cationic polymers covalently attached to chymotrypsin showed high mucin binding, while zwitterionic, uncharged, and anionic polymers showed no mucin binding. Cationic polymers also increased chymotrypsin activity from pH 6-8, while zwitterionic polymers had no effect, and uncharged and anionic polymers decreased enzyme activity. Lastly, cationic polymers decreased the tendency of chymotrypsin to structurally unfold at extremely low pH, while uncharged and anionic polymers induced unfolding more quickly. We hypothesized that when polymers are covalently attached to the surface of a protein, the degree to which those polymers interact with the protein surface is the predominant determinant of whether the polymer will stabilize or inactivate the protein. Preferential interactions between the polymer and the protein lead to removal of water from the surface of the protein, and this, we believe, inactivates the enzyme.

Different Results of IgE Binding- and Crosslinking-Based Allergy Tests Caused by Allergen Immobilization.

PubMed

Okamoto-Uchida, Yoshimi; Nakamura, Ryosuke; Matsuzawa, Yumiko; Soma, Megumi; Kawakami, Hiroshi; Ishii-Watabe, Akiko; Nishimaki-Mogami, Tomoko; Teshima, Reiko; Saito, Yoshiro

2016-01-01

The physicochemical nature of allergen molecules differ from the liquid phase to the solid phase. However, conventional allergy tests are based on the detection of immunoglobulin (Ig)E binding to immobilized allergens. We recently developed an in vitro allergy testing method using a luciferase-reporting humanized rat mast cell line to detect IgE crosslinking-induced luciferase expression (EXiLE test). The aim of the present study was to evaluate the effects of antigen immobilization on the results of different in vitro allergy tests using two anti-ovalbumin (OVA) antibodies (Abs), E-C1 and E-G5, with different properties in the OVA-induced allergic reaction. Both Abs showed clear binding to OVA with an enzyme-linked immunosorbent assay and by BIAcore analysis. However, only E-C1 potentiated EXiLE response for the liquid-phase OVA. On the other hand, OVA immobilized on solid-phase induced EXiLE responses in both E-C1 Ab- and E-G5 Ab-sensitized mast cells. Western blotting of OVA indicated that E-C1 Ab binds both to OVA monomers and dimers, unlike E-G5 Ab, which probably binds only to the OVA dimer. These results suggest that antigen immobilization enhanced IgE crosslinking ability through multimerization of allergen molecules in the solid phase, resulting in an increase in false positives in IgE binding-based conventional in vitro allergy tests. These findings shed light on the physicochemical nature of antigens as an important factor for the development and evaluation of in vitro allergy tests and suggest that mast cell activation-based allergy testing with liquid-phase allergens is a promising strategy to evaluate the physiological interactions of IgE and allergens.

Efficacy of Flaxseed Flour as Bind Enhancing Agent on the Quality of Extended Restructured Mutton Chops

PubMed Central

Sharma, Heena; Sharma, Brahma Deo; Mendiratta, S. K.; Talukder, Suman; Ramasamy, Giriprasad

2014-01-01

Consumers have become very conscious about their nutrition and well being due to changes in their socio-economic lifestyle and rapid urbanization. Therefore, development of technology for production of low cost and functional meat products is urgently required. One such approach is innovative restructuring technology in which binding of meat pieces still remains the main challenge and extension of product is generally associated with poor binding and texture. Thus, the present study was envisaged as an attempt to solve this problem by the incorporation of flaxseed flour (FF) as bind enhancing agent. The FF was used at three different levels viz., 0.5%, 1%, and 1.5% to replace lean meat in pre-standardized restructured mutton chops formulation. The products were subjected to analysis for physico-chemical, sensory and textural properties. Cooking yield, moisture percentage and fat percentage increased with increase in the level of incorporation of FF, however, protein percent and pH decreased with increase in the level of incorporation. Shear force value of product incorporated with 1.5% FF was significantly higher (p<0.01) than control and product containing 0.5% FF level. Among the sensory attributes, product with 1% flaxseed flour showed significantly higher values (p<0.05) for general appearance, binding, texture and overall acceptability. Hardness showed significant increasing (p<0.01) values with increasing levels of incorporation of flaxseed flour, however all other parameters of texture profile analysis showed a decreasing trend. On the basis of sensory scores and physico-chemical properties, the optimum incorporation level of FF was adjudged as 1%. Products incorporated with optimum level of flaxseed flour (1%) were also assessed for water activity and microbiological quality during the storage period of 15 days. It was found that the extended restructured product could be safely stored under refrigeration (4°C±1°C) in low density polyethylene (LDPE) pouches for 15 days without marked deterioration in sensory and microbiological quality. Thus, it was concluded that flaxseed flour can be used as a good bind enhancing agent in extended restructured meat products at an economic cost. PMID:25049949

A novel approach to investigate the effect of methionine oxidation on pharmacokinetic properties of therapeutic antibodies

PubMed Central

Stracke, Jan; Emrich, Thomas; Rueger, Petra; Schlothauer, Tilman; Kling, Lothar; Knaupp, Alexander; Hertenberger, Hubert; Wolfert, Andreas; Spick, Christian; Lau, Wilma; Drabner, Georg; Reiff, Ulrike; Koll, Hans; Papadimitriou, Apollon

2014-01-01

Preserving the chemical and structural integrity of therapeutic antibodies during manufacturing and storage is a major challenge during pharmaceutical development. Oxidation of Fc methionines Met252 and Met428 is frequently observed, which leads to reduced affinity to FcRn and faster plasma clearance if present at high levels. Because oxidation occurs in both positions simultaneously, their individual contribution to the concomitant changes in pharmacokinetic properties has not been clearly established. A novel pH-gradient FcRn affinity chromatography method was applied to isolate three antibody oxidation variants from an oxidized IgG1 preparation based on their FcRn binding properties. Physico-chemical characterization revealed that the three oxidation variants differed predominantly in the number of oxMet252 per IgG (0, 1, or 2), but not significantly in the content of oxMet428. Corresponding to the increase in oxMet252 content, stepwise reduction of FcRn affinity in vitro, as well as faster clearance and shorter terminal half-life, in huFcRn-transgenic mice were observed. A single Met252 oxidation per antibody had no significant effect on pharmacokinetics (PK) compared with unmodified IgG. Importantly, only molecules with both heavy chains oxidized at Met252 exhibited significantly faster clearance. In contrast, Met428 oxidation had no apparent negative effect on PK and even led to somewhat improved FcRn binding and slower clearance. This minor effect, however, seemed to be abrogated by the dominant effect of Met252 oxidation. The novel approach of functional chromatographic separation of IgG oxidation variants followed by physico-chemical and biological characterization has yielded the first experimentally-backed explanation for the unaltered PK properties of antibody preparations containing relatively high Met252 and Met428 oxidation levels. PMID:25517308

Sequence-Based Prediction of RNA-Binding Proteins Using Random Forest with Minimum Redundancy Maximum Relevance Feature Selection.

PubMed

Ma, Xin; Guo, Jing; Sun, Xiao

2015-01-01

The prediction of RNA-binding proteins is one of the most challenging problems in computation biology. Although some studies have investigated this problem, the accuracy of prediction is still not sufficient. In this study, a highly accurate method was developed to predict RNA-binding proteins from amino acid sequences using random forests with the minimum redundancy maximum relevance (mRMR) method, followed by incremental feature selection (IFS). We incorporated features of conjoint triad features and three novel features: binding propensity (BP), nonbinding propensity (NBP), and evolutionary information combined with physicochemical properties (EIPP). The results showed that these novel features have important roles in improving the performance of the predictor. Using the mRMR-IFS method, our predictor achieved the best performance (86.62% accuracy and 0.737 Matthews correlation coefficient). High prediction accuracy and successful prediction performance suggested that our method can be a useful approach to identify RNA-binding proteins from sequence information.

Sorption of organic carbon compounds to the fine fraction of surface and Subsurface Soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jagadamma, Sindhu; Mayes, Melanie; Zinn, Yuri

2014-01-01

Dissolved organic carbon (DOC) transported from the soil surface is stabilized in deeper soil profiles by physicochemical sorption processes. However, it is unclear how different forms of organic carbon (OC) compounds common in soil organic matter interact with soil minerals in the surface (A) and subsurface (B) horizons. We added four compounds (glucose, starch, cinnamic acid and stearic acid) to the silt- and clay-sized fraction (fine fraction) of A and B horizons of eight soils from varying climates (3 temperate, 3 tropical, 1 arctic and 1 sub-arctic). Equilibriumbatch experiments were conducted using 0 to 100 mg C L 1 ofmore » 14C-labeled compounds for 8 h. Sorption parameters (maximum sorption capacity, Qmax and binding coefficient, k) calculated by fitting sorption data to the Langmuir equation showed that Qmax of A and B horizons was very similar for all compounds. Both Qmax and k values were related to sorbate properties, with Qmax being lowest for glucose (20 500 mg kg 1), highest for stearic acid (20,000 200,000 mg kg 1), and intermediate for both cinnamic acid (200 4000 mg kg 1) and starch (400 6000 mg kg 1). Simple linear regression analysis revealed that physicochemical properties of the sorbents influenced the Qmax of cinnamic acid and stearic acid, but not glucose and starch. The sorbent properties did not show predictive ability for binding coefficient k. By using the fine fraction as sorbent, we found that the mineral fractions of A horizons are equally reactive as the B horizons irrespective of soil organic carbon content.« less

High abundance androgen receptor in goldfish brain: characteristics and seasonal changes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pasmanik, M.; Callard, G.V.

1988-08-01

Testosterone (T) exerts its actions in brain directly via androgen receptors or, after aromatization to estradiol, via estrogen receptors. Brain aromatase activity in teleost fish is 100-1000 times greater than in mammals and would be expected to significantly reduce the quantity of androgen available for receptor binding. Experiments were carried out on the goldfish Carassius auratus to determine if androgen receptors are present in teleost brain and whether their physicochemical properties reflect elevated aromatase. Cytosolic and nuclear extracts were assayed with the use of (/sup 3/H)T and charcoal, Sephadex LH-20, or DNA-cellulose chromatography to separate bound and free steroids. Bindingmore » activity was saturable and had an equally high affinity for T and 5 alpha-dihydrotestosterone. Although mibolerone was a relatively weak competitor, the putative teleost androgen 11-ketotestosterone, methyltrienolone (R1881), estradiol, progesterone, and cortisol were poor ligands. Characteristics that distinguish this receptor from a steroid-binding protein in goldfish serum are the presence of binding activity in both nuclear and cytosolic extracts, a low rate of ligand-receptor dissociation, electrophoretic mobility, sedimentation properties in low vs. high salt, and tissue distribution. DNA cellulose-adhering and nonadhering forms were detected, but these did not differ in other variables measured. Although goldfish androgen receptors resembled those of mammals in all important physicochemical characteristics, they were unusually abundant compared to levels in rat brain, but comparable to levels in prostate and other male sex hormone target organs. Moreover, there were seasonal variations in total receptors, with a peak at spawning (April) 4- to 5-fold higher than values in reproductively inactive fish.« less

Intracellular Drug Concentrations and Transporters: Measurement, Modeling, and Implications for the Liver

PubMed Central

Chu, X; Korzekwa, K; Elsby, R; Fenner, K; Galetin, A; Lai, Y; Matsson, P; Moss, A; Nagar, S; Rosania, GR; Bai, JPF; Polli, JW; Sugiyama, Y; Brouwer, KLR

2013-01-01

Intracellular concentrations of drugs and metabolites are often important determinants of efficacy, toxicity, and drug interactions. Hepatic drug distribution can be affected by many factors, including physicochemical properties, uptake/efflux transporters, protein binding, organelle sequestration, and metabolism. This white paper highlights determinants of hepatocyte drug/metabolite concentrations and provides an update on model systems, methods, and modeling/simulation approaches used to quantitatively assess hepatocellular concentrations of molecules. The critical scientific gaps and future research directions in this field are discussed. PMID:23588320

Phage Display Derived IgNAR V Region Binding Domains for Therapeutic Development.

PubMed

Ubah, Obinna C; Barelle, Caroline J; Buschhaus, Magdalena J; Porter, Andrew J

2016-01-01

Phage display technology has revolutionized the science of drug discovery by transforming the generation and manipulation of ligands, such as antibody fragments, enzymes, and peptides. The basis of this technology is the expression of recombinant proteins or peptides fused to a phage coat protein, and subsequent isolation of ligands based on a variety of catalytic, physicochemical/binding kinetic and/or biological characteristics. An incredible number of diagnostic and therapeutic domains have been successfully isolated using phage display technology. The variable domain of the New Antigen Receptors (VNAR) found in cartilaginous fish, is also amenable to phage display selection. Whilst not an antibody, VNARs are unquestionable the oldest (450 million years), and smallest antigen binding, single-domains so far identified in the vertebrate kingdom. Their role as an integral part of the adaptive immune system of sharks has been well established, enhancing our understanding of the evolutionary origins of humoral immunity and the unusual but divergent ancestry of the VNARs themselves. VNARs exhibit remarkable physicochemical properties, such as small size, stability in extreme conditions, solubility, molecular flexibility, high affinity and selectivity for target. The purpose of this review is to illustrate the important role phage display has played in the isolation and characterization of potent therapeutic and diagnostic VNAR domains. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Impact of protein modification on the protein corona on nanoparticles and nanoparticle-cell interactions.

PubMed

Treuel, Lennart; Brandholt, Stefan; Maffre, Pauline; Wiegele, Sarah; Shang, Li; Nienhaus, G Ulrich

2014-01-28

Recent studies have firmly established that cellular uptake of nanoparticles is strongly affected by the presence and the physicochemical properties of a protein adsorption layer around these nanoparticles. Here, we have modified human serum albumin (HSA), a serum protein often used in model studies of protein adsorption onto nanoparticles, to alter its surface charge distribution and investigated the consequences for protein corona formation around small (radius ∼5 nm), dihydrolipoic acid-coated quantum dots (DHLA-QDs) by using fluorescence correlation spectroscopy. HSA modified by succinic anhydride (HSAsuc) to generate additional carboxyl groups on the protein surface showed a 3-fold decreased binding affinity toward the nanoparticles. A 1000-fold enhanced affinity was observed for HSA modified by ethylenediamine (HSAam) to increase the number of amino functions on the protein surface. Remarkably, HSAsuc formed a much thicker protein adsorption layer (8.1 nm) than native HSA (3.3 nm), indicating that it binds in a distinctly different orientation on the nanoparticle, whereas the HSAam corona (4.6 nm) is only slightly thicker. Notably, protein binding to DHLA-QDs was found to be entirely reversible, independent of the modification. We have also measured the extent and kinetics of internalization of these nanoparticles without and with adsorbed native and modified HSA by HeLa cells. Pronounced variations were observed, indicating that even small physicochemical changes of the protein corona may affect biological responses.

Zebavidin - An Avidin-Like Protein from Zebrafish

PubMed Central

Taskinen, Barbara; Zmurko, Joanna; Ojanen, Markus; Kukkurainen, Sampo; Parthiban, Marimuthu; Määttä, Juha A. E.; Leppiniemi, Jenni; Jänis, Janne; Parikka, Mataleena; Turpeinen, Hannu; Rämet, Mika; Pesu, Marko; Johnson, Mark S.; Kulomaa, Markku S.; Airenne, Tomi T.; Hytönen, Vesa P.

2013-01-01

The avidin protein family members are well known for their high affinity towards D-biotin and high structural stability. These properties make avidins valuable tools for a wide range of biotechnology applications. We have identified a new member of the avidin family in the zebrafish (Danio rerio) genome, hereafter called zebavidin. The protein is highly expressed in the gonads of both male and female zebrafish and in the gills of male fish, but our data suggest that zebavidin is not crucial for the developing embryo. Biophysical and structural characterisation of zebavidin revealed distinct properties not found in any previously characterised avidins. Gel filtration chromatography and native mass spectrometry suggest that the protein forms dimers in the absence of biotin at low ionic strength, but assembles into tetramers upon binding biotin. Ligand binding was analysed using radioactive and fluorescently labelled biotin and isothermal titration calorimetry. Moreover, the crystal structure of zebavidin in complex with biotin was solved at 2.4 Å resolution and unveiled unique ligand binding and subunit interface architectures; the atomic-level details support our physicochemical observations. PMID:24204770

Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method.

PubMed

Petukh, Marharyta; Li, Minghui; Alexov, Emil

2015-07-01

A new methodology termed Single Amino Acid Mutation based change in Binding free Energy (SAAMBE) was developed to predict the changes of the binding free energy caused by mutations. The method utilizes 3D structures of the corresponding protein-protein complexes and takes advantage of both approaches: sequence- and structure-based methods. The method has two components: a MM/PBSA-based component, and an additional set of statistical terms delivered from statistical investigation of physico-chemical properties of protein complexes. While the approach is rigid body approach and does not explicitly consider plausible conformational changes caused by the binding, the effect of conformational changes, including changes away from binding interface, on electrostatics are mimicked with amino acid specific dielectric constants. This provides significant improvement of SAAMBE predictions as indicated by better match against experimentally determined binding free energy changes over 1300 mutations in 43 proteins. The final benchmarking resulted in a very good agreement with experimental data (correlation coefficient 0.624) while the algorithm being fast enough to allow for large-scale calculations (the average time is less than a minute per mutation).

sc-PDB: a database for identifying variations and multiplicity of 'druggable' binding sites in proteins.

PubMed

Meslamani, Jamel; Rognan, Didier; Kellenberger, Esther

2011-05-01

The sc-PDB database is an annotated archive of druggable binding sites extracted from the Protein Data Bank. It contains all-atoms coordinates for 8166 protein-ligand complexes, chosen for their geometrical and physico-chemical properties. The sc-PDB provides a functional annotation for proteins, a chemical description for ligands and the detailed intermolecular interactions for complexes. The sc-PDB now includes a hierarchical classification of all the binding sites within a functional class. The sc-PDB entries were first clustered according to the protein name indifferent of the species. For each cluster, we identified dissimilar sites (e.g. catalytic and allosteric sites of an enzyme). SCOPE AND APPLICATIONS: The classification of sc-PDB targets by binding site diversity was intended to facilitate chemogenomics approaches to drug design. In ligand-based approaches, it avoids comparing ligands that do not share the same binding site. In structure-based approaches, it permits to quantitatively evaluate the diversity of the binding site definition (variations in size, sequence and/or structure). The sc-PDB database is freely available at: http://bioinfo-pharma.u-strasbg.fr/scPDB.

Co-Processed Chitin-Mannitol as a New Excipient for Oro-Dispersible Tablets

PubMed Central

Daraghmeh, Nidal; Chowdhry, Babur Z.; Leharne, Stephen A.; Al Omari, Mahmoud M. H.; Badwan, Adnan A.

2015-01-01

This study describes the preparation, characterization and performance of a novel excipient for use in oro-dispersible tablets (ODT). The excipient (Cop–CM) consists of chitin and mannitol. The excipient with optimal physicochemical properties was obtained at a chitin: mannitol ratio of 2:8 (w/w) and produced by roll compaction (RC). Differential scanning calorimetry (DSC), Fourier transform-Infrared (FT-IR), X-ray powder diffraction (XRPD) and scanning electron microscope (SEM) techniques were used to characterize Cop–CM, in addition to characterization of its powder and ODT dosage form. The effect of particle size distribution of Cop–CM was investigated and found to have no significant influence on the overall tablet physical properties. The compressibility parameter (a) for Cop–CM was calculated from a Kawakita plot and found to be higher (0.661) than that of mannitol (0.576) due to the presence of the highly compressible chitin (0.818). Montelukast sodium and domperidone ODTs produced, using Cop–CM, displayed excellent physicochemical properties. The exceptional binding, fast wetting and superdisintegration properties of Cop–CM, in comparison with commercially available co-processed ODT excipients, results in a unique multifunctional base which can successfully be used in the formulation of oro-dispersible and fast immediate release tablets. PMID:25830680

New phthalimide-appended Schiff bases: Studies of DNA binding, molecular docking and antioxidant activities.

PubMed

Nayab, Pattan Sirajuddin; Akrema; Ansari, Istikhar A; Shahid, Mohammad; Rahisuddin

2017-08-01

Herein, we investigated new phthalimide-based Schiff base molecules as promising DNA-binding and free radical scavenging agents. Physicochemical properties of these molecules were demonstrated on the basis of elemental analysis, ultraviolet-visible (UV-Vis), infra-red (IR), 1 H and 13 C nuclear magnetic resonance (NMR) spectroscopy. All spectral data are agreed well with the proposed Schiff base framework. The DNA-binding potential of synthesized compounds were investigated by means of UV-visible, fluorescence, iodide quenching, circular dichroism, viscosity and thermal denaturation studies. The intrinsic binding constants (K b ) were calculated from absorption studies were found to be 1.1 × 10 4 and 1.0 × 10 4  M -1 for compounds 2a and 2b suggesting that compound 2a binding abilities with DNA were stronger than the compound 2b. Our studies showed that the presented compounds interact with DNA through groove binding. Molecular docking studies were carried out to predict the binding between Ct-DNA and test compounds. Interestingly, in silico predictions were corroborated with in vitro DNA-binding conclusions. Furthermore, the title compounds displayed remarkable antioxidant activity compared with reference standard. Copyright © 2016 John Wiley & Sons, Ltd.

Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage

PubMed Central

Bozek, Katarzyna; Lengauer, Thomas; Sierra, Saleta; Kaiser, Rolf; Domingues, Francisco S.

2013-01-01

The relationship of HIV tropism with disease progression and the recent development of CCR5-blocking drugs underscore the importance of monitoring virus coreceptor usage. As an alternative to costly phenotypic assays, computational methods aim at predicting virus tropism based on the sequence and structure of the V3 loop of the virus gp120 protein. Here we present a numerical descriptor of the V3 loop encoding its physicochemical and structural properties. The descriptor allows for structure-based prediction of HIV tropism and identification of properties of the V3 loop that are crucial for coreceptor usage. Use of the proposed descriptor for prediction results in a statistically significant improvement over the prediction based solely on V3 sequence with 3 percentage points improvement in AUC and 7 percentage points in sensitivity at the specificity of the 11/25 rule (95%). We additionally assessed the predictive power of the new method on clinically derived ‘bulk’ sequence data and obtained a statistically significant improvement in AUC of 3 percentage points over sequence-based prediction. Furthermore, we demonstrated the capacity of our method to predict therapy outcome by applying it to 53 samples from patients undergoing Maraviroc therapy. The analysis of structural features of the loop informative of tropism indicates the importance of two loop regions and their physicochemical properties. The regions are located on opposite strands of the loop stem and the respective features are predominantly charge-, hydrophobicity- and structure-related. These regions are in close proximity in the bound conformation of the loop potentially forming a site determinant for the coreceptor binding. The method is available via server under http://structure.bioinf.mpi-inf.mpg.de/. PMID:23555214

Development and validation of a bioassay to evaluate binding of adalimumab to cell membrane-anchored TNFα using flow cytometry detection.

PubMed

Camacho-Sandoval, Rosa; Sosa-Grande, Eréndira N; González-González, Edith; Tenorio-Calvo, Alejandra; López-Morales, Carlos A; Velasco-Velázquez, Marco; Pavón-Romero, Lenin; Pérez-Tapia, Sonia Mayra; Medina-Rivero, Emilio

2018-06-05

Physicochemical and structural properties of proteins used as active pharmaceutical ingredients of biopharmaceuticals are determinant to carry out their biological activity. In this regard, the assays intended to evaluate functionality of biopharmaceuticals provide confirmatory evidence that they contain the appropriate physicochemical properties and structural conformation. The validation of the methodologies used for the assessment of critical quality attributes of biopharmaceuticals is a key requirement for manufacturing under GMP environments. Herein we present the development and validation of a flow cytometry-based methodology for the evaluation of adalimumab's affinity towards membrane-bound TNFα (mTNFα) on recombinant CHO cells. This in vitro methodology measures the interaction between an in-solution antibody and its target molecule onto the cell surface through a fluorescent signal. The characteristics evaluated during the validation exercise showed that this methodology is suitable for its intended purpose. The assay demonstrated to be accurate (r 2  = 0.92, slope = 1.20), precise (%CV ≤ 18.31) and specific (curve fitting, r 2  = 0.986-0.997) to evaluate binding of adalimumab to mTNFα. The results obtained here provide evidence that detection by flow cytometry is a viable alternative for bioassays used in the pharmaceutical industry. In addition, this methodology could be standardized for the evaluation of other biomolecules acting through the same mechanism of action. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Prediction of kinase-inhibitor binding affinity using energetic parameters

PubMed Central

Usha, Singaravelu; Selvaraj, Samuel

2016-01-01

The combination of physicochemical properties and energetic parameters derived from protein-ligand complexes play a vital role in determining the biological activity of a molecule. In the present work, protein-ligand interaction energy along with logP values was used to predict the experimental log (IC50) values of 25 different kinase-inhibitors using multiple regressions which gave a correlation coefficient of 0.93. The regression equation obtained was tested on 93 kinase-inhibitor complexes and an average deviation of 0.92 from the experimental log IC50 values was shown. The same set of descriptors was used to predict binding affinities for a test set of five individual kinase families, with correlation values > 0.9. We show that the protein-ligand interaction energies and partition coefficient values form the major deterministic factors for binding affinity of the ligand for its receptor. PMID:28149052

Physicochemical properties of quinoa starch.

PubMed

Li, Guantian; Wang, Sunan; Zhu, Fan

2016-02-10

Physicochemical properties of quinoa starches isolated from 26 commercial samples from a wide range of collection were studied. Swelling power (SP), water solubility index (WSI), amylose leaching (AML), enzyme susceptibility, pasting, thermal and textural properties were analyzed. Apparent amylose contents (AAM) ranged from 7.7 to 25.7%. Great variations in the diverse physicochemical properties were observed. Correlation analysis showed that AAM was the most significant factor related to AML, WSI, and pasting parameters. Correlations among diverse physicochemical parameters were analyzed. Principal component analysis using twenty three variables were used to visualize the difference among samples. Six principal components were extracted which could explain 88.8% of the total difference. The wide variations in physicochemical properties could contribute to innovative utilization of quinoa starch for food and non-food applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

The study of zinc ions binding to casein.

PubMed

Pomastowski, P; Sprynskyy, M; Buszewski, B

2014-08-01

The presented research was focused on physicochemical study of casein properties and the kinetics of zinc ions binding to the protein. Moreover, a fast and simple method of casein extraction from cow's milk has been proposed. Casein isoforms, zeta potential (ζ) and particle size of the separated caseins were characterized with the use of capillary electrophoresis, zeta potential analysis and field flow fractionation (FFF) technique, respectively. The kinetics of the metal-binding process was investigated in batch adsorption experiments. Intraparticle diffusion model, first-order and zero-order kinetic models were applied to test the kinetic experimental data. Analysis of changes in infrared bands registered for casein before and after zinc binding was also performed. The obtained results showed that the kinetic process of zinc binding to casein is not homogeneous but is expressed with an initial rapid stage with about 70% of zinc ions immobilized by casein and with a much slower second step. Maximum amount of bound zinc in the experimental conditions was 30.04mgZn/g casein. Copyright © 2014 Elsevier B.V. All rights reserved.

Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key.

PubMed

Haupt, V Joachim; Daminelli, Simone; Schroeder, Michael

2013-01-01

Drug repositioning applies established drugs to new disease indications with increasing success. A pre-requisite for drug repurposing is drug promiscuity (polypharmacology) - a drug's ability to bind to several targets. There is a long standing debate on the reasons for drug promiscuity. Based on large compound screens, hydrophobicity and molecular weight have been suggested as key reasons. However, the results are sometimes contradictory and leave space for further analysis. Protein structures offer a structural dimension to explain promiscuity: Can a drug bind multiple targets because the drug is flexible or because the targets are structurally similar or even share similar binding sites? We present a systematic study of drug promiscuity based on structural data of PDB target proteins with a set of 164 promiscuous drugs. We show that there is no correlation between the degree of promiscuity and ligand properties such as hydrophobicity or molecular weight but a weak correlation to conformational flexibility. However, we do find a correlation between promiscuity and structural similarity as well as binding site similarity of protein targets. In particular, 71% of the drugs have at least two targets with similar binding sites. In order to overcome issues in detection of remotely similar binding sites, we employed a score for binding site similarity: LigandRMSD measures the similarity of the aligned ligands and uncovers remote local similarities in proteins. It can be applied to arbitrary structural binding site alignments. Three representative examples, namely the anti-cancer drug methotrexate, the natural product quercetin and the anti-diabetic drug acarbose are discussed in detail. Our findings suggest that global structural and binding site similarity play a more important role to explain the observed drug promiscuity in the PDB than physicochemical drug properties like hydrophobicity or molecular weight. Additionally, we find ligand flexibility to have a minor influence.

Nano-Sized Cyclodextrin-Based Molecularly Imprinted Polymer Adsorbents for Perfluorinated Compounds—A Mini-Review

PubMed Central

Karoyo, Abdalla H.; Wilson, Lee D.

2015-01-01

Recent efforts have been directed towards the design of efficient and contaminant selective remediation technology for the removal of perfluorinated compounds (PFCs) from soils, sediments, and aquatic environments. While there is a general consensus on adsorption-based processes as the most suitable methodology for the removal of PFCs from aquatic environments, challenges exist regarding the optimal materials design of sorbents for selective uptake of PFCs. This article reviews the sorptive uptake of PFCs using cyclodextrin (CD)-based polymer adsorbents with nano- to micron-sized structural attributes. The relationship between synthesis of adsorbent materials and their structure relate to the overall sorption properties. Hence, the adsorptive uptake properties of CD-based molecularly imprinted polymers (CD-MIPs) are reviewed and compared with conventional MIPs. Further comparison is made with non-imprinted polymers (NIPs) that are based on cross-linking of pre-polymer units such as chitosan with epichlorohydrin in the absence of a molecular template. In general, MIPs offer the advantage of selectivity, chemical tunability, high stability and mechanical strength, ease of regeneration, and overall lower cost compared to NIPs. In particular, CD-MIPs offer the added advantage of possessing multiple binding sites with unique physicochemical properties such as tunable surface properties and morphology that may vary considerably. This mini-review provides a rationale for the design of unique polymer adsorbent materials that employ an intrinsic porogen via incorporation of a macrocyclic compound in the polymer framework to afford adsorbent materials with tunable physicochemical properties and unique nanostructure properties. PMID:28347047

Lattice energy calculation - A quick tool for screening of cocrystals and estimation of relative solubility. Case of flavonoids

NASA Astrophysics Data System (ADS)

Kuleshova, L. N.; Hofmann, D. W. M.; Boese, R.

2013-03-01

Cocrystals (or multicomponent crystals) have physico-chemical properties that are different from crystals of pure components. This is significant in drug development, since the desired properties, e.g. solubility, stability and bioavailability, can be tailored by binding two substances into a single crystal without chemical modification of an active component. Here, the FLEXCRYST program suite, implemented with a data mining force field, was used to estimate the relative stability and, consequently, the relative solubility of cocrystals of flavonoids vs their pure crystals, stored in the Cambridge Structural Database. The considerable potency of this approach for in silico screening of cocrystals, as well as their relative solubility, was demonstrated.

Approaching Pharmacological Space: Events and Components.

PubMed

Vistoli, Giulio; Pedretti, Alessandro; Mazzolari, Angelica; Testa, Bernard

2018-01-01

With a view to introducing the concept of pharmacological space and its potential applications in investigating and predicting the toxic mechanisms of xenobiotics, this opening chapter describes the logical relations between conformational behavior, physicochemical properties and binding spaces, which are seen as the three key elements composing the pharmacological space. While the concept of conformational space is routinely used to encode molecular flexibility, the concepts of property spaces and, particularly, of binding spaces are more innovative. Indeed, their descriptors can find fruitful applications (a) in describing the dynamic adaptability a given ligand experiences when inserted into a specific environment, and (b) in parameterizing the flexibility a ligand retains when bound to a biological target. Overall, these descriptors can conveniently account for the often disregarded entropic factors and as such they prove successful when inserted in ligand- or structure-based predictive models. Notably, and although binding space parameters can clearly be derived from MD simulations, the chapter will illustrate how docking calculations, despite their static nature, are able to evaluate ligand's flexibility by analyzing several poses for each ligand. Such an approach, which represents the founding core of the binding space concept, can find various applications in which the related descriptors show an impressive enhancing effect on the statistical performances of the resulting predictive models.

[Strategy of molecular design of drugs: the unification of macro-properties and micro-structures of a molecule].

PubMed

Guo, Zong-Ru

2008-03-01

The interaction of a drug with the organism involves both the disposition of a drug by the organism and the action of a drug on the organism. The disposition of various exogenous substances, including drugs, complies with general rules. The underlying physical and chemical changes to different drugs in view of time and space, i. e. pharmacokinetics, share common characteristics, that is the tout ensemble of a molecule and its macroscopic properties convey direct effect on the pharmacokinetic behavior as the tendency and consequence of biological evolution. The action of a drug on the organism, on the other hand, implicates the physico-chemical binding of a drug molecule to the target protein, which induces pharmacological and toxicological effects. The biological reactions, no matter beneficial or adverse, are all specific and individual manifestation of the drug molecule and determined by the interactive binding between definitive atoms or groups of the drug molecule and the macromolecular target in three-dimension. Such critical atoms, groups, or fragments responsible for the interaction reflect the microscopic structures of drug molecules and are called pharmacophore. In this context, a drug molecule is presumed as an assembly of macroscopic property and microscopic structure, with the macroscopic properties determining the absorption, distribution, metabolism and elimination of drugs and the microscopic structure coining pharmacological action. The knowledge of the internal relationship between macroscopy/microscopy and PK/PD conduces to comprehension of drug action and guides molecular drug design, because this conception facilitates the identification of structural features necessary for biological response, and the determination of factors modulating the physico-chemical and pharmacokinetic properties. The factors determining macro-properties include molecular weight, solubility, charge, lipophilicity (partition), and polar surface area, etc., which are destined by molecular scaffolds and/or side chain(s) apart from pharmacophore. The features of micro-structures contributing to specific activity contain hydrogen bonding donor and acceptor, positive and negative charge centers, hydrophobic centers and centers of aromatic rings. Different combinations and spacial arrangements of these features determine the distinct activity presented. The macro-property and micro-structure are integrated into a single molecule, and are inseparable. The macro-property reflects overall contribution of atoms and groups in the micro-structure. On the other hand, structural changes aimed to adjust macroscopic property usually alter the relative position of the microscopic structure. The goal of molecular drug design is to integrate the macroscopic and microscopic factors in optimized manner. In the early stage of molecular design, both macroscopic property and microscopic structure should be considered to make pharmacodynamics, pharmacokinetics, and physico-chemical properties in optimal match. Therefore, it required the existence of structural overlapping among acceptable pharmacokinetics, visible developing potential and specific pharmacodynamics. The larger the scope of overlapping, the higher the possibility to be a drug.

β -Cyclodextrin polymer binding to DNA: Modulating the physicochemical parameters

NASA Astrophysics Data System (ADS)

Rocha, J. C. B.; Silva, E. F.; Oliveira, M. F.; Sousa, F. B.; Teixeira, A. V. N. C.; Rocha, M. S.

2017-05-01

Cyclodextrins and cyclodextrins-modified molecules have interesting and appealing properties due to their capacity to host components that are normally insoluble or poorly soluble in water. In this work, we investigate the interaction of a β -cyclodextrin polymer (poly-β -CD) with λ -DNA. The polymers are obtained by the reaction of β -CD with epichlorohydrin in alkaline conditions. We have used optical tweezers to characterize the changes of the mechanical properties of DNA molecules by increasing the concentration of poly-β -CD in the sample. The physical chemistry of the interaction is then deduced from these measurements by using a recently developed quenched-disorder statistical model. It is shown that the contour length of the DNA does not change in the whole range of poly-β -CD concentration (<300 μ M ). On the other hand, significant alterations were observed in the persistence length that identifies two binding modes corresponding to the clustering of ˜2.6 and ˜14 polymer molecules along the DNA double helix, depending on the polymer concentration. Comparing these results with the ones obtained for monomeric β -CD, it was observed that the concentration of CD that alters the DNA persistence length is considerably smaller when in the polymeric form. Also, the binding constant of the polymer-DNA interaction is three orders of magnitude higher than the one found for native (monomeric) β -CD. These results show that the polymerization of the β -CD strongly increases its binding affinity to the DNA molecule. This property can be wisely used to modulate the binding of cyclodextrins to the DNA double helix.

Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments.

PubMed

Rocha, M S

2015-09-01

In this review we focus on the idea of establishing connections between the mechanical properties of DNA-ligand complexes and the physical chemistry of DNA-ligand interactions. This type of connection is interesting because it opens the possibility of performing a robust characterization of such interactions by using only one experimental technique: single molecule stretching. Furthermore, it also opens new possibilities in comparing results obtained by very different approaches, in particular when comparing single molecule techniques to ensemble-averaging techniques. We start the manuscript reviewing important concepts of DNA mechanics, from the basic mechanical properties to the Worm-Like Chain model. Next we review the basic concepts of the physical chemistry of DNA-ligand interactions, revisiting the most important models used to analyze the binding data and discussing their binding isotherms. Then, we discuss the basic features of the single molecule techniques most used to stretch DNA-ligand complexes and to obtain "force × extension" data, from which the mechanical properties of the complexes can be determined. We also discuss the characteristics of the main types of interactions that can occur between DNA and ligands, from covalent binding to simple electrostatic driven interactions. Finally, we present a historical survey of the attempts to connect mechanics to physical chemistry for DNA-ligand systems, emphasizing a recently developed fitting approach useful to connect the persistence length of DNA-ligand complexes to the physicochemical properties of the interaction. Such an approach in principle can be used for any type of ligand, from drugs to proteins, even if multiple binding modes are present.

Defining Desirable Central Nervous System Drug Space through the Alignment of Molecular Properties, in Vitro ADME, and Safety Attributes

PubMed Central

2010-01-01

As part of our effort to increase survival of drug candidates and to move our medicinal chemistry design to higher probability space for success in the Neuroscience therapeutic area, we embarked on a detailed study of the property space for a collection of central nervous system (CNS) molecules. We carried out a thorough analysis of properties for 119 marketed CNS drugs and a set of 108 Pfizer CNS candidates. In particular, we focused on understanding the relationships between physicochemical properties, in vitro ADME (absorption, distribution, metabolism, and elimination) attributes, primary pharmacology binding efficiencies, and in vitro safety data for these two sets of compounds. This scholarship provides guidance for the design of CNS molecules in a property space with increased probability of success and may lead to the identification of druglike candidates with favorable safety profiles that can successfully test hypotheses in the clinic. PMID:22778836

On the nature of cavities on protein surfaces: application to the identification of drug-binding sites.

PubMed

Nayal, Murad; Honig, Barry

2006-06-01

In this article we introduce a new method for the identification and the accurate characterization of protein surface cavities. The method is encoded in the program SCREEN (Surface Cavity REcognition and EvaluatioN). As a first test of the utility of our approach we used SCREEN to locate and analyze the surface cavities of a nonredundant set of 99 proteins cocrystallized with drugs. We find that this set of proteins has on average about 14 distinct cavities per protein. In all cases, a drug is bound at one (and sometimes more than one) of these cavities. Using cavity size alone as a criterion for predicting drug-binding sites yields a high balanced error rate of 15.7%, with only 71.7% coverage. Here we characterize each surface cavity by computing a comprehensive set of 408 physicochemical, structural, and geometric attributes. By applying modern machine learning techniques (Random Forests) we were able to develop a classifier that can identify drug-binding cavities with a balanced error rate of 7.2% and coverage of 88.9%. Only 18 of the 408 cavity attributes had a statistically significant role in the prediction. Of these 18 important attributes, almost all involved size and shape rather than physicochemical properties of the surface cavity. The implications of these results are discussed. A SCREEN Web server is available at http://interface.bioc.columbia.edu/screen. 2006 Wiley-Liss, Inc.

Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions

PubMed Central

Laine, Elodie; Carbone, Alessandra

2015-01-01

Protein-protein interactions (PPIs) are essential to all biological processes and they represent increasingly important therapeutic targets. Here, we present a new method for accurately predicting protein-protein interfaces, understanding their properties, origins and binding to multiple partners. Contrary to machine learning approaches, our method combines in a rational and very straightforward way three sequence- and structure-based descriptors of protein residues: evolutionary conservation, physico-chemical properties and local geometry. The implemented strategy yields very precise predictions for a wide range of protein-protein interfaces and discriminates them from small-molecule binding sites. Beyond its predictive power, the approach permits to dissect interaction surfaces and unravel their complexity. We show how the analysis of the predicted patches can foster new strategies for PPIs modulation and interaction surface redesign. The approach is implemented in JET2, an automated tool based on the Joint Evolutionary Trees (JET) method for sequence-based protein interface prediction. JET2 is freely available at www.lcqb.upmc.fr/JET2. PMID:26690684

A mechanistic physicochemical model of carbon dioxide transport in blood.

PubMed

O'Neill, David P; Robbins, Peter A

2017-02-01

A number of mathematical models have been produced that, given the Pco 2 and Po 2 of blood, will calculate the total concentrations for CO 2 and O 2 in blood. However, all these models contain at least some empirical features, and thus do not represent all of the underlying physicochemical processes in an entirely mechanistic manner. The aim of this study was to develop a physicochemical model of CO 2 carriage by the blood to determine whether our understanding of the physical chemistry of the major chemical components of blood together with their interactions is sufficiently strong to predict the physiological properties of CO 2 carriage by whole blood. Standard values are used for the ionic composition of the blood, the plasma albumin concentration, and the hemoglobin concentration. All K m values required for the model are taken from the literature. The distribution of bicarbonate, chloride, and H + ions across the red blood cell membrane follows that of a Gibbs-Donnan equilibrium. The system of equations that results is solved numerically using constraints for mass balance and electroneutrality. The model reproduces the phenomena associated with CO 2 carriage, including the magnitude of the Haldane effect, very well. The structural nature of the model allows various hypothetical scenarios to be explored. Here we examine the effects of 1) removing the ability of hemoglobin to form carbamino compounds; 2) allowing a degree of Cl - binding to deoxygenated hemoglobin; and 3) removing the chloride (Hamburger) shift. The insights gained could not have been obtained from empirical models. This study is the first to incorporate a mechanistic model of chloride-bicarbonate exchange between the erythrocyte and plasma into a full physicochemical model of the carriage of carbon dioxide in blood. The mechanistic nature of the model allowed a theoretical study of the quantitative significance for carbon dioxide transport of carbamino compound formation; the putative binding of chloride to deoxygenated hemoglobin, and the chloride (Hamburger) shift. Copyright © 2017 the American Physiological Society.

A mechanistic physicochemical model of carbon dioxide transport in blood

PubMed Central

O’Neill, David P.

2017-01-01

A number of mathematical models have been produced that, given the Pco2 and Po2 of blood, will calculate the total concentrations for CO2 and O2 in blood. However, all these models contain at least some empirical features, and thus do not represent all of the underlying physicochemical processes in an entirely mechanistic manner. The aim of this study was to develop a physicochemical model of CO2 carriage by the blood to determine whether our understanding of the physical chemistry of the major chemical components of blood together with their interactions is sufficiently strong to predict the physiological properties of CO2 carriage by whole blood. Standard values are used for the ionic composition of the blood, the plasma albumin concentration, and the hemoglobin concentration. All Km values required for the model are taken from the literature. The distribution of bicarbonate, chloride, and H+ ions across the red blood cell membrane follows that of a Gibbs-Donnan equilibrium. The system of equations that results is solved numerically using constraints for mass balance and electroneutrality. The model reproduces the phenomena associated with CO2 carriage, including the magnitude of the Haldane effect, very well. The structural nature of the model allows various hypothetical scenarios to be explored. Here we examine the effects of 1) removing the ability of hemoglobin to form carbamino compounds; 2) allowing a degree of Cl− binding to deoxygenated hemoglobin; and 3) removing the chloride (Hamburger) shift. The insights gained could not have been obtained from empirical models. NEW & NOTEWORTHY This study is the first to incorporate a mechanistic model of chloride-bicarbonate exchange between the erythrocyte and plasma into a full physicochemical model of the carriage of carbon dioxide in blood. The mechanistic nature of the model allowed a theoretical study of the quantitative significance for carbon dioxide transport of carbamino compound formation; the putative binding of chloride to deoxygenated hemoglobin, and the chloride (Hamburger) shift. PMID:27881667

Noncoded amino acids in protein engineering: Structure-activity relationship studies of hirudin-thrombin interaction.

PubMed

De Filippis, Vincenzo; Acquasaliente, Laura; Pontarollo, Giulia; Peterle, Daniele

2018-01-01

The advent of recombinant DNA technology allowed to site-specifically insert, delete, or mutate almost any amino acid in a given protein, significantly improving our knowledge of protein structure, stability, and function. Nevertheless, a quantitative description of the physical and chemical basis that makes a polypeptide chain to efficiently fold into a stable and functionally active conformation is still elusive. This mainly originates from the fact that nature combined, in a yet unknown manner, different properties (i.e., hydrophobicity, conformational propensity, polarizability, and hydrogen bonding capability) into the 20 standard natural amino acids, thus making difficult, if not impossible, to univocally relate the change in protein stability or function to the alteration of physicochemical properties caused by amino acid exchange(s). In this view, incorporation of noncoded amino acids with tailored side chains, allowing to finely tune the structure at a protein site, would facilitate to dissect the effects of a given mutation in terms of one or a few physicochemical properties, thus much expanding the scope of physical organic chemistry in the study of proteins. In this review, relevant applications from our laboratory will be presented on the use of noncoded amino acids in structure-activity relationships studies of hirudin binding to thrombin. © 2017 International Union of Biochemistry and Molecular Biology, Inc.

The Importance of Being Tyrosine: Lessons in Molecular Recognition from Minimalist Synthetic Binding Proteins

PubMed Central

Koide, Shohei; Sidhu, Sachdev S.

2010-01-01

Summary Combinatorial libraries built with severely restricted chemical diversity have yielded highly functional synthetic binding proteins. Structural analyses of these minimalist binding sites have revealed the dominant role of large tyrosine residues for mediating molecular contacts and of small serine/glycine residues for providing space and flexibility. The concept of using limited residue types to construct optimized binding proteins mirrors findings in the field of small molecule drug development, where it has been proposed that most drugs are built from a limited set of side chains presented by diverse frameworks. The physicochemical properties of tyrosine make it the amino acid that is most effective for mediating molecular recognition, and protein engineers have taken advantage of these characteristics to build tyrosine-rich protein binding sites that outperform natural proteins in terms of affinity and specificity. Knowledge from preceding studies can be used to improve current designs, and thus, synthetic protein libraries will continue to evolve and improve. In the near future, it seems likely that synthetic binding proteins will supersede natural antibodies for most purposes, and moreover, synthetic proteins will enable many new applications beyond the scope of natural proteins. PMID:19298050

Raman crystallography of RNA.

PubMed

Gong, Bo; Chen, Jui-Hui; Yajima, Rieko; Chen, Yuanyuan; Chase, Elaine; Chadalavada, Durga M; Golden, Barbara L; Carey, Paul R; Bevilacqua, Philip C

2009-10-01

Raman crystallography is the application of Raman spectroscopy to single crystals. This technique has been applied to a variety of protein molecules where it has provided unique information about biopolymer folding, substrate binding, and catalysis. Here, we describe the application of Raman crystallography to functional RNA molecules. RNA represents unique opportunities and challenges for Raman crystallography. One issue that confounds studies of RNA is its tendency to adopt multiple non-functional folds. Raman crystallography has the advantage that it isolates a single state of the RNA within the crystal and can evaluate its fold, metal ion binding properties (ligand identity, stoichiometry, and affinity), proton binding properties (identity, stoichiometry, and affinity), and catalytic potential. In particular, base-specific stretches can be identified and then associated with the binding of metal ions and protons. Because measurements are carried out in the hanging drop at ambient, rather than cryo, conditions and because RNA crystals tend to be approximately 70% solvent, RNA dynamics and conformational changes become experimentally accessible. This review focuses on experimental setup and procedures, acquisition and interpretation of Raman data, and determination of physicochemical properties of the RNA. Raman crystallographic and solution biochemical experiments on the HDV RNA enzyme are summarized and found to be in excellent agreement. Remarkably, characterization of the crystalline state has proven to help rather than hinder functional characterization of functional RNA, most likely because the tendency of RNA to fold heterogeneously is limited in a crystalline environment. Future applications of Raman crystallography to RNA are briefly discussed.

Acceleration of Binding Site Comparisons by Graph Partitioning.

PubMed

Krotzky, Timo; Klebe, Gerhard

2015-08-01

The comparison of protein binding sites is a prominent task in computational chemistry and has been studied in many different ways. For the automatic detection and comparison of putative binding cavities the Cavbase system has been developed which uses a coarse-grained set of pseudocenters to represent the physicochemical properties of a binding site and employs a graph-based procedure to calculate similarities between two binding sites. However, the comparison of two graphs is computationally quite demanding which makes large-scale studies such as the rapid screening of entire databases hardly feasible. In a recent work, we proposed the method Local Cliques (LC) for the efficient comparison of Cavbase binding sites. It employs a clique heuristic to detect the maximum common subgraph of two binding sites and an extended graph model to additionally compare the shape of individual surface patches. In this study, we present an alternative to further accelerate the LC method by partitioning the binding-site graphs into disjoint components prior to their comparisons. The pseudocenter sets are split with regard to their assigned phyiscochemical type, which leads to seven much smaller graphs than the original one. Applying this approach on the same test scenarios as in the former comprehensive way results in a significant speed-up without sacrificing accuracy. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Protein binding hot spots prediction from sequence only by a new ensemble learning method.

PubMed

Hu, Shan-Shan; Chen, Peng; Wang, Bing; Li, Jinyan

2017-10-01

Hot spots are interfacial core areas of binding proteins, which have been applied as targets in drug design. Experimental methods are costly in both time and expense to locate hot spot areas. Recently, in-silicon computational methods have been widely used for hot spot prediction through sequence or structure characterization. As the structural information of proteins is not always solved, and thus hot spot identification from amino acid sequences only is more useful for real-life applications. This work proposes a new sequence-based model that combines physicochemical features with the relative accessible surface area of amino acid sequences for hot spot prediction. The model consists of 83 classifiers involving the IBk (Instance-based k means) algorithm, where instances are encoded by important properties extracted from a total of 544 properties in the AAindex1 (Amino Acid Index) database. Then top-performance classifiers are selected to form an ensemble by a majority voting technique. The ensemble classifier outperforms the state-of-the-art computational methods, yielding an F1 score of 0.80 on the benchmark binding interface database (BID) test set. http://www2.ahu.edu.cn/pchen/web/HotspotEC.htm .

Interactions of Indole Derivatives with β-Cyclodextrin: A Quantitative Structure-Property Relationship Study

PubMed Central

Šoškić, Milan; Porobić, Ivana

2016-01-01

Retention factors for 31 indole derivatives, most of them with auxin activity, were determined by high-performance liquid chromatography, using bonded β-cyclodextrin as a stationary phase. A three-parameter QSPR (quantitative structure-property relationship) model, based on physico-chemical and structural descriptors was derived, which accounted for about 98% variations in the retention factors. The model suggests that the indole nucleus occupies the relatively apolar cavity of β-cyclodextrin while the carboxyl group of the indole -3-carboxylic acids makes hydrogen bonds with the hydroxyl groups of β-cyclodextrin. The length and flexibility of the side chain containing carboxyl group strongly affect the binding of these compounds to β-cyclodextrin. Non-acidic derivatives, unlike the indole-3-carboxylic acids, are poorly retained on the column. A reasonably well correlation was found between the retention factors of the indole-3-acetic acids and their relative binding affinities for human serum albumin, a carrier protein in the blood plasma. A less satisfactory correlation was obtained when the retention factors of the indole derivatives were compared with their affinities for auxin-binding protein 1, a plant auxin receptor. PMID:27124734

Insights on the mechanism of action of immunostimulants in relation to their pharmacological potency. The effects of imidazoquinolines on TLR8.

PubMed

Kubli-Garfias, Carlos; Vázquez-Ramírez, Ricardo; Trejo-Muñoz, Cynthia; Berber, Arturo

2017-01-01

Imidazoquinolines are powerful immunostimulants (IMMS) that function through Toll-like receptors, particularly TLR7 and TLR8. In addition to enhancing the immune response, IMMS also function as antineoplastic drugs and vaccine adjuvants. These small compounds display almost the same molecular structure, except in some cases in which atom in position 1 varies and changes the imidazole characteristics. A variable acyclic side chain is also always attached at atom in position 2, while another chain may be attached at atom in position 1. These structural differences alter immune responses, such as the production of interferon regulatory factor and nuclear factor-κB (IRF-NFκB). In this work, quantum mechanics theory and computational chemistry methods were applied to study the physicochemical properties of the crystal binding site of TLR8 complexed with the following six IMMS molecules: Hybrid-2, XG1-236, DS802, CL075, CL097 and R848 (resiquimod). The PDB IDs of the crystals were: 4R6A, 4QC0, 4QBZ, 3W3K, 3W3J, and 3W3N respectively. Thus, were calculated, the total energy, solvation energy, interaction energy (instead of free energy) of the system and interaction energy of the polar region of the IMMS. Additionally, the dipole moment, electrostatic potential, polar surface, atomic charges, hydrogen bonds, and polar and hydrophobic interactions, among others, were assessed. Together, these properties revealed important differences among the six TLR8-immunostimulant complexes, reflected as different interaction energies and therefore different electrostatic environments and binding energies. Remarkably, the interaction energy of a defined polar region composed of the highly polarized N3, N5 atoms and the N11 amino group, acted as a polar pharmacophore that correlates directly with the reported immunopharmacological potency of the six complexed molecules. Based on these results, it was concluded that accurate physicochemical analysis of the crystal binding site could reveal the binding energy (measured as interaction energy) and associated molecular mechanism of action between IMMS and TLR8. These findings may facilitate the development and design of improved small molecules with IMMS properties that are targeted to the TLR system and have enhanced pharmacological effectiveness and reduced toxicity.

Insights on the mechanism of action of immunostimulants in relation to their pharmacological potency. The effects of imidazoquinolines on TLR8

PubMed Central

Kubli-Garfias, Carlos; Vázquez-Ramírez, Ricardo; Trejo-Muñoz, Cynthia; Berber, Arturo

2017-01-01

Imidazoquinolines are powerful immunostimulants (IMMS) that function through Toll-like receptors, particularly TLR7 and TLR8. In addition to enhancing the immune response, IMMS also function as antineoplastic drugs and vaccine adjuvants. These small compounds display almost the same molecular structure, except in some cases in which atom in position 1 varies and changes the imidazole characteristics. A variable acyclic side chain is also always attached at atom in position 2, while another chain may be attached at atom in position 1. These structural differences alter immune responses, such as the production of interferon regulatory factor and nuclear factor-κB (IRF-NFκB). In this work, quantum mechanics theory and computational chemistry methods were applied to study the physicochemical properties of the crystal binding site of TLR8 complexed with the following six IMMS molecules: Hybrid-2, XG1-236, DS802, CL075, CL097 and R848 (resiquimod). The PDB IDs of the crystals were: 4R6A, 4QC0, 4QBZ, 3W3K, 3W3J, and 3W3N respectively. Thus, were calculated, the total energy, solvation energy, interaction energy (instead of free energy) of the system and interaction energy of the polar region of the IMMS. Additionally, the dipole moment, electrostatic potential, polar surface, atomic charges, hydrogen bonds, and polar and hydrophobic interactions, among others, were assessed. Together, these properties revealed important differences among the six TLR8-immunostimulant complexes, reflected as different interaction energies and therefore different electrostatic environments and binding energies. Remarkably, the interaction energy of a defined polar region composed of the highly polarized N3, N5 atoms and the N11 amino group, acted as a polar pharmacophore that correlates directly with the reported immunopharmacological potency of the six complexed molecules. Based on these results, it was concluded that accurate physicochemical analysis of the crystal binding site could reveal the binding energy (measured as interaction energy) and associated molecular mechanism of action between IMMS and TLR8. These findings may facilitate the development and design of improved small molecules with IMMS properties that are targeted to the TLR system and have enhanced pharmacological effectiveness and reduced toxicity. PMID:28582454

Health effects of residential wood smoke particles: the importance of combustion conditions and physicochemical particle properties

PubMed Central

Kocbach Bølling, Anette; Pagels, Joakim; Yttri, Karl Espen; Barregard, Lars; Sallsten, Gerd; Schwarze, Per E; Boman, Christoffer

2009-01-01

Background Residential wood combustion is now recognized as a major particle source in many developed countries, and the number of studies investigating the negative health effects associated with wood smoke exposure is currently increasing. The combustion appliances in use today provide highly variable combustion conditions resulting in large variations in the physicochemical characteristics of the emitted particles. These differences in physicochemical properties are likely to influence the biological effects induced by the wood smoke particles. Outline The focus of this review is to discuss the present knowledge on physicochemical properties of wood smoke particles from different combustion conditions in relation to wood smoke-induced health effects. In addition, the human wood smoke exposure in developed countries is explored in order to identify the particle characteristics that are relevant for experimental studies of wood smoke-induced health effects. Finally, recent experimental studies regarding wood smoke exposure are discussed with respect to the applied combustion conditions and particle properties. Conclusion Overall, the reviewed literature regarding the physicochemical properties of wood smoke particles provides a relatively clear picture of how these properties vary with the combustion conditions, whereas particle emissions from specific classes of combustion appliances are less well characterised. The major gaps in knowledge concern; (i) characterisation of the atmospheric transformations of wood smoke particles, (ii) characterisation of the physicochemical properties of wood smoke particles in ambient and indoor environments, and (iii) identification of the physicochemical properties that influence the biological effects of wood smoke particles. PMID:19891791

A study on the electrical, optical, and physicochemical properties of poly(MMA-co-MAA)/ poly(3,4-ethylenedioxythiophene) hybrid thin films.

PubMed

Han, Yong-Hyeon; Kim, Hyeong Eun; Hwangbo, Kyung-Hee; Yim, Jin-Heong; Cho, Kuk Young

2013-08-01

Poly(3,4-ethylenedioxythiophene) (PEDOT) has good properties as a conductive polymer such as high conductivity, optical transmittance, and chemical stability, while offering relatively weak physicochemical properties. The main purpose of this paper is to improve physicochemical properties such as solvent resistance and pencil hardness of PEDOT. Carboxyl groups in the poly(MMA-co-MAA) polymer chains can effectively crosslink each other in the presence of aziridine, resulting in physicochemically robust PEDOT/poly(MMA-co-MAA) hybrid conductive films. The electrical conductivity, optical properties, and physicochemical properties of the hybrid conductive film were compared by varying the solid content and poly(MMA-co-MAA) portion in the coating precursor solution. From the results, the transparency and surface resistance of the hybrid film show a tendency to decrease with increasing solid content in the coating precursor. Moreover, solvent resistance and hardness were dramatically enhanced by hybridization of PEDOT and crosslinked poly(MMA-co-MAA) due to curing reactions between carboxyl groups. The chemical composition of 30 wt-% of poly(MMA-co-MAA) (MMA:MAA mole ratio 9:1) and 3 wt-% - 5 wt-% of aziridine yields the best physicochemical properties of poly(MMA-co-MAA)/PEDOT hybrid thin films.

Analysis of CD44-Hyaluronan Interactions in an Artificial Membrane System

PubMed Central

Wolny, Patricia M.; Banerji, Suneale; Gounou, Céline; Brisson, Alain R.; Day, Anthony J.; Jackson, David G.; Richter, Ralf P.

2010-01-01

CD44 is a major cell surface receptor for the large polydisperse glycosaminoglycan hyaluronan (HA). Binding of the long and flexible HA chains is thought to be stabilized by the multivalent nature of the sugar molecule. In addition, high and low molecular weight forms of HA provoke distinct proinflammatory and anti-inflammatory effects upon binding to CD44 and can deliver either proliferative or antiproliferative signals in appropriate cell types. Despite the importance of such interactions, however, neither the stoichiometry of multivalent HA binding at the cell surface nor the molecular basis for functional distinction between different HA size categories is understood. Here we report on the design of a supported lipid bilayer system that permits quantitative analysis of multivalent binding through presentation of CD44 in a stable, natively oriented manner and at controlled density. Using this system in combination with biophysical techniques, we show that the amount of HA binding to bilayers that are densely coated with CD44 increases as a function of HA size, with half-maximal saturation at ∼30 kDa. Moreover, reversible binding was confined to the smaller HA species (molecular weight of ≤10 kDa), whereas the interaction was essentially irreversible with larger polymers. The amount of bound HA decreased with decreasing receptor surface density, but the stability of binding was not affected. From a physico-chemical perspective, the binding properties of HA share many similarities with the typical behavior of a flexible polymer as it adsorbs onto a homogeneously attractive surface. These findings provide new insight into the multivalent nature of CD44-HA interactions and suggest a molecular basis for the distinct biological properties of different size fractions of hyaluronan. PMID:20663884

The oxygen-binding properties of hemocyanin from the mollusk Concholepas concholepas.

PubMed

González, Andrea; Nova, Esteban; Del Campo, Miguel; Manubens, Augusto; De Ioannes, Alfredo; Ferreira, Jorge; Becker, María Inés

2017-12-01

Hemocyanins have highly conserved copper-containing active sites that bind oxygen. However, structural differences among the hemocyanins of various mollusks may affect their physicochemical properties. Here, we studied the oxygen-binding cooperativity and affinity of Concholepas concholepas hemocyanin (CCH) and its two isolated subunits over a wide range of temperatures and pH values. Considering the differences in the quaternary structures of CCH and keyhole limpet hemocyanin (KLH), we hypothesized that the heterodidecameric CCH has different oxygen-binding parameters than the homodidecameric KLH. A novel modification of the polarographic method was applied in which rat liver submitochondrial particles containing cytochrome c oxidase were introduced to totally deplete oxygen of the test solution using ascorbate as the electron donor. This method was both sensitive and reproducible. The results showed that CCH, like other hemocyanins, exhibits cooperativity, showing an inverse relationship between the oxygen-binding parameters and temperature. According to their Hill coefficients, KLH has greater cooperativity than CCH at physiological pH; however, CCH is less sensitive to pH changes than KLH. Appreciable differences in binding behavior were found between the CCH subunits: the cooperativity of CCH-A was not only almost double that of CCH-B, but it was also slightly superior to that of CCH, thus suggesting that the oxygen-binding domains of the CCH subunits are different in their primary structure. Collectively, these data suggest that CCH-A is the main oxygen-binding domain in CCH; CCH-B may play a more structural role, perhaps utilizing its surprising predisposition to form tubular polymers, unlike CCH-A, as demonstrated here using electron microscopy. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of K and Pt promoters on the performance of cobalt catalyst supported on CNTs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zabidi, Noor Asmawati Mohd, E-mail: noorasmawati-mzabidi@petronas.com.my; Ali, Sardar, E-mail: alikhan-635@yahoo.com; Subbarao, Duvvuri, E-mail: duvvuri-subbarao@petronas.com.my

2014-10-24

This paper presents a comparative study on the effects of incorporation of potassium (K) and platinum (Pt) as promoters on the physicochemical properties of cobalt catalyst. The catalyst was prepared by a wet impregnation method on a CNTs support. Samples were characterized using transmission electron microscopy (TEM), H{sub 2}-temperature-programmed reduction (TPR) and X-ray photoelectron spectroscopy (XPS) techniques. Fischer-Tropsch Synthesis (FTS) was carried out in a fixed-bed microreactor at 543 K and 1 atm, with H{sub 2}/CO = 2v/v and space velocity, SV of 12 L/g.h for 5 hours. The K-promoted and Pt-promoted Co catalysts have different physicochemical properties and catalytic performances comparedmore » to that of the un-promoted Co catalyst. XPS analysis revealed that K and Pt promoters induced electronic modifications as exhibited by the shifts in the Co binding energies. Incorporation of 0.06 wt% K and 0.06 wt% Pt in Co/CNTs catalyst resulted in an increase in the CO conversion and C{sub 5+} selectivity and a decrease in methane selectivity. Potassium was found to be a better promoter for Co/CNTs catalyst compared to platinum.« less

Effects of K and Pt promoters on the performance of cobalt catalyst supported on CNTs

NASA Astrophysics Data System (ADS)

Zabidi, Noor Asmawati Mohd; Ali, Sardar; Subbarao, Duvvuri

2014-10-01

This paper presents a comparative study on the effects of incorporation of potassium (K) and platinum (Pt) as promoters on the physicochemical properties of cobalt catalyst. The catalyst was prepared by a wet impregnation method on a CNTs support. Samples were characterized using transmission electron microscopy (TEM), H2-temperature-programmed reduction (TPR) and X-ray photoelectron spectroscopy (XPS) techniques. Fischer-Tropsch Synthesis (FTS) was carried out in a fixed-bed microreactor at 543 K and 1 atm, with H2/ CO = 2v / v and space velocity, SV of 12 L/g.h for 5 hours. The K-promoted and Pt-promoted Co catalysts have different physicochemical properties and catalytic performances compared to that of the un-promoted Co catalyst. XPS analysis revealed that K and Pt promoters induced electronic modifications as exhibited by the shifts in the Co binding energies. Incorporation of 0.06 wt% K and 0.06 wt% Pt in Co/CNTs catalyst resulted in an increase in the CO conversion and C5+ selectivity and a decrease in methane selectivity. Potassium was found to be a better promoter for Co/CNTs catalyst compared to platinum.

A Study of Physicochemical Properties of Subcutaneous Fat of the Abdomen and its Implication in Abdominal Obesity.

PubMed

Pandey, Arvind Kumar; Kumar, Pramod; Kodavoor, Srinivas Aithal; Kotian, Sushma Rama; Yathdaka, Sudhakar Narahari; Nayak, Dayanand; Souza, Anne D; Souza, Antony Sylvan D

2016-05-01

The lower abdominal obesity is more resistant to absorption as compared to that of upper abdomen. Differences in the physicochemical properties of the subcutaneous fat of the upper and lower abdomen may be responsible for this variation. There is paucity of the scientific literature on the physicochemical properties of the subcutaneous fat of abdomen. The present study was undertaken to create a database of physicochemical properties of abdominal subcutaneous fat. The samples of subcutaneous fat from upper and lower abdomen were collected from 40 fresh autopsied bodies (males 33, females 7). The samples were prepared for physicochemical analysis using organic and inorganic solvents. Various physicochemical properties of the fat samples analysed were surface tension, viscosity, specific gravity, specific conductivity, iodine value and thermal properties. Data was analysed by paired and independent sample t-tests. There was a statistically significant difference in all the physicochemical parameters between males and females except surface tension (organic) and surface tension (inorganic) of upper abdominal fat, and surface tension (organic) of lower abdominal fat. In males, viscosity of upper abdominal fat was more compared to that of lower abdomen (both organic and inorganic) unlike the specific conductivity that was higher for the lower abdominal fat as compared to that of the upper abdomen. In females there were statistically significant higher values of surface tension (inorganic) and specific gravity (organic) of the upper abdomen fat as compared to that of lower abdomen. The initial and final weight loss of the lower abdominal fat as indicated by Thermo Gravimetric Analysis was significantly more in males than in female. The difference in the physicochemical properties of subcutaneous fat between upper and lower abdomen and between males and females could be responsible for the variant behaviour of subcutaneous abdominal fat towards resorption.

Nature and consequences of non-covalent interactions between flavonoids and macronutrients in foods.

PubMed

Bordenave, Nicolas; Hamaker, Bruce R; Ferruzzi, Mario G

2014-01-01

Many of the potential health benefits of flavonoids have been associated with their specific chemical and biological properties including their ability to interact and bind non-covalently to macronutrients in foods. While flavonoid-protein interactions and binding have been the subject of intensive study, significantly less is understood about non-covalent interactions with carbohydrates and lipids. These interactions with macronutrients are likely to impact both the flavonoid properties in foods, such as their radical scavenging activity, and the food or beverage matrix itself, including their taste, texture and other sensorial properties. Overall, non-covalent binding of flavonoids with macronutrients is primarily driven by van der Waals interactions. From the flavonoid perspective, these interactions are modulated by characteristics such as degree of polymerization, molecular flexibility, number of external hydroxyl groups, or number of terminal galloyl groups. From the macronutrient standpoint, electrostatic and ionic interactions are generally predominant with carbohydrates, while hydrophobic interactions are generally predominant with lipids and mainly limited to interactions with flavonols. All of these interactions are involved in flavonoid-protein interactions. While primarily associated with undesirable characteristics in foods and beverages, such as astringency, negative impact on macronutrient digestibility and hazing, more recent efforts have attempted to leverage these interactions to develop controlled delivery systems or strategies to enhance flavonoids bioavailability. This paper aims at reviewing the fundamental bases for non-covalent interactions, their occurrence in food and beverage systems and their impact on the physico-chemical, organoleptic and some nutritional properties of food.

Hybrid ligand-alkylating agents targeting telomeric G-quadruplex structures.

PubMed

Doria, Filippo; Nadai, Matteo; Folini, Marco; Di Antonio, Marco; Germani, Luca; Percivalle, Claudia; Sissi, Claudia; Zaffaroni, Nadia; Alcaro, Stefano; Artese, Anna; Richter, Sara N; Freccero, Mauro

2012-04-14

The synthesis, physico-chemical properties and biological effects of a new class of naphthalene diimides (NDIs) capable of reversibly binding telomeric DNA and alkylate it through an electrophilic quinone methide moiety (QM), are reported. FRET and circular dichroism assays showed a marked stabilization and selectivity towards telomeric G4 DNA folded in a hybrid topology. NDI-QMs' alkylating properties revealed a good reactivity on single nucleosides and selectivity towards telomeric G4. A selected NDI was able to significantly impair the growth of melanoma cells by causing telomere dysfunction and down-regulation of telomerase expression. These findings points to our hybrid ligand-alkylating NDIs as possible tools for the development of novel targeted anticancer therapies. This journal is © The Royal Society of Chemistry 2012

Key physicochemical properties of nanomaterials in view of their toxicity: an exploratory systematic investigation for the example of carbon-based nanomaterial

NASA Astrophysics Data System (ADS)

Salieri, Beatrice; Pasteris, Andrea; Netkueakul, Woranan; Hischier, Roland

2017-03-01

Currently, a noncomprehensive understanding of the physicochemical properties of carbon-based nanomaterial (CBNs), which may affect toxic effects, is still observable. In this study, an exploratory systematic investigation into the key physicochemical properties of multiwall carbon nanotube (MWCNT), single-wall carbon nanotube (SWCNT), and C60-fullerene on their ecotoxicity has been undertaken. We undertook an extensive survey of the literature pertaining to the ecotoxicity of organism representative of the trophic level of algae, crustaceans, and fish. Based on this, a set of data reporting both the physicochemical properties of carbon-based nanomaterial and the observed toxic effect has been established. The relationship between physicochemical properties and observed toxic effect was investigated based on various statistical approaches. Specifically, analysis of variance by one-way ANOVA was used to assess the effect of categorical properties (use of a dispersant or treatments in the test medium, type of carbon-based nanomaterial, i.e., SWCNT, MWCNT, C60-fullerene, functionalization), while multiple regression analysis was used to assess the effect of quantitative properties (i.e., diameter length of nanotubes, secondary size) on the toxicity values. The here described investigations revealed significant relationships among the physicochemical properties and observed toxic effects. The research was mainly affected by the low availability of data and also by the low variability of the studies collected. Overall, our results demonstrate that the here proposed and applied approach could have a major role in identifying the physicochemical properties of relevance for the toxicity of nanomaterial. However, the future success of the approach would require that the ENMs and the experimental conditions used in the toxicity studies are fully characterized.

DNABP: Identification of DNA-Binding Proteins Based on Feature Selection Using a Random Forest and Predicting Binding Residues.

PubMed

Ma, Xin; Guo, Jing; Sun, Xiao

2016-01-01

DNA-binding proteins are fundamentally important in cellular processes. Several computational-based methods have been developed to improve the prediction of DNA-binding proteins in previous years. However, insufficient work has been done on the prediction of DNA-binding proteins from protein sequence information. In this paper, a novel predictor, DNABP (DNA-binding proteins), was designed to predict DNA-binding proteins using the random forest (RF) classifier with a hybrid feature. The hybrid feature contains two types of novel sequence features, which reflect information about the conservation of physicochemical properties of the amino acids, and the binding propensity of DNA-binding residues and non-binding propensities of non-binding residues. The comparisons with each feature demonstrated that these two novel features contributed most to the improvement in predictive ability. Furthermore, to improve the prediction performance of the DNABP model, feature selection using the minimum redundancy maximum relevance (mRMR) method combined with incremental feature selection (IFS) was carried out during the model construction. The results showed that the DNABP model could achieve 86.90% accuracy, 83.76% sensitivity, 90.03% specificity and a Matthews correlation coefficient of 0.727. High prediction accuracy and performance comparisons with previous research suggested that DNABP could be a useful approach to identify DNA-binding proteins from sequence information. The DNABP web server system is freely available at http://www.cbi.seu.edu.cn/DNABP/.

Igs expressed by chronic lymphocytic leukemia B cells show limited binding-site structure variability.

