Manipulating Fatty Acid Biosynthesis in Microalgae for Biofuel through Protein-Protein Interactions

PubMed Central

Blatti, Jillian L.; Beld, Joris; Behnke, Craig A.; Mendez, Michael; Mayfield, Stephen P.; Burkart, Michael D.

2012-01-01

Microalgae are a promising feedstock for renewable fuels, and algal metabolic engineering can lead to crop improvement, thus accelerating the development of commercially viable biodiesel production from algae biomass. We demonstrate that protein-protein interactions between the fatty acid acyl carrier protein (ACP) and thioesterase (TE) govern fatty acid hydrolysis within the algal chloroplast. Using green microalga Chlamydomonas reinhardtii (Cr) as a model, a structural simulation of docking CrACP to CrTE identifies a protein-protein recognition surface between the two domains. A virtual screen reveals plant TEs with similar in silico binding to CrACP. Employing an activity-based crosslinking probe designed to selectively trap transient protein-protein interactions between the TE and ACP, we demonstrate in vitro that CrTE must functionally interact with CrACP to release fatty acids, while TEs of vascular plants show no mechanistic crosslinking to CrACP. This is recapitulated in vivo, where overproduction of the endogenous CrTE increased levels of short-chain fatty acids and engineering plant TEs into the C. reinhardtii chloroplast did not alter the fatty acid profile. These findings highlight the critical role of protein-protein interactions in manipulating fatty acid biosynthesis for algae biofuel engineering as illuminated by activity-based probes. PMID:23028438

Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design.

PubMed

Xie, Neng-Zhong; Du, Qi-Shi; Li, Jian-Xiu; Huang, Ri-Bo

2015-01-01

Three strong interactions between amino acid side chains (salt bridge, cation-π, and amide bridge) are studied that are stronger than (or comparable to) the common hydrogen bond interactions, and play important roles in protein-protein interactions. Quantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations. The energies of three types of amino acid side chain interactions in gaseous phase and in aqueous solutions are calculated using high level quantum chemical methods and basis sets. Typical examples of amino acid salt bridge, cation-π, and amide bridge interactions are analyzed, including the inhibitor design targeting neuraminidase (NA) enzyme of influenza A virus, and the ligand binding interactions in the HCV p7 ion channel. The inhibition mechanism of the M2 proton channel in the influenza A virus is analyzed based on strong amino acid interactions. (1) The salt bridge interactions between acidic amino acids (Glu- and Asp-) and alkaline amino acids (Arg+, Lys+ and His+) are the strongest residue-residue interactions. However, this type of interaction may be weakened by solvation effects and broken by lower pH conditions. (2) The cation- interactions between protonated amino acids (Arg+, Lys+ and His+) and aromatic amino acids (Phe, Tyr, Trp and His) are 2.5 to 5-fold stronger than common hydrogen bond interactions and are less affected by the solvation environment. (3) The amide bridge interactions between the two amide-containing amino acids (Asn and Gln) are three times stronger than hydrogen bond interactions, which are less influenced by the pH of the solution. (4) Ten of the twenty natural amino acids are involved in salt bridge, or cation-, or amide bridge interactions that often play important roles in protein-protein, protein-peptide, protein-ligand, and protein-DNA interactions.

Acid-Base Interactions of Polystyrene Sulfonic Acid in Amorphous Solid Dispersions Using a Combined UV/FTIR/XPS/ssNMR Study.

PubMed

Song, Yang; Zemlyanov, Dmitry; Chen, Xin; Nie, Haichen; Su, Ziyang; Fang, Ke; Yang, Xinghao; Smith, Daniel; Byrn, Stephen; Lubach, Joseph W

2016-02-01

This study investigates the potential drug-excipient interactions of polystyrene sulfonic acid (PSSA) and two weakly basic anticancer drugs, lapatinib (LB) and gefitinib (GB), in amorphous solid dispersions. Based on the strong acidity of the sulfonic acid functional group, PSSA was hypothesized to exhibit specific intermolecular acid-base interactions with both model basic drugs. Ultraviolet (UV) spectroscopy identified red shifts, which correlated well with the color change observed in lapatinib-PSSA solutions. Fourier transform infrared (FTIR) spectra suggest the protonation of the quinazoline nitrogen atom in both model compounds, which agrees well with data from the crystalline ditosylate salt of lapatinib. X-ray photoelectron spectroscopy (XPS) detected increases in binding energy of the basic nitrogen atoms in both lapatinib and gefitinib, strongly indicating protonation of these nitrogen atoms. (15)N solid-state NMR spectroscopy provided direct spectroscopic evidence for protonation of the quinazoline nitrogen atoms in both LB and GB, as well as the secondary amine nitrogen atom in LB and the tertiary amine nitrogen atom in GB. The observed chemical shifts in the LB-PSSA (15)N spectrum also agree very well with the lapatinib ditosylate salt where proton transfer is known. Additionally, the dissolution and physical stability behaviors of both amorphous solid dispersions were examined. PSSA was found to significantly improve the dissolution of LB and GB and effectively inhibit the crystallization of LB and GB under accelerated storage conditions due to the beneficial strong intermolecular acid-base interaction between the sulfonic acid groups and basic nitrogen centers.

Abscisic Acid-Cytokinin Antagonism Modulates Resistance Against Pseudomonas syringae in Tobacco.

PubMed

Großkinsky, Dominik K; van der Graaff, Eric; Roitsch, Thomas

2014-12-01

Phytohormones are known as essential regulators of plant defenses, with ethylene, jasmonic acid, and salicylic acid as the central immunity backbone, while other phytohormones have been demonstrated to interact with this. Only recently, a function of the classic phytohormone cytokinin in plant immunity has been described in Arabidopsis, rice, and tobacco. Although interactions of cytokinins with salicylic acid and auxin have been indicated, the complete network of cytokinin interactions with other immunity-relevant phytohormones is not yet understood. Therefore, we studied the interaction of kinetin and abscisic acid as a negative regulator of plant immunity to modulate resistance in tobacco against Pseudomonas syringae. By analyzing infection symptoms, pathogen proliferation, and accumulation of the phytoalexin scopoletin as a key mediator of kinetin-induced resistance in tobacco, antagonistic interaction of these phytohormones in plant immunity was identified. Kinetin reduced abscisic acid levels in tobacco, while increased abscisic acid levels by exogenous application or inhibition of abscisic acid catabolism by diniconazole neutralized kinetin-induced resistance. Based on these results, we conclude that reduction of abscisic acid levels by enhanced abscisic acid catabolism strongly contributes to cytokinin-mediated resistance effects. Thus, the identified cytokinin-abscisic acid antagonism is a novel regulatory mechanism in plant immunity.

Solid-state supramolecular architectures formed by co-crystallization of melamine and 2-, 3- and 4-fluorophenylacetic acids

NASA Astrophysics Data System (ADS)

Perpétuo, Genivaldo Julio; Janczak, Jan

2018-01-01

A family of supramolecular complexes of melamine with fluorophenylacetic acid isomers using solvent-assisted and evaporation-based techniques has been prepared. Crystallization of melamine with 2-fluorophenylacetic acid yield hydrated ionic supramolecular complex (1), whereas crystallization of melamine with 3- and 4-fluorophenylacetic acids leads to formation of neutral supramolecular complexes (2, 3), all with base to acid ratio of 1:2. The supramolecular assembly is driven by the noncovalent interactions, most commonly by the hydrogen bonds. The components of the crystal 1 interact via Nsbnd H⋯O and Osbnd H⋯N hydrogen bonds with R22(8) and R32(10) graphs forming ionic supramolecular complex, whereas the components in the crystals 2 and 3 interact with a graph of R22(8) forming neutral supramolecular complexes. The singly protonated melamin-1-ium residues in 1 interact each other via a pair of Nsbnd H⋯N hydrogen bonds forming one dimensional chains along [-110] that interact via Nsbnd H⋯O with deprotonated and neutral 2-fluorophenylacetic acid units and water molecules forming ribbon. In 2 and 3 co-crystals the melamine interacts with 3- and 4-fluorophenylacetic acids via a pair of Nsbnd H⋯O hydrogen bonds forming pseudo one-dimensional supramolecular chains along [010] direction. Hirshfeld surface and analysis of 2D fingerprint plots have been analysed both quantitatively and qualitatively interactions that governing the supramolecular organisation. The IR and Raman vibrational characterization of the supramolecular complexes 1-3 was supported by the spectra of their deuterated analogues.

Green Tea Catechin-Based Complex Micelles Combined with Doxorubicin to Overcome Cardiotoxicity and Multidrug Resistance

PubMed Central

Cheng, Tangjian; Liu, Jinjian; Ren, Jie; Huang, Fan; Ou, Hanlin; Ding, Yuxun; Zhang, Yumin; Ma, Rujiang; An, Yingli; Liu, Jianfeng; Shi, Linqi

2016-01-01

Chemotherapy for cancer treatment has been demonstrated to cause some side effects on healthy tissues and multidrug resistance of the tumor cells, which greatly limits therapeutic efficacy. To address these limitations and achieve better therapeutic efficacy, combination therapy based on nanoparticle platforms provides a promising approach through delivering different agents simultaneously to the same destination with synergistic effect. In this study, a novel green tea catechin-based polyion complex (PIC) micelle loaded with doxorubicin (DOX) and (-)-Epigallocatechin-3-O-gallate (EGCG) was constructed through electrostatic interaction and phenylboronic acid-catechol interaction between poly(ethylene glycol)-block-poly(lysine-co-lysine-phenylboronic acid) (PEG-PLys/PBA) and EGCG. DOX was co-loaded in the PIC micelles through π-π stacking interaction with EGCG. The phenylboronic acid-catechol interaction endowed the PIC micelles with high stability under physiological condition. Moreover, acid cleavability of phenylboronic acid-catechol interaction in the micelle core has significant benefits for delivering EGCG and DOX to same destination with synergistic effects. In addition, benefiting from the oxygen free radicals scavenging activity of EGCG, combination therapy with EGCG and DOX in the micelle core could protect the cardiomyocytes from DOX-mediated cardiotoxicity according to the histopathologic analysis of hearts. Attributed to modulation of EGCG on P-glycoprotein (P-gp) activity, this kind of PIC micelles could effectively reverse multidrug resistance of cancer cells. These results suggested that EGCG based PIC micelles could effectively overcome DOX induced cardiotoxicity and multidrug resistance. PMID:27375779

Green Tea Catechin-Based Complex Micelles Combined with Doxorubicin to Overcome Cardiotoxicity and Multidrug Resistance.

PubMed

Cheng, Tangjian; Liu, Jinjian; Ren, Jie; Huang, Fan; Ou, Hanlin; Ding, Yuxun; Zhang, Yumin; Ma, Rujiang; An, Yingli; Liu, Jianfeng; Shi, Linqi