PubMed

Marcatili, Paolo; Ghiotto, Fabio; Tenca, Claudya; Chailyan, Anna; Mazzarello, Andrea N; Yan, Xiao-Jie; Colombo, Monica; Albesiano, Emilia; Bagnara, Davide; Cutrona, Giovanna; Morabito, Fortunato; Bruno, Silvia; Ferrarini, Manlio; Chiorazzi, Nicholas; Tramontano, Anna; Fais, Franco

2013-06-01

Ag selection has been suggested to play a role in chronic lymphocytic leukemia (CLL) pathogenesis, but no large-scale analysis has been performed so far on the structure of the Ag-binding sites (ABSs) of leukemic cell Igs. We sequenced both H and L chain V(D)J rearrangements from 366 CLL patients and modeled their three-dimensional structures. The resulting ABS structures were clustered into a small number of discrete sets, each containing ABSs with similar shapes and physicochemical properties. This structural classification correlates well with other known prognostic factors such as Ig mutation status and recurrent (stereotyped) receptors, but it shows a better prognostic value, at least in the case of one structural cluster for which clinical data were available. These findings suggest, for the first time, to our knowledge, on the basis of a structural analysis of the Ab-binding sites, that selection by a finite quota of antigenic structures operates on most CLL cases, whether mutated or unmutated.

Albumin-Encapsulated Liposomes: A Novel Drug Delivery Carrier With Hydrophobic Drugs Encapsulated in the Inner Aqueous Core.

PubMed

Okamoto, Yuko; Taguchi, Kazuaki; Yamasaki, Keishi; Sakuragi, Mina; Kuroda, Shun'ichi; Otagiri, Masaki

2018-01-01

Liposomes are clinically used in drug delivery, but loading hydrophobic substances is limited to the hydrophobic space of a lipid membrane, despite the fact that it is favorable to encapsulate substances into the inner aqueous core of liposome, from a drug stability of view. We report herein on the preparation of a liposome with bovine serum albumin encapsulated (BSA-liposome). Using this system, it is possible to encapsulate hydrophobic drugs in the inner aqueous core of the liposome based on the hypothesis that the water solubility of hydrophobic drugs is increased when bound to albumin. The physicochemical properties of the prepared BSA-liposomes could be easily regulated and the loading of hydrophobic drugs in the inner aqueous core of the liposome was dramatically improved by virtue of the drug-binding properties of albumin. An in vivo safety and pharmacokinetic study showed that BSA-liposomes possess favorable properties as a drug carrier, including biocompatibility and a stealth effect. This new type of hydrophobic drug carrier, an albumin-liposome, has the potential for use in delivering numerous hydrophobic drugs that typically bind to albumin. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Immunoreactive Proteins of Bifidobacterium longum ssp. longum CCM 7952 and Bifidobacterium longum ssp. longum CCDM 372 Identified by Gnotobiotic Mono-Colonized Mice Sera, Immune Rabbit Sera and Non-immune Human Sera

PubMed Central

Górska, Sabina; Dylus, Ewa; Rudawska, Angelika; Brzozowska, Ewa; Srutkova, Dagmar; Schwarzer, Martin; Razim, Agnieszka; Kozakova, Hana; Gamian, Andrzej

2016-01-01

The Bifidobacteria show great diversity in the cell surface architecture which may influence the physicochemical properties of the bacterial cell and strain specific properties. The immunomodulatory role of bifidobacteria has been extensively studied, however studies on the immunoreactivity of their protein molecules are very limited. Here, we compared six different methods of protein isolation and purification and we report identification of immunogenic and immunoreactive protein of two human Bifidobacterium longum ssp. longum strains. We evaluated potential immunoreactive properties of proteins employing polyclonal sera obtained from germ free mouse, rabbit and human. The protein yield was isolation method-dependent and the reactivity of proteins detected by SDS-PAGE and Western blotting was heterogeneous and varied between different serum samples. The proteins with the highest immunoreactivity were isolated, purified and have them sequenced. Among the immunoreactive proteins we identified enolase, aspartokinase, pyruvate kinase, DnaK (B. longum ssp. longum CCM 7952) and sugar ABC transporter ATP-binding protein, phosphoglycerate kinase, peptidoglycan synthethase penicillin-binding protein 3, transaldolase, ribosomal proteins and glyceraldehyde 3-phosphate dehydrogenase (B. longum ssp. longum CCDM 372). PMID:27746766

Immunoreactive Proteins of Bifidobacterium longum ssp. longum CCM 7952 and Bifidobacterium longum ssp. longum CCDM 372 Identified by Gnotobiotic Mono-Colonized Mice Sera, Immune Rabbit Sera and Non-immune Human Sera.

PubMed

Górska, Sabina; Dylus, Ewa; Rudawska, Angelika; Brzozowska, Ewa; Srutkova, Dagmar; Schwarzer, Martin; Razim, Agnieszka; Kozakova, Hana; Gamian, Andrzej

2016-01-01

The Bifidobacteria show great diversity in the cell surface architecture which may influence the physicochemical properties of the bacterial cell and strain specific properties. The immunomodulatory role of bifidobacteria has been extensively studied, however studies on the immunoreactivity of their protein molecules are very limited. Here, we compared six different methods of protein isolation and purification and we report identification of immunogenic and immunoreactive protein of two human Bifidobacterium longum ssp. longum strains. We evaluated potential immunoreactive properties of proteins employing polyclonal sera obtained from germ free mouse, rabbit and human. The protein yield was isolation method-dependent and the reactivity of proteins detected by SDS-PAGE and Western blotting was heterogeneous and varied between different serum samples. The proteins with the highest immunoreactivity were isolated, purified and have them sequenced. Among the immunoreactive proteins we identified enolase, aspartokinase, pyruvate kinase, DnaK ( B. longum ssp. longum CCM 7952) and sugar ABC transporter ATP-binding protein, phosphoglycerate kinase, peptidoglycan synthethase penicillin-binding protein 3, transaldolase, ribosomal proteins and glyceraldehyde 3-phosphate dehydrogenase ( B. longum ssp. longum CCDM 372).

Development of Seaweed-based Biopolymers for Edible Films and Lectins

NASA Astrophysics Data System (ADS)

Praseptiangga, D.

2017-04-01

Marine macroalgae (seaweeds) as one of important groups of biopolymers play an important role in human life. Biopolymers have been studied regarding their film-forming properties to produce edible films intended as food packaging and active ingredient carriers. Edible film, a thin layer or which is an integral part of food and can be eaten together with, have been used to avoid food quality deterioration due to physico-chemical changes, texture changes, or chemical reactions. Film-forming materials can be utilized individually or as mixed composite blends. Proteins and polysaccharides used for their mechanical and structural properties, and hydrophobic substances (lipids, essential oils, and emulsifiers) to provide good moisture barrier properties. In addition, bioactive substances from marine natural products, including seaweeds, have been explored for being used in the fields of medicine, food science, pharmaceutical science, biochemistry, and glycobiology. Among them, lectins or carbohydrate-binding proteins from seaweeds have recently been remarked. Lectins (hemagglutinins) are widely distributed in nature and also good candidates in such prospecting of seaweeds. They are useful as convenient tools to discriminate differences in carbohydrate structures and reveal various biological activities through binding and interacting to carbohydrates, suggesting that they are promising candidates for medicinal and clinical application.

Preparation, characterization and binding behaviors of host-guest inclusion complexes of metoclopramide hydrochloride with α- and β-cyclodextrin molecules

NASA Astrophysics Data System (ADS)

Barman, Siti; Barman, Biraj Kumar; Roy, Mahendra Nath

2018-03-01

The supramolecular interaction of metoclopramide hydrochloride (MP) with α-cyclodextrin (α-CD) and β-cyclodextrin (β-CD) has been inspected by ultraviolet-visible (UV-vis) light, infra-red (IR) light, fluorescence and 1H NMR spectroscopy. The formation of an inclusion complex greatly affects the physical-chemical properties of the guest molecules, such as solubility, chemical reactivity and the spectroscopic and electrochemical properties. Thus the changes in the spectral properties and physico-chemical properties confirm the inclusion complex formation. Surface tension, conductivity studies and Job's plot indicate a 1: 1 stoichiometry of the MP:CD host-guest inclusion complexes. The binding/association constants have been evaluated by both UV-Vis and fluorescence spectroscopic study indicating a higher degree of encapsulation for β-cyclodextrin (β-CD). Furthermore, the negative value of thermodynamic parameter (ΔG°) of the host-guest system suggests that the inclusion process proceeded spontaneously at 298.15 K. Based on the NMR data, the plausible mode of interaction of MP:α-CD and MP:β-CD complexes were proposed, which suggested that lipophilic aromatic ring of the MP entered into the cavity of CDs from the wider side, with the amide (sbnd CONH) and methoxy (-OMe) residues inside the CD cavity.

Physicochemical properties and cell-based bioactivity of Pu'erh tea polysaccharide conjugates.

PubMed

Chen, Xiao-Qiang; Zhang, Zhi-Fa; Gao, Zhi-Ming; Huang, Yi; Wu, Zheng-Qi

2017-11-01

Polysaccharide conjugates were prepared from Pu'erh tea and fractionated by DEAE-cellulose DE-52 column chromatography to yield one unexplored polysaccharide-conjugate fraction termed TPC-P with a molecular weight of 251,200Da. DVS (dynamic vapour sorption) result discovered that the humidity condition of long-term preservation for TPC-P is below 70% RH. Although it contained proteins, TPC-P could not bind to the Coomassie Brilliant Blue dyes G250 and R250. The "shoulder-shaped" ultroviolet absorption peak in TPC-P UV-vis scanning spectum ascribe theabrownins that inevitably adsorbed the polysaccharide conjugate. Zeta potential results demonstrated TPC-P aqueous solution merely presented the negative charge properties of polysaccharides instead of acid-base property of its protein section, and had more stability in greater than pH 5.5. No precipitation or haze occurred in the three TPC-P/EGCG aqueous mixtures during their being stored for 12h. The phase separation was observed in aqueous mixtures of TPC-P and type B gelatin. TPC-P possessed the fine stability as a function of temperature heating and cooling between 0 and 55°C. It is proposed that some properties of the covalent binding protein of TPC-P were "shielded" by its polysaccharide chains. Copyright © 2017 Elsevier B.V. All rights reserved.

Amylopectin molecular structure in relation to physicochemical properties of quinoa starch.

PubMed

Li, Guantian; Zhu, Fan

2017-05-15

Structure-function relationships of starch components remain a subject of research interest. Quinoa starch has very small granules (∼2μm) with unique properties. In this study, nine quinoa starches varied greatly in composition, structure, and physicochemical properties were selected for the analysis of structure-function relationships. Pearson correlation analysis revealed that the properties related to gelatinization such as swelling power, water solubility index, crystallinity, pasting, and thermal properties are much affected by the amylopectin chain profile and amylose content. The parameters of gel texture and amylose leaching are much related to amylopectin internal structure. Other properties such as enzyme susceptibility and particle size distribution are also strongly correlated with starch composition and amylopectin structure. Interesting findings indicate the importance of amylopectin internal structure and individual unit chain profile in determining the physicochemical properties of starch. This work highlights some relationships among composition, amylopectin structure and physicochemical properties of quinoa starch. Copyright © 2017 Elsevier Ltd. All rights reserved.

Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations.

PubMed

Liu, Kai; Watanabe, Etsurou; Kokubo, Hironori

2017-02-01

The binding mode prediction is of great importance to structure-based drug design. The discrimination of various binding poses of ligand generated by docking is a great challenge not only to docking score functions but also to the relatively expensive free energy calculation methods. Here we systematically analyzed the stability of various ligand poses under molecular dynamics (MD) simulation. First, a data set of 120 complexes was built based on the typical physicochemical properties of drug-like ligands. Three potential binding poses (one correct pose and two decoys) were selected for each ligand from self-docking in addition to the experimental pose. Then, five independent MD simulations for each pose were performed with different initial velocities for the statistical analysis. Finally, the stabilities of ligand poses under MD were evaluated and compared with the native one from crystal structure. We found that about 94% of the native poses were maintained stable during the simulations, which suggests that MD simulations are accurate enough to judge most experimental binding poses as stable properly. Interestingly, incorrect decoy poses were maintained much less and 38-44% of decoys could be excluded just by performing equilibrium MD simulations, though 56-62% of decoys were stable. The computationally-heavy binding free energy calculation can be performed only for these survived poses.

Differentiation of δ, μ, and κ opioid receptor agonists based on pharmacophore development and computed physicochemical properties

NASA Astrophysics Data System (ADS)

Filizola, Marta; Villar, Hugo O.; Loew, Gilda H.

2001-04-01

Compounds that bind with significant affinity to the opioid receptor types, δ, μ, and κ, with different combinations of activation and inhibition at these three receptors could be promising behaviorally selective agents. Working on this hypothesis, the chemical moieties common to three different sets of opioid receptor agonists with significant affinity for each of the three receptor types δ, μ, or κ were identified. Using a distance analysis approach, common geometric arrangements of these chemical moieties were found for selected δ, μ, or κ opioid agonists. The chemical and geometric commonalities among agonists at each opioid receptor type were then compared with a non-specific opioid recognition pharmacophore recently developed. The comparison provided identification of the additional requirements for activation of δ, μ, and κ opioid receptors. The distance analysis approach was able to clearly discriminate κ-agonists, while global molecular properties for all compounds were calculated to identify additional requirements for activation of δ and μ receptors. Comparisons of the combined geometric and physicochemical properties calculated for each of the three sets of agonists allowed the determination of unique requirements for activation of each of the three opioid receptors. These results can be used to improve the activation selectivity of known opioid agonists and as a guide for the identification of novel selective opioid ligands with potential therapeutic usefulness.

Effects of Soy Protein Hydrolysates Prepared by Varying Subcritical Media on the Physicochemical Properties of Pork Patties

PubMed Central

Davaatseren, Munkhtugs

2016-01-01

This study investigated the effect of soy protein hydrolysates (SPH) prepared by varying subcritical media on the physicochemical properties of pork patties. For resource of SPH, two different soybean species (Glycine max Merr.) of Daewonkong (DWK) and Saedanbaek (SDB) were selected. SPH was prepared by subcritical processing at 190℃ and 25 MPa under three different of media (water, 20% ethanol and 50% ethanol). Solubility and free amino group content revealed that water was better to yield larger amount of SPH than ethanol/water mixtures, regardless of species. Molecular weight (Mw) distribution of SPH was also similar between two species, while slightly different Mw distribution was obtained by subcritical media. For pork patty application, 50% ethanol treatment showed clear red color comparing to control after 14 d of storage. In addition, ethanol treatment had better oxidative stability than control and water treatment based on thiobarbituric acid-reactive substances (TBARS) analysis. For eating quality, although 20% ethanol treatment in SDB showed slightly higher cooking loss than control, generally addition of SPH did not affect the water-binding properties and hardness of pork patties. Consequently, the present study indicated that 50% ethanol was the best subcritical media to produce SPH possessing antioxidant activity, and the SPH produced from DWK exhibited better antioxidant activity than that produced SDB. PMID:27499657

Insights into physicochemical and functional properties of polysaccharides sequentially extracted from onion (Allium cepa L.).

PubMed

Zhu, Dan-Ye; Ma, Yi-Long; Wang, Cai-Hong; Wang, Hao; Ren, Ya-Fei; Zhang, Jian-Guo; Thakur, Kiran; Wei, Zhao-Jun

2017-12-01

Onion polysaccharides (ACLP) were sequentially extracted with four different solvents (hot buffer, chelating agent, dilute alkaline and concentrated alkaline) and obtained four fractions, named as HBSS, CHSS, DASS and CASS, respectively. The present studies characterized the ACLP concerning its physicochemical and functional properties. Monosaccharides analysis revealed that mannose (81.68%) was the dominant sugar in HBSS and galactose (67.59%) was the most in CASS. Similarly, CHSS and DASS possessed mannose and galactose as major sugar, which were 25.80% and 31.37%, 20.33% and 33.96%, respectively. The obtained molecular weight of ACLPs were 7.702×10 3 (HBSS), 4.690×10 3 (CHSS), 4.943×10 3 (DASS) and 1.390×10 3 kDa (CASS). CASS resulted in the strongest solubility, fat-binding capacity, foam capacity and foam stability whereas, HBSS showed the highest thermal stability. DASS showed the best hygroscopicity and the best moisture retention was obtained by CHSS. Subsequently, the emulsifying activity and emulsifying stability were the highest for HBSS and the longest for of CASS, respectively. The rheological properties of CHSS exhibited the largest viscosity. Our results indicated that all factions could be considered as functional polysaccharides according to their respective characteristics, which have vast potential in food production. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of Soy Protein Hydrolysates Prepared by Varying Subcritical Media on the Physicochemical Properties of Pork Patties.

PubMed

Lee, Yun-Kyung; Ko, Bo-Bae; Davaatseren, Munkhtugs; Hong, Geun-Pyo

2016-01-01

This study investigated the effect of soy protein hydrolysates (SPH) prepared by varying subcritical media on the physicochemical properties of pork patties. For resource of SPH, two different soybean species (Glycine max Merr.) of Daewonkong (DWK) and Saedanbaek (SDB) were selected. SPH was prepared by subcritical processing at 190℃ and 25 MPa under three different of media (water, 20% ethanol and 50% ethanol). Solubility and free amino group content revealed that water was better to yield larger amount of SPH than ethanol/water mixtures, regardless of species. Molecular weight (Mw) distribution of SPH was also similar between two species, while slightly different Mw distribution was obtained by subcritical media. For pork patty application, 50% ethanol treatment showed clear red color comparing to control after 14 d of storage. In addition, ethanol treatment had better oxidative stability than control and water treatment based on thiobarbituric acid-reactive substances (TBARS) analysis. For eating quality, although 20% ethanol treatment in SDB showed slightly higher cooking loss than control, generally addition of SPH did not affect the water-binding properties and hardness of pork patties. Consequently, the present study indicated that 50% ethanol was the best subcritical media to produce SPH possessing antioxidant activity, and the SPH produced from DWK exhibited better antioxidant activity than that produced SDB.

Interaction of Colloidal Gold Nanoparticles with Model Serum Proteins: The Nanoparticle-Protein 'Corona' from a PhysicoChemical Viewpoint

NASA Astrophysics Data System (ADS)

Dominguez Medina, Sergio

When nanoparticles come in contact with biological fluids they become coated with a mixture of proteins present in the media, forming what is known as the nanoparticle-protein 'corona'. This corona changes the nanoparticles' original surface properties and plays a central role in how these get screened by cellular receptors. In the context of biomedical research, this presents a bottleneck for the transition of nanoparticles from research laboratories to clinical settings. It is therefore fundamental to probe these nanoparticle-protein interactions in order to understand the different physico-chemical mechanisms involved. This thesis is aimed to investigate the exposure of colloidal gold nanoparticles to model serum proteins, particularly serum albumin, the main transporter of molecular compounds in the bloodstream of mammals. A set of experimental tools based on optical microscopy and spectroscopy were developed in order to probe these interactions in situ. First, the intrinsic photoluminescence and elastic scattering of individual gold nanoparticles were investigated in order to understand its physical origin. These optical signals were then used to measure the size of the nanoparticles while in Brownian diffusion using fluctuation correlation spectroscopy. This spectroscopic tool was then applied to detect the binding of serum albumin onto the nanoparticle surface, increasing its hydrodynamic size. By performing a binding isotherm as a function of protein concentration, it was determined that serum albumin follows an anti-cooperative binding mechanism on negatively charged gold nanoparticles. This protein monolayer substantially enhanced the stability of the colloid, preventing their aggregation in saline solutions with ionic strength higher than biological media. Cationic gold nanoparticles in contrast, aggregated when serum albumin was present at a low protein-to-nanoparticle ratio, but prevented aggregation if exposed in excess. Single-molecule fluorescence microscopy revealed that under low protein-to-nanoparticle binding ratios, serum albumin irreversibly unfolds upon adsorption and spreads across the available nanoparticle surface area. Unfolded proteins then interact with one another, triggering nanoparticle aggregation. Fibrinogen and globulin also triggered aggregation when exposed to cationic nanoparticles. In an effort to relate these physico-chemical observations to relevant biological parameters, the uptake of protein coated gold nanoparticles by a model cancer cell line was investigated under different incubation conditions. Those nanoparticles pre-incubated with bovine serum albumin before fetal bovine serum were found to be uptaken three times more than those only incubated in serum.

Some pungent arguments against the physico-chemical theories of the origin of the genetic code and corroborating the coevolution theory.

PubMed

Di Giulio, Massimo

2017-02-07

Whereas it is extremely easy to prove that "if the biosynthetic relationships between amino acids were fundamental in the structuring of the genetic code, then their physico-chemical properties might also be revealed in the genetic code table"; it is, on the contrary, impossible to prove that "if the physico-chemical properties of amino acids were fundamental in the structuring of the genetic code, then the presence of the biosynthetic relationships between amino acids should not be revealed in the genetic code". And, given that in the genetic code table are mirrored both the biosynthetic relationships between amino acids and their physico-chemical properties, all this would be a test that would falsify the physico-chemical theories of the origin of the genetic code. That is to say, if the physico-chemical properties of amino acids had a fundamental role in organizing the genetic code, then we would not have duly revealed the presence - in the genetic code - of the biosynthetic relationships between amino acids, and on the contrary this has been observed. Therefore, this falsifies the physico-chemical theories of genetic code origin. Whereas, the coevolution theory of the origin of the genetic code would be corroborated by this analysis, because it would be able to give a description of evolution of the genetic code more coherent with the indisputable empirical observations that link both the biosynthetic relationships of amino acids and their physico-chemical properties to the evolutionary organization of the genetic code. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of oxidation on the plasmonic properties of aluminum nanoclusters.

PubMed

Douglas-Gallardo, Oscar A; Soldano, Germán J; Mariscal, Marcelo M; Sánchez, Cristián Gabriel

2017-11-16

The scouting of alternative plasmonic materials able to enhance and extend the optical properties of noble metal nanostructures is on the rise. Aluminum is endowed with a set of interesting properties which turn it into an attractive plasmonic material. Here we present the optical and electronic features of different aluminum nanostructures stemming from a multilevel computational study. Molecular Dynamics (MD) simulations using a reactive force field (ReaxFF), carefully validated with Density Functional Theory (DFT), were employed to mimic the oxidation of icosahedral aluminum nanoclusters. Resulting structures with different oxidation degrees were then studied through the Time-Dependent Density Functional Tight Binding (TD-DFTB) method. A similar approach was used in aluminum nanoclusters with a disordered structure to study how the loss of crystallinity affects the optical properties. To the best of our knowledge, this is the first report that addresses this issue from the fully atomistic time-dependent approach by means of two different and powerful simulation tools able to describe quantum and physicochemical properties associated with nanostructured particles.

Comprehensive Characterization of Reference Standard Lots of HIV-1 Subtype C Gp120 Proteins for Clinical Trials in Southern African Regions

PubMed Central

Wang, Zihao; Lorin, Clarisse; Koutsoukos, Marguerite; Franco, David; Bayat, Babak; Zhang, Ying; Carfi, Andrea; Barnett, Susan W.; Porter, Frederick

2016-01-01

Two HIV-1 subtype C gp120 protein candidates were the selected antigens for several experimental vaccine regimens now under evaluation in HVTN 100 Phase I/II clinical trial aiming to support the start of the HVTN 702 Phase IIb/III trial in southern Africa, which is designed to confirm and extend the partial protection seen against HIV-1 infection in the RV144 Thai trial. Here, we report the comprehensive physicochemical characterization of the gp120 reference materials that are representative of the clinical trial materials. Gp120 proteins were stably expressed in Chinese Hamster Ovary (CHO) cells and subsequently purified and formulated. A panel of analytical techniques was used to characterize the physicochemical properties of the two protein molecules. When formulated in the AS01 Adjuvant System, the bivalent subtype C gp120 antigens elicited 1086.C- and TV1.C-specific binding antibody and CD4+ T cell responses in mice. All the characteristics were highly representative of the Clinical Trial Materials (CTM). Data from this report demonstrate the immunogenicity of the gp120 antigens, provide comprehensive characterization of the molecules, set the benchmark for assessment of current and future CTM lots, and lay the physicochemical groundwork for interpretation of future clinical trial data. PMID:27187483

A Study of Physicochemical Properties of Subcutaneous Fat of the Abdomen and its Implication in Abdominal Obesity

PubMed Central

Kumar, Pramod; Kodavoor, Srinivas Aithal; Kotian, Sushma Rama; Yathdaka, Sudhakar Narahari; Nayak, Dayanand; Souza, Anne D; Souza, Antony Sylvan D

2016-01-01

Introduction The lower abdominal obesity is more resistant to absorption as compared to that of upper abdomen. Differences in the physicochemical properties of the subcutaneous fat of the upper and lower abdomen may be responsible for this variation. There is paucity of the scientific literature on the physicochemical properties of the subcutaneous fat of abdomen. Aim The present study was undertaken to create a database of physicochemical properties of abdominal subcutaneous fat. Materials and Methods The samples of subcutaneous fat from upper and lower abdomen were collected from 40 fresh autopsied bodies (males 33, females 7). The samples were prepared for physicochemical analysis using organic and inorganic solvents. Various physicochemical properties of the fat samples analysed were surface tension, viscosity, specific gravity, specific conductivity, iodine value and thermal properties. Data was analysed by paired and independent sample t-tests. Results There was a statistically significant difference in all the physicochemical parameters between males and females except surface tension (organic) and surface tension (inorganic) of upper abdominal fat, and surface tension (organic) of lower abdominal fat. In males, viscosity of upper abdominal fat was more compared to that of lower abdomen (both organic and inorganic) unlike the specific conductivity that was higher for the lower abdominal fat as compared to that of the upper abdomen. In females there were statistically significant higher values of surface tension (inorganic) and specific gravity (organic) of the upper abdomen fat as compared to that of lower abdomen. The initial and final weight loss of the lower abdominal fat as indicated by Thermo Gravimetric Analysis was significantly more in males than in female Conclusion The difference in the physicochemical properties of subcutaneous fat between upper and lower abdomen and between males and females could be responsible for the variant behaviour of subcutaneous abdominal fat towards resorption. PMID:27437272

Proteochemometric model for predicting the inhibition of penicillin-binding proteins

NASA Astrophysics Data System (ADS)

Nabu, Sunanta; Nantasenamat, Chanin; Owasirikul, Wiwat; Lawung, Ratana; Isarankura-Na-Ayudhya, Chartchalerm; Lapins, Maris; Wikberg, Jarl E. S.; Prachayasittikul, Virapong

2015-02-01

Neisseria gonorrhoeae infection threatens to become an untreatable sexually transmitted disease in the near future owing to the increasing emergence of N. gonorrhoeae strains with reduced susceptibility and resistance to the extended-spectrum cephalosporins (ESCs), i.e. ceftriaxone and cefixime, which are the last remaining option for first-line treatment of gonorrhea. Alteration of the penA gene, encoding penicillin-binding protein 2 (PBP2), is the main mechanism conferring penicillin resistance including reduced susceptibility and resistance to ESCs. To predict and investigate putative amino acid mutations causing β-lactam resistance particularly for ESCs, we applied proteochemometric modeling to generalize N. gonorrhoeae susceptibility data for predicting the interaction of PBP2 with therapeutic β-lactam antibiotics. This was afforded by correlating publicly available data on antimicrobial susceptibility of wild-type and mutant N. gonorrhoeae strains for penicillin-G, cefixime and ceftriaxone with 50 PBP2 protein sequence data using partial least-squares projections to latent structures. The generated model revealed excellent predictability ( R 2 = 0.91, Q 2 = 0.77, Q Ext 2 = 0.78). Moreover, our model identified amino acid mutations in PBP2 with the highest impact on antimicrobial susceptibility and provided information on physicochemical properties of amino acid mutations affecting antimicrobial susceptibility. Our model thus provided insight into the physicochemical basis for resistance development in PBP2 suggesting its use for predicting and monitoring novel PBP2 mutations that may emerge in the future.

Effects of losartan treatment on the physicochemical properties of diabetic rat bone.

PubMed

Donmez, Baris Ozgur; Unal, Mustafa; Ozdemir, Semir; Ozturk, Nihal; Oguz, Nurettin; Akkus, Ozan

2017-03-01

Inhibitors of the renin-angiotensin system used to treat several diseases have also been shown to be effective on bone tissue, suggesting that angiotensin-converting enzyme inhibitors and angiotensin receptor blockers may reduce fracture risk. The present study investigated the effects of losartan on the physicochemical and biomechanical properties of diabetic rat bone. Losartan (5 mg/kg/day) was administered via oral gavage for 12 weeks. Bone mineral density (BMD) was measured using dual-energy X-ray absorptiometry. Whole femurs were tested under tension to evaluate the biomechanical properties of bone. The physicochemical properties of bone were analyzed by Fourier transform infrared spectroscopy. Although losartan did not recover decreases in the BMD of diabetic bone, it recovered the physicochemical (mineral and collagen matrix) properties of diabetic rat bone. Furthermore, losartan also recovered ultimate tensile strength of diabetic rat femurs. Losartan, an angiotensin II type 1 receptor blocker, has a therapeutic effect on the physicochemical properties of diabetic bone resulting in improvement of bone strength at the material level. Therefore, specific inhibition of this pathway at the receptor level shows potential as a therapeutic target for diabetic patients suffering from bone diseases such as osteopenia.

Abbott Physicochemical Tiering (APT)--a unified approach to HTS triage.

PubMed

Cox, Philip B; Gregg, Robert J; Vasudevan, Anil

2012-07-15

The selection of the highest quality chemical matter from high throughput screening (HTS) is the ultimate aim of any triage process. Typically there are many hundreds or thousands of hits capable of modulating a given biological target in HTS with a wide range of physicochemical properties that should be taken into consideration during triage. Given the multitude of physicochemical properties that define drug-like space, a system needs to be in place that allows for a rapid selection of chemical matter based on a prioritized range of these properties. With this goal in mind, we have developed a tool, coined Abbott Physicochemical Tiering (APT) that enables hit prioritization based on ranges of these important physicochemical properties. This tool is now used routinely at Abbott to help prioritize hits out of HTS during the triage process. Herein we describe how this tool was developed and validated using Abbott internal high throughput ADME data (HT-ADME). Copyright © 2012 Elsevier Ltd. All rights reserved.

Detecting Local Ligand-Binding Site Similarity in Non-Homologous Proteins by Surface Patch Comparison

PubMed Central

Sael, Lee; Kihara, Daisuke

2012-01-01

Functional elucidation of proteins is one of the essential tasks in biology. Function of a protein, specifically, small ligand molecules that bind to a protein, can be predicted by finding similar local surface regions in binding sites of known proteins. Here, we developed an alignment free local surface comparison method for predicting a ligand molecule which binds to a query protein. The algorithm, named Patch-Surfer, represents a binding pocket as a combination of segmented surface patches, each of which is characterized by its geometrical shape, the electrostatic potential, the hydrophobicity, and the concaveness. Representing a pocket by a set of patches is effective to absorb difference of global pocket shape while capturing local similarity of pockets. The shape and the physicochemical properties of surface patches are represented using the 3D Zernike descriptor, which is a series expansion of mathematical 3D function. Two pockets are compared using a modified weighted bipartite matching algorithm, which matches similar patches from the two pockets. Patch-Surfer was benchmarked on three datasets, which consist in total of 390 proteins that bind to one of 21 ligands. Patch-Surfer showed superior performance to existing methods including a global pocket comparison method, Pocket-Surfer, which we have previously introduced. Particularly, as intended, the accuracy showed large improvement for flexible ligand molecules, which bind to pockets in different conformations. PMID:22275074

Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison.

PubMed

Sael, Lee; Kihara, Daisuke

2012-04-01

Functional elucidation of proteins is one of the essential tasks in biology. Function of a protein, specifically, small ligand molecules that bind to a protein, can be predicted by finding similar local surface regions in binding sites of known proteins. Here, we developed an alignment free local surface comparison method for predicting a ligand molecule which binds to a query protein. The algorithm, named Patch-Surfer, represents a binding pocket as a combination of segmented surface patches, each of which is characterized by its geometrical shape, the electrostatic potential, the hydrophobicity, and the concaveness. Representing a pocket by a set of patches is effective to absorb difference of global pocket shape while capturing local similarity of pockets. The shape and the physicochemical properties of surface patches are represented using the 3D Zernike descriptor, which is a series expansion of mathematical 3D function. Two pockets are compared using a modified weighted bipartite matching algorithm, which matches similar patches from the two pockets. Patch-Surfer was benchmarked on three datasets, which consist in total of 390 proteins that bind to one of 21 ligands. Patch-Surfer showed superior performance to existing methods including a global pocket comparison method, Pocket-Surfer, which we have previously introduced. Particularly, as intended, the accuracy showed large improvement for flexible ligand molecules, which bind to pockets in different conformations. Copyright © 2011 Wiley Periodicals, Inc.

Influence of succinylation on physicochemical property of yak casein micelles.

PubMed

Yang, Min; Yang, Jitao; Zhang, Yuan; Zhang, Weibing

2016-01-01

Succinylation is a chemical-modification method that affects the physicochemical characteristics and functional properties of proteins. This study assessed the influence of succinylation on the physicochemical properties of yak casein micelles. The results revealed that surface hydrophobicity indices decreased with succinylation. Additionally, denaturation temperature and denaturation enthalpy decreased with increasing succinylation level, except at 82%. The buffering properties of yak casein micelles were affected by succinylation. It was found that chemical modification contributed to a slight shift of the buffering peak towards a lower pH value and a markedly increase of the maximum buffering values of yak casein micelles at pH 4.5-6.0 and pH < 3. Succinylation increased yak casein micellar hydration and whiteness values. The findings obtained from this study will provide the basic information on the physicochemical properties of native and succinylated yak casein micelles. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effects of the physicochemical properties of gold nanostructures on cellular internalization

PubMed Central

Zhang, Jinchao; Wang, Paul C.; Liang, Xing-Jie

2015-01-01

Unique physicochemical properties of Au nanomaterials make them potential star materials in biomedical applications. However, we still know a little about the basic problem of what really matters in fabrication of Au nanomaterials which can get into biological systems, especially cells, with high efficiency. An understanding of how the physicochemical properties of Au nanomaterials affect their cell internalization is of significant interest. Studies devoted to clarify the functions of various properties of Au nanostructures such as size, shape and kinds of surface characteristics in cell internalization are under way. These fundamental investigations will give us a foundation for constructing Au nanomaterial-based biomedical devices in the future. In this review, we present the current advances and rationales in study of the relationship between the physicochemical properties of Au nanomaterials and cell uptake. We also provide a perspective on the Au nanomaterial-cell interaction research. PMID:26813673

Dinitrosyl iron complexes and S-nitrosothiols are two possible forms for stabilization and transport of nitric oxide in biological systems.

PubMed

Vanin, A F

1998-07-01

The physicochemical properties, mechanisms of synthesis and decomposition of dinitrosyl iron complexes (DNICs) with thiol-containing ligands and of S-nitrosothiols (RS-NO), and the potential role of these compounds in storage and transport of NO in biological systems are reviewed. Special attention is given to the phenomenon of mutual transformation of DNIC and RS-NO catalyzed by Fe2+. Each Fe2+ binds two neutral NO molecules in the DNICs, catalyzes their mutual oxidation--reduction with formation of nitrous oxide and nitrosonium ions appearing in the DNICs. These ions S-nitrosate thiol-compounds with RS-NO formation. Fe2+ binds two RS-NO molecules and catalyzes their mutual oxidation--reduction followed by decomposition of the resulting molecules. Mutual conversion of DNICs and RS-NO regulated by iron, thiol, and NO levels is suggested to provide NO transport in cells and tissues.

G protein-membrane interactions II: Effect of G protein-linked lipids on membrane structure and G protein-membrane interactions.

PubMed

Casas, Jesús; Ibarguren, Maitane; Álvarez, Rafael; Terés, Silvia; Lladó, Victoria; Piotto, Stefano P; Concilio, Simona; Busquets, Xavier; López, David J; Escribá, Pablo V

2017-09-01

G proteins often bear myristoyl, palmitoyl and isoprenyl moieties, which favor their association with the membrane and their accumulation in G Protein Coupled Receptor-rich microdomains. These lipids influence the biophysical properties of membranes and thereby modulate G protein binding to bilayers. In this context, we showed here that geranylgeraniol, but neither myristate nor palmitate, increased the inverted hexagonal (H II ) phase propensity of phosphatidylethanolamine-containing membranes. While myristate and palmitate preferentially associated with phosphatidylcholine membranes, geranylgeraniol favored nonlamellar-prone membranes. In addition, Gαi 1 monomers had a higher affinity for lamellar phases, while Gβγ and Gαβγ showed a marked preference for nonlamellar prone membranes. Moreover, geranylgeraniol enhanced the binding of G protein dimers and trimers to phosphatidylethanolamine-containing membranes, yet it decreased that of monomers. By contrast, both myristate and palmitate increased the Gαi 1 preference for lamellar membranes. Palmitoylation reinforced the binding of the monomer to PC membranes and myristoylation decreased its binding to PE-enriched bilayer. Finally, binding of dimers and trimers to lamellar-prone membranes was decreased by palmitate and myristate, but it was increased in nonlamellar-prone bilayers. These results demonstrate that co/post-translational G protein lipid modifications regulate the membrane lipid structure and that they influence the physico-chemical properties of membranes, which in part explains why G protein subunits sort to different plasma membrane domains. This article is part of a Special Issue entitled: Membrane Lipid Therapy: Drugs Targeting Biomembranes edited by Pablo V. Escribá. Copyright © 2017 Elsevier B.V. All rights reserved.

Pectin gelation with chlorhexidine: Physico-chemical studies in dilute solutions.

PubMed

Lascol, Manon; Bourgeois, Sandrine; Guillière, Florence; Hangouët, Marie; Raffin, Guy; Marote, Pedro; Lantéri, Pierre; Bordes, Claire

2016-10-05

Low methoxyl pectin is known to gel with divalent cations (e.g. Ca(2+), Zn(2+)). In this study, a new way of pectin gelation in the presence of an active pharmaceutical ingredient, chlorhexidine (CX), was highlighted. Thus chlorhexidine interactions with pectin were investigated and compared with the well-known pectin/Ca(2+) binding model. Gelation mechanisms were studied by several physico-chemical methods such as zeta potential, viscosity, size measurements and binding isotherm was determined by Proton Nuclear Magnetic Resonance Spectroscopy ((1)H NMR). The binding process exhibited similar first two steps for both divalent ions: a stoichiometric monocomplexation of the polymer followed by a dimerization step. However, stronger interactions were observed between pectin and chlorhexidine. Moreover, the dimerization step occurred under stoichiometric conditions with chlorhexidine whereas non-stoichiometric conditions were involved with calcium ions. In the case of chlorhexidine, an additional intermolecular binding occurred in a third step. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparative evaluation of physicochemical properties of jatropha curcas seed oil for coolant-lubricant application

NASA Astrophysics Data System (ADS)

Murad, Muhamad Nasir; Sharif, Safian; Rahim, Erween Abd.; Abdullah, Rozaini

2017-09-01

Increased attention to environmental issues due to industrial activities has forced the authorities raise awareness and implement regulations to reduce the use of mineral oil. Some vegetable oils unexplored or less explored, particularly the non-edible oils such as Jatropha curcas oil (JCO) and others. Physicochemical properties of JCO is compared with others edible oils, synthetic ester and fatty alcohol to obtain a viable alternative in metal cutting fluids. The oil was found to show the suitability of properties for coolant-lubricant applications in term of its physicochemical properties and better in flash point and viscosity value.

Nanoparticle-blood interactions: the implications on solid tumour targeting.

PubMed

Lazarovits, James; Chen, Yih Yang; Sykes, Edward A; Chan, Warren C W

2015-02-18

Nanoparticles are suitable platforms for cancer targeting and diagnostic applications. Typically, less than 10% of all systemically administered nanoparticles accumulate in the tumour. Here we explore the interactions of blood components with nanoparticles and describe how these interactions influence solid tumour targeting. In the blood, serum proteins adsorb onto nanoparticles to form a protein corona in a manner dependent on nanoparticle physicochemical properties. These serum proteins can block nanoparticle tumour targeting ligands from binding to tumour cell receptors. Additionally, serum proteins can also encourage nanoparticle uptake by macrophages, which decreases nanoparticle availability in the blood and limits tumour accumulation. The formation of this protein corona will also increase the nanoparticle hydrodynamic size or induce aggregation, which makes nanoparticles too large to enter into the tumour through pores of the leaky vessels, and prevents their deep penetration into tumours for cell targeting. Recent studies have focused on developing new chemical strategies to reduce or eliminate serum protein adsorption, and rescue the targeting potential of nanoparticles to tumour cells. An in-depth and complete understanding of nanoparticle-blood interactions is key to designing nanoparticles with optimal physicochemical properties with high tumour accumulation. The purpose of this review article is to describe how the protein corona alters the targeting of nanoparticles to solid tumours and explains current solutions to solve this problem.

Physicochemical characterization and biocompatibility of alginate-polycation microcapsules designed for islet transplantation

NASA Astrophysics Data System (ADS)

Tam, Susan Kimberly

Microencapsulation represents a method for immunoprotecting transplanted therapeutic cells or tissues from graft rejection using a physical barrier. This approach is advantageous in that it eliminates the need to induce long-term immunosuppression and allows the option of transplanting non-cadaveric cell sources, such as animal cells and stem cell-derived tissues. The microcapsules that we have investigated are designed to immunoprotect islets of Langerhans (i.e. clusters of insulin-secreting cells), with the goal of treating insulin-dependent diabetes. With the aid of techniques for physicochemical analysis, this research focused on understanding which properties of the microcapsule are the most important for determining its biocompatibility. The objective of this work was to elucidate correlations between the chemical make-up, physicochemical properties, and in vivo biocompatibility of alginate-based microcapsules. Our approach was based on the hypothesis that the immune response to the microcapsules is governed by, and can therefore be controlled by, specific physicochemical properties of the microcapsule and its material components. The experimental work was divided into five phases, each associated with a specific aim : (1) To prove that immunoglobulins adsorb to the surface of alginate-polycation microcapsules, and to correlate this adsorption with the microcapsule chemistry. (2) To test interlaboratory reproducibility in making biocompatible microcapsules, and evaluate the suitability of our materials and fabrication protocols for subsequent studies. (3) To determine which physicochemical properties of alginates affect the in vivo biocompatibility of their gels. (4) To determine which physiochemical properties of alginate-polycation microcapsules are most important for determining their in vivo biocompatibility (5) To determine whether a modestly immunogenic membrane hinders or helps the ability of the microcapsule to immunoprotect islet xenografts in diabetic mice. To achieve these aims, extensive physicochemical analyses of the alginates and microcapsules were carried out. Among the properties of the alginates that were investigated include their purity (LAL assay, microBCA), chemical composition (nuclear magnetic resonance, NMR), elemental composition (x-ray photoelectron spectroscopy, XPS), and hydrophilicity (contact angle technique). As for the microcapsules, we also examined their surface chemical composition (XPS), hydrophilicity, as well as alginate-polycation interactions (Fourier transform infrared spectroscopy, FTIR), and membrane strength (osmotic swelling). The results of this research led to a number of important conclusions about the biocompatibility of alginates and alginate-based microcapsules. First of all, purifying an alginate does not guarantee its biocompatibility. Indeed, we provided evidence that both the alginate chemical composition (i.e. relative content of mannuronate and guluronate) and its intrinsic viscosity influence the extent of host cell adhesion to alginate gel beads. Using a biocompatible alginate, we then provided evidence that microcapsule biocompatibility is greatly compromised by its polycationic membrane. We showed that this membrane is responsible for the adsorption of opsonizing proteins in vitro and the adhesion of immune cells in vivo. That said, the severity of inflammatory response to the membrane can vary, and this depended on the microcapsule design, including the choice of alginate and polycation type. Results of our physicochemical analyses suggested that the most important factor determining biocompatibility is the ability of the polycation to diffuse into, and subsequently bind to, the alginate gel core. Moreover, adding a final coating of alginate had no significant effect on reversing the effects of the membrane on various microcapsule properties (surface composition, hydrophobicity, stability), nor did this coating reduce its immunogenicity. Although we repeatedly provided evidence that the microcapsule membrane is the main problem for biocompatibility, we also demonstrated that the severity of this problem can vary according to the fabrication details. This is an important note, as it confirms the possibility of achieving optimal microcapsule biocompatibility if the interactions between the alginate and polycation are ideal. (Abstract shortened by UMI.)

Demonstrating In-Cell Target Engagement Using a Pirin Protein Degradation Probe (CCT367766)

PubMed Central

2017-01-01

Demonstrating intracellular protein target engagement is an essential step in the development and progression of new chemical probes and potential small molecule therapeutics. However, this can be particularly challenging for poorly studied and noncatalytic proteins, as robust proximal biomarkers are rarely known. To confirm that our recently discovered chemical probe 1 (CCT251236) binds the putative transcription factor regulator pirin in living cells, we developed a heterobifunctional protein degradation probe. Focusing on linker design and physicochemical properties, we generated a highly active probe 16 (CCT367766) in only three iterations, validating our efficient strategy for degradation probe design against nonvalidated protein targets. PMID:29240418

Caffeine and sulfadiazine interact differently with human serum albumin: A combined fluorescence and molecular docking study

NASA Astrophysics Data System (ADS)

Islam, Mullah Muhaiminul; Sonu, Vikash K.; Gashnga, Pynsakhiat Miki; Moyon, N. Shaemningwar; Mitra, Sivaprasad

2016-01-01

The interaction and binding behavior of the well-known drug sulfadiazine (SDZ) and psychoactive stimulant caffeine (CAF) with human serum albumin (HSA) was monitored by in vitro fluorescence titration and molecular docking calculations under physiological condition. The quenching of protein fluorescence on addition of CAF is due to the formation of protein-drug complex in the ground state; whereas in case of SDZ, the experimental results were explained on the basis of sphere of action model. Although both these compounds bind preferentially in Sudlow's site 1 of the protein, the association constant is approximately two fold higher in case of SDZ (∼4.0 × 104 M-1) in comparison with CAF (∼9.3 × 102 M-1) and correlates well with physico-chemical properties like pKa and lipophilicity of the drugs. Temperature dependent fluorescence study reveals that both SDZ and CAF bind spontaneously with HSA. However, the binding of SDZ with the protein is mainly governed by the hydrophobic forces in contrast with that of CAF; where, the interaction is best explained in terms of electrostatic mechanism. Molecular docking calculation predicts the binding of these drugs in different location of sub-domain IIA in the protein structure.

Physico-chemical properties of manufactured nanomaterials - Characterisation and relevant methods. An outlook based on the OECD Testing Programme.

PubMed

Rasmussen, Kirsten; Rauscher, Hubert; Mech, Agnieszka; Riego Sintes, Juan; Gilliland, Douglas; González, Mar; Kearns, Peter; Moss, Kenneth; Visser, Maaike; Groenewold, Monique; Bleeker, Eric A J

2018-02-01

Identifying and characterising nanomaterials require additional information on physico-chemical properties and test methods, compared to chemicals in general. Furthermore, regulatory decisions for chemicals are usually based upon certain toxicological properties, and these effects may not be equivalent to those for nanomaterials. However, regulatory agencies lack an authoritative decision framework for nanomaterials that links the relevance of certain physico-chemical endpoints to toxicological effects. This paper investigates various physico-chemical endpoints and available test methods that could be used to produce such a decision framework for nanomaterials. It presents an overview of regulatory relevance and methods used for testing fifteen proposed physico-chemical properties of eleven nanomaterials in the OECD Working Party on Manufactured Nanomaterials' Testing Programme, complemented with methods from literature, and assesses the methods' adequacy and applications limits. Most endpoints are of regulatory relevance, though the specific parameters depend on the nanomaterial and type of assessment. Size (distribution) is the common characteristic of all nanomaterials and is decisive information for classifying a material as a nanomaterial. Shape is an important particle descriptor. The octanol-water partitioning coefficient is undefined for particulate nanomaterials. Methods, including sample preparation, need to be further standardised, and some new methods are needed. The current work of OECD's Test Guidelines Programme regarding physico-chemical properties is highlighted. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Rapid experimental measurements of physicochemical properties to inform models and testing.

PubMed

Nicolas, Chantel I; Mansouri, Kamel; Phillips, Katherine A; Grulke, Christopher M; Richard, Ann M; Williams, Antony J; Rabinowitz, James; Isaacs, Kristin K; Yau, Alice; Wambaugh, John F

2018-05-02

The structures and physicochemical properties of chemicals are important for determining their potential toxicological effects, toxicokinetics, and route(s) of exposure. These data are needed to prioritize the risk for thousands of environmental chemicals, but experimental values are often lacking. In an attempt to efficiently fill data gaps in physicochemical property information, we generated new data for 200 structurally diverse compounds, which were rigorously selected from the USEPA ToxCast chemical library, and whose structures are available within the Distributed Structure-Searchable Toxicity Database (DSSTox). This pilot study evaluated rapid experimental methods to determine five physicochemical properties, including the log of the octanol:water partition coefficient (known as log(K ow ) or logP), vapor pressure, water solubility, Henry's law constant, and the acid dissociation constant (pKa). For most compounds, experiments were successful for at least one property; log(K ow ) yielded the largest return (176 values). It was determined that 77 ToxPrint structural features were enriched in chemicals with at least one measurement failure, indicating which features may have played a role in rapid method failures. To gauge consistency with traditional measurement methods, the new measurements were compared with previous measurements (where available). Since quantitative structure-activity/property relationship (QSAR/QSPR) models are used to fill gaps in physicochemical property information, 5 suites of QSPRs were evaluated for their predictive ability and chemical coverage or applicability domain of new experimental measurements. The ability to have accurate measurements of these properties will facilitate better exposure predictions in two ways: 1) direct input of these experimental measurements into exposure models; and 2) construction of QSPRs with a wider applicability domain, as their predicted physicochemical values can be used to parameterize exposure models in the absence of experimental data. Published by Elsevier B.V.

Impact of heating on sensory properties of French Protected Designation of Origin (PDO) blue cheeses. Relationships with physicochemical parameters.

PubMed

Bord, Cécile; Guerinon, Delphine; Lebecque, Annick

2016-07-01

The aim of this study was to measure the impact of heating on the sensory properties of blue-veined cheeses in order to characterise their sensory properties and to identify their specific sensory typology associated with physicochemical parameters. Sensory profiles were performed on a selection of Protected Designation of Origin (PDO) cheeses representing the four blue-veined cheese categories produced in the Massif Central (Fourme d'Ambert, Fourme de Montbrison, Bleu d'Auvergne and Bleu des Causses). At the same time, physicochemical parameters were measured in these cheeses. The relationship between these two sets of data was investigated. Four types of blue-veined cheeses displayed significantly different behaviour after heating and it is possible to discriminate these cheese categories through specific sensory attributes. Fourme d'Ambert and Bleu d'Auvergne exhibited useful culinary properties: they presented good meltability, stretchability and a weak oiling-off. However, basic tastes (salty, bitter and sour) are also sensory attributes which can distinguish heated blue cheeses. The relationship between the sensory and physicochemical data indicated a correlation suggesting that some of these sensory properties may be explained by certain physicochemical parameters of heated cheeses. © The Author(s) 2015.

TSCA Work Plan Chemical Technical Supplement – Physicochemical Properties and Environmental Fate of the Brominated Phthalates Cluster (BPC) Chemicals

EPA Pesticide Factsheets

TSCA Work Plan Chemical Technical Supplement – Physicochemical Properties and Environmental Fate of the Brominated Phthalates Cluster (BPC) Chemicals -- Brominated Phthalates Cluster Flame Retardants.

Assessing Analytical Similarity of Proposed Amgen Biosimilar ABP 501 to Adalimumab.

PubMed

Liu, Jennifer; Eris, Tamer; Li, Cynthia; Cao, Shawn; Kuhns, Scott

2016-08-01

ABP 501 is being developed as a biosimilar to adalimumab. Comprehensive comparative analytical characterization studies have been conducted and completed. The objective of this study was to assess analytical similarity between ABP 501 and two adalimumab reference products (RPs), licensed by the United States Food and Drug Administration (adalimumab [US]) and authorized by the European Union (adalimumab [EU]), using state-of-the-art analytical methods. Comprehensive analytical characterization incorporating orthogonal analytical techniques was used to compare products. Physicochemical property comparisons comprised the primary structure related to amino acid sequence and post-translational modifications including glycans; higher-order structure; primary biological properties mediated by target and receptor binding; product-related substances and impurities; host-cell impurities; general properties of the finished drug product, including strength and formulation; subvisible and submicron particles and aggregates; and forced thermal degradation. ABP 501 had the same amino acid sequence and similar post-translational modification profiles compared with adalimumab RPs. Primary structure, higher-order structure, and biological activities were similar for the three products. Product-related size and charge variants and aggregate and particle levels were also similar. ABP 501 had very low residual host-cell protein and DNA. The finished ABP 501 drug product has the same strength with regard to protein concentration and fill volume as adalimumab RPs. ABP 501 and the RPs had a similar stability profile both in normal storage and thermal stress conditions. Based on the comprehensive analytical similarity assessment, ABP 501 was found to be similar to adalimumab with respect to physicochemical and biological properties.

The physicochemical properties of the low-temperature ionic liquid silver bromide-1-butyl-3-methylimidazolium bromide

NASA Astrophysics Data System (ADS)

Grishina, E. P.; Ramenskaya, L. M.; Pimenova, A. M.

2009-11-01

The physicochemical properties of the low-temperature ionic liquid based on 1-butyl-3-methylimidazolium bromide (BMImBr) and silver bromide were studied. Differential scanning calorimetry, Fourier transform IR spectroscopy, densimetry, viscometry, and conductometry measurements were performed to determine the dependences of the parameters under study on the concentration of AgBr. It was shown that the temperature and concentration behavior of the physicochemical properties of BMImBr-AgBr melts characterized the interaction between the system components with the formation of complex particles.

Real-Time Ligand Binding Pocket Database Search Using Local Surface Descriptors

PubMed Central

Chikhi, Rayan; Sael, Lee; Kihara, Daisuke

2010-01-01

Due to the increasing number of structures of unknown function accumulated by ongoing structural genomics projects, there is an urgent need for computational methods for characterizing protein tertiary structures. As functions of many of these proteins are not easily predicted by conventional sequence database searches, a legitimate strategy is to utilize structure information in function characterization. Of a particular interest is prediction of ligand binding to a protein, as ligand molecule recognition is a major part of molecular function of proteins. Predicting whether a ligand molecule binds a protein is a complex problem due to the physical nature of protein-ligand interactions and the flexibility of both binding sites and ligand molecules. However, geometric and physicochemical complementarity is observed between the ligand and its binding site in many cases. Therefore, ligand molecules which bind to a local surface site in a protein can be predicted by finding similar local pockets of known binding ligands in the structure database. Here, we present two representations of ligand binding pockets and utilize them for ligand binding prediction by pocket shape comparison. These representations are based on mapping of surface properties of binding pockets, which are compactly described either by the two dimensional pseudo-Zernike moments or the 3D Zernike descriptors. These compact representations allow a fast real-time pocket searching against a database. Thorough benchmark study employing two different datasets show that our representations are competitive with the other existing methods. Limitations and potentials of the shape-based methods as well as possible improvements are discussed. PMID:20455259

Real-time ligand binding pocket database search using local surface descriptors.

PubMed

Chikhi, Rayan; Sael, Lee; Kihara, Daisuke

2010-07-01

Because of the increasing number of structures of unknown function accumulated by ongoing structural genomics projects, there is an urgent need for computational methods for characterizing protein tertiary structures. As functions of many of these proteins are not easily predicted by conventional sequence database searches, a legitimate strategy is to utilize structure information in function characterization. Of particular interest is prediction of ligand binding to a protein, as ligand molecule recognition is a major part of molecular function of proteins. Predicting whether a ligand molecule binds a protein is a complex problem due to the physical nature of protein-ligand interactions and the flexibility of both binding sites and ligand molecules. However, geometric and physicochemical complementarity is observed between the ligand and its binding site in many cases. Therefore, ligand molecules which bind to a local surface site in a protein can be predicted by finding similar local pockets of known binding ligands in the structure database. Here, we present two representations of ligand binding pockets and utilize them for ligand binding prediction by pocket shape comparison. These representations are based on mapping of surface properties of binding pockets, which are compactly described either by the two-dimensional pseudo-Zernike moments or the three-dimensional Zernike descriptors. These compact representations allow a fast real-time pocket searching against a database. Thorough benchmark studies employing two different datasets show that our representations are competitive with the other existing methods. Limitations and potentials of the shape-based methods as well as possible improvements are discussed.

IspE Inhibitors Identified by a Combination of In Silico and In Vitro High-Throughput Screening

PubMed Central

Tidten-Luksch, Naomi; Grimaldi, Raffaella; Torrie, Leah S.; Frearson, Julie A.; Hunter, William N.; Brenk, Ruth

2012-01-01

CDP-ME kinase (IspE) contributes to the non-mevalonate or deoxy-xylulose phosphate (DOXP) pathway for isoprenoid precursor biosynthesis found in many species of bacteria and apicomplexan parasites. IspE has been shown to be essential by genetic methods and since it is absent from humans it constitutes a promising target for antimicrobial drug development. Using in silico screening directed against the substrate binding site and in vitro high-throughput screening directed against both, the substrate and co-factor binding sites, non-substrate-like IspE inhibitors have been discovered and structure-activity relationships were derived. The best inhibitors in each series have high ligand efficiencies and favourable physico-chemical properties rendering them promising starting points for drug discovery. Putative binding modes of the ligands were suggested which are consistent with established structure-activity relationships. The applied screening methods were complementary in discovering hit compounds, and a comparison of both approaches highlights their strengths and weaknesses. It is noteworthy that compounds identified by virtual screening methods provided the controls for the biochemical screens. PMID:22563402

Comparative studies on drug binding to the purified and pharmaceutical-grade human serum albumins: Bridging between basic research and clinical applications of albumin.

PubMed

Ashrafi-Kooshk, Mohammad Reza; Ebrahimi, Farangis; Ranjbar, Samira; Ghobadi, Sirous; Moradi, Nastaran; Khodarahmi, Reza

2015-09-01

Human serum albumin (HSA), the most abundant protein in blood plasma, is a monomeric multidomain protein that possesses an extraordinary capacity for binding, so that serves as a circulating depot for endogenous and exogenous compounds. During the heat sterilization process, the structure of pharmaceutical-grade HSA may change and some of its activities may be lost. In this study, to provide deeper insight on this issue, we investigated drug-binding and some physicochemical properties of purified albumin (PA) and pharmaceutical-grade albumin (PGA) using two known drugs (indomethacin and ibuprofen). PGA displayed significantly lower drug binding capacity compared to PA. Analysis of the quenching and thermodynamic parameters indicated that intermolecular interactions between the drugs and the proteins are different from each other. Surface hydrophobicity as well as the stability of PGA decreased compared to PA, also surface hydrophobicity of PA and PGA increased upon drugs binding. Also, kinetic analysis of pseudo-esterase activities indicated that Km and Vmax parameters for PGA enzymatic activity are more and less than those of PA, respectively. This in vitro study demonstrates that the specific drug binding of PGA is significantly reduced. Such studies can act as connecting bridge between basic research discoveries and clinical applications. Copyright © 2015 The International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

Relationship between performance deterioration of a polyamide reverse osmosis membrane used in a seawater desalination plant and changes in its physicochemical properties.

PubMed

Suzuki, Tasuma; Tanaka, Ryohei; Tahara, Marina; Isamu, Yuya; Niinae, Masakazu; Lin, Lin; Wang, Jingbo; Luh, Jeanne; Coronell, Orlando

2016-09-01

While it is known that the performance of reverse osmosis membranes is dependent on their physicochemical properties, the existing literature studying membranes used in treatment facilities generally focuses on foulant layers or performance changes due to fouling, not on the performance and physicochemical changes that occur to the membranes themselves. In this study, the performance and physicochemical properties of a polyamide reverse osmosis membrane used for three years in a seawater desalination plant were compared to those of a corresponding unused membrane. The relationship between performance changes during long-term use and changes in physicochemical properties was evaluated. The results showed that membrane performance deterioration (i.e., reduced water flux, reduced contaminant rejection, and increased fouling propensity) occurred as a result of membrane use in the desalination facility, and that the main physicochemical changes responsible for performance deterioration were reduction in PVA coating coverage and bromine uptake by polyamide. The latter was likely promoted by oxidant residual in the membrane feed water. Our findings indicate that the optimization of membrane materials and processes towards maximizing the stability of the PVA coating and ensuring complete removal of oxidants in feed waters would minimize membrane performance deterioration in water purification facilities. Copyright © 2016 Elsevier Ltd. All rights reserved.

NANOSILVER MOVEMENT THROUGH BIOLOGICAL BARRIERS RELATES TO PHYSICOCHEMICAL PROPERTIES

EPA Science Inventory

Linking the physicochemical (PC) properties of engineered nanomaterials (NM) to their biological activity is critical for identifying their (toxic) mode of action, and developing appropriate and effective risk assessment guidelines. Particle surface charge (zeta potential), surfa...

Cationic drug pharmacokinetics in diseased livers determined by fibrosis index, hepatic protein content, microsomal activity, and nature of drug.

PubMed

Hung, Daniel Y; Chang, Ping; Cheung, Kee; McWhinney, Brett; Masci, Paul P; Weiss, Michael; Roberts, Michael S

2002-06-01

The disposition kinetics of six cationic drugs in perfused diseased and normal rat livers were determined by multiple indicator dilution and related to the drug physicochemical properties and liver histopathology. A carbon tetrachloride (CCl(4))-induced acute hepatocellular injury model had a higher fibrosis index (FI), determined by computer-assisted image analysis, than did an alcohol-induced chronic hepatocellular injury model. The alcohol-treated group had the highest hepatic alpha(1)-acid glycoprotein, microsomal protein (MP), and cytochrome P450 (P450) concentrations. Various pharmacokinetic parameters could be related to the octanol-water partition coefficient (log P(app)) of the drug as a surrogate for plasma membrane partition coefficient and affinity for MP or P450, the dependence being lower in the CCl(4)-treated group and higher in the alcohol-treated group relative to controls. Stepwise regression analysis showed that hepatic extraction ratio, permeability-surface area product, tissue-binding constant, intrinsic clearance, partition ratio of influx (k(in)) and efflux rate constant (k(out)), and k(in)/k(out) were related to physicochemical properties of drug (log P(app) or pK(a)) and liver histopathology (FI, MP, or P450). In addition, hepatocyte organelle ion trapping of cationic drugs was evident in all groups. It is concluded that fibrosis-inducing hepatic disease effects on cationic drug disposition in the liver may be predicted from drug properties and liver histopathology.

Evaluation of Particle Size Influence on Proximate Composition, Physicochemical, Techno-Functional and Physio-Functional Properties of Flours Obtained from Persimmon (Diospyros kaki Trumb.) Coproducts.

PubMed

Lucas-González, Raquel; Viuda-Martos, Manuel; Pérez-Álvarez, José Ángel; Fernández-López, Juana

2017-03-01

The aim of the work was to study the influence of particle size in the composition, physicochemical, techno-functional and physio-functional properties of two flours obtained from persimmon (Diospyros kaki Trumb. cvs. 'Rojo Brillante' (RBF) and 'Triump' (THF) coproducts. The cultivar (RBF and THF) and particle size significantly affected all parameters under study, although depending on the evaluated property, only one of these effects predominated. Carbohydrates (38.07-46.98 g/100 g) and total dietary fiber (32.07-43.57 g/100 g) were the main components in both flours (RBF and THF). Furthermore, insoluble dietary fiber represented more than 68% of total dietary fiber content. All color properties studied were influenced by cultivar and particle size. For both cultivars, the lower particle size, the higher lightness and hue values. RBF flours showed high values for emulsifying activity (69.33-74.00 mL/mL), while THF presented high values for water holding capacity (WHC: 9.47-12.19 g water/g sample). The bile holding capacity (BHC) and fat/oil binding values were, in general, higher in RBF (19.61-12.19 g bile/g sample and 11.98-9.07, respectively) than THF (16.12-12.40 g bile/g sample and 9.78-7.96, respectively). The effect of particle size was really evident in both WHC and BHC. Due to their dietary fiber content, techno-functional and physio-functional properties, persimmon flours seem to have a good profile to be used as potential functional ingredient.

Application of 3D-QSAR for identification of descriptors defining bioactivity of antimicrobial peptides.

PubMed

Bhonsle, Jayendra B; Venugopal, Divakaramenon; Huddler, Donald P; Magill, Alan J; Hicks, Rickey P

2007-12-27

In our laboratory, a series of antimicrobial peptides have been developed, where the resulting 3D-physicochemical properties are controlled by the placement of amino acids with well-defined properties (hydrophobicity, charge density, electrostatic potential, and so on) at specific locations along the peptide backbone. These peptides exhibited different in vitro activity against Staphylococcus aureus (SA) and Mycobacterium ranae (MR) bacteria. We hypothesized that the differences in the biological activity is a direct manifestation of different physicochemical interactions that occur between the peptides and the cell membranes of the bacteria. 3D-QSAR analysis has shown that, within this series, specific physicochemical properties are responsible for antibacterial activity and selectivity. There are five physicochemical properties specific to the SA QSAR model, while five properties are specific to the MR QSAR model. These results support the hypothesis that, for any particular AMP, organism selectivity and potency are controlled by the chemical composition of the target cell membrane.

Physicochemical Property Guidelines for Modern Agrochemicals.

PubMed

Zhang, Yu; Lorsbach, Beth; Castetter, Scott; Lambert, William T; Kister, Jeremy; Wang, Nick X; Klittich, Carla; Roth, Joshua; Sparks, Thomas C; Loso, Mike R

2018-04-17

The relentless need for the discovery and development of new agrochemicals continues due to driving forces such as loss of existing products through the development of resistance, the necessity for products with more favorable environmental and toxicological profiles, shifting pest spectra, and the changing agricultural needs and practices of the farming community. These new challenges underscore the demand for novel, high quality starting points to accelerate the discovery of new agrochemicals that address market challenges. This article discusses the efforts to identify the optimum ranges of physicochemical properties of agrochemicals through analysis of modern commercial products. Specifically, we reviewed literature studies examining physicochemical property effects and analyzed the properties typical of successful fungicides, herbicides, and insecticides (chewing and sap-feeding pests). From the analysis, a new set of physicochemical property guidelines for each discipline, as well as building block class, are proposed. These new guidelines should significantly aid in the discovery of next generation agrochemicals. This article is protected by copyright. All rights reserved.

Prescribed fires effects on physico-chemical properties and quantity of runoff and soil erosion in a Mediterranean forest

NASA Astrophysics Data System (ADS)

Esteban Lucas-Borja, Manuel; Plaza Alvaréz, Pedro Antonio; Sagra, Javier; Alfaro Sánchez, Raquel; Moya, Daniel; Ferrandiz Gotor, Pablo; De las Heras Ibañez, Jorge

2017-04-01

Wildfires have an important influence in forest ecosystems. Contrary to high severity fire, which may have negative impacts on the ecosystems, low severity induce small changes on soil properties. Thus and in order to reduce fire risk, low-severity prescribed fires have been widely used as a fuel reduction tool and silvicultural treatment in Mediterranean forest ecosystems. However, fire may alter microsite conditions and little is known about the impact of prescribed burning on the physico-chemical properties of runoff. In this study, we compared the effects of prescribed burning on physico-chemical properties and quantity of runoff and soil erosion during twelve months after a low severity prescribed fire applied in twelve 16 m2 plot (6 burned plots and 6 control plots used for comparison) set up in the Lezuza forest (Albacete, central-eastern Spain). Physico-chemical properties and quantity of runoff and soil losses were monitored after each rainfall event (five rainfall events in total). Also, different forest stand characteristics (slope, tree density, basal area and shrub/herbal cover) affecting each plot were measured. Results showed that forest stand characteristics were very similar in all used plots. Also, physico-chemical runoff properties were highly modified after the prescribed fire, increasing water pH, carbonates, bicarbonates, total dissolved solids and organic matter content dissolved in water. Electrical conductivity, calcium, sodium, chloride and magnesium were not affected by prescribed fire. Soil losses were highly related to precipitation intensity and tree interception. Tree intercepted the rainfall and significantly reduced soil losses and also runoff quantity. In conclusion and after the first six-month experiment, the influence of prescribed fires on physico-chemical runoff properties should be taken into account for developing proper prescribed burnings guidelines.

Biometal binding-site mimicry with modular, hetero-bifunctionally modified architecture encompassing a Trp/His motif: insights into spatiotemporal noncovalent interactions from a comparative spectroscopic study.

PubMed

Yang, Chi Ming

2011-03-28

Metal-site Trp/His interactions are crucial to diverse metalloprotein functions. This paper presents a study using metal-motif mimicry to capture and dissect the static and transient components of physicochemical properties underlying the Trp/His aromatic side-chain noncovalent interactions across the first- and second-coordination spheres of biometal ions. Modular biomimetic constructs, EDTA-(L-Trp, L-His) or EWH and DTPA-(L-Trp, L-His) or DWH, featuring a function-significant Trp/His pair, enabled extracting the putative hydrophobic/hydrophilic aromatic interactions surrounding metal centers. Fluorescence, circular dichroism (CD) spectroscopic titrations and ESI mass spectrometry demonstrated that both the constructs stoichiometrically bind to Ca(2+), Co(2+), Cu(2+), Ni(2+), Mn(2+), Zn(2+), Cd(2+), and Fe(2+), and such binding was strongly coupled to stereospecific side-chain structure reorientations of the Trp indole and His imidazole rings. A mechanistic dichotomy corresponding to the participation of the indole unit in the binding event was revealed by a scaffold-platform correlation of steady-state fluorescence-response landscape, illuminating that secondary-coordination-sphere ligand cation-π interactions were immediately followed by subsequent transient physicochemical processes including through-space energy transfer, charge transfer and/or electron transfer, depending on the type of metals. The fluorescence quenching of Trp side chain by 3d metal ions can be ascribed to through-space d-π interactions. While the fluorescence titration was capable of illuminating a two-component energetic model, clean isosbestic/isodichroic points in the CD titration spectra indicated that the metallo-constructs, such as Cu(2+)-EWH complex, fold thermodynamically by means of a two-state equilibrium. Further, the metal-ion dependence of Trp conformational variation in the modular architecture of metal-bound scaffolds was evidenced unambiguously by the CD spectra and supported by MMFF calculations; both were capable of distinguishing between the coordination geometry and the preference for metal binding mode. The study thus helps understand how aromatic rings around metal-sites have unique capabilities through the control of the spatiotemporal distribution of noncovalent interaction elements to achieve diverse chemical functionality.

PREDICTION OF PHYSICOCHEMICAL PROCESSES FOR ENVIRONMENTAL MODELING BY COMPUTER

EPA Science Inventory

The major differences among behavioral profiles of molecules in the environment are attributable to their physicochemical properties. For most chemicals, only fragmentary knowledge exists about those properties that determine each compound's environmental fate. A chemical-by-ch...

Emerging Energetic Materials: Synthesis, Physicochemical, and Detonation Properties

USDA-ARS?s Scientific Manuscript database

This book summarizes the science and technology of new generation high energy and insensitive explosives. The objective is to provide the professionals with comprehensive information on synthesis, physicochemical, and detonation properties of the explosives. Potential technologies applicable for tre...

Interaction studies reveal specific recognition of an anti-inflammatory polyphosphorhydrazone dendrimer by human monocytes

NASA Astrophysics Data System (ADS)

Ledall, Jérémy; Fruchon, Séverine; Garzoni, Matteo; Pavan, Giovanni M.; Caminade, Anne-Marie; Turrin, Cédric-Olivier; Blanzat, Muriel; Poupot, Rémy

2015-10-01

Dendrimers are nano-materials with perfectly defined structure and size, and multivalency properties that confer substantial advantages for biomedical applications. Previous work has shown that phosphorus-based polyphosphorhydrazone (PPH) dendrimers capped with azabisphosphonate (ABP) end groups have immuno-modulatory and anti-inflammatory properties leading to efficient therapeutic control of inflammatory diseases in animal models. These properties are mainly prompted through activation of monocytes. Here, we disclose new insights into the molecular mechanisms underlying the anti-inflammatory activation of human monocytes by ABP-capped PPH dendrimers. Following an interdisciplinary approach, we have characterized the physicochemical and biological behavior of the lead ABP dendrimer with model and cell membranes, and compared this experimental set of data to predictive computational modelling studies. The behavior of the ABP dendrimer was compared to the one of an isosteric analog dendrimer capped with twelve azabiscarboxylate (ABC) end groups instead of twelve ABP end groups. The ABC dendrimer displayed no biological activity on human monocytes, therefore it was considered as a negative control. In detail, we show that the ABP dendrimer can bind both non-specifically and specifically to the membrane of human monocytes. The specific binding leads to the internalization of the ABP dendrimer by human monocytes. On the contrary, the ABC dendrimer only interacts non-specifically with human monocytes and is not internalized. These data indicate that the bioactive ABP dendrimer is recognized by specific receptor(s) at the surface of human monocytes.Dendrimers are nano-materials with perfectly defined structure and size, and multivalency properties that confer substantial advantages for biomedical applications. Previous work has shown that phosphorus-based polyphosphorhydrazone (PPH) dendrimers capped with azabisphosphonate (ABP) end groups have immuno-modulatory and anti-inflammatory properties leading to efficient therapeutic control of inflammatory diseases in animal models. These properties are mainly prompted through activation of monocytes. Here, we disclose new insights into the molecular mechanisms underlying the anti-inflammatory activation of human monocytes by ABP-capped PPH dendrimers. Following an interdisciplinary approach, we have characterized the physicochemical and biological behavior of the lead ABP dendrimer with model and cell membranes, and compared this experimental set of data to predictive computational modelling studies. The behavior of the ABP dendrimer was compared to the one of an isosteric analog dendrimer capped with twelve azabiscarboxylate (ABC) end groups instead of twelve ABP end groups. The ABC dendrimer displayed no biological activity on human monocytes, therefore it was considered as a negative control. In detail, we show that the ABP dendrimer can bind both non-specifically and specifically to the membrane of human monocytes. The specific binding leads to the internalization of the ABP dendrimer by human monocytes. On the contrary, the ABC dendrimer only interacts non-specifically with human monocytes and is not internalized. These data indicate that the bioactive ABP dendrimer is recognized by specific receptor(s) at the surface of human monocytes. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03884g

Fabrication of novel dental nanocomposites and investigation their physicochemical and biological properties

NASA Astrophysics Data System (ADS)

Jaymand, Mehdi; lotfi, Mehrdad; Abbasian, Mojtaba

2018-03-01

This article evaluates physicochemical, mechanical, and biological properties of a series of novel dental nanocomposites that fabricated from multifunctional methacrylate-based dental monomers, triethyleneglycol dimethacrylate (TEGDMA) monomer, and modified silica nanoparticles (SiO2 NPs). The antibacterial activities of the monomers were investigated against lactobacillus plantarum by standard agar disk diffusion method. The cytotoxicity characteristics of the monomers and fabricated nanocomposites were evaluated by MTT and trypan blue cell viability tests, respectively against NIH3T3 cell line. In addition, the mechanical properties, as well as physicochemical characteristics including water sorption, sol fraction, and double bond conversion were also investigated. According to the results, the formulated nanocomposites have potential to apply as dental nanocomposites mainly due to their acceptable physicochemical, mechanical and biological characteristics.