2016-01-01

Chemotherapy for cancer treatment has been demonstrated to cause some side effects on healthy tissues and multidrug resistance of the tumor cells, which greatly limits therapeutic efficacy. To address these limitations and achieve better therapeutic efficacy, combination therapy based on nanoparticle platforms provides a promising approach through delivering different agents simultaneously to the same destination with synergistic effect. In this study, a novel green tea catechin-based polyion complex (PIC) micelle loaded with doxorubicin (DOX) and (-)-Epigallocatechin-3-O-gallate (EGCG) was constructed through electrostatic interaction and phenylboronic acid-catechol interaction between poly(ethylene glycol)-block-poly(lysine-co-lysine-phenylboronic acid) (PEG-PLys/PBA) and EGCG. DOX was co-loaded in the PIC micelles through π-π stacking interaction with EGCG. The phenylboronic acid-catechol interaction endowed the PIC micelles with high stability under physiological condition. Moreover, acid cleavability of phenylboronic acid-catechol interaction in the micelle core has significant benefits for delivering EGCG and DOX to same destination with synergistic effects. In addition, benefiting from the oxygen free radicals scavenging activity of EGCG, combination therapy with EGCG and DOX in the micelle core could protect the cardiomyocytes from DOX-mediated cardiotoxicity according to the histopathologic analysis of hearts. Attributed to modulation of EGCG on P-glycoprotein (P-gp) activity, this kind of PIC micelles could effectively reverse multidrug resistance of cancer cells. These results suggested that EGCG based PIC micelles could effectively overcome DOX induced cardiotoxicity and multidrug resistance.

Fluorescent sensors based on boronic acids

NASA Astrophysics Data System (ADS)

Cooper, Christopher R.; James, Tony D.

1999-05-01

Sensor systems have long been needed for detecting the presence in solution of certain chemically or biologically important species. Sensors are used in a wide range of applications from simple litmus paper that shows a single color change in acidic or basic environments to complex biological assays that use enzymes, antibodies and antigens to display binding events. With this work the use of boronic acids in the design and synthesis of sensors for saccharides (diols) will be presented. The fluorescent sensory systems rely on photoinduced electron transfer (PET) to modulate the observed fluorescence. When saccharides form cyclic boronate esters with boronic acids, the Lewis acidity of the boronic acid is enhanced and therefore the Lewis acid-base interaction between the boronic acid and a neighboring amine is strengthened. The strength of this acid-base interaction modulates the PET from the amine (acting as a quencher) to anthracene (acting as a fluorophore). These compounds show increased fluorescence at neutral pH through suppression of the PET from nitrogen to anthracene on saccharide binding. The general strategy for the development of saccharide selective systems will be discussed. The potential of the boronic acid based systems will be illustrated using the development of glucose and glucosamine selective fluorescent sensors as examples.

Fluorescence Turn-on Enantioselective Recognition of both Chiral Acidic Compounds and α-Amino Acids by a Chiral Tetraphenylethylene Macrocycle Amine.

PubMed

Feng, Hai-Tao; Zhang, Xing; Zheng, Yan-Song

2015-08-21

New chiral tetraphenylethylene (TPE) macrocycles bearing optically pure amine groups were synthesized and found to have a discriminating ability between the two enantiomers of not only chiral acidic compounds but also α-amino acids by enantioselective aggregation and aggregation-induced emission (AIE) effects. NMR spectra, including 2D-NOESY, disclosed that the host-guest interaction of the macrocycle receptor played a key role in addition to the acid-base interactions.

A nuclear magnetic resonance study of the dynamics of organofluorine interactions with a dissolved humic acid.

PubMed

Longstaffe, James G; Courtier-Murias, Denis; Simpson, Andre J

2016-02-01

A quantitative understanding of the dynamics of the interactions between organofluorine compounds and humic acids will contribute to an improved understanding of the role that Natural Organic Matter plays as a mediator in the fate, transport and distribution of these contaminants in the environment. Here, Nuclear Magnetic Resonance (NMR) spectroscopy-based diffusion measurements are used to estimate the association dynamics between dissolved humic acid and selected organofluorine compounds: pentafluoroaniline, pentafluorophenol, potassium perfluorooctane sulfonate, and perfluorooctanoic acid. Under the conditions used here, the strength of the association with humic acid increases linearly as temperature decreases for all compounds except for perfluorooctanoic acid, which exhibits divergent behavior with a non-linear decrease in the extent of interaction as temperature decreases. A general interaction mechanism controlled largely by desolvation effects is suggested for all compounds examined here except for perfluorooctanoic acid, which exhibits a specific mode of interaction consistent with a proteinaceous binding site. Reverse Heteronuclear Saturation Transfer Difference NMR is used to confirm the identity and nature of the humic acid binding sites. Copyright © 2015 Elsevier Ltd. All rights reserved.

Is there an attractive interaction between two methyl groups?

NASA Astrophysics Data System (ADS)

Zhuo, Hong-Ying; Jiang, Li-Xia; Li, Qing-Zhong; Li, Wen-Zuo; Cheng, Jian-Bo

2014-07-01

A weak interaction was found between the two methyl groups in the complexes of XCH3-CH3BH2 (X = F, CN, NO2, HCO, and SOCH3), where the former methyl group acts as a Lewis acid and the latter one as a Lewis base. This directional interaction has small interaction energy, accompanied with some small changes in geometry and spectroscopy. Stronger Lewis acids FYH3 (Y = Si, Ge, and Sn) as well as Lewis bases CH3BeH and CH3MgH were compared. Dispersion energy is the major source of attraction and electrostatic contribution grows up to exceed dispersion energy for stronger interactions.

The acid tolerance response and pH adaptation of Enterococcus faecalis in extract of lime Citrus aurantiifolia from Aceh Indonesia.

PubMed

Mubarak, Zaki; Soraya, Cut

2018-01-01

Background:  The objective of the present study was to evaluate the acid tolerance response and pH adaptation when Enterococcus faecalis interacted with extract of lime ( Citrus aurant iifolia ). Methods : We used E. faecalis ATCC 29212 and lime extract from Aceh, Indonesia. The microbe was analyzed for its pH adaptation, acid tolerance response, and adhesion assay using a light microscope with a magnification of x1000. Further, statistical tests were performed to analyze both correlation and significance of the acid tolerance and pH adaptation as well as the interaction activity. Results : E. faecalis was able to adapt to a very acidic environment (pH 2.9), which was characterized by an increase in its pH (reaching 4.2) at all concentrations of the lime extract (p < 0.05). E. faecalis was also able to provide acid tolerance response to lime extract based on spectrophotometric data (595 nm) (p < 0.05). Also, the interaction activity of E. faecalis in different concentrations of lime extract was relatively stable within 6 up to 12 hours (p < 0.05), but it became unstable within 24-72 hours (p > 0.05) based on the mass profiles of its interaction activity. Conclusions : E. faecalis can adapt to acidic environments (pH 2.9-4.2); it is also able to tolerate acid generated by Citrus auranti ifolia extract, revealing a stable interaction in the first 6-12 hours.

Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites.

PubMed

Jelínek, Jan; Škoda, Petr; Hoksza, David

2017-12-06

Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino acids take part in a PPI has been an active field of research for some time, the quality of in-silico methods is still far from perfect. We have developed a novel prediction method called INSPiRE which benefits from a knowledge base built from data available in Protein Data Bank. All proteins involved in PPIs were converted into labeled graphs with nodes corresponding to amino acids and edges to pairs of neighboring amino acids. A structural neighborhood of each node was then encoded into a bit string and stored in the knowledge base. When predicting PPIs, INSPiRE labels amino acids of unknown proteins as interface or non-interface based on how often their structural neighborhood appears as interface or non-interface in the knowledge base. We evaluated INSPiRE's behavior with respect to different types and sizes of the structural neighborhood. Furthermore, we examined the suitability of several different features for labeling the nodes. Our evaluations showed that INSPiRE clearly outperforms existing methods with respect to Matthews correlation coefficient. In this paper we introduce a new knowledge-based method for identification of protein-protein interaction sites called INSPiRE. Its knowledge base utilizes structural patterns of known interaction sites in the Protein Data Bank which are then used for PPI prediction. Extensive experiments on several well-established datasets show that INSPiRE significantly surpasses existing PPI approaches.

Hydrogen bonded binary molecular adducts derived from exobidentate N-donor ligand with dicarboxylic acids: Acid⋯imidazole hydrogen-bonding interactions in neutral and ionic heterosynthons

NASA Astrophysics Data System (ADS)

Kathalikkattil, Amal Cherian; Damodaran, Subin; Bisht, Kamal Kumar; Suresh, Eringathodi

2011-01-01

Four new binary molecular compounds between a flexible exobidentate N-heterocycle and a series of dicarboxylic acids have been synthesized. The N-donor 1,4-bis(imidazol-1-ylmethyl)benzene (bix) was reacted with flexible and rigid dicarboxylic acids viz., cyclohexane-1,4-dicarboxylic acid (H 2chdc), naphthalene-1,4-dicarboxylic acid (H 2npdc) and 1H-pyrazole-3,5-dicarboxylic acid (H 2pzdc), generating four binary molecular complexes. X-ray crystallographic investigation of the molecular adducts revealed the primary intermolecular interactions carboxylic acid⋯amine (via O-H⋯N) as well as carboxylate⋯protonated amine (via N-H +⋯O -) within the binary compounds, generating layered and two-dimensional sheet type H-bonded networks involving secondary weak interactions (C-H⋯O) including the solvent of crystallization. Depending on the differences in p Ka values of the selected base/acid (Δp Ka), diverse H-bonded supramolecular assemblies could be premeditated. This study demonstrates the H-bonding interactions between imidazole/imidazolium cation and carboxylic acid/carboxylate anion in providing sufficient driving force for the directed assembly of binary molecular complexes. In the two-component solid form of hetero synthons involving bix and dicarboxylic acid, only H 2chdc exist as cocrystal with bix, while all the other three compounds crystallized exclusively as salt, in agreement with the Δp Ka values predicted for the formation of salts/cocrystals from the base and acid used in the synthesis of supramolecular solids.

Stacking interactions in PUF-RNA complexes

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

Yiling Koh, Yvonne; Wang, Yeming; Qiu, Chen

2012-07-02

Stacking interactions between amino acids and bases are common in RNA-protein interactions. Many proteins that regulate mRNAs interact with single-stranded RNA elements in the 3' UTR (3'-untranslated region) of their targets. PUF proteins are exemplary. Here we focus on complexes formed between a Caenorhabditis elegans PUF protein, FBF, and its cognate RNAs. Stacking interactions are particularly prominent and involve every RNA base in the recognition element. To assess the contribution of stacking interactions to formation of the RNA-protein complex, we combine in vivo selection experiments with site-directed mutagenesis, biochemistry, and structural analysis. Our results reveal that the identities of stackingmore » amino acids in FBF affect both the affinity and specificity of the RNA-protein interaction. Substitutions in amino acid side chains can restrict or broaden RNA specificity. We conclude that the identities of stacking residues are important in achieving the natural specificities of PUF proteins. Similarly, in PUF proteins engineered to bind new RNA sequences, the identity of stacking residues may contribute to 'target' versus 'off-target' interactions, and thus be an important consideration in the design of proteins with new specificities.« less

Quantitative thermodynamic predication of interactions between nucleic acid and non-nucleic acid species using Microsoft excel.