More than a simple lipophilic contact: a detailed thermodynamic analysis of nonbasic residues in the s1 pocket of thrombin.

PubMed

Baum, Bernhard; Mohamed, Menshawy; Zayed, Mohamed; Gerlach, Christof; Heine, Andreas; Hangauer, David; Klebe, Gerhard

2009-07-03

The field of medicinal chemistry aims to design and optimize small molecule leads into drug candidates that may positively interfere with pathological disease situations in humans or combat the growth of infective pathogens. From the plethora of crystal structures of protein-inhibitor complexes we have learned how molecules recognize each other geometrically, but we still have rather superficial understanding of why they bind to each other. This contribution surveys a series of 26 thrombin inhibitors with small systematic structural differences to elucidate the rationale for their widely deviating binding affinity from 185 microM to 4 nM as recorded by enzyme kinetic measurements. Five well-resolved (resolution 2.30 - 1.47 A) crystal structures of thrombin-inhibitor complexes and an apo-structure of the uncomplexed enzyme (1.50 A) are correlated with thermodynamic data recorded by isothermal titration calorimetry with 12 selected inhibitors from the series. Taking solubility data into account, the variation in physicochemical properties allows conclusions to be reached about the relative importance of the enthalpic binding features as well as to estimate the importance of the parameters more difficult to capture, such as residual ligand entropy and desolvation properties. The collected data reveal a comprehensive picture of the thermodynamic signature that explains the so far poorly understood attractive force experienced by m-chloro-benzylamides to thrombin.

Deposition of chemically reactive and repellent sites on biosensor chips for reduced non-specific binding.

PubMed

Gandhiraman, R P; Gubala, V; Le, N C H; Nam, Le Cao Hoai; Volcke, C; Doyle, C; James, B; Daniels, S; Williams, D E

2010-08-01

The performances of new polymeric materials with excellent optical properties and good machinability have led the biomedical diagnostics industry to develop cheap disposable biosensor platforms appropriate for point of care applications. Zeonor, a type of cycloolefin polymer (COP), is one such polymer that presents an excellent platform for biosensor chips. These polymer substrates have to be modified to have suitable physico-chemical properties for immobilizing proteins. In this work, we have demonstrated the amine functionalization of COP substrates, by plasma enhanced chemical vapour deposition (PECVD), through codeposition of ethylene diamine and 3-aminopropyltriethoxysilane precursors, for building chemistries on the plastic chip. The elemental composition, adhesion, ageing and reactivity of the plasma polymerized film were examined. The Si-O functionality present in amino silane contributed for a good interfacial adhesion of the coating to COP substrates and also acted as a network building layer for plasma polymerization. Wet chemical modification was then carried out on the amine functionalized chips to create chemically reactive isothiocyanate sites and protein repellent fluorinated sites on the same chip. The density of the reactive and repellent sites was altered by choosing appropriate mixtures of homofunctional phenyldiisothiocyanate (PDITC), pentafluoroisothiocyanate (5FITC) and phenylisothiocyanate (PITC) compounds. By tailoring the density of reactive binding sites and protein repellent sites, the non-specific binding of ssDNA has been decreased to a significant extent. Copyright 2010 Elsevier B.V. All rights reserved.

Synthesis and characterization of a new Inonotus obliquus polysaccharide-iron(III) complex.

PubMed

Wang, Jia; Chen, Haixia; Wang, Yanwei; Xing, Lisha

2015-04-01

A new Inonotus obliquus polysaccharide-iron(III) complex (IOPS-iron) was synthesized and characterized. The preparation conditions of IOPS-iron(III) were optimized and the physicochemical properties were characterized by physicochemical methods, scanning electron microscopy (SEM), electron paramagnetic resonance (EPR) spectroscopy, fourier transform infrared (FTIR) spectroscopy, circular dichroism (CD) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy, respectively. The highest iron content of IOPS-iron(III) complex (19.40%) was obtained at the conditions: the ratio of IOPS and FeCl3 • 6H2O was 3:5 (w/w), the pH value of alkali solution was 10, the reaction temperature was 30 °C and the reaction time was 6h. The iron(III) was shown to be bound through the binding sites of the polysaccharide IOPS and it could form spatially separated iron centers on the polysaccharide backbone. IOPS-iron(III) complex was found to have good digestive availability and antioxidant activities in the in vitro assays, which suggested the IOPS-iron(III) complex might be used as a new iron supplement candidate. Copyright © 2015 Elsevier B.V. All rights reserved.

Interaction of firefly luciferase and silver nanoparticles and its impact on enzyme activity

NASA Astrophysics Data System (ADS)

Käkinen, Aleksandr; Ding, Feng; Chen, Pengyu; Mortimer, Monika; Kahru, Anne; Ke, Pu Chun

2013-08-01

We report on the dose-dependent inhibition of firefly luciferase activity induced by exposure of the enzyme to 20 nm citrate-coated silver nanoparticles (AgNPs). The inhibition mechanism was examined by characterizing the physicochemical properties and biophysical interactions of the enzyme and the AgNPs. Consistently, binding of the enzyme induced an increase in zeta potential from -22 to 6 mV for the AgNPs, triggered a red-shift of 44 nm in the absorbance peak of the AgNPs, and rendered a ‘protein corona’ of 20 nm in thickness on the nanoparticle surfaces. However, the secondary structures of the enzyme were only marginally affected upon formation of the protein corona, as verified by circular dichroism spectroscopy measurement and multiscale discrete molecular dynamics simulations. Rather, inductively coupled plasma mass spectrometry measurement revealed a significant ion release from the AgNPs. The released silver ions could readily react with the cysteine residues and N-groups of the enzyme to alter the physicochemical environment of their neighboring catalytic site and subsequently impair the enzymatic activity.

Lipids and lipid binding proteins: a perfect match.

PubMed

Glatz, Jan F C

2015-02-01

Lipids serve a great variety of functions, ranging from structural components of biological membranes to signaling molecules affecting various cellular functions. Several of these functions are related to the unique physico-chemical properties shared by all lipid species, i.e., their hydrophobicity. The latter, however, is accompanied by a poor solubility in an aqueous environment and thus a severe limitation in the transport of lipids in aqueous compartments such as blood plasma and the cellular soluble cytoplasm. Specific proteins which can reversibly and non-covalently associate with lipids, designated as lipid binding proteins or lipid chaperones, greatly enhance the aqueous solubility of lipids and facilitate their transport between tissues and within tissue cells. Importantly, transport of lipids across biological membranes also is facilitated by specific (membrane-associated) lipid binding proteins. Together, these lipid binding proteins determine the bio-availability of their ligands, and thereby markedly influence the subsequent processing, utilization, or signaling effect of lipids. The bio-availability of specific lipid species thus is governed by the presence of specific lipid binding proteins, the affinity of these proteins for distinct lipid species, and the presence of competing ligands (including pharmaceutical compounds). Recent studies suggest that post-translational modifications of lipid binding proteins may have great impact on lipid-protein interactions. As a result, several levels of regulation exist that together determine the bio-availability of lipid species. This short review discusses the significance of lipid binding proteins and their potential application as targets for therapeutic intervention. Copyright © 2014 Elsevier Ltd. All rights reserved.

Toward the Understanding of MNEI Sweetness from Hydration Map Surfaces

PubMed Central

De Simone, Alfonso; Spadaccini, Roberta; Temussi, Piero A.; Fraternali, Franca

2006-01-01

The binding mechanism of sweet proteins to their receptor, a G-protein-coupled receptor, is not supported by direct structural information. In principle, the key groups responsible for biological activity (glucophores) can be localized on a small structural unit (sweet finger) or spread on a larger surface area. A recently proposed model, called “wedge model”, implies a large surface of interaction with the receptor. To explore this model in greater detail, it is necessary to examine the physicochemical features of the surfaces of sweet proteins, since their interaction with the receptor, with respect to that of small sweeteners, is more dependent on general physicochemical properties of the interface, such as electrostatic potential and hydration. In this study, we performed exhaustive molecular dynamics simulations in explicit water of the sweet protein MNEI and of its structural mutant G-16A, whose sweetness is one order of magnitude lower than that of MNEI. Solvent density and self-diffusion calculated from molecular dynamics simulations suggest a likely area of interaction delimited by four stretches arranged as a tetrahedron whose shape is complementary to that of a cavity on the surface of the receptor, in agreement with the wedge model. The suggested area of interaction is amazingly consistent with known mutagenesis data. In addition, the asymmetric hydration of the only helix in both proteins hints at a specific role for this secondary structure element in orienting the protein during the binding process. PMID:16461400

Predictive Models of Nanotoxicity: Relationship of Physicochemical Properties to Particle Movement Through Biological Barriers

EPA Science Inventory

Understanding the linkage between the physicochemical (PC) properties of nanoparticles (NP) and their activation of biological systems is poorly understood, yet fundamental to predicting nanotoxicity, idenitifying mode of actions and developing appropriate and effective regul...

Engineering of Fc Fragments with Optimized Physicochemical Properties Implying Improvement of Clinical Potentials for Fc-Based Therapeutics.

PubMed

Yang, Chunpeng; Gao, Xinyu; Gong, Rui

2017-01-01

Therapeutic monoclonal antibodies and Fc-fusion proteins are successfully used in treatment of various diseases mainly including cancer, immune disease, and viral infection, which belong to the Fc-based therapeutics. In recent years, engineered Fc-derived antibody domains have also shown potential for Fc-based therapeutics. To increase the druggability of Fc-based therapeutic candidates, many efforts have been made in optimizing physicochemical properties and functions mediated by Fc fragment. The desired result is that we can simultaneously obtain Fc variants with increased physicochemical properties in vitro and capacity of mediating appropriate functions in vivo . However, changes of physicochemical properties of Fc may result in alternation of Fc-mediated functions and vice versa , which leads to undesired outcomes for further development of Fc-based therapeutics. Therefore, whether modified Fc fragments are suitable for achievement of expected clinical results or not needs to be seriously considered. Now, this question comes to be noticed and should be figured out to make better translation from the results of laboratory into clinical applications. In this review, we summarize different strategies on engineering physicochemical properties of Fc, and preliminarily elucidate the relationships between modified Fc in vitro and the subsequent therapeutic influence in vivo .

Engineering of Fc Fragments with Optimized Physicochemical Properties Implying Improvement of Clinical Potentials for Fc-Based Therapeutics

PubMed Central

Yang, Chunpeng; Gao, Xinyu; Gong, Rui

2018-01-01

Therapeutic monoclonal antibodies and Fc-fusion proteins are successfully used in treatment of various diseases mainly including cancer, immune disease, and viral infection, which belong to the Fc-based therapeutics. In recent years, engineered Fc-derived antibody domains have also shown potential for Fc-based therapeutics. To increase the druggability of Fc-based therapeutic candidates, many efforts have been made in optimizing physicochemical properties and functions mediated by Fc fragment. The desired result is that we can simultaneously obtain Fc variants with increased physicochemical properties in vitro and capacity of mediating appropriate functions in vivo. However, changes of physicochemical properties of Fc may result in alternation of Fc-mediated functions and vice versa, which leads to undesired outcomes for further development of Fc-based therapeutics. Therefore, whether modified Fc fragments are suitable for achievement of expected clinical results or not needs to be seriously considered. Now, this question comes to be noticed and should be figured out to make better translation from the results of laboratory into clinical applications. In this review, we summarize different strategies on engineering physicochemical properties of Fc, and preliminarily elucidate the relationships between modified Fc in vitro and the subsequent therapeutic influence in vivo. PMID:29375551

Effects of excipients on the tensile strength, surface properties and free volume of Klucel® free films of pharmaceutical importance

NASA Astrophysics Data System (ADS)

Gottnek, Mihály; Süvegh, Károly; Pintye-Hódi, Klára; Regdon, Géza

2013-08-01

The physicochemical properties of polymers planned to be applied as mucoadhesive films were studied. Two types of Klucel® hydroxypropylcellulose (LF and MF) were used as film-forming polymers. Hydroxypropylcellulose was incorporated in 2 w/w% with glycerol and xylitol as excipients and lidocaine base as an active ingredient at 5, 10 or 15 w/w% of the mass of the film-forming polymer. The free volume changes of the films were investigated by positron annihilation lifetime spectroscopy, the mechanical properties of the samples were measured with a tensile strength tester and contact angles were determined to assess the surface properties of the films. It was found that the Klucel® MF films had better physicochemical properties than those of the LF films. Klucel® MF as a film-forming polymer with lidocaine base and both excipients at 5 w/w% exhibited physicochemical properties and good workability. The excipients proved to exert strong effects on the physicochemical properties of the tested systems and it is very important to study them intensively in preformulation studies in the pharmaceutical technology in order to utilise their benefits and to avoid any disadvantageous effects.

Linear and Branched PEIs (Polyethylenimines) and Their Property Space.

PubMed

Lungu, Claudiu N; Diudea, Mircea V; Putz, Mihai V; Grudziński, Ireneusz P

2016-04-13

A chemical property space defines the adaptability of a molecule to changing conditions and its interaction with other molecular systems determining a pharmacological response. Within a congeneric molecular series (compounds with the same derivatization algorithm and thus the same brute formula) the chemical properties vary in a monotonic manner, i.e., congeneric compounds share the same chemical property space. The chemical property space is a key component in molecular design, where some building blocks are functionalized, i.e., derivatized, and eventually self-assembled in more complex systems, such as enzyme-ligand systems, of which (physico-chemical) properties/bioactivity may be predicted by QSPR/QSAR (quantitative structure-property/activity relationship) studies. The system structure is determined by the binding type (temporal/permanent; electrostatic/covalent) and is reflected in its local electronic (and/or magnetic) properties. Such nano-systems play the role of molecular devices, important in nano-medicine. In the present article, the behavior of polyethylenimine (PEI) macromolecules (linear LPEI and branched BPEI, respectively) with respect to the glucose oxidase enzyme GOx is described in terms of their (interacting) energy, geometry and topology, in an attempt to find the best shape and size of PEIs to be useful for a chosen (nanochemistry) purpose.

Linear and Branched PEIs (Polyethylenimines) and Their Property Space

PubMed Central

Lungu, Claudiu N.; Diudea, Mircea V.; Putz, Mihai V.; Grudziński, Ireneusz P.

2016-01-01

A chemical property space defines the adaptability of a molecule to changing conditions and its interaction with other molecular systems determining a pharmacological response. Within a congeneric molecular series (compounds with the same derivatization algorithm and thus the same brute formula) the chemical properties vary in a monotonic manner, i.e., congeneric compounds share the same chemical property space. The chemical property space is a key component in molecular design, where some building blocks are functionalized, i.e., derivatized, and eventually self-assembled in more complex systems, such as enzyme-ligand systems, of which (physico-chemical) properties/bioactivity may be predicted by QSPR/QSAR (quantitative structure-property/activity relationship) studies. The system structure is determined by the binding type (temporal/permanent; electrostatic/covalent) and is reflected in its local electronic (and/or magnetic) properties. Such nano-systems play the role of molecular devices, important in nano-medicine. In the present article, the behavior of polyethylenimine (PEI) macromolecules (linear LPEI and branched BPEI, respectively) with respect to the glucose oxidase enzyme GOx is described in terms of their (interacting) energy, geometry and topology, in an attempt to find the best shape and size of PEIs to be useful for a chosen (nanochemistry) purpose. PMID:27089324

Fragment Screening of Soluble Epoxide Hydrolase for Lead Generation-Structure-Based Hit Evaluation and Chemistry Exploration.

PubMed

Xue, Yafeng; Olsson, Thomas; Johansson, Carina A; Öster, Linda; Beisel, Hans-Georg; Rohman, Mattias; Karis, David; Bäckström, Stefan

2016-03-04

Soluble epoxide hydrolase (sEH) is involved in the regulation of many biological processes by metabolizing the key bioactive lipid mediator, epoxyeicosatrienoic acids. For the development of sEH inhibitors with improved physicochemical properties, we performed both a fragment screening and a high-throughput screening aiming at an integrated hit evaluation and lead generation. Followed by a joint dose-response analysis to confirm the hits, the identified actives were then effectively triaged by a structure-based hit-classification approach to three prioritized series. Two distinct scaffolds were identified as tractable starting points for potential lead chemistry work. The oxoindoline series bind at the right-hand side of the active-site pocket with hydrogen bonds to the protein. The 2-phenylbenzimidazole-4-sulfonamide series bind at the central channel with significant induced fit, which has not been previously reported. On the basis of the encouraging initial results, we envision that a new lead series with improved properties could be generated if a vector is found that could merge the cyclohexyl functionality of the oxoindoline series with the trifluoromethyl moiety of the 2-phenylbenzimidazole-4-sulfonamide series. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Self-Motion Depending on the Physicochemical Properties of Esters as the Driving Force

ERIC Educational Resources Information Center

Nakata, Satoshi; Matsuo, Kyoko; Kirisaka, Junko

2007-01-01

The self-motion of an ester boat is investigated depending on the physicochemical properties of the surface-active substance. The results show that the ester boat moves towards the higher surface tension generating as the driving force.

Molecular modeling of polymers 16. Gaseous diffusion in polymers: a quantitative structure-property relationship (QSPR) analysis.

PubMed

Patel, H C; Tokarski, J S; Hopfinger, A J

1997-10-01

The purpose of this study was to identify the key physicochemical molecular properties of polymeric materials responsible for gaseous diffusion in the polymers. Quantitative structure-property relationships, QSPRs were constructed using a genetic algorithm on a training set of 16 polymers for which CO2, N2, O2 diffusion constants were measured. Nine physicochemical properties of each of the polymers were used in the trial basis set for QSPR model construction. The linear cross-correlation matrices were constructed and investigated for colinearity among the members of the training sets. Common water diffusion measures for a limited training set of six polymers was used to construct a "semi-QSPR" model. The bulk modulus of the polymer was overwhelmingly found to be the dominant physicochemical polymer property that governs CO2, N2 and O2 diffusion. Some secondary physicochemical properties controlling diffusion, including conformational entropy, were also identified as correlation descriptors. Very significant QSPR diffusion models were constructed for all three gases. Cohesive energy was identified as the main correlation physicochemical property with aqueous diffusion measures. The dominant role of polymer bulk modulus on gaseous diffusion makes it difficult to develop criteria for selective transport of gases through polymers. Moreover, high bulk moduli are predicted to be necessary for effective gas barrier materials. This property requirement may limit the processing and packaging features of the material. Aqueous diffusion in polymers may occur by a different mechanism than gaseous diffusion since bulk modulus does not correlate with aqueous diffusion, but rather cohesive energy of the polymer.

Metallofullerenol Gd@C82(OH)22 distracts the proline-rich-motif from putative binding on the SH3 domain

NASA Astrophysics Data System (ADS)

Kang, Seung-Gu; Huynh, Tien; Zhou, Ruhong

2013-03-01

Biocompatibility is often regarded as one important aspect of de novo designed nanomaterials for biosafety. However, the toxicological effect, appearing along with its latency, is much more difficult to address by linearly mapping physicochemical properties of related nanomaterials with biological effects such as immune or cellular regulatory responses due to the complicated protein-protein interactions. Here, we investigate a potential interference of a metallofullerenol, Gd@C82(OH)22, on the function of SH3 domain, a highly promiscuous protein-protein interaction mediator involved in signaling and regulatory pathways through its binding with the proline-rich motif (PRM) peptides, using the atomistic molecular dynamics simulation. Our study shows that when only Gd@C82(OH)22 and the SH3 domain are present (without the PRM ligand), Gd@C82(OH)22 can interact with the SH3 domain by either directly blocking the hydrophobic active site or binding with a hydrophilic off-site with almost equal probability, which can be understood from its intrinsic amphiphilic nature. In a binding competition with the PRM onto the SH3 domain, however, the on-site binding mode is depleted while Gd@C82(OH)22 effectively intercepts the PRM from the putative binding site of the SH3 domain, implying that Gd@C82(OH)22 can disturb protein-protein interactions mediated by the SH3 domain. Despite a successful surface modification in an aqueous biological medium and a more recent demonstration as potential de novo cancer therapeutics, our study indicates that greater attention is needed in assessing the potential cytotoxicity of these nanomaterials.Biocompatibility is often regarded as one important aspect of de novo designed nanomaterials for biosafety. However, the toxicological effect, appearing along with its latency, is much more difficult to address by linearly mapping physicochemical properties of related nanomaterials with biological effects such as immune or cellular regulatory responses due to the complicated protein-protein interactions. Here, we investigate a potential interference of a metallofullerenol, Gd@C82(OH)22, on the function of SH3 domain, a highly promiscuous protein-protein interaction mediator involved in signaling and regulatory pathways through its binding with the proline-rich motif (PRM) peptides, using the atomistic molecular dynamics simulation. Our study shows that when only Gd@C82(OH)22 and the SH3 domain are present (without the PRM ligand), Gd@C82(OH)22 can interact with the SH3 domain by either directly blocking the hydrophobic active site or binding with a hydrophilic off-site with almost equal probability, which can be understood from its intrinsic amphiphilic nature. In a binding competition with the PRM onto the SH3 domain, however, the on-site binding mode is depleted while Gd@C82(OH)22 effectively intercepts the PRM from the putative binding site of the SH3 domain, implying that Gd@C82(OH)22 can disturb protein-protein interactions mediated by the SH3 domain. Despite a successful surface modification in an aqueous biological medium and a more recent demonstration as potential de novo cancer therapeutics, our study indicates that greater attention is needed in assessing the potential cytotoxicity of these nanomaterials. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr33756a

Fragment-Based Discovery of Pyrimido[1,2-b]indazole PDE10A Inhibitors.

PubMed

Chino, Ayaka; Seo, Ryushi; Amano, Yasushi; Namatame, Ichiji; Hamaguchi, Wataru; Honbou, Kazuya; Mihara, Takuma; Yamazaki, Mayako; Tomishima, Masaki; Masuda, Naoyuki

2018-01-01

In this study, we report the identification of potent pyrimidoindazoles as phosphodiesterase10A (PDE10A) inhibitors by using the method of fragment-based drug discovery (FBDD). The pyrazolopyridine derivative 2 was found to be a fragment hit compound which could occupy a part of the binding site of PDE10A enzyme by using the method of the X-ray co-crystal structure analysis. On the basis of the crystal structure of compound 2 and PDE10A protein, a number of compounds were synthesized and evaluated, by means of structure-activity relationship (SAR) studies, which culminated in the discovery of a novel pyrimidoindazole derivative 13 having good physicochemical properties.

Selective detection of Mg2+ ions via enhanced fluorescence emission using Au–DNA nanocomposites

PubMed Central

Basu, Tanushree; Rana, Khyati; Das, Niranjan

2017-01-01

The biophysical properties of DNA-modified Au nanoparticles (AuNPs) have attracted a great deal of research interest for various applications in biosensing. AuNPs have strong binding capability to the phosphate and sugar groups in DNA, rendering unique physicochemical properties for detection of metal ions. The formation of Au–DNA nanocomposites is evident from the observed changes in the optical absorption, plasmon band, zeta potential, DLS particle size distribution, as well as TEM and AFM surface morphology analysis. Circular dichroism studies also revealed that DNA-functionalized AuNP binding caused a conformational change in the DNA structure. Due to the size and shape dependent plasmonic interactions of AuNPs (33–78 nm) with DNA, the resultant Au–DNA nanocomposites (NCs) exhibit superior fluorescence emission due to chemical binding with Ca2+, Fe2+ and Mg2+ ions. A significant increase in fluorescence emission (λex = 260 nm) of Au–DNA NCs was observed after selectively binding with Mg2+ ions (20–800 ppm) in an aqueous solution where a minimum of 100 ppm Mg2+ ions was detected based on the linearity of concentration versus fluorescence intensity curve (λem = 400 nm). The effectiveness of Au–DNA nanocomposites was further verified by comparing the known concentration (50–120 ppm) of Mg2+ ions in synthetic tap water and a real life sample of Gelusil (300–360 ppm Mg2+), a widely used antacid medicine. Therefore, this method could be a sensitive tool for the estimation of water hardness after careful preparation of a suitably designed Au–DNA nanostructure. PMID:28487819

Effect of the cyclobutane cytidine dimer on the properties of Escherichia coli DNA photolyase.

PubMed

Murphy, Anar K; Tammaro, Margaret; Cortazar, Frank; Gindt, Yvonne M; Schelvis, Johannes P M

2008-11-27

Cyclobutane pyrimidine dimer (CPD) photolyases are structure specific DNA-repair enzymes that specialize in the repair of CPDs, the major photoproducts that are formed upon irradiation of DNA with ultraviolet light. The purified enzyme binds a flavin adenine dinucleotide (FAD), which is in the neutral radical semiquinone (FADH(*)) form. The CPDs are repaired by a light-driven, electron transfer from the anionic hydroquinone (FADH(-)) singlet excited state to the CPD, which is followed by reductive cleavage of the cyclobutane ring and subsequent monomerization of the pyrimidine bases. CPDs formed between two adjacent thymidine bases (T< >T) are repaired with greater efficiency than those formed between two adjacent cytidine bases (C< >C). In this paper, we investigate the changes in Escherichia coli photolyase that are induced upon binding to DNA containing C< >C lesions using resonance Raman, UV-vis absorption, and transient absorption spectroscopies, spectroelectrochemistry, and computational chemistry. The binding of photolyase to a C< >C lesion modifies the energy levels of FADH(*), the rate of charge recombination between FADH(-) and Trp(306)(*), and protein-FADH(*) interactions differently than binding to a T< >T lesion. However, the reduction potential of the FADH(-)/FADH(*) couple is modified in the same way with both substrates. Our calculations show that the permanent electric dipole moment of C< >C is stronger (12.1 D) and oriented differently than that of T< >T (8.7 D). The possible role of the electric dipole moment of the CPD in modifying the physicochemical properties of photolyase as well as in affecting CPD repair will be discussed.

Physicochemical properties of betaine monohydrate-carboxylic acid mixtures

NASA Astrophysics Data System (ADS)

Zahrina, I.; Nasikin, M.; Mulia, K.

2018-05-01

Green solvents are widely used to minimize environmental problems associated with the use of volatile organic solvents in many industries. DES are new green solvents in recent. The physicochemical properties of DES can be varied by properly combining of salts with different hydrogen bond donors. The objective of this work is to investigate the effect of varying molar ratios on the physicochemical properties of betaine monohydrate-carboxylic acid (i.e,. propionic or acetic acid) mixtures. Properties of mixtures were measured at 40°C. The viscosity, polarity scale (ENR), density, pH, and water content tend to decrease with the decrease in a molar ratio of betaine monohydrate to acid. Conversely, the ionic conductivity was increased. The physicochemical properties of these mixtures depend on the hydrogen bonding interactions between betaine, water and acid molecules. Betaine monohydratecarboxylic acid mixtures have wide range of polarity, low viscosity, high ionic conductivity, and density higher than 1 g·cm-3 that make them fit for numerous various applications. Additionally, due to these mixtures have acidic pH, it should be properly selected of metal type to minimize corrosion problems in industrial application.

A comparative study of the antihyaluronidase, antiurease, antioxidant, antimicrobial and physicochemical properties of different unifloral degrees of chestnut (Castanea sativa Mill.) honeys.

PubMed

Kolayli, Sevgi; Can, Zehra; Yildiz, Oktay; Sahin, Huseyin; Karaoglu, Sengul Alpay

2016-01-01

This study was planned to investigate some physicochemical and anti-inflammatory, antioxidant, antimicrobial properties of three different degrees of unifloral characters of chestnut honeys. Antihyaluronidase, antiurease and antimicrobial activities were evaluated as anti-inflammatory characteristics. Total phenolic contents, flavonoids, tannins, phenolic profiles, ferric-reducing antioxidant power (FRAP), scavenging activities of 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid (ABTS + ) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals were evaluated as antioxidant properties. Color, optical rotation, conductivity, moisture, pH and ash content were evaluated as physicochemical parameters, and some sugars content, prolin, diastase, HMF and minerals (Na, K, Ca, P, Fe, Cu and Zn) were evaluated as chemical and biochemical parameters. All studied physicochemical and biological active properties were changed in line with the unifloral character of the chestnut honeys. A higher unifloral character was found associated with greater apitherapeutic capacity of the honey, as well as biological active compounds.

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

PubMed Central

2013-01-01

Background Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity. Results We present an advanced software tool entitled MOLE 2.0, which has been designed to analyze molecular channels and pores. Benchmark tests against other available software tools showed that MOLE 2.0 is by comparison quicker, more robust and more versatile. As a new feature, MOLE 2.0 estimates physicochemical properties of the identified channels, i.e., hydropathy, hydrophobicity, polarity, charge, and mutability. We also assessed the variability in physicochemical properties of eighty X-ray structures of two members of the cytochrome P450 superfamily. Conclusion Estimated physicochemical properties of the identified channels in the selected biomacromolecules corresponded well with the known functions of the respective channels. Thus, the predicted physicochemical properties may provide useful information about the potential functions of identified channels. The MOLE 2.0 software is available at http://mole.chemi.muni.cz. PMID:23953065

Preparation and Physicochemical Properties of Vinblastine Microparticles by Supercritical Antisolvent Process

PubMed Central

Zhang, Xiaonan; Zhao, Xiuhua; Zu, Yuangang; Chen, Xiaoqiang; Lu, Qi; Ma, Yuliang; Yang, Lei

2012-01-01

The objective of the study was to prepare vinblastine microparticles by supercritical antisolvent process using N-methyl-2-pyrrolidone as solvent and carbon dioxide as antisolvent and evaluate its physicochemical properties. The effects of four process variables, pressure, temperature, drug concentration and drug solution flow rate, on drug particle formation during the supercritical antisolvent process, were investigated. Particles with a mean particle size of 121 ± 5.3 nm were obtained under the optimized process conditions (precipitation temperature 60 °C, precipitation pressure 25 MPa, vinblastine concentration 2.50 mg/mL and vinblastine solution flow rate 6.7 mL/min). The vinblastine was characterized by scanning electron microscopy, X-ray diffraction, Fourier-transform infrared spectroscopy, mass spectrometry and dissolution test. It was concluded that physicochemical properties of crystalline vinblastine could be improved by physical modification, such as particle size reduction and generation of amorphous state using the supercritical antisolvent process. Furthermore, the supercritical antisolvent process was a powerful methodology for improving the physicochemical properties of vinblastine. PMID:23202916

Physicochemical properties and oral bioavailability of ursolic acid nanoparticles using supercritical anti-solvent (SAS) process.

PubMed

Yang, Lei; Sun, Zhen; Zu, Yuangang; Zhao, Chunjian; Sun, Xiaowei; Zhang, Zhonghua; Zhang, Lin

2012-05-01

The objective of the study was to prepare ursolic acid (UA) nanoparticles using the supercritical anti-solvent (SAS) process and evaluate its physicochemical properties and oral bioavailability. The effects of four process variables, pressure, temperature, drug concentration and drug solution flow rate, on drug particle formation during SAS process, were investigated. Particles with mean particle size ranging from 139.2±19.7 to 1039.8±65.2nm were obtained by varying the process parameters. The UA was characterised by scanning electron microscopy, X-ray diffraction, Fourier-transform infrared spectroscopy, thermal gravimetric analysis, specific surface area, dissolution test and bioavailability test. It was concluded that physicochemical properties and bioavailability of crystalline UA could be improved by physical modification, such as particle size reduction and generation of amorphous state using SAS process. Further, SAS process was a powerful methodology for improving the physicochemical properties and bioavailability of UA. Copyright © 2011 Elsevier Ltd. All rights reserved.

Fused heterocycles bearing bridgehead nitrogen as potent HIV-1 NNRTIs. Part 3: optimization of [1,2,4]triazolo[1,5-a]pyrimidine core via structure-based and physicochemical property-driven approaches.

PubMed

Huang, Boshi; Li, Cuicui; Chen, Wenmin; Liu, Tao; Yu, Mingyan; Fu, Lu; Sun, Yueyue; Liu, Huiqing; De Clercq, Erik; Pannecouque, Christophe; Balzarini, Jan; Zhan, Peng; Liu, Xinyong

2015-03-06

In our arduous efforts to develop new potent HIV-1 non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs), novel piperidine-linked [1,2,4]triazolo[1,5-a]pyrimidine derivatives were designed, synthesized and evaluated for their antiviral activities in MT-4 cell cultures. Biological results showed that all of the title compounds displayed moderate to excellent activities against wild-type (wt) HIV-1 strain (IIIB) with EC50 values ranging from 8.1 nM to 2284 nM in a cell-based assay. Among them, the most promising analog 7d possessed an EC50 value of 8.1 nM against wt HIV-1, which was much more potent than the reference drugs DDI, 3 TC, NVP and DLV. Additionally, 7d demonstrated weak activity against the double mutant HIV-1 strain (K103N + Y181C), and was more efficient than NVP in a RT inhibition assay. Besides, some measured and calculated physicochemical properties of 7d, like log P and water solubility, as well as the structure-activity relationships (SARs) analysis have been discussed in detail. Furthermore, the binding mode of the active compound 7d was rationalized by molecular simulation studies. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Cholesterol-based cationic lipids for gene delivery: contribution of molecular structure factors to physico-chemical and biological properties.

PubMed

Sheng, Ruilong; Luo, Ting; Li, Hui; Sun, Jingjing; Wang, Zhao; Cao, Amin

2014-04-01

In this work, we prepared a series of cholesterol-based cationic (Cho-cat) lipids bearing cholesterol hydrophobe, natural amino acid headgroups (lysine/histidine) and linkage (carbonate ester/ether) bonds. In which, the natural amino acid headgroups made dominant contribution to their physico-chemical and biological properties. Among the lipids, the l-lysine headgroup bearing lipids (Cho-es/et-Lys) showed higher pDNA binding affinity and were able to form larger sized and higher surface charged lipoplexes than that of l-histidine headgroup bearing lipids (Cho-es/et-His), they also demonstrated higher transfection efficacy and higher membrane disruption capacities than that of their l-histidine headgroup bearing counterparts. However, compared to the contributions of the headgroups, the (carbonate ester/ether) linkage bonds showed much less affects. Besides, it could be noted that, Cho-es/et-Lys lipids exhibited very high luciferase gene transfection efficiency that almost reached the transfection level of "gold standard" bPEI-25k, made them potential transfection reagents for practical application. Moreover, the results facilitated the understanding for the structure-activity relationship of the cholesterol-based cationic lipids, and also paved a simple and efficient way for achieving high transfection efficiency by modification of suitable headgroups on lipid gene carriers. Copyright © 2014 Elsevier B.V. All rights reserved.

New approaches for the reliable in vitro assessment of binding affinity based on high-resolution real-time data acquisition of radioligand-receptor binding kinetics.

PubMed

Zeilinger, Markus; Pichler, Florian; Nics, Lukas; Wadsak, Wolfgang; Spreitzer, Helmut; Hacker, Marcus; Mitterhauser, Markus

2017-12-01

Resolving the kinetic mechanisms of biomolecular interactions have become increasingly important in early-phase drug development. Since traditional in vitro methods belong to dose-dependent assessments, binding kinetics is usually overlooked. The present study aimed at the establishment of two novel experimental approaches for the assessment of binding affinity of both, radiolabelled and non-labelled compounds targeting the A 3 R, based on high-resolution real-time data acquisition of radioligand-receptor binding kinetics. A novel time-resolved competition assay was developed and applied to determine the K i of eight different A 3 R antagonists, using CHO-K1 cells stably expressing the hA 3 R. In addition, a new kinetic real-time cell-binding approach was established to quantify the rate constants k on and k off , as well as the dedicated K d of the A 3 R agonist [ 125 I]-AB-MECA. Furthermore, lipophilicity measurements were conducted to control influences due to physicochemical properties of the used compounds. Two novel real-time cell-binding approaches were successfully developed and established. Both experimental procedures were found to visualize the kinetic binding characteristics with high spatial and temporal resolution, resulting in reliable affinity values, which are in good agreement with values previously reported with traditional methods. Taking into account the lipophilicity of the A 3 R antagonists, no influences on the experimental performance and the resulting affinity were investigated. Both kinetic binding approaches comprise tracer administration and subsequent binding to living cells, expressing the dedicated target protein. Therefore, the experiments resemble better the true in vivo physiological conditions and provide important markers of cellular feedback and biological response.

The human mitochondrial single-stranded DNA-binding protein displays distinct kinetics and thermodynamics of DNA binding and exchange

PubMed Central

Qian, Yufeng; Johnson, Kenneth A.

2017-01-01

The human mitochondrial ssDNA-binding protein (mtSSB) is a homotetrameric protein, involved in mtDNA replication and maintenance. Although mtSSB is structurally similar to SSB from Escherichia coli (EcoSSB), it lacks the C-terminal disordered domain, and little is known about the biophysics of mtSSB–ssDNA interactions. Here, we characterized the kinetics and thermodynamics of mtSSB binding to ssDNA by equilibrium titrations and stopped-flow kinetic measurements. We show that the mtSSB tetramer can bind to ssDNA in two distinct binding modes: (SSB)30 and (SSB)60, defined by DNA binding site sizes of 30 and 60 nucleotides, respectively. We found that the binding mode is modulated by magnesium ion and NaCl concentration, but unlike EcoSSB, the mtSSB does not show negative intersubunit cooperativity. Global fitting of both the equilibrium and kinetic data afforded estimates for the rate and equilibrium constants governing the formation of (SSB)60 and (SSB)30 complexes and for the transitions between the two binding modes. We found that the mtSSB tetramer binds to ssDNA with a rate constant near the diffusion limit (2 × 109 m−1 s−1) and that longer DNA (≥60 nucleotides) rapidly wraps around all four monomers, as revealed by FRET assays. We also show that the mtSSB tetramer can directly transfer from one ssDNA molecule to another via an intermediate with two DNA molecules bound to the mtSSB. In conclusion, our results indicate that human mtSSB shares many physicochemical properties with EcoSSB and that the differences may be explained by the lack of an acidic, disordered C-terminal tail in human mtSSB protein. PMID:28615444

[Cytochemical localization and properties of selected nucleolytic enzymes].

PubMed

Sierakowska, Halina

2015-01-01

In the article there are shortly outlined studies on cytochemical localization of selected nucleolytic enzymes carried out between 1957-1986 by David Shugar and his coworkers. The histochemical localization of several nucleolytic enzymes in animal and plant tissues was determined by synthesis of specific substrates, alpha-naphthyl esters of 5'- and 3'-nucleotides and their derivatives. In rat tissues phosphodiesterase I was localized in the plasma membrane whereas phosphodiesterase II in the lizosomes, reflecting their physiological roles. The localization of pancreatic type ribonuclease in animal tissues was determined, indicating its role in extracellular digestion. Plant nucleotide pyrophosphatase was localized in several tissues, purified to near homogeneity from potato tubers and its properties and substrate specificity were determined. Application of this enzyme for removal of m7GMP from the "cap" of eukaryotic mRNA allowed to elucidate the role of "cap" in mRNA binding to ribosomes in the process of translation. Furthermore, cyclic nucleotide phosphodiesterase was isolated from potato tubers and its physicochemical properties, oligomeric structure and substrate specificity were elucidated.

Effect of pH adjustment, homogenization and diafiltration on physicochemical, reconstitution, functional and rheological properties of medium protein milk protein concentrates (MPC70).

PubMed

Meena, Ganga Sahay; Singh, Ashish Kumar; Gupta, Vijay Kumar; Borad, Sanket; Arora, Sumit; Tomar, Sudhir Kumar

2018-04-01

Poor solubility is the major limiting factor in commercial applications of milk protein concentrates (MPC) powders. Retentate treatments such as pH adjustment using disodium phosphate (Na 2 HPO 4 ), also responsible for calcium chelation with homogenization and; its diafiltration with 150 mM NaCl solution were hypothesized to improve the functional properties of treated MPC70 powders. These treatments significantly improved the solubility, heat stability, water binding, dispersibility, bulk density, flowability, buffer index, foaming and emulsifying capacity of treated powders over control. Rheological behaviour of reconstituted MPC solutions was best explained by Herschel Bulkley model. Compared to rough, large globular structures with dents in control; majorly intact, separate, smaller particles of smooth surface, without any aggregation were observed in SEM micrograph of treated powders. Applied treatments are easy, cost-effective and capable to improve functional properties of treated powders that could replace control MPC70 powder in various food applications where protein functionality is of prime importance.

A global optimization algorithm for protein surface alignment

PubMed Central

2010-01-01

Background A relevant problem in drug design is the comparison and recognition of protein binding sites. Binding sites recognition is generally based on geometry often combined with physico-chemical properties of the site since the conformation, size and chemical composition of the protein surface are all relevant for the interaction with a specific ligand. Several matching strategies have been designed for the recognition of protein-ligand binding sites and of protein-protein interfaces but the problem cannot be considered solved. Results In this paper we propose a new method for local structural alignment of protein surfaces based on continuous global optimization techniques. Given the three-dimensional structures of two proteins, the method finds the isometric transformation (rotation plus translation) that best superimposes active regions of two structures. We draw our inspiration from the well-known Iterative Closest Point (ICP) method for three-dimensional (3D) shapes registration. Our main contribution is in the adoption of a controlled random search as a more efficient global optimization approach along with a new dissimilarity measure. The reported computational experience and comparison show viability of the proposed approach. Conclusions Our method performs well to detect similarity in binding sites when this in fact exists. In the future we plan to do a more comprehensive evaluation of the method by considering large datasets of non-redundant proteins and applying a clustering technique to the results of all comparisons to classify binding sites. PMID:20920230

Studies on molecular properties prediction and histamine H3 receptor affinities of novel ligands with uracil-based motifs.

PubMed

Lipani, Luca; Odadzic, Dalibor; Weizel, Lilia; Schwed, Johannes-Stephan; Sadek, Bassem; Stark, Holger

2014-10-30

The histamine H3 receptor (H3R) plays a role in cognitive and memory processes and is involved in different neurological disorders, including Alzheimer's disease, schizophrenia, and narcolepsy. Therefore, several hH3R antagonists/inverse agonists entered clinical phases for a broad spectrum of mainly centrally occurring diseases. However, many other promising candidates failed due to their pharmacokinetic profile, mostly because of their strong lipophilicity accompanied with low solubility. Analysis of previous potential H3R selective antagonists/inverse agonists, e.g. pitolisant, revealed promising results concerning physicochemical properties and drug-likeness. Herein, a series of new hH3R ligands 8-20 consisting of piperidin-1-yl or piperidin-1-yl-propoxyphenyl coupled to different uracil, thymine, and 5,6-dimethyluracil related moieties, were synthesized, evaluated on their binding properties at the hH3R and the estimation of different physicochemical and drug-likeness properties. Due to the coupling to various positions at pyrimidine-2,4-(1H,3H)-dione, affinity at hH3Rs and drug-likeness parameters have been improved. For instance, compound 9 showed in addition to high affinity at the hH3R (pKi (hH3R) = 8.14) clog S, clog P, LE, LipE, and drug-likeness score values of -4.36, 3.47, 0.34, 4.63, and 1.54, respectively. Also, the methyl substituted analog 17 (pKi (hH3R) = 8.15) revealed LE, LipE and drug-likeness score values of -3.29, 2.47, 0.49, 5.52, and 1.76, respectively. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

20180318 - Rapid collection of experimental physicochemical property data to inform various models and testing methods (ACS Spring)

EPA Science Inventory

In order to determine the potential toxicological effects, toxicokinetics, and route(s) of exposure for chemicals, their structures and corresponding physicochemical properties are required. With this data, the risk for thousands of environmental chemicals can be prioritized. How...

Physicochemical and biological characterization of single-walled and double-walled carbon nanotubes in biological media.

PubMed

Liu, Wen-Te; Bien, Mauo-Ying; Chuang, Kai-Jen; Chang, Ta-Yuan; Jones, Tim; BéruBé, Kelly; Lalev, Georgi; Tsai, Dai-Hua; Chuang, Hsiao-Chi; Cheng, Tsun-Jen

2014-09-15

To study the toxicity of nanoparticles under relevant conditions, it is important to reproducibly disperse nanoparticles in biological media in in vitro and in vivo studies. Here, single-walled nanotubes (SWNTs) and double-walled nanotubes (DWNTs) were physicochemically and biologically characterized when dispersed in phosphate-buffered saline (PBS) and bovine serum albumin (BSA). BSA-SWNT/DWNT interaction resulted in a reduction of aggregation and an increase in particle stabilization. Based on the protein sequence coverage and protein binding results, DWNTs exhibited higher protein binding than SWNTs. SWNT and DWNT suspensions in the presence of BSA increased interleukin-6 (IL-6) levels and reduced tumor necrosis factor-alpha (TNF-α) levels in A549 cells as compared to corresponding samples in the absence of BSA. We next determined the effects of SWNTs and DWNTs on pulmonary protein modification using bronchoalveolar lavage fluid (BALF) as a surrogate collected form BALB/c mice. The BALF proteins bound to SWNTs (13 proteins) and DWNTs (11 proteins), suggesting that these proteins were associated with blood coagulation pathways. Lastly, we demonstrated the importance of physicochemical and biological alterations of SWNTs and DWNTs when dispersed in biological media, since protein binding may result in the misinterpretation of in vitro results and the activation of protein-regulated biological responses. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Divergent unprotected peptide macrocyclisation by palladium-mediated cysteine arylation.

PubMed

Rojas, Anthony J; Zhang, Chi; Vinogradova, Ekaterina V; Buchwald, Nathan H; Reilly, John; Pentelute, Bradley L; Buchwald, Stephen L

2017-06-01

Macrocyclic peptides are important therapeutic candidates due to their improved physicochemical properties in comparison to their linear counterparts. Here we detail a method for a divergent macrocyclisation of unprotected peptides by crosslinking two cysteine residues with bis-palladium organometallic reagents. These synthetic intermediates are prepared in a single step from commercially available aryl bis-halides. Two bioactive linear peptides with cysteine residues at i , i + 4 and i , i + 7 positions, respectively, were cyclised to introduce a diverse array of aryl and bi-aryl linkers. These two series of macrocyclic peptides displayed similar linker-dependent lipophilicity, phospholipid affinity, and unique volume of distributions. Additionally, one of the bioactive peptides showed target binding affinity that was predominantly affected by the length of the linker. Collectively, this divergent strategy allowed rapid and convenient access to various aryl linkers, enabling the systematic evaluation of the effect of appending unit on the medicinal properties of macrocyclic peptides.

Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review

PubMed Central

Paquet, Eric; Viktor, Herna L.

2015-01-01

Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods. PMID:25785262

Physico-chemical properties and cytotoxic effects of sugar-based surfactants: Impact of structural variations.

PubMed

Lu, Biao; Vayssade, Muriel; Miao, Yong; Chagnault, Vincent; Grand, Eric; Wadouachi, Anne; Postel, Denis; Drelich, Audrey; Egles, Christophe; Pezron, Isabelle

2016-09-01

Surfactants derived from the biorefinery process can present interesting surface-active properties, low cytotoxicity, high biocompatibility and biodegradability. They are therefore considered as potential sustainable substitutes to currently used petroleum-based surfactants. To better understand and anticipate their performances, structure-property relationships need to be carefully investigated. For this reason, we applied a multidisciplinary approach to systematically explore the effect of subtle structural variations on both physico-chemical properties and biological effects. Four sugar-based surfactants, each with an eight carbon alkyl chain bound to a glucose or maltose head group by an amide linkage, were synthesized and evaluated together along with two commercially available standard surfactants. Physico-chemical properties including solubility, Krafft point, surface-tension lowering and critical micellar concentration (CMC) in water and biological medium were explored. Cytotoxicity evaluation by measuring proliferation index and metabolic activity against dermal fibroblasts showed that all surfactants studied may induce cell death at low concentrations (below their CMC). Results revealed significant differences in both physico-chemical properties and cytotoxic effects depending on molecule structural features, such as the position of the linkage on the sugar head-group, or the orientation of the amide linkage. Furthermore, the cytotoxic response increased with the reduction of surfactant CMC. This study underscores the relevance of a methodical and multidisciplinary approach that enables the consideration of surfactant solution properties when applied to biological materials. Overall, our results will contribute to a better understanding of the concomitant impact of surfactant structure at physico-chemical and biological levels. Copyright © 2016 Elsevier B.V. All rights reserved.

A Comparative Molecular Similarity Index Analysis (CoMSIA) study identifies an HLA-A2 binding supermotif

NASA Astrophysics Data System (ADS)

Doytchinova, Irini A.; Flower, Darren R.

2002-08-01

The 3D-QSAR CoMSIA technique was applied to a set of 458 peptides binding to the five most widespread HLA-A2-like alleles: A*0201, A*0202, A*0203, A*0206 and A*6802. Models comprising the main physicochemical properties (steric bulk, electron density, hydrophobicity and hydrogen-bond formation abilities) were obtained with acceptable predictivity ( q 2 ranged from 0.385 to 0.683). The use of coefficient contour maps allowed an A2-supermotif to be identified based on common favoured and disfavoured areas. The CoMSIA definition for the best HLA-A2 binder is as follows: hydrophobic aromatic amino acid at position 1; hydrophobic bulky side chains at positions 2, 6 and 9; non-hydrogen-bond-forming amino acids at position 3; small aliphatic hydrogen-bond donors at position 4; aliphatic amino acids at position 5; small aliphatic side chains at position 7; and small aliphatic hydrophilic and hydrogen-bond forming amino acids at position 8.

Effect of processing on physicochemical characteristics and bioefficacy of β-lactoglobulin-epigallocatechin-3-gallate complexes.

PubMed

Lestringant, Pauline; Guri, Anilda; Gülseren, Ibrahim; Relkin, Perla; Corredig, Milena

2014-08-20

Varying amounts of epigallocatechin-3-gallate (EGCG) were encapsulated in β-lactoglobulin (β-Lg) nanoparticles, either native or processed, denoted as heated or desolvated protein. The stability, physical properties, and bioactivity of the β-Lg-EGCG complexes were tested. Native β-Lg-EGCG complexes showed comparable stability and binding efficacy (EGCG/β-Lg molar ratio of 1:1) to heated β-Lg nanoparticles (1% and 5% protein w/w). The sizes of heated and desolvated β-Lg nanoparticles were comparable, but the latter showed the highest binding affinity for EGCG. The presence of EGCG complexed with β-Lg did not affect the interfacial tension of the protein when tested at the soy oil-water interface but caused a decrease in dilational elasticity. All β-Lg complexes (native, heated, or desolvated) showed a decrease in cellular proliferation similar to that of free ECGC. In summary, protein-EGCG complexes did not alter the bioefficacy of EGCG and contributed to increased stability with storage, demonstrating the potential benefits of nanoencapsulation.

Improving Nonspecific Binding and Solubility: Bicycloalkyl Groups and Cubanes as para-Phenyl Bioisosteres.

PubMed

Auberson, Yves P; Brocklehurst, Cara; Furegati, Markus; Fessard, Thomas C; Koch, Guido; Decker, Andrea; La Vecchia, Luigi; Briard, Emmanuelle

2017-04-20

Bicycloalkyl groups have been previously described as phenyl group bioisosteres. This article describes the synthesis of new building blocks allowing their introduction into complex molecules, and explores their use as a means to modify the physicochemical properties of drug candidates and improve the quality of imaging agents. In particular, the replacement of an aromatic ring with a bicyclo[1.1.1]pentane-1,3-diyl (BCP) group improves aqueous solubility by at least 50-fold, and markedly decreases nonspecific binding (NSB) as measured by CHI(IAM), the chromatographic hydrophobicity index on immobilized artificial membranes. Structural variations with the bicyclo[2.2.2]octane-1,4-diyl group led to more lipophilic molecules and did not show the same benefits regarding NSB or solubility, whereas substitutions with cubane-1,4-diyl showed improvements for both parameters. These results confirm the potential advantages of both BCP and cubane motifs as bioisosteric replacements for optimizing para-phenyl-substituted molecules. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular modelling and synthesis of spiroimidazolidine-2,4-diones with dual activities as hypoglycemic agents and selective inhibitors of aldose reductase.

PubMed

Salem, Manar G; Abdel Aziz, Yasmine M; Elewa, Marwa; Elshihawy, Hosam A; Said, Mohamed M

2018-05-02

Novel derivatives of spiroimidazolidinedione were synthesized and evaluated as hypoglycemic agents through binding to sulfonylurea receptor 1 (SUR1) in pancreatic beta-cells. Their selectivity index was calculated against both aldehyde reductase (ALR1) and aldose reductase (ALR2). Aldehyde reductase is a key enzyme in the polyol pathway that is involved in the etiology of the secondary diabetic complications. All structures were confirmed by microanalysis and by IR, 1 H NMR, 13 C NMR and EI-MS spectroscopy. The investigated compounds were subjected to molecular docking and an in silico prediction study to determine their free energy of binding (ΔG) values and predict their physicochemical properties and drug-likeness scores. Compound 1'-(5-chlorothiophene-2-ylsulfonyl)spiro[cyclohexane-1,5'-imidazolidine]-2',4'-dione showed IC 50 0.47 µM and 79% reduction in blood glucose level with a selectivity index 127 for ALR2. Copyright © 2018 Elsevier Inc. All rights reserved.

Effect of germination on the physicochemical and antioxidant characteristics of rice flour from three rice varieties from Nigeria.

PubMed

Chinma, Chiemela Enyinnaya; Anuonye, Julian Chukwuemeka; Simon, Omotade Comfort; Ohiare, Raliat Ozavize; Danbaba, Nahemiah

2015-10-15

This study determined the effect of germination (48 h) on the physicochemical and antioxidant characteristics of rice flour from three rice varieties from Nigeria. Local rice varieties (Jamila, Jeep and Kwandala) were evaluated and compared to an improved variety (MR 219). Physicochemical and antioxidant properties of flours were determined using standard methods. Protein, magnesium, phosphorus, potassium and antioxidant properties of rice flours increased after germination while phytic acid and total starch contents decreased. Foaming capacity and stability of rice flours increased after germination. Germination resulted to changes in pasting and thermal characteristics of rice flours. Germinated rice flours had better physicochemical and antioxidant properties with reduced phytic acid and starch contents compared to MR 219, which can be utilized as functional ingredients in the preparation of rice-based products. Copyright © 2015 Elsevier Ltd. All rights reserved.

Nanoparticles-cell association predicted by protein corona fingerprints

NASA Astrophysics Data System (ADS)

Palchetti, S.; Digiacomo, L.; Pozzi, D.; Peruzzi, G.; Micarelli, E.; Mahmoudi, M.; Caracciolo, G.

2016-06-01

In a physiological environment (e.g., blood and interstitial fluids) nanoparticles (NPs) will bind proteins shaping a ``protein corona'' layer. The long-lived protein layer tightly bound to the NP surface is referred to as the hard corona (HC) and encodes information that controls NP bioactivity (e.g. cellular association, cellular signaling pathways, biodistribution, and toxicity). Decrypting this complex code has become a priority to predict the NP biological outcomes. Here, we use a library of 16 lipid NPs of varying size (Ø ~ 100-250 nm) and surface chemistry (unmodified and PEGylated) to investigate the relationships between NP physicochemical properties (nanoparticle size, aggregation state and surface charge), protein corona fingerprints (PCFs), and NP-cell association. We found out that none of the NPs' physicochemical properties alone was exclusively able to account for association with human cervical cancer cell line (HeLa). For the entire library of NPs, a total of 436 distinct serum proteins were detected. We developed a predictive-validation modeling that provides a means of assessing the relative significance of the identified corona proteins. Interestingly, a minor fraction of the HC, which consists of only 8 PCFs were identified as main promoters of NP association with HeLa cells. Remarkably, identified PCFs have several receptors with high level of expression on the plasma membrane of HeLa cells.In a physiological environment (e.g., blood and interstitial fluids) nanoparticles (NPs) will bind proteins shaping a ``protein corona'' layer. The long-lived protein layer tightly bound to the NP surface is referred to as the hard corona (HC) and encodes information that controls NP bioactivity (e.g. cellular association, cellular signaling pathways, biodistribution, and toxicity). Decrypting this complex code has become a priority to predict the NP biological outcomes. Here, we use a library of 16 lipid NPs of varying size (Ø ~ 100-250 nm) and surface chemistry (unmodified and PEGylated) to investigate the relationships between NP physicochemical properties (nanoparticle size, aggregation state and surface charge), protein corona fingerprints (PCFs), and NP-cell association. We found out that none of the NPs' physicochemical properties alone was exclusively able to account for association with human cervical cancer cell line (HeLa). For the entire library of NPs, a total of 436 distinct serum proteins were detected. We developed a predictive-validation modeling that provides a means of assessing the relative significance of the identified corona proteins. Interestingly, a minor fraction of the HC, which consists of only 8 PCFs were identified as main promoters of NP association with HeLa cells. Remarkably, identified PCFs have several receptors with high level of expression on the plasma membrane of HeLa cells. Electronic supplementary information (ESI) available: Table S1. Cell viability (%) and cell association of the different nanoparticles used. Table S2. Total number of identified proteins on the different nanoparticles used. Tables S3-S18. Top 25 most abundant corona proteins identified in the protein corona of nanoparticles NP2-NP16 following 1 hour incubation with HP. Table S19. List of descriptors used. Table S20. Potential targets of protein corona fingerprints with its own interaction score (mentha) and the expression median value in Hela cells. Fig. S1 and S2. Effect of exposure to human plasma on size and zeta potential of NPs. Fig. S3. Predictive modeling of nanoparticle-cell association. See DOI: 10.1039/c6nr03898k

Use of an integrated approach to characterize the physicochemical properties of foundry green sands

USDA-ARS?s Scientific Manuscript database

A fresh green sand, spent green sand, and a weathered spent green sand from a landfill were analyzed using diffractometry, electron microscopy, granulometry, spectrometry, and thermogravimetry. Our objective was to understand how the physicochemical properties of the green sands change from their o...

Improvement in storage stability of infrared dried rough rice

USDA-ARS?s Scientific Manuscript database

The objective of this study was to develop infrared drying (IRD) method to improve the stability of physicochemical properties of rough rice during storage. The effect of IRD on the physicochemical properties of stored rough rice was compared with that of hot air drying (HAD) and ambient air drying ...

Linking the Physicochemical Properities of Titania with Its Biocidal Properities

EPA Science Inventory

LINKING THE PHYSICOCHEMICAL PROPERTIES OF TITANIA WITH ITS BIOCIDAL PROPERTIES. C. Han1, L. Putvin2, M. Pelaez1, H. Zamankhan3, H. Choi3, D. Betancourt4a, D. Dionysiou1. B. Veronesi4b, 1 Department of Biomedical, Chemical and Environmental Engineering, University of Cincinnati...

Some Physicochemical Properties of Faience Masses with the Utilization of Perlite and Diatomite,

DTIC Science & Technology

Physicochemical properties of faience (15-35 percent perlite or 5 percent diatomite ) were studied. The addition of 35 percent perlite lowered the...The strength increased. The effect of diatomite was not as pronounced, but the addition of diatomite prevented the formation of cristobalite. In

Effect of nitrogen rate and the environment on physicochemical properties of selected high amylose rice cultivars

USDA-ARS?s Scientific Manuscript database

Genetic marker haplotypes for the Waxy and alk genes are associated with amylose content and gelatinization temperature, respectively, and are used by breeders to develop rice cultivars that have physicochemical properties desired by the parboiling and canning industries. Cultivars that provide cons...

Effect of physicochemical properties of peptides from soy protein on their antimicrobial activity.

PubMed

Xiang, Ning; Lyu, Yuan; Zhu, Xiao; Bhunia, Arun K; Narsimhan, Ganesan

2017-08-01

Antimicrobial peptides (AMPs) kill microbial cells through insertion and damage/permeabilization of the cytoplasmic cell membranes and has applications in food safety and antibiotic replacement. Soy protein is an attractive, abundant natural source for commercial production of AMPs. In this research, explicit solvent molecular dynamics (MD) simulation was employed to investigate the effects of (i) number of total and net charges, (ii) hydrophobicity (iii) hydrophobic moment and (iv) helicity of peptides from soy protein on their ability to bind to lipid bilayer and their transmembrane aggregates to form pores. Interaction of possible AMP segments from soy protein with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPC/POPG) bilayers, a mimic of bacterial cell membrane, was investigated. Pore formation was insensitive to helicity and occurred for hydrophobicity threshold in the range of -0.3-0kcal/mol, hydrophobic moment threshold of 0.3kcal/mol, net charge threshold of 2. Though low hydrophobicity and high number of charges help in the formation of water channel for transmembrane aggregates, insertion of peptides with these properties requires overcome of energy barrier, as shown by potential of mean force calculations, thereby resulting in low antimicrobial activity. Experimental evaluation of antimicrobial activity of these peptides against Gram positive L. monocytogenes and Gram negative E. coli as obtained by spot-on-lawn assay was consistent with simulation results. These results should help in the development of guidelines for selection of peptides with antimicrobial activity based on their physicochemical properties. Copyright © 2017 Elsevier Inc. All rights reserved.

Probing binding hot spots at protein-RNA recognition sites.

PubMed

Barik, Amita; Nithin, Chandran; Karampudi, Naga Bhushana Rao; Mukherjee, Sunandan; Bahadur, Ranjit Prasad

2016-01-29

We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein-RNA interfaces to probe the binding hot spots at protein-RNA recognition sites. We find that the degree of conservation varies across the RNA binding proteins; some evolve rapidly compared to others. Additionally, irrespective of the structural class of the complexes, residues at the RNA binding sites are evolutionary better conserved than those at the solvent exposed surfaces. For recognitions involving duplex RNA, residues interacting with the major groove are better conserved than those interacting with the minor groove. We identify multi-interface residues participating simultaneously in protein-protein and protein-RNA interfaces in complexes where more than one polypeptide is involved in RNA recognition, and show that they are better conserved compared to any other RNA binding residues. We find that the residues at water preservation site are better conserved than those at hydrated or at dehydrated sites. Finally, we develop a Random Forests model using structural and physicochemical attributes for predicting binding hot spots. The model accurately predicts 80% of the instances of experimental ΔΔG values in a particular class, and provides a stepping-stone towards the engineering of protein-RNA recognition sites with desired affinity. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

On the binding affinity of macromolecular interactions: daring to ask why proteins interact

PubMed Central

Kastritis, Panagiotis L.; Bonvin, Alexandre M. J. J.

2013-01-01

Interactions between proteins are orchestrated in a precise and time-dependent manner, underlying cellular function. The binding affinity, defined as the strength of these interactions, is translated into physico-chemical terms in the dissociation constant (Kd), the latter being an experimental measure that determines whether an interaction will be formed in solution or not. Predicting binding affinity from structural models has been a matter of active research for more than 40 years because of its fundamental role in drug development. However, all available approaches are incapable of predicting the binding affinity of protein–protein complexes from coordinates alone. Here, we examine both theoretical and experimental limitations that complicate the derivation of structure–affinity relationships. Most work so far has concentrated on binary interactions. Systems of increased complexity are far from being understood. The main physico-chemical measure that relates to binding affinity is the buried surface area, but it does not hold for flexible complexes. For the latter, there must be a significant entropic contribution that will have to be approximated in the future. We foresee that any theoretical modelling of these interactions will have to follow an integrative approach considering the biology, chemistry and physics that underlie protein–protein recognition. PMID:23235262

Seeking potential anticonvulsant agents that target GABAA receptors using experimental and theoretical procedures

NASA Astrophysics Data System (ADS)

Saavedra-Vélez, Margarita Virginia; Correa-Basurto, José; Matus, Myrna H.; Gasca-Pérez, Eloy; Bello, Martiniano; Cuevas-Hernández, Roberto; García-Rodríguez, Rosa Virginia; Trujillo-Ferrara, José; Ramos-Morales, Fernando Rafael

2014-12-01

The aim of this study was to identify compounds that possess anticonvulsant activity by using a pentylenetetrazol (PTZ)-induced seizure model. Theoretical studies of a set of ligands, explored the binding affinities of the ligands for the GABAA receptor (GABAAR), including some benzodiazepines. The ligands satisfy the Lipinski rules and contain a pharmacophore core that has been previously reported to be a GABAAR activator. To select the ligands with the best physicochemical properties, all of the compounds were analyzed by quantum mechanics and the energies of the highest occupied molecular orbital and lowest unoccupied molecular orbital were determined. Docking calculations between the ligands and the GABAAR were used to identify the complexes with the highest Gibbs binding energies. The identified compound D1 (dibenzo( b,f)(1,4)diazocine-6,11(5H,12H)-dione) was synthesized, experimentally tested, and the GABAAR-D1 complex was submitted to 12-ns-long molecular dynamics (MD) simulations to corroborate the binding conformation obtained by docking techniques. MD simulations were also used to analyze the decomposition of the Gibbs binding energy of the residues involved in the stabilization of the complex. To validate our theoretical results, molecular docking and MD simulations were also performed for three reference compounds that are currently in commercial use: clonazepam (CLZ), zolpidem and eszopiclone. The theoretical results show that the GABAAR-D1, and GABAAR-CLZ complexes bind to the benzodiazepine binding site, share a similar map of binding residues, and have similar Gibbs binding energies and entropic components. Experimental studies using a PTZ-induced seizure model showed that D1 possesses similar activity to CLZ, which corroborates the predicted binding free energy identified by theoretical calculations.

Contribution of engineered nanomaterials physicochemical properties to mast cell degranulation

NASA Astrophysics Data System (ADS)

Johnson, Monica M.; Mendoza, Ryan; Raghavendra, Achyut J.; Podila, Ramakrishna; Brown, Jared M.

2017-03-01

The rapid development of engineered nanomaterials (ENMs) has grown dramatically in the last decade, with increased use in consumer products, industrial materials, and nanomedicines. However, due to increased manufacturing, there is concern that human and environmental exposures may lead to adverse immune outcomes. Mast cells, central to the innate immune response, are one of the earliest sensors of environmental insult and have been shown to play a role in ENM-mediated immune responses. Our laboratory previously determined that mast cells are activated via a non-FcɛRI mediated response following silver nanoparticle (Ag NP) exposure, which was dependent upon key physicochemical properties. Using bone marrow-derived mast cells (BMMCs), we tested the hypothesis that ENM physicochemical properties influence mast cell degranulation. Exposure to 13 physicochemically distinct ENMs caused a range of mast degranulation responses, with smaller sized Ag NPs (5 nm and 20 nm) causing the most dramatic response. Mast cell responses were dependent on ENMs physicochemical properties such as size, apparent surface area, and zeta potential. Surprisingly, minimal ENM cellular association by mast cells was not correlated with mast cell degranulation. This study suggests that a subset of ENMs may elicit an allergic response and contribute to the exacerbation of allergic diseases.

Physicochemical Profiles of the Marketed Agrochemicals and Clues for Agrochemical Lead Discovery and Screening Library Development.

PubMed

Rao, Hanbing; Huangfu, Changxin; Wang, Yanying; Wang, Xianxiang; Tang, Tiansheng; Zeng, Xianyin; Li, Zerong; Chen, Yuzong

2015-05-01

Combinatorial chemistry, high-throughput and virtual screening technologies have been extensively used for discovering agrochemical leads from chemical libraries. The knowledge of the physicochemical properties of the marketed agrochemicals is useful for guiding the design and selection of such libraries. Since the earlier profiling of marketed agrochemicals, the number and types of marketed agrochemicals have significantly increased. Recent studies have shown the change of some physicochemical properties of oral drugs with time. There is a need to also profile the physicochemical properties of the marketed agrochemicals. In this work, we analyzed the key physicochemical properties of 1751 marketed agrochemicals in comparison with the previously-analyzed herbicides and insecticides, 106 391 natural products and 57 548 diverse synthetic libraries compounds. Our study revealed the distribution profiles and evolution trend of different types of agrochemicals that in many respects are broadly similar to the reported profiles for oral drugs, with the most marked difference being that agrochemicals have a lower number of hydrogen bond donors. The derived distribution patterns provided the rule of thumb guidelines for selecting potential agrochemical leads and also provided clues for further improving the libraries for agrochemical lead discovery. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Clay facial masks: physicochemical stability at different storage temperatures.

PubMed

Zague, Vivian; de Almeida Silva, Diego; Baby, André Rolim; Kaneko, Telma Mary; Velasco, Maria Valéria Robles

2007-01-01

Clay facial masks--formulations that contain a high percentage of solids dispersed in a liquid vehicle--have become of special interest due to specific properties presented by clays, such as particle size, cooling index, high adsorption capacity, and plasticity. Although most of the physicochemical properties of clay dispersions have been studied, specific aspects concerning the physicochemical stability of clay mask products remain unclear. This work aimed at investigating the accelerated physicochemical stability of clay mask formulations stored at different temperatures. Formulations were subjected to centrifuge testing and to thermal treatment for 15 days, during which temperature was varied from -5.0 degrees to 45.0 degrees C. The apparent viscosity and visual aspect (homogeneity) of all formulations were affected by temperature variation, whereas color, odor, and pH value remained unaltered. These results, besides the estimation of physicochemical stability under aging, can be useful in determining the best storage conditions for clay-based formulations.

The influence of convection drying on the physicochemical properties of yacón (Smallanthus sonchifolius)

NASA Astrophysics Data System (ADS)

Salinas, Juan Gabriel; Alvarado, Juan Antonio; Bergenståhl, Björn; Tornberg, Eva

2018-04-01

Yacón root is a natural source of fructans, which has many potential benefits. Convective drying has been applied to increase the shelf life of yacón roots. However, this processing may lead to detrimental effects on the physicochemical functionality. The drying was investigated using different conditions (drying temperatures of 45 °C, 50 °C and 55 °C at a drying air velocity of 2 m/s and 60 °C at a drying air velocity of 2 m/s, 3 m/s and 4 m/s). The dried samples were compared to the original yacón with regard to their physicochemical properties. From all the properties that were studied, the color of the dried material and the elastic modulus of the reconstituted yacón were the most important properties being minimized respectively. The results of this investigation indicate that the best drying conditions, where the physicochemical properties of the samples are kept closest to the original material, are obtained either by using temperatures of 55 °C and 2 m/s or using higher temperatures but increasing the air velocity.

Effect of Hydrothermal Treatment on the Physicochemical, Rheological, and Oil-Resistant Properties of Rice Flour

USDA-ARS?s Scientific Manuscript database

Rice flour was thermo-mechanically modified by steam jet-cooking and the physico-chemical and rheological properties of the resulting product were characterized. Then, its performance in frying batters was evaluated as an oil barrier. Compared to native rice flour, the steam jet-cooked rice flour ...

Effect of acidity on the physicochemical properties of α- and β-chitin nanofibers.

PubMed

Suenaga, Shin; Totani, Kazuhide; Nomura, Yoshihiro; Yamashita, Kazuhiko; Shimada, Iori; Fukunaga, Hiroshi; Takahashi, Nobuhide; Osada, Mitsumasa

2017-09-01

We have investigated whether acidity can be used to control the physicochemical properties of chitin nanofibers (ChNFs). In this study, we define acidity as the molar ratio of dissociated protons from the acid to the amino groups in the raw chitin powder. The effect of acidity on the physicochemical properties of α- and β-ChNFs was compared. The transmittance and viscosity of the β-ChNFs drastically and continuously increased with increasing acidity, while those of the α-ChNFs were not affected by acidity. These differences are because of the higher ability for cationization based on the more flexible crystal structure of β-chitin than α-chitin. In addition, the effect of the acid species on the transmittance of β-ChNFs was investigated. The transmittance of β-ChNFs can be expressed by the acidity regardless of the acid species, such as hydrochloric acid, phosphoric acid, and acetic acid. These results indicate that the acidity defined in this work is an effective parameter to define and control the physicochemical properties of ChNFs. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of spent mushroom compost application on the physicochemical properties of a degraded soil

NASA Astrophysics Data System (ADS)

Gümüş, İlknur; Şeker, Cevdet

2017-11-01

Under field and laboratory conditions, the application of organic amendments has generally shown an improvement in soil physicochemical properties. Here, spent mushroom compost (SMC) is proposed as a suitable organic amendment for soil structure restoration. Our study assessed the impact of SMC on the physicochemical properties of a weak-structured and physically degraded soil. The approach involved the establishment of a pot experiment with SMC applications into soil (control, 0.5, 1, 2, 4 and 8 %). Soils were incubated at field capacity (-33 kPa) for 21, 42, and 62 days under laboratory conditions. SMC applications into the soil significantly increased the aggregate stability (AS) and decreased the modulus of rupture. The application of SMC at rates of 1, 2, 4, and 8 % significantly increased the total nitrogen and soil organic carbon contents of the degraded soil at all incubation periods (p < 0.05). The results obtained in this study indicate that the application of SMC can improve soil physicochemical properties, which may benefit farmers, land managers, and mushroom growers.

Effect of Microwave Irradiation on the Physicochemical and Digestive Properties of Lotus Seed Starch.

PubMed

Zeng, Shaoxiao; Chen, Bingyan; Zeng, Hongliang; Guo, Zebin; Lu, Xu; Zhang, Yi; Zheng, Baodong

2016-03-30

The objective of this study is to investigate the effect of microwave irradiation on the physicochemical and digestive properties of lotus seed starch. The physicochemical properties of lotus seed starch were characterized by light microscopy, (1)H NMR, FT-IR spectroscopy, and HPSEC-MALLS-RI. The starch-water interaction and crystalline region increased due to the changed water distribution of starch granules and the increase of the double-helix structure. The swelling power, amylose leaching, molecular properties, and radius of gyration reduced with the increasing microwave power, which further affected the sensitivity of lotus seed starch to enzymatic degradation. Furthermore, the resistant starch and slowly digestible starch increased with the increasing microwave irradiation, which further resulted in their decreasing hydrolysis index and glycemic index. The digestive properties of lotus seed starch were mainly influenced by the reduced branching degree of amylopectin and the strong amylose-amylose interaction.

Structure Property Relationships of Carboxylic Acid Isosteres.

PubMed

Lassalas, Pierrik; Gay, Bryant; Lasfargeas, Caroline; James, Michael J; Tran, Van; Vijayendran, Krishna G; Brunden, Kurt R; Kozlowski, Marisa C; Thomas, Craig J; Smith, Amos B; Huryn, Donna M; Ballatore, Carlo

2016-04-14

The replacement of a carboxylic acid with a surrogate structure, or (bio)-isostere, is a classical strategy in medicinal chemistry. The general underlying principle is that by maintaining the features of the carboxylic acid critical for biological activity, but appropriately modifying the physicochemical properties, improved analogs may result. In this context, a systematic assessment of the physicochemical properties of carboxylic acid isosteres would be desirable to enable more informed decisions of potential replacements to be used for analog design. Herein we report the structure-property relationships (SPR) of 35 phenylpropionic acid derivatives, in which the carboxylic acid moiety is replaced with a series of known isosteres. The data set generated provides an assessment of the relative impact on the physicochemical properties that these replacements may have compared to the carboxylic acid analog. As such, this study presents a framework for how to rationally apply isosteric replacements of the carboxylic acid functional group.

Spectral Study of the Interaction of Myoglobin with Tannin

NASA Astrophysics Data System (ADS)

Grigoryan, K. R.; Sargsyan, L. S.

2016-07-01

The interaction of myoglobin with tannin (tannic acid) at 298.15 and 303.15 K was studied by fluorescence and absorption spectroscopy in the UV region. The physicochemical and thermodynamic binding parameters (the fluorescence quenching mechanism, the bonding constant, the number of binding sites, the type of interaction) and parameters of the formed complex were determined. It was found that binding of myoglobin with tannic acid does not lead to significant changes in the electronic state of the heme ring of myoglobin.

Phosphatidylserine lipids and membrane order precisely regulate the activity of Polybia-MP1 peptide.

PubMed

Alvares, Dayane S; Ruggiero Neto, João; Ambroggio, Ernesto E

2017-06-01

Polybia-MP1 (IDWKKLLDAAKQIL-NH 2 ) is a lytic peptide from the Brazilian wasp venom with known anti-cancer properties. Previous evidence indicates that phosphatidylserine (PS) lipids are relevant for the lytic activity of MP1. In agreement with this requirement, phosphatidylserine lipids are translocated to the outer leaflet of cells, and are available for MP1 binding, depending on the presence of liquid-ordered domains. Here, we investigated the effect of PS on MP1 activity when this lipid is reconstituted in membranes of giant or large liposomes with different lipid-phase states. By monitoring the membrane and soluble luminal content of giant unilamellar vesicles (GUVs), using fluorescence confocal microscopy, we were able to determine that MP1 has a pore-forming activity at the membrane level. Liquid-ordered domains, which were phase-separated within the membrane of GUVs, influenced the pore-forming activity of MP1. Experiments evaluating the membrane-binding and lytic activity of MP1 on large unilamellar vesicles (LUVs), with the same lipid composition as GUVs, demonstrated that there was synergy between liquid-ordered domains and PS, which enhanced both activities. Based on our findings, we propose that the physicochemical properties of cancer cell membranes, which possess a much higher concentration of PS than normal cells, renders them susceptible to MP1 binding and lytic pore formation. These results can be correlated with MP1's potent and selective anti-cancer activity and pave the way for future research to develop cancer therapies that harness and exploit the properties of MP1. Copyright © 2017 Elsevier B.V. All rights reserved.

Interaction of vasicine with calf thymus DNA: Molecular docking, spectroscopic and differential scanning calorimetric insights

NASA Astrophysics Data System (ADS)

R. S., Sai Murali; R. S., Sai Siddhardha; Rajesh Babu, D.; Venketesh, S.; Basavaraju, R.; Nageswara Rao, G.

2017-06-01

The present study brings out the interaction between vasicine, an alkaloid and Adhatoda vasica Nees with double stranded DNA. The physico-chemical interaction between small molecules and nucleic acids is a major area of focus in screening drugs against various cancers. Molecular probing in our study using Molecular Operating Environment (MOE) has revealed interaction of vasicine with DNA double helix. Here we report the interaction of vasicine with Calf thymus DNA. We present for the first time the results obtained from UV-visible, fluorescence spectroscopic and differential scanning calorimetric techniques that suggest a moderate to strong electrostatic, hydrophobic and van der Waals interactions mediating the DNA binding properties of vasicine, leading to disruption of DNA secondary structure.

In Vivo Fate of Carbon Nanotubes with Different Physicochemical Properties for Gene Delivery Applications.

PubMed

Cifuentes-Rius, Anna; Boase, Nathan R B; Font, Ines; Coronas, Nuria; Ramos-Perez, Victor; Thurecht, Kristofer J; Borrós, Salvador

2017-04-05

Gene therapy has arisen as a pioneering technique to treat diseases by direct employment of nucleic acids as medicine. The major historical problem is to develop efficient and safe systems for the delivery of therapeutic genes into the target cells. Carbon nanotubes (CNTs) have demonstrated considerable promise as delivery vectors due to their (i) high aspect ratio and (ii) capacity to translocate through plasma membranes, known as the nanoneedle effect. To leverage these advantages, close attention needs to be paid to the physicochemical characteristics of the CNTs used. CNTs with different diameters (thinner and thicker) were treated by chemical oxidation to produce shorter fragments. Rigid (thick) and flexible (thin) CNTs, and their shortened versions, were coated with polyallylamine (ppAA) by plasma-enhanced chemical vapor deposition. The ppAA coating leads to a positively charged CNT surface that is able to electrostatically bind the green fluorescent protein plasmid reporter. This study shows how rigidity and length can affect their (i) behavior in biological media, (ii) ability to transfect in vitro, and (iii) biodistribution in vivo. This study also generates a set of basic design rules for the development of more efficient CNT-based gene-delivery vectors.

Physicochemical properties and biological activities of DEAE-derivatized Sphingomonas gellan.

PubMed

Yoo, Sang-Ho; Lee, Kyung Hee; Lee, Ji-Soo; Cha, Jaeho; Park, Cheon Seok; Lee, Hyeon Gyu

2005-08-10

Physicochemical characteristics and biological activities of Sphingomonas gellan (S-gellan) were investigated. The S-gellan weight fractions of Glc and GlcUA were 0.45 and 0.25, respectively, and the molar ratio of Glc:Rha:GlcUA was approximately 4:2:3. The S-gellan was chemically derivatized with diethylaminoethyl chloride-HCl (DEAE-HCl), and the resulting modified S-gellan contained both positive and negative charges. The elemental and IR analyses were conducted to confirm the successful incorporation of DEAE groups into S-gellan. A large increase in nitrogen fraction was observed from the derivatized S-gellan by elemental analysis. The IR absorption bands induced by C-H, C-N, and C-O-C stretching were noticeable at 2950, 1310-1380, and 1000-1150 cm(-1), respectively, resulting from the DEAE substitution. The characteristic CH3 and CH2 peaks originated from the DEAE group were detected in the 1H NMR spectrum of the derivatized S-gellan as well. The solubility of native S-gellan was improved almost twice from 40% to 75% after DEAE derivatization, while water holding capacity (WHC) drastically decreased from 10026% to 245%. Oil binding capacity (OBC) of S-gellan also significantly dropped from 1528% to 331% after the derivatization. The bile acid binding capacity of S-gellan was indirectly determined by measuring the holding capability of cholic acid inside the dialysis membrane (MWCO 12,000-14,000 Da). Once S-gellan was DEAE derivatized, there was substantial increase in the cholic acid retardation index (CRI). Up to 9 h of dialysis, the derivatized S-gellan released 29.3% less of cholic acid compared to the control group that did not contain S-gellan. From these results of the improved water solubility and stronger bile acid binding capacity, it would be suggested that the DEAE-derivatized S-gellan has more advantages than gellan itself for functional food applications.

Synthesis, spectroscopic studies, DFT calculations, electrochemical evaluation, BSA binding and molecular docking of an aroylhydrazone -based cis-dioxido Mo(VI) complex

NASA Astrophysics Data System (ADS)

Mohamadi, Maryam; Faghih-Mirzaei, Ehsan; Ebrahimipour, S. Yousef; Sheikhshoaie, Iran; Haase, Wolfgang; Foro, Sabine

2017-07-01

A cis-dioxido Mo(VI) complex, [MoO2(L)(MeOH)], [L2-: (3-methoxy-2-oxidobenzylidene) benzohydrazonate], has been synthesized and characterized using physicochemical and spectroscopic techniques including elemental analysis, FT-IR, 1HNMR, UV-Vis spectroscopy, molar conductivity and single crystal X-ray diffraction. DFT calculations in the ground state of the complex were carried out using hybrid functional B3LYP with DGDZVP as basis set. Non-linear optical properties including electric dipole moment (μ), polarizability (α) and molecular first hyperpolarizability (β) of the compound were also computed. The values of linear polarizability and first hyperpolarizability obtained for the studied molecule indicated that the compound could be a good candidate of nonlinear optical materials. TD-DFT calculation and molecular electrostatic potential (MEP) were also performed. The thermodynamic properties (heat capacity, entropy, and enthalpy) of the complex at different temperatures have been calculated. The interaction of a synthesized complex, with bovine serum albumin was also thoroughly investigated using experimental and theoretical studies. UV-Vis absorption and fluorescence quenching techniques were used to determine the binding parameters as well as the mechanism of the interaction. The values of binding constants were in the range of 104-105 M-1 demonstrating a moderate interaction between the synthesized complex and BSA making the protein suitable for transportation and delivery of the compound. Thermodynamic parameters were also indicating a binding through van der Waals force or hydrogen bond of [MoO2(L)(MeOH)] to BSA. The results obtained from docking studies were consistent to those obtained from experimental studies.

insilico Characterization and Homology Modeling of Arabitol Dehydrogenase (ArDH) from Candida albican.

PubMed

Sarwar, Muhammad Waseem; Saleem, Irum Baddisha; Ali, Asif; Abbas, Farhat

2013-01-01

Arabitol dehydrogenase (ArDH) is involved in the production of different sugar alcohols like arabitol, sorbitol, mannitol, erythritol and xylitol by using five carbon sugars as substrate. Arabinose, d-ribose, d-ribulose, xylose and d-xylulose are known substrate of this enzyme. ArDH is mainly produced by osmophilic fungi for the conversion of ribulose to arabitol under stress conditions. Recently this enzyme has been used by various industries for the production of pharmaceutically important sugar alcohols form cheap source than glucose. But the information at structure level as well as its binding energy analysis with different substrates was missing. The present study was focused on sequence analysis, insilico characterization and substrate binding analysis of ArDH from a fungus specie candida albican. Sequence analysis and physicochemical properties showed that this protein is highly stable, negatively charged and having more hydrophilic regions, these properties made this enzyme to bind with number of five carbon sugars as substrate. The predicted 3D model will helpful for further structure based studies. Docking analysis provided free energies of binding of each substrate from a best pose as arabinose -9.8224calK/mol, dribose -11.3701Kcal/mol, d-ribulose -8.9230Kcal/mol, xylose -9.7007Kcal/mol and d-xylulose 9.7802Kcal/mol. Our study provided insight information of structure and interactions of ArDH with its substrate. These results obtained from this study clearly indicate that d-ribose is best substrate for ArDH for the production of sugar alcohols. This information will be helpful for better usage of this enzyme for hyper-production of sugar alcohols by different industries.

insilico Characterization and Homology Modeling of Arabitol Dehydrogenase (ArDH) from Candida albican

PubMed Central

Sarwar, Muhammad Waseem; Saleem, Irum Baddisha; Ali, Asif; Abbas, Farhat

2013-01-01

Background: Arabitol dehydrogenase (ArDH) is involved in the production of different sugar alcohols like arabitol, sorbitol, mannitol, erythritol and xylitol by using five carbon sugars as substrate. Arabinose, d-ribose, d-ribulose, xylose and d-xylulose are known substrate of this enzyme. ArDH is mainly produced by osmophilic fungi for the conversion of ribulose to arabitol under stress conditions. Recently this enzyme has been used by various industries for the production of pharmaceutically important sugar alcohols form cheap source than glucose. But the information at structure level as well as its binding energy analysis with different substrates was missing. Results: The present study was focused on sequence analysis, insilico characterization and substrate binding analysis of ArDH from a fungus specie candida albican. Sequence analysis and physicochemical properties showed that this protein is highly stable, negatively charged and having more hydrophilic regions, these properties made this enzyme to bind with number of five carbon sugars as substrate. The predicted 3D model will helpful for further structure based studies. Docking analysis provided free energies of binding of each substrate from a best pose as arabinose -9.8224calK/mol, dribose -11.3701Kcal/mol, d-ribulose -8.9230Kcal/mol, xylose -9.7007Kcal/mol and d-xylulose 9.7802Kcal/mol. Conclusion: Our study provided insight information of structure and interactions of ArDH with its substrate. These results obtained from this study clearly indicate that d-ribose is best substrate for ArDH for the production of sugar alcohols. This information will be helpful for better usage of this enzyme for hyper-production of sugar alcohols by different industries. PMID:24391356

Physicochemical properties of an insensitive munitions compound, N-methyl-4-nitroaniline (MNA).

PubMed

Boddu, Veera M; Abburi, Krishnaiah; Maloney, Stephen W; Damavarapu, Reddy

2008-06-30

Accurate information on physicochemical properties of an organic contaminant is essential for predicting its environmental impact and fate. These properties also provide invaluable information for the overall understanding of environmental distribution, biotransformation, and potential treatment processes. In this study the aqueous solubility (Sw), octanol-water partition coefficient (Kow), and Henry's law constant (K(H)) were determined for an insensitive munitions (IM) compound, N-methyl-4-nitroaniline (MNA), at 298.15, 308.15, and 318.15 K. Effect of ionic strength on solubility, using electrolytes such as NaCl and CaCl2, was also studied. The data on the physicochemical parameters were correlated using the standard Van't Hoff equation. All three properties exhibited a linear relationship with reciprocal temperature. The enthalpy and entropy of phase transfer were derived from the experimental data.

Exploring and validating physicochemical properties of mangiferin through GastroPlus® software

PubMed Central

Khurana, Rajneet Kaur; Kaur, Ranjot; Kaur, Manninder; Kaur, Rajpreet; Kaur, Jasleen; Kaur, Harpreet; Singh, Bhupinder

2017-01-01

Aim: Mangiferin (Mgf), a promising therapeutic polyphenol, exhibits poor oral bioavailability. Hence, apt delivery systems are required to facilitate its gastrointestinal absorption. The requisite details on its physicochemical properties have not yet been well documented in literature. Accordingly, in order to have explicit insight into its physicochemical characteristics, the present work was undertaken using GastroPlus™ software. Results: Aqueous solubility (0.38 mg/ml), log P (-0.65), Peff (0.16 × 10-4 cm/s) and ability to act as P-gp substrate were defined. Potency to act as a P-gp substrate was verified through Caco-2 cells, while Peff was estimated through single pass intestinal perfusion studies. Characterization of Mgf through transmission electron microscopy, differential scanning calorimetry, infrared spectroscopy and powder x-ray diffraction has also been reported. Conclusion: The values of physicochemical properties for Mgf reported in the current manuscript would certainly enable the researchers to develop newer delivery systems for Mgf. PMID:28344830

Effect of partial reduction of pork meat on the physicochemical and sensory quality of dry ripened sausages: development of a healthy venison salchichon.

PubMed

Utrilla, M C; García Ruiz, A; Soriano, A

2014-12-01

The minimum percentage of pork meat to be added to traditional venison salchichon has been determined in order to ensure a nutritionally healthier product without impairing physicochemical or sensory properties. Six types of salchichon were made using lean venison and a varying amount of pork meat (40%, 30%, 25%, 20%, 15% and 10%). All types displayed appropriate physicochemical properties (pH, aw, moisture loss) and color (L*, a*, b*) during ripening, as well as adequate levels of lipolysis (acidity index) and lipid oxidation (TBARS). Moreover, reduction of the amount of pork meat in salchichon prompted an increase in the relative percentage of polyunsaturated fatty acids. It was concluded that in making venison salchichon, the addition of a 25% pork meat is sufficient to ensure a satisfactory ripening process and physicochemical characteristics, optimal organoleptic properties and a higher percentage of polyunsaturated fatty acids than that found in traditional venison salchichon. Copyright © 2014 Elsevier Ltd. All rights reserved.

Assessment of physicochemical and antioxidant characteristics of Quercus pyrenaica honeydew honeys.

PubMed

Shantal Rodríguez Flores, M; Escuredo, Olga; Carmen Seijo, M

2015-01-01

Consumers are exhibiting increasing interest in honeydew honey, principally due to its functional properties. Some plants can be sources of honeydew honey, but in north-western Spain, this honey type only comes from Quercus pyrenaica. In the present study, the melissopalynological and physicochemical characteristics and the antioxidant properties of 32 honeydew honey samples are described. Q. pyrenaica honeydew honey was defined by its colour, high pH, phenols and flavonoids. Multivariate statistical techniques were used to analyse the influence of the production year on the honey's physicochemical parameters and polyphenol content. Differences among the honey samples were found, showing that weather affected the physicochemical composition of the honey samples. Optimal conditions for oak growth favoured the production of honeydew honey. Copyright © 2014 Elsevier Ltd. All rights reserved.

Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ

PubMed Central

Hritz, Jozef; Läppchen, Tilman

2010-01-01

The FtsZ protein is a self-polymerizing GTPase that plays a central role in bacterial cell division. Several C8-substituted GTP analogs are known to inhibit the polymerization of FtsZ by competing for the same binding site as its endogenous activating ligand GTP. Free energy calculations of the relative binding affinities to FtsZ for a set of five C8-substituted GTP analogs were performed. The calculated values agree well with the available experimental data, and the main contribution to the free energy differences is determined to be the conformational restriction of the ligands. The dihedral angle distributions around the glycosidic bond of these compounds in water are known to vary considerably depending on the physicochemical properties of the substituent at C8. However, within the FtsZ protein, this substitution has a negligible influence on the dihedral angle distributions, which fall within the narrow range of −140° to −90° for all investigated compounds. The corresponding ensemble average of the coupling constants 3J(C4,H1′) is calculated to be 2.95 ± 0.1 Hz. The contribution of the conformational selection of the GTP analogs upon binding was quantified from the corresponding populations. The obtained restraining free energy values follow the same trend as the relative binding affinities to FtsZ, indicating their dominant contribution. PMID:20559630

DNA-magnetic Particle Binding Analysis by Dynamic and Electrophoretic Light Scattering.

PubMed

Haddad, Yazan; Dostalova, Simona; Kudr, Jiri; Zitka, Ondrej; Heger, Zbynek; Adam, Vojtech

2017-11-09

Isolation of DNA using magnetic particles is a field of high importance in biotechnology and molecular biology research. This protocol describes the evaluation of DNA-magnetic particles binding via dynamic light scattering (DLS) and electrophoretic light scattering (ELS). Analysis by DLS provides valuable information on the physicochemical properties of particles including particle size, polydispersity, and zeta potential. The latter describes the surface charge of the particle which plays major role in electrostatic binding of materials such as DNA. Here, a comparative analysis exploits three chemical modifications of nanoparticles and microparticles and their effects on DNA binding and elution. Chemical modifications by branched polyethylenimine, tetraethyl orthosilicate and (3-aminopropyl)triethoxysilane are investigated. Since DNA exhibits a negative charge, it is expected that zeta potential of particle surface will decrease upon binding of DNA. Forming of clusters should also affect particle size. In order to investigate the efficiency of these particles in isolation and elution of DNA, the particles are mixed with DNA in low pH (~6), high ionic strength and dehydration environment. Particles are washed on magnet and then DNA is eluted by Tris-HCl buffer (pH = 8). DNA copy number is estimated using quantitative polymerase chain reaction (PCR). Zeta potential, particle size, polydispersity and quantitative PCR data are evaluated and compared. DLS is an insightful and supporting method of analysis that adds a new perspective to the process of screening of particles for DNA isolation.

IDENTIFICATION OF PHARMACEUTICAL EXCIPIENT BEHAVIOR OF CHICKPEA (CICER ARIETINUM) STARCH IN GLICLAZIDE IMMEDIATE RELEASE TABLETS.

PubMed

Meka, Venkata Srikanth; Yee, Phung; Sheshala, Ravi

2016-01-01

In the past few years, there are number of researchers carrying out their research on the excipients derived from polysaccharides and some of these researches show that natural excipients are comparable and can serve as an alternative to the synthetic excipients. Hence, the objectives of this research are to characterize the naturally sourced chickpea starch powder and to study the pharmaceutical excipient behavior of chickpea starch in gliclazide immediate release (IR) tablets. In this research, the binding properties of chickpea starch were compared to that of povidone, whereas the disintegrant properties of chickpea starch were compared to those of crospovidone, croscarmellose sodium and sodium starch glycolate. Flow property of chickpea starch was assessed with the measurement of bulk density, tapped density, compressibility index and angle of repose. Calibration curve for gliclazide in phosphate buffer pH 7.4 was developed. Gliclazide IR tablets were then produced with direct compression method. Physicochemical characteristics of the tablets, including thickness, tablet weight uniformity, hardness, disintegration time and friability were evaluated. Then, in vitro dissolution studies were performed by following United States Pharmacopeia (USP) dissolution method. The dissolution results were analyzed and compared with t30, t50, dissolution efficiency (DE). Lastly, drug-excipient compatibility studies, including Fourier transform infrared (FTIR) spectroscopic analysis and differential scanning calorimetric (DSC) analysis were carried out. Fair flow property was observed in the chickpea starch powder. Furthermore, the tablets produced passed all the tests in physicochemical characteristics evaluation except hardness and disintegration test. Additionally, in vitro dissolution studies show that chickpea starch acted as a disintegrant instead of a binder in gliclazide IR tablets and its disintegrant properties were comparable to those of crospovidone, croscarmellose sodium and sodium starch glycolate. Besides that, gliclazide was also compatible with the excipients used. Chickpea starch acted as a disintegrant in gliclazide IR tablets, instead of a binder. Therefore, chickpea starch can be a promising disintegrant in gliclazide IR tablets.

Relationship between complement activation, cellular uptake and surface physicochemical aspects of novel PEG-modified nanocapsules.

PubMed

Mosqueira, V C; Legrand, P; Gulik, A; Bourdon, O; Gref, R; Labarre, D; Barratt, G

2001-11-01

The aim of our work was to examine the relationship between modifications of the surface of nanocapsules (NC) by adsorption or covalent grafting of poly(ethylene oxide) (PEG), and changes in their phospholipid (PL) content on complement activation (C3 cleavage) and on uptake by macrophages. The physicochemical characterization of the NC included an investigation of their properties, such as surface charge, size, hydrophilicity, morphology and homogeneity. This is the first time that such properties have been correlated with biological interactions for NC, a novel carrier system with a structure more complex than nanospheres. C3 crossed immunoelectrophoresis revealed the reduced activation for NC with longer PEG chain and higher density, although all formulations induced C3 cleavage to a lesser or greater extent. NC bearing PEG covalently bound to the surface were weaker activators of complement than plain PLA [poly(D,L-lactide)] NC or nanospheres (NS). Furthermore, the fluorescent/confocal microscopy of J774A1 cells in contact with NC reveal a dramatically reduced interaction with PEG-bearing NC. However, the way in which PEG was attached (covalent or adsorbed) seemed to affect the mechanism of uptake. Taken together, these results suggest that the low level of protein binding to NC covered with a high density of 20kDa PEG chains is likely to be due to the steric barriers surrounding these particles, which prevents protein adsorption and reduces their interaction with macrophages.

Interactions between suspension characteristics and physicochemical properties of silver and copper oxide nanoparticles: a case study for optimizing nanoparticle stock suspensions using a central composite design.

PubMed

Son, Jino; Vavra, Janna; Li, Yusong; Seymour, Megan; Forbes, Valery

2015-04-01

The preparation of a stable nanoparticle stock suspension is the first step in nanotoxicological studies, but how different preparation methods influence the physicochemical properties of nanoparticles in a solution, even in Milli-Q water, is often under-appreciated. In this study, a systematic approach using a central composite design (CCD) was employed to investigate the effects of sonication time and suspension concentration on the physicochemical properties (i.e. hydrodynamic diameter, zeta potential and ion dissolution) of silver (Ag) and copper oxide (CuO) nanoparticles (NPs) and to identify optimal conditions for suspension preparation in Milli-Q water; defined as giving the smallest particle sizes, highest suspension stability and lowest ion dissolution. Indeed, all the physicochemical properties of AgNPs and CuONPs varied dramatically depending on how the stock suspensions were prepared and differed profoundly between nanoparticle types, indicating the importance of suspension preparation. Moreover, the physicochemical properties of AgNPs and CuONPs, at least in simple media (Milli-Q water), behaved in predictable ways as a function of sonication time and suspension concentration, confirming the validity of our models. Overall, the approach allows systematic assessment of the influence of various factors on key properties of nanoparticle suspensions, which will facilitate optimization of the preparation of nanoparticle stock suspensions and improve the reproducibility of nanotoxicological results. We recommend that further attention be given to details of stock suspension preparation before conducting nanotoxicological studies as these can have an important influence on the behavior and subsequent toxicity of nanoparticles. Copyright © 2014 Elsevier Ltd. All rights reserved.

Quantifying protein-protein interactions in high throughput using protein domain microarrays.

PubMed

Kaushansky, Alexis; Allen, John E; Gordus, Andrew; Stiffler, Michael A; Karp, Ethan S; Chang, Bryan H; MacBeath, Gavin

2010-04-01

Protein microarrays provide an efficient way to identify and quantify protein-protein interactions in high throughput. One drawback of this technique is that proteins show a broad range of physicochemical properties and are often difficult to produce recombinantly. To circumvent these problems, we have focused on families of protein interaction domains. Here we provide protocols for constructing microarrays of protein interaction domains in individual wells of 96-well microtiter plates, and for quantifying domain-peptide interactions in high throughput using fluorescently labeled synthetic peptides. As specific examples, we will describe the construction of microarrays of virtually every human Src homology 2 (SH2) and phosphotyrosine binding (PTB) domain, as well as microarrays of mouse PDZ domains, all produced recombinantly in Escherichia coli. For domains that mediate high-affinity interactions, such as SH2 and PTB domains, equilibrium dissociation constants (K(D)s) for their peptide ligands can be measured directly on arrays by obtaining saturation binding curves. For weaker binding domains, such as PDZ domains, arrays are best used to identify candidate interactions, which are then retested and quantified by fluorescence polarization. Overall, protein domain microarrays provide the ability to rapidly identify and quantify protein-ligand interactions with minimal sample consumption. Because entire domain families can be interrogated simultaneously, they provide a powerful way to assess binding selectivity on a proteome-wide scale and provide an unbiased perspective on the connectivity of protein-protein interaction networks.

Detecting site-specific physicochemical selective pressures: applications to the Class I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system.

PubMed

Sainudiin, Raazesh; Wong, Wendy Shuk Wan; Yogeeswaran, Krithika; Nasrallah, June B; Yang, Ziheng; Nielsen, Rasmus

2005-03-01

Models of codon substitution are developed that incorporate physicochemical properties of amino acids. When amino acid sites are inferred to be under positive selection, these models suggest the nature and extent of the physicochemical properties under selection. This is accomplished by first partitioning the codons on the basis of some property of the encoded amino acids. This partition is used to parametrize the rates of property-conserving and property-altering base substitutions at the codon level by means of finite mixtures of Markov models that also account for codon and transition:transversion biases. Here, we apply this method to two positively selected receptors involved in ligand-recognition: the class I alleles of the human major histocompatibility complex (MHC) of known structure and the S-locus receptor kinase (SRK) of the sporophytic self-incompatibility system (SSI) in cruciferous plants (Brassicaceae), whose structure is unknown. Through likelihood ratio tests we demonstrate that at some sites, the positively selected MHC and SRK proteins are under physicochemical selective pressures to alter polarity, volume, polarity and/or volume, and charge to various extents. An empirical Bayes approach is used to identify sites that may be important for ligand recognition in these proteins.

Computational and Statistical Analyses of Amino Acid Usage and Physico-Chemical Properties of the Twelve Late Embryogenesis Abundant Protein Classes

PubMed Central

Jaspard, Emmanuel; Macherel, David; Hunault, Gilles

2012-01-01

Late Embryogenesis Abundant Proteins (LEAPs) are ubiquitous proteins expected to play major roles in desiccation tolerance. Little is known about their structure - function relationships because of the scarcity of 3-D structures for LEAPs. The previous building of LEAPdb, a database dedicated to LEAPs from plants and other organisms, led to the classification of 710 LEAPs into 12 non-overlapping classes with distinct properties. Using this resource, numerous physico-chemical properties of LEAPs and amino acid usage by LEAPs have been computed and statistically analyzed, revealing distinctive features for each class. This unprecedented analysis allowed a rigorous characterization of the 12 LEAP classes, which differed also in multiple structural and physico-chemical features. Although most LEAPs can be predicted as intrinsically disordered proteins, the analysis indicates that LEAP class 7 (PF03168) and probably LEAP class 11 (PF04927) are natively folded proteins. This study thus provides a detailed description of the structural properties of this protein family opening the path toward further LEAP structure - function analysis. Finally, since each LEAP class can be clearly characterized by a unique set of physico-chemical properties, this will allow development of software to predict proteins as LEAPs. PMID:22615859

Physico-chemical properties and extrusion behaviour of selected common bean varieties.

PubMed

Natabirwa, Hedwig; Muyonga, John H; Nakimbugwe, Dorothy; Lungaho, Mercy

2018-03-01

Extrusion processing offers the possibility of processing common beans industrially into highly nutritious and functional products. However, there is limited information on properties of extrudates from different bean varieties and their association with raw material characteristics and extrusion conditions. In this study, physico-chemical properties of raw and extruded Bishaz, K131, NABE19, Roba1 and RWR2245 common beans were determined. The relationships between bean characteristics and extrusion conditions on the extrudate properties were analysed. Extrudate physico-chemical and pasting properties varied significantly (P < 0.05) among bean varieties. Expansion ratio and water solubility decreased, while bulk density, water absorption, peak and breakdown viscosities increased as feed moisture increased. Protein exhibited significant positive correlation (P < 0.05) with water solubility index, and negative correlations (P < 0.05) with water absorption, bulk density and pasting viscosities. Iron and dietary fibre showed positive correlation while total ash exhibited negative correlation with peak viscosity, final viscosity and setback. Similar trends were observed in principal component analysis. Extrudate physico-chemical properties were found to be associated with beans protein, starch, iron, zinc and fibre contents. Therefore, bean chemical composition may serve as an indicator for beans extrusion behaviour and could be useful in selection of beans for extrusion. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Correlation between physicochemical properties of modified clinoptilolite and its performance in the removal of ammonia-nitrogen.

PubMed

Dong, Yingbo; Lin, Hai; He, Yinhai

2017-03-01

The physicochemical properties of the 24 modified clinoptilolite samples and their ammonia-nitrogen removal rates were measured to investigate the correlation between them. The modified clinoptilolites obtained by acid modification, alkali modification, salt modification, and thermal modification were used to adsorb ammonia-nitrogen. The surface area, average pore width, macropore volume, mecropore volume, micropore volume, cation exchange capacity (CEC), zeta potential, silicon-aluminum ratios, and ammonia-nitrogen removal rate of the 24 modified clinoptilolite samples were measured. Subsequently, the linear regression analysis method was used to research the correlation between the physicochemical property of the different modified clinoptilolite samples and the ammonia-nitrogen removal rate. Results showed that the CEC was the major physicochemical property affecting the ammonia-nitrogen removal performance. According to the impacts from strong to weak, the order was CEC > silicon-aluminum ratios > mesopore volume > micropore volume > surface area. On the contrary, the macropore volume, average pore width, and zeta potential had a negligible effect on the ammonia-nitrogen removal rate. The relational model of physicochemical property and ammonia-nitrogen removal rate of the modified clinoptilolite was established, which was ammonia-nitrogen removal rate = 1.415[CEC] + 173.533 [macropore volume] + 0.683 [surface area] + 4.789[Si/Al] - 201.248. The correlation coefficient of this model was 0.982, which passed the validation of regression equation and regression coefficients. The results of the significance test showed a good fit to the correlation model.

Influence of homogenization treatment on physicochemical properties and enzymatic hydrolysis rate of pure cellulose fibers.

PubMed

Jacquet, N; Vanderghem, C; Danthine, S; Blecker, C; Paquot, M

2013-02-01

The aim of this study is to compare the effect of different homogenization treatments on the physicochemical properties and the hydrolysis rate of a pure bleached cellulose. Results obtained show that homogenization treatments improve the enzymatic hydrolysis rate of the cellulose fibers by 25 to 100 %, depending of the homogenization treatment applied. Characterization of the samples showed also that homogenization had an impact on some physicochemical properties of the cellulose. For moderate treatment intensities (pressure below 500 b and degree of homogenization below 25), an increase of water retention values (WRV) that correlated to the increase of the hydrolysis rate was highlighted. Result also showed that the overall crystallinity of the cellulose properties appeared not to be impacted by the homogenization treatment. For higher treatment intensities, homogenized cellulose samples developed a stable tridimentional network that contributes to decrease cellulase mobility and slowdown the hydrolysis process.

Presence of Fluorescent Carbon Nanoparticles in Baked Lamb: Their Properties and Potential Application for Sensors.

PubMed

Wang, Haitao; Xie, Yisha; Liu, Shan; Cong, Shuang; Song, Yukun; Xu, Xianbing; Tan, Mingqian

2017-08-30

The presence of nanoparticles in food has drawn much attention in recent years. Fluorescent carbon nanoparticles are a new class of nanostructures; however, the distribution and physicochemical properties of such nanoparticles in food remain unclear. Herein, the presence of fluorescent carbon nanoparticles in baked lamb was confirmed, and their physicochemical properties were investigated. The fluorescent carbon nanoparticles from baked lamb emit strong blue fluorescence under ultraviolet light with a 10% fluorescent quantum yield. The nanoparticles are roughly spherical in appearance with a diameter of around 2.0 nm. Hydroxyl, amino, and carboxyl groups exist on the surface of nanoparticles. In addition, the nanoparticles could serve as a fluorescence sensor for glucose detection through an oxidation-reduction reaction. This work is the first report on fluorescent carbon nanoparticles present in baked lamb, which provides valuable insight into the physicochemical properties of such nanoparticles and their potential application in sensors.

Spatial and vertical distribution of soil physico-chemical properties and the content of heavy metals in the pedosphere in Poland

Treesearch

Marek Degorski

1998-01-01

The lithological and petrographical characteristics of soil pedogenesis was determined, and the spatial and vertical distribution of some soil physico-chemical properties (including heavy metal content) were studied along two transects in Poland. The genetic horizon for 22 soil profiles were described for particle size and petrographic composition, quartz grain...

Hydrophobicity and Charge Shape Cellular Metabolite Concentrations

PubMed Central

Bar-Even, Arren; Noor, Elad; Flamholz, Avi; Buescher, Joerg M.; Milo, Ron

2011-01-01

What governs the concentrations of metabolites within living cells? Beyond specific metabolic and enzymatic considerations, are there global trends that affect their values? We hypothesize that the physico-chemical properties of metabolites considerably affect their in-vivo concentrations. The recently achieved experimental capability to measure the concentrations of many metabolites simultaneously has made the testing of this hypothesis possible. Here, we analyze such recently available data sets of metabolite concentrations within E. coli, S. cerevisiae, B. subtilis and human. Overall, these data sets encompass more than twenty conditions, each containing dozens (28-108) of simultaneously measured metabolites. We test for correlations with various physico-chemical properties and find that the number of charged atoms, non-polar surface area, lipophilicity and solubility consistently correlate with concentration. In most data sets, a change in one of these properties elicits a ∼100 fold increase in metabolite concentrations. We find that the non-polar surface area and number of charged atoms account for almost half of the variation in concentrations in the most reliable and comprehensive data set. Analyzing specific groups of metabolites, such as amino-acids or phosphorylated nucleotides, reveals even a higher dependence of concentration on hydrophobicity. We suggest that these findings can be explained by evolutionary constraints imposed on metabolite concentrations and discuss possible selective pressures that can account for them. These include the reduction of solute leakage through the lipid membrane, avoidance of deleterious aggregates and reduction of non-specific hydrophobic binding. By highlighting the global constraints imposed on metabolic pathways, future research could shed light onto aspects of biochemical evolution and the chemical constraints that bound metabolic engineering efforts. PMID:21998563

MoRFPred-plus: Computational Identification of MoRFs in Protein Sequences using Physicochemical Properties and HMM profiles.

PubMed

Sharma, Ronesh; Bayarjargal, Maitsetseg; Tsunoda, Tatsuhiko; Patil, Ashwini; Sharma, Alok

2018-01-21

Intrinsically Disordered Proteins (IDPs) lack stable tertiary structure and they actively participate in performing various biological functions. These IDPs expose short binding regions called Molecular Recognition Features (MoRFs) that permit interaction with structured protein regions. Upon interaction they undergo a disorder-to-order transition as a result of which their functionality arises. Predicting these MoRFs in disordered protein sequences is a challenging task. In this study, we present MoRFpred-plus, an improved predictor over our previous proposed predictor to identify MoRFs in disordered protein sequences. Two separate independent propensity scores are computed via incorporating physicochemical properties and HMM profiles, these scores are combined to predict final MoRF propensity score for a given residue. The first score reflects the characteristics of a query residue to be part of MoRF region based on the composition and similarity of assumed MoRF and flank regions. The second score reflects the characteristics of a query residue to be part of MoRF region based on the properties of flanks associated around the given residue in the query protein sequence. The propensity scores are processed and common averaging is applied to generate the final prediction score of MoRFpred-plus. Performance of the proposed predictor is compared with available MoRF predictors, MoRFchibi, MoRFpred, and ANCHOR. Using previously collected training and test sets used to evaluate the mentioned predictors, the proposed predictor outperforms these predictors and generates lower false positive rate. In addition, MoRFpred-plus is a downloadable predictor, which makes it useful as it can be used as input to other computational tools. https://github.com/roneshsharma/MoRFpred-plus/wiki/MoRFpred-plus:-Download. Copyright © 2017 Elsevier Ltd. All rights reserved.

An FPGA Implementation to Detect Selective Cationic Antibacterial Peptides

PubMed Central

Polanco González, Carlos; Nuño Maganda, Marco Aurelio; Arias-Estrada, Miguel; del Rio, Gabriel

2011-01-01

Exhaustive prediction of physicochemical properties of peptide sequences is used in different areas of biological research. One example is the identification of selective cationic antibacterial peptides (SCAPs), which may be used in the treatment of different diseases. Due to the discrete nature of peptide sequences, the physicochemical properties calculation is considered a high-performance computing problem. A competitive solution for this class of problems is to embed algorithms into dedicated hardware. In the present work we present the adaptation, design and implementation of an algorithm for SCAPs prediction into a Field Programmable Gate Array (FPGA) platform. Four physicochemical properties codes useful in the identification of peptide sequences with potential selective antibacterial activity were implemented into an FPGA board. The speed-up gained in a single-copy implementation was up to 108 times compared with a single Intel processor cycle for cycle. The inherent scalability of our design allows for replication of this code into multiple FPGA cards and consequently improvements in speed are possible. Our results show the first embedded SCAPs prediction solution described and constitutes the grounds to efficiently perform the exhaustive analysis of the sequence-physicochemical properties relationship of peptides. PMID:21738652

Characterization of rice physicochemical properties local rice germplasm from Tana Toraja regency of South Sulawesi

NASA Astrophysics Data System (ADS)

Masniawati, A.; Marwah Asrul, Nur Al; Johannes, E.; Asnady, M.

2018-03-01

The research about the characterization of physicochemical properties from local rice germplasm of Tana Toraja’s Regency, South Sulawesi aims to determine the physicochemical properties of rice as a parameter to indicate the quality of cooking. Local varieties categorized as germplasm that needs to be protected for future varietal improvement.In this research, the researchers used seven varieties of local rice. The parameters analyzed including physicochemical properties of amylose content, protein content, gel consistency, and gelatinization temperature. Percentage of amylose content ranged from 2 to 18 %. Pare Bumbungan and Pare Lalodo are categorized as waxy rice and Pare Ambo, Pare Bau, Pare Kobo, Pare Rogon and Pare Tallang are categorized as low amylose content. The percentage of protein content ranged from 7.3 to 9.5 %. Gelatinization temperature of rice showed high gelatinization temperature. Pare Bumbungan, Pare Kobo, Pare Lalodo, and Pare Rogon are categorized as soft gel consistency (˃50 mm). Pare Ambo, Pare Bau and Pare Tallang are categorized as medium gel consistency (36-50m). Pare Rogon and Pare Kobo are two kinds of rice varieties according to the quality of cooking criteria for consumers in Indonesia.

Physicochemical and Antioxidant Properties of Rice Bran Oils Produced from Colored Rice Using Different Extraction Methods.

PubMed

Mingyai, Sukanya; Kettawan, Aikkarach; Srikaeo, Khongsak; Singanusong, Riantong

2017-06-01

This study investigated the physicochemical and antioxidant properties of rice bran oil (RBO) produced from the bran of three rice varities; Khao Dawk Mali 105 (white rice), Red Jasmine rice (red rice) and Hom-nin rice (black rice) using three extraction methods including cold-press extraction (CPE), solvent extraction (SE) and supercritical CO 2 extraction (SC-CO 2 ). Yields, color, acid value (AV), free fatty acid (FFA), peroxide value (PV), iodine value (IV), total phenolic compound (TPC), γ-oryzanol, α-tocopherol and fatty acid profile were analyzed. It was found that the yields obtained from SE, SC-CO 2 and CPE extractions were 17.35-20.19%, 14.76-18.16% and 3.22-6.22%, respectively. The RBO from the bran of red and black rice samples exhibited high antioxidant activities. They also contained higher amount of γ-oryzanol and α-tocopherol than those of white rice sample. In terms of extraction methods, SC-CO 2 provided better qualities of RBO as evidenced by their physicochemical and antioxidant properties. This study found that RBO produced from the bran of black rice samples using SC-CO 2 extraction method showed the best physicochemical and antioxidant properties.

Humic Substances in Organic Wastes and their Effects on Amended Soils

NASA Astrophysics Data System (ADS)

Senesi, N.; Ciavatta, C.; Plaza, C.

2009-04-01

Soil humic substances (HS) are universally recognized to play a major role in a wide number of agronomic and environmental processes. For example, soil HS are able to bind mineral particles together, thus promoting a good soil structure, constitute an important source of nutrients for plants and microorganisms, contribute largely to the acid-base buffering capacity of soils, and exert a marked control on the biological availability, physico-chemical behavior, and environmental fate of toxic metal ions and xenobiotics. For these reasons, the knowledge of the short- and long-term effects of organic amendments on the status, quality, and reactivity of indigenous soil HS is of paramount importance. The objective of this presentation is to provide an overview of the chemical and physico-chemical data available in the literature for the evaluation of the effects of organic wastes of various origin and nature used as soil amendments on the composition, structure, and chemical reactivity of native soil HS. In general, HS-like components of organic wastes are typically characterized by a relatively larger presence of aliphatic, amide, and polysaccharide structures, simple structural components of wide molecular heterogeneity, smaller contents of oxygen, acidic functional groups, and organic free radicals, and smaller degrees of aromatic ring polycondensation, polymerization, and humification than native soil HS. Further, with respect to native soil HS, HS-like fractions from organic wastes generally exhibit smaller binding capacities and affinities for metal ions and organic xenobiotics. Appropriate treatment processes of raw organic wastes able to produce environmentally safe and agronomically efficient soil amendments, such as composting, yield HS-like fractions characterized by chemical and physico-chemical features that approach those of native soil HS. In general, aliphatic, polysaccharide, and lignin structures and S- and N-containing groups of the HS-like fractions of organic wastes can be partially incorporated into native soil HS determining modifications at various extents of their composition, structure, and chemistry. The changes occurred in amended soil HS are more evident when untreated organic materials are used. However, with increasing time after land application, the effects observed become less and less apparent with a clear trend to approach the molecular properties typical of native soil HS.

Fatty Acid Binding Proteins Expressed at the Human Blood-Brain Barrier Bind Drugs in an Isoform-Specific Manner.

PubMed

Lee, Gordon S; Kappler, Katharina; Porter, Christopher J H; Scanlon, Martin J; Nicolazzo, Joseph A

2015-10-01

To examine the expression of fatty acid binding proteins (FABPs) at the human blood-brain barrier (BBB) and to assess their ability to bind lipophilic drugs. mRNA and protein expression of FABP subtypes in immortalized human brain endothelial (hCMEC/D3) cells were examined by RT-qPCR and Western blot, respectively. FABPs that were found in hCMEC/D3 cells (hFABPs) were recombinantly expressed and purified from Escherichia coli C41(DE3) cells. Drug binding to these hFABPs was assessed using a fluorescence assay, which measured the ability of a panel of lipophilic drugs to displace the fluorescent probe compound 1-anilinonaphthalene-8-sulfonic acid (ANS). hFABP3, 4 and 5 were expressed in hCMEC/D3 cells at the mRNA and protein level. The competitive ANS displacement assay demonstrated that, in general, glitazones preferentially bound to hFABP5 (Ki: 1.0-28 μM) and fibrates and fenamates preferentially bound to hFABP4 (Ki: 0.100-17 μM). In general, lipophilic drugs appeared to show weaker affinities for hFABP3 relative to hFABP4 and hFABP5. No clear correlation was observed between the molecular structure or physicochemical properties of the drugs and their ability to displace ANS from hFABP3, 4 and 5. hFABP3, 4 and 5 are expressed at the human BBB and bind differentially to a diverse range of lipophilic drugs. The unique expression and binding patterns of hFABPs at the BBB may therefore influence drug disposition into the brain.

Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets

PubMed Central

2012-01-01

Background To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. Results We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. Conclusions SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery. PMID:23281852

Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.

PubMed

Chiu, Yi-Yuan; Lin, Chun-Yu; Lin, Chih-Ta; Hsu, Kai-Cheng; Chang, Li-Zen; Yang, Jinn-Moon

2012-01-01

To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.

Exploring selectivity requirements for COX-2 versus COX-1 binding of 2-(5-phenyl-pyrazol-1-yl)-5-methanesulfonylpyridines using topological and physico-chemical parameters.

PubMed

Chakraborty, Santanu; Sengupta, Chandana; Roy, Kunal

2005-04-01

Considering the current need for development of selective cyclooxygenase-2 (COX-2) inhibitors, an attempt has been made to explore physico-chemical requirements of 2-(5-phenyl-pyrazol-1-yl)-5-methanesulfonylpyridines for binding with COX-1 and COX-2 enzyme subtypes and also to explore the selectivity requirements. In this study, E-states of different common atoms of the molecules (calculated according to Kier & Hall), first order valence connectivity and physicochemical parameters (hydrophobicity pi, Hammett sigma and molar refractivity MR of different ring substituents) were used as independent variables along with suitable dummy parameters in the stepwise regression method. The best equation describing COX-1 binding affinity [n = 25, Q2 = 0.606, R(a)2 = 0.702, R2 = 0.752, R = 0.867, s = 0.447, F = 15.2 (df 4, 20)] suggests that the COX-1 binding affinity increases in the presence of a halogen substituent at R1 position and a p-alkoxy or p-methylthio substituent at R2 position. Furthermore, a difluoromethyl group is preferred over a trifluoromethyl group at R position for the COX-1 binding. The best equation describing COX-2 binding affinity [n = 32, Q2 = 0.622, R(a)2= 0.692, R2 = 0.732, R = 0.856, s = 0.265, F = 18.4 (df 4, 27)] shows that the COX-2 binding affinity increases with the presence of a halogen substituent at R1 position and increase of size of R2 substituents. However, it decreases in case of simultaneous presence of 3-chloro and 4-methoxy groups on the phenyl nucleus and in the presence of highly lipophilic R2 substituents. The best selectivity relation [n = 25, Q2 = 0.455, R(a)2 = 0.605, R2 = 0.670, R = 0.819, s = 0.423, F = 10.2 (df 4, 20)] suggests that the COX-2 selectivity decreases in the presence of p-alkoxy group and electron-withdrawing para substituents at R2 position. Again, a trifluoro group is conductive for the selectivity instead of a difluoromethyl group at R position. Furthermore, branching may also play significant role in determining the selectivity as evidenced from the connectivity parameter.

Production and physicochemical properties of carboxymethyl cellulose films enriched with spent coffee grounds polysaccharides.

PubMed

Ballesteros, Lina F; Cerqueira, Miguel A; Teixeira, José A; Mussatto, Solange I

2018-01-01

Extracts rich in polysaccharides were obtained by alkali pretreatment (PA) or autohydrolysis (PB) of spent coffee grounds, and incorporated into a carboxymethyl cellulose (CMC)-based film aiming at the development of bio-based films with new functionalities. Different concentrations of PA or PB (up to 0.20% w/v) were added to the CMC-based film and the physicochemical properties of the final films were determined. Scanning electron microscopy, Fourier-transform infrared spectroscopy, X-ray diffraction, thermogravimetric analysis, as well as determinations of optical and mechanical properties, moisture content, solubility in water, water vapor permeability, contact angle and sorption isotherms were performed. The addition of PA or PB resulted in important changes in the properties of the CMC-based film, mainly in color and opacity. The polysaccharides incorporation significantly improved the light barrier of the film and provided an enhancement or at least a preservation in the physicochemical properties. Copyright © 2017 Elsevier B.V. All rights reserved.

Interaction studies reveal specific recognition of an anti-inflammatory polyphosphorhydrazone dendrimer by human monocytes.

PubMed

Ledall, Jérémy; Fruchon, Séverine; Garzoni, Matteo; Pavan, Giovanni M; Caminade, Anne-Marie; Turrin, Cédric-Olivier; Blanzat, Muriel; Poupot, Rémy

2015-11-14

Dendrimers are nano-materials with perfectly defined structure and size, and multivalency properties that confer substantial advantages for biomedical applications. Previous work has shown that phosphorus-based polyphosphorhydrazone (PPH) dendrimers capped with azabisphosphonate (ABP) end groups have immuno-modulatory and anti-inflammatory properties leading to efficient therapeutic control of inflammatory diseases in animal models. These properties are mainly prompted through activation of monocytes. Here, we disclose new insights into the molecular mechanisms underlying the anti-inflammatory activation of human monocytes by ABP-capped PPH dendrimers. Following an interdisciplinary approach, we have characterized the physicochemical and biological behavior of the lead ABP dendrimer with model and cell membranes, and compared this experimental set of data to predictive computational modelling studies. The behavior of the ABP dendrimer was compared to the one of an isosteric analog dendrimer capped with twelve azabiscarboxylate (ABC) end groups instead of twelve ABP end groups. The ABC dendrimer displayed no biological activity on human monocytes, therefore it was considered as a negative control. In detail, we show that the ABP dendrimer can bind both non-specifically and specifically to the membrane of human monocytes. The specific binding leads to the internalization of the ABP dendrimer by human monocytes. On the contrary, the ABC dendrimer only interacts non-specifically with human monocytes and is not internalized. These data indicate that the bioactive ABP dendrimer is recognized by specific receptor(s) at the surface of human monocytes.

Effect of ultrafine grinding on physicochemical and antioxidant properties of dietary fiber from wine grape pomace.

PubMed

Zhu, Feng-Mei; Du, Bin; Li, Jun

2014-01-01

Wine grape pomace dietary fiber powders were prepared by superfine grinding, whose effects were investigated on the composition, functional and antioxidant properties of the wine grape pomace dietary fiber products. The results showed that superfine grinding could effectively pulverize the fiber particles to submicron scale. As particle size decrease, the functional properties (water-holding capacity, water-retention capacity, swelling capacity, oil-binding capacity, and nitrite ion absorption capacity) of wine grape pomace dietary fiber were significantly (p < 0.05) decreased and a redistribution of fiber components from insoluble to soluble fractions was observed. The antioxidant activities of wine grape pomace and dietary fiber before and after grinding were in terms of DPPH radical scavenging activity, ABTS diammonium salt radical scavenging activity, ferric reducing antioxidant power, and total phenolic content. Compared with dietary fiber before and after grinding, micronized insoluble dietary fiber showed increased ABTS radical scavenging activity, ferric reducing antioxidant power, and total phenolic content yet decreased DPPH radical scavenging activity. Positive correlations were detected between ABTS radical scavenging activity, ferric reducing antioxidant power, and total phenolic content.

Effects of countercations on the structures and redox and spectroscopic properties of diruthenium catecholate complexes with ligand-unsupported Ru-Ru bonds.

PubMed

Chang, Ho-Chol; Mochizuki, Katsunori; Kitagawa, Susumu

2005-05-30

The molecular structures and physicochemical properties of diruthenium complexes with ligand-unsupported Ru-Ru bonds, generally formulated as [A2{Ru2(DTBCat)4}] (DTB = 3,5- or 3,6-di-tert-butyl; Cat(2-) = catecholate), were studied in detail by changing the countercations. First, the binding structures of the cations in a family of [{A(DME)n}2{Ru2(3,5-DTBCat)4}] (n = 2 for A+ = Li+ and Na+ and n = 1 for A+ = K+ and Rb+) were systematically examined to reveal the effects of the cations on the molecular structures and electrochemical properties. Second, the complex (n-Bu4N)2[Ru2(3,6-DTBCat)4] with a cation-free structure was synthesized using tetra-n-butylammonium cations. The complex clearly demonstrates first that the ligand-unsupported Ru-Ru bonds are essentially stabilized by the dianionic nature of the catecholate derivatives without any other bridging or supporting species. In contrast, the redox potentials and absorption spectra of the complexes can sensitively respond to the countercations depending upon the polarity of the solvents.

Gadolinium-Based Contrast Agents for MR Cancer Imaging

PubMed Central

Zhou, Zhuxian; Lu, Zheng-Rong

2013-01-01

Magnetic resonance imaging (MRI) is a clinical imaging modality effective for anatomical and functional imaging of diseased soft tissues, including solid tumors. MRI contrast agents have been routinely used for detecting tumor at an early stage. Gadolinium based contrast agents are the most commonly used contrast agents in clinical MRI. There have been significant efforts to design and develop novel Gd(III) contrast agents with high relaxivity, low toxicity and specific tumor binding. The relaxivity of the Gd(III) contrast agents can be increased by proper chemical modification. The toxicity of Gd(III) contrast agents can be reduced by increasing the agents’ thermodynamic and kinetic stability, as well as optimizing their pharmacokinetic properties. The increasing knowledge in the field of cancer genomics and biology provides an opportunity for designing tumor-specific contrast agents. Various new Gd(III) chelates have been designed and evaluated in animal models for more effective cancer MRI. This review outlines the design and development, physicochemical properties, and in vivo properties of several classes of Gd(III)-based MR contrast agents for tumor imaging. PMID:23047730

Preparation and physicochemical properties of protein concentrate and isolate produced from Acacia tortilis (Forssk.) Hayne ssp. raddiana.

PubMed

Embaby, Hassan E; Swailam, Hesham M; Rayan, Ahmed M

2018-02-01

The composition and physicochemical properties of defatted acacia flour (DFAF), acacia protein concentrate (APC) and acacia protein isolate (API) were evaluated. The results indicated that API had lower, ash and fat content, than DFAF and APC. Also, significant difference in protein content was noticed among DFAF, APC and API (37.5, 63.7 and 91.8%, respectively). Acacia protein concentrate and isolates were good sources of essential amino acids except cystine and methionine. The physicochemical and functional properties of acacia protein improved with the processing of acacia into protein concentrate and protein isolate. The results of scanning electron micrographs showed that DFAF had a compact structure; protein concentrate were, flaky, and porous type, and protein isolate had intact flakes morphology.

Synthesis and physico-chemical characterization of a polysialate-hydroxyapatite composite for potential biomedical application

NASA Astrophysics Data System (ADS)

Zoulgami, M.; Lucas-Girot, A.; Michaud, V.; Briard, P.; Gaudé, J.; Oudadesse, H.

2002-09-01

New composite materials based on aluminosilicate materials were developed to be used in orthopaedic or maxillo-facial surgery. They are called geopolymers or polysialate-siloxo (PSS) and were studied alone or mixed with hydroxyapatite (HAP). The properties of these materials were investigated for potential use in biological or surgery applications. In this work, the chemistry involved in materials preparation was described. Samples were characterized by some physico-chemical methods like X-ray diffraction (XRD), infrared spectrometry (IR) and electron dispersion X-ray spectrometry (EDX). Results indicate that the mixing hydroxyapatite-geopolymer (PSS) leads to a neutral porous composite material with interesting physico-chemical properties. A preliminary evaluation of its cytotoxicity reveals an harmlessness towards fibroblasts. These properties allow to envisage this association as a potential biomaterial.

Physicochemical properties of precursors of Al2O3-ZrO2 oxide ceramics prepared by electrochemical method

NASA Astrophysics Data System (ADS)

Petrova, E. V.; Dresvyannikov, A. F.; Ahmadi Daryakenari, M.; Khairullina, A. I.

2016-05-01

Scanning electron microscopy, X-ray, and thermal analysis are used to examine the structure and properties of dispersive systems based on aluminum and zirconium oxides prepared electrochemically. The effect the conditions of synthesis have on the structure and morphology of Al2O3-ZrO2 particles is studied. It is shown that the effect of an electric field on the reaction medium allows us to adjust the physicochemical properties and morphology.

A motif detection and classification method for peptide sequences using genetic programming.

PubMed

Tomita, Yasuyuki; Kato, Ryuji; Okochi, Mina; Honda, Hiroyuki

2008-08-01

An exploration of common rules (property motifs) in amino acid sequences has been required for the design of novel sequences and elucidation of the interactions between molecules controlled by the structural or physical environment. In the present study, we developed a new method to search property motifs that are common in peptide sequence data. Our method comprises the following two characteristics: (i) the automatic determination of the position and length of common property motifs by calculating the physicochemical similarity of amino acids, and (ii) the quick and effective exploration of motif candidates that discriminates the positives and negatives by the introduction of genetic programming (GP). Our method was evaluated by two types of model data sets. First, the intentionally buried property motifs were searched in the artificially derived peptide data containing intentionally buried property motifs. As a result, the expected property motifs were correctly extracted by our algorithm. Second, the peptide data that interact with MHC class II molecules were analyzed as one of the models of biologically active peptides with buried motifs in various lengths. Twofold MHC class II binding peptides were identified with the rule using our method, compared to the existing scoring matrix method. In conclusion, our GP based motif searching approach enabled to obtain knowledge of functional aspects of the peptides without any prior knowledge.

Chances and limitations of nanosized titanium dioxide practical application in view of its physicochemical properties

NASA Astrophysics Data System (ADS)

Bogdan, Janusz; Jackowska-Tracz, Agnieszka; Zarzyńska, Joanna; Pławińska-Czarnak, Joanna

2015-02-01

Nanotechnology is a field of science that is nowadays developing in a dynamic way. It seems to offer almost endless opportunities of contribution to many areas of economy and human activity, in general. Thanks to nanotechnology, the so-called nanomaterials can be designed. They present structurally altered materials, with their physical, chemical and biological properties entirely differing from properties of the same materials manufactured in microtechnology. Nanotechnology creates a unique opportunity to modify the matter at the level of atoms and particles. Therefore, it has become possible to obtain items displaying new, useful properties, i.e. self-disinfecting and self-cleaning surfaces. Those surfaces are usually covered by a thin layer of a photocatalyst. The role of the photocatalyst is most of the time performed by the nanosized titanium dioxide (nano-TiO2). Excitation of nano-TiO2 by ultraviolet radiation initiates advanced oxidation processes and reactions leading to the creation of oxygen vacancies that bind water particles. As a result, photocatalytic surfaces are given new properties. Those properties can then be applied in a variety of disciplines, such as medicine, food hygiene, environmental protection or building industry. Practically, the applications include inactivation of microorganisms, degradation of toxins, removing pollutants from buildings and manufacturing of fog-free windows or mirrors.

The property distance index PD predicts peptides that cross-react with IgE antibodies

PubMed Central

Ivanciuc, Ovidiu; Midoro-Horiuti, Terumi; Schein, Catherine H.; Xie, Liping; Hillman, Gilbert R.; Goldblum, Randall M.; Braun, Werner

2009-01-01

Similarities in the sequence and structure of allergens can explain clinically observed cross-reactivities. Distinguishing sequences that bind IgE in patient sera can be used to identify potentially allergenic protein sequences and aid in the design of hypo-allergenic proteins. The property distance index PD, incorporated in our Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP/), may identify potentially cross-reactive segments of proteins, based on their similarity to known IgE epitopes. We sought to obtain experimental validation of the PD index as a quantitative predictor of IgE cross-reactivity, by designing peptide variants with predetermined PD scores relative to three linear IgE epitopes of Jun a 1, the dominant allergen from mountain cedar pollen. For each of the three epitopes, 60 peptides were designed with increasing PD values (decreasing physicochemical similarity) to the starting sequence. The peptides synthesized on a derivatized cellulose membrane were probed with sera from patients who were allergic to Jun a 1, and the experimental data were interpreted with a PD classification method. Peptides with low PD values relative to a given epitope were more likely to bind IgE from the sera than were those with PD values larger than 6. Control sequences, with PD values between 18 and 20 to all the three epitopes, did not bind patient IgE, thus validating our procedure for identifying negative control peptides. The PD index is a statistically validated method to detect discrete regions of proteins that have a high probability of cross-reacting with IgE from allergic patients. PMID:18950868

Ferrocene-pyrimidine conjugates: Synthesis, electrochemistry, physicochemical properties and antiplasmodial activities.

PubMed

Chopra, Rakesh; de Kock, Carmen; Smith, Peter; Chibale, Kelly; Singh, Kamaljit

2015-07-15

The promise of hybrid antimalarial agents and the precedence set by the antimalarial drug ferroquine prompted us to design ferrocene-pyrimidine conjugates. Herein, we report the synthesis, electrochemistry and anti-plasmodial evaluation of ferrocenyl-pyrimidine conjugates against chloroquine susceptible NF54 strain of the malaria parasite Plasmodium falciparum. Also their physicochemical properties have been studied. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Phosphorothioate backbone modifications of nucleotide-based drugs are potent platelet activators

PubMed Central

Flierl, Ulrike; Nero, Tracy L.; Lim, Bock; Arthur, Jane F.; Yao, Yu; Jung, Stephanie M.; Gitz, Eelo; Pollitt, Alice Y.; Zaldivia, Maria T.K.; Jandrot-Perrus, Martine; Schäfer, Andreas; Nieswandt, Bernhard; Andrews, Robert K.; Parker, Michael W.; Gardiner, Elizabeth E.

2015-01-01

Nucleotide-based drug candidates such as antisense oligonucleotides, aptamers, immunoreceptor-activating nucleotides, or (anti)microRNAs hold great therapeutic promise for many human diseases. Phosphorothioate (PS) backbone modification of nucleotide-based drugs is common practice to protect these promising drug candidates from rapid degradation by plasma and intracellular nucleases. Effects of the changes in physicochemical properties associated with PS modification on platelets have not been elucidated so far. Here we report the unexpected binding of PS-modified oligonucleotides to platelets eliciting strong platelet activation, signaling, reactive oxygen species generation, adhesion, spreading, aggregation, and thrombus formation in vitro and in vivo. Mechanistically, the platelet-specific receptor glycoprotein VI (GPVI) mediates these platelet-activating effects. Notably, platelets from GPVI function–deficient patients do not exhibit binding of PS-modified oligonucleotides, and platelet activation is fully abolished. Our data demonstrate a novel, unexpected, PS backbone–dependent, platelet-activating effect of nucleotide-based drug candidates mediated by GPVI. This unforeseen effect should be considered in the ongoing development programs for the broad range of upcoming and promising DNA/RNA therapeutics. PMID:25646267

Identification of DNA-binding proteins using multi-features fusion and binary firefly optimization algorithm.

PubMed

Zhang, Jian; Gao, Bo; Chai, Haiting; Ma, Zhiqiang; Yang, Guifu

2016-08-26

DNA-binding proteins (DBPs) play fundamental roles in many biological processes. Therefore, the developing of effective computational tools for identifying DBPs is becoming highly desirable. In this study, we proposed an accurate method for the prediction of DBPs. Firstly, we focused on the challenge of improving DBP prediction accuracy with information solely from the sequence. Secondly, we used multiple informative features to encode the protein. These features included evolutionary conservation profile, secondary structure motifs, and physicochemical properties. Thirdly, we introduced a novel improved Binary Firefly Algorithm (BFA) to remove redundant or noisy features as well as select optimal parameters for the classifier. The experimental results of our predictor on two benchmark datasets outperformed many state-of-the-art predictors, which revealed the effectiveness of our method. The promising prediction performance on a new-compiled independent testing dataset from PDB and a large-scale dataset from UniProt proved the good generalization ability of our method. In addition, the BFA forged in this research would be of great potential in practical applications in optimization fields, especially in feature selection problems. A highly accurate method was proposed for the identification of DBPs. A user-friendly web-server named iDbP (identification of DNA-binding Proteins) was constructed and provided for academic use.

The isolated MUC5AC gene product from human ocular mucin displays intramolecular conformational heterogeneity.

PubMed

Round, Andrew N; McMaster, Terence J; Miles, Mervyn J; Corfield, Anthony P; Berry, Monica

2007-06-01

Atomic force microscopy (AFM) has been used to show that human ocular mucins contain at least three distinct polymer conformations, separable by isopycnic density gradient centrifugation. In this work we have used affinity purification against the anti(mucin peptide core) monoclonal antibody 45M1 to isolate MUC5AC gene products, a major component of human ocular mucins. AFM images confirm that the affinity-purified polymers adopt distinct conformations that coidentify with two of those observed in the parent population, and further reveal that these two different conformations can be present within the same polymer. AFM images of the complexes formed after incubation of 45M1 with the parent sample reveal different rates of binding to the two MUC5AC polymer types. The variability of gene products within a mucin population was revealed by analyzing the height distributions along the polymer contour and periodicities in distances between occupied antibody binding sites. AFM analysis of mucin polymers at the single molecule level provides new information about the genetic origins of individual polymers and the contributions of glycosylation to the physicochemical properties of mucins, which can be correlated with information obtained from biochemistry, antibody binding assays, and molecular biology techniques.

Interaction of vasicine with calf thymus DNA: Molecular docking, spectroscopic and differential scanning calorimetric insights.

PubMed

R S, Sai Murali; R S, Sai Siddhardha; D, Rajesh Babu; S, Venketesh; R, Basavaraju; G, Nageswara Rao

2017-06-05

The present study brings out the interaction between vasicine, an alkaloid and Adhatoda vasica Nees with double stranded DNA. The physico-chemical interaction between small molecules and nucleic acids is a major area of focus in screening drugs against various cancers. Molecular probing in our study using Molecular Operating Environment (MOE) has revealed interaction of vasicine with DNA double helix. Here we report the interaction of vasicine with Calf thymus DNA. We present for the first time the results obtained from UV-visible, fluorescence spectroscopic and differential scanning calorimetric techniques that suggest a moderate to strong electrostatic, hydrophobic and van der Waals interactions mediating the DNA binding properties of vasicine, leading to disruption of DNA secondary structure. Copyright © 2017 Elsevier B.V. All rights reserved.

Recent advances in dendrimer-based nanovectors for tumor-targeted drug and gene delivery

PubMed Central

Kesharwani, Prashant; Iyer, Arun K.

2015-01-01

Advances in the application of nanotechnology in medicine have given rise to multifunctional smart nanocarriers that can be engineered with tunable physicochemical characteristics to deliver one or more therapeutic agent(s) safely and selectively to cancer cells, including intracellular organelle-specific targeting. Dendrimers having properties resembling biomolecules, with well-defined 3D nanopolymeric architectures, are emerging as a highly attractive class of drug and gene delivery vector. The presence of numerous peripheral functional groups on hyperbranched dendrimers affords efficient conjugation of targeting ligands and biomarkers that can recognize and bind to receptors overexpressed on cancer cells for tumor-cell-specific delivery. The present review compiles the recent advances in dendrimer-mediated drug and gene delivery to tumors by passive and active targeting principles with illustrative examples. PMID:25555748

A Coordination Chemistry Approach to Fine-Tune the Physicochemical Parameters of Lanthanide Complexes Relevant to Medical Applications.

PubMed

Le Fur, Mariane; Molnár, Enikő; Beyler, Maryline; Kálmán, Ferenc K; Fougère, Olivier; Esteban-Gómez, David; Rousseaux, Olivier; Tripier, Raphaël; Tircsó, Gyula; Platas-Iglesias, Carlos

2018-03-02

The geometric features of two pyclen-based ligands possessing identical donor atoms but different site organization have a profound impact in their complexation properties toward lanthanide ions. The ligand containing two acetate groups and a picolinate arm arranged in a symmetrical fashion (L1) forms a Gd 3+ complex being two orders of magnitude less stable than its dissymmetric analogue GdL2. Besides, GdL1 experiences a much faster dissociation following the acid-catalyzed mechanism than GdL2. On the contrary, GdL1 exhibits a lower exchange rate of the coordinated water molecule compared to GdL2. These very different properties are related to different strengths of the Gd-ligand bonds associated to steric effects, which hinder the coordination of a water molecule in GdL2 and the binding of acetate groups in GdL1. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bioconversion of Chitin to Bioactive Chitooligosaccharides: Amelioration and Coastal Pollution Reduction by Microbial Resources.

PubMed

Kumar, Manish; Brar, Amandeep; Vivekanand, V; Pareek, Nidhi

2018-04-10

Chitin-metabolizing products are of high industrial relevance in current scenario due to their wide biological applications, relatively lower cost, greater abundance, and sustainable supply. Chitooligosaccharides have remarkably wide spectrum of applications in therapeutics such as antitumor agents, immunomodulators, drug delivery, gene therapy, wound dressings, as chitinase inhibitors to prevent malaria. Hypocholesterolemic and antimicrobial activities of chitooligosaccharides make them a molecule of choice for food industry, and their functional profile depends on the physicochemical characteristics. Recently, chitin-based nanomaterials are also gaining tremendous importance in biomedical and agricultural applications. Crystallinity and insolubility of chitin imposes a major hurdle in the way of polymer utilization. Chemical production processes are known to produce chitooligosaccharides with variable degree of polymerization and properties along with ecological concerns. Biological production routes mainly involve chitinases, chitosanases, and chitin-binding proteins. Development of bio-catalytic production routes for chitin will not only enhance the production of commercially viable chitooligosaccharides with defined molecular properties but will also provide a means to combat marine pollution with value addition.

Intracellular production of hydrogels and synthetic RNA granules by multivalent enhancers

PubMed Central

Nakamura, Hideki; Lee, Albert A.; Afshar, Ali Sobhi; Watanabe, Shigeki; Rho, Elmer; Razavi, Shiva; Suarez, Allison; Lin, Yu-Chun; Tanigawa, Makoto; Huang, Brian; DeRose, Robert; Bobb, Diana; Hong, William; Gabelli, Sandra B.; Goutsias, John; Inoue, Takanari

2018-01-01

Non-membrane bound, hydrogel-like entities, such as RNA granules, nucleate essential cellular functions through their unique physico-chemical properties. However, these intracellular hydrogels have not been as extensively studied as their extracellular counterparts, primarily due to technical challenges in probing these materials in situ. Here, by taking advantage of a chemically inducible dimerization paradigm, we developed iPOLYMER, a strategy for rapid induction of protein-based hydrogels inside living cells. A series of biochemical and biophysical characterizations, in conjunction with computational modeling, revealed that the polymer network formed in the cytosol resembles a physiological hydrogel-like entity that behaves as a size-dependent molecular sieve. We studied several properties of the gel and functionalized it with RNA binding motifs that sequester polyadenine-containing nucleotides to synthetically mimic RNA granules. Therefore, we here demonstrate that iPOLYMER presents a unique and powerful approach to synthetically reconstitute hydrogel-like structures including RNA granules in intact cells. PMID:29115293

Collagen hydrogels incorporated with surface-aminated mesoporous nanobioactive glass: Improvement of physicochemical stability and mechanical properties is effective for hard tissue engineering.