PubMed

Zou, Jiaqi; Li, Na

2013-09-01

Proper design of nucleic acid sequences is crucial for many applications. We have previously established a thermodynamics-based quantitative model to help design aptamer-based nucleic acid probes by predicting equilibrium concentrations of all interacting species. To facilitate customization of this thermodynamic model for different applications, here we present a generic and easy-to-use platform to implement the algorithm of the model with Microsoft(®) Excel formulas and VBA (Visual Basic for Applications) macros. Two Excel spreadsheets have been developed: one for the applications involving only nucleic acid species, the other for the applications involving both nucleic acid and non-nucleic acid species. The spreadsheets take the nucleic acid sequences and the initial concentrations of all species as input, guide the user to retrieve the necessary thermodynamic constants, and finally calculate equilibrium concentrations for all species in various bound and unbound conformations. The validity of both spreadsheets has been verified by comparing the modeling results with the experimental results on nucleic acid sequences reported in the literature. This Excel-based platform described here will allow biomedical researchers to rationalize the sequence design of nucleic acid probes using the thermodynamics-based modeling even without relevant theoretical and computational skills. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Multi-gas interaction modeling on decorated semiconductor interfaces: A novel Fermi distribution-based response isotherm and the inverse hard/soft acid/base concept

NASA Astrophysics Data System (ADS)

Laminack, William; Gole, James

2015-12-01

A unique MEMS/NEMS approach is presented for the modeling of a detection platform for mixed gas interactions. Mixed gas analytes interact with nanostructured decorating metal oxide island sites supported on a microporous silicon substrate. The Inverse Hard/Soft acid/base (IHSAB) concept is used to assess a diversity of conductometric responses for mixed gas interactions as a function of these nanostructured metal oxides. The analyte conductometric responses are well represented using a combination diffusion/absorption-based model for multi-gas interactions where a newly developed response absorption isotherm, based on the Fermi distribution function is applied. A further coupling of this model with the IHSAB concept describes the considerations in modeling of multi-gas mixed analyte-interface, and analyte-analyte interactions. Taking into account the molecular electronic interaction of both the analytes with each other and an extrinsic semiconductor interface we demonstrate how the presence of one gas can enhance or diminish the reversible interaction of a second gas with the extrinsic semiconductor interface. These concepts demonstrate important considerations in the array-based formats for multi-gas sensing and its applications.

Hydrophobic interactions between polymethacrylic acid and sodium laureth sulfate in aqueous solutions

NASA Astrophysics Data System (ADS)

Yaremko, Z. M.; Fedushinskaya, L. B.; Burka, O. A.; Soltys, M. N.

2014-09-01

The role of hydrophobic interaction in the development of associative processes is demonstrated, based on the concentration dependences of the viscosity and pH of binary solutions of polymethacrylic acid as an anionic polyelectrolyte and sodium laureth sulfate as an anionic surfactant. It is found that the inflection point on the dependence of the difference between the pH values of binary solutions of polymethacrylic acid and sodium laureth sulfate on the polyelectrolyte concentration is a criterion for determining the predominant contribution from hydrophobic interaction, as is the inflection point on the dependence of pH of individual solutions of polymethacrylic acid on the polyelectrolyte concentration.

Impact of humic/fulvic acid on the removal of heavy metals from aqueous solutions using nanomaterials: a review.

PubMed

Tang, Wang-Wang; Zeng, Guang-Ming; Gong, Ji-Lai; Liang, Jie; Xu, Piao; Zhang, Chang; Huang, Bin-Bin

2014-01-15

Nowadays nanomaterials have been widely used to remove heavy metals from water/wastewater due to their large surface area and high reactivity. Humic acid (HA) and fulvic acid (FA) exist ubiquitously in aquatic environments and have a variety of functional groups which allow them to complex with metal ions and interact with nanomaterials. These interactions can not only alter the environmental behavior of nanomaterials, but also influence the removal and transportation of heavy metals by nanomaterials. Thus, the interactions and the underlying mechanisms involved warrant specific investigations. This review outlined the effects of HA/FA on the removal of heavy metals from aqueous solutions by various nanomaterials, mainly including carbon-based nanomaterials, iron-based nanomaterials and photocatalytic nanomaterials. Moreover, mechanisms involved in the interactions were discussed and potential environmental implications of HA/FA to nanomaterials and heavy metals were evaluated. © 2013.

Edible bioactive fatty acid-cellulosic derivative composites used in food-packaging applications.

PubMed

Sebti, Issam; Ham-Pichavant, Frédérique; Coma, Véronique

2002-07-17

To develop biodegradable packaging that both acts as a moisture barrier and as antimicrobial activity, nisin and stearic acid were incorporated into a hydroxy propyl methyl cellulose (HPMC) based film. Fifteen percent (w/w HPMC) of stearic acid improved film moisture barrier. However, film mechanical resistance and film antimicrobial activity on Listeria monocytogenes and Staphylococcus aureus pathogenic strains were both reduced. This lower film inhibitory activity was due to interactions between nisin and stearic acid. The molecular interaction was modeled, and an equation was developed to calculate the nisin concentration needed to be incorporated into the film matrix to obtain a desired residual antimicrobial activity. Because the molecular interactions were pH dependent, the impact of the pH of the film-forming solution on film inhibitory activity was investigated. Adjusting the pH to 3 totally avoided stearic acid and nisin interaction, inducing a high film inhibitory activity.

Use of Synthetic Antibodies Targeted to the Jak/Stat Pathway in Breast Cancer

DTIC Science & Technology

2011-03-01

substance P ( SP ), a neuropeptide that is rapidly internalized upon interaction with the neurokinin-1 receptor ( NK1R ). Cargos in the form of...based on substance P ( SP ), an 11 amino acid neuropeptide that is rapidly internalized through specific interaction with the neurokinin-1 receptor...EM IS TR Y Results Engineering a Delivery Vehicle Based on Substance P . Substance P ( SP ) is an 11 amino acid neuropeptide that is

Nucleic acid-functionalized transition metal nanosheets for biosensing applications

PubMed Central

Mo, Liuting; Li, Juan; Liu, Qiaoling; Qiu, Liping; Tan, Weihong

2017-01-01

In clinical diagnostics, as well as food and environmental safety practices, biosensors are powerful tools for monitoring biological or biochemical processes. Two-dimensional (2D) transition metal nanomaterials, including transition metal chalcogenides (TMCs) and transition metal oxides (TMOs), are receiving growing interest for their use in biosensing applications based on such unique properties as high surface area and fluorescence quenching abilities. Meanwhile, nucleic acid probes based on Watson-Crick base-pairing rules are also being widely applied in biosensing based on their excellent recognition capability. In particular, the emergence of functional nucleic acids in the 1980s, especially aptamers, has substantially extended the recognition capability of nucleic acids to various targets, ranging from small organic molecules and metal ions to proteins and cells. Based on π-π stacking interaction between transition metal nanosheets and nucleic acids, biosensing systems can be easily assembled. Therefore, the combination of 2D transition metal nanomaterials and nucleic acids brings intriguing opportunities in bioanalysis and biomedicine. In this review, we summarize recent advances of nucleic acid-functionalized transition metal nanosheets in biosensing applications. The structure and properties of 2D transition metal nanomaterials are first discussed, emphasizing the interaction between transition metal nanosheets and nucleic acids. Then, the applications of nucleic acid-functionalized transition metal nanosheet-based biosensors are discussed in the context of different signal transducing mechanisms, including optical and electrochemical approaches. Finally, we provide our perspectives on the current challenges and opportunities in this promising field. PMID:27020066

Nucleic acid-functionalized transition metal nanosheets for biosensing applications.

PubMed

Mo, Liuting; Li, Juan; Liu, Qiaoling; Qiu, Liping; Tan, Weihong

2017-03-15

In clinical diagnostics, as well as food and environmental safety practices, biosensors are powerful tools for monitoring biological or biochemical processes. Two-dimensional (2D) transition metal nanomaterials, including transition metal chalcogenides (TMCs) and transition metal oxides (TMOs), are receiving growing interest for their use in biosensing applications based on such unique properties as high surface area and fluorescence quenching abilities. Meanwhile, nucleic acid probes based on Watson-Crick base-pairing rules are also being widely applied in biosensing based on their excellent recognition capability. In particular, the emergence of functional nucleic acids in the 1980s, especially aptamers, has substantially extended the recognition capability of nucleic acids to various targets, ranging from small organic molecules and metal ions to proteins and cells. Based on π-π stacking interaction between transition metal nanosheets and nucleic acids, biosensing systems can be easily assembled. Therefore, the combination of 2D transition metal nanomaterials and nucleic acids brings intriguing opportunities in bioanalysis and biomedicine. In this review, we summarize recent advances of nucleic acid-functionalized transition metal nanosheets in biosensing applications. The structure and properties of 2D transition metal nanomaterials are first discussed, emphasizing the interaction between transition metal nanosheets and nucleic acids. Then, the applications of nucleic acid-functionalized transition metal nanosheet-based biosensors are discussed in the context of different signal transducing mechanisms, including optical and electrochemical approaches. Finally, we provide our perspectives on the current challenges and opportunities in this promising field. Copyright © 2016 Elsevier B.V. All rights reserved.

Influences of acid-base property of membrane on interfacial interactions related with membrane fouling in a membrane bioreactor based on thermodynamic assessment.

PubMed

Zhao, Leihong; Qu, Xiaolu; Zhang, Meijia; Lin, Hongjun; Zhou, Xiaoling; Liao, Bao-Qiang; Mei, Rongwu; Hong, Huachang

2016-08-01

Failure of membrane hydrophobicity in predicting membrane fouling requires a more reliable indicator. In this study, influences of membrane acid base (AB) property on interfacial interactions in two different interaction scenarios in a submerged membrane bioreactor (MBR) were studied according to thermodynamic approaches. It was found that both the polyvinylidene fluoride (PVDF) membrane and foulant samples in the MBR had relatively high electron donor (γ(-)) component and low electron acceptor (γ(+)) component. For both of interaction scenarios, AB interaction was the major component of the total interaction. The results showed that, the total interaction monotonically decreased with membrane γ(-), while was marginally affected by membrane γ(+), suggesting that γ(-) could act as a reliable indicator for membrane fouling prediction. This study suggested that membrane modification for fouling mitigation should orient to improving membrane surface γ(-) component rather than hydrophilicity. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dispersion Interactions between Urea and Nucleobases Contribute to the Destabilization of RNA by Urea in Aqueous Solution

PubMed Central

Kasavajhala, Koushik; Bikkina, Swetha; Patil, Indrajit; MacKerell, Alexander D.; Priyakumar, U. Deva

2015-01-01

Urea has long been used to investigate protein folding and, more recently, RNA folding. Studies have proposed that urea denatures RNA by participating in stacking interactions and hydrogen bonds with nucleic acid bases. In this study, the ability of urea to form unconventional stacking interactions with RNA bases is investigated using ab initio calculations (RI-MP2 and CCSD(T) methods with the aug-cc-pVDZ basis set). A total of 29 stable nucleobase-urea stacked complexes are identified in which the intermolecular interaction energies (up to −14 kcal/mol) are dominated by dispersion effects. Natural bond orbital (NBO) and atoms in molecules (AIM) calculations further confirm strong interactions between urea and nucleobases. Calculations on model systems with multiple urea and water molecules interacting with a guanine base lead to a hypothesis that urea molecules along with water are able to form cage-like structures capable of trapping nucleic acid bases in extrahelical states by forming both hydrogen bonded and dispersion interactions, thereby contributing to the unfolding of RNA in the presence of urea in aqueous solution. PMID:25668757

Nanostructure-directed physisorption vs chemisorption at semiconductor interfaces: the inverse of the HSAB concept.