PubMed

El-Fiqi, Ahmed; Lee, Jae Ho; Lee, Eun-Jung; Kim, Hae-Won

2013-12-01

Collagen (Col) hydrogels have poor physicochemical and mechanical properties and are susceptible to substantial shrinkage during cell culture, which limits their potential applications in hard tissue engineering. Here, we developed novel nanocomposite hydrogels made of collagen and mesoporous bioactive glass nanoparticles (mBGns) with surface amination, and addressed the effects of mBGn addition (Col:mBG = 2:1, 1:1 and 1:2) and its surface amination on the physicochemical and mechanical properties of the hydrogels. The amination of mBGn was shown to enable chemical bonding with collagen molecules. As a result, the nanocomposite hydrogels exhibited a significantly improved physicochemical and mechanical stability. The hydrolytic and enzymatic degradation of the Col-mBGn hydrogels were slowed down due to the incorporation of mBGn and its surface amination. The mechanical properties of the hydrogels, specifically the resistance to loading as well as the stiffness, significantly increased with the addition of mBGn and its aminated form, as assessed by a dynamic mechanical analysis. Mesenchymal stem cells cultivated within the Col-mBGn hydrogels were highly viable, with enhanced cytoskeletal extensions, due to the addition of surface aminated mBGn. While the Col hydrogel showed extensive shrinkage (down to ∼20% of initial size) during a few days of culture, the shrinkage of the mBGn-added hydrogel was substantially reduced, and the aminated mBGn-added hydrogel had no observable shrinkage over 21 days. Results demonstrated the effective roles of aminated mBGn in significantly improving the physicochemical and mechanical properties of Col hydrogel, which are ultimately favorable for applications in stem cell culture for bone tissue engineering. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Deciphering complex patterns of class-I HLA-peptide cross-reactivity via hierarchical grouping.

PubMed

Mukherjee, Sumanta; Warwicker, Jim; Chandra, Nagasuma

2015-07-01

T-cell responses in humans are initiated by the binding of a peptide antigen to a human leukocyte antigen (HLA) molecule. The peptide-HLA complex then recruits an appropriate T cell, leading to cell-mediated immunity. More than 2000 HLA class-I alleles are known in humans, and they vary only in their peptide-binding grooves. The polymorphism they exhibit enables them to bind a wide range of peptide antigens from diverse sources. HLA molecules and peptides present a complex molecular recognition pattern, as many peptides bind to a given allele and a given peptide can be recognized by many alleles. A powerful grouping scheme that not only provides an insightful classification, but is also capable of dissecting the physicochemical basis of recognition specificity is necessary to address this complexity. We present a hierarchical classification of 2010 class-I alleles by using a systematic divisive clustering method. All-pair distances of alleles were obtained by comparing binding pockets in the structural models. By varying the similarity thresholds, a multilevel classification was obtained, with 7 supergroups, each further subclassifying to yield 72 groups. An independent clustering performed based only on similarities in their epitope pools correlated highly with pocket-based clustering. Physicochemical feature combinations that best explain the basis of clustering are identified. Mutual information calculated for the set of peptide ligands enables identification of binding site residues contributing to peptide specificity. The grouping of HLA molecules achieved here will be useful for rational vaccine design, understanding disease susceptibilities and predicting risk of organ transplants.

Rational engineering of physicochemical properties of nanomaterials for biomedical applications with nanotoxicological perspectives.

PubMed

Navya, P N; Daima, Hemant Kumar

2016-01-01

Innovative engineered nanomaterials are at the leading edge of rapidly emerging fields of nanobiotechnology and nanomedicine. Meticulous synthesis, unique physicochemical properties, manifestation of chemical or biological moieties on the surface of materials make engineered nanostructures suitable for a variety of biomedical applications. Besides, tailored nanomaterials exhibit entirely novel therapeutic applications with better functionality, sensitivity, efficiency and specificity due to their customized unique physicochemical and surface properties. Additionally, such designer made nanomaterials has potential to generate series of interactions with various biological entities including DNA, proteins, membranes, cells and organelles at nano-bio interface. These nano-bio interactions are driven by colloidal forces and predominantly depend on the dynamic physicochemical and surface properties of nanomaterials. Nevertheless, recent development and atomic scale tailoring of various physical, chemical and surface properties of nanomaterials is promising to dictate their interaction in anticipated manner with biological entities for biomedical applications. As a result, rationally designed nanomaterials are in extensive demand for bio-molecular detection and diagnostics, therapeutics, drug and gene delivery, fluorescent labelling, tissue engineering, biochemical sensing and other pharmaceuticals applications. However, toxicity and risk associated with engineered nanomaterials is rather unclear or not well understood; which is gaining considerable attention and the field of nanotoxicology is evolving promptly. Therefore, this review explores current knowledge of articulate engineering of nanomaterials for biomedical applications with special attention on potential toxicological perspectives.

Rational engineering of physicochemical properties of nanomaterials for biomedical applications with nanotoxicological perspectives

NASA Astrophysics Data System (ADS)

Navya, P. N.; Daima, Hemant Kumar

2016-02-01

Innovative engineered nanomaterials are at the leading edge of rapidly emerging fields of nanobiotechnology and nanomedicine. Meticulous synthesis, unique physicochemical properties, manifestation of chemical or biological moieties on the surface of materials make engineered nanostructures suitable for a variety of biomedical applications. Besides, tailored nanomaterials exhibit entirely novel therapeutic applications with better functionality, sensitivity, efficiency and specificity due to their customized unique physicochemical and surface properties. Additionally, such designer made nanomaterials has potential to generate series of interactions with various biological entities including DNA, proteins, membranes, cells and organelles at nano-bio interface. These nano-bio interactions are driven by colloidal forces and predominantly depend on the dynamic physicochemical and surface properties of nanomaterials. Nevertheless, recent development and atomic scale tailoring of various physical, chemical and surface properties of nanomaterials is promising to dictate their interaction in anticipated manner with biological entities for biomedical applications. As a result, rationally designed nanomaterials are in extensive demand for bio-molecular detection and diagnostics, therapeutics, drug and gene delivery, fluorescent labelling, tissue engineering, biochemical sensing and other pharmaceuticals applications. However, toxicity and risk associated with engineered nanomaterials is rather unclear or not well understood; which is gaining considerable attention and the field of nanotoxicology is evolving promptly. Therefore, this review explores current knowledge of articulate engineering of nanomaterials for biomedical applications with special attention on potential toxicological perspectives.

Stabilizers influence drug–polymer interactions and physicochemical properties of disulfiram-loaded poly-lactide-co-glycolide nanoparticles

PubMed Central

Hoda, Muddasarul; Sufi, Shamim Akhtar; Cavuturu, Bindumadhuri; Rajagopalan, Rukkumani

2018-01-01

Aim: Stabilizers are known to be an integral component of polymeric nanostructures. Ideally, they manipulate physicochemical properties of nanoparticles. Based on this hypothesis, we demonstrated that disulfiram (drug) and Poly-lactide-co-glycolide (polymer) interactions and physicochemical properties of their nanoparticles formulations are significantly influenced by the choice of stabilizers. Methodology: Electron microscopy, differential scanning calorimetry, x-ray diffraction, Raman spectrum analysis, isothermal titration calorimetry and in silico docking studies were performed. Results & discussion: Polysorbate 80 imparted highest crystallinity while Triton-X 100 imparted highest rigidity, possibly influencing drug bioavailability, blood-retention time, cellular uptake and sustained drug release. All the molecular interactions were hydrophobic in nature and entropy driven. Therefore, polymeric nanoparticles may be critically manipulated to streamline the passive targeting of drug-loaded nanoparticles. PMID:29379637

Effect of drying procedures on the physicochemical properties and antioxidant activities of polysaccharides from Crassostrea gigas

PubMed Central

Zheng, Yaxu; Qu, Min; Jin, Qiao; Tong, Changqing

2017-01-01

Crassostrea gigas polysaccharides (CGP) were obtained by different drying methods: freeze-drying (FD), spray-drying (SD) or rotary evaporation-drying (RED). The physicochemical properties of CGP were evaluated on the basis of polysaccharide content, protein content, color characteristics, FT-IR spectroscopy, differential scanning calorimetry (DSC), and scanning electron microscopy (SEM). Antioxidant activities were researched three different free radicals, including DPPH free radicals, ABTS free radicals and reducing power. The results demonstrated that FDCGP, SDCGP and REDCGP have different physicochemical properties and antioxidant activities. Contrasted with FDCGP and REDCGP, SDCGP exhibited stronger antioxidant abilities. Therefore, considering the polysaccharides appearances and antioxidant activities, the spray drying method is a decent selection for the preparation of such polysaccharides, and it should be selected for application in the food industry. PMID:29176846

Data on physicochemical properties of active films derived from plantain flour/PCL blends developed under reactive extrusion conditions.

PubMed

Gutiérrez, Tomy J; Alvarez, Vera A

2017-12-01

The data given below relates to the research paper entitled: "Eco-friendly films prepared from plantain flour/PCL blends under reactive extrusion conditions using zirconium octanoate as a catalyst", recently published by our research group [1]. This article provides information concerning the physicochemical properties of the above-mentioned film systems: thickness, density, opacity, moisture content and surface moisture.

METAL OXIDE NANOPARTICLES

DOE Office of Scientific and Technical Information (OSTI.GOV)

FERNANDEZ-GARCIA,M.; RODGRIGUEZ, J.A.

2007-10-01

This chapter covers the fundamental science, synthesis, characterization, physicochemical properties and applications of oxide nanomaterials. Explains fundamental aspects that determine the growth and behavior of these systems, briefly examines synthetic procedures using bottom-up and top-down fabrication technologies, discusses the sophisticated experimental techniques and state of the art theory results used to characterize the physico-chemical properties of oxide solids and describe the current knowledge concerning key oxide materials with important technological applications.

Composition, structure, physicochemical properties, and modifications of cassava starch.

PubMed

Zhu, Fan

2015-05-20

Cassava is highly tolerant to harsh climatic conditions and has great productivity on marginal lands. The supply of cassava starch, the major component of the root, is thus sustainable and cheap. This review summarizes the current knowledge of the composition, physical and chemical structures, physicochemical properties, nutritional quality, and modifications of cassava starch. Research opportunities to better understand this starch are provided. Copyright © 2014 Elsevier Ltd. All rights reserved.

Physicochemical properties and biocompatibility of N-trimethyl chitosan: effect of quaternization and dimethylation.

PubMed

Jintapattanakit, Anchalee; Mao, Shirui; Kissel, Thomas; Junyaprasert, Varaporn Buraphacheep

2008-10-01

The aim of this research was to investigate the effect of degrees of quaternization (DQ) and dimethylation (DD) on physicochemical properties and cytotoxicity of N-trimethyl chitosan (TMC). TMC was synthesized by reductive methylation of chitosan in the presence of a strong base at elevated temperature and polymer characteristics were investigated. The number of methylation process and duration of reaction were demonstrated to affect the DQ and DD. An increased number of reaction steps increased DQ and decreased DD, while an extended duration of reaction increased both DQ and DD. The molecular weight of TMC was in the range of 60-550kDa. From the Mark-Houwink equation, it was found that TMC in 2% acetic acid/0.2M sodium acetate behaved as a spherical structure, approximating a random coil. The highest solubility was found with TMC of an intermediate DQ (40%) regardless of DD and molecular weight. The effect of DD on the physicochemical properties and cytotoxicity was obviously observed when proportion of DD to DQ was higher than 1. TMC with relatively high DD showed reduction in both solubility and mucoadhesion and hence decreased cytotoxicity. However, the influence of DD was insignificant when DQ of TMC was higher than 40% at which physicochemical properties and cytotoxicity were mainly dependent upon DQ.

Physical modification of palm kernel meal improved available carbohydrate, physicochemical properties and in vitro digestibility in economic freshwater fish.

PubMed

Thongprajukaew, Karun; Yawang, Pinya; Dudae, Lateepah; Bilanglod, Husna; Dumrongrittamatt, Terdtoon; Tantikitti, Chutima; Kovitvadhi, Uthaiwan

2013-12-01

Unavailable carbohydrates are an important limiting factor for utilization of palm kernel meal (PKM) as aquafeed ingredients. The aim of this study was to improve available carbohydrate from PKM. Different physical modifications including water soaking, microwave irradiation, gamma irradiation and electron beam, were investigated in relation to chemical composition, physicochemical properties and in vitro carbohydrate digestibility using digestive enzymes from economic freshwater fish. Modified methods had significant (P < 0.05) effects on chemical composition by decreasing crude fiber and increasing available carbohydrates. Improvements in physicochemical properties of PKM, such as water solubility, microstructure, relative crystallinity and lignocellulosic spectra, were mainly achieved by soaking and microwave irradiation. Carbohydrate digestibility varied among the physical modifications tested (P < 0.05) and three fish species had different abilities to digest PKM. Soaking was the appropriate modification for increasing carbohydrate digestion specifically in Nile tilapia (Oreochromis niloticus), whereas either soaking or microwave irradiation was effective for striped snakehead (Channa striata). For walking catfish (Clarias batrachus), carbohydrate digestibility was similar among raw, soaked and microwave-irradiated PKM. These findings suggest that soaking and microwave irradiation could be practical methods for altering appropriate physicochemical properties of PKM as well as increasing carbohydrate digestibility in select economic freshwater fish. © 2013 Society of Chemical Industry.

Physicochemical mechanisms of plasma-liquid interactions within plasma channels in liquid

NASA Astrophysics Data System (ADS)

Franclemont, Joshua; Fan, Xiangru; Mededovic Thagard, Selma

2015-10-01

The goal of this study is to advance the fundamental understanding of the physical and chemical mechanisms by which excited radical species produced by electrical plasmas directly in water, OH radicals especially, induce chemical changes in aqueous organic compounds and to exploit this for the development and optimization of drinking and wastewater plasma-based treatment systems. To achieve this goal, this study measured and correlated the production rate of hydrogen peroxide (H2O2) with physicochemical properties of 11 organic compounds. The observed individual correlations between the investigated physicochemical properties and the resulting H2O2 concentrations were used to develop an equation that would allow predicting the measured H2O2 concentration from physicochemical properties of a compound. Results reveal that the production rate of H2O2 directly depends on the surface tension of the solution and compounds’ bulk liquid concentration, hydrophobicity (K ow value), and molecular volume. Other properties such as vapor pressure, Henry’s constant, enthalpy of vaporization, ionization energy, electron affinity, and molecular dipole moment do not affect the H2O2 chemistry. K ow value and surface tension of the solution determine the compound’s concentration at the plasma interface. Once at the interface, the molecular volume determines the rate at which the molecule will react with OH radicals.

Physicochemical properties of quinoa flour as affected by starch interactions.

PubMed

Li, Guantian; Zhu, Fan

2017-04-15

There has been growing interest in whole grain quinoa flour for new product development due to the unique nutritional benefits. The quality of quinoa flour is much determined by the properties of its major component starch as well as non-starch components. In this study, composition and physicochemical properties of whole grain flour from 7 quinoa samples have been analyzed. Flour properties have been correlated to the flour composition and the properties of isolated quinoa starches through chemometrics. Great variations in chemical composition, swelling power, water soluble index, enzyme susceptibility, pasting, gel texture, and thermal properties of the flour have been observed. Correlation analysis showed that thermal properties and enzyme susceptibility of quinoa flour are highly influenced by the starch. Interactions of starch with non-starch components, including lipids, protein, dietary fibre, phenolics, and minerals, greatly impacted the flour properties. For example, peak gelatinization temperature of the flour is positively correlated to that of the starch (r=0.948, p<0.01) and negatively correlated to the lipid content (r=-0.951, p<0.01). Understanding the roles of starch and other components in physicochemical properties of quinoa flour provides a basis for better utilization of this specialty crop. Copyright © 2016 Elsevier Ltd. All rights reserved.

Beware of ligand efficiency (LE): understanding LE data in modeling structure-activity and structure-economy relationships.

PubMed

Polanski, Jaroslaw; Tkocz, Aleksandra; Kucia, Urszula

2017-09-11

On the one hand, ligand efficiency (LE) and the binding efficiency index (BEI), which are binding properties (B) averaged versus the heavy atom count (HAC: LE) or molecular weight (MW: BEI), have recently been declared a novel universal tool for drug design. On the other hand, questions have been raised about the mathematical validity of the LE approach. In fact, neither the critics nor the advocates are precise enough to provide a generally understandable and accepted chemistry of the LE metrics. In particular, this refers to the puzzle of the LE trends for small and large molecules. In this paper, we explain the chemistry and mathematics of the LE type of data. Because LE is a weight metrics related to binding per gram, its hyperbolic decrease with an increasing number of heavy atoms can be easily understood by its 1/MW dependency. Accordingly, we analyzed how this influences the LE trends for ligand-target binding, economic big data or molecular descriptor data. In particular, we compared the trends for the thermodynamic ∆G data of a series of ligands that interact with 14 different target classes, which were extracted from the BindingDB database with the market prices of a commercial compound library of ca. 2.5 mln synthetic building blocks. An interpretation of LE and BEI that clearly explains the observed trends for these parameters are presented here for the first time. Accordingly, we show that the main misunderstanding of the chemical meaning of the BEI and LE parameters is their interpretation as molecular descriptors that are connected with a single molecule, while binding is a statistical effect in which a population of ligands limits the formation of ligand-receptor complexes. Therefore, LE (BEI) should not be interpreted as a molecular (physicochemical) descriptor that is connected with a single molecule but as a property (binding per gram). Accordingly, the puzzle of the surprising behavior of LE is explained by the 1/MW dependency. This effect clearly explains the hyperbolic LE trend not as a real increase in binding potency but as a physical limitation due to the different population of ligands with different MWs in a 1 g sample available for the formation of ligand-receptor complexes. Graphical abstract .

A physicochemical study of sugar palm (Arenga Pinnata) starch films plasticized by glycerol and sorbitol

NASA Astrophysics Data System (ADS)

Poeloengasih, Crescentiana D.; Pranoto, Yudi; Hayati, Septi Nur; Hernawan, Rosyida, Vita T.; Prasetyo, Dwi J.; Jatmiko, Tri H.; Apriyana, Wuri; Suwanto, Andri

2016-02-01

The present work explores the physicochemical characteristics of sugar palm starch film for a potential hard capsule purpose. Sugar palm (Arenga pinnata) starch films were plasticized with glycerol or sorbitol in various concentrations (30% up to 50% w/w starch). Their effects on physicochemical properties of the films were investigated. The results showed that sugar palm starch was successfully developed as the main material of film using casting method. Incorporation of both glycerol or sorbitol affected the properties of films in different ways. It was found that thickness and solubility increased as plasticizer concentration increased, whereas retraction ratio, swelling degree and swelling thickness decreased with the increased plasticizer concentration.

Physicochemical properties of extrudates from white yam and bambara nut blends

NASA Astrophysics Data System (ADS)

Oluwole, O. B.; Olapade, A. A.; Awonorin, S. O.; Henshaw, F. O.

2013-01-01

This study was conducted to investigate effects of extrusion conditions on physicochemical properties of blend of yam and bambara nut flours. A blend of white yam grit (750 μm) and Bambara nut flour (500 μm) in a ratio of 4:1, respectively was extrusion cooked at varying screw speeds 50-70 r.p.m., feed moisture 12.5-17.5% (dry basis) and barrel temperatures 130-150°C. The extrusion variables employed included barrel temperature, screw speed, and feed moisture content, while the physicochemical properties of the extrudates investigated were the expansion ratio, bulk density, and trypsin inhibition activity. The results revealed that all the extrusion variables had significant effects (p<0.05) on the product properties considered in this study. The expansion ratio values ranged 1.55-2.06, bulk density values ranged 0.76-0.94 g cm-3, while trypsin inhibition activities were 1.01-8.08 mg 100 g-1 sample.

The effects of chilling stress after anthesis on the physicochemical properties of rice (Oryza sativa L) starch.

PubMed

Zhu, Dawei; Wei, Haiyan; Guo, Baowei; Dai, Qigen; Wei, Cunxu; Gao, Hui; Hu, Yajie; Cui, Peiyuan; Li, Min; Huo, Zhongyang; Xu, Ke; Zhang, Hongcheng

2017-12-15

This study investigates the effect of chilling stress, over a period of three days after anthesis, on the physicochemical properties of starches derived from six rice cultivars. Chilling stress significantly affected the grain characteristics and physicochemical properties of rice starches, except for those of two varieties, NJ 9108 and ZD 18. In the other four rice cultivars subjected to chilling stress, the content of medium, and large sized granules showed a decrease, and an increase, respectively. Amylose content increased as a result of chilling stress, thereby resulting in starch with a lower swelling power, water solubility, and higher retrogradation enthalpy and gelatinization temperature. Chilling stress led to deterioration of cooked rice quality as determined by the pasting properties of starch. This study indicated that among the cultivars studied, the two rice varieties most resistant to chilling stress after rice anthesis were NJ 9108 and ZD 18. Copyright © 2017 Elsevier Ltd. All rights reserved.

Influence of physicochemical properties of rice flour on oil uptake of tempura frying batter.

PubMed

Nakamura, Sumiko; Ohtsubo, Ken'ichi

2010-01-01

The physicochemical properties of rice flour and wheat flour influenced the oil uptake of tempura frying batter. Rice flour was better than wheat flour in the overall quality and crispness of the fried tempura batter. Rice flour resisted oil absorption more than wheat flour, and a higher level of apparent starch amylose and higher consistency/breakdown ratio of the pasting properties led to a lower oil uptake of the batter. Super hard EM10 rice showed the highest apparent amylose content and higher consistency/breakdown ratio than the other flour samples, the batter from EM10 revealing the lowest oil content after frying among all the batters examined. The apparent amylose content, consistency/breakdown ratio and oil absorption index are proposed as useful guides for oil absorption when frying from among the physicochemical properties that influence the oil content of fried batter. Our proposal for the "oil absorption index" could be a simple, although not perfect method for estimating the oil content of batter flour.

Evaluation of physicochemical properties and antioxidant activities of kombucha "Tea Fungus" during extended periods of fermentation.

PubMed

Amarasinghe, Hashani; Weerakkody, Nimsha S; Waisundara, Viduranga Y

2018-05-01

Kombucha fermentation is traditionally carried out by inoculating a previously grown tea fungal mat into a freshly prepared tea broth and incubating under aerobic conditions for 7-10 days. In this study, four kombucha beverages were prepared by placing the tea fungal mats in sugared Sri Lankan black tea at varying concentrations for a period of 8 weeks. The antioxidant activities, physicochemical, and qualitative properties were monitored prior to the commencement of the fermentation process, one day after the inoculation with the microorganisms and subsequently on a weekly basis. All samples displayed a statistically significant decrease ( p  <   .05) in the antioxidant activity at the end of 8 weeks, which was indicative of the decreasing functional properties of the beverage. The physicochemical properties indicated increased acidity and turbidity, which might decrease consumer appeal of the fermented beverage. Further studies are necessary to test the accumulation of organic acids, nucleic acids, and toxicity of kombucha on human organs following the extended period of fermentation.

Chemical and Functional Properties of Chia Seed (Salvia hispanica L.) Gum

PubMed Central

Segura-Campos, Maira Rubi; Ciau-Solís, Norma; Rosado-Rubio, Gabriel; Chel-Guerrero, Luis; Betancur-Ancona, David

2014-01-01

Chia (Salvia hispanica L.) constitutes a potential alternative raw material and ingredient in food industry applications due to its dietary fiber content. Gum can be extracted from its dietary fiber fractions for use as an additive to control viscosity, stability, texture, and consistency in food systems. The gum extracted from chia seeds was characterized to determine their quality and potential as functional food additives. The extracted chia gum contained 26.2% fat and a portion was submitted to fat extraction, producing two fractions: gum with fat (FCG) and gum partly defatted (PDCG). Proximal composition and physicochemical characterization showed these fractions to be different (P < 0.05). The PDCG had higher protein, ash, and carbohydrates content than the FCG, in addition to higher water-holding (110.5 g water/g fiber) and water-binding capacities (0.84 g water/g fiber). The FCG had greater oil-holding capacity (25.7 g oil/g fiber) and water absorption capacity (44 g water/g fiber). In dispersion trials, the gums exhibited a non-Newtonian fluid behavior, specifically shear thinning or pseudoplastic type. PDCG had more viscosity than FCG. Chia seed is an excellent natural source of gum with good physicochemical and functional qualities, and is very promising for use in food industry. PMID:26904622

Molecular properties of food allergens.

PubMed

Breiteneder, Heimo; Mills, E N Clare

2005-01-01

Plant food allergens belong to a rather limited number of protein families and are also characterized by a number of biochemical and physicochemical properties, many of which are also shared by food allergens of animal origin. These include thermal stability and resistance to proteolysis, which are enhanced by an ability to bind ligands, such as metal ions, lipids, or steroids. Other types of lipid interaction, including membranes or other lipid structures, represent another feature that might promote the allergenic properties of certain food proteins. A structural feature clearly related to stability is intramolecular disulfide bonds alongside posttranslational modifications, such as N-glycosylation. Some plant food allergens, such as the cereal seed storage prolamins, are rheomorphic proteins with polypeptide chains that adopt an ensemble of secondary structures resembling unfolded or partially folded proteins. Other plant food allergens are characterized by the presence of repetitive structures, the ability to form oligomers, and the tendency to aggregate. A summary of our current knowledge regarding the molecular properties of food allergens is presented. Although we cannot as yet predict the allergenicity of a given food protein, understanding of the molecular properties that might predispose them to becoming allergens is an important first step and will undoubtedly contribute to the integrative allergenic risk assessment process being adopted by regulators.

Towards the chemometric dissection of peptide - HLA-A*0201 binding affinity: comparison of local and global QSAR models

NASA Astrophysics Data System (ADS)

Doytchinova, Irini A.; Walshe, Valerie; Borrow, Persephone; Flower, Darren R.

2005-03-01

The affinities of 177 nonameric peptides binding to the HLA-A*0201 molecule were measured using a FACS-based MHC stabilisation assay and analysed using chemometrics. Their structures were described by global and local descriptors, QSAR models were derived by genetic algorithm, stepwise regression and PLS. The global molecular descriptors included molecular connectivity χ indices, κ shape indices, E-state indices, molecular properties like molecular weight and log P, and three-dimensional descriptors like polarizability, surface area and volume. The local descriptors were of two types. The first used a binary string to indicate the presence of each amino acid type at each position of the peptide. The second was also position-dependent but used five z-scales to describe the main physicochemical properties of the amino acids forming the peptides. The models were developed using a representative training set of 131 peptides and validated using an independent test set of 46 peptides. It was found that the global descriptors could not explain the variance in the training set nor predict the affinities of the test set accurately. Both types of local descriptors gave QSAR models with better explained variance and predictive ability. The results suggest that, in their interactions with the MHC molecule, the peptide acts as a complicated ensemble of multiple amino acids mutually potentiating each other.

Determination of physiochemical properties of palm oil methyl ester catalyzed by waste cockle shells

NASA Astrophysics Data System (ADS)

Nasir, Nurul Fitriah; Latif, Noradila Abdul; Bakar, Sharifah Adzila Syed Abu; Rahman, Mohd Nasrull Abdul; Selamat, Siti Norhidayah; Nasharudin, Nurul Nadirah

2017-04-01

Waste cockle shell can be used as a source of calcium oxide (CaO) in catalyzing a transesterification reaction to produce biodiesel or fatty acid methyl ester (FAME). This aim of this paper is to determine the physicochemical properties of (FAME) which utilize waste cockle shells in the transesterification reaction process. In this study, the catalyst was prepared using high temperature furnace (700°C) for 4 h. The molar ratio of methanol to oil was fixed at 9:1 and the reaction temperature and catalyst concentration were varied from 65 -70 °C, and 10-30 wt. %, respectively for transesterification reaction. The reaction time was also fixed at 3 h. The analyzed physicochemical properties were density, viscosity, flash point and net heat of combustion. The results obtained from the analysis found that reaction temperature 65°C with 30% of catalyst concentration has produced the physical properties of FAME that comply the biodiesel standards. The results suggest that reaction temperature and catalyst concentration have influence on the value of physicochemical properties of FAME produced.

Effect of dietary pomegranate seed oil on laying hen performance and physicochemical properties of eggs.

PubMed

Kostogrys, Renata B; Filipiak-Florkiewicz, Agnieszka; Dereń, Katarzyna; Drahun, Anna; Czyżyńska-Cichoń, Izabela; Cieślik, Ewa; Szymczyk, Beata; Franczyk-Żarów, Magdalena

2017-04-15

The objective of the study was to determine the effects of pomegranate seed oil, used as a source of punicic acid (CLnA) in the diets of laying hens, on the physicochemical properties of eggs. Forty Isa Brown laying hens (26weeks old) were equally subjected to 4 dietary treatments (n=10) and fed a commercial layer diet supplying 2.5% sunflower oil (control) or three levels (0.5, 1.0 and 1.5%) of punicic acid in the diets. After 12weeks of feeding the hens, eggs collection began. Sixty eggs - randomly selected from each group - were analysed for physicochemical properties. Eggs naturally enriched with CLnA preserve their composition and conventional properties in most of the analysed parameters (including chemical composition, physical as well as organoleptic properties). Dietary CLnA had positive impact on the colour of the eggs' yolk, whereas the hardness of hard-boiled egg yolks was not affected. Additionally, increasing dietary CLnA led to an increase not only the CLnA concentrations, but also CLA in egg-yolk lipids. Copyright © 2016. Published by Elsevier Ltd.

Influence of mannitol concentration on the physicochemical, mechanical and pharmaceutical properties of lyophilised mannitol.

PubMed

Kaialy, Waseem; Khan, Usman; Mawlud, Shadan

2016-08-20

Mannitol is a pharmaceutical excipient that is receiving increased popularity in solid dosage forms. The aim of this study was to provide comparative evaluation on the effect of mannitol concentration on the physicochemical, mechanical, and pharmaceutical properties of lyophilised mannitol. The results showed that the physicochemical, mechanical and pharmaceutical properties of lyophilised mannitol powders are strong functions of mannitol concentration. By decreasing mannitol concentration, the true density, bulk density, cohesivity, flowability, netcharge-to-mass ratio, and relative degree of crystallinity of LM were decreased, whereas the breakability, size distribution, and size homogeneity of lyophilised mannitol particles were increased. The mechanical properties of lyophilised mannitol tablets improved with decreasing mannitol concentration. The use of lyophilised mannitol has profoundly improved the dissolution rate of indomethacin from tablets in comparison to commercial mannitol. This improvement exhibited an increasing trend with decreasing mannitol concentration. In conclusion, mannitols lyophilised from lower concentrations are more desirable in tableting than mannitols from higher concentrations due to their better mechanical and dissolution properties. Copyright © 2016 Elsevier B.V. All rights reserved.

A study of relations between physicochemical properties of crude oils and microbiological characteristics of reservoir microflora

NASA Astrophysics Data System (ADS)

Yashchenko, I. G.; Polishchuk, Yu. M.; Peremitina, T. O.

2015-10-01

The dependence of the population and activity of reservoir microflora upon the chemical composition and viscosity of crude oils has been investigated, since it allows the problem of improvement in the technologies and enhancement of oil recovery as applied to production of difficult types of oils with anomalous properties (viscous, heavy, waxy, high resin) to be solved. The effect of the chemical composition of the oil on the number, distribution, and activity of reservoir microflora has been studied using data on the microbiological properties of reservoir water of 16 different fields in oil and gas basins of Russia, Mongolia, China, and Vietnam. Information on the physicochemical properties of crude oils of these fields has been obtained from the database created at the Institute of Petroleum Chemistry, Siberian Branch on the physicochemical properties of oils throughout the world. It has been found that formation water in viscous oil reservoirs is char acterized by a large population of heterotrophic and sulfate reducing bacteria and the water of oil fields with a high paraffin content, by population of denitrifying bacteria.

Vaginal Microbicide Film Combinations of Two Reverse Transcriptase Inhibitors, EFdA and CSIC, for the Prevention of HIV-1 Sexual Transmission.

PubMed

Zhang, Wei; Hu, Minlu; Shi, Yuan; Gong, Tiantian; Dezzutti, Charlene S; Moncla, Bernard; Sarafianos, Stefan G; Parniak, Michael A; Rohan, Lisa C

2015-09-01

EFdA is a potent nucleoside reverse transcriptase inhibitor (NRTI) with activity against a wide spectrum of wild-type and drug resistant HIV-1 variants. CSIC is a tight-binding non-nucleoside reverse transcriptase inhibitor (NNRTI) with demonstrated anti-HIV properties important for use in topical prevention of HIV transmission. The objective of this study was to develop and characterize film-formulated EFdA and CSIC for use as a female-controlled vaginal microbicide to prevent sexual transmission of HIV. Assessments of EFdA- and CSIC-loaded films included physicochemical characteristics, in vitro cytotoxicity, epithelia integrity studies, compatibility with the normal vaginal Lactobacillus flora and anti-HIV bioactivity evaluations. No significant change in physicochemical properties or biological activity of the combination films were noted during 3 months storage. In vitro cytotoxicity and bioactivity testing showed that 50% cytotoxic concentration (CC50) of either EFdA or CSIC was several orders of magnitude higher than the 50% effective concentration (EC50) values. Film-formulated EFdA and CSIC combination showed additive inhibitory activity against wild type and drug-resistant variants of HIV. Epithelial integrity studies demonstrated that the combination vaginal film had a much lower toxicity to HEC-1A monolayers compared to that of VCF®, a commercial vaginal film product containing nonoxynol-9. Polarized ectocervical explants showed films with drug alone or in combination were effective at preventing HIV infection. Our data suggest that vaginal microbicide films containing a combination of the NRTI EFdA and the NNRTI CSIC have potential to prevent HIV-1 sexual transmission.

Thermodynamic investigations of protein's behaviour with ionic liquids in aqueous medium studied by isothermal titration calorimetry.

PubMed

Bharmoria, Pankaj; Kumar, Arvind

2016-05-01

While a number of reports appear on ionic liquids-proteins interactions, their thermodynamic behaviour using suitable technique like isothermal titration calorimetry is not systematically presented. Isothermal titration calorimetry (ITC) is a key technique which can directly measure the thermodynamic contribution of IL binding to protein, particularly the enthalpy, heat capacities and binding stoichiometry. Ionic liquids (ILs), owing to their unique and tunable physicochemical properties have been the central area of scientific research besides graphene in the last decade, and growing unabated. Their encounter with proteins in the biological system is inevitable considering their environmental discharge though most of them are recyclable for a number of cycles. In this article we will cover the thermodynamics of proteins upon interaction with ILs as osmolyte and surfactant. The up to date literature survey of IL-protein interactions using isothermal titration calorimetry will be discussed and parallel comparison with the results obtained for such studies with other techniques will be highlighted to demonstrate the accuracy of ITC technique. Net stability of proteins can be obtained from the difference in the free energy (ΔG) of the native (folded) and denatured (unfolded) state using the Gibbs-Helmholtz equation (ΔG=ΔH-TΔS). Isothermal titration calorimetry can directly measure the heat changes upon IL-protein interactions. Calculation of other thermodynamic parameters such as entropy, binding constant and free energy depends upon the proper fitting of the binding isotherms using various fitting models. Copyright © 2015 Elsevier B.V. All rights reserved.

Thermodynamic Insights into the Binding of Mono- and Dicationic Imidazolium Surfactant Ionic Liquids with Methylcellulose in the Diluted Regime.

PubMed

Ziembowicz, Francieli Isa; Bender, Caroline Raquel; Frizzo, Clarissa Piccinin; Martins, Marcos Antonio Pinto; de Souza, Thiane Deprá; Kloster, Carmen Luisa; Santos Garcia, Irene Teresinha; Villetti, Marcos Antonio

2017-09-07

Alkylimidazolium salts are an important class of ionic liquids (ILs) due to their self-assembly capacity when in solution and due to their potential applications in chemistry and materials science. Therefore, detailed knowledge of the physicochemical properties of this class of ILs and their mixtures with natural polymers is highly desired. This work describes the interactions between a homologous series of mono- (C n MIMBr) and dicationic imidazolium (C n (MIM) 2 Br 2 ) ILs with cellulose ethers in aqueous medium. The effects of the alkyl chain length (n = 10, 12, 14, and 16), type, and concentration range of ILs (below and above their cmc) on the binding to methylcellulose (MC) were evaluated. The thermodynamic parameters showed that the interactions are favored by the increase of the IL hydrocarbon chain length, and that the binding of monocationic ILs to MC is driven by entropy. The monocationic ILs bind more effectively on the methoxyl group of MC when compared to dicationic ILs, and this outcome may be rationalized by considering the structural difference between the conventional (C n MIMBr) and the bolaform (C n (MIM) 2 Br 2 ) surfactant ILs. The C 16 MIMBr interacts more strongly with hydroxypropylcellulose when compared to methylcellulose, indicating that the strength of the interaction also depends on the hydrophobicity of the cellulose ethers. Our findings highlight that several parameters should be taken into account when designing new complex formulations.

Protein nanopore-based, single-molecule exploration of copper binding to an antimicrobial-derived, histidine-containing chimera peptide.

PubMed

Mereuta, Loredana; Schiopu, Irina; Asandei, Alina; Park, Yoonkyung; Hahm, Kyung-Soo; Luchian, Tudor

2012-12-11

Metal ions binding exert a crucial influence upon the aggregation properties and stability of peptides, and the propensity of folding in various substates. Herein, we demonstrate the use of the α-HL protein as a powerful nanoscopic tool to probe Cu(2+)-triggered physicochemical changes of a 20 aminoacids long, antimicrobial-derived chimera peptide with a His residue as metal-binding site, and simultaneously dissect the kinetics of the free- and Cu(2+)-bound peptide interaction to the α-HL pore. Combining single-molecule electrophysiology on reconstituted lipid membranes and fluorescence spectroscopy, we show that the association rate constant between the α-HL pore and a Cu(2+)-free peptide is higher than that of a Cu(2+)-complexed peptide. We posit that mainly due to conformational changes induced by the bound Cu(2+) on the peptide, the resulting complex encounters a higher energy barrier toward its association with the protein pore, stemming most likely from an extra entropy cost needed to fit the Cu(2+)-complexed peptide within the α-HL lumen region. The lower dissociation rate constant of the Cu(2+)-complexed peptide from α-HL pore, as compared to that of Cu(2+)-free peptide, supports the existence of a deeper free energy well for the protein interaction with a Cu(2+)-complexed peptide, which may be indicative of specific Cu(2+)-mediated contributions to the binding of the Cu(2+)-complexed peptide within the pore lumen.

Characterization of cookies made from wheat flour blended with buckwheat flour and effect on antioxidant properties.

PubMed

Jan, Ulfat; Gani, Adil; Ahmad, Mudasir; Shah, Umar; Baba, Waqas N; Masoodi, F A; Maqsood, Sajid; Gani, Asir; Wani, Idress Ahmed; Wani, S M

2015-10-01

Buckwheat flour was incorporated into wheat flour at different levels (0, 20, 40, 60, 80, and 100 %) and the physicochemical, functional and antioxidant properties of the blended flour were studied. This study also investigated the effect of buckwheat on the retention of antioxidant properties of cookies during baking. The results showed significant variation in physicochemical and functional properties of the blended flour. The addition of buckwheat flour into wheat flour also increased the antioxidant properties of blended flour proportionally, but metal chelating properties decreased. The incorporation of buckwheat in wheat flour helped in better retention of antioxidant potential of cookies during baking process as buckwheat cookies (100 % buckwheat) showed greater percentage increase in antioxidant properties than control (100 % wheat). Quality characteristics of cookies such as hardness and spread ratio decreased, while as non-enzymatic browning (NEB) increased significantly with increase in the proportion of buckwheat flour in wheat flour. The Overall acceptability of cookies by sensory analysis was highest at 40 % level of blending. This study concluded that addition of buckwheat in wheat flour, may not only improve the physico-chemical and functional properties of the blended flour but may also enhance the nutraceutical potential of the product prepared from it.

Sunlight affects aggregation and deposition of graphene oxide in the aquatic environment.

EPA Science Inventory

In this study, we investigate the role of simulated sunlight on the physicochemical properties, aggregation, and deposition of graphene oxide (GO) in aquatic environments. Results show that light exposure under varied environmental conditions significantly impacts the physicochem...

Physicochemical Properties of Dietary Fibers from Artocarpus camansi Fruit

NASA Astrophysics Data System (ADS)

Suryanti, V.; Kusumaningsih, T.; Rumingtyas, Y. S.

2017-04-01

The objective of this work was to investigate the dietary fiber (DF) contents of Artocorpus camansi (breadnut) fruit and examine their physicochemical properties, such as water-holding capacity (WAC), oil-holding capacity (OHC) and water absorption capacity (WAC). This fruit flour contained of both water soluble fibers (SDF), such as pectin (1.95%) and gum (0.4%), and water insoluble fibers (IDF) (89.25%). The IDF content of this fruit was significantly high in respect to other DF sources. The WHC, OHC and WAC of IDF were 4.10, 2.60 and 4.0%, respectively. Moreover, the WHC, OHC and WHC of total dietary fibers (TDF) were 4.2, 4.3 and 4.6%, respectively. The results showed that the DF of fruit flour had good physicochemical properties. The findings suggested that there is a potential application of A. camansi of fruit as functional ingredients in the food industry.

Effect of egg albumen protein addition on physicochemical properties and nanostructure of gelatin from fish skin.

PubMed

Cai, Luyun; Feng, Jianhui; Peng, Xichun; Regenstein, Joe M; Li, Xiuxia; Li, Jianrong; Zhao, Wei

2016-12-01

The physicochemical properties and nanostructure of mixtures of egg albumen protein (EAP) and gelatin from under-utilised grass carp ( Ctenopharyngodon idella ) skins were studied. The gelatin with 1% EAP had an acceptable gel strength. The addition of 5% EAP significantly increased the melting and gelling temperatures of gelatin gels. Additionally, the colour turned white and the crystallinity was higher in gelatin gels with gradient concentrations of EAP (1, 3, and 5%). Gelatin with 5% EAP had the highest G' values while gelatin with 1% EAP had the lowest G' values. Atomic force microscopy showed the heterogeneous nanostructure of fish gelatin, and a simple coacervate with a homogeneous distribution was only observed with the addition of 1% EAP, indicating interaction between gelatin and EAP. These results showed that EAP effect fish gelatin's physicochemical and nanostructure properties and has potential applications in foods and pharmaceuticals.

Effect of physicochemical action on the aggregative properties of detonation-synthesized nanodiamonds

NASA Astrophysics Data System (ADS)

Fan, Z. W.; Ilnitska, H.; Lysakovskyi, V.; Ivakhnenko, S.; Kovalenko, T.

2018-01-01

The results of researches of physicochemical action on aggregate properties of nanodiamond are presented. The kinetics of aggregation of nanodiamond powder was studied as a function of time, temperature, and pH of the solution. The effect of the sp2-sp3 hybridization ratio of carbon in nanodiamond powders on their aggregation was studied. It is shown that the presence of non-diamond carbon in detonation synthesis nanodiamond powders leads to the increase of the mean diameters of particles, i.e., their agglomeration. The theoretical justification of the aggregation mechanism is proposed. It is shown that it is possible to control aggregative properties of nanodiamond powders by physicochemical influences, e.g., gas-phase thermal treatment to reduce the size of agglomerates and to create a well-developed reconstructed surface of diamond particles with a low content of functional groups on their surface.

Manganese in occupational arc welding fumes--aspects on physiochemical properties, with focus on solubility.

PubMed

Taube, Fabian

2013-01-01

Physicochemical properties, such as particle sizes, composition, and solubility of welding fumes are decisive for the bioaccessibility of manganese and thereby for the manganese cytotoxic and neurotoxic effects arising from various welding fumes. Because of the diverse results within the research on welding fume solubility, this article aims to review and discuss recent literature on physicochemical properties of gas metal arc welding, shielded metal arc welding, and flux-cored arc welding fumes, with focus on solubility properties. This article also presents a short introduction to the literature on arc welding techniques, health effects from manganese, and occupational exposure to manganese among welders.

Effect of cream fermentation on microbiological, physicochemical and rheological properties of L. helveticus-butter.

PubMed

Ewe, Joo-Ann; Loo, Su-Yi

2016-06-15

The primary objective of this study was to evaluate the physicochemical and rheological properties of butter produced by Lactobacillus helveticus fermented cream. The incorporation of putative probiotic - the L. helveticus, to ferment cream prior to butter production was anticipated to alter the nutritional composition of butter. Changes in crude macronutrients and the resultant modification relating to textural properties of butter induced upon metabolic activities of L. helveticus in cream were focused in this research. Fermented butter (LH-butter) was produced by churning the cream that was fermented by lactobacilli at 37 °C for 24 h. Physicochemical analysis, proximate analysis and rheology properties of LH-butter were compared with butter produced using unfermented cream (control). LH-butter showed a significantly (P<0.05) higher fat content and acid value; lower moisture and ash; and was softer than the control. Cream fermentation modified nutritional and textural properties of butter in which LH-butter contained higher health beneficial unsaturated fatty acids than the control and thus rendered the product softer. Its enrichment with probiotics could thus further enhance its functional property. Copyright © 2016 Elsevier Ltd. All rights reserved.

Cyclodextrins improving the physicochemical and pharmacological properties of antidepressant drugs: a patent review.

PubMed

Diniz, Tâmara Coimbra; Pinto, Tiago Coimbra Costa; Menezes, Paula Dos Passos; Silva, Juliane Cabral; Teles, Roxana Braga de Andrade; Ximenes, Rosana Christine Cavalcanti; Guimarães, Adriana Gibara; Serafini, Mairim Russo; Araújo, Adriano Antunes de Souza; Quintans Júnior, Lucindo José; Almeida, Jackson Roberto Guedes da Silva

2018-01-01

Depression is a serious mood disorder and is one of the most common mental illnesses. Despite the availability of several classes of antidepressants, a substantial percentage of patients are unresponsive to these drugs, which have a slow onset of action in addition to producing undesirable side effects. Some scientific evidence suggests that cyclodextrins (CDs) can improve the physicochemical and pharmacological profile of antidepressant drugs (ADDs). The purpose of this paper is to disclose current data technology prospects involving antidepressant drugs and cyclodextrins. Areas covered: We conducted a patent review to evaluate the antidepressive activity of the compounds complexed in CDs, and we analyzed whether these complexes improved their physicochemical properties and pharmacological action. The present review used 8 specialized patent databases for patent research, using the term 'cyclodextrin' combined with 'antidepressive agents' and its related terms. We found 608 patents. In the end, considering the inclusion criteria, 27 patents reporting the benefits of complexation of ADDs with CDs were included. Expert opinion: The use of CDs can be considered an important tool for the optimization of physicochemical and pharmacological properties of ADDs, such as stability, solubility and bioavailability.

Does gamma irradiation affect physicochemical properties of honey?

PubMed

Hussein, S Z; Yusoff, K M; Makpol, S; Mohd Yusof, Y A

2014-01-01

Honey is a supersaturated solution of sugars, enriched with proteins, minerals, vitamins, organic acids and polyphenols. Gamma irradiation is a physical technique of food preservation which protects the honey from insects' and microbial contamination during storage. We investigated the effect of gamma irradiation on physicochemical properties in two types of Malaysian honey, Gelam and Nenas. Both honeys were irradiated at the dose 25 kGy in a cobalt-60 irradiator. The physicochemical properties pH, moisture, acidity, color, and sugar content as well as vitamins C and E, hydroxymethylfurfural (HMF) and mineral contents, for the irradiated and non-irradiated honeys were assessed. The results revealed that pH, acidity, minerals and sugar contents in both types of honey were not affected significantly by gamma irradiation, while moisture, vitamin E contents and HMF level decreased significantly with gamma irradiation. However, significant increased in color intensity and vitamin C were observed after gamma irradiation for both types of honey. In summary, gamma irradiation treatment of honey (in the dose mentioned above) did not cause significant changes in the physicochemical and mineral contents, except for significant alterations in color intensity, moisture, vitamins (C and E), and HMF contents.

Key fuel properties and engine performances of diesel-ethanol blends, using tetrahydrofuran as surfactant additive

NASA Astrophysics Data System (ADS)

Molea, A.; Visuian, P.; Barabás, I.; Suciu, R. C.; Burnete, N. V.

2017-10-01

In this paper there were presented researches related to preparation and characterization of physicochemical properties of diesel-ethanol blends stabilized with tetrahydrofuran as surfactant, in order to be used as fuels in compression ignition engines. The main spray characteristics and engine performances of these blends were evaluated by using AVL Fire software. In the first stage of the studies, commercial diesel was mixed with ethanol, in different concentrations (between 2% and 15% v/v), followed by the addition of tetrahydrofuran (THF) until the blends were miscible, i.e. the blends were stabilized. The experiments were done at room temperature (22 °C). The obtained blends were characterized in order to determine the chemical composition and physicochemical properties, i.e. density, kinematic viscosity, surface tension. UV-Vis spectroscopy was utilized in order to determine a semi-quantitative evaluation regarding the chemical composition of the prepared blends and chemical interaction between diesel, ethanol and THF. Based on the determined properties, the fuel spray characteristics, engine performances and emission characteristics were evaluated by simulation using the AVL Fire software. The obtained results regarding physicochemical properties of blends were compared with diesel. Some improvements were observed when operating with the prepared blends compared to diesel with respect to engine performances and emission characteristics. Based on physicochemical evaluation and computer simulation, it was demonstrated that diesel-ethanol-tetrahydrofuran blends can be used as alternative fuel in compression ignition engines.

An ultrastable conjugate of silver nanoparticles and protein formed through weak interactions

NASA Astrophysics Data System (ADS)

Brahmkhatri, Varsha P.; Chandra, Kousik; Dubey, Abhinav; Atreya, Hanudatta S.

2015-07-01

In recent years, silver nanoparticles (AgNPs) have attracted significant attention owing to their unique physicochemical, optical, conductive and antimicrobial properties. One of the properties of AgNPs which is crucial for all applications is their stability. In the present study we unravel a mechanism through which silver nanoparticles are rendered ultrastable in an aqueous solution in complex with the protein ubiquitin (Ubq). This involves a dynamic and reversible association and dissociation of ubiquitin from the surface of AgNP. The exchange occurs at a rate much greater than 25 s-1 implying a residence time of <40 ms for the protein. The AgNP-Ubq complex remains stable for months due to steric stabilization over a wide pH range compared to unconjugated AgNPs. NMR studies reveal that the protein molecules bind reversibly to AgNP with an approximate dissociation constant of 55 μM and undergo fast exchange. At pH > 4 the positively charged surface of the protein comes in contact with the citrate capped AgNP surface. Further, NMR relaxation-based experiments suggest that in addition to the dynamic exchange, a conformational rearrangement of the protein takes place upon binding to AgNP. The ultrastability of the AgNP-Ubq complex was found to be useful for its anti-microbial activity, which allowed the recycling of this complex multiple times without the loss of stability. Altogether, the study provides new insights into the mechanism of protein-silver nanoparticle interactions and opens up new avenues for its application in a wide range of systems.In recent years, silver nanoparticles (AgNPs) have attracted significant attention owing to their unique physicochemical, optical, conductive and antimicrobial properties. One of the properties of AgNPs which is crucial for all applications is their stability. In the present study we unravel a mechanism through which silver nanoparticles are rendered ultrastable in an aqueous solution in complex with the protein ubiquitin (Ubq). This involves a dynamic and reversible association and dissociation of ubiquitin from the surface of AgNP. The exchange occurs at a rate much greater than 25 s-1 implying a residence time of <40 ms for the protein. The AgNP-Ubq complex remains stable for months due to steric stabilization over a wide pH range compared to unconjugated AgNPs. NMR studies reveal that the protein molecules bind reversibly to AgNP with an approximate dissociation constant of 55 μM and undergo fast exchange. At pH > 4 the positively charged surface of the protein comes in contact with the citrate capped AgNP surface. Further, NMR relaxation-based experiments suggest that in addition to the dynamic exchange, a conformational rearrangement of the protein takes place upon binding to AgNP. The ultrastability of the AgNP-Ubq complex was found to be useful for its anti-microbial activity, which allowed the recycling of this complex multiple times without the loss of stability. Altogether, the study provides new insights into the mechanism of protein-silver nanoparticle interactions and opens up new avenues for its application in a wide range of systems. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03047a

A facile strategy to design zeolite L crystals with tunable morphology and surface architecture.

PubMed

Lupulescu, Alexandra I; Kumar, Manjesh; Rimer, Jeffrey D

2013-05-01

Tailoring the anisotropic growth rates of materials to achieve desired structural outcomes is a pervasive challenge in synthetic crystallization. Here we discuss a method to selectively control the growth of zeolite crystals, which are used extensively in a wide range of industrial applications. This facile method cooperatively tunes crystal properties, such as morphology and surface architecture, through the use of inexpensive, commercially available chemicals with specificity for binding to crystallographic surfaces and mediating anisotropic growth. We examined over 30 molecules as potential zeolite growth modifiers (ZGMs) of zeolite L (LTL type) crystallization. ZGM efficacy was quantified through a combination of macroscopic (bulk) and microscopic (surface) investigations that identified modifiers capable of dramatically altering the cylindrical morphology of LTL crystals. We demonstrate an ability to tailor properties critical to zeolite performance, such as external porous surface area, crystal shape, and pore length, which can enhance sorbate accessibility to LTL pores, tune the supramolecular organization of guest-host composites, and minimize the diffusion path length, respectively. We report that a synergistic combination of ZGMs and the judicious adjustment of synthesis parameters produce LTL crystals with unique surface features, and a range of length-to-diameter aspect ratios spanning 3 orders of magnitude. A systematic examination of different ZGM structures and molecular compositions (i.e., hydrophobicity and binding moieties) reveal interesting physicochemical properties governing their efficacy and specificity. Results of this study suggest this versatile strategy may prove applicable for a host of framework types to produce unrivaled materials that have eluded more conventional techniques.

Effects of different radio-opacifying agents on physicochemical and biological properties of a novel root-end filling material

PubMed Central

Lü, Xiao-Ying; Liu, Gen-Di

2018-01-01

Background/Purpose Radio-opacity is an essential attribute of ideal root-end filling materials because it is important for clinicians to observe root canal filling and to facilitate the follow-up instructions. The novel root-end filling material (NRFM) has good cytocompatibility and physicochemical properties but low intrinsic radio-opacity value. To improve its radio-opacity value, three novel radio-opaque root-end filling materials (NRRFMs) were developed by adding barium sulphate (NRFM-Ba), bismuth trioxide (NRFM-Bi) and zirconium dioxide (NRFM-Zr) to NRFM, respectively. The purpose of this study was to identify the suitable radio-opacifier for NRFM through evaluating their physicochemical and biological properties, in comparison with NRFM and glass ionomer cement (GIC). Methods NRRFMs were characterized using X-ray diffraction (XRD) and Fourier transform infrared spectrophotometry (FTIR). Physicochemical properties including setting time, compressive strength, porosity, pH variation, solubility, washout resistance, contact angle and radiopacity were investigated. Cytocompatibility of both freshly mixed and set NRRFMs was investigated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Alkaline phosphatase (ALP) activity assay and alizarin red staining were used to investigate the osteogenic differentiation potential of NRFM-Zr. Data were analyzed using two-way ANOVA (pH variation, solubility and ALP activity) and one-way ANOVA (for the other variables). Results (1) NRRFMs were primarily composed of hydroxyapatite, calcium carboxylate salt and the corresponding radio-opacity agents (barium sulphate, bismuth trioxide or zirconium dioxide). (2) Besides similar physicochemical properties in terms of setting time, pH variation, solubility, washout resistance and contact angle to NRFM, NRFM-Bi and NRFM-Zr exhibited lower porosity and greater compressive strength after being set for 7 days and their radio-opacity were greater than the 3 mm aluminium thickness specified in ISO 6876 (2001). (3) MTT assay revealed that freshly mixed and set NRFM-Zr presented better cell viability than NRFM-Ba and NRFM-Bi at 24 hours and 48 hours (P<0.05). (4) NRFM-Zr significantly enhanced ALP activity and calcium formation of human osteoblast-like Saos-2 cells when compared with negative group and GIC (P<0.05). Conclusion NRFM-Zr presents desirable physicochemical and biological properties, thus zirconium dioxide may be a suitable radio-opacifier for NRFM. PMID:29420559

Effects of different radio-opacifying agents on physicochemical and biological properties of a novel root-end filling material.

PubMed

Chen, Yao-Zhong; Lü, Xiao-Ying; Liu, Gen-Di

2018-01-01

Radio-opacity is an essential attribute of ideal root-end filling materials because it is important for clinicians to observe root canal filling and to facilitate the follow-up instructions. The novel root-end filling material (NRFM) has good cytocompatibility and physicochemical properties but low intrinsic radio-opacity value. To improve its radio-opacity value, three novel radio-opaque root-end filling materials (NRRFMs) were developed by adding barium sulphate (NRFM-Ba), bismuth trioxide (NRFM-Bi) and zirconium dioxide (NRFM-Zr) to NRFM, respectively. The purpose of this study was to identify the suitable radio-opacifier for NRFM through evaluating their physicochemical and biological properties, in comparison with NRFM and glass ionomer cement (GIC). NRRFMs were characterized using X-ray diffraction (XRD) and Fourier transform infrared spectrophotometry (FTIR). Physicochemical properties including setting time, compressive strength, porosity, pH variation, solubility, washout resistance, contact angle and radiopacity were investigated. Cytocompatibility of both freshly mixed and set NRRFMs was investigated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Alkaline phosphatase (ALP) activity assay and alizarin red staining were used to investigate the osteogenic differentiation potential of NRFM-Zr. Data were analyzed using two-way ANOVA (pH variation, solubility and ALP activity) and one-way ANOVA (for the other variables). (1) NRRFMs were primarily composed of hydroxyapatite, calcium carboxylate salt and the corresponding radio-opacity agents (barium sulphate, bismuth trioxide or zirconium dioxide). (2) Besides similar physicochemical properties in terms of setting time, pH variation, solubility, washout resistance and contact angle to NRFM, NRFM-Bi and NRFM-Zr exhibited lower porosity and greater compressive strength after being set for 7 days and their radio-opacity were greater than the 3 mm aluminium thickness specified in ISO 6876 (2001). (3) MTT assay revealed that freshly mixed and set NRFM-Zr presented better cell viability than NRFM-Ba and NRFM-Bi at 24 hours and 48 hours (P<0.05). (4) NRFM-Zr significantly enhanced ALP activity and calcium formation of human osteoblast-like Saos-2 cells when compared with negative group and GIC (P<0.05). NRFM-Zr presents desirable physicochemical and biological properties, thus zirconium dioxide may be a suitable radio-opacifier for NRFM.

Gelling ability of kefiran in the presence of sucrose and fructose and physicochemical characterization of the resulting cryogels.

PubMed

Zavala, Lucía; Roberti, Paula; Piermaria, Judith A; Abraham, Analía G

2015-08-01

In this work, the influence of sucrose and fructose on the gel-forming capacity of kefiran was investigated as well as the physicochemical characteristics of the resulting gels. The addition of sugar to gel-forming solutions did not alter the pseudoplastic flow properties of kefiran solutions and after one freeze-thaw cycle translucent gels with high water-holding capability were obtained. A highly porous matrix was revealed by microscopy whose pore size varied with sugar concentration. Sucrose and fructose had different effects on the rheological characteristics of sugar-kefiran gels. An increment in the strength of the gels with progressive concentrations of sucrose was evidenced by an increase in the elastic modulus (G'), indicating that sucrose reinforces the binding interactions between the polymer molecules (p ≤ 0.05). A drastic reduction in elastic modulus occurred, however, when 50.0 % w/w sucrose was added to kefiran gels, resulting in less elasticity. In contrast, when fructose was added to kefiran gels, elastic modulus decreased slightly with progressive sugar concentrations up to 10 %, thereafter increasing up to 50 % (p ≤ 0.05). Supplementation with up to 30 % sugar contributed to water retention and increased the viscous modulus. The relative increment in the elastic and viscous moduli elevated the loss tangent (tanδ) depending on the type and concentration of sugar. Sugars (sucrose, fructose) present in the matrix of the polysaccharide networks modified water-polymer and polymer-polymer interactions and consequently changed the gels' physicochemical characteristics, thus allowing the possibility of selecting the appropriate formulation through tailor-made kefiran cryogels.

Influence of pH control in the formation of inclusion bodies during production of recombinant sphingomyelinase-D in Escherichia coli.

PubMed

Castellanos-Mendoza, Andrea; Castro-Acosta, Ricardo M; Olvera, Alejandro; Zavala, Guadalupe; Mendoza-Vera, Miguel; García-Hernández, Enrique; Alagón, Alejandro; Trujillo-Roldán, Mauricio A; Valdez-Cruz, Norma A

2014-09-12

Inclusion bodies (IBs) are aggregated proteins that form clusters when protein is overexpressed in heterologous expression systems. IBs have been considered as non-usable proteins, but recently they are being used as functional materials, catalytic particles, drug delivery agents, immunogenic structures, and as a raw material in recombinant therapeutic protein purification. However, few studies have been made to understand how culture conditions affect the protein aggregation and the physicochemical characteristics that lead them to cluster. The objective of our research was to understand how pH affects the physicochemical properties of IBs formed by the recombinant sphingomyelinase-D of tick expressed in E. coli BL21-Gold (DE3) by evaluating two pH culture strategies. Uncontrolled pH culture conditions favored recombinant sphingomyelinase-D aggregation and IB formation. The IBs of sphingomyelinase-D produced under controlled pH at 7.5 and after 24 h were smaller (<500 nm) than those produced under uncontrolled pH conditions (>500 nm). Furthermore, the composition, conformation and β-structure formation of the aggregates were different. Under controlled pH conditions in comparison to uncontrolled conditions, the produced IBs presented higher resistance to denaturants and proteinase-K degradation, presented β-structure, but apparently as time passes the IBs become compacted and less sensitive to amyloid dye binding. The manipulation of the pH has an impact on IB formation and their physicochemical characteristics. Particularly, uncontrolled pH conditions favored the protein aggregation and sphingomyelinase-D IB formation. The evidence may lead to find methodologies for bioprocesses to obtain biomaterials with particular characteristics, extending the application possibilities of the inclusion bodies.

Liposomes for Topical Use: A Physico-Chemical Comparison of Vesicles Prepared from Egg or Soy Lecithin

PubMed Central

Budai, Lívia; Kaszás, Nóra; Gróf, Pál; Lenti, Katalin; Maghami, Katayoon; Antal, István; Klebovich, Imre; Petrikovics, Ilona; Budai, Marianna

2013-01-01

Developments in nanotechnology and in the formulation of liposomal systems provide the opportunity for cosmetic dermatology to design novel delivery systems. Determination of their physico-chemical parameters has importance when developing a nano-delivery system. The present study highlights some technological aspects/characteristics of liposomes formulated from egg or soy lecithins for topical use. Alterations in the pH, viscosity, surface tension, and microscopic/macroscopic appearance of these vesicular systems were investigated. The chemical composition of the two types of lecithin was checked by mass spectrometry. Caffeine, as a model molecule, was encapsulated into multilamellar vesicles prepared from the two types of lecithin: then zeta potential, membrane fluidity, and encapsulation efficiency were compared. According to our observations, samples prepared from the two lecithins altered the pH in opposite directions: egg lecithin increased it while soy lecithin decreased it with increased lipid concentration. Our EPR spectroscopic results showed that the binding of caffeine did not change the membrane fluidity in the temperature range of possible topical use (measured between 2 and 50 °C). Combining our results on encapsulation efficiency for caffeine (about 30% for both lecithins) with those on membrane fluidity data, we concluded that the interaction of caffeine with the liposomal membrane does not change the rotational motion of the lipid molecules close to the head group region. In conclusion, topical use of egg lecithin for liposomal formulations can be preferred if there are no differences in the physico-chemical properties due to the encapsulated drugs, because the physiological effects of egg lecithin vesicles on skin are significantly better than that of soy lecithin liposomes. PMID:24482779

Thermal Oxidation Induces Lipid Peroxidation and Changes in the Physicochemical Properties and β-Carotene Content of Arachis Oil

PubMed Central

Falade, Ayodeji Osmund

2015-01-01

This study sought to investigate the effect of thermal oxidation on the physicochemical properties, malondialdehyde, and β-carotene content of arachis oil. Pure arachis oil was heated for 20 mins with a corresponding temperature of 220°C. Thereafter, changes in the physicochemical properties (acid, iodine, and peroxide values) of the oil samples were determined. Subsequently, the level of lipid peroxidation was determined using change in malondialdehyde content. Then, the total carotenoid and β-carotene contents were evaluated using spectrophotometric method and high performance liquid chromatography, respectively. The results of the study revealed a significant increase (P < 0.05) in the acid and peroxide values and malondialdehyde concentration of the heated oil when compared with the fresh arachis oil. In contrast, a significant decrease (P < 0.05) was observed in the iodine value, total carotenoid, 13-cis-, 15-cis-, trans-, and 9-cis-β-carotene, and total β-carotene content of the heated oil. Hence, thermal oxidation induced lipid peroxidation and caused changes in the physicochemical properties and carotenoid contents of arachis oil, thereby reducing its nutritive value and health benefit. Therefore, cooking and frying with arachis oil for a long period might not be appropriate as this might lead to a loss of significant amount of the insignificant β-carotene in arachis oil. PMID:26904665

Study on biogenic amines in various dry salted fish consumed in China

NASA Astrophysics Data System (ADS)

Wu, Yanyan; Chen, Yufeng; Li, Laihao; Yang, Xianqing; Yang, Shaoling; Lin, Wanling; Zhao, Yongqiang; Deng, Jianchao

2016-08-01

This study was carried out to investigate the biogenic amines (BAs), physicochemical property and microorganisms in dry salted fish, a traditional aquatic food consumed in China. Forty three samples of dry salted fish were gathered from retail and wholesale markets and manufacturers, which had been produced in various regions in China. Cadaverine (CAD) and putrescine (PUT) were quantitatively the most common biogenic amines. About 14% of the samples exceeded the histamine content standards established by the FDA and/or EU. The highest histamine content was found in Silver pomfret ( Pampus argenteus) (347.79 mg kg-1). Five of forty three samples exceeded the acceptable content of TYR (100 mg kg-1), and 23.26% of dried-salted fish contained high contents of biogenic amines (above 600 mg kg-1). In addition, species, regions, pickling processes and drying methods made the physicochemical property, microorganisms and biogenic amines in dry salted fish to be different to some extents. The total plate count (TPC) was much higher than that of total halophilic bacteria in all samples. The biogenic amines, physicochemical property and microbiological counts exhibited large variations among samples. Furthermore, no significant correlation between biogenic amines and physicochemical property and TPC was observed. This study indicated that dry salted fish may still present healthy risk for BAs, depending on the processing methods, storage conditions among others.

Jujube honey from China: physicochemical characteristics and mineral contents.

PubMed

Zhou, Juan; Suo, Zhirong; Zhao, Pinpin; Cheng, Ni; Gao, Hui; Zhao, Jing; Cao, Wei

2013-03-01

We investigated and compared the physicochemical properties (moisture, color, ash, pH, electrical conductivity, free acidity, lactonic acidity, total acidity, fructose, glucose, sucrose, diastase activity, and HMF) and mineral contents (Al, Ca, Co, Cr, Cu, Fe, K, Li, Mg, Mn, Na, Ni, As, Cd, Pb, and Zn), as well as total proline and total protein contents of 23 jujube honey samples collected from different regions of China. The mineral content was determined by inductively coupled plasma-optical emission spectrometry (ICP-OES). The physicochemical values were in the range of approved limits (conforming to EU legislation) in all 23 samples. The physicochemical properties of jujube honey showed significant variations among samples. The mean pH value of the jujube honeys was 6.71. The most abundant minerals were potassium, calcium, sodium, and magnesium, ranging between 1081.4 and 2642.9, 97.1 and 194.2, 7.79 and 127.8, and 10.36 and 24.67 mg/kg, respectively, and potassium made up 71% of the total mineral content. This study demonstrated remarkable variation in physicochemical parameters and mineral contents of jujube honey, mainly depending on its geographic source. © 2013 Institute of Food Technologists®

Distribution of lacosamide in the rat brain assessed by in vitro slice technique.

PubMed

Gáll, Zsolt; Vancea, Szende

2018-01-01

Lacosamide is a newer anticonvulsant and is the only one that enhances the slow inactivation of voltage gated sodium channels. It is also claimed to have disease-modifying potential, but its pharmacokinetic properties have been much less discussed in the literature. In rats, lacosamide shows restricted distribution to tissues, and the brain-to-plasma partition coefficient (K p ) is only 0.553. In this study, the brain disposition of lacosamide was evaluated in rat brains, and its neuropharmacokinetic parameters (i.e., protein binding and intracellular accumulation) were assessed using in vitro methods. Brain slice experiments and brain homogenate binding studies were performed for several drugs acting on the central nervous system, and drugs were assayed by using a liquid chromatography-mass spectrometry system. By applying a combined approach, it was found that (1) the unbound volume of distribution in the brain for lacosamide (V u,brain  = 1.37) was lower than that of other classical anticonvulsants; (2) the unbound fraction of lacosamide in the brain (0.899) was slightly lower than its unbound fraction in plasma (0.96); (3) the unbound intracellular-to-extracellular concentration ratio of lacosamide was 1.233, meaning that lacosamide was accumulated in the intracellular space because of its physicochemical properties and zwitterionic structure; and (4) the unbound brain-to-plasma concentration ratio of lacosamide was lower than the total brain-to-plasma concentration ratio (K p,uu,brain  = 0.42 vs. K p  = 0.553). In conclusion, the limited brain distribution of lacosamide is not related to its nonspecific protein-binding capacity; rather, an active transport mechanism across the blood-brain barrier may be involved, which reduces the anticonvulsant and/or antiepileptogenic actions of this drug.

In silico approaches to predict the potential of milk protein-derived peptides as dipeptidyl peptidase IV (DPP-IV) inhibitors.

PubMed

Nongonierma, Alice B; Mooney, Catherine; Shields, Denis C; FitzGerald, Richard J

2014-07-01

Molecular docking of a library of all 8000 possible tripeptides to the active site of DPP-IV was used to determine their binding potential. A number of tripeptides were selected for experimental testing, however, there was no direct correlation between the Vina score and their in vitro DPP-IV inhibitory properties. While Trp-Trp-Trp, the peptide with the best docking score, was a moderate DPP-IV inhibitor (IC50 216μM), Lineweaver and Burk analysis revealed its action to be non-competitive. This suggested that it may not bind to the active site of DPP-IV as assumed in the docking prediction. Furthermore, there was no significant link between DPP-IV inhibition and the physicochemical properties of the peptides (molecular mass, hydrophobicity, hydrophobic moment (μH), isoelectric point (pI) and charge). LIGPLOTs indicated that competitive inhibitory peptides were predicted to have both hydrophobic and hydrogen bond interactions with the active site of DPP-IV. DPP-IV inhibitory peptides generally had a hydrophobic or aromatic amino acid at the N-terminus, preferentially a Trp for non-competitive inhibitors and a broader range of residues for competitive inhibitors (Ile, Leu, Val, Phe, Trp or Tyr). Two of the potent DPP-IV inhibitors, Ile-Pro-Ile and Trp-Pro (IC50 values of 3.5 and 44.2μM, respectively), were predicted to be gastrointestinally/intestinally stable. This work highlights the needs to test the assumptions (i.e. competitive binding) of any integrated strategy of computational and experimental screening, in optimizing screening. Future strategies targeting allosteric mechanisms may need to rely more on structure-activity relationship modeling, rather than on docking, in computationally selecting peptides for screening. Copyright © 2014 Elsevier Inc. All rights reserved.

Effect of hydroxypropylcellulose and Tween 80 on physicochemical properties and bioavailability of ezetimibe-loaded solid dispersion.

PubMed

Rashid, Rehmana; Kim, Dong Wuk; Din, Fakhar Ud; Mustapha, Omer; Yousaf, Abid Mehmood; Park, Jong Hyuck; Kim, Jong Oh; Yong, Chul Soon; Choi, Han-Gon

2015-10-05

The purpose of this research was to evaluate the effect of the HPC (hydroxypropylcellulose) and Tween 80 on the physicochemical properties and oral bioavailability of ezetimibe-loaded solid dispersions. The binary solid dispersions were prepared with drug and various amounts of HPC. Likewise, ternary solid dispersions were prepared with different ratios of drug, HPC and Tween 80. Both types of solid dispersions were prepared using the solvent evaporation method. Their aqueous solubility, physicochemical properties, dissolution and oral bioavailability were investigated in comparison with the drug powder. All the solid dispersions significantly improved the drug solubility and dissolution. As the amount of HPC increased in the binary solid dispersions to 10-fold, the drug solubility and dissolution were increased accordingly. However, further increase in HPC did not result in significant differences among them. Similarly, up to 0.1-fold, Tween 80 increased the drug solubility in the ternary solid dispersions followed by no significant change. However, Tween 80 hardly affected the drug dissolution. The physicochemical analysis proved that the drug in binary and ternary solid dispersion was existed in the amorphous form. The particle-size measurements of these formulations were also not significantly different from each other, which showed that Tween 80 had no impact on physicochemical properties. The ezetimibe-loaded binary and ternary solid dispersions gave 1.6- and 1.8-fold increased oral bioavailability in rats, respectively, as compared to the drug powder; however, these values were not significantly different from each other. Thus, HPC greatly affected the solubility, dissolution and oral bioavailability of drug, but Tween 80 hardly did. Furthermore, this ezetimibe-loaded binary solid dispersion prepared only with HPC would be suggested as a potential formulation for oral administration of ezetimibe. Copyright © 2015 Elsevier Ltd. All rights reserved.

Investigation on physicochemical properties of plasma-activated water for the application of medical device sterilization

NASA Astrophysics Data System (ADS)

Abuzairi, Tomy; Ramadhanty, Savira; Puspohadiningrum, Dini Fithriaty; Ratnasari, Anita; Poespawati, Nji Raden; Purnamaningsih, Retno Wigajatri

2018-02-01

Plasma activated water (PAW) is a new approach to bacterial inactivation while ensuring safety and maintaining the properties of the material sterilized. Reported research imply that PAW has been effective for inactivation of bacteria. In this paper, plasma treatment using atmospheric pressure plasma was demonstrated. Physicochemical properties such as pH, temperature, ORP, and nitrite concentration were assessed. The results suggest that plasma treatment causes acidification on water and generate reactive species, creating an environment suitable for killing bacteria. Therefore, plasma activated water is an assuring method for medical devices sterilization.

Isolation and purification of wheat germ agglutinin and analysis of its properties

NASA Astrophysics Data System (ADS)

Wang, Han

2017-12-01

In this paper, the wheat germ agglutinin was isolated and purified by affinity chromatography of chicken ovomucoid as ligand. The physicochemical properties were analyzed. The chicken ovomucoid was isolated from egg white and conjugated to affinity chromatography column agarose gel to prepare affinity adsorbent. The crude extract of wheat germ was freezedried by affinity chromatography. The physicochemical properties were analyzed by SDSpolyacrylamide gel electrophoresis and isoelectric focusing electrophoresis. And the relative molecular mass and isoelectric point of wheat germ agglutinin were obtained, and the high efficiency of purification of wheat germ agglutinin was proved by affinity chromatography.

Heterocyclic cationic gemini surfactants: a comparative overview of their synthesis, self-assembling, physicochemical, and biological properties.

PubMed

Sharma, Vishnu Dutt; Ilies, Marc A

2014-01-01

Gemini surfactants (GS) are presently receiving substantial attention due to their special self-assembling properties and unique interfacial activity. This comprehensive review is focused on positively charged heterocyclic GS, presenting their major synthetic access routes and examining the impact of structural elements on physicochemical and aggregation properties of this class of amphiphiles. Interaction of geminis surfactants with cells and their biological properties as novel transfection agents are emphasized through a detailed structure-activity relationship analysis. Throughout the review we have also presented the properties of selected ammonium GS, simple surfactants and lipid congeners, in order to emphasize the advantages conferred by using heterocyclic polar heads in GS design. © 2012 Wiley Periodicals, Inc.

Static and transport properties of alkyltrimethylammonium cation-based room-temperature ionic liquids.

PubMed

Seki, Shiro; Tsuzuki, Seiji; Hayamizu, Kikuko; Serizawa, Nobuyuki; Ono, Shimpei; Takei, Katsuhito; Doi, Hiroyuki; Umebayashi, Yasuhiro

2014-05-01

We have measured physicochemical properties of five alkyltrimethylammonium cation-based room-temperature ionic liquids and compared them with those obtained from computational methods. We have found that static properties (density and refractive index) and transport properties (ionic conductivity, self-diffusion coefficient, and viscosity) of these ionic liquids show close relations with the length of the alkyl chain. In particular, static properties obtained by experimental methods exhibit a trend complementary to that by computational methods (refractive index ∝ [polarizability/molar volume]). Moreover, the self-diffusion coefficient obtained by molecular dynamics (MD) simulation was consistent with the data obtained by the pulsed-gradient spin-echo nuclear magnetic resonance technique, which suggests that computational methods can be supplemental tools to predict physicochemical properties of room-temperature ionic liquids.

The Effects of Molecular Properties on Ready Biodegradation of Aromatic Compounds in the OECD 301B CO2 Evolution Test.

PubMed

He, Mei; Mei, Cheng-Fang; Sun, Guo-Ping; Li, Hai-Bei; Liu, Lei; Xu, Mei-Ying

2016-07-01

Ready biodegradation is the primary biodegradability of a compound, which is used for discriminating whether a compound could be rapidly and readily biodegraded in the natural ecosystems in a short period and has been applied extensively in the environmental risk assessment of many chemicals. In this study, the effects of 24 molecular properties (including 2 physicochemical parameters, 10 geometrical parameters, 6 topological parameters, and 6 electronic parameters) on the ready biodegradation of 24 kinds of synthetic aromatic compounds were investigated using the OECD 301B CO2 Evolution test. The relationship between molecular properties and ready biodegradation of these aromatic compounds varied with molecular properties. A significant inverse correlation was found for the topological parameter TD, five geometrical parameters (Rad, CAA, CMA, CSEV, and N c), and the physicochemical parameter K ow, and a positive correlation for two topological parameters TC and TVC, whereas no significant correlation was observed for any of the electronic parameters. Based on the correlations between molecular properties and ready biodegradation of these aromatic compounds, the importance of molecular properties was demonstrated as follows: geometrical properties > topological properties > physicochemical properties > electronic properties. Our study first demonstrated the effects of molecular properties on ready biodegradation by a number of experiment data under the same experimental conditions, which should be taken into account to better guide the ready biodegradation tests and understand the mechanisms of the ready biodegradation of aromatic compounds.

Interactions of cisplatin analogues with lysozyme: a comparative analysis.

PubMed

Ferraro, Giarita; De Benedictis, Ilaria; Malfitano, Annamaria; Morelli, Giancarlo; Novellino, Ettore; Marasco, Daniela

2017-10-01

The biophysical characterization of drug binding to proteins plays a key role in structural biology and in the discovery and optimization of drug discovery processes. The search for optimal combinations of biophysical techniques that can correctly and efficiently identify and quantify binding of metal-based drugs to their final target is challenging, due to the physicochemical properties of these agents. Different cisplatin derivatives have shown different citotoxicities in most common cancer lines, suggesting that they exert their biological activity via different mechanisms of action. Here we carried out a comparative analysis, by studying the behaviours of three Pt-compounds under the same experimental conditions and binding assays to properly deepen the determinants of the different MAOs. Indeed we compared the results obtained using surface plasmon resonance, isothermal titration calorimetry, fluorescence spectroscopy and thermal shift assays based on circular dichroism experiments in the characterization of the formation of adducts obtained upon reaction of cisplatin, carboplatin and iodinated analogue of cisplatin, cis-Pt (NH 3 ) 2 I 2 , with the model protein hen egg white lysozyme, both at neutral and acid pHs. Further we reasoned on the applicability of employed techniques for the study the thermodynamics and kinetics of the reaction of a metallodrug with a protein and to reveal which information can be obtained using a combination of these analyses. Data were discussed on the light of the existing structural data collected on the platinated protein.

Mathematical Modeling of Herpes Simplex Virus Distribution in Solid Tumors: Implications for Cancer Gene Therapy

PubMed Central

Mok, Wilson; Stylianopoulos, Triantafyllos; Boucher, Yves; Jain, Rakesh K.

2010-01-01

Purpose Although oncolytic viral vectors show promise for the treatment of various cancers, ineffective initial distribution and propagation throughout the tumor mass often limit the therapeutic response. A mathematical model is developed to describe the spread of herpes simplex virus from the initial injection site. Experimental Design The tumor is modeled as a sphere of radius R. The model incorporates reversible binding, interstitial diffusion, viral degradation, and internalization and physiologic parameters. Three species are considered as follows: free interstitial virus, virus bound to cell surfaces, and internalized virus. Results This analysis reveals that both rapid binding and internalization as well as hindered diffusion contain the virus to the initial injection volume, with negligible spread to the surrounding tissue. Unfortunately, increasing the dose to saturate receptors and promote diffusion throughout the tumor is not a viable option: the concentration necessary would likely compromise safety. However, targeted modifications to the virus that decrease the binding affinity have the potential to increase the number of infected cells by 1.5-fold or more. An increase in the effective diffusion coefficient can result in similar gains. Conclusions This analysis suggests criteria by which the potential response of a tumor to oncolytic herpes simplex virus therapy can be assessed. Furthermore, it reveals the potential of modifications to the vector delivery method, physicochemical properties of the virus, and tumor extracellular matrix composition to enhance efficacy. PMID:19318482

Development of new PTK7-targeting aptamer-fluorescent and -radiolabelled probes for evaluation as molecular imaging agents: Lymphoma and melanoma in vivo proof of concept.

PubMed

Calzada, Victoria; Moreno, María; Newton, Jessica; González, Joel; Fernández, Marcelo; Gambini, Juan Pablo; Ibarra, Manuel; Chabalgoity, Alejandro; Deutscher, Susan; Quinn, Thomas; Cabral, Pablo; Cerecetto, Hugo

2017-02-01

Aptamers are single-stranded oligonucleotides that recognize molecular targets with high affinity and specificity. Aptamer that selectively bind to the protein tyrosine kinase-7 (PTK7) receptor, overexpressed on many cancers, has been labelled as probes for molecular imaging of cancer. Two new PTK7-targeting aptamer probes were developed by coupling frameworks from the fluorescent dye AlexaFluor647 or the 6-hydrazinonicotinamide (HYNIC) chelator-labelled to 99m Tc. The derivatizations via a 5'-aminohexyl terminal linker were done at room temperature and under mild buffer conditions. Physicochemical and biological controls for both imaging agents were performed verifying the integrity of the aptamer-conjugates by HPLC. Recognition of melanoma (B16F1) and lymphoma (A20) mouse cell lines by the aptamer was studied using cell binding, flow cytometry and confocal microscopy. Finally, in vivo imaging studies in tumour-bearing mice were performed. The new probes were able to bind to melanoma and lymphoma cell lines in vitro, the in vivo imaging in tumour-bearing mice showed different uptake behaviours showing for the fluorescent conjugate good uptake by B cell lymphoma while the radiolabelled conjugate did not display tumour uptake due to its high extravascular distribution, and both showed rapid clearance properties in tumour-bearing mice. Copyright © 2016 Elsevier Ltd. All rights reserved.

Beneficial reuse of fly ashes in geotechnical engineering with physicochemical and electron microscopic methods.

DOT National Transportation Integrated Search

2013-06-01

The sedimentation behavior of fine grained soil is largely dependent on its pore fluid chemistry. Physicochemical properties of the : pore fluid, such as ionic strength and pH, could greatly influence the micro structure of kaolinite which in turn in...

Application of ultra high pressure (UHP) in starch chemistry.

PubMed

Kim, Hyun-Seok; Kim, Byung-Yong; Baik, Moo-Yeol

2012-01-01

Ultra high pressure (UHP) processing is an attractive non-thermal technique for food treatment and preservation at room temperature, with the potential to achieve interesting functional effects. The majority of UHP process applications in food systems have focused on shelf-life extension associated with non-thermal sterilization and a reduction or increase in enzymatic activity. Only a few studies have investigated modifications of structural characteristics and/or protein functionalities. Despite the rapid expansion of UHP applications in food systems, limited information is available on the effects of UHP on the structural and physicochemical properties of starch and/or its chemical derivatives included in most processed foods as major ingredients or minor additives. Starch and its chemical derivatives are responsible for textural and physical properties of food systems, impacting their end-use quality and/or shelf-life. This article reviews UHP processes for native (unmodified) starch granules and their effects on the physicochemical properties of UHP-treated starch. Furthermore, functional roles of UHP in acid-hydrolysis, hydroxypropylation, acetylation, and cross-linking reactions of starch granules, as well as the physicochemical properties of UHP-assisted starch chemical derivatives, are discussed.

Effect of white, red and black ginseng on physicochemical properties and ginsenosides.

PubMed

Jin, Yan; Kim, Yeon-Ju; Jeon, Ji-Na; Wang, Chao; Min, Jin-Woo; Noh, Hae-Yong; Yang, Deok-Chun

2015-06-01

A systematic comparison of the ginsenosides and physicochemical properties of white ginseng (WG), red ginseng (RG) and black ginseng (BG) was performed. The purpose of the present study was to identify the effects of the physicochemical properties by steaming process. During the steaming process, ginsenosides transform into specific ginsenosides by hydrolysis, dehydration and isomerization at C-3, C-6 or C-20. Steaming ginseng led to a significant increase in reducing sugar, acidic polysaccharide and phenolic compounds content. Antioxidative properties were investigated using the DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging activity, compared with BHA (Butylated hydroxyanisole). RG and BG exhibited higher antioxidant activity than WG. The maximum residue level for Benzo(a)pyrene was established to 5 μg/kg in food products. The levels of benzo(a)pyrene in WG and RG were not detected. Benzo(a)pyrene was detected in the BG, the content was 0.17 μg/kg. The scientific achievements of the present study could help consumers to choose different type of ginseng products available on the market.

Study on the Antimicrobial Properties of Citrate-Based Biodegradable Polymers

PubMed Central

Su, Lee-Chun; Xie, Zhiwei; Zhang, Yi; Nguyen, Kytai Truong; Yang, Jian

2014-01-01

Citrate-based polymers possess unique advantages for various biomedical applications since citric acid is a natural metabolism product, which is biocompatible and antimicrobial. In polymer synthesis, citric acid also provides multiple functional groups to control the crosslinking of polymers and active binding sites for further conjugation of biomolecules. Our group recently developed a number of citrate-based polymers for various biomedical applications by taking advantage of their controllable chemical, mechanical, and biological characteristics. In this study, various citric acid derived biodegradable polymers were synthesized and investigated for their physicochemical and antimicrobial properties. Results indicate that citric acid derived polymers reduced bacterial proliferation to different degrees based on their chemical composition. Among the studied polymers, poly(octamethylene citrate) showed ~70–80% suppression to microbe proliferation, owing to its relatively higher ratio of citric acid contents. Crosslinked urethane-doped polyester elastomers and biodegradable photoluminescent polymers also exhibited significant bacteria reduction of ~20 and ~50% for Staphylococcus aureus and Escherichia coli, respectively. Thus, the intrinsic antibacterial properties in citrate-based polymers enable them to inhibit bacteria growth without incorporation of antibiotics, silver nanoparticles, and other traditional bacteria-killing agents suggesting that the citrate-based polymers are unique beneficial materials for wound dressing, tissue engineering, and other potential medical applications where antimicrobial property is desired. PMID:25023605

Assessment of Human Lung Macrophages After Exposure to Multi-Walled Carbon Nanotubes. Part 1. Cytotoxicity

DTIC Science & Technology

2011-01-01

animals) to gain a better understanding between their physicochemical properties and bio -effects. Keywords: U937 Cell, MWNTs, MWNT-COOH, ROS. 1...complex (i.e., cells vs. whole animals) to gain a better understanding between their physicochemical properties and bio -effects. 4. MATERIAL AND METHODS...Roach, G. A. M. Reynolds, and T. R. Webb, Tox. Sci. 77, 117 (2004). 3. C. W. Lam, J. T. James , R. McCluskey, and R. L. Hunter, Toxicol. Lett. 77, 126

Synthesis and Evaluation of Neuroprotective Selenoflavanones

PubMed Central

Choi, Yong-Sung; Kim, Dong-Myung; Kim, Yoon-Jung; Yang, Sai; Lee, Kyung-Tae; Ryu, Jong Hoon; Jeong, Jin-Hyun

2015-01-01

The physicochemical properties and antioxidant activity of a molecule could be improved by the substitution of an oxygen atom in a molecule with selenium. We synthesized selenoflavanones and flavanones to evaluate their neuroprotective effects. The selenoflavanones showed improved physicochemical properties, suggestive of the ability to pass through the blood-brain barrier (BBB). They showed in vitro antioxidant effects against hydrogen peroxide, and did not result in severe cytotoxicity. Moreover, infarction volumes in a transient ischemia mouse model were significantly reduced by the selenoflavanone treatments. PMID:26690420

Pharmaceutical cocrystals: an overview.

PubMed

Qiao, Ning; Li, Mingzhong; Schlindwein, Walkiria; Malek, Nazneen; Davies, Angela; Trappitt, Gary

2011-10-31

Pharmaceutical cocrystals are emerging as a new class of solid drugs with improved physicochemical properties, which has attracted increased interests from both industrial and academic researchers. In this paper a brief and systematic overview of pharmaceutical cocrystals is provided, with particular focus on cocrystal design strategies, formation methods, physicochemical property studies, characterisation techniques, and recent theoretical developments in cocrystal screening and mechanisms of cocrystal formations. Examples of pharmaceutical cocrystals are also summarised in this paper. Copyright © 2011 Elsevier B.V. All rights reserved.

Recognition of functional sites in protein structures.

PubMed

Shulman-Peleg, Alexandra; Nussinov, Ruth; Wolfson, Haim J

2004-06-04

Recognition of regions on the surface of one protein, that are similar to a binding site of another is crucial for the prediction of molecular interactions and for functional classifications. We first describe a novel method, SiteEngine, that assumes no sequence or fold similarities and is able to recognize proteins that have similar binding sites and may perform similar functions. We achieve high efficiency and speed by introducing a low-resolution surface representation via chemically important surface points, by hashing triangles of physico-chemical properties and by application of hierarchical scoring schemes for a thorough exploration of global and local similarities. We proceed to rigorously apply this method to functional site recognition in three possible ways: first, we search a given functional site on a large set of complete protein structures. Second, a potential functional site on a protein of interest is compared with known binding sites, to recognize similar features. Third, a complete protein structure is searched for the presence of an a priori unknown functional site, similar to known sites. Our method is robust and efficient enough to allow computationally demanding applications such as the first and the third. From the biological standpoint, the first application may identify secondary binding sites of drugs that may lead to side-effects. The third application finds new potential sites on the protein that may provide targets for drug design. Each of the three applications may aid in assigning a function and in classification of binding patterns. We highlight the advantages and disadvantages of each type of search, provide examples of large-scale searches of the entire Protein Data Base and make functional predictions.

Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping

PubMed Central

Ben-Shimon, Avraham; Niv, Masha Y.

2011-01-01

Protein kinases are key signaling enzymes that catalyze the transfer of γ-phosphate from an ATP molecule to a phospho-accepting residue in the substrate. Unraveling the molecular features that govern the preference of kinases for particular residues flanking the phosphoacceptor is important for understanding kinase specificities toward their substrates and for designing substrate-like peptidic inhibitors. We applied ANCHORSmap, a new fragment-based computational approach for mapping amino acid side chains on protein surfaces, to predict and characterize the preference of kinases toward Arginine binding. We focus on positions P−2 and P−5, commonly occupied by Arginine (Arg) in substrates of basophilic Ser/Thr kinases. The method accurately identified all the P−2/P−5 Arg binding sites previously determined by X-ray crystallography and produced Arg preferences that corresponded to those experimentally found by peptide arrays. The predicted Arg-binding positions and their associated pockets were analyzed in terms of shape, physicochemical properties, amino acid composition, and in-silico mutagenesis, providing structural rationalization for previously unexplained trends in kinase preferences toward Arg moieties. This methodology sheds light on several kinases that were described in the literature as having non-trivial preferences for Arg, and provides some surprising departures from the prevailing views regarding residues that determine kinase specificity toward Arg. In particular, we found that the preference for a P−5 Arg is not necessarily governed by the 170/230 acidic pair, as was previously assumed, but by several different pairs of acidic residues, selected from positions 133, 169, and 230 (PKA numbering). The acidic residue at position 230 serves as a pivotal element in recognizing Arg from both the P−2 and P−5 positions. PMID:22125489

G-quadruplex induced stabilization by 2′-deoxy-2′-fluoro-d-arabinonucleic acids (2′F-ANA)

PubMed Central

Peng, Chang Geng; Damha, Masad J.

2007-01-01

The impact of 2′-deoxy-2′-fluoroarabinonucleotide residues (2′F-araN) on different G-quadruplexes derived from a thrombin-binding DNA aptamer d(G2T2G2TGTG2T2G2), an anti-HIV phosphorothioate aptamer PS-d(T2G4T2) and a DNA telomeric sequence d(G4T4G4) via UV thermal melting (Tm) and circular dichroism (CD) experiments has been investigated. Generally, replacement of deoxyguanosines that adopt the anti conformation (anti-guanines) with 2′F-araG can stabilize G-quartets and maintain the quadruplex conformation, while replacement of syn-guanines with 2′F-araG is not favored and results in a dramatic switch to an alternative quadruplex conformation. It was found that incorporation of 2′F-araG or T residues into a thrombin-binding DNA G-quadruplex stabilizes the complex (ΔTm up to ∼+3°C/2′F-araN modification); 2′F-araN units also increased the half-life in 10% fetal bovine serum (FBS) up to 48-fold. Two modified thrombin-binding aptamers (PG13 and PG14) show an approximately 4-fold increase in binding affinity to thrombin, as assessed via a nitrocellulose filter binding assay, both with increased thermal stability (∼1°C/2′F-ANA modification increase in Tm) and nuclease resistance (4–7-fold) as well. Therefore, the 2′-deoxy-2′-fluoro-d-arabinonucleic acid (2′F-ANA) modification is well suited to tune (and improve) the physicochemical and biological properties of naturally occurring DNA G-quartets. PMID:17636049

Potential Functional Byproducts from Guava Purée Processing.

PubMed

Lim, Si Yi; Tham, Paik Yean; Lim, Hilary Yi Ler; Heng, Wooi Shin; Chang, Ying Ping

2018-05-10

The valorization of guava waste requires compositional and functional studies. We tested three byproducts of guava purée processing, namely refiner, siever, and decanter. We analyzed the chemical composition and quantified the prebiotic activity score and selected carbohydrates; we also determined the water holding (WHC), oil holding (OHC), cation exchange capacities, bile acid binding, and glucose dialysis retardation (GDR) of the solid fraction and the antioxidative and α-amylase inhibitory capacities (AIC) of the ethanolic extract. Refiner contained 7.7% lipid, 7.08% protein and a relatively high phytate content; it had a high prebiotic activity score and possessed the highest binding capacity with deoxycholic acid. Siever contained high levels of low molecular weight carbohydrates and total tannin but relatively low crude fiber and cellulose contents. It had the highest binding with chenodeoxycholic acid (74.8%), and exhibited the highest 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging capacity. Decanter was rich in cellulose and had a high prebiotic activity score. The WHC and OHC values of decanter were within a narrow range and also exhibited the highest binding with cholic acid (86.6%), and the highest values of GDR and AIC. The refiner waste could be included in animal feed but requires further processing to reduce the high phytate levels. All three guava byproducts had the potential to be a source of antioxidant dietary fiber (DF), a finding that warrants further in vivo study. To differing extents, the guava byproducts exhibited useful physicochemical binding properties and so possessed the potential for health-promoting activity. These byproducts could also be upgraded to other marketable products so the manufacturers of processed guava might be able to develop their businesses sustainably by making better use of them. © 2018 Institute of Food Technologists®.

repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects.

PubMed

Liu, Bin; Liu, Fule; Fang, Longyun; Wang, Xiaolong; Chou, Kuo-Chen

2015-04-15

In order to develop powerful computational predictors for identifying the biological features or attributes of DNAs, one of the most challenging problems is to find a suitable approach to effectively represent the DNA sequences. To facilitate the studies of DNAs and nucleotides, we developed a Python package called representations of DNAs (repDNA) for generating the widely used features reflecting the physicochemical properties and sequence-order effects of DNAs and nucleotides. There are three feature groups composed of 15 features. The first group calculates three nucleic acid composition features describing the local sequence information by means of kmers; the second group calculates six autocorrelation features describing the level of correlation between two oligonucleotides along a DNA sequence in terms of their specific physicochemical properties; the third group calculates six pseudo nucleotide composition features, which can be used to represent a DNA sequence with a discrete model or vector yet still keep considerable sequence-order information via the physicochemical properties of its constituent oligonucleotides. In addition, these features can be easily calculated based on both the built-in and user-defined properties via using repDNA. The repDNA Python package is freely accessible to the public at http://bioinformatics.hitsz.edu.cn/repDNA/. bliu@insun.hit.edu.cn or kcchou@gordonlifescience.org Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A blueprint for the synthesis and characterisation of thin graphene oxide with controlled lateral dimensions for biomedicine

NASA Astrophysics Data System (ADS)

Filipe Rodrigues, Artur; Newman, Leon; Lozano, Neus; Mukherjee, Sourav P.; Fadeel, Bengt; Bussy, Cyrill; Kostarelos, Kostas

2018-07-01

Graphene-based materials (GBMs) have ignited a revolution in material science and technology, with electronic, optical and mechanical properties that are of relevant interest for a wide range of applications. To support the development of these enabling technologies, a global research effort has been invested to assess their hazard and biocompatibility. Different production methods have however generated a diverse collection of GBMs with different physicochemical properties, leading to a variety of biological outcomes that are still not fully understood. To better understand the biological interactions of GBMs with biological systems and allow the design of safer materials, a thorough physicochemical characterisation is therefore highly recommended. The aim of the present work was to produce a blueprint for the synthesis and characterisation of non-pyrogenic graphene oxide (GO) flakes with three different controlled lateral dimensions, which could be further used for either hazard assessment or biomedical proof-of-concept studies. A battery of techniques used to characterise the physicochemical properties of the GO samples included atomic force microscopy, transmission electron microscopy, Fourier-transformed infra-red spectroscopy, x-ray photoelectron spectroscopy and Raman spectroscopy. The combination of these different techniques confirmed that only the lateral dimension varied among the GO materials produced, without significant change in any other of their fundamental physicochemical properties, such as the thickness or surface chemistry. The proposed systematic approach in GO batch production for biology will hopefully contribute to a better understanding of the material properties that govern their interactions with biological systems and offer a blueprint towards standardisation of biologically relevant 2D materials.

Dynamic aspects of antibody:oligosaccharide complexes characterized by molecular dynamics simulations and saturation transfer difference nuclear magnetic resonance.

PubMed

Theillet, François-Xavier; Frank, Martin; Vulliez-Le Normand, Brigitte; Simenel, Catherine; Hoos, Sylviane; Chaffotte, Alain; Bélot, Frédéric; Guerreiro, Catherine; Nato, Farida; Phalipon, Armelle; Mulard, Laurence A; Delepierre, Muriel

2011-12-01

Carbohydrates are likely to maintain significant conformational flexibility in antibody (Ab):carbohydrate complexes. As demonstrated herein for the protective monoclonal Ab (mAb) F22-4 recognizing the Shigella flexneri 2a O-antigen (O-Ag) and numerous synthetic oligosaccharide fragments thereof, the combination of molecular dynamics simulations and nuclear magnetic resonance saturation transfer difference experiments, supported by physicochemical analysis, allows us to determine the binding epitope and its various contributions to affinity without using any modified oligosaccharides. Moreover, the methods used provide insights into ligand flexibility in the complex, thus enabling a better understanding of the Ab affinities observed for a representative set of synthetic O-Ag fragments. Additionally, these complementary pieces of information give evidence to the ability of the studied mAb to recognize internal as well as terminal epitopes of its cognate polysaccharide antigen. Hence, we show that an appropriate combination of computational and experimental methods provides a basis to explore carbohydrate functional mimicry and receptor binding. The strategy may facilitate the design of either ligands or carbohydrate recognition domains, according to needed improvements of the natural carbohydrate:receptor properties. © The Author 2011. Published by Oxford University Press. All rights reserved.

Expression and purification of short hydrophobic elastin-like polypeptides with maltose-binding protein as a solubility tag.

PubMed

Bataille, Laure; Dieryck, Wilfrid; Hocquellet, Agnès; Cabanne, Charlotte; Bathany, Katell; Lecommandoux, Sébastien; Garbay, Bertrand; Garanger, Elisabeth

2015-06-01

Elastin-like polypeptides (ELPs) are biodegradable polymers with interesting physico-chemical properties for biomedical and biotechnological applications. The recombinant expression of hydrophobic elastin-like polypeptides is often difficult because they possess low transition temperatures, and therefore form aggregates at sub-ambient temperatures. To circumvent this difficulty, we expressed in Escherichia coli three hydrophobic ELPs (VPGIG)n with variable lengths (n=20, 40, and 60) in fusion with the maltose-binding protein (MBP). Fusion proteins were soluble and yields of purified MBP-ELP ranged between 66 and 127mg/L culture. After digestion of the fusion proteins by enterokinase, the ELP moiety was purified by using inverse transition cycling. The purified fraction containing ELP40 was slightly contaminated by traces of undigested fusion protein. Purification of ELP60 was impaired because of co-purification of the MBP tag during inverse transition cycling. ELP20 was successfully purified to homogeneity, as assessed by gel electrophoresis and mass spectrometry analyses. The transition temperature of ELP20 was measured at 15.4°C in low salt buffer. In conclusion, this method can be used to produce hydrophobic ELP of low molecular mass. Copyright © 2015 Elsevier Inc. All rights reserved.

The Nature of the Interactions in Triethanolammonium-Based Ionic Liquids. A Quantum Chemical Study.

PubMed

Fedorova, Irina V; Safonova, Lyubov P

2018-05-10

Structural features and interionic interactions play a crucial role in determining the overall stability of ionic liquids and their physicochemical properties. Therefore, we performed high-level quantum-chemical study of different cation-anion pairs representing the building units of protic ionic liquids based on triethanolammonium cation and anions of sulfuric, nitric, phosphoric, and phosphorus acids to provide essential insight into these phenomena at the molecular level. It was shown that every structure is stabilized through multiple H bonds between the protons in the N-H and O-H groups of the cation and different oxygen atoms of the anion acid. Using atoms in molecules topological parameters and natural bond orbital analysis, we determined the nature and strength of these interactions. Our calculations suggest that the N-H group of the cation has more proton donor-like character than the O-H group that makes the N-H···O hydrogen bonds stronger. A close relation between the binding energies of these ion pairs and experimental melting points was established: the smaller the absolute value of the binding energy between ions, the lower is the melting point.

Mannan-binding lectin of the sea urchin Strongylocentrotus nudus.

PubMed

Bulgakov, Aleksandr A; Eliseikina, Marina G; Kovalchuk, Svetlana N; Petrova, Irina Yu; Likhatskaya, Galina N; Shamshurina, Ekaterina V; Rasskazov, Valery A

2013-02-01

A novel lectin specific to low-branched mannans (MBL-SN) was isolated from coelomic plasma of the sea urchin Strongylocentrotus nudus by combining anion-exchange liquid chromatography on DEAE Toyopearl 650 M, affinity chromatography on mannan-Sepharose and gel filtration on the Sephacryl S-200. The molecular mass of MBL-SN was estimated by sodium dodecyl sulphate polyacrylamide gel electrophoresis under non-reducing conditions to be about 34 kDa. MBL-SN was shown to be a dimer with two identical subunits of about 17 kDa. The native MBL-SN exists as a tetramer. The physico-chemical properties of MBL-SN indicate that it belongs to C-type mannan-binding lectins. The cDNA encoding MBL-SN was cloned from the total cDNA of S. nudus coelomocytes and encodes a 17-kDa protein of 144 amino acid residues that contains a single carbohydrate-recognition domain of C-type lectins. Prediction of the MBL-SN tertiary structure using comparative modelling revealed that MBL-SN is an α/β-protein with eight β-strands and two α-helices. Comparison of the MBL-SN model with available three-dimensional structures of C-type lectins revealed that they share a common fold pattern.

Investigation of the Interaction Between Human Serum Albumin and Two Drugs as Binary and Ternary Systems.

PubMed

Abdollahpour, Nooshin; Soheili, Vahid; Saberi, Mohammad Reza; Chamani, Jamshidkhan

2016-12-01

Human serum albumin (HSA) is the most frequent protein in blood plasma. Albumin transports various compounds, preserves osmotic pressure, and buffers pH. A unique feature of albumin is its ability to bind drugs and other bioactive molecules. However, it is important to consider binary and ternary systems of two pharmaceuticals to estimate the effect of the first drug on the second one and physicochemical properties. Different techniques including time-resolved, second-derivative and anisotropy fluorescence spectroscopy, resonance light scattering (RLS), critical induced aggregation concentration (C CIAC ), particle size, zeta potential and stability analysis were employed in this assessment to elucidate the binding behavior of Amlodipine and Aspirin to HSA. Moreover, isothermal titration calorimetric techniques were performed and the QSAR properties were applied to analyze the hydration energy and log P. Multiple sequence alignments were also used to predict the structure and biological characteristics of the HSA binding site. Time-resolved fluorescence spectroscopy showed interaction of both drugs to HSA based on a static quenching mechanism. Subsequently, second-derivative fluorescence spectroscopy presented different values of parameter H in binary and ternary systems, which were suggested that tryptophan was in a more polar environment in the ternary system than in a binary system. Moreover, the polydispersity index and results from mean number measurements revealed that the presence of the second drug caused a decrease in the stability of systems and increased the heterogeneity of complex. It is also, observed that the gradual addition of HSA has led to a marked increase in fluorescence anisotropy (r) of Amlodipine and Aspirin which can be suggested that the drugs were located in a restricted environment of the protein as confirmed by Red Edge Excitation Shift (REES) studies. The isothermal titration calorimetric technique demonstrated that the interaction of the drugs with HSA was an enthalpically-driven process. The present experiment showed that the binding of Amlodipine and Aspirin to HSA induced a conformational change of HSA. It was also identified that the protein binding of the first drug could be affected by the second drug. Such results can be of great use for understanding the pharmacokinetic and pharmacodynamic mechanisms of drugs.

Application of ultrasound treatment for improving the physicochemical, functional and rheological properties of myofibrillar proteins.

PubMed

Amiri, Amir; Sharifian, Parisa; Soltanizadeh, Nafiseh

2018-05-01

The aim of this study was to evaluate the impact of duration (10, 20 and 30min) and power (100 and 300W) of high-intensity ultrasound (20kHz) on physicochemical properties of beef myofibrillar proteins in order to investigate novel process for modification of its functional characteristics. Results showed that augmentation of duration and power of ultrasound led to enhance pH. Also, the water holding capacity and gel strength were improved by increasing pH. The highest value in pH, reactive sulfhydryl content, water holding capacity and gel strength was obtained in sample subjected to 30min of ultrasound at 300W. The particle size distribution of the proteins was decreased after ultrasound treatment because of the cavitation force of ultrasound waves. In this circumstance, an improvement of emulsifying properties can be obtained. Ultrasonic waves had significant effects on the rheological properties of myofibrillar proteins. Treated samples were more elastic and stiffer than control, although the inverse trend was observed after 30min treatment at each power. Finally, a reducing trend in viscosity was observed by increasing time and power of sonication. Ultrasonic treatment could successfully improve functional properties with effect on physicochemical properties of myofibrillar proteins. Copyright © 2018 Elsevier B.V. All rights reserved.

Correlation between soil physicochemical properties and vegetation parameters in secondary tropical forest in Sabal, Sarawak, Malaysia

NASA Astrophysics Data System (ADS)

Karyati, K.; Ipor, I. B.; Jusoh, I.; Wasli, M. E.

2018-04-01

The tree growth is influenced by soil morphological and physicochemical properties in the site. The purpose of this study was to describe correlation between soil properties under various stage secondary forests and vegetation parameters, such as floristic structure parameters and floristic diversity indices. The vegetation surveys were conducted in 5, 10, and 20 years old at secondary tropical forests in Sarawak, Malaysia. Nine sub plots sized 20 m × 20 m were established within each study site. The Pearson analysis showed that soil physicochemical properties were significantly correlated to floristic structure parameters and floristic diversity indices. The result of PCA clarified the correlation among most important soil properties, floristic structure parameters, and floristic diversity indices. The PC1 represented cation retention capacity and soil texture which were little affected by the fallow age and its also were correlated by floristic structure and diversity. The PC2 was linked to the levels of soil acidity. This property reflected the remnant effects of ash addition and fallow duration, and the significant correlation were showed among pH (H2O), floristic structure and diversity. The PC3 represented the soil compactness. The soil hardness could be influenced by fallow period and it was also correlated by floristic structure.

Physicochemical and morphological properties of plasticized poly(vinyl alcohol)-agar biodegradable films.

PubMed

Madera-Santana, T J; Freile-Pelegrín, Y; Azamar-Barrios, J A

2014-08-01

The effects of the addition of glycerol (GLY) on the physicochemical and morphological properties of poly(vinyl alcohol) (PVA)-agar films were reported. PVA-agar films were prepared by solution cast method, and the addition of GLY in PVA-agar films altered the optical properties, resulting in a decrease in opacity values and in the color difference (ΔE) of the films. Structural characterization using Fourier transformation infrared (FTIR) spectroscopy and X-ray diffraction (XRD) indicated that the presence of GLY altered the intensity of the bands (from 1200 to 800cm(-1)) and crystallinity. The characterization of the thermal properties indicated that an increase in the agar content produces a decrease in the melting temperature and augments the heat of fusion. Similar tendencies were observed in plasticized films, but at different magnification. The formulation that demonstrated the lowest mechanical properties contained 25wt.% agar, whereas the formulation that contained 75wt.% agar demonstrated a significant improvement. The water vapor transmission rate (WVTR) and surface morphology analysis demonstrated that the structure of PVA-agar films is reorganized upon GLY addition. The physicochemical properties of PVA-agar films using GLY as a plasticizer provide information for the application of this formulation as packaging material for specific food applications. Copyright © 2014 Elsevier B.V. All rights reserved.

A Novel Selective Inverse Agonist of the CB2 Receptor as a Radiolabeled Tool Compound for Kinetic Binding Studies.

PubMed

Martella, Andrea; Sijben, Huub; Rufer, Arne C; Grether, Uwe; Fingerle, Juergen; Ullmer, Christoph; Hartung, Thomas; IJzerman, Adriaan P; van der Stelt, Mario; Heitman, Laura H

2017-10-01

The endocannabinoid system, and in particular the cannabinoid type 2 receptor (CB2R), raised the interest of many medicinal chemistry programs for its therapeutic relevance in several (patho)physiologic processes. However, the physico-chemical properties of tool compounds for CB2R (e.g., the radioligand [ 3 H]CP55,940) are not optimal, despite the research efforts in developing effective drugs to target this system. At the same time, the importance of drug-target binding kinetics is growing since the kinetic binding profile of a ligand may provide important insights for the resulting in vivo efficacy. In this context we synthesized and characterized [ 3 H]RO6957022, a highly selective CB2R inverse agonist, as a radiolabeled tool compound. In equilibrium and kinetic binding experiments [ 3 H]RO6957022 showed high affinity for human CB2R with fast association ( k on ) and moderate dissociation ( k off ) kinetics. To demonstrate the robustness of [ 3 H]RO6957022 binding, affinity studies were carried out for a wide range of CB2R reference ligands, spanning the range of full, partial, and inverse agonists. Finally, we used [ 3 H]RO6957022 to study the kinetic binding profiles (i.e., k on and k off values) of selected synthetic and endogenous (i.e., 2-arachidonoylglycerol, anandamide, and noladin ether) CB2R ligands by competition association experiments. All tested ligands, and in particular the endocannabinoids, displayed distinct kinetic profiles, shedding more light on their mechanism of action and the importance of association rates in the determination of CB2R affinity. Altogether, this study shows that the use of a novel tool compound, i.e., [ 3 H]RO6957022, can support the development of novel ligands with a repertoire of kinetic binding profiles for CB2R. Copyright © 2017 by The American Society for Pharmacology and Experimental Therapeutics.

Antioxidant properties, physico-chemical characteristics and proximate composition of five wild fruits of Manipur, India.

PubMed

Sharma, Ph Baleshwor; Handique, Pratap Jyoti; Devi, Huidrom Sunitibala

2015-02-01

Antioxidant properties, physico-chemical characteristics and proximate composition of five wild fruits viz., Garcinia pedunculata, Garcinia xanthochymus, Docynia indica, Rhus semialata and Averrhoa carambola grown in Manipur, India were presented in the current study. The order of the antioxidant activity and reducing power of the fruit samples was found as R. semialata > D. indica > G. xanthochymus > A. carambola > G. pedunculata. Good correlation coefficient (R(2) > 0.99) was found among the three methods applied to determine antioxidant activity. Total phenolic content was positively correlated (R(2) = 0.960) with the antioxidant activity however, total flavonoid content was not positively correlated with the antioxidant activity. Physico-chemical and proximate composition of these fruits is documented for the first time.

PHYSICOCHEMICAL MECHANISMS RESPONSIBLE FOR THE FILTRATION AND MOBILIZATION OF A FILAMENTOUS BACTERIOPHAGE IN QUARTZ SAND. (R824775)

EPA Science Inventory

This study examines the influence of pore water chemistry on the filtration and physicochemical properties of a male-specific filamentous bacteriophage isolated from
chlorinated effluent of the San Jose Creek Water Reclamation Plant in Los Angeles County, California. The isola...

Impacts of fungal stalk rot pathogens on physicochemical properties of sorghum grain

USDA-ARS?s Scientific Manuscript database

Stalk rot diseases are among the most ubiquitous and damaging fungal diseases of sorghum worldwide. Although reports of quantitative stalk rot yield losses are available, the impact of stalk rot on the physicochemical attributes of sorghum grain is currently unknown. This study was conducted to test...

Relationship between physicochemical characteristics of flour and sugar-snap cookie quality in Korean wheat cultivar

USDA-ARS?s Scientific Manuscript database

The relationship of physicochemical properties of flour, including particle size of flour, damaged starch, SDS-sedimentation volume, gluten content and four solvent retention capacity (SRC) values with cookie baking quality, including cookie diameter and thickness was evaluated using 30 Korean wheat...

Changes in some physicochemical properties and fatty acid composition of irradiated meatballs during storage.

PubMed

Gecgel, Umit

2013-06-01

Meatball samples were irradiated using a (60)Co irradiation source (with the dose of 1, 3, 5 and 7 kGy) and stored (1, 2 and 3 weeks at 4°C) to appraise some physicochemical properties and the fatty acid composition. The physicochemical results showed no significant differences in moisture, protein, fat and ash content of meatballs because of irradiation. However, total acidity, peroxide and thiobarbituric acid (TBA) values increased significantly as a result of irradiation doses and storage period. The fatty acid profile in meatball samples changed with irradiation. While saturated fatty acids (C16:0, C17:0, C18:0, and C20:0) increased with irradiation, monounsaturated (C14:1, C15:1, C18:1, and C20:1) and polyunsaturated (C18:2, C18:3, and C22:2) fatty acids decreased with irradiation. Trans fatty acids (C16:1trans, C18:1trans, C18:2trans, C18:3trans) increased with increasing irradiation doses. Meatball samples irradiated at 7 kGy had the highest total trans fatty acid content. This research shows that some physicochemical properties and fatty acid composition of meatballs can be changed by gamma irradiation.

Physicochemical properties and combustion behavior of duckweed during wet torrefaction.

PubMed

Zhang, Shuping; Chen, Tao; Li, Wan; Dong, Qing; Xiong, Yuanquan

2016-10-01

Wet torrefaction of duckweed was carried out in the temperature range of 130-250°C to evaluate the effects on physicochemical properties and combustion behavior. The physicochemical properties of duckweed samples were investigated by ultimate analysis, proximate analysis, FTIR, XRD and SEM techniques. It was found that wet torrefaction improved the fuel characteristics of duckweed samples resulting from the increase in fixed carbon content, HHVs and the decrease in nitrogen and sulfur content and atomic ratios of O/C and H/C. It can be seen from the results of FTIR, XRD and SEM analyses that the dehydration, decarboxylation, solid-solid conversion, and condensation polymerization reactions were underwent during wet torrefaction. In addition, the results of thermogravimetric analysis (TGA) in air indicated that wet torrefaction resulted in significant changes on combustion behavior and combustion kinetics parameters. Duckweed samples after wet torrefaction behaved more char-like and gave better combustion characteristics than raw sample. Copyright © 2016 Elsevier Ltd. All rights reserved.

Physico-chemical and antioxidant properties of four mango (Mangifera indica L.) cultivars in China.

PubMed

Liu, Feng-Xia; Fu, Shu-Fang; Bi, Xiu-Fang; Chen, Fang; Liao, Xiao-Jun; Hu, Xiao-Song; Wu, Ji-Hong

2013-05-01

Four principal mango cultivars (Tainong No.1, Irwin, JinHwang and Keitt) grown in southern China were selected, and their physico-chemical and antioxidant properties were characterized and compared. Of all the four cultivars, Tainong No.1 had highest content of total phenols, ρ-coumaric acid, sinapic acid, quercetin, titratable acidity, citric acid, malic acid, fructose, higher antioxidant activities (DPPH, FRAP) and L(*), lower pH, PPO activity and individual weight. Keitt mangoes showed significantly (p<0.05) higher contents of β-carotene, ρ-hydroxybenzoic acid, sucrose, total sugar, total soluble solid, catechin, succinic acid and higher PPO activity. JinHwang mangoes exhibited significantly (p<0.05) higher individual weight and PPO activity, but had lower content of total phenols, β-carotene and lower antioxidant activity. Principal component analysis (PCA) allowed the four mango cultivars to be differentiated clearly based on all these physico-chemical and antioxidant properties determined in the study. Copyright © 2012 Elsevier Ltd. All rights reserved.

Effects of whey protein concentrate, feed moisture and temperature on the physicochemical characteristics of a rice-based extruded flour.

PubMed

Teba, Carla da Silva; Silva, Erika Madeira Moreira da; Chávez, Davy William Hidalgo; Carvalho, Carlos Wanderlei Piler de; Ascheri, José Luis Ramírez

2017-08-01

The influence of whey protein concentrate (WPC), feed moisture and temperature on the physicochemical properties of rice-based extrudates has been investigated. WPC (0.64-7.36g/100g rice) was extruded under 5 moisture (16.64-23.36g/100g) and 5 temperature (106.36-173.64°C) established by a 3 2 central composite rotational design. Physicochemical properties [color, porosimetry, crystallinity, water solubility and absorption, pasting properties, reconstitution test, proximate composition, amino acids, minerals and electrophoresis] were determined. WPC and feed moisture increased redness, yellowness and decreased luminosity. Feed moisture and temperature increased density and total volume pore. WPC and moisture increased crystallinity, but only WPC increased solubility and decrease the retrogradation tendency. Increasing temperature increased the viscosity of the extrudates. The addition of WPC improved the nutritional composition of the extrudates, especially proteins. It is suggested that the extrusion process positively affected the retention of most of the polypeptides chains. Copyright © 2017 Elsevier Ltd. All rights reserved.

Physicochemical properties and in vitro digestibility of sorghum starch altered by high hydrostatic pressure.

PubMed

Liu, Hang; Fan, Huanhuan; Cao, Rong; Blanchard, Christopher; Wang, Min

2016-11-01

A nonthermal processing technology, high hydrostatic pressure (HHP) treatment, was investigated to assess its influence on the physicochemical properties and in vitro digestibility of sorghum starch (SS). There was no change in the 'A'-type crystalline pattern of SS after the pressure treatments at 120-480MPa. However, treatment at 600MPa produced a pattern similar to 'B'-type crystalline. HHP treatment also resulted in SS granules with rough surfaces. Measured amylose content, water absorption capacity, alkaline water retention, pasting temperature and thermostability increased with increasing pressure levels, while the oil absorption capacity, swelling power, relative crystallinity and viscosity decreased. Compared with native starch, HHP-modified SS samples had lower in vitro hydrolysis, reduced amount of rapidly digestible starch, as well as increased levels of slowly digestible starch and resistant starch. These results indicate that HHP treatment is an effective modification method for altering in vitro digestibility and physicochemical properties of SS. Copyright © 2016 Elsevier B.V. All rights reserved.

Chemical composition and functional characteristics of dietary fiber-rich powder obtained from core of maize straw.

PubMed

Lv, Jin-Shun; Liu, Xiao-Yan; Zhang, Xiao-Pan; Wang, Lin-Shuang

2017-07-15

A novel dietary fiber (MsCDF) based core of maize straw (Core) was prepared by using high boiling solvent of sodium peroxide by high pressure pretreatment (HBSHP). The composition of MsCDF, and several physicochemical properties for MsCDF related to its nutritional quality were investigated. The results revealed that the MsCDF contains high contents total dietary fiber (TDF), soluble dietary fiber (SDF), insoluble dietary fiber (IDF) and two main monosaccharaides, xylose and glucose. Meanwhile, the studies of physicochemical properties of MsCDF indicated that MsCDF performed well water-holding capacity (WHC), oil-holding capacity (OHC), Swelling, solubility (SOL), Glucose dialysis retardation index (GDRI) and adsorption capacity on cholesterol. The results of this study serve as evidence that MsCDF can be used as a functional food additive, Core can be used as a crude material to produce MsCDF and the technology of HBSHP can be used to modify the physico-chemical properties of Core. Copyright © 2017 Elsevier Ltd. All rights reserved.

A comparative study of composting the solid fraction of dairy manure with or without bulking material: Performance and microbial community dynamics.

PubMed

Zhong, Xiao-Zhong; Ma, Shi-Chun; Wang, Shi-Peng; Wang, Ting-Ting; Sun, Zhao-Yong; Tang, Yue-Qin; Deng, Yu; Kida, Kenji

2018-01-01

The present study compared the development of various physicochemical properties and the composition of microbial communities involved in the composting process in the solid fraction of dairy manure (SFDM) with a sawdust-regulated SFDM (RDM). The changes in several primary physicochemical properties were similar in the two composting processes, and both resulted in mature end-products within 48days. The bacterial communities in both composting processes primarily comprised Proteobacteria and Bacteroidetes. Firmicutes were predominant in the thermophilic phase, whereas Chloroflexi, Planctomycetes, and Nitrospirae were more abundant in the final mature phase. Furthermore, the succession of bacteria in both groups proceeded in a similar pattern, suggesting that the effects of the bulking material on bacterial dynamics were minor. These results demonstrate the feasibility of composting using only the SFDM, reflected by the evolution of physicochemical properties and the microbial communities involved in the composting process. Copyright © 2017 Elsevier Ltd. All rights reserved.

Physicochemical properties of beta-glucan in differently processed oat foods influence glycemic response.

PubMed

Regand, Alejandra; Tosh, Susan M; Wolever, Thomas M S; Wood, Peter J

2009-10-14

To assess the effect of food processing on the capacity of oat beta-glucan to attenuate postprandial glycemia, isocaloric crisp bread, granola, porridge, and pasta containing 4 g of beta-glucan as well as control products with low beta-glucan content were prepared. The physicochemical properties (viscosity, peak molecular weight (M(p)), and concentration (C)) of beta-glucan in in-vitro-digestion extracts were evaluated, and fasting and postprandial blood glucose concentrations were measured in human subjects. Porridge and granola had the highest efficacy in attenuating the peak blood glucose response (PBGR) because of their high M(p) and viscosity. beta-Glucan depolymerization in bread and pasta reduced beta-glucan bioactivity. Pastas, known to have low glycemic responses, showed the lowest PBGR. The analyses of these products with previously reported data indicated that 73% of the bioactivity in reducing PBGR can be explained by M(p) x C. Characterizing the physicochemical properties of beta-glucan in bioactive foods aids functional food development.

Effect of banana pulp and peel flour on physicochemical properties and in vitro starch digestibility of yellow alkaline noodles.

PubMed

Ramli, Saifullah; Alkarkhi, Abbas F M; Shin Yong, Yeoh; Min-Tze, Liong; Easa, Azhar Mat

2009-01-01

The present study describes the utilization of banana--Cavendish (Musa acuminata L., cv cavendshii) and Dream (Musa acuminata colla. AAA, cv 'Berangan')--pulp and peel flours as functional ingredients in yellow alkaline noodles. Noodles were prepared by partial substitution of wheat flour with ripe banana pulp or peel flours. In most cases, the starch hydrolysis index, predicted glycaemic index (pGI) and physicochemical properties of cooked noodles were affected by banana flour addition. In general, the pGI values of cooked noodles were in the order; banana peel noodles < banana pulp noodles < control noodles. Since the peel flour was higher in total dietary fibre but lower in resistant starch contents than the pulp flour, the low pGI of banana peel noodles was mainly due to its high dietary fibre content. In conclusion, banana pulp and peel flour could be useful for controlling starch hydrolysis of yellow noodles, even though some physicochemical properties of the noodles were altered.

The hemolymph of caterpillars Spodoptera littoralis: physico-chemical properties and ionic composition compared to culture media.

PubMed

Smagghe, G; Van Leeuwen, T

2004-01-01

In this paper, we determined some physico-chemical properties like osmotic pressure, pH and electrical conductivity of the hemolymph from caterpillars of Spodoptera littoralis (Lepidoptera: Noctuidae) during the last larval instar. It was of interest that we observed an increase in osmotic pressure with the increase in age in the last instar that may concur with the start of histolysis at metamorphosis. These physicochemical properties were then compared to those of Grace's and modified Grace's tissue culture medium. In addition, concentrations of the cations Na, K, Ca and Mg, and the anions Cl, NO3, PO4 and SO4 were determined in the insect hemolymph of S. littoralis. The cations K and Mg reached high values with a percent of about 52% of the total amount of cations. The concentration of sodium was low. The total sum of the anions consisted about 56 meq/1, and this allows to neutralise about 45 % of the total cations.

Importance of asparagine on the conformational stability and chemical reactivity of selected anti-inflammatory peptides

NASA Astrophysics Data System (ADS)

Soriano-Correa, Catalina; Barrientos-Salcedo, Carolina; Campos-Fernández, Linda; Alvarado-Salazar, Andres; Esquivel, Rodolfo O.

2015-08-01

Inflammatory response events are initiated by a complex series of molecular reactions that generate chemical intermediaries. The structure and properties of peptides and proteins are determined by the charge distribution of their side chains, which play an essential role in its electronic structure and physicochemical properties, hence on its biological functionality. The aim of this study was to analyze the effect of changing one central amino acid, such as substituting asparagine for aspartic acid, from Cys-Asn-Ser in aqueous solution, by assessing the conformational stability, physicochemical properties, chemical reactivity and their relationship with anti-inflammatory activity; employing quantum-chemical descriptors at the M06-2X/6-311+G(d,p) level. Our results suggest that asparagine plays a more critical role than aspartic acid in the structural stability, physicochemical features, and chemical reactivity of these tripeptides. Substituent groups in the side chain cause significant changes on the conformational stability and chemical reactivity, and consequently on their anti-inflammatory activity.

Effect of high hydrostatic pressure and retrogradation treatments on structural and physicochemical properties of waxy wheat starch.

PubMed

Hu, Xiao-Pei; Zhang, Bao; Jin, Zheng-Yu; Xu, Xue-Ming; Chen, Han-Qing

2017-10-01

In this study, the effects of high hydrostatic pressure and retrogradation (HHPR) treatments on in vitro digestibility, structural and physicochemical properties of waxy wheat starch were investigated. The waxy wheat starch slurries (10%, w/v) were treated with high hydrostatic pressures of 300, 400, 500, 600MPa at 20°C for 30min, respectively, and then retrograded at 4°C for 4d. The results indicated that the content of slowly digestible starch (SDS) in HHPR-treated starch samples increased with increasing pressure level, and it reached the maximum (31.12%) at 600MPa. HHPR treatment decreased the gelatinization temperatures, the gelatinization enthalpy, the relative crystallinity and the peak viscosity of the starch samples. Moreover, HHPR treatment destroyed the surface and interior structures of starch granules. These results suggest that the in vitro digestibility, physicochemical, and structural properties of waxy wheat starch are effectively modified by HHPR. Copyright © 2017 Elsevier Ltd. All rights reserved.

Influence of pectinase treatment on the physicochemical properties of potato flours.

PubMed

Kim, Eun-Jung; Kim, Hyun-Seok

2015-01-15

Untreated and pectinase-treated potato flours from Atlantic and Superior cultivars were characterised to identify the effects of pectinase treatment on their physicochemical properties. Steam-cooked potato whole-tissues were treated with and without pectinase to prepare the dehydrated potato flours. Untreated and pectinase-treated potato flours were investigated with respect to morphology, chemical composition, starch leaching, swelling power, gelatinization, and pasting viscosity. Upon viewing with scanning electron microscopy and light microscopy, the pectinase-treated (relative to untreated) potato flours revealed that the retrograded starch materials were present in intact parenchyma cells, apparently exhibiting granular structures. Their protein and ash contents were reduced through pectinase treatment. While starch leachate contents were lower for the pectinase-treated potato flours, the opposite trend in swelling powers was observed. Pectinase-treated potato flours exhibited higher melting temperatures and pasting viscosities than untreated counterparts. Overall, the modification of potato flour morphology by pectinase treatment may result in alteration of physicochemical properties of potato flours. Copyright © 2014 Elsevier Ltd. All rights reserved.

Chemical composition and physicochemical properties of tropical red seaweed, Gracilaria changii.

PubMed

Chan, Pei Teng; Matanjun, Patricia

2017-04-15

A study on the proximate composition, minerals, vitamins, carotenoids, amino acids, fatty acids profiles and some physicochemical properties of freeze dried Gracilaria changii was conducted. It was discovered that this seaweed was high in dietary fibre (64.74±0.82%), low in fat (0.30±0.02%) and Na/K ratio (0.12±0.02). The total amino acid content was 91.90±7.70% mainly essential amino acids (55.87±2.15mgg -1 ) which were comparable to FAO/WHO requirements. The fatty acid profiles were dominated by the polyunsaturated fatty acids particularly docosahexaenoic (48.36±6.76%) which led to low ω6/ω3, atherogenic, and thrombogenic index. The physicochemical properties of this seaweed namely the water holding and the swelling capacity were comparable to some commercial fibre rich products. This study suggested that G. changii could be potentially used as ingredients to improve nutritive value and texture of functional foods for human consumption. Copyright © 2016 Elsevier Ltd. All rights reserved.

Characterization of textural, rheological, thermal, microstructural, and water mobility in wheat flour dough and bread affected by trehalose.

PubMed

Peng, Bo; Li, Youqian; Ding, Shiyong; Yang, Jun

2017-10-15

The study aims to elucidate the effects of trehalose on the mechanical, thermal, and rheological properties of wheat flour dough and water distribution in bread. Texture profile analysis, DSC, farinograph, extensograph, and frequency sweep were applied in dough. The results from SEM revealed that the gluten film became less notable with the presence of trehalose. The kinetics of staling process, low-field 1 H NMR, and water-binding capacity were employed to characterize physicochemical properties of bread. Trehalose decreased the staling rate constant k, indicating an inhibitory effect on firming process in bread. Trehalose had the ability to retain water by hindering the interaction among water molecules, gluten and starch, thus relatively increasing the immobility of the part of water represented by T 22 in low-field 1 H NMR tests. Trehalose restricted water mobilization during storage, resulting in a better water-holding capacity. Our findings reveal that trehalose could be an improver in dough and bread-making performance, as well as an antistaling agent in bread. Copyright © 2017 Elsevier Ltd. All rights reserved.

Electronic structure of an anticancer drug DC81 and its interaction with DNA base pairs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tiwari, Gargi, E-mail: gargi.tiwari@rediffmail.com; Sharma, Dipendra, E-mail: d-11sharma@rediffmail.com; Dwivedi, K. K., E-mail: dwivedikarunesh4@gmail.com

The drug, 8-Hydroxy-7-methoxy-pyrrolo-[2,1-c][1,4] benzodiazepine-5-one, commonly christened as DC81 belongs to the pyrrolo-[2,1-c][1,4]benzodiazepine (PBDs) family. It is a member of the group of naturally occurring antitumour antibiotics produced by various Streptomyces species. The antitumour activity of DC81 is attributed to its sequence specific interaction with G-C rich DNA region in particular, for Pu-G-Pu motifs. In the present paper, physico-chemical properties DC81 have been carried out using an ab-initio method, HF/6-31G(d,p) with GAMESS program. MEP, HOMO and LUMO surfaces have been scanned. Ionization potential, electron affinity, electronegativity, global hardness and softness of the drug have been calculated. Further, drug-DNA interactions have beenmore » examined using modified second order perturbation theory along with multicentred-multipole expansion technique. Results have been discussed in the light of other theoretical and experimental observations. Efforts have been made to elucidate the binding patterns and thereby biological properties of the drug.« less

Electronic structure of an anticancer drug DC81 and its interaction with DNA base pairs

NASA Astrophysics Data System (ADS)

Tiwari, Gargi; Sharma, Dipendra; Dwivedi, K. K.; Dwivedi, M. K.

2016-05-01

The drug, 8-Hydroxy-7-methoxy-pyrrolo-[2,1-c][1,4] benzodiazepine-5-one, commonly christened as DC81 belongs to the pyrrolo-[2,1-c][1,4]benzodiazepine (PBDs) family. It is a member of the group of naturally occurring antitumour antibiotics produced by various Streptomyces species. The antitumour activity of DC81 is attributed to its sequence specific interaction with G-C rich DNA region in particular, for Pu-G-Pu motifs. In the present paper, physico-chemical properties DC81 have been carried out using an ab-initio method, HF/6-31G(d,p) with GAMESS program. MEP, HOMO and LUMO surfaces have been scanned. Ionization potential, electron affinity, electronegativity, global hardness and softness of the drug have been calculated. Further, drug-DNA interactions have been examined using modified second order perturbation theory along with multicentred-multipole expansion technique. Results have been discussed in the light of other theoretical and experimental observations. Efforts have been made to elucidate the binding patterns and thereby biological properties of the drug.

Osteoblast response to zirconia-hybridized pyrophosphate-stabilized amorphous calcium phosphate

PubMed Central

Whited, Bryce M.; Skrtic, Drago; Love, Brian J.

2006-01-01

Calcium phosphate bioceramics, such as hydroxyapatite, have long been used as bone substitutes because of their proven biocompatibility and bone binding properties in vivo. Recently, a zirconia-hybridized pyrophosphate-stabilized amorphous calcium phosphate (Zr-ACP) has been synthesized, which is more soluble than hydroxyapatite and allows for controlled release of calcium and phosphate ions. These ions have been postulated to increase osteoblast differentiation and mineralization in vitro. The focus of this work is to elucidate the physicochemical properties of Zr-ACP and to measure cell response to Zr-ACP in vitro using a MC3T3-E1 mouse calvarial-derived osteoprogenitor cell line. Cells were cultured in osteogenic medium and mineral was added to culture at different stages in cell maturation. Culture in the presence of Zr-ACP showed significant increases in cell proliferation, alkaline phosphatase activity (ALP), and osteopontin (OPN) synthesis, whereas collagen synthesis was unaffected. In addition, calcium and phosphate ion concentrations and medium pH were found to transiently increase with the addition of Zr-ACP, and are hypothesized to be responsible for the osteogenic effect of Zr-ACP. PMID:16278876

PHYSICOCHEMICAL PROPERTY CALCULATIONS

EPA Science Inventory

Computer models have been developed to estimate a wide range of physical-chemical properties from molecular structure. The SPARC modeling system approaches calculations as site specific reactions (pKa, hydrolysis, hydration) and `whole molecule' properties (vapor pressure, boilin...

Swirling cavitation improves the emulsifying properties of commercial soy protein isolate.

PubMed

Yang, Feng; Liu, Xue; Ren, Xian'e; Huang, Yongchun; Huang, Chengdu; Zhang, Kunming

2018-04-01

Since emulsifying properties are important functional properties of soy protein, many physical, chemical, and enzymatic methods have been applied to treat soy protein to improve emulsifying properties. In this study, we investigated the effects of swirling cavitation at different pressures and for different times on emulsifying and physicochemical properties of soy protein isolate (SPI). The SPI treated with swirling cavitation showed a significant decrease in particle size and increase in solubility. Emulsions formed from treated SPI had higher emulsifying activity and emulsifying stability indexes, smaller oil droplet sizes, lower flocculation indexes, higher adsorbed proteins, lower interfacial protein concentrations, and lower creaming indexes than those formed from untreated SPI, indicating that swirling cavitation improved the emulsifying properties of the SPI. Furthermore, swirling cavitation treatment significantly enhanced the surface hydrophobicity, altered the disulfide bond and exposed sulfhydryl group contents of the SPI. The secondary structure of the SPI was also influenced by swirling cavitation, with an increase in β-sheet content and a decrease in α-helix, β-turn, and random coil contents. In addition, several significant correlations between physicochemical and emulsifying properties were revealed by Pearson correlation analysis, suggesting that the physicochemical changes observed in treated SPI, including the decreased particle size, increased solubility and surface hydrophobicity, and enhanced β-sheet formation, may explain the improved emulsifying properties of the isolate. Thus, our findings implied that swirling cavitation treatment may be an effective technique to improve the emulsifying properties of SPI. Copyright © 2017 Elsevier B.V. All rights reserved.

Pharmaceutical Cocrystals and Their Physicochemical Properties

PubMed Central

2009-01-01

Over the last 20 years, the number of publications outlining the advances in design strategies, growing techniques, and characterization of cocrystals has continued to increase significantly within the crystal engineering field. However, only within the last decade have cocrystals found their place in pharmaceuticals, primarily due to their ability to alter physicochemical properties without compromising the structural integrity of the active pharmaceutical ingredient (API) and thus, possibly, the bioactivity. This review article will highlight and discuss the advances made over the last 10 years pertaining to physical and chemical property improvements through pharmaceutical cocrystalline materials and, hopefully, draw closer the fields of crystal engineering and pharmaceutical sciences. PMID:19503732

Effects of volumetric expansion in molecular crystals: A quantum mechanical investigation on aspirin and paracetamol most stable polymorphs

NASA Astrophysics Data System (ADS)

Adhikari, Kapil; Flurchick, Kenneth M.; Valenzano, Loredana

2015-02-01

This work reports a study performed at hybrid semi-empirical density functional level (B3LYP-D2*) of the physico-chemical properties of aspirin (acetylsalicylic acid) and paracetamol (acetaminophen) in their most stable crystalline forms. It is shown how effects arising from volumetric expansions influence the properties of the materials. Structural, energetic, and vibrational properties are in good agreement with experimental values reported at temperatures far from 0 K. Results show that the proposed approach is reliable enough to reproduce effects of volumetric expansion on lattice energies and other measurable physico-chemical observables related to inter-molecular forces.

Vaginal microbicide film combinations of two reverse transcriptase inhibitors, EFdA and CSIC, for the prevention of HIV-1 sexual transmission

PubMed Central

Zhang, Wei; Hu, Minlu; Shi, Yuan; Gong, Tiantian; Dezzutti, Charlene S.; Moncla, Bernard; Sarafianos, Stefan G.; Parniak, Michael A.; Rohan, Lisa C.

2015-01-01

Purpose EFdA is a potent nucleoside reverse transcriptase inhibitor (NRTI) with activity against a wide spectrum of wild-type and drug resistant HIV-1 variants. CSIC is a tight-binding non-nucleoside reverse transcriptase inhibitor (NNRTI) with demonstrated anti-HIV properties important for use in topical prevention of HIV transmission. The objective of this study was to develop and characterize film-formulated EFdA and CSIC for use as a female-controlled vaginal microbicide to prevent sexual transmission of HIV. Methods Assessments of EFdA- and CSIC-loaded films included physicochemical characteristics, in vitro cytotoxicity, epithelia integrity studies, compatibility with the normal vaginal Lactobacillus flora and anti-HIV bioactivity evaluations. Results No significant change in physicochemical properties or biological activity of the combination films were noted during 3 months storage. In vitro cytotoxicity and bioactivity testing showed that 50% cytotoxic concentration (CC50) of either EFdA or CSIC was several orders of magnitude higher than the 50% effective concentration (EC50) values. Film-formulated EFdA and CSIC combination showed additive inhibitory activity against wild type and drug-resistant variants of HIV. Epithelial integrity studies demonstrated that the combination vaginal film had a much lower toxicity to HEC-1A monolayers compared to that of VCF®, a commercial vaginal film product containing nonoxynol-9. Polarized ectocervical explants showed films with drug alone or in combination were effective at preventing HIV infection. Conclusions Our data suggest that vaginal microbicide films containing a combination of the NRTI EFdA and the NNRTI CSIC have potential to prevent HIV-1 sexual transmission. PMID:25794967

Removal of micro pollutants using activated biochars and powdered activated carbon in water

NASA Astrophysics Data System (ADS)

Kim, E.; Jung, C.; Han, J.; Son, A.; Yoon, Y.

2015-12-01

Recent studies have suggested that emerging micropollutants containing endocrine disrupting compounds (EDCs); bisphenol A, 17 α-ethinylestradiol, 17 β-estradiol and pharmaceuticals and personal care products (PPCPs); sulfamethoxazole, carbamazepine, ibuprofen, atenolol, benzophenone, benzotriazole, caffeine, gemfibrozil, primidone, triclocarban in water have been linked to ecological impacts, even at trace concentrations (sub ug/L). Adsorption with adsorbent such as activated carbon having a high-binding affinity has been widely used to eliminate various contaminants in the aqueous phase. Recently, an efficient treatment strategy for EDCs and PPCPs has been considered by using cost effective adsorption particularly with biochar in aqueous environmentIn this study, the objective of this study is to determine the removal of 13 target EDCs/PPCPs having different physicochemical properties by a biochar at various water quality conditions (pH (3.5, 7, and 10.5), background ions (NaCl, CaCl2, Na₂SO₄), ionic strength, natural organic matter (NOM)). The activated biochar produced in a laboratory was also characterized by using conventional analytical methods as well as advanced solid-state nuclear magnetic resonance (NMR) techniques, which answer how these properties determine the competitive adsorption characteristics and mechanisms of EDCs and PPCPs.The primary findings suggest that micropollutants can be removed more effectively by the biochar than the commercially available powdered activated carbon. At pH values below the pKa of each compound, the adsorption affinity toward adsorbents increased significantly with the pH, whereas the adsorption affinity decreased significantly at the pH above the pKa values. Na+ did not significantly impact adsorption, while increasing the concentration of Ca2+lead to increase in the adsorption of these micropollutants. NOM adsorption with humic acids on these adsorbents disturbed adsorption capacity of the target compounds as occupying active adsorption sites and interacting with EDCs/PPCPs. Conclusion that can be drawn thus far is that the biochar shows great physicochemical properties for adsorption to reduce the micropollutants.

Variations in Physicochemical Properties of a Traditional Mercury-Based Nanopowder Formulation: Need for Standard Manufacturing Practices

PubMed Central

Kamath, S. U.; Pemiah, B.; Rajan, K. S.; Krishnaswamy, S.; Sethuraman, S.; Krishnan, U. M.

2014-01-01

Rasasindura is a mercury-based nanopowder synthesized using natural products through mechanothermal processing. It has been used in the Ayurvedic system of medicine since time immemorial for various therapeutic purposes such as rejuvenation, treatment of syphilis and in genital disorders. Rasasindura is said to be composed of mercury, sulphur and organic moieties derived from the decoction of plant extracts used during its synthesis. There is little scientific understanding of the preparation process so far. Though metallic mercury is incorporated deliberately for therapeutic purposes, it certainly raises toxicity concerns. The lack of gold standards in manufacturing of such drugs leads to a variation in the chemical composition of the final product. The objective of the present study was to assess the physicochemical properties of Rasasindura samples of different batches purchased from different manufacturers and assess the extent of deviation and gauge its impact on human health. Modern characterization techniques were employed to analyze particle size and morphology, surface area, zeta potential, elemental composition, crystallinity, thermal stability and degradation. Average particle size of the samples observed through scanning electron microscope ranged from 5-100 nm. Mercury content was found to be between 84 and 89% from elemental analysis. Despite batch-to-batch and manufacturer-to-manufacturer variations in the physicochemical properties, all the samples contained mercury in the form of HgS. These differences in the physicochemical properties may ultimately impact its biological outcome. PMID:25593382

CdTe quantum dots: aqueous phase synthesis, stability studies and protein conjugation for development of biosensors

NASA Astrophysics Data System (ADS)

Borse, Vivek; Sadawana, Mayur; Srivastava, Rohit

2016-04-01

Synthesis of quantum dots (QDs) in aqueous medium is advantageous as compared to the organic solvent mediated synthesis, as the aqueous synthesis is less toxic, reagent effective, easily reproducible and importantly, synthesized QDs have biological compatibility. The QDs should be aqueous in nature for use in cell imaging, drug labeling, tracking and delivery. Structural modifications are necessary to enable their use in biosensing application. In this work, mercaptopropionic acid capped cadmium telluride QDs (MPA-CdTe QDs) were synthesized by hydrothermal method and characterized by various techniques. Water and various biochemical buffers were used to study the fluorescence intensity stability of the QDs at different physicochemical conditions. QDs stored in 4° C showed excellent stability of fluorescence intensity values as compared to the samples stored at room temperature. Staphylococcal protein A (SPA) was conjugated with the QDs (SPA-QDs) and characterized using UV and fluorescence spectroscopy, zeta potential, HRTEM, FTIR, and AFM. Blue shift was observed in the fluorescence emission spectra that may be due to reduction in the surface charge as carboxyl groups on QDs were replaced by amino groups of SPA. This SPA conjugated to QDs enables binding of the C-terminal of antibodies on its surface allowing N-terminal binding site remain free to bind with antigenic biomarkers. Thus, the biosensor i.e. antibody bound on SPA-QDs would bind to the antigenic biomarkers in sample and the detection system could be developed. As QDs have better fluorescence properties than organic dyes, this biosensor will provide high sensitivity and quantitative capability in diagnostics.

Molecular Docking, Synthesis And Biological Evaluation Of Sulphonylureas/Guanidine Derivatives As Promising Antidiabetics Agent.