PubMed

Gole, James L; Ozdemir, Serdar

2010-08-23

A concept, complementary to that of hard and soft acid-base interactions (HSAB-dominant chemisorption) and consistent with dominant physisorption to a semiconductor interface, is presented. We create a matrix of sensitivities and interactions with several basic gases. The concept, based on the reversible interaction of hard-acid surfaces with soft bases, hard-base surfaces with soft acids, or vice versa, corresponds 1) to the inverse of the HSAB concept and 2) to the selection of a combination of semiconductor interface and analyte materials, which can be used to direct a physisorbed vs chemisorbed interaction. The technology, implemented on nanopore coated porous silicon micropores, results in the coupling of acid-base chemistry with the depletion or enhancement of majority carriers in an extrinsic semiconductor. Using the inverse-HSAB (IHSAB) concept, significant and predictable changes in interface sensitivity for a variety of gases can be implemented. Nanostructured metal oxide particle depositions provide selectivity and complement a highly efficient electrical contact to a porous silicon nanopore covered microporous interface. The application of small quantities (much less than a monolayer) of nanostructured metals, metal oxides, and catalysts which focus the physisorbtive and chemisorbtive interactions of the interface, can be made to create a range of notably higher sensitivities for reversible physisorption. This is exemplified by an approach to reversible, sensitive, and selective interface responses. Nanostructured metal oxides developed from electroless gold (Au(x)O), tin (SnO(2)), copper (Cu(x)O), and nickel (NiO) depositions, nanoalumina, and nanotitania are used to demonstrate the IHSAB concept and provide for the detection of gases, including NH(3), PH(3), CO, NO, and H(2)S, in an array-based format to the sub-ppm level.

Characterization of the Adsorption of Nucleic Acid Bases onto Ferrihydrite via Fourier Transform Infrared and Surface-Enhanced Raman Spectroscopy and X-ray Diffractometry.

PubMed

Canhisares-Filho, José E; Carneiro, Cristine E A; de Santana, Henrique; Urbano, Alexandre; da Costa, Antonio C S; Zaia, Cássia T B V; Zaia, Dimas A M

2015-09-01

Minerals could have played an important role in concentration, protection, and polymerization of biomolecules. Although iron is the fourth most abundant element in Earth's crust, there are few works in the literature that describe the use of iron oxide-hydroxide in prebiotic chemistry experiments. In the present work, the interaction of adenine, thymine, and uracil with ferrihydrite was studied under conditions that resemble those of prebiotic Earth. At acidic pH, anions in artificial seawater decreased the pH at the point of zero charge (pHpzc) of ferrihydrite; and at basic pH, cations increased the pHpzc. The adsorption of nucleic acid bases onto ferrihydrite followed the order adenine > uracil > thymine. Adenine adsorption peaked at neutral pH; however, for thymine and uracil, adsorption increased with increasing pH. Electrostatic interactions did not appear to play an important role on the adsorption of nucleic acid bases onto ferrihydrite. Adenine adsorption onto ferrihydrite was higher in distilled water compared to artificial seawater. After ferrihydrite was mixed with artificial seawaters or nucleic acid bases, X-ray diffractograms and Fourier transform infrared spectra did not show any change. Surface-enhanced Raman spectroscopy showed that the interaction of adenine with ferrihydrite was not pH-dependent. In contrast, the interactions of thymine and uracil with ferrihydrite were pH-dependent such that, at basic pH, thymine and uracil lay flat on the surface of ferrihydrite, and at acidic pH, thymine and uracil were perpendicular to the surface. Ferrihydrite adsorbed much more adenine than thymine; thus adenine would have been better protected against degradation by hydrolysis or UV radiation on prebiotic Earth.

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

Hamdani, Hazrina Yusof, E-mail: hazrina@mfrlab.org; Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas; Artymiuk, Peter J., E-mail: p.artymiuk@sheffield.ac.uk

A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graphmore » theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods.« less

Acid-base homeostasis in the human system

NASA Technical Reports Server (NTRS)

White, R. J.

1974-01-01

Acid-base regulation is a cooperative phenomena in vivo with body fluids, extracellular and intracellular buffers, lungs, and kidneys all playing important roles. The present account is much too brief to be considered a review of present knowledge of these regulatory systems, and should be viewed, instead, as a guide to the elements necessary to construct a simple model of the mutual interactions of the acid-base regulatory systems of the body.

The interaction between ApoA2 -265T>C polymorphism and dietary fatty acids intake on oxidative stress in patients with type 2 diabetes mellitus.

PubMed

Zamani, Elham; Sadrzadeh-Yeganeh, Haleh; Sotoudeh, Gity; Keramat, Laleh; Eshraghian, Mohammadreza; Rafiee, Masoumeh; Koohdani, Fariba

2017-08-01

Apolipoprotein A2 (APOA2) -265T>C polymorphism has been studied in relation to oxidative stress and various dietary fatty acids. Since the interaction between APOA2 polymorphism and dietary fatty acids on oxidative stress has not yet discussed, we aimed to investigate the interaction on oxidative stress in type 2 diabetes mellitus (T2DM) patients. The subjects were 180 T2DM patients with known APOA2 genotype, either TT, TC or CC. Superoxide dismutase (SOD) activity was determined by colorimetric method. Total antioxidant capacity (TAC) and serum level of 8-isoprostane F2α were measured by spectrophotometry and ELISA, respectively. Dietary intake was collected through a food frequency questionnaire. Based on the median intake, fatty acids intake was dichotomized into high or low groups. The interaction between APOA2 polymorphism and dietary fatty acids intake was analyzed by ANCOVA multivariate interaction model. Higher than median intake of omega-6 polyunsaturated fatty acids (n-6 PUFA) was associated with increased serum level of 8-isoprostane F2α in subjects with TT/TC genotype (p = 0.004), and higher than median intake of omega-3 polyunsaturated fatty acids (n-3 PUFA) was associated with increased serum SOD activity in CC genotype (p < 0.001). There was a statistically significant interaction between APOA2 polymorphism and n-6 PUFA intake on 8-isoprostane F2α concentration as well as n-3 PUFA intake on serum SOD activity (p-interaction = 0.04 and 0.02, respectively). The current study shows the interaction between APOA2 polymorphism and dietary fatty acids intake on oxidative stress. More investigations on different populations are required to confirm the interaction.