PubMed

Panchal, Ishan; Sen, Dhrubo Jyoti; Patel, Ashish D; Shah, Umang; Patel, Mehul; Navle, Archana; Bhavsar, Vashisth

2017-10-02

A series of novel sulphonylureas/guanidine derivatives were designed, synthesized, and evaluated for the treatment of diabetes mellitus. In this study, the designed compounds were docked with AKR1C1 complexes by using glide docking program and docking calculations were performed to predict the binding affinity of the designed compounds with the binding pocket of protein 4YVP and QikProp program was used to predict the ADME/T properties of the analogues. All the targeted derivatives were synthesized and purified by recrystallization. Synthesize compounds were characterized by various physicochemical and various spectroscopic techniques like melting point, thin layer chromatography, infrared spectroscopy (KBr pellets), mass spectroscopy(m/z), 1H NMR (DMSO-d6), and 13C NMR. The synthesized compounds were further studied for biological evolution by alloxan (150 mg/dl, intraperitonial) induced diabetic rat model for in-vivo studies. Among all the synthesized derivatives, 5c and 5d were most potent as per binding energy. Compound 5i have shown a better plasma glucose reduction compared to glibenclamide. Hence, it will further use as a lead compound to develop a more such kind of agent. The docking study revealed that in all designed sulphonylureas/guanidine series of compounds 5c and 5d were found to be most potent compounds as per the binding energy compared to glibenclamide. With the help of details study of in vivo biological activity we observed that compound 5i gives better result compared to glibenclamide as standard. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Influence of selected physicochemical parameters on microbiological activity of mucks.

NASA Astrophysics Data System (ADS)

Całka, A.; Sokołowska, Z.; Warchulska, P.; Dąbek-Szreniawska, M.

2009-04-01

One of the basic factor decided about soil fertility are microorganisms that together with flora, determine trend and character of biochemical processes as well totality of fundamental transformations connected with biogeochemistry and physicochemical properties of soil. Determination of general bacteria number, quantity of selected groups of microorganisms and investigation of respiration intensity let estimate microbiological activity of soil. Intensity of microbiological processes is directly connected with physicochemical soil parameters. In that case, such structural parameters as bulk density, porosity, surface or carbon content play significant role. Microbiological activity also changes within the bounds of mucks with different stage of humification and secondary transformation. Knowledge of relations between structural properties, microorganism activity and degree of transformation and humification can lead to better understanding microbiological processes as well enable to estimate microbiological activity at given physicochemical conditions and at progressing process of soil transformation. The study was carried out on two peaty-moorsh (muck) soils at different state of secondary transformation and humification degree. Soil samples were collected from Polesie Lubelskie (layer depth: 5 - 25 cm). Investigated mucks originated from soils formed from low peatbogs. Soil sample marked as I belonged to muck group weakly secondary transformed. Second sample (II) represented soil group with middle stage of secondary transformation. The main purpose of the research was to examine the relations between some physicochemical and surface properties and their biological activity. Total number and respiration activity of microorganisms were determined. The effectiveness of utilizing the carbon substances from the soil by the bacteria increased simultaneously with the transformation state of the peat-muck soils. Quantity of organic carbon decreased distinctly in the soil at the higher stage of secondary transformation and it influenced quantity and activity of soil microorganisms. Bulk density and surface increased with increasing secondary transformation degree. On the other hand, porosity decreased with increasing secondary transformation index. Process of secondary transformation influenced the soil environment for the microbes by changing the physicochemical properties. This way it influenced the number of microorganisms and caused changes of biological activity in the soils.

Targeted therapy using nanotechnology: focus on cancer

PubMed Central

Sanna, Vanna; Pala, Nicolino; Sechi, Mario

2014-01-01

Recent advances in nanotechnology and biotechnology have contributed to the development of engineered nanoscale materials as innovative prototypes to be used for biomedical applications and optimized therapy. Due to their unique features, including a large surface area, structural properties, and a long circulation time in blood compared with small molecules, a plethora of nanomaterials has been developed, with the potential to revolutionize the diagnosis and treatment of several diseases, in particular by improving the sensitivity and recognition ability of imaging contrast agents and by selectively directing bioactive agents to biological targets. Focusing on cancer, promising nanoprototypes have been designed to overcome the lack of specificity of conventional chemotherapeutic agents, as well as for early detection of precancerous and malignant lesions. However, several obstacles, including difficulty in achieving the optimal combination of physicochemical parameters for tumor targeting, evading particle clearance mechanisms, and controlling drug release, prevent the translation of nanomedicines into therapy. In spite of this, recent efforts have been focused on developing functionalized nanoparticles for delivery of therapeutic agents to specific molecular targets overexpressed on different cancer cells. In particular, the combination of targeted and controlled-release polymer nanotechnologies has resulted in a new programmable nanotherapeutic formulation of docetaxel, namely BIND-014, which recently entered Phase II clinical testing for patients with solid tumors. BIND-014 has been developed to overcome the limitations facing delivery of nanoparticles to many neoplasms, and represents a validated example of targeted nanosystems with the optimal biophysicochemical properties needed for successful tumor eradication. PMID:24531078

Tunable recognition of the steroid α-face by adjacent π-electron density

PubMed Central

Friščić, T.; Lancaster, R. W.; Fábián, L.; Karamertzanis, P. G.

2010-01-01

We report a previously unknown recognition motif between the α-face of the steroid hydrocarbon backbone and π-electron-rich aromatic substrates. Our study is based on a systematic and comparative analysis of the solid-state complexation of four steroids with 24 aromatic molecules. By using the solid state as a medium for complexation, we circumvent solubility and solvent competition problems that are inherent to the liquid phase. Characterization is performed using powder and single crystal X-ray diffraction, infrared solid-state spectroscopy and is complemented by a comprehensive cocrystal structure prediction methodology that surpasses earlier computational approaches in terms of realism and complexity. Our combined experimental and theoretical approach reveals that the α⋯π stacking is of electrostatic origin and is highly dependent on the steroid backbone’s unsaturated and conjugated character. We demonstrate that the α⋯π stacking interaction can drive the assembly of molecules, in particular progesterone, into solid-state complexes without the need for additional strong interactions. It results in a marked difference in the solid-state complexation propensities of different steroids with aromatic molecules, suggesting a strong dependence of the steroid-binding affinity and even physicochemical properties on the steroid’s A-ring structure. Hence, the hydrocarbon part of the steroid is a potentially important variable in structure-activity relationships for establishing the binding and signaling properties of steroids, and in the manufacture of pharmaceutical cocrystals. PMID:20624985

The role of chlorophyll b in photosynthesis: Hypothesis

PubMed Central

Eggink, Laura L; Park, Hyoungshin; Hoober, J Kenneth

2001-01-01

Background The physico-chemical properties of chlorophylls b and c have been known for decades. Yet the mechanisms by which these secondary chlorophylls support assembly and accumulation of light-harvesting complexes in vivo have not been resolved. Presentation Biosynthetic modifications that introduce electronegative groups on the periphery of the chlorophyll molecule withdraw electrons from the pyrrole nitrogens and thus reduce their basicity. Consequently, the tendency of the central Mg to form coordination bonds with electron pairs in exogenous ligands, a reflection of its Lewis acid properties, is increased. Our hypothesis states that the stronger coordination bonds between the Mg atom in chlorophyll b and chlorophyll c and amino acid sidechain ligands in chlorophyll a/b- and a/c-binding apoproteins, respectively, enhance their import into the chloroplast and assembly of light-harvesting complexes. Testing Several apoproteins of light-harvesting complexes, in particular, the major protein Lhcb1, are not detectable in leaves of chlorophyll b-less plants. A direct test of the hypothesis – with positive selection – is expression, in mutant plants that synthesize only chlorophyll a, of forms of Lhcb1 in which weak ligands are replaced with stronger Lewis bases. Implications The mechanistic explanation for the effects of deficiencies in chlorophyll b or c points to the need for further research on manipulation of coordination bonds between these chlorophylls and chlorophyll-binding proteins. Understanding these interactions will possibly lead to engineering plants to expand their light-harvesting antenna and ultimately their productivity. PMID:11710960

Relating physico-chemical properties of frozen green peas (Pisum sativum L.) to sensory quality.

PubMed

Nleya, Kathleen M; Minnaar, Amanda; de Kock, Henriëtte L

2014-03-30

The acceptability of frozen green peas depends on their sensory quality. There is a need to relate physico-chemical parameters to sensory quality. In this research, six brands of frozen green peas representing product sold for retail and caterer's markets were purchased and subjected to descriptive sensory evaluation and physico-chemical analyses (including dry matter content, alcohol insoluble solids content, starch content, °Brix, residual peroxidase activity, size sorting, hardness using texture analysis and colour measurements) to assess and explain product quality. The sensory quality of frozen green peas, particularly texture properties, were well explained using physico-chemical methods of analysis notably alcohol insoluble solids, starch content, hardness and °Brix. Generally, retail class peas were of superior sensory quality to caterer's class peas although one caterer's brand was comparable to the retail brands. Retail class peas were sweeter, smaller, greener, more moist and more tender than the caterer's peas. Retail class peas also had higher °Brix, a(*) , hue and chroma values; lower starch, alcohol insoluble solids, dry matter content and hardness measured. The sensory quality of frozen green peas can be partially predicted by measuring physico-chemical parameters particularly °Brix and to a lesser extent hardness by texture analyser, alcohol insoluble solids, dry matter and starch content. © 2013 Society of Chemical Industry.

An assessment of strontium sorption onto bentonite buffer material in waste repository.

PubMed

Pathak, Pankaj

2017-03-01

In the present study, changes occurring in sorption characteristics of a representative bentonite (WIn-BT) exposed to SrCl 2 (0.001-0.1 M) under the pH range of 1-13 were investigated. Such interaction revealed a significant variation in surface charge density and binding energy of ions with respect to bentonite, and alteration in their physicochemical properties viz., specific surface area, cation exchange capacity, thermal and mechanical behaviour were observed. The distribution coefficients (k d ) calculated for sorption onto virgin (UCBT) and contaminated bentonite (CBT) indicated a greater influence of mineralogical changes occurred with variance of pH and strontium concentration. Notably, the sorption mechanism clearly elucidates the effect of structural negative charge and existence of anionic metal species onto CBT, and depicted the reason behind significant k d values at highly acidic and alkaline pH. The maximum k d of UCBT and CBT (0.001M SrCl2) were 8.99 and 2.92 L/kg, respectively, at the soil pH 8.5; whereas it was 2.37 and 1.23 L/kg at pH 1 for the CBT (0.1M SrCl2) and CBT (0.01M SrCl2) , respectively. The findings of this study can be useful to identify the physicochemical parameters of candidate buffer material and sorption reversibility in waste repository.

The Effect of Physicochemical Modification on the Function of Antibodies Induced by Anti-Nicotine Vaccine in Mice

PubMed Central

Thorn, Jennifer M.; Bhattacharya, Keshab; Crutcher, Renata; Sperry, Justin; Isele, Colleen; Kelly, Barbara; Yates, Libbey; Zobel, James; Zhang, Ningli; Davis, Heather L.; McCluskie, Michael J.

2017-01-01

Smoking remains one of the major causes of morbidity and mortality worldwide. One approach to assisting smoking cessation is via anti-nicotine vaccines, composed of nicotine-like haptens conjugated to a carrier protein plus adjuvant(s). We have previously shown that the carrier, hapten, linker, hapten load, degree of conjugate aggregation, and presence of adducts can each influence the function (nicotine-binding capacity) of the antibody (Ab) induced. Herein, we extend those findings and show that tertiary structure is also critical to the induction of functional immune responses and that this can be influenced by conjugation conditions. We evaluated immunogenicity in mice using six lots of NIC7-CRM, a conjugate of 5-aminoethoxy-nicotine (Hapten 7), and a single point (glycine 52 to glutamic acid) mutant nontoxic form of diphtheria toxin, cross-reactive material 197 (CRM197), which were synthesized under different reaction conditions resulting in conjugates with equivalent molecular characteristics (hapten load, aggregates, adducts), but a different tertiary structure. When tested in mice, better functional responses (reduced nicotine in the brain of immunized animals relative to non-immunized controls) were obtained with conjugates with a more closed structure than those with an open conformation. These studies highlight the need for a better understanding of the physicochemical properties of small molecule conjugate vaccines. PMID:28513561

De novo active sites for resurrected Precambrian enzymes

NASA Astrophysics Data System (ADS)

Risso, Valeria A.; Martinez-Rodriguez, Sergio; Candel, Adela M.; Krüger, Dennis M.; Pantoja-Uceda, David; Ortega-Muñoz, Mariano; Santoyo-Gonzalez, Francisco; Gaucher, Eric A.; Kamerlin, Shina C. L.; Bruix, Marta; Gavira, Jose A.; Sanchez-Ruiz, Jose M.

2017-07-01

Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.

Drug Distribution. Part 1. Models to Predict Membrane Partitioning.

PubMed

Nagar, Swati; Korzekwa, Ken

2017-03-01

Tissue partitioning is an important component of drug distribution and half-life. Protein binding and lipid partitioning together determine drug distribution. Two structure-based models to predict partitioning into microsomal membranes are presented. An orientation-based model was developed using a membrane template and atom-based relative free energy functions to select drug conformations and orientations for neutral and basic drugs. The resulting model predicts the correct membrane positions for nine compounds tested, and predicts the membrane partitioning for n = 67 drugs with an average fold-error of 2.4. Next, a more facile descriptor-based model was developed for acids, neutrals and bases. This model considers the partitioning of neutral and ionized species at equilibrium, and can predict membrane partitioning with an average fold-error of 2.0 (n = 92 drugs). Together these models suggest that drug orientation is important for membrane partitioning and that membrane partitioning can be well predicted from physicochemical properties.

Structural characterization of pharmaceutical heparins prepared from different animal tissues.

PubMed

Fu, Li; Li, Guoyun; Yang, Bo; Onishi, Akihiro; Li, Lingyun; Sun, Peilong; Zhang, Fuming; Linhardt, Robert J

2013-05-01

Although most pharmaceutical heparin used today is obtained from porcine intestine, heparin has historically been prepared from bovine lung and ovine intestine. There is some regulatory concern about establishing the species origin of heparin. This concern began with the outbreak of mad cow disease in the 1990s and was exacerbated during the heparin shortage in the 2000s and the heparin contamination crisis of 2007-2008. Three heparins from porcine, ovine, and bovine were characterized through state-of-the-art carbohydrate analysis methods with a view profiling their physicochemical properties. Differences in molecular weight, monosaccharide and disaccharide composition, oligosaccharide sequence, and antithrombin III-binding affinity were observed. These data provide some insight into the variability of heparins obtained from these three species and suggest some analytical approaches that may be useful in confirming the species origin of a heparin active pharmaceutical ingredient. Copyright © 2013 Wiley Periodicals, Inc.

Intracellular production of hydrogels and synthetic RNA granules by multivalent molecular interactions

NASA Astrophysics Data System (ADS)

Nakamura, Hideki; Lee, Albert A.; Afshar, Ali Sobhi; Watanabe, Shigeki; Rho, Elmer; Razavi, Shiva; Suarez, Allister; Lin, Yu-Chun; Tanigawa, Makoto; Huang, Brian; Derose, Robert; Bobb, Diana; Hong, William; Gabelli, Sandra B.; Goutsias, John; Inoue, Takanari

2018-01-01

Some protein components of intracellular non-membrane-bound entities, such as RNA granules, are known to form hydrogels in vitro. The physico-chemical properties and functional role of these intracellular hydrogels are difficult to study, primarily due to technical challenges in probing these materials in situ. Here, we present iPOLYMER, a strategy for a rapid induction of protein-based hydrogels inside living cells that explores the chemically inducible dimerization paradigm. Biochemical and biophysical characterizations aided by computational modelling show that the polymer network formed in the cytosol resembles a physiological hydrogel-like entity that acts as a size-dependent molecular sieve. We functionalize these polymers with RNA-binding motifs that sequester polyadenine-containing nucleotides to synthetically mimic RNA granules. These results show that iPOLYMER can be used to synthetically reconstitute the nucleation of biologically functional entities, including RNA granules in intact cells.

Amyloid fibers provide structural integrity to Bacillus subtilis biofilms.

PubMed

Romero, Diego; Aguilar, Claudio; Losick, Richard; Kolter, Roberto

2010-02-02

Bacillus subtilis forms biofilms whose constituent cells are held together by an extracellular matrix. Previous studies have shown that the protein TasA and an exopolysaccharide are the main components of the matrix. Given the importance of TasA in biofilm formation, we characterized the physicochemical properties of this protein. We report that purified TasA forms fibers of variable length and 10-15 nm in width. Biochemical analyses, in combination with the use of specific dyes and microscopic analyses, indicate that TasA forms amyloid fibers. Consistent with this hypothesis, TasA fibers required harsh treatments (e.g., formic acid) to be depolymerized. When added to a culture of a tasA mutant, purified TasA restored wild-type biofilm morphology, indicating that the purified protein retained biological activity. We propose that TasA forms amyloid fibers that bind cells together in the biofilm.

EXTRACTION AND PHYSICO-CHEMICAL STUDIES OF DIASTASE-LIKE ENZYME FROM PIPER BETLE PETIOLES: PART 1

PubMed Central

Ramasarma, G.V.S; Dutta, Sadhan Kumar

1995-01-01

Petioles of the plant piper betle-bengal variety have been subjected for extraction employing standard procedure and the crude extract obtained has been evaluated for its diastase like activity and other physico-chemical properties to investigate further its possible biological and pharmacological activities. PMID:22556729

Synthesis and physicochemical characterizations and antimicrobial activity of ZnO nanoparticles

NASA Astrophysics Data System (ADS)

Sharma, Bhumika K.; Patel, Kinjal; Roy, Debesh R.

2018-05-01

Nanoparticles exhibit very interesting and useful physicochemical properties when they interact with substrates and goes through some physicochemical and/or biological processes. ZnO is known to be a highly demanding nanomaterial due to its discreet properties, shapes and sizes. A detail experimental study on the synthesis, characterization and antibacterial activity of ZnO nanoparticles (NPs) is performed. ZnO NPs are synthesized using chemical precipitation method. The understanding of crystal structure, morphology and elemental compositions are explained using Powder X-Ray Diffraction (XRD) and Field Emission Scanning Electron Microscope (FE-SEM) respectively. Fourier transform infrared spectroscopy (FTIR) is performed to achieve the information on the presence of various functional groups. The antibacterial activity of these ZnO NPs is investigated in terms of Zone of Inhibition (ZOI) against Escherichia coli (Gram negative) microorganisms.

Radiotracer properties determined by high performance liquid chromatography: a potential tool for brain radiotracer discovery.

PubMed

Tavares, Adriana Alexandre S; Lewsey, James; Dewar, Deborah; Pimlott, Sally L

2012-01-01

Previously, development of novel brain radiotracers has largely relied on simple screening tools. Improved selection methods at the early stages of radiotracer discovery and an increased understanding of the relationships between in vitro physicochemical and in vivo radiotracer properties are needed. We investigated if high performance liquid chromatography (HPLC) methodologies could provide criteria for lead candidate selection by comparing HPLC measurements with radiotracer properties in humans. Ten molecules, previously used as radiotracers in humans, were analysed to obtain the following measures: partition coefficient (Log P); permeability (P(m)); percentage of plasma protein binding (%PPB); and membrane partition coefficient (K(m)). Relationships between brain entry measurements (Log P, P(m) and %PPB) and in vivo brain percentage injected dose (%ID); and K(m) and specific binding in vivo (BP(ND)) were investigated. Log P values obtained using in silico packages and flask methods were compared with Log P values obtained using HPLC. The modelled associations with %ID were stronger for %PPB (r(2)=0.65) and P(m) (r(2)=0.77) than for Log P (r(2)=0.47) while 86% of BP(ND) variance was explained by K(m). Log P values were variable dependant on the methodology used. Log P should not be relied upon as a predictor of blood-brain barrier penetration during brain radiotracer discovery. HPLC measurements of permeability, %PPB and membrane interactions may be potentially useful in predicting in vivo performance and hence allow evaluation and ranking of compound libraries for the selection of lead radiotracer candidates at early stages of radiotracer discovery. Copyright © 2012 Elsevier Inc. All rights reserved.

Atomic evidence that modification of H-bonds established with amino acids critical for host-cell binding induces sterile immunity against malaria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patarroyo, Manuel E., E-mail: mepatarr@mail.com; Universidad Nacional de Colombia, Bogota; Cifuentes, Gladys

Based on the 3D X-ray crystallographic structures of relevant proteins of the malaria parasite involved in invasion to host cells and 3D NMR structures of High Activity Binding Peptides (HABPs) and their respective analogues, it was found that HABPs are rendered into highly immunogenic and sterile immunity inducers in the Aotus experimental model by modifying those amino acids that establish H-bonds with other HABPs or binding to host's cells. This finding adds striking and novel physicochemical principles, at the atomic level, for a logical and rational vaccine development methodology against infectious disease, among them malaria.

Nisin as a Food Preservative: Part 1: Physicochemical Properties, Antimicrobial Activity, and Main Uses.

PubMed

Gharsallaoui, Adem; Oulahal, Nadia; Joly, Catherine; Degraeve, Pascal

2016-06-10

Nisin is a natural preservative for many food products. This bacteriocin is mainly used in dairy and meat products. Nisin inhibits pathogenic food borne bacteria such as Listeria monocytogenes and many other Gram-positive food spoilage microorganisms. Nisin can be used alone or in combination with other preservatives or also with several physical treatments. This paper reviews physicochemical and biological properties of nisin, the main factors affecting its antimicrobial effectiveness, and its food applications as an additive directly incorporated into food matrices.

Distribution of trace elements in certain ecological components and animal products in a dairy farm at Tirupati, Chittoor District, Andhra Pradesh, India.

PubMed

Raghu, V

2013-12-01

Biogeochemical characteristics of the cattle are dealt based on the observations made in Ayurveda in the light of modern scientific developments in applied environmental geochemistry. The biogeochemical characteristics of certain important ecological components and animal products of the stall-fed animals were studied. For this purpose, a dairy farm of Tirumala-Tirupati Devasthanams, a religious organization in Tirupati, Chittoor District, Andhra Pradesh was selected. This study is intended to trace out the trace element interactions in the ecological components (soil, water, fodder, feed) of the stall-fed animals and their output components viz. dung, urine and milk. Physical, physico-chemical properties and certain trace elements were determined for composite samples of ecological components and dung, urine, and milk of stall-fed animals. The variations in the distribution of pH and EC of urine and milk reflect the variations in their physico-chemical or hydro-chemical properties. As mentioned in Ayurveda, not only the properties of milk but also the properties of dung and urine reflect their diet and conditions of their habitat. Even though the diet is the same, the cows of different breeds yield milk of variable physical, physico-chemical properties and trace element composition which can be attributed to their body colour, substantiating Ayurveda.

Fractionation, physicochemical property and immunological activity of polysaccharides from Cassia obtusifolia.

PubMed

Feng, Lei; Yin, Junyi; Nie, Shaoping; Wan, Yiqun; Xie, Mingyong

2016-10-01

The seeds of Cassia obtusifolia are widely used as a drink in Asia and an additive in food industry. Considerable amounts of water-soluble polysaccharides were found in the whole seeds, while conflicting results on structure characteristics have been reported, and few studies have been reported on physicochemical properties and immunomodulatory activities. In the present study, gradient ethanol precipitation was applied to fractionate the water-soluble polysaccharide (CP), and two sub-fractions CP-30 (30% ethanol precipitate) and CP-40 (40% ethanol precipitate) were obtained. Different rheological properties for CP-30 and CP-40 were found, indicating the differences in structure characteristics between CP-30 and CP-40. Chemical properties, including molecular weight, monosaccharide composition, and glycosidic linkage were investigated. Compared with CP-30, CP-40 had lower molecular weight and higher content of xylose. The immunomodulatory effects of CP, CP-30 and CP-40 were assessed. All of them were found to possess significant immunomodulation activities, while varied effects of them on macrophage functions were observed. The aim of the present study was to develop a simple and efficient method to purify cassia polysaccharides, and investigate their physicochemical properties and biological activities, which was meaningful for their potential use in food industry and folk medicine. Copyright © 2016. Published by Elsevier B.V.

Estimation of Melting Points of Organics.

PubMed

Yalkowsky, Samuel H; Alantary, Doaa

2018-05-01

Unified physicochemical property estimation relationships is a system of empirical and theoretical relationships that relate 20 physicochemical properties of organic molecules to each other and to chemical structure. Melting point is a key parameter in the unified physicochemical property estimation relationships scheme because it is a determinant of several other properties including vapor pressure, and solubility. This review describes the first-principals calculation of the melting points of organic compounds from structure. The calculation is based on the fact that the melting point, T m , is equal to the ratio of the heat of melting, ΔH m , to the entropy of melting, ΔS m . The heat of melting is shown to be an additive constitutive property. However, the entropy of melting is not entirely group additive. It is primarily dependent on molecular geometry, including parameters which reflect the degree of restriction of molecular motion in the crystal to that of the liquid. Symmetry, eccentricity, chirality, flexibility, and hydrogen bonding, each affect molecular freedom in different ways and thus make different contributions to the total entropy of fusion. The relationships of these entropy determining parameters to chemical structure are used to develop a reasonably accurate means of predicting the melting points over 2000 compounds. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Two-level QSAR network (2L-QSAR) for peptide inhibitor design based on amino acid properties and sequence positions.

PubMed

Du, Q S; Ma, Y; Xie, N Z; Huang, R B

2014-01-01

In the design of peptide inhibitors the huge possible variety of the peptide sequences is of high concern. In collaboration with the fast accumulation of the peptide experimental data and database, a statistical method is suggested for peptide inhibitor design. In the two-level peptide prediction network (2L-QSAR) one level is the physicochemical properties of amino acids and the other level is the peptide sequence position. The activity contributions of amino acids are the functions of physicochemical properties and the sequence positions. In the prediction equation two weight coefficient sets {ak} and {bl} are assigned to the physicochemical properties and to the sequence positions, respectively. After the two coefficient sets are optimized based on the experimental data of known peptide inhibitors using the iterative double least square (IDLS) procedure, the coefficients are used to evaluate the bioactivities of new designed peptide inhibitors. The two-level prediction network can be applied to the peptide inhibitor design that may aim for different target proteins, or different positions of a protein. A notable advantage of the two-level statistical algorithm is that there is no need for host protein structural information. It may also provide useful insight into the amino acid properties and the roles of sequence positions.

Influence of internal composition on physicochemical properties of alginate aqueous-core capsules.

PubMed

Ben Messaoud, Ghazi; Sánchez-González, Laura; Probst, Laurent; Desobry, Stéphane

2016-05-01

To enhance physicochemical properties of alginate aqueous-core capsules, conventional strategies were focused in literature on designing composite and coated capsules. In the present study, own effect of liquid-core composition on mechanical and release properties was investigated. Capsules were prepared by dripping a CaCl2 solution into an alginate gelling solution. Viscosity of CaCl2 solution was adjusted by adding cationic, anionic and non-ionic naturally derived polymers, respectively chitosan, xanthan gum and guar gum. In parallel, uniform alginate hydrogels were prepared by different methods (pouring, in situ forming and mixing). Mechanical stability of capsules and plane hydrogels were respectively evaluated by compression experiments and small amplitude oscillatory shear rheology and then correlated. Capsules permeability was evaluated by monitoring diffusion of encapsulated cochineal dye, riboflavin and BSA. The core-shell interactions were investigated by ATR-FTIR. Results showed that inner polymer had an impact on membrane stability and could act as an internal coating or provide mechanical reinforcement. Mechanical properties of alginate capsules were in a good agreement with rheological behavior of plane hydrogels. Release behavior of the entrapped molecules changed considerably. This study demonstrated the importance of aqueous-core composition, and gave new insights for possible adjusting of microcapsules physicochemical properties by modulating core-shell interactions. Copyright © 2016 Elsevier Inc. All rights reserved.

Human β-Synuclein Rendered Fibrillogenic by Designed Mutations

PubMed Central

Zibaee, Shahin; Fraser, Graham; Jakes, Ross; Owen, David; Serpell, Louise C.; Crowther, R. Anthony; Goedert, Michel

2010-01-01

Filamentous inclusions made of α-synuclein are found in nerve cells and glial cells in a number of human neurodegenerative diseases, including Parkinson disease, dementia with Lewy bodies, and multiple system atrophy. The assembly and spreading of these inclusions are likely to play an important role in the etiology of common dementias and movement disorders. Both α-synuclein and the homologous β-synuclein are abundantly expressed in the central nervous system; however, β-synuclein is not present in the pathological inclusions. Previously, we observed a poor correlation between filament formation and the presence of residues 73–83 of α-synuclein, which are absent in β-synuclein. Instead, filament formation correlated with the mean β-sheet propensity, charge, and hydrophilicity of the protein (global physicochemical properties) and β-strand contiguity calculated by a simple algorithm of sliding averages (local physicochemical property). In the present study, we rendered β-synuclein fibrillogenic via one set of point mutations engineered to enhance global properties and a second set engineered to enhance predominantly β-strand contiguity. Our findings show that the intrinsic physicochemical properties of synucleins influence their fibrillogenic propensity via two distinct but overlapping modalities. The implications for filament formation and the pathogenesis of neurodegenerative diseases are discussed. PMID:20833719

Lutetium(III) acetate phthalocyanines for photodynamic therapy applications: Synthesis and photophysicochemical properties.

PubMed

Mantareva, Vanya; Durmuş, Mahmut; Aliosman, Meliha; Stoineva, Ivanka; Angelov, Ivan

2016-06-01

The development of new water-soluble photosensitizers for photodynamic therapy (PDT) applications is a very active research topic. Efforts have been made to obtain the far-red absorbing phthalocyanine complexes with molecular design that facilitates the uptake and selectivity for a high PDT efficiency. The monomolecular lutetium(III) acetate phthalocyanines (LuPcs) substituted with methylpyridyloxy groups at non-peripheral (5) and peripheral (6) positions were synthesized by following the modification of the well-known synthetical routes. The photo-physicochemical properties of the both quaternized LuPcs were evaluated by the steady-state and time-resolved spectroscopy. The photochemical technique was applied to study the generation of the singlet oxygen. Two water-soluble and cationic LuPcs were synthesized and chemically characterized. The photo-physicochemical properties of absorption (675 and 685nm) and the red shifted fluorescence (704 and 721nm) as well as the fluorescence lifetimes (2.24 and 3.27ns) were studied. The promising values of singlet oxygen quantum yields (0.32 for 5 and 0.35 for 6) were determined. Lutetium(III) acetate phthalocyanine complexes were synthesized and evaluated with physicochemical properties suitable for future photodynamic therapy applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Modified β-Cyclodextrin Inclusion Complex to Improve the Physicochemical Properties of Albendazole. Complete In Vitro Evaluation and Characterization

PubMed Central

García, Agustina; Leonardi, Darío; Salazar, Mario Oscar; Lamas, María Celina

2014-01-01

The potential use of natural cyclodextrins and their synthetic derivatives have been studied extensively in pharmaceutical research and development to modify certain properties of hydrophobic drugs. The ability of these host molecules of including guest molecules within their cavities improves notably the physicochemical properties of poorly soluble drugs, such as albendazole, the first chosen drug to treat gastrointestinal helminthic infections. Thus, the aim of this work was to synthesize a beta cyclodextrin citrate derivative, to analyze its ability to form complexes with albendazole and to evaluate its solubility and dissolution rate. The synthesis progress of the cyclodextrin derivative was followed by electrospray mass spectrometry and the acid-base titration of the product. The derivative exhibited an important drug affinity. Nuclear magnetic resonance experiments demonstrated that the tail and the aromatic ring of the drug were inside the cavity of the cyclodextrin derivative. The inclusion complex was prepared by spray drying and full characterized. The drug dissolution rate displayed exceptional results, achieving 100% drug release after 20 minutes. The studies indicated that the inclusion complex with the cyclodextrin derivative improved remarkably the physicochemical properties of albendazole, being a suitable excipient to design oral dosage forms. PMID:24551084

Analysis of Physicochemical Properties for Drugs of Natural Origin.

PubMed

Camp, David; Garavelas, Agatha; Campitelli, Marc

2015-06-26

The impact of time, therapy area, and route of administration on 13 physicochemical properties calculated for 664 drugs developed from a natural prototype was investigated. The mean values for the majority of properties sampled over five periods from pre-1900 to 2013 were found to change in a statistically significant manner. In contrast, lipophilicity and aromatic ring count remained relatively constant, suggesting that these parameters are the most important for successful prosecution of a natural product drug discovery program if the route of administration is not focused exclusively on oral availability. An examination by therapy area revealed that anti-infective agents had the most differences in physicochemical property profiles compared with other areas, particularly with respect to lipophilicity. However, when this group was removed, the variation between the mean values for lipophilicity and aromatic ring count across the remaining therapy areas was again found not to change in a meaningful manner, further highlighting the importance of these two parameters. The vast majority of drugs with a natural progenitor were formulated for either oral and/or injectable administration. Injectables were, on average, larger and more polar than drugs developed for oral, topical, and inhalation routes.

Molecular-Level Control of Ciclopirox Olamine Release from Poly(ethylene oxide)-Based Mucoadhesive Buccal Films: Exploration of Structure-Property Relationships with Solid-State NMR.

PubMed

Urbanova, Martina; Gajdosova, Marketa; Steinhart, Miloš; Vetchy, David; Brus, Jiri

2016-05-02

Mucoadhesive buccal films (MBFs) provide an innovative way to facilitate the efficient site-specific delivery of active compounds while simultaneously separating the lesions from the environment of the oral cavity. The structural diversity of these complex multicomponent and mostly multiphase systems as well as an experimental strategy for their structural characterization at molecular scale with atomic resolution were demonstrated using MBFs of ciclopirox olamine (CPX) in a poly(ethylene oxide) (PEO) matrix as a case study. A detailed description of each component of the CPX/PEO films was followed by an analysis of the relationships between each component and the physicochemical properties of the MBFs. Two distinct MBFs were identified by solid-state NMR spectroscopy: (i) at low API (active pharmaceutical ingredient) loading, a nanoheterogeneous solid solution of CPX molecularly dispersed in an amorphous PEO matrix was created; and (ii) at high API loading, a pseudoco-crystalline system containing CPX-2-aminoethanol nanocrystals incorporated into the interlamellar space of a crystalline PEO matrix was revealed. These structural differences were found to be closely related to the mechanical and physicochemical properties of the prepared MBFs. At low API loading, the polymer chains of PEO provided sufficient quantities of binding sites to stabilize the CPX that was molecularly dispersed in the highly amorphous semiflexible polymer matrix. Consequently, the resulting MBFs were soft, with low tensile strength, plasticity, and swelling index, supporting rapid drug release. At high CPX content, however, the active compounds and the polymer chains simultaneously cocrystallized, leaving the CPX to form nanocrystals grown directly inside the spherulites of PEO. Interfacial polymer-drug interactions were thus responsible not only for the considerably enhanced plasticity of the system but also for the exclusive crystallization of CPX in the thermodynamically most stable polymorphic form, Form I, which exhibited reduced dissolution kinetics. The bioavailability of CPX olamine formulated as PEO-based MBFs can thus be effectively controlled by inducing the complete dispersion and/or microsegregation and nanocrystallization of CPX olamine in the polymer matrix. Solid-state NMR spectroscopy is an efficient tool for exploring structure-property relationships in these complex pharmaceutical solids.

Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction.

PubMed

Daberdaku, Sebastian; Ferrari, Carlo

2018-02-06

The correct determination of protein-protein interaction interfaces is important for understanding disease mechanisms and for rational drug design. To date, several computational methods for the prediction of protein interfaces have been developed, but the interface prediction problem is still not fully understood. Experimental evidence suggests that the location of binding sites is imprinted in the protein structure, but there are major differences among the interfaces of the various protein types: the characterising properties can vary a lot depending on the interaction type and function. The selection of an optimal set of features characterising the protein interface and the development of an effective method to represent and capture the complex protein recognition patterns are of paramount importance for this task. In this work we investigate the potential of a novel local surface descriptor based on 3D Zernike moments for the interface prediction task. Descriptors invariant to roto-translations are extracted from circular patches of the protein surface enriched with physico-chemical properties from the HQI8 amino acid index set, and are used as samples for a binary classification problem. Support Vector Machines are used as a classifier to distinguish interface local surface patches from non-interface ones. The proposed method was validated on 16 classes of proteins extracted from the Protein-Protein Docking Benchmark 5.0 and compared to other state-of-the-art protein interface predictors (SPPIDER, PrISE and NPS-HomPPI). The 3D Zernike descriptors are able to capture the similarity among patterns of physico-chemical and biochemical properties mapped on the protein surface arising from the various spatial arrangements of the underlying residues, and their usage can be easily extended to other sets of amino acid properties. The results suggest that the choice of a proper set of features characterising the protein interface is crucial for the interface prediction task, and that optimality strongly depends on the class of proteins whose interface we want to characterise. We postulate that different protein classes should be treated separately and that it is necessary to identify an optimal set of features for each protein class.

Preparation and physicochemical characterization of spray-dried and jet-milled microparticles containing bosentan hydrate for dry powder inhalation aerosols.

PubMed

Lee, Hyo-Jung; Kang, Ji-Hyun; Lee, Hong-Goo; Kim, Dong-Wook; Rhee, Yun-Seok; Kim, Ju-Young; Park, Eun-Seok; Park, Chun-Woong

2016-01-01

The objectives of this study were to prepare bosentan hydrate (BST) microparticles as dry powder inhalations (DPIs) via spray drying and jet milling under various parameters, to comprehensively characterize the physicochemical properties of the BST hydrate microparticles, and to evaluate the aerosol dispersion performance and dissolution behavior as DPIs. The BST microparticles were successfully prepared for DPIs by spray drying from feeding solution concentrations of 1%, 3%, and 5% (w/v) and by jet milling at grinding pressures of 2, 3, and 4 MPa. The physicochemical properties of the spray-dried (SD) and jet-milled (JM) microparticles were determined via scanning electron microscopy, atomic force microscopy, dynamic light scattering particle size analysis, Karl Fischer titration, surface analysis, pycnometry, differential scanning calorimetry, powder X-ray diffraction, and Fourier transform infrared spectroscopy. The in vitro aerosol dispersion performance and drug dissolution behavior were evaluated using an Anderson cascade impactor and a Franz diffusion cell, respectively. The JM microparticles exhibited an irregular corrugated surface and a crystalline solid state, while the SD microparticles were spherical with a smooth surface and an amorphous solid state. Thus, the in vitro aerosol dispersion performance and dissolution behavior as DPIs were considerably different due to the differences in the physicochemical properties of the SD and JM microparticles. In particular, the highest grinding pressures under jet milling exhibited excellent aerosol dispersion performance with statistically higher values of 56.8%±2.0% of respirable fraction and 33.8%±2.3% of fine particle fraction and lower mass median aerodynamic diameter of 5.0±0.3 μm than the others ( P <0.05, analysis of variance/Tukey). The drug dissolution mechanism was also affected by the physicochemical properties that determine the dissolution kinetics of the SD and JM microparticles, which were well fitted into the Higuchi and zero-order models, respectively.

Physicochemical characterisation of fluids and soft foods frequently mixed with oral drug formulations prior to administration to children.

PubMed

Kersten, E; Barry, A; Klein, S

2016-03-01

Oral drug administration to children poses specific pharmaceutical challenges that are often not seen to the same extent in adults, and whose occurrence may also be age dependent. When an age-appropriate dosage form is not available, manipulation of adult dosage forms (e.g., splitting and crushing of tablets or opening of capsules) has been reported as a means to facilitate administration to children. To enhance swallowability and/or mask an unpleasant taste of the dosage form to be administered, crushed/split tablets or the contents of capsules are often mixed with food or drinks or suspended in a vehicle prior to administration. However, it seems that the risks and benefits of an approach whereby the dosage form is modified prior to administration in this manner are everything but clear. The aim of the present study was to gain an overview of the physicochemical properties of a number of fluids, soft foods and suspension vehicles that are commonly reported to be mixed with oral medications before administration to children to improve patient acceptability. For this purpose, physicochemical parameters of 15 different fluids, soft foods and suspension vehicles were measured. These included pH, buffer capacity, osmolality, surface tension and viscosity. Results of the study clearly show the differences in physicochemical properties of the test candidates. It is thus obvious that the type of fluid/food mixed with a drug product before administration may have a significant impact on bioavailability of the drug administered. Therefore, a risk-based assessment of such practices considering API properties, formulation features and physicochemical properties of the fluids and foods intended to be co-administered with the dosage form, in conjunction with the anatomical and physiological maturity of the gastro-intestinal tract in the intended paediatric population, should be an essential part of paediatric oral formulation development.

Physicochemical characterization of 3,6-diHydroxyflavone binding BSA immobilized on PEG-coated silver nanoparticles

NASA Astrophysics Data System (ADS)

Voicescu, Mariana; Ionescu, Sorana; Calderon-Moreno, Jose M.; Nistor, Cristina L.

2017-02-01

Studies based on silver nanoparticles (SNPs) and polyethylene glycols (PEGs) are mainly in the pharmaceutical field, with PEG as good "vehicle" to transport protein-based drugs. In this work, physicochemical characteristics of 3,6-diHydroxyflavone (3,6-diHF) binding bovine serum albumin (BSA) on PEG (Tween20, L64, and Myrj52)-coated SNPs have been investigated by steady-state and time-resolved fluorescence spectroscopy. These interactions give rise to the formation of intermolecular and intramolecular H bonds. As a subject of interest, the effect of temperature (30-60 °C) on the H bonds was studied by steady-state fluorescence. The size distribution and zeta potential of SNPs were determined by dynamic light scattering (DLS). Scanning electron microscopy (SEM) analysis revealed the spherical nature of particles with average diameter 40-80 nm. The structure, stability, dynamics, and conformational changes in adsorbed BSA protein on the PEG-coated SNPs surface have been also investigated by steady-state/lifetime fluorescence and circular dichroism spectroscopy. The results have relevance in the oxidative stress and drug delivery processes.

Interleukin-13 conjugated quantum dots for identification of glioma initiating cells and their extracellular vesicles.

PubMed

Madhankumar, A B; Mrowczynski, Oliver D; Patel, Suhag R; Weston, Cody L; Zacharia, Brad E; Glantz, Michael J; Siedlecki, Christopher A; Xu, Li-Chong; Connor, James R

2017-08-01

Cadmium selenide (CdSe) based quantum dots modified with polyethylene glycol and chemically linked to interleukin-13 (IL13) were prepared with the aim of identifying the high affinity receptor (IL13Rα2) which is expressed in glioma stem cells and exosomes secreted by these cancer stem cells. IL13 conjugated quantum dots (IL13QD) were thoroughly characterized for their physicochemical properties including particle size and surface morphology. Furthermore, the specific binding of the IL13QD to glioma cells and to glioma stem cells (GSC) was verified using a competitive binding study. The exosomes were isolated from the GSC conditioned medium and the expression of IL13Rα2 in the GSC and exosomes was verified. The binding property of IL13QD to the tumor associated exosomes was initially confirmed by transmission electron microscopy. The force of attraction between the quantum dots and U251 glioma cells and the exosomes was investigated by atomic force microscopy, which indicated a higher force of binding interaction between the IL13QD and IL13Rα2 expressing glioma cells and exosomes secreted by glioma stem cells. Flow cytometry of the IL13QD and exosomes from the culture media and cerebrospinal fluid (CSF) of patients with glioma tumors indicated a distinctly populated complex pattern different from that of non-targeted quantum dots and bovine serum albumin (BSA) conjugated quantum dots confirming specific binding potential of the IL13QD to the tumor associated exosomes. The results of this study demonstrate that IL13QD can serve as an ex vivo marker for glioma stem cells and exosomes that can inform diagnosis and prognosis of patients harboring malignant disease. Functionalized quantum dots are flexible semiconductor nanomaterials which have an immense application in biomedical research. In particular, when they are functionalized with biomolecules like proteins or antibodies, they have the specialized ability to detect the expression of receptors and antigens in cells and tissues. In this study we designed a cytokine (interleukin-13) functionalized quantum dot to detect a cancer associated receptor expressed in cancer stem cells and the extracellular vesicles (exosomes) secreted by the cancer cells themselves. The binding pattern of these cytokine modified quantum dots to the cancer stem cells and exosomes alters the physical properties of the complex in the fixed and suspended form. This altered binding pattern can be monitored by a variety of techniques, including transmission electron microscopy, atomic force microscopy and flow cytometry, and subsequent characterization of this quantum dot binding profile provides useful data that can be utilized as a fingerprint to detect cancer disease progression. This type of functionalized quantum dot fingerprint is especially useful for invasive cancers including brain and other metastatic cancers and may allow for earlier detection of disease progression or recurrence, thus saving the lives of patients suffering from this devastating disease. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Evolution of the physicochemical properties of marketed drugs: can history foretell the future?

PubMed

Faller, Bernard; Ottaviani, Giorgio; Ertl, Peter; Berellini, Giuliano; Collis, Alan

2011-11-01

A set of diverse bioactive molecules, relevant from a medicinal chemistry viewpoint, was assembled and used to navigate the physicochemical property space of new and old, or traditional drugs against a larger set of 12,000 diverse bioactive small molecules. Most drugs on the market only occupy a fraction of the property space of the bioactive molecules, whereas new molecular entities (NMEs) approved since 2002 are moving away from this traditional drug space. In this new territory, semi-empirical rules derived from knowledge accumulated from historic, older molecules are not necessarily valid and different liabilities become more prominent. Copyright © 2011 Elsevier Ltd. All rights reserved.

Assessing therapeutic relevance of biologically interesting, ampholytic substances based on their physicochemical and spectral characteristics with chemometric tools

NASA Astrophysics Data System (ADS)

Judycka, U.; Jagiello, K.; Bober, L.; Błażejowski, J.; Puzyn, T.

2018-06-01

Chemometric tools were applied to investigate the biological behaviour of ampholytic substances in relation to their physicochemical and spectral properties. Results of the Principal Component Analysis suggest that size of molecules and their electronic and spectral characteristics are the key properties required to predict therapeutic relevance of the compounds examined. These properties were used for developing the structure-activity classification model. The classification model allows assessing the therapeutic behaviour of ampholytic substances on the basis of solely values of descriptors that can be obtained computationally. Thus, the prediction is possible without necessity of carrying out time-consuming and expensive laboratory tests, which is its main advantage.

Estimating the physicochemical properties of polyhalogenated aromatic and aliphatic compounds using UPPER: part 2. Aqueous solubility, octanol solubility and octanol-water partition coefficient.

PubMed

Admire, Brittany; Lian, Bo; Yalkowsky, Samuel H

2015-01-01

The UPPER (Unified Physicochemical Property Estimation Relationships) model uses additive and non-additive parameters to estimate 20 biologically relevant properties of organic compounds. The model has been validated by Lian and Yalkowsky (2014) on a data set of 700 hydrocarbons. Recently, Admire et al. (2014) expanded the model to predict the boiling and melting points of 1288 polyhalogenated benzenes, biphenyls, dibenzo-p-dioxins, diphenyl ethers, anisoles and alkanes. In this work, 19 new group descriptors are determined and used to predict the aqueous solubilities, octanol solubilities and the octanol-water coefficients. Copyright © 2014 Elsevier Ltd. All rights reserved.

Mechanisms of carbon nanotube-induced pulmonary fibrosis: a physicochemical characteristic perspective.

PubMed

Duke, Katherine S; Bonner, James C

2018-05-01

Carbon nanotubes (CNTs) are engineered nanomaterials (ENMs) with numerous beneficial applications. However, they could pose a risk to human health from occupational or consumer exposures. Rodent models demonstrate that exposure to CNTs via inhalation, instillation, or aspiration results in pulmonary fibrosis. The severity of the fibrogenic response is determined by various physicochemical properties of the nanomaterial such as residual metal catalyst content, rigidity, length, aggregation status, or surface charge. CNTs are also increasingly functionalized post-synthesis with organic or inorganic agents to modify or enhance surface properties. The mechanisms of CNT-induced fibrosis involve oxidative stress, innate immune responses of macrophages, cytokine and growth factor production, epithelial cell injury and death, expansion of the pulmonary myofibroblast population, and consequent extracellular matrix accumulation. A comprehensive understanding of how physicochemical properties affect the fibrogenic potential of various types of CNTs should be considered in combination with genetic variability and gain or loss of function of specific genes encoding secreted cytokines, enzymes, or intracellular cell signaling molecules. Here, we cover the current state of the literature on mechanisms of CNT-exposed pulmonary fibrosis in rodent models with a focus on physicochemical characteristics as principal drivers of the mechanisms leading to pulmonary fibrosis. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Respiratory Disease Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials. © 2017 Wiley Periodicals, Inc.

Principal Physicochemical Methods Used to Characterize Dendrimer Molecule Complexes Used as Genetic Therapy Agents, Nanovaccines or Drug Carriers.

PubMed

Alberto, Rodríguez Fonseca Rolando; Joao, Rodrigues; de Los Angeles, Muñoz-Fernández María; Alberto, Martínez Muñoz; Manuel Jonathan, Fragoso Vázquez; José, Correa Basurto

2017-08-30

Nanomedicine is the application of nanotechnology to medicine. This field is related to the study of nanodevices and nanomaterials applied to various medical uses, such as in improving the pharmacological properties of different molecules. Dendrimers are synthetic nanoparticles whose physicochemical properties vary according to their chemical structure. These molecules have been extensively investigated as drug nanocarriers to improve drug solubility and as sustained-release systems. New therapies such as gene therapy and the development of nanovaccines can be improved by the use of dendrimers. The biophysical and physicochemical characterization of nucleic acid/peptide-dendrimer complexes is crucial to identify their functional properties prior to biological evaluation. In that sense, it is necessary to first identify whether the peptide-dendrimer or nucleic aciddendrimer complexes can be formed and whether the complex can dissociate under the appropriate conditions at the target cells. In addition, biophysical and physicochemical characterization is required to determine how long the complexes remain stable, what proportion of peptide or nucleic acid is required to form the complex or saturate the dendrimer, and the size of the complex formed. In this review, we present the latest information on characterization systems for dendrimer-nucleic acid, dendrimer-peptide and dendrimer-drug complexes with several biotechnological and pharmacological applications. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Impacts of Solar PV Arrays on Physicochemical Properties of Soil

NASA Astrophysics Data System (ADS)

Cagle, A.; Choi, C. S.; Macknick, J.; Ravi, S.; Bickhart, R.

2017-12-01

The deployment of renewable energy technologies, such as solar photovoltaics (PV), is rapidly escalating. While PV can provide clean, renewable energy, there is uncertainty regarding its potential positive and/or negative impacts on the local environment. Specifically, its effects on the physicochemical properties of the underlying soil have not been systematically quantified. This study facilitates the discussion on the effects of PV installations related to the following questions: i. How do soil moisture, infiltration rates, total organic carbon, and nitrogen contents vary spatially under a PV array? ii. How do these physicochemical properties compare to undisturbed and adjacent land covered in native vegetation? iii. Are these variations statistically significant to provide insight on whether PV installations have beneficial or detrimental impacts on soil? We address these questions through field measurements of soil moisture, infiltration, grain particle size distribution, total organic carbon, and nitrogen content at a 1-MW solar PV array located at the National Renewable Energy Laboratory in Golden, Colorado. We collect data via multiple transects underneath the PV array as as well as in an adjacent plot of undisturbed native vegetation. Measurements are taken at four positions under the solar panels; the east-facing edge, center area under the panel, west-facing edge, and interspace between panel rows to capture differences in sun exposure as well as precipitation runoff of panels. Measurements are collected before and after a precipitation event to capture differences in soil moisture and infiltration rates. Results of this work can provide insights for research fields associated with the co-location of agriculture and PV installations as well as the long term ecological impacts of solar energy development. Trends in physicochemical properties under and between solar panels can affect the viability of co-location of commercial crops in PV arrays, the ability to grow native vegetation groundcover, and also the revegetation of a solar PV landscape after decommissioning. This study helps to illuminate the range of physicochemical properties of soils underlying solar PV arrays, addressing a key research gap and encouraging further research in the area.

Physicochemical stability and in vitro bioaccessibility of ß-carotene nanoemulsions stabilized with whey protein-dextran conjugates

USDA-ARS?s Scientific Manuscript database

In this study, ß-carotene (BC)-loaded nanoemulsions encapsulated with native whey protein isolate (WPI) and WPI-dextran (DT, 5 kDa, 20 kDa, and 70 kDa) conjugates were prepared and the effects of glycosylation with various molecular weight DTs on the physicochemical property, lipolysis, and BC bioac...

Influence of vacuum drying temperature on: physico-chemical composition and antioxidant properties of murta berries

USDA-ARS?s Scientific Manuscript database

Murta (Ugni molinae T.) berries were vacuum dried at a constant pressure of 15 kPa. The effects of processing temperatures (50, 60, 70, 80 and 90 °C) on the physico-chemical characteristics, the phenolic and flavonoid compounds, the antioxidant activity (measured by DPPH and ORAC) and the sugar and ...

Structural and physico-chemical properties of insoluble rice bran fiber: effect of acid–base induced modifications

USDA-ARS?s Scientific Manuscript database

The structural modifications of insoluble rice bran fiber (IRBF) by sequential regimes of sulphuric acid (H2SO4) and their effects on the physicochemical attributes were studied. The increment of H2SO4 concentration resulted in decreased water holding capacity that ultimately enhanced the oil bindin...

Physicochemical and functional properties of dietary fiber from maca (Lepidium meyenii Walp.) liquor residue.

PubMed

Chen, Jinjin; Zhao, Qingsheng; Wang, Liwei; Zha, Shenghua; Zhang, Lijun; Zhao, Bing

2015-11-05

Using maca (Lepidium meyenii) liquor residue as the raw material, dietary fiber (DF) was prepared by chemical (MCDF) and enzymatic (MEDF) methods, respectively, of which the physicochemical and functional properties were comparatively studied. High contents of DF were found in MCDF (55.63%) and MEDF (81.10%). Both fibers showed good functional properties, including swelling capacity, water holding capacity, oil holding capacity, glucose adsorption capacity and glucose retardation index. MEDF showed better functional properties, which could be attributed to its higher content of DF, more irregular surface and more abundant monosaccharide composition. The results herein suggest that maca DF prepared by enzymatic method from liquor residue is a good functional ingredient in food products. Copyright © 2015 Elsevier Ltd. All rights reserved.

Physicochemical properties of collagen solutions cross-linked by glutaraldehyde.

PubMed

Tian, Zhenhua; Li, Conghu; Duan, Lian; Li, Guoying

2014-06-01

The physicochemical properties of collagen solutions (5 mg/ml) cross-linked by various amounts of glutaraldehyde (GTA) [GTA/collagen (w/w) = 0-0.5] under acidic condition (pH 4.00) were examined. Based on the results of the determination of residual amino group content, sodium dodecyl sulphate-polyacrylamide gel electrophoresis, dynamic rheological measurements, differential scanning calorimetry and atomic force microscopy (AFM), it was proved that the collagen solutions possessed strikingly different physicochemical properties depending on the amount of GTA. At low GTA amounts [GTA/collagen (w/w) ≤ 0.1], the residual amino group contents of the cross-linked collagens decreased largely from 100% to 32.76%, accompanied by an increase in the molecular weight. Additionally, increases of the fiber diameter and the values of G', G″ and η* were measured, while the thermal denaturation temperature (Td) did not change visibly and the fluidity of collagen samples was still retained with increasing the GTA amount. When the ratio of GTA to collagen exceeded 0.1, although the residual amino group content only decreased by ~8.2%, the cross-linked collagen solution [GTA/collagen (w/w) = 0.3] displayed a clear loss of flow and a sudden rise (~2.0 °C) of the Td value compared to the uncross-linked collagen solution, probably illustrating that the collagen solution was converted into a gel with mature network structure-containing nuclei observed in AFM image. It was conjectured that the physicochemical properties of the collagen solutions might be in connection with the cross-linking between collagen molecules from the same aggregate or different aggregates.

Toward a systematic exploration of nano-bio interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bai, Xue; Liu, Fang; Liu, Yin

Many studies of nanomaterials make non-systematic alterations of nanoparticle physicochemical properties. Given the immense size of the property space for nanomaterials, such approaches are not very useful in elucidating fundamental relationships between inherent physicochemical properties of these materials and their interactions with, and effects on, biological systems. Data driven artificial intelligence methods such as machine learning algorithms have proven highly effective in generating models with good predictivity and some degree of interpretability. They can provide a viable method of reducing or eliminating animal testing. However, careful experimental design with the modelling of the results in mind is a proven andmore » efficient way of exploring large materials spaces. This approach, coupled with high speed automated experimental synthesis and characterization technologies now appearing, is the fastest route to developing models that regulatory bodies may find useful. We advocate greatly increased focus on systematic modification of physicochemical properties of nanoparticles combined with comprehensive biological evaluation and computational analysis. This is essential to obtain better mechanistic understanding of nano-bio interactions, and to derive quantitatively predictive and robust models for the properties of nanomaterials that have useful domains of applicability. - Highlights: • Nanomaterials studies make non-systematic alterations to nanoparticle properties. • Vast nanomaterials property spaces require systematic studies of nano-bio interactions. • Experimental design and modelling are efficient ways of exploring materials spaces. • We advocate systematic modification and computational analysis to probe nano-bio interactions.« less

Environmental and biological applications and implications of soft and condensed nanomaterials

NASA Astrophysics Data System (ADS)

Chen, Pengyu

Recent innovations and growth of nanotechnology have spurred exciting technological and commercial developments of nanomaterails. Their appealing physical and physicochemical properties offer great opportunities in biological and environmental applications, while in the meantime may compromise human health and environmental sustainability through either unintentional exposure or intentional discharge. Accordingly, this dissertation exploits the physicochemical behavior of soft dendritic polymers for environmental remediation and condensed nano ZnO tetrapods for biological sensing (Chapter two-four), and further delineate the environmental implications of such nanomaterials using algae- the major constituent of the aquatic food chain-as a model system (Chapter five). This dissertation is presented as follows. Chapter one presents a general review of the characteristic properties, applications, forces dictating nanomaterials, and their biological and environmental implications of the most produced and studied soft and condensed nanomaterials. In addition, dendritic polymers and ZnO nanomaterials are thoroughly reviewed separately. Chapter two investigates the physicochemical properties of poly(amidoamine)-tris(hydroxymethyl)amidomethane- dendrimer for its potential applications in water purification. The binding mechanisms and capacities of this dendrimer in hosting major environmental pollutants including cationic copper, anionic nitrate, and polyaromatic phenanthrene are discussed. Chapter three exploits a promising use of dendrimers for removal of potentially harmful discharged nanoparticles (NPs). Specifically, fullerenols are used as a model nanomaterial, and their interactions with two different generations of dendrimers are studied using spectrophotometry and thermodynamics methods. Chapter four elucidates two novel optical schemes for sensing environmental pollutants and biological compounds using dendrimer-gold nanowire complex and gold-coated ZnO tetrapods, respectively. The surface plasmon resonance of gold nanowires and NPs are utilized for enhancing the detection limits of Cu(II) down to nanomolar level and protein/lipids down to picomolar level. Chapter five justifies the growing concern of the environmental implications of nanomaterials in light of the increasing environmental and biological applications of nanomaterials based on the previous chapters, using ZnO NPs and single-celled green algae, Chlorella sp. as a model system. Chapter six summarized the key findings in this dissertation and presents future work stimulated by this PhD research. In summary, the key scientific contributions of this dissertation are: 1). we have performed the first study on the versatility of a trifunctional dendrimer for hosting cationic, anionic, and polyaromatic chemical contaminants; 2). we have demonstrated for the first time the concept that a soft, biocompatible nanoparticle—a dendrimer, can be used for hosting discharged, harmful nanoparticles for environmental remediation; and 3). we have shown for the first time the impact of nanoparticles on aquatic organisms is bidirectional.

Effect of casein and inulin addition on physico-chemical characteristics of low fat camel dairy cream.

PubMed

Ziaeifar, Leila; Labbafi Mazrae Shahi, Mohsen; Salami, Maryam; Askari, Gholam R

2018-05-21

The effect of the addition of the camel casein fraction on some physico-chemical properties of low fat camel milk cream was studied. Oil-in-water emulsions, 25, 30, and 35 (w/w) fat, were prepared using inulin, camel skim milk, milk fat and variable percentages of casein (1, 2, and 3% w/w). The droplet size, ζ-potential, surface protein concentration, viscosity and surface tension of low fat dairy creams was measured. Cream containing 2% (w/w) casein had better stability. The modifications in physico-chemical properties appeared to be driven by changes in particle size distribution caused by droplet aggregation. The cream containing 2% casein leads to a gradual decrease in droplet size, as the particle size decreased, apparent viscosity increased. When casein concentration increased, ζ-potential decreased due to combination of c terminal (negative charge) with the surface of fat particles but steric repulsion improved textural properties. Cream with 30% fat and 2% casein had the best result. Copyright © 2018 Elsevier B.V. All rights reserved.

Physicochemical properties of β-carotene emulsions stabilized by chlorogenic acid-lactoferrin-glucose/polydextrose conjugates.

PubMed

Liu, Fuguo; Wang, Di; Xu, Honggao; Sun, Cuixia; Gao, Yanxiang

2016-04-01

In this study, the influence of chlorogenic acid (CA)-lactoferrin (LF)-glucose (Glc) conjugate and CA-LF-polydextrose (PD) conjugate on the physicochemical characteristics of β-carotene emulsions was investigated. Novel emulsifiers were formed during Maillard reaction between CA-LF conjugate and Glc/PD. The physicochemical properties of β-carotene emulsions were characterized by droplet size, ζ-potential, rheological behavior, transmission changes during centrifugal sedimentation and β-carotene degradation. Results showed that the covalent attachment of Glc or PD to CA-LF conjugate effectively increased the hydrophilicity of the oil droplets surfaces and strengthened the steric repulsion between the oil droplets. Glucose was better than polydextrose for the conjugation with CA-LF conjugate to stabilize β-carotene emulsions. In comparison with LF and CA-LF-Glc/PD mixtures, CA-LF-Glc/PD ternary conjugates exhibited better emulsifying properties and improved physical stability of β-carotene emulsions during the freeze-thaw treatment. In addition, CA-LF-Glc/PD conjugates significantly enhanced chemical stability of β-carotene in the emulsions against ultraviolet light exposure. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cheminformatics Applications and Physicochemical Property ...

EPA Pesticide Factsheets

The registration of new chemicals under the Toxic Substances Control Act (TSCA) and new pesticides under the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) requires knowledge of the process science underlying the transport and transformation of organic chemicals in natural ecosystems. The purpose of this presentation is to demonstrate how cheminformatics, using chemical terms language in combination with the output of physicochemical property calculators, can be employed to encode this knowledge and make it available to the appropriate decision makers. The encoded process science is realized through the execution of reaction libraries in simulators such as EPA’s Chemical Transformation Simulator (CTS). In support of the CTS, reaction libraries have, or are currently being developed for a number of transformation processes including hydrolysis, abiotic reduction, photolysis and disinfection by-product formation. Examples of how the process science in the peer-reviewed literature is being encoded will be presented. The purpose of this presentation is to demonstrate how cheminformatics, using chemical terms language in combination with the output of physicochemical property calculators, can be employed to encode this knowledge and make it available to the appropriate decision makers.

Germinated barley as a functional ingredient in chicken sausages: effect on physicochemical and technological properties at different levels.

PubMed

Kim, Hyun-Wook; Hwang, Ko-Eun; Song, Dong-Heon; Kim, Yong-Jae; Ham, Youn-Kyung; Jeong, Tae-Jun; Choi, Yun-Sang; Kim, Cheon-Jei

2016-01-01

The objective of this study was to evaluate the effect of germinated barley (GB) levels on physicochemical and technological properties of cooked chicken sausages. The chicken sausages were formulated with 0-4 % GB. Addition of GB increased pH and yellowness but decreased lightness of the cooked chicken sausages. However, there was no difference in redness among treatments (P > 0.05). Based on the positive effects of GB on measurements related to water and/or fat retention ability, such as emulsion stability, cooking loss, and thawing loss, such results depended upon the added amount of GB. In addition, apparent viscosity increased with increasing levels of GB, resulting in hardness, springiness, and chewiness (P < 0.05). These results could be associated with polysaccharides contained in GB, such as insoluble fiber, β-glucan, and starch. Therefore, our results suggests that GB could be a functional ingredient to improve physicochemical and technological properties of chicken sausages and optimal level of GB was determined as minimum 2 %.

Experimental and Molecular Modeling Evaluation of the Physicochemical Properties of Proline-Based Deep Eutectic Solvents.

PubMed

van den Bruinhorst, Adriaan; Spyriouni, Theodora; Hill, Jörg-Rüdiger; Kroon, Maaike C

2018-01-11

The liquid range and applicability of deep eutectic solvents (DESs) are determined by their physicochemical properties. In this work, the physicochemical properties of glycolic acid:proline and malic acid:proline were evaluated experimentally and with MD simulations at five different ratios. Both DESs exhibited esterification upon preparation, which affected the viscosity in particular. In order to minimize oligomer formation and water release, three different experimental preparation methods were explored, but none could prevent esterification. The experimental and calculated densities of the DESs were found to be in good agreement. The measured and modeled glass transition temperature showed similar trends with composition, as did the experimental viscosity and the calculated diffusivities. The MD simulations provided additional insight at the atomistic level, showing that at acid-rich compositions, the acid-acid hydrogen bonding (HB) interactions prevail. Malic acid-based DESs show stronger acid-acid HB interactions than glycolic acid-based ones, possibly explaining its extreme viscosity. Upon the addition of proline, the interspecies interactions become predominant, confirming the formation of the widely assumed HB network between the DESs constituents in the liquid phase.

Physicochemical properties of natural actomyosin from threadfin bream (Nemipterus spp.) induced by high hydrostatic pressure.

PubMed

Zhou, Aimei; Lin, Liying; Liang, Yan; Benjakul, Soottawat; Shi, Xiaoling; Liu, Xin

2014-08-01

Changes of physicochemical properties in natural actomyosin (NAM) from threadfin bream (Nemipterus spp.) induced by high hydrostatic pressure (200, 400, 600MPa for 10, 30, 50min) were studied. The increase in turbidity of NAM was coincidental with the decrease in protein solubility with increasing pressure and time, suggesting the formation of protein aggregates. SDS-PAGE showed that polymerisation and degradation of myosin heavy chain were induced by high pressure. Ca(2+)-ATPase activity of NAM treated by high pressure was lost, suggesting the denaturation of myosin and the dissociation of actomyosin complex. Surface hydrophobicity of NAM increased when the pressure and pressurization time increased, indicating that the exposed hydrophobic residues increased upon application of high pressure. Decrease in total sulfhydryl content and increase in surface-reactive sulfhydryl content of NAM samples were observed with the extension of pressurizing time, indicating the formation of disulphide bonds through oxidation of SH groups or disulphide interchanges. The above changes of physicochemical properties suggested conformational changes of NAM from muscle of threadfin bream induced by high hydrostatic pressure. Copyright © 2014 Elsevier Ltd. All rights reserved.

A critical review on the spray drying of fruit extract: effect of additives on physicochemical properties.

PubMed

Krishnaiah, Duduku; Nithyanandam, Rajesh; Sarbatly, Rosalam

2014-01-01

Spray drying accomplishes drying while particles are suspended in the air and is one method in the family of suspended particle processing systems, along with fluid-bed drying, flash drying, spray granulation, spray agglomeration, spray reaction, spray cooling, and spray absorption. This drying process is unique because it involves both particle formation and drying. The present paper reviews spray drying of fruit extracts, such as acai, acerola pomace, gac, mango, orange, cactus pear, opuntia stricta fruit, watermelon, and durian, and the effects of additives on physicochemical properties such as antioxidant activity, total carotenoid content, lycopene and β-carotene content, hygroscopy, moisture content, volatile retention, stickiness, color, solubility, glass transition temperature, bulk density, rehydration, caking, appearance under electron microscopy, and X-ray powder diffraction. The literature clearly demonstrates that the effect of additives and encapsulation play a vital role in determining the physicochemical properties of fruit extract powder. The technical difficulties in spray drying of fruit extracts can be overcome by modifying the spray dryer design. It also reveals that spray drying is a novel technology for converting fruit extract into powder form.

Effect of ultrasound-assisted freezing on the physico-chemical properties and volatile compounds of red radish.

PubMed

Xu, Bao-Guo; Zhang, Min; Bhandari, Bhesh; Cheng, Xin-Feng; Islam, Md Nahidul

2015-11-01

Power ultrasound, which can enhance nucleation rate and crystal growth rate, can also affect the physico-chemical properties of immersion frozen products. In this study, the influence of slow freezing (SF), immersion freezing (IF) and ultrasound-assisted freezing (UAF) on physico-chemical properties and volatile compounds of red radish was investigated. Results showed that ultrasound application significantly improved the freezing rate; the freezing time of ultrasound application at 0.26 W/cm(2) was shorten by 14% and 90%, compared to IF and SF, respectively. UAF products showed significant (p<0.05) reduction in drip loss and phytonutrients (anthocyanins, vitamin C and phenolics) loss. Compared to SF products, IF and UAF products showed better textural preservation and higher calcium content. The radish tissues exhibited better cellular structures under ultrasonic power intensities of 0.17 and 0.26 W/cm(2) with less cell separation and disruption. Volatile compound data revealed that radish aromatic profile was also affected in the freezing process. Copyright © 2015 Elsevier B.V. All rights reserved.

Influence of the inlet air temperature in a fluid bed coating process on drug release from shellac-coated pellets.

PubMed

Farag, Yassin; Leopold, Claudia Sabine

2011-03-01

Since the introduction of aqueous ammoniacal solutions, shellac regained importance for pharmaceutical applications. However, as shellac is a material obtained from natural resources, its quality and thus its physicochemical properties may vary depending on its origin and the type of refining. In this study theophylline pellets were coated with aqueous solutions of three different commercially available shellac types. The inlet air temperature of the coating process was varied, and its influence on drug release from the coated pellet formulations was investigated. Film formation was correlated to the physicochemical and mechanical properties of the investigated shellac types. Pellets coated at lower temperatures showed distinct cracks in the coating film resulting in a loss of the barrier function during dissolution testing. These cracks were nonreversible by additional curing. The physicochemical and mechanical properties of the investigated shellac types varied significantly and could hardly be related to the drug release performance of the investigated formulations. Obviously, with shellac a minimum inlet air temperature must be exceeded to achieve a coherent coating film. This temperature was dependent on the investigated shellac type.

Comparative Effects of Gamma Irradiation and Ozone Treatment on Hygienic Quality of Korean Red Ginseng Powder

NASA Astrophysics Data System (ADS)

Byun, Myung-Woo; Yook, Hong-Sun; Kang, Il-Jun; Chung, Cha-Kwon; Kwon, Joong-Ho; Choi, Kang-Ju

1998-06-01

For the purpose of improving hygienic quality of Korean red ginseng powder, the comparative effects of gamma irradiation and ozone treatment on the microbial and physicochemical properties were investigated. Gamma irradiation at 7.5 kGy resulted in sterilization of total aerobic bacteria, molds and coliforms below detective levels, while ozone treatment for 8 hours up to 18 ppm did not sufficiently eliminate the microorganisms of the red ginseng powder. Physicochemical properties including compositions of the red ginseng saponin (ginsenosides) and fatty acids, pH and hydrogen doanting activity were not significantly changed by gamma irradiation, whereas, ozone treatment caused significant changes in fatty acid compositions, TBA value, pH, acidity and hydrogen donating activity. The results from this study led us to conclude that gamma irradiation was more effective than ozone treatment both for the improvement of hygienic quality and for the maintenance of physicochemical quality of red ginseng powder.

Application of Spectroscopic Methods for Structural Analysis of Chitin and Chitosan

PubMed Central

Kumirska, Jolanta; Czerwicka, Małgorzata; Kaczyński, Zbigniew; Bychowska, Anna; Brzozowski, Krzysztof; Thöming, Jorg; Stepnowski, Piotr

2010-01-01

Chitin, the second most important natural polymer in the world, and its N-deacetylated derivative chitosan, have been identified as versatile biopolymers for a broad range of applications in medicine, agriculture and the food industry. Two of the main reasons for this are firstly the unique chemical, physicochemical and biological properties of chitin and chitosan, and secondly the unlimited supply of raw materials for their production. These polymers exhibit widely differing physicochemical properties depending on the chitin source and the conditions of chitosan production. The presence of reactive functional groups as well as the polysaccharide nature of these biopolymers enables them to undergo diverse chemical modifications. A complete chemical and physicochemical characterization of chitin, chitosan and their derivatives is not possible without using spectroscopic techniques. This review focuses on the application of spectroscopic methods for the structural analysis of these compounds. PMID:20559489

The Comparative Effect of Carrot and Lemon Fiber as a Fat Replacer on Physico-chemical, Textural, and Organoleptic Quality of Low-fat Beef Hamburger.

PubMed

Soncu, Eda Demirok; Kolsarıcı, Nuray; Çiçek, Neslihan; Öztürk, Görsen Salman; Akoğlu, Ilker T; Arıcı, Yeliz Kaşko

2015-01-01

This study was designed to determine the usability of lemon fiber (LF-2%, 4%, 6%) and carrot fiber (CF-2%, 4%, 6%) to produce low-fat beef hamburgers. To that end, a certain amount of fat was replaced with each fiber. The proximate composition, pH value, cholesterol content, cooking characteristics, color, texture profile, and sensory properties of low-fat beef hamburgers were investigated. LF increased moisture content and cooking yield due to its better water binding properties, while CF caused higher fat and cholesterol contents owing to its higher fat absorption capacity (p<0.05). LF resulted in a lighter, redder, and more yellow color (p<0.05). Hardness, gumminess, springiness, and chewiness parameters decreased when the usage level of both fibers increased (p<0.05). However, more tender, gummy, springy, and smoother hamburgers were produced by the addition of CF in comparison with LF (p<0.05). Moreover, hamburgers including CF were rated with higher sensory scores (p<0.05). In conclusion, LF demonstrated better technological results in terms of cooking yield, shrinkage, moisture retention, and fat retention. However it is suggested that CF produces better low-fat hamburgers since up to 2% CF presented sensory and textural properties similar to those of regular hamburgers.

Fine-tuning the physicochemical properties of peptide-based blood-brain barrier shuttles.

PubMed

Ghasemy, Somaye; García-Pindado, Júlia; Aboutalebi, Fatemeh; Dormiani, Kianoush; Teixidó, Meritxell; Malakoutikhah, Morteza

2018-05-01

N-methylation is a powerful method to modify the physicochemical properties of peptides. We previously found that a fully N-methylated tetrapeptide, Ac-(N-MePhe) 4 -CONH 2 , was more lipophilic than its non-methylated analog Ac-(Phe) 4 -CONH 2 . In addition, the former crossed artificial and cell membranes while the latter did not. Here we sought to optimize the physicochemical properties of peptides and address how the number and position of N-methylated amino acids affect these properties. To this end, 15 analogs of Ac-(Phe) 4 -CONH 2 were designed and synthesized in solid-phase. The solubility of the peptides in water and their lipophilicity, as measured by ultra performance liquid chromatography (UPLC) retention times, were determined. To study the permeability of the peptides, the Parallel Artificial Membrane Permeability Assay (PAMPA) was used as an in vitro model of the blood-brain barrier (BBB). Contrary to the parent peptide, the 15 analogs crossed the artificial membrane, thereby showing that N-methylation improved permeability. We also found that N-methylation enhanced lipophilicity but decreased the water solubility of peptides. Our results showed that both the number and position of N-methylated residues are important factors governing the physicochemical properties of peptides. There was no correlation between the number of N-methylated amide bonds and any of the properties measured. However, for the peptides consecutively N-methylated from the N-terminus to the C-terminus (p1, p5, p11, p12 and p16), lipophilicity correlated well with the number of N-methylated amide bonds and the permeability of the peptides. Moreover, the peptides were non-toxic to HEK293T cells, as determined by the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay. Copyright © 2018 Elsevier Ltd. All rights reserved.

IDM-PhyChm-Ens: intelligent decision-making ensemble methodology for classification of human breast cancer using physicochemical properties of amino acids.

PubMed

Ali, Safdar; Majid, Abdul; Khan, Asifullah

2014-04-01

Development of an accurate and reliable intelligent decision-making method for the construction of cancer diagnosis system is one of the fast growing research areas of health sciences. Such decision-making system can provide adequate information for cancer diagnosis and drug discovery. Descriptors derived from physicochemical properties of protein sequences are very useful for classifying cancerous proteins. Recently, several interesting research studies have been reported on breast cancer classification. To this end, we propose the exploitation of the physicochemical properties of amino acids in protein primary sequences such as hydrophobicity (Hd) and hydrophilicity (Hb) for breast cancer classification. Hd and Hb properties of amino acids, in recent literature, are reported to be quite effective in characterizing the constituent amino acids and are used to study protein foldings, interactions, structures, and sequence-order effects. Especially, using these physicochemical properties, we observed that proline, serine, tyrosine, cysteine, arginine, and asparagine amino acids offer high discrimination between cancerous and healthy proteins. In addition, unlike traditional ensemble classification approaches, the proposed 'IDM-PhyChm-Ens' method was developed by combining the decision spaces of a specific classifier trained on different feature spaces. The different feature spaces used were amino acid composition, split amino acid composition, and pseudo amino acid composition. Consequently, we have exploited different feature spaces using Hd and Hb properties of amino acids to develop an accurate method for classification of cancerous protein sequences. We developed ensemble classifiers using diverse learning algorithms such as random forest (RF), support vector machines (SVM), and K-nearest neighbor (KNN) trained on different feature spaces. We observed that ensemble-RF, in case of cancer classification, performed better than ensemble-SVM and ensemble-KNN. Our analysis demonstrates that ensemble-RF, ensemble-SVM and ensemble-KNN are more effective than their individual counterparts. The proposed 'IDM-PhyChm-Ens' method has shown improved performance compared to existing techniques.

Characterization of the solvent properties of oleochemical carbonates

USDA-ARS?s Scientific Manuscript database

Oleophilic carbonates, such as hexadecyl carbonate, can be characterized with respect to their solvent properties using inverse gas chromatography (IGC). Physicochemical properties of these renewable lipid derivatives are of importance for applications such as their use as phase change materials, fu...

Nano-QSPR Modelling of Carbon-Based Nanomaterials Properties.

PubMed

Salahinejad, Maryam

2015-01-01

Evaluation of chemical and physical properties of nanomaterials is of critical importance in a broad variety of nanotechnology researches. There is an increasing interest in computational methods capable of predicting properties of new and modified nanomaterials in the absence of time-consuming and costly experimental studies. Quantitative Structure- Property Relationship (QSPR) approaches are progressive tools in modelling and prediction of many physicochemical properties of nanomaterials, which are also known as nano-QSPR. This review provides insight into the concepts, challenges and applications of QSPR modelling of carbon-based nanomaterials. First, we try to provide a general overview of QSPR implications, by focusing on the difficulties and limitations on each step of the QSPR modelling of nanomaterials. Then follows with the most significant achievements of QSPR methods in modelling of carbon-based nanomaterials properties and their recent applications to generate predictive models. This review specifically addresses the QSPR modelling of physicochemical properties of carbon-based nanomaterials including fullerenes, single-walled carbon nanotube (SWNT), multi-walled carbon nanotube (MWNT) and graphene.

Physicochemical characterization of lignin recovered from microwave-assisted delignified lignocellulosic biomass for use in biobased materials

Treesearch

Jiulong Xie; Chung-Yun Hse; Todd F. Shupe; Tingxing Hu

2015-01-01

Lignocellulosic biomass (Moso Bamboo, Chinese tallow tree wood, switchgrass, and pine wood) was subjected to a novel delignification process using microwave energy in a binary glycerol/methanol solvent. The physicochemical properties of the recovered lignin were analyzed prior to its application in the fabrication of polylactic acid (PLA)–lignin composites. The results...

Inactive enzymatic mutant proteins (phosphoglycerate mutase and enolase) as sugar binders for ribulose-1,5-bisphosphate regeneration reactors

PubMed Central

De, Debojyoti; Dutta, Debajyoti; Kundu, Moloy; Mahato, Sourav; Schiavone, Marc T; Chaudhuri, Surabhi; Giri, Ashok; Gupta, Vidya; Bhattacharya, Sanjoy K

2005-01-01

Background Carbon dioxide fixation bioprocess in reactors necessitates recycling of D-ribulose1,5-bisphosphate (RuBP) for continuous operation. A radically new close loop of RuBP regenerating reactor design has been proposed that will harbor enzyme-complexes instead of purified enzymes. These reactors will need binders enabling selective capture and release of sugar and intermediate metabolites enabling specific conversions during regeneration. In the current manuscript we describe properties of proteins that will act as potential binders in RuBP regeneration reactors. Results We demonstrate specific binding of 3-phosphoglycerate (3PGA) and 3-phosphoglyceraldehyde (3PGAL) from sugar mixtures by inactive mutant of yeast enzymes phosphoglycerate mutase and enolase. The reversibility in binding with respect to pH and EDTA has also been shown. No chemical conversion of incubated sugars or sugar intermediate metabolites were found by the inactive enzymatic proteins. The dissociation constants for sugar metabolites are in the micromolar range, both proteins showed lower dissociation constant (Kd) for 3-phosphoglycerate (655–796 μM) compared to 3-phosphoglyceraldehyde (822–966 μM) indicating higher affinity for 3PGA. The proteins did not show binding to glucose, sucrose or fructose within the sensitivity limits of detection. Phosphoglycerate mutase showed slightly lower stability on repeated use than enolase mutants. Conclusions The sugar and their intermediate metabolite binders may have a useful role in RuBP regeneration reactors. The reversibility of binding with respect to changes in physicochemical factors and stability when subjected to repeated changes in these conditions are expected to make the mutant proteins candidates for in-situ removal of sugar intermediate metabolites for forward driving of specific reactions in enzyme-complex reactors. PMID:15689239

Kinetics of bacterial phospholipase C activity at micellar interfaces: effect of substrate aggregate microstructure and a model for the kinetic parameters.

PubMed

Singh, Jasmeet; Ranganathan, Radha; Hajdu, Joseph

2008-12-25

Activity at micellar interfaces of bacterial phospholipase C from Bacillus cereus on phospholipids solubilized in micelles was investigated with the goal of elucidating the role of the interface microstructure and developing further an existing kinetic model. Enzyme kinetics and physicochemical characterization of model substrate aggregates were combined, thus enabling the interpretation of kinetics in the context of the interface. Substrates were diacylphosphatidylcholine of different acyl chain lengths in the form of mixed micelles with dodecyldimethylammoniopropanesulfonate. An early kinetic model, reformulated to reflect the interfacial nature of the kinetics, was applied to the kinetic data. A better method of data treatment is proposed, use of which makes the presence of microstructure effects quite transparent. Models for enzyme-micelle binding and enzyme-lipid binding are developed, and expressions incorporating the microstructural properties are derived for the enzyme-micelle dissociation constant K(s) and the interface Michaelis-Menten constant, K(M). Use of these expressions in the interface kinetic model brings excellent agreement between the kinetic data and the model. Numerical values for the thermodynamic and kinetic parameters are determined. Enzyme-lipid binding is found to be an activated process with an acyl chain length dependent free energy of activation that decreases with micelle lipid molar fraction with a coefficient of about -15RT and correlates with the tightness of molecular packing in the substrate aggregate. Thus, the physical insight obtained includes a model for the kinetic parameters that shows that these parameters depend on the substrate concentration and acyl chain length of the lipid. Enzyme-micelle binding is indicated to be hydrophobic and solvent mediated with a dissociation constant of 1.2 mM.

Physicochemical properties and starch digestibility of Chinese noodles in relation to optimal cooking time.

PubMed

Ye, Xiaoting; Sui, Zhongquan

2016-03-01

Changes in the physicochemical properties and starch digestibility of white salted noodles (WSN) at different cooking stage were investigated. The noodles were dried in fresh air and then cooked for 2-12 min by boiling in distilled water to determine the properties of cooking quality, textural properties and optical characteristic. For starch digestibility, dry noodles were milled and sieved into various particle size classes ranging from 0.5 mm to 5.0 mm, and hydrolyzed by porcine pancreatic α-amylase. The optimal cooking time of WSN determined by squeezing between glasses was 6 min. The results showed that the kinetics of solvation of starch and protein molecules were responsible for changes of the physicochemical properties of WSN during cooking. The susceptibility of starch to α-amylase was influenced by the cooking time, particle size and enzyme treatment. The greater value of rapidly digestible starch (RDS) and lower value of slowly digestible starch (SDS) and resistant starch (RS) were reached at the optimal cooking stage ranging between 63.14-71.97%, 2.47-10.74% and 23.94-26.88%, respectively, indicating the susceptibility on hydrolysis by enzyme was important in defining the cooked stage. The study suggested that cooking quality and digestibility were not correlated but the texture greatly controls the digestibility of the noodles. Copyright © 2015 Elsevier B.V. All rights reserved.

Physicochemical and FTIR Study of Diesel-Hydrogen Peroxide Fuel Blend

NASA Astrophysics Data System (ADS)

Saad Khan, Muhammad; Ahmed, Iqbal; Lal, Bhajan; Idris, Al-Amin; Albeirutty, Muhammad H.; Ayoub, Muhammad; Sufian, Suriati binti

2018-04-01

Physicochemical properties of combustion fuels play a key role in determining the qualitative and quantitative characteristics, reliability and health effects associated with emissions. This paper reports the preparation of polysaccharide (PS) based emulsifier for stable blending of petroleum diesel-hydrogen peroxide (H2O2) and investigated the influence of H2O2 as diesel fuel blends on the physicochemical properties and characteristics. The quantity of PS-emulsifier was kept at 5 volume % (vol. %) and the volume ratio of H2O2 were varied 5-15 vol. % to reference diesel (RD), respectively. The blended diesel/H2O2 fuel were prepared under inert oxygen (O2) gas closed heating system; afterthought, physiochemical properties of diesel/H2O2 blend were evaluated at standard ASTM D-975 testing method. The kinetic properties show the interaction of RD and H2O2 blend at presence of PS emulsifier which exhibit the phenomenon to diminish the interfacial tension among the two different phases to form a homogenized stable solution. Results revealed that H2O2 is capable of enhancing the diesel fuel properties and showed that the addition of H2O2 in a diesel fuel blend are lied within the ranges of standard ASTM D-975. Due to further oxygen atom present in H2O2, it can facilitate the combustion process which ultimately effect on exhaust emission.

Estimating the physicochemical properties of polyhalogenated aromatic and aliphatic compounds using UPPER: part 1. Boiling point and melting point.

PubMed

Admire, Brittany; Lian, Bo; Yalkowsky, Samuel H

2015-01-01

The UPPER (Unified Physicochemical Property Estimation Relationships) model uses enthalpic and entropic parameters to estimate 20 biologically relevant properties of organic compounds. The model has been validated by Lian and Yalkowsky on a data set of 700 hydrocarbons. The aim of this work is to expand the UPPER model to estimate the boiling and melting points of polyhalogenated compounds. In this work, 19 new group descriptors are defined and used to predict the transition temperatures of an additional 1288 compounds. The boiling points of 808 and the melting points of 742 polyhalogenated compounds are predicted with average absolute errors of 13.56 K and 25.85 K, respectively. Copyright © 2014 Elsevier Ltd. All rights reserved.

Applicability of vacuum impregnation to modify physico-chemical, sensory and nutritive characteristics of plant origin products--a review.

PubMed

Radziejewska-Kubzdela, Elżbieta; Biegańska-Marecik, Róża; Kidoń, Marcin

2014-09-19

Vacuum impregnation is a non-destructive method of introducing a solution with a specific composition to the porous matrices of fruit and vegetables. Mass transfer in this process is a result of mechanically induced differences in pressure. Vacuum impregnation makes it possible to fill large volumes of intercellular spaces in tissues of fruit and vegetables, thus modifying physico-chemical properties and sensory attributes of products. This method may be used, e.g., to reduce pH and water activity of the product, change its thermal properties, improve texture, color, taste and aroma. Additionally, bioactive compounds may be introduced together with impregnating solutions, thus improving health-promoting properties of the product or facilitating production of functional food.

Improving Physical Properties via C–H Oxidation: Chemical and Enzymatic Approaches

PubMed Central

Michaudel, Quentin; Journot, Guillaume; Regueiro-Ren, Alicia; Goswami, Animesh; Guo, Zhiwei; Tully, Thomas P.; Zou, Lufeng; Ramabhadran, Raghunath O.; Houk, Kendall N.

2014-01-01

Physicochemical properties constitute a key factor for the success of a drug candidate. Whereas many strategies to improve the physicochemical properties of small heterocycle-type leads exist, complex hydrocarbon skeletons are more challenging to derivatize due to the absence of functional groups. A variety of C–H oxidation methods have been explored on the betulin skeleton to improve the solubility of this very bioactive, yet poorly water soluble, natural product. Capitalizing on the innate reactivity of the molecule, as well as the few molecular handles present on the core, allowed for oxidations at different positions across the pentacyclic structure. Enzymatic oxidations afforded several orthogonal oxidations to chemical methods. Solubility measurements showed an enhancement for many of the synthesized compounds. PMID:25244630

Porous nano-cerium oxide wood chip biochar composites for aqueous levofloxacin removal and sorption mechanism insights.

PubMed

Yi, Shengze; Sun, Yuanyuan; Hu, Xin; Xu, Hongxia; Gao, Bin; Wu, Jichun

2017-01-14

The adsorption removal of levofloxacin (LEV), a widely used fluoroquinolone antibiotic, by using the biochars derived from the pyrolysis of pine wood chip pretreated with cerium trichloride was investigated through batch sorption experiments and multiple characterization techniques. The differences in the basic physicochemical properties between Ce-impregnated biochars and the pristine biochars were confirmed by the analysis of elemental compositions, specific surface areas, energy dispersive spectrometry, X-ray diffraction, and thermo-gravimetry. FT-IR spectra of the pre- and post-sorption biochars confirmed the chemical adsorption for LEV sorption onto the biochars. Large shifts in the binding energy of Ce 3d , O 1s , C 1s , and N 1s regions on the pre- and post-sorption biochars indicated the surface complexation of LEV molecule onto the biochars. The binding species of Ce 4+ and Ce 3+ identified by X-ray photoelectron spectroscopy reflect the role of Ce oxides during sorption. Batch adsorption showed the significant enhancement of adsorption capacity for LEV after the Ce modification. Batch adsorption kinetic data fitted well with the pseudo-second-order model. Both the Langmuir and the Freundlich models reproduced the isotherm data well. Findings from this work indicated that Ce-impregnated biochars can be effective for the removal of aqueous LEV.

Non-covalent Small-Molecule Kelch-like ECH-Associated Protein 1-Nuclear Factor Erythroid 2-Related Factor 2 (Keap1-Nrf2) Inhibitors and Their Potential for Targeting Central Nervous System Diseases.

PubMed

Pallesen, Jakob S; Tran, Kim T; Bach, Anders

2018-05-29

The transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2) has a protective effect against oxidative stress and plays a major role in inflammation and central nervous system (CNS) diseases. Inhibition of the protein-protein interaction (PPI) between Nrf2 and its repressor protein, Kelch-like ECH-associated protein 1 (Keap1), leads to translocation of Nrf2 from the cytosol to the nucleus and expression of detoxifying antioxidant enzymes. To date, several non-covalent small-molecule Keap1-Nrf2 inhibitors have been identified; however, many of them contain carboxylic acids and are rather large in size, which likely prevents or decreases CNS permeability. This Perspective describes current small-molecule Keap1-Nrf2 inhibitors with experimental evidence for the ability to inhibit the Keap1-Nrf2 interaction by binding to Keap1 in a non-covalent manner. Binding data, biostructural studies, and biological activity are summarized for the inhibitors, and their potential as CNS tool compounds is discussed by analyzing physicochemical properties, including CNS multiparameter optimization (MPO) scoring algorithms. Finally, several strategies for identifying CNS-targeting Keap1 inhibitors are described.

Discovery, clinical development, and therapeutic uses of bisphosphonates.

PubMed

Licata, Angelo A

2005-04-01

To review the literature concerning the history, development, and therapeutic uses of bisphosphonates. English-language articles were identified through a search of MEDLINE (through December 2004) using the key word bisphosphonate. Reference lists of pivotal studies, reviews, and full prescribing information for the approved agents were also examined. Selected studies included those that discussed the discovery and initial applications of bisphosphonates, as well as their historical development, pharmacokinetic and pharmacodynamic properties, and current therapeutic uses. Bisphosphonates structurally resemble pyrophosphates (naturally occurring polyphosphates) and have demonstrated similar physicochemical effects to pyrophosphates. In addition, bisphosphonates reduce bone turnover and resist hydrolysis when administered orally. The information gained from initial work with etidronate generated a considerable scientific effort to design new and more effective bisphosphonates. The PCP moiety in the general bisphosphonate structure is essential for binding to hydroxyapatite and allows for a number of chemical variations by changing the 2 lateral side chains (designated R(1) and R(2)). The R(1) side chain determines binding affinity to hydroxyapatite, and the R(2) side chain determines antiresorptive potency. Accordingly, each bisphosphonate has its own characteristic profile of activity. The bisphosphonates reduce bone turnover, increase bone mass, and decrease fracture risk and therefore have a significant place in the management of skeletal disorders including osteoporosis, Paget's disease, bone metastases, osteogenesis imperfecta, and heterotopic ossification.

Synthesis and physicochemical properties of the furan dicarboxylic acid, 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid, an inhibitor of plasma protein binding in uraemia.

PubMed

Costigan, M G; Gilchrist, T L; Lindup, W E

1996-06-01

The furan dicarboxylic acid, 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (5-propyl FPA) accumulates in the plasma of patients with chronic renal failure and is a major contributor to the drug binding defect of uraemic plasma. This acid has also been implicated in several other aspects of the uraemic syndrome: anaemia, irregularities of thyroid function, neurological symptoms and inhibition of active tubular secretion. The acid is not commercially available and its synthesis, starting with Meldrum's acid and methyl succinyl chloride, is described. The pKa values were measured by titration and values of 3.2 and 3.6 respectively were assigned to the carboxylic acid groups attached directly to the ring at position 3 and at position 2 (on the side-chain). The partition coefficient (log P) between hydrochloric acid and octanol was 1.2 and the distribution coefficient (log D; octanol-phosphate buffer pH 7.4) was -0.59. The pKa values and the degree of hydrophobic character of 5-propyl FPA are consistent with those of other protein-bound acids which undergo active tubular secretion by the kidney and this substance may serve as an endogenous marker for the effects of drugs and disease on this process.

Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods

PubMed Central

Du, Xing; Li, Yi; Xia, Yuan-Ling; Ai, Shi-Meng; Liang, Jing; Sang, Peng; Ji, Xing-Lai; Liu, Shu-Qun

2016-01-01

Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms. Proteins, an important class of biological macromolecules, realize their functions through binding to themselves or other molecules. A detailed understanding of the protein–ligand interactions is therefore central to understanding biology at the molecular level. Moreover, knowledge of the mechanisms responsible for the protein-ligand recognition and binding will also facilitate the discovery, design, and development of drugs. In the present review, first, the physicochemical mechanisms underlying protein–ligand binding, including the binding kinetics, thermodynamic concepts and relationships, and binding driving forces, are introduced and rationalized. Next, three currently existing protein-ligand binding models—the “lock-and-key”, “induced fit”, and “conformational selection”—are described and their underlying thermodynamic mechanisms are discussed. Finally, the methods available for investigating protein–ligand binding affinity, including experimental and theoretical/computational approaches, are introduced, and their advantages, disadvantages, and challenges are discussed. PMID:26821017

Implications of interfacial characteristics of food foaming agents in foam formulations.

PubMed

Rodríguez Patino, Juan M; Carrera Sánchez, Cecilio; Rodríguez Niño, Ma Rosario

2008-08-05

The manufacture of food dispersions (emulsions and foams) with specific quality attributes depends on the selection of the most appropriate raw materials and processing conditions. These dispersions being thermodynamically unstable require the use of emulsifiers (proteins, lipids, phospholipids, surfactants etc.). Emulsifiers typically coexist in the interfacial layer with specific functions in the processing and properties of the final product. The optimum use of emulsifiers depends on our knowledge of their interfacial physico-chemical characteristics - such as surface activity, amount adsorbed, structure, thickness, topography, ability to desorb (stability), lateral mobility, interactions between adsorbed molecules, ability to change conformation, interfacial rheological properties, etc. -, the kinetics of film formation and other associated physico-chemical properties at fluid interfaces. These monolayers constitute well defined systems for the analysis of food colloids at the micro- and nano-scale level, with several advantages for fundamental studies. In the present review we are concerned with the analysis of physico-chemical properties of emulsifier films at fluid interfaces in relation to foaming. Information about the above properties would be very helpful in the prediction of optimised formulations for food foams. We concluded that at surface pressures lower than that of monolayer saturation the foaming capacity is low, or even zero. A close relationship was observed between foaming capacity and the rate of diffusion of the foaming agent to the air-water interface. However, the foam stability correlates with the properties of the film at long-term adsorption.

Physicochemical properties of chitooligosaccharide prepared by using chitosanase from Stenotrophomonas maltophilia KPU 2123

NASA Astrophysics Data System (ADS)

Fawzya, Y. N.; Rahmawati, A.; Patantis, G.

2018-03-01

Study on the physicochemical properties of chitooligosaccharide (COS) prepared by hydrolysis of chitosan using chitosanase from Stenotrophomonas maltophilia KPU 2123 has been carried out. Hydrolysis process was conducted by reacting the soluble chitosan with 8 U·g-1 chitosan of chitosanase for 0; 8; 16 and 24 h incubation and stopped by addition of 0.25 M NaOH until reached pH 7. The COS was obtained as supernatant after being centrifugation. The liquid COS were then freeze-dried and analyzed their physicochemical properties, which comprised yield, viscosity, moisture and ash content, the degree of deacetylation (DD), as well as lead (Pb), arsenic (As) content and analyses of COS by Thin Layer Chromatography (TLC). The optimum hydrolysis time was found to be 16 h with the COS viscosity was 8.50 ± 0.87 cPs. The high COS yield was related to high ash content, i.e. 251.70 ± 77.97 % and 50.45 ± 3.19 % (db), respectively. There was lead (Pb) and arsenic (As) metals detected, i.e. 4.4 ppm and 0.1 ppm, respectively. However, they still met the requirement of Pb and As content in a commercial COS referred. Based on the COS properties, desalination process should be applied in the preparation of COS by enzymatic method.

Physicochemical and Rheological Properties of a Dairy Dessert, Enriched with Chickpea Flour.

PubMed

Aguilar-Raymundo, Victoria Guadalupe; Vélez-Ruiz, Jorge Fernando

2018-02-18

Dairy desserts are complex mixtures and matrices including main components such as milk, sugar, starch, hydrocolloids, colorants and flavors, with a proteinaceous structure; they are widely consumed and present a semisolid consistency. In this work, the physicochemical and rheological properties of a dairy dessert with the addition of chickpea flour (raw and cooked, at four concentrations) were studied to determine the effect of the flour. The results indicated that luminosity (L*: 62.75-83.29), pH (6.35-7.11) and acidity (1.56-3.56) changed with the type of flour. The flow properties of the custards exhibited a non-Newtonian behavior that was well fitted by three flow models. The studied custard systems were stored for twelve days at 4 °C. The physicochemical and flow properties of the custards changed notably as a function of flour addition and storage time. From all samples, only four were analyzed with oscillatory tests, showing their mechanical spectra with elastic behavior. The dessert texture was also measured, founding that those formulated with Blanco Noroeste chickpea flour exhibited the highest values of hardness (0.356-0.391 Newton (N)) through the twelve days. It can be concluded that those custard systems with the highest content of flour presented a very good response as a potential new dairy product.

Complexation of rice starch/flour and maize oil through heat moisture treatment: Structural, in vitro digestion and physicochemical properties.

PubMed

Chen, Xu; He, Xiaowei; Fu, Xiong; Zhang, Bin; Huang, Qiang

2017-05-01

This study investigated structural, in vitro digestion and physicochemical properties of normal rice starch (NRS)/flour (NRF) complexed with maize oil (MO) through heat-moisture treatment (HMT). The NRS-/NRF-MO complex displayed an increased pasting temperature and a decreased peak viscosity. After HMT, less ordered Maltese and more granule fragments were observed for NRS-/NRF-MO complex. Meanwhile, more aggregation was observed in the HMT samples with higher moisture contents. We found that higher onset temperature, lower enthalpy change and relative crystallinity of the NRS-/NRF-MO complex were associated with a higher moisture content of HMT samples. The higher moisture content of HMT was also favorable for the amylose-lipid complex formation. Differences in starch digestion properties were found for NRS-MO and NRF-MO complex. All of the NRS/NRF complexed MO after cooking showed lower rapidly digestible starch (RDS) contents compared with the control sample, therein NRS-/NRF- MO 20% exhibited the highest sum of the slowly digestible starch and resistant starch contents. In general, HMT had a greater impact on the in vitro digestion and physicochemical properties of flour samples compared with starch counterparts. Copyright © 2017 Elsevier B.V. All rights reserved.

Investigation of Methylene Blue Release from Functional Polymeric Systems Using Dielectric Analysis.

PubMed

Bruschi, Marcos Luciano; Junqueira, Mariana Volpato; Borghi-Pangoni, Fernanda Belincanta; Yu, Tao; Andrews, Gavin Paul; Jones, David Simon

2018-01-01

Methylene blue (MB) is a photosensitizer used in photodynamic therapy (PDT) to treat colorectal cancer tumors and leishmaniasis infection. The clinical efficacy of PDT using MB is dependent on the physicochemical characteristics of the formulation. Bioadhesive thermoresponsive systems containing poloxamer 407 and Carbopol 934P have been proposed as platforms for PDT. However, the effect of MB on the physicochemical properties of these platforms is not fully understood, particularly in light of the MB availability. The aim of this study was to investigate the dielectric characteristics of functional polymeric systems containing MB and their influence on mucoadhesion and drug release. Binary polymeric systems containing different concentrations of poloxamer 407, Carbopol 934P and MB were evaluated as dielectric and mucoadhesive properties, as well as in vitro drug release profile. MB, temperature and polymeric composition influenced the physicochemical properties of the systems. The presence of MB altered the supramolecular structure of the preparations. The mucoadhesive properties of systems were influenced by MB presence and the formulation with the lowest amount of MB displayed faster release. The lower MB concentration in the systems displayed better results in terms of ionic mobility and drug release, and is indicative of a suitable clinical performance. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Investigation of interaction between Pax-5 isoforms and thioredoxin using de novo modelling methods.

PubMed

Cuperlovic-Culf, Miroslava; Robichaud, Gilles A; Nardini, Michel; Ouellette, Rodney J

2003-01-01

Pax-5 transcription factor plays a crucial role in B-cell development, activation and differentiation. In murine B-cells four different isoforms of Pax-5 have been identified, and their role in the regulation of the activity of the wild-type protein was revealed although still not fully understood. Using theoretical methods, we investigated the properties of one region of the Pax-5e and Pax-5d isoforms (named UDE domain) and we present a possible theoretical model for the interaction of this domain with thioredoxin that have been previously postulated based on the experimental results. Domain UDE (MW 4.8 kDa) is characterised by an extremely high ratio of positively charged residues (8) in comparisons to negatively charged amino acids (3), as well as unusually large concentrations of prolines (11.6%) and cysteines (4.7%). This is indicative of its role in protein-protein interaction. The experimental 3D structure for either UDE domain or for any analogous sequence is not yet available, and therefore we resorted to various bioinformatics methods in order to predict the secondary and 3D structure from the primary sequence of UDE. Physicochemical properties of the predicted UDE structure gave more indication about possibilities for UDE-thioredoxin binding. In addition, UDE domain was shown to have both sequence and structure analogous to a segment of NAD-reducing hydrogenase HOXS a subunit which is believed to interact with thioredoxin. These studies showed that the UDE domain in Pax-5d and Pax-5e represents an ideal binding site for thioredoxin and we developed a model of UDE-TRX complex with two disulphide bridges. The active site of thioredoxin remained exposed after binding to UDE in this model and therefore binding of thioredoxin to Pax-5d could explain the unexpectedly high resistance of this isoform to oxidation. The complex between thioredoxin and Pax-5e can be a method for transportation of thioredoxin into the nucleus and also into the the vicinity of Pax-5a, explaining the observed activator role of Pax-5e.

Kinetics of NO and O2 binding to a maleimide poly(ethylene glycol)-conjugated human haemoglobin

PubMed Central

2004-01-01

The hypertensive effect observed with most cell-free haemoglobins has been proposed to result from NO scavenging. However, a newly developed PEG [poly(ethylene glycol)]-conjugated haemoglobin, MalPEG-Hb [maleimide-activated PEG-conjugated haemoglobin], is non-hypertensive with unique physicochemical properties: high O2 affinity, low co-operativity and large molecular radius. It is therefore of interest to compare the ligand-binding properties of MalPEG-Hb with unmodified cell-free HbA (stroma-free human haemoglobin). NO association rates for deoxy and oxyMalPEG-Hb and HbA were found to be identical. These results confirm the lack of correlation between hypertension and NO for a similar modified haemoglobin with high molecular radius and low p50 (pO2 at which haemoglobin is half-saturated with O2) [Rohlfs, Bruner, Chiu, Gonzales, Gonzales, Magde, Magde, Vandegriff and Winslow (1998) J. Biol. Chem. 273, 12128–12134]. The R-state O2 association kinetic constants were also the same for the two haemoglobins. However, even though the p50 of MalPEG-Hb is approx. half of that of HbA, the biphasic O2 dissociation rates measured at relatively high pO2 (150 Torr) were 2-fold higher, giving rise to a 2-fold lower R-state equilibrium association constant for MalPEG-Hb compared with HbA. Thus the O2 affinity of MalPEG-Hb is higher only at pO2 values lower than the intersection point of the O2 equilibrium curves for MalPEG-Hb and HbA. In summary, the present studies found similar rates of NO binding to HbA and MalPEG-Hb, eliminating the possibility that the lack of vasoactivity of MalPEG-Hb is simply the result of reduced molecular reactivity with NO. Alternatively, the unique O2-binding characteristics with low p50 and co-operativity suggest that the ‘R-state’ conformation of MalPEG-Hb is in a more T-state configuration and restricted from conformational change. PMID:15175010

Properties of the recombinant TNF-binding proteins from variola, monkeypox, and cowpox viruses are different.

PubMed

Gileva, Irina P; Nepomnyashchikh, Tatiana S; Antonets, Denis V; Lebedev, Leonid R; Kochneva, Galina V; Grazhdantseva, Antonina V; Shchelkunov, Sergei N

2006-11-01

Tumor necrosis factor (TNF), a potent proinflammatory and antiviral cytokine, is a critical extracellular immune regulator targeted by poxviruses through the activity of virus-encoded family of TNF-binding proteins (CrmB, CrmC, CrmD, and CrmE). The only TNF-binding protein from variola virus (VARV), the causative agent of smallpox, infecting exclusively humans, is CrmB. Here we have aligned the amino acid sequences of CrmB proteins from 10 VARV, 14 cowpox virus (CPXV), and 22 monkeypox virus (MPXV) strains. Sequence analyses demonstrated a high homology of these proteins. The regions homologous to cd00185 domain of the TNF receptor family, determining the specificity of ligand-receptor binding, were found in the sequences of CrmB proteins. In addition, a comparative analysis of the C-terminal SECRET domain sequences of CrmB proteins was performed. The differences in the amino acid sequences of these domains characteristic of each particular orthopoxvirus species were detected. It was assumed that the species-specific distinctions between the CrmB proteins might underlie the differences in these physicochemical and biological properties. The individual recombinant proteins VARV-CrmB, MPXV-CrmB, and CPXV-CrmB were synthesized in a baculovirus expression system in insect cells and isolated. Purified VARV-CrmB was detectable as a dimer with a molecular weight of 90 kDa, while MPXV- and CPXV-CrmBs, as monomers when fractioned by non-reducing SDS-PAGE. The CrmB proteins of VARV, MPXV, and CPXV differed in the efficiencies of inhibition of the cytotoxic effects of human, mouse, or rabbit TNFs in L929 mouse fibroblast cell line. Testing of CrmBs in the experimental model of LPS-induced shock using SPF BALB/c mice detected a pronounced protective effect of VARV-CrmB. Thus, our data demonstrated the difference in anti-TNF activities of VARV-, MPXV-, and CPXV-CrmBs and efficiency of VARV-CrmB rather than CPXV- or MPXV-CrmBs against LPS-induced mortality in mice.

Histamine monolith versatility to purify supercoiled plasmid deoxyribonucleic acid from Escherichia coli lysate.

PubMed

Sousa, A; Almeida, A M; Černigoj, U; Sousa, F; Queiroz, J A

2014-08-15

Preparation of high quantities of supercoiled plasmid DNA of pharmaceutical grade purity is a research area where intensive investigation is being performed. From this standpoint, several downstream methods have been proposed, among them the monolithic chromatographic strategies owing to excellent mass transfer properties of monolithic supports and their high binding capacity for large biomolecules. The present study explores the physicochemical properties of histamine ligand in a supercoiled plasmid DNA purification process from an Escherichia coli clarified lysate, where the emphasis is given to the elution strategy that allows higher selectivity and efficient removal of other impurities besides the open circular isoform. The combination of high NaCl concentration and acidic pH allowed the elimination of 89% of RNA during the preparative loading of the lysate sample. The results of the purification strategy with ascending sodium chloride gradient revealed that 97% of supercoiled plasmid DNA was recovered with a purity degree of 99%. In addition, using a combined purification strategy with ascending sodium chloride (capture step) and then descending ammonium sulfate (polishing step) gradient, it was achieved a lower supercoiled plasmid DNA recovery yield of 79% with a purity degree of 92%, although the dynamic binding capacity under these conditions was higher than in the previous strategy. A significant reduction of host contents, such as proteins, RNA and genomic DNA, was obtained in both purification strategies. Accordingly, histamine is a useful and versatile ligand that allows the desirable supercoiled plasmid purification with high yield and purity level. Copyright © 2014. Published by Elsevier B.V.

Implementation of steady state approximation for modelling of reaction kinetic of UV catalysed hydrogen peroxide oxidation of starch

NASA Astrophysics Data System (ADS)

Kumoro, Andri Cahyo; Retnowati, Diah Susetyo; Ratnawati, Budiyati, Catarina Sri

2015-12-01

With regard to its low viscosity, high stability, clarity, film forming and binding properties, oxidised starch has been widely used in various applications specifically in the food, paper, textile, laundry finishing and binding materials industries. A number of methods have been used to produce oxidised starch through reactions with various oxidizing agents, such as hydrogen peroxide, air oxygen, ozone, bromine, chromic acid, permanganate, nitrogen dioxide and hypochlorite. Unfortunately, most of previous works reported in the literatures were focused on the study of reaction mechanism and physicochemical properties characterization of the oxidised starches produced without investigation of the reaction kinetics of the oxidation process. This work aimed to develop a simple kinetic model for UV catalysed hydrogen peroxide oxidation of starch through implementation of steady state approximation for the radical reaction rates. The model was then verified using experimental data available in the literature. The model verification revealed that the proposed model shows its good agreement with the experimental data as indicated by an average absolute relative error of only 2.45%. The model also confirmed that carboxyl groups are oxidised further by hydroxyl radical. The carbonyl production rate was found to follow first order reaction with respect to carbonyl concentration. Similarly, carboxyl production rate also followed first order reaction with respect to carbonyl concentration. The apparent reaction rate constant for carbonyl formation and oxidation were 6.24 × 104 s-1 and 1.01 × 104 M-1.s-1, respectively. While apparent reaction rate constant for carboxyl oxidation was 4.86 × 104 M-1.s-1.

Superposition and alignment of labeled point clouds.

PubMed

Fober, Thomas; Glinca, Serghei; Klebe, Gerhard; Hüllermeier, Eyke

2011-01-01

Geometric objects are often represented approximately in terms of a finite set of points in three-dimensional euclidean space. In this paper, we extend this representation to what we call labeled point clouds. A labeled point cloud is a finite set of points, where each point is not only associated with a position in three-dimensional space, but also with a discrete class label that represents a specific property. This type of model is especially suitable for modeling biomolecules such as proteins and protein binding sites, where a label may represent an atom type or a physico-chemical property. Proceeding from this representation, we address the question of how to compare two labeled points clouds in terms of their similarity. Using fuzzy modeling techniques, we develop a suitable similarity measure as well as an efficient evolutionary algorithm to compute it. Moreover, we consider the problem of establishing an alignment of the structures in the sense of a one-to-one correspondence between their basic constituents. From a biological point of view, alignments of this kind are of great interest, since mutually corresponding molecular constituents offer important information about evolution and heredity, and can also serve as a means to explain a degree of similarity. In this paper, we therefore develop a method for computing pairwise or multiple alignments of labeled point clouds. To this end, we proceed from an optimal superposition of the corresponding point clouds and construct an alignment which is as much as possible in agreement with the neighborhood structure established by this superposition. We apply our methods to the structural analysis of protein binding sites.

The effect of inulin as a fat substitute on the physicochemical and sensory properties of chicken sausages.

PubMed

Alaei, Fereshteh; Hojjatoleslamy, Mohammad; Hashemi Dehkordi, Seyyed Majid

2018-03-01

Due to its high thermal resistance and compatibility with the sausage emulsion system, the long-chain inulin can be used as a fat substitute in the formulation of this product. This study was conducted to investigate the effect of inulin on the physicochemical, textural, and sensory properties of chicken sausages. The study included treatments of 25%, 50%, 75%, and 100% substitution. After preparing the samples, their physicochemical, textural, calorimetric, and sensory properties were evaluated. The treatment of 100% substitution of inulin had the maximum amount of sugar (29.90%), moisture (72.63%), protein (51.34), ash (6.95%), and salt (4.02%) (dry basis). The fat content was decreased with the increased levels of inulin substitution (p < .05). The increased amount of inulin reduced hardness, cohesiveness, gumminess, and stringiness, but increased springiness and chewiness up to the 25% substitution of inulin. The highest color difference and hue angle were related to 100% substitution treatment. The sensory evaluation of the samples showed that with the increase in the amount of inulin, the mean scores of the factors including color, appearance, and texture were increased, but the mean scores of smell and mouthfeel were decreased. Overall, the substitution of the entire fat existing in the formulation of the sausage with inulin led to the best physicochemical, textural, colorimetric, and sensory results. The use of inulin could be recommended as a fat substitute in the formulation of chicken sausages.

Phospholipids fatty acids of drinking water reservoir sedimentary microbial community: Structure and function responses to hydrostatic pressure and other physico-chemical properties.

PubMed

Chai, Bei-Bei; Huang, Ting-Lin; Zhao, Xiao-Guang; Li, Ya-Jiao

2015-07-01

Microbial communities in three drinking water reservoirs, with different depth in Xi'an city, were quantified by phospholipids fatty acids analysis and multivariate statistical analysis was employed to interpret their response to different hydrostatic pressure and other physico-chemical properties of sediment and overlying water. Principle component analyses of sediment characteristics parameters showed that hydrostatic pressure was the most important effect factor to differentiate the overlying water quality from three drinking water reservoirs from each other. NH4+ content in overlying water was positive by related to hydrostatic pressure, while DO in water-sediment interface and sediment OC in sediment were negative by related with it. Three drinking water reservoir sediments were characterized by microbial communities dominated by common and facultative anaerobic Gram-positive bacteria, as well as, by sulfur oxidizing bacteria. Hydrostatic pressure and physico-chemical properties of sediments (such as sediment OC, sediment TN and sediment TP) were important effect factors to microbial community structure, especially hydrostatic pressure. It is also suggested that high hydrostatic pressure and low dissolved oxygen concentration stimulated Gram-positive and sulfate-reducing bacteria (SRB) bacterial population in drinking water reservoir sediment. This research supplied a successful application of phospholipids fatty acids and multivariate analysis to investigate microbial community composition response to different environmental factors. Thus, few physico-chemical factors can be used to estimate composition microbial of community as reflected by phospholipids fatty acids, which is difficult to detect.

Covalent modification of a ten-residue cationic antimicrobial peptide with levofloxacin

NASA Astrophysics Data System (ADS)

Rodriguez, Carlos; Papanastasiou, Emilios; Juba, Melanie; Bishop, Barney

2014-09-01

The rampant spread of antibiotic resistant bacteria has spurred interest in alternative strategies for developing next-generation antibacterial therapies. As such, there has been growing interest in cationic antimicrobial peptides (CAMPs) and their therapeutic applications. Modification of CAMPs via conjugation to auxiliary compounds, including small molecule drugs, is a new approach to developing effective, broad-spectrum antibacterial agents with novel physicochemical properties and versatile antibacterial mechanisms. Here, we’ve explored design parameters for engineering CAMPs conjugated to small molecules with favorable physicochemical and antibacterial properties by covalently affixing a fluoroquinolone antibiotic, levofloxacin, to the ten-residue CAMP Pep-4. Relative to the unmodified Pep-4, the conjugate was found to demonstrate substantially increased antibacterial potency under high salt concentrations. Historically, it has been observed that most CAMPs lose antibacterial effectiveness in such high ionic strength environments, a fact that has presented a challenge to their development as therapeutics. Physicochemical studies revealed that P4LC was more hydrophobic than Pep-4, while mechanistic findings indicated that the conjugate was more effective at disrupting bacterial membrane integrity. Although the inherent antibacterial effect of the incorporated levofloxacin molecules did not appear to be substantially realized in this conjugate, these findings nevertheless suggest that covalent attachment of small molecule antibiotics with favorable physicochemical properties to CAMPs could be a promising strategy for enhancing peptide performance and overall therapeutic potential. These results have broader applicability to the development of future CAMP-antibiotic conjugates for potential therapeutic applications.

Sludge Biochar Amendment and Alfalfa Revegetation Improve Soil Physicochemical Properties and Increase Diversity of Soil Microbes in Soils from a Rare Earth Element Mining Wasteland

PubMed Central

Inubushi, Kazuyuki; Liang, Jian; Zhu, Sipin; Wei, Zhenya; Guo, Xiaobin; Luo, Xianping

2018-01-01

Long-term unregulated mining of ion-adsorption clays (IAC) in China has resulted in severe ecological destruction and created large areas of wasteland in dire need of rehabilitation. Soil amendment and revegetation are two important means of rehabilitation of IAC mining wasteland. In this study, we used sludge biochar prepared by pyrolysis of municipal sewage sludge as a soil ameliorant, selected alfalfa as a revegetation plant, and conducted pot trials in a climate-controlled chamber. We investigated the effects of alfalfa revegetation, sludge biochar amendment, and their combined amendment on soil physicochemical properties in soil from an IAC mining wasteland as well as the impact of sludge biochar on plant growth. At the same time, we also assessed the impacts of these amendments on the soil microbial community by means of the Illumina Miseq sequences method. Results showed that alfalfa revegetation and sludge biochar both improved soil physicochemical properties and microbial community structure. When alfalfa revegetation and sludge biochar amendment were combined, we detected additive effects on the improvement of soil physicochemical properties as well as increases in the richness and diversity of bacterial and fungal communities. Redundancy analyses suggested that alfalfa revegetation and sludge biochar amendment significantly affected soil microbial community structure. Critical environmental factors consisted of soil available K, pH, organic matter, carbon–nitrogen ratio, bulk density, and total porosity. Sludge biochar amendment significantly promoted the growth of alfalfa and changed its root morphology. Combining alfalfa the revegetation with sludge biochar amendment may serve to not only achieve the revegetation of IAC mining wasteland, but also address the challenge of municipal sludge disposal by making the waste profitable. PMID:29751652

Significant Differences in Physicochemical Properties of Human Immunoglobulin Kappa and Lambda CDR3 Regions.

PubMed

Townsend, Catherine L; Laffy, Julie M J; Wu, Yu-Chang Bryan; Silva O'Hare, Joselli; Martin, Victoria; Kipling, David; Fraternali, Franca; Dunn-Walters, Deborah K

2016-01-01

Antibody variable regions are composed of a heavy and a light chain, and in humans, there are two light chain isotypes: kappa and lambda. Despite their importance in receptor editing, the light chain is often overlooked in the antibody literature, with the focus being on the heavy chain complementarity-determining region (CDR)-H3 region. In this paper, we set out to investigate the physicochemical and structural differences between human kappa and lambda light chain CDR regions. We constructed a dataset containing over 29,000 light chain variable region sequences from IgM-transcribing, newly formed B cells isolated from human bone marrow and peripheral blood. We also used a published human naïve dataset to investigate the CDR-H3 properties of heavy chains paired with kappa and lambda light chains and probed the Protein Data Bank to investigate the structural differences between kappa and lambda antibody CDR regions. We found that kappa and lambda light chains have very different CDR physicochemical and structural properties, whereas the heavy chains with which they are paired do not differ significantly. We also observed that the mean CDR3 N nucleotide addition in the kappa, lambda, and heavy chain gene rearrangements are correlated within donors but can differ between donors. This indicates that terminal deoxynucleotidyl transferase may work with differing efficiencies between different people but the same efficiency in the different classes of immunoglobulin chain within one person. We have observed large differences in the physicochemical and structural properties of kappa and lambda light chain CDR regions. This may reflect different roles in the humoral immune response.

Significant Differences in Physicochemical Properties of Human Immunoglobulin Kappa and Lambda CDR3 Regions

PubMed Central

Townsend, Catherine L.; Laffy, Julie M. J.; Wu, Yu-Chang Bryan; Silva O’Hare, Joselli; Martin, Victoria; Kipling, David; Fraternali, Franca; Dunn-Walters, Deborah K.

2016-01-01

Antibody variable regions are composed of a heavy and a light chain, and in humans, there are two light chain isotypes: kappa and lambda. Despite their importance in receptor editing, the light chain is often overlooked in the antibody literature, with the focus being on the heavy chain complementarity-determining region (CDR)-H3 region. In this paper, we set out to investigate the physicochemical and structural differences between human kappa and lambda light chain CDR regions. We constructed a dataset containing over 29,000 light chain variable region sequences from IgM-transcribing, newly formed B cells isolated from human bone marrow and peripheral blood. We also used a published human naïve dataset to investigate the CDR-H3 properties of heavy chains paired with kappa and lambda light chains and probed the Protein Data Bank to investigate the structural differences between kappa and lambda antibody CDR regions. We found that kappa and lambda light chains have very different CDR physicochemical and structural properties, whereas the heavy chains with which they are paired do not differ significantly. We also observed that the mean CDR3 N nucleotide addition in the kappa, lambda, and heavy chain gene rearrangements are correlated within donors but can differ between donors. This indicates that terminal deoxynucleotidyl transferase may work with differing efficiencies between different people but the same efficiency in the different classes of immunoglobulin chain within one person. We have observed large differences in the physicochemical and structural properties of kappa and lambda light chain CDR regions. This may reflect different roles in the humoral immune response. PMID:27729912

Assisted phytostabilization of a multicontaminated mine technosol using biochar amendment: Early stage evaluation of biochar feedstock and particle size effects on As and Pb accumulation of two Salicaceae species (Salix viminalis and Populus euramericana).

PubMed

Lebrun, Manhattan; Miard, Florie; Nandillon, Romain; Léger, Jean-Christophe; Hattab-Hambli, Nour; Scippa, Gabriella S; Bourgerie, Sylvain; Morabito, Domenico

2018-03-01

Soil contamination by metal(loid)s is one of the most important environmental problem. It leads to loss of environment biodiversity and soil functions and can have harmful effects on human health. Therefore, contaminated soils could be remediated, using phytoremediation. Indeed, plant growth will improve soil conditions while accumulating metal(loid)s and modifying their mobility. However, due to the poor fertility and high metal(loid)s levels of these soils, amendments, like biochar, has to be applied. This study was performed on a former mine technosol contaminated by As and Pb and aimed to study (i) the effect of biochar on soil physico-chemical properties and plant phytostabilization potential (ii) biochar feedstock and particle size effects. In this goal, a mesocosm experiment was set up using four different biochars, obtained from two feedstocks (lightwood and pinewood) and harboring two particle sizes (inf. 0.1 mm and 0.2-0.4 mm) and two Salicaceae species. Soil and soil pore water physico-chemical properties as well as plant growth and metal(loid)s distribution were assessed. The results showed that biochar was efficient in improving soil physico-chemical properties and reducing Pb soil pore water concentrations. This amelioration allowed plant growth and increased dry weight production of both species. Regarding metal(loid)s distribution, willow and poplar showed an As and Pb accumulation in roots and low translocation towards edible parts, i.e stems and leaves, which shows a phytostabilization potential. Finally, the 2 biochar parameters, feedstock and particle size, only affected soil and soil pore water physico-chemical properties while having no effect on plant growth. Copyright © 2017 Elsevier Ltd. All rights reserved.

The effects of rice straw biochar on indigenous microbial community and enzymes activity in heavy metal-contaminated sediment.

PubMed

Huang, Danlian; Liu, Linshan; Zeng, Guangming; Xu, Piao; Huang, Chao; Deng, Linjing; Wang, Rongzhong; Wan, Jia

2017-05-01

Owning to the potential in carbon sequestration and other environmental benefits, biochar has been widely used for in-situ environmental remediation. Understanding the biological effects of biochar is essential. The goal of this study was to explore the response of indigenous microbes under the stress of different concentrations of biochar. The results showed that biochar could significantly change physicochemical properties, enzymes activity and microbial community composition depending on biochar concentration and incubation time. When the concentration of biochar was 50 mg kg -1 , the activities of invertase and alkaline phosphatase were obviously inhibited. Meanwhile, bacterial 16S rRNA and fungal 18S rRNA coding gene copies were decreased by 74% and 25%, respectively after 90 days of incubation. Additionally, the bacterial community succession occurred and the relative intensity of dominant species decreased when treated with high concentration of biochar. However, the activity of urease and alkaline phosphatase, as well as bacterial and fungal abundance, were increased when sediment was treated with 10 mg kg -1 biochar. Relationships among physicochemical properties, heavy metals and microbes were analyzed by correlation analysis and redundancy analysis (RDA). Correlations between invertase activity and pH value in the experiment were significantly negative. Redundancy analysis showed physicochemical properties and heavy metals explained 92% of the variation in the bacterial DGGE profiles and organic matter content explained the majority (45%) of the variation. This study indicated that indigenous microbes could be affected by biochar either directly or indirectly via changing the physicochemical properties and heavy metals of sediment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Model resin composites incorporating ZnO-NP: activity against S. mutans and physicochemical properties characterization

PubMed Central

Brandão, Natasha Lamego; Portela, Maristela Barbosa; Maia, Luciane Cople; Antônio, Andréa; Silva, Vanessa Loureiro Moreira e

2018-01-01

Abstract Although resin composites are widely used in the clinical practice, the development of recurrent caries at composite-tooth interface still remains as one of the principal shortcomings to be overcome in this field. Objectives To evaluate the activity against S. mutans biofilm of model resin composites incorporating different concentrations of ZnO-nanoparticles (ZnO-NP) and characterize their physicochemical properties. Materials and Methods Different concentrations of ZnO-NP (wt.%): E1=0, E2=0.5, E3=1, E4=2, E5=5 and E6=10 were incorporated into a model resin composite consisting of Bis-GMA-TEGDMA and barium borosilicate particles. The activity against S. mutans biofilm was evaluated by metabolic activity and lactic acid production. The following physicochemical properties were characterized: degree of conversion (DC%), flexural strength (FS), elastic modulus (EM), hardness (KHN), water sorption (Wsp), water solubility (Wsl) and translucency (TP). Results E3, E4, E5 and E6 decreased the biofilm metabolic activity and E5 and E6 decreased the lactic acid production (p<0.05). E6 presented the lowest DC% (p<0.05). No significant difference in FS and EM was found for all resin composites (p>0.05). E5 and E6 presented the lowest values of KHN (p<0.05). E6 presented a higher Wsp than E1 (p<0.05) and the highest Wsl (p<0.05). The translucency significantly decreased as the ZnO- NP concentration increased (p<0.05). Conclusions The incorporation of 2 – 5 wt.% of ZnO-NP could endow antibacterial activity to resin composites, without jeopardizing their physicochemical properties. PMID:29742262

Ion-ion correlation, solvent excluded volume and pH effects on physicochemical properties of spherical oxide nanoparticles.

PubMed

Ovanesyan, Zaven; Aljzmi, Amal; Almusaynid, Manal; Khan, Asrar; Valderrama, Esteban; Nash, Kelly L; Marucho, Marcelo

2016-01-15

One major source of complexity in the implementation of nanoparticles in aqueous electrolytes arises from the strong influence that biological environments has on their physicochemical properties. A key parameter for understanding the molecular mechanisms governing the physicochemical properties of nanoparticles is the formation of the surface charge density. In this article, we present an efficient and accurate approach that combines a recently introduced classical solvation density functional theory for spherical electrical double layers with a surface complexation model to account for ion-ion correlation and excluded volume effects on the surface titration of spherical nanoparticles. We apply the proposed computational approach to account for the charge-regulated mechanisms on the surface chemistry of spherical silica (SiO2) nanoparticles. We analyze the effects of the nanoparticle size, as well as pH level and electrolyte concentration of the aqueous solution on the nanoparticle's surface charge density and Zeta potential. We validate our predictions for 580Å and 200Å nanoparticles immersed in acid, neutral and alkaline mono-valent aqueous electrolyte solutions against experimental data. Our results on mono-valent electrolyte show that the excluded volume and ion-ion correlations contribute significantly to the surface charge density and Zeta potential of the nanoparticle at high electrolyte concentration and pH levels, where the solvent crowding effects and electrostatic screening have shown a profound influence on the protonation/deprotonation reactions at the liquid/solute interface. The success of this approach in describing physicochemical properties of silica nanoparticles supports its broader application to study other spherical metal oxide nanoparticles. Copyright © 2015 Elsevier Inc. All rights reserved.

Model resin composites incorporating ZnO-NP: activity against S. mutans and physicochemical properties characterization.

PubMed

Brandão, Natasha Lamego; Portela, Maristela Barbosa; Maia, Luciane Cople; Antônio, Andréa; Silva, Vanessa Loureiro Moreira E; Silva, Eduardo Moreira da

2018-01-01

Although resin composites are widely used in the clinical practice, the development of recurrent caries at composite-tooth interface still remains as one of the principal shortcomings to be overcome in this field. Objectives To evaluate the activity against S. mutans biofilm of model resin composites incorporating different concentrations of ZnO-nanoparticles (ZnO-NP) and characterize their physicochemical properties. Materials and Methods Different concentrations of ZnO-NP (wt.%): E1=0, E2=0.5, E3=1, E4=2, E5=5 and E6=10 were incorporated into a model resin composite consisting of Bis-GMA-TEGDMA and barium borosilicate particles. The activity against S. mutans biofilm was evaluated by metabolic activity and lactic acid production. The following physicochemical properties were characterized: degree of conversion (DC%), flexural strength (FS), elastic modulus (EM), hardness (KHN), water sorption (Wsp), water solubility (Wsl) and translucency (TP). Results E3, E4, E5 and E6 decreased the biofilm metabolic activity and E5 and E6 decreased the lactic acid production (p<0.05). E6 presented the lowest DC% (p<0.05). No significant difference in FS and EM was found for all resin composites (p>0.05). E5 and E6 presented the lowest values of KHN (p<0.05). E6 presented a higher Wsp than E1 (p<0.05) and the highest Wsl (p<0.05). The translucency significantly decreased as the ZnO- NP concentration increased (p<0.05). Conclusions The incorporation of 2 - 5 wt.% of ZnO-NP could endow antibacterial activity to resin composites, without jeopardizing their physicochemical properties.

Sludge Biochar Amendment and Alfalfa Revegetation Improve Soil Physicochemical Properties and Increase Diversity of Soil Microbes in Soils from a Rare Earth Element Mining Wasteland.

PubMed

Luo, Caigui; Deng, Yangwu; Inubushi, Kazuyuki; Liang, Jian; Zhu, Sipin; Wei, Zhenya; Guo, Xiaobin; Luo, Xianping

2018-05-11

Long-term unregulated mining of ion-adsorption clays (IAC) in China has resulted in severe ecological destruction and created large areas of wasteland in dire need of rehabilitation. Soil amendment and revegetation are two important means of rehabilitation of IAC mining wasteland. In this study, we used sludge biochar prepared by pyrolysis of municipal sewage sludge as a soil ameliorant, selected alfalfa as a revegetation plant, and conducted pot trials in a climate-controlled chamber. We investigated the effects of alfalfa revegetation, sludge biochar amendment, and their combined amendment on soil physicochemical properties in soil from an IAC mining wasteland as well as the impact of sludge biochar on plant growth. At the same time, we also assessed the impacts of these amendments on the soil microbial community by means of the Illumina Miseq sequences method. Results showed that alfalfa revegetation and sludge biochar both improved soil physicochemical properties and microbial community structure. When alfalfa revegetation and sludge biochar amendment were combined, we detected additive effects on the improvement of soil physicochemical properties as well as increases in the richness and diversity of bacterial and fungal communities. Redundancy analyses suggested that alfalfa revegetation and sludge biochar amendment significantly affected soil microbial community structure. Critical environmental factors consisted of soil available K, pH, organic matter, carbon⁻nitrogen ratio, bulk density, and total porosity. Sludge biochar amendment significantly promoted the growth of alfalfa and changed its root morphology. Combining alfalfa the revegetation with sludge biochar amendment may serve to not only achieve the revegetation of IAC mining wasteland, but also address the challenge of municipal sludge disposal by making the waste profitable.

Removal of pharmaceuticals, perfluoroalkyl substances and other micropollutants from wastewater using lignite, Xylit, sand, granular activated carbon (GAC) and GAC+Polonite® in column tests - Role of physicochemical properties.

PubMed

Rostvall, Ande; Zhang, Wen; Dürig, Wiebke; Renman, Gunno; Wiberg, Karin; Ahrens, Lutz; Gago-Ferrero, Pablo

2018-06-15

This study evaluated the performance of five different sorbents (granular activated carbon (GAC), GAC + Polonite ® (GAC + P), Xylit, lignite and sand) for a set of 83 micropollutants (MPs) (pharmaceuticals, perfluoroalkyl substances (PFASs), personal care products, artificial sweeteners, parabens, pesticide, stimulants), together representing a wide range of physicochemical properties. Treatment with GAC and GAC + P provided the highest removal efficiencies, with average values above 97%. Removal rates were generally lower for Xylit (on average 74%) and lignite (on average 68%), although they proved to be highly efficient for a few individual MPs. The average removal efficiency for sand was only 47%. It was observed that the MPs behaved differently depending on their physicochemical properties. The physicochemical properties of PFASs (i.e. molecular weight, topological molecular surface area, log octanol water partition coefficient (K ow ) and distribution coefficient between octanol and water (log D)) were positively correlated to observed removal efficiency for the sorbents Xylit, lignite and sand (p < 0.05), indicating a strong influence of perfluorocarbon chain length and associated hydrophobic characteristics. In contrast, for the other MPs the ratio between apolar and polar surface area (SA/SP) was positively correlated with the removal efficiency, indicating that hydrophobic adsorption may be a key feature of their sorption mechanisms. GAC showed to be the most promising filter medium to improve the removal of MPs in on-site sewage treatment facilities. However, more studies are needed to evaluate the removal of MPs in field trials. Copyright © 2018 Elsevier Ltd. All rights reserved.

Characterizing a Full Spectrum of Physico-Chemical Properties of Ginsenosides Rb1 and Rg1 to Be Proposed as Standard Reference Materials

PubMed Central

Kim, Il-Woung; Hong, Hee-Do; Choi, Sang Yoon; Hwang, Da-Hye; Her, Youl; Kim, Si-Kwan

2011-01-01

Good manufacturing practice (GMP)-based quality control is an integral component of the common technical document, a formal documentation process for applying a marketing authorization holder to those countries where ginseng is classified as a medicine. In addition, authentication of the physico-chemical properties of ginsenoside reference materials, and qualitative and quantitative batch analytical data based on validated analytical procedures are prerequisites for certifying GMP. Therefore, the aim of this study was to propose an authentication process for isolated ginsenosides Rb1 and Rg1 as reference materials (RM) and for these compounds to be designated as RMs for ginseng preparations throughout the world. Ginsenoside Rb1 and Rg1 were isolated by Diaion HP-20 adsorption chromatography, silica gel flash chromatography, recrystallization, and preparative HPLC. HPLC fractions corresponding to those two ginsenosides were recrystallized in appropriate solvents for the analysis of physico-chemical properties. Documentation of the isolated ginsenosides was made according to the method proposed by Gaedcke and Steinhoff. The ginsenosides were subjected to analyses of their general characteristics, identification, purity, content quantitation, and mass balance tests. The isolated ginsenosides were proven to be a single compound when analyzed by three different HPLC systems. Also, the water content was found to be 0.940% for Rb1 and 0.485% for Rg1, meaning that the net mass balance for ginsenoside Rb1 and Rg1 were 99.060% and 99.515%, respectively. From these results, we could assess and propose a full spectrum of physicochemical properties for the ginsenosides Rb1 and Rg1 as standard reference materials for GMP-based quality control. PMID:23717096

Physicochemical and Functional Properties of Vegetable and Cereal Proteins as Potential Sources of Novel Food Ingredients

PubMed Central

Soria-Hernández, Cintya; Serna-Saldívar, Sergio

2015-01-01

Summary Proteins from vegetable and cereal sources are an excellent alternative to substitute animal-based counterparts because of their reduced cost, abundant supply and good nutritional value. The objective of this investigation is to study a set of vegetable and cereal proteins in terms of physicochemical and functional properties. Twenty protein sources were studied: five soya bean flour samples, one pea flour and fourteen newly developed blends of soya bean and maize germ (five concentrates and nine hydrolysates). The physicochemical characterization included pH (5.63 to 7.57), electrical conductivity (1.32 to 4.32 mS/cm), protein content (20.78 to 94.24% on dry mass basis), free amino nitrogen (0.54 to 2.87 mg/g) and urease activity (0.08 to 2.20). The functional properties showed interesting differences among proteins: water absorption index ranged from 0.41 to 18.52, the highest being of soya and maize concentrates. Nitrogen and water solubility ranged from 10.14 to 74.89% and from 20.42 to 95.65%, respectively. Fat absorption and emulsification activity indices ranged from 2.59 to 4.72 and from 3936.6 to 52 399.2 m2/g respectively, the highest being of pea flour. Foam activity (66.7 to 475.0%) of the soya and maize hydrolysates was the best. Correlation analyses showed that hydrolysis affected solubility-related parameters whereas fat-associated indices were inversely correlated with water-linked parameters. Foam properties were better of proteins treated with low heat, which also had high urease activity. Physicochemical and functional characterization of the soya and maize protein concentrates and hydrolysates allowed the identification of differences regarding other vegetable and cereal protein sources such as pea or soya bean. PMID:27904358

Physicochemical and Pharmacological Characterization of Permanently Charged Opioids.

PubMed

Mazak, Karoly; Noszal, Bela; Hosztafi, Sandor

2017-01-01

The main aim of synthesizing permanently charged opioids is to ensure that they do not enter the central nervous system. Such drugs can provide analgesic activity with reduced sedation and other side effects on the central nervous system. We undertook a search of bibliographic databases for peer-reviewed research literature and also summarized our published results in this field. The present review focuses on the characterization of permanently charged opioids by various physicochemical methods, and in vitro as well as in vivo tests. The basicity and lipophilicity of opioid alkaloids are discussed at the microscopic, speciesspecific level. Glucuronide conjugates of opioids are also reviewed. Whereas the primary metabolite morphine-3-glucuronide does not bind to opioid receptors with high affinity, morphine-6-glucuronide is a potent analgesic, at least, partly due to its unexpectedly high lipophilicity. We discuss the quaternary ammonium opioid derivatives of a permanent positive charge, detailing their antinociceptive activity and effects on gastrointestinal motility in various in vivo animal tests and in vitro studies. Compounds with antagonistic activity are also reviewed. The last part of our study concentrates on sulfate conjugates of morphine derivatives that display unique pharmacological properties because they carry a negative charge at any pH value in the human body. In conclusion, the findings of this review confirm the importance of permanently charged opioids in the investigated fields of pharmacology. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Aromaticity at the water-hydrocarbon core interface of the membrane

PubMed Central

Lizardi-Ortiz, José E.; Hyzinski-García, María C.; Fernández-Gerena, José L.; Osorio-Martínez, Karen M.; Velázquez-Rivera, Eric; Valle-Avilés, Félix L.; Lasalde-Dominicci, José A.

2011-01-01

Almost all lipid-exposed transmembrane domains of integral proteins contain aromatic residues flanking the hydrophobic segment of the domains. These residues generally reside close to the carbonyl region of the membrane, and several structural and functional roles have been associated to these residues. Although the roles and physicochemical reasons for aromatic preference have been extensively studied using model systems, few studies have been done in a native membrane system. To gain insight about the mechanistic implication for this aromatic preference, we selected position αF426 of the muscle-type nicotinic acetylcholine receptor (nAChR). αF426 is a lipid-exposed residue at the extracellular segment of the αM4 transmembrane domain and is highly conserved among different nAChR subunits and species. We used site-directed mutagenesis, α-Bungarotoxin-binding assay, and two-electrodes voltage clamp in Xenopus laevis oocytes to characterize mutations at position αF426, which impart different physicochemical properties like volume, polarity, hydrogen bonds, aromaticity and net electrical charge. All mutations except the aromatic residues resulted in a significant reduction of the nAChR cell-surface levels and the macroscopic currents to acetylcholine. These results suggest that position αF426 contributes to structural stability and open-close transitions of the nAChR. Finally, the present study also provides information about how intermolecular interactions at position α426 modulate open-close transitions of the nAChR. PMID:18836298

Physicochemical properties of kiwifruit starch.

PubMed

Li, Dongxing; Zhu, Fan

2017-04-01

Three varieties of golden kiwifruit (Actinidia chinensis) (Gold3, Gold9 and Hort16A) were collected at the commercial harvesting time, and physicochemical properties of starches from core and outer pericarp were studied. Starch contents (dry weight basis) in outer pericarp and core tissues ranged from 38.6 to 51.8% and 34.6 to 40.7%, respectively. All the kiwifruit starches showed B-type polymorph. Compared to the outer pericarp starches, amylose content and enzyme susceptibility of core starches were higher, and the degree of crystallinity, granule size and gelatinization parameters of core starches were somewhat lower. This suggests different biosynthetic properties between these two starches. The enthalpy changes of gelatinization of outer pericarp starches were high (∼21J/g). Rheological properties of outer pericarp starches were compared with normal maize and potato starches showed high yield stress of flow properties. This study revealed the unique properties of kiwifruit starch among various types of starches. Copyright © 2016 Elsevier Ltd. All rights reserved.

How Lipid Membranes Affect Pore Forming Toxin Activity.

PubMed

Rojko, Nejc; Anderluh, Gregor

2015-12-15

Pore forming toxins (PFTs) evolved to permeate the plasma membrane of target cells. This is achieved in a multistep mechanism that usually involves binding of soluble protein monomer to the lipid membrane, oligomerization at the plane of the membrane, and insertion of part of the polypeptide chain across the lipid membrane to form a conductive channel. Introduced pores allow uncontrolled transport of solutes across the membrane, inflicting damage to the target cell. PFTs are usually studied from the perspective of structure-function relationships, often neglecting the important role of the bulk membrane properties on the PFT mechanism of action. In this Account, we discuss how membrane lateral heterogeneity, thickness, and fluidity influence the pore forming process of PFTs. In general, lipid molecules are more accessible for binding in fluid membranes due to steric reasons. When PFT specifically binds ordered domains, it usually recognizes a specific lipid distribution pattern, like sphingomyelin (SM) clusters or SM/cholesterol complexes, and not individual lipid species. Lipid domains were also suggested to act as an additional concentration platform facilitating PFT oligomerization, but this is yet to be shown. The last stage in PFT action is the insertion of the transmembrane segment across the membranes to build the transmembrane pore walls. Conformational changes are a spontaneous process, and sufficient free energy has to be available for efficient membrane penetration. Therefore, fluid bilayers are permeabilized more readily in comparison to highly ordered and thicker liquid ordered lipid phase (Lo). Energetically more costly insertion into the Lo phase can be driven by the hydrophobic mismatch between the thinner liquid disordered phase (Ld) and large protein complexes, which are unable to tilt like single transmembrane segments. In the case of proteolipid pores, membrane properties can directly modulate pore size, stability, and even selectivity. Finally, events associated with pore formation can modulate properties of the lipid membrane and affect its organization. Model membranes do not necessarily reproduce the physicochemical properties of the native cellular membrane, and caution is needed when transferring results from model to native lipid membranes. In this context, the utilization of novel approaches that enable studying PFTs on living cells at a single molecule level should reveal complex protein-lipid membrane interactions in greater detail.

SPEER-SERVER: a web server for prediction of protein specificity determining sites

PubMed Central

Chakraborty, Abhijit; Mandloi, Sapan; Lanczycki, Christopher J.; Panchenko, Anna R.; Chakrabarti, Saikat

2012-01-01

Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or proteins. Identification of SDS through experimental techniques is a slow, difficult and tedious job. Hence, it is very important to develop efficient computational methods that can more expediently identify SDS. Herein, we present Specificity prediction using amino acids’ Properties, Entropy and Evolution Rate (SPEER)-SERVER, a web server that predicts SDS by analyzing quantitative measures of the conservation patterns of protein sites based on their physico-chemical properties and the heterogeneity of evolutionary changes between and within the protein subfamilies. This web server provides an improved representation of results, adds useful input and output options and integrates a wide range of analysis and data visualization tools when compared with the original standalone version of the SPEER algorithm. Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/. PMID:22689646

Physico-chemical studies of the experimental and theoretical properties of organic nonlinear optical material 4-chloro-4'methoxy benzylideneaniline

NASA Astrophysics Data System (ADS)

George, Merin; John, Nimmy L.; Saravana Kumar, M.; Subashini, A.; Sajan, D.

2017-01-01

The FT-IR, FT-Raman and UV-visible spectral analysis of 4-chloro 4'-methoxy benzylidene aniline were done experimentally and interpreted with the aid of normal coordinate analysis based on density functional theory (DFT) at the B3LYP/6-311++G (d, p) level of theory. Natural Bond orbital analysis was performed to understand the charge transfer interactions and reactive sites within the system. HOMO-LUMO analysis and first static and dynamic hyperpolarizability calculations were carried out in order to confirm the NLO activity of CMOBA. Photophysical characterization was done to understand the fluorescence emission and lifetime of CMOBA leading to application in blue OLEDs. The Molecular Electrostatic Potential Map was simulated to identify the active sites for electrophilic and nucleophilic attack or the active sites of the molecule which can bind to proteins. Molecular docking analysis revealed its potential as an inhibitor for different proteins which are responsible for cancer and many inflammatory diseases such as rheumatoid arthritis, inflammatory bowel disease, Crohn's disease and psoriasis. Experimental studies of invitro antiproliferative effect by MTT assay verified the anticancer properties of CMOBA.