Fundamental Understanding of the Interaction of Acid Gases with CeO 2 : From Surface Science to Practical Catalysis

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

Tumuluri, Uma; Rother, Gernot; Wu, Zili

Acid gases including CO 2, SO 2, and NO x are ubiquitous in large-scale energy applications including heterogeneous catalysis. The adverse environmental and health effects of these acid gases have resulted in high interest in the research and development of technologies to remove or convert these acid gases. The main challenge for the development of these technologies is to develop catalysts that are highly efficient, stable, and cost-effective, and many catalysts have been reported in this regard. CeO 2 and CeO 2-based catalysts have gained prominence in the removal and conversion of CO 2, SO 2, and NO x becausemore » of their structural robustness and redox and acid–base properties. In this article, we provide a brief overview of the application of CeO 2 and CeO 2-based catalysts for the removal of CO 2, SO 2, and NO x gases with an emphasis on the fundamental understanding of the interactions of these acid gases with CeO 2. The studies summarized in this review range from surface science using single crystals and thin films with precise crystallographic planes to practical catalysis applications of nanocrystalline and polycrystalline CeO 2 materials with defects and dopants. After an introduction to the properties of CeO 2 surfaces, their catalytic properties for conversions of different acid gases are reviewed and discussed. Lastly, we find that the surface atomic structure, oxygen vacancies, and surface acid–base properties of CeO 2 play vital roles in the surface chemistry and structure evolution during the interactions of acid gases with CeO 2 and CeO 2-based catalysts.« less

Fundamental Understanding of the Interaction of Acid Gases with CeO 2 : From Surface Science to Practical Catalysis

DOE PAGES

Tumuluri, Uma; Rother, Gernot; Wu, Zili

2016-03-21

Acid gases including CO 2, SO 2, and NO x are ubiquitous in large-scale energy applications including heterogeneous catalysis. The adverse environmental and health effects of these acid gases have resulted in high interest in the research and development of technologies to remove or convert these acid gases. The main challenge for the development of these technologies is to develop catalysts that are highly efficient, stable, and cost-effective, and many catalysts have been reported in this regard. CeO 2 and CeO 2-based catalysts have gained prominence in the removal and conversion of CO 2, SO 2, and NO x becausemore » of their structural robustness and redox and acid–base properties. In this article, we provide a brief overview of the application of CeO 2 and CeO 2-based catalysts for the removal of CO 2, SO 2, and NO x gases with an emphasis on the fundamental understanding of the interactions of these acid gases with CeO 2. The studies summarized in this review range from surface science using single crystals and thin films with precise crystallographic planes to practical catalysis applications of nanocrystalline and polycrystalline CeO 2 materials with defects and dopants. After an introduction to the properties of CeO 2 surfaces, their catalytic properties for conversions of different acid gases are reviewed and discussed. Lastly, we find that the surface atomic structure, oxygen vacancies, and surface acid–base properties of CeO 2 play vital roles in the surface chemistry and structure evolution during the interactions of acid gases with CeO 2 and CeO 2-based catalysts.« less

A Systems Model for Ursodeoxycholic Acid Metabolism in Healthy and Patients With Primary Biliary Cirrhosis

PubMed Central

Dobbins, RL; O'Connor‐Semmes, RL; Young, MA

2016-01-01

A systems model was developed to describe the metabolism and disposition of ursodeoxycholic acid (UDCA) and its conjugates in healthy subjects based on pharmacokinetic (PK) data from published studies in order to study the distribution of oral UDCA and potential interactions influencing therapeutic effects upon interruption of its enterohepatic recirculation. The base model was empirically adapted to patients with primary biliary cirrhosis (PBC) based on current understanding of disease pathophysiology and clinical measurements. Simulations were performed for patients with PBC under two competing hypotheses: one for inhibition of ileal absorption of both UDCA and conjugates and the other only of conjugates. The simulations predicted distinctly different bile acid distribution patterns in plasma and bile. The UDCA model adapted to patients with PBC provides a platform to investigate a complex therapeutic drug interaction among UDCA, UDCA conjugates, and inhibition of ileal bile acid transport in this rare disease population. PMID:27537780

Nucleic acid-based nanoengineering: novel structures for biomedical applications

PubMed Central

Li, Hanying; LaBean, Thomas H.; Leong, Kam W.

2011-01-01

Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson–Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine. PMID:23050076

Protein- protein interaction detection system using fluorescent protein microdomains

DOEpatents

Waldo, Geoffrey S.; Cabantous, Stephanie

2010-02-23

The invention provides a protein labeling and interaction detection system based on engineered fragments of fluorescent and chromophoric proteins that require fused interacting polypeptides to drive the association of the fragments, and further are soluble and stable, and do not change the solubility of polypeptides to which they are fused. In one embodiment, a test protein X is fused to a sixteen amino acid fragment of GFP (.beta.-strand 10, amino acids 198-214), engineered to not perturb fusion protein solubility. A second test protein Y is fused to a sixteen amino acid fragment of GFP (.beta.-strand 11, amino acids 215-230), engineered to not perturb fusion protein solubility. When X and Y interact, they bring the GFP strands into proximity, and are detected by complementation with a third GFP fragment consisting of GFP amino acids 1-198 (strands 1-9). When GFP strands 10 and 11 are held together by interaction of protein X and Y, they spontaneous association with GFP strands 1-9, resulting in structural complementation, folding, and concomitant GFP fluorescence.

ReaxFF molecular dynamics simulation of intermolecular structure formation in acetic acid-water mixtures at elevated temperatures and pressures

NASA Astrophysics Data System (ADS)

Sengul, Mert Y.; Randall, Clive A.; van Duin, Adri C. T.

2018-04-01

The intermolecular structure formation in liquid and supercritical acetic acid-water mixtures was investigated using ReaxFF-based molecular dynamics simulations. The microscopic structures of acetic acid-water mixtures with different acetic acid mole fractions (1.0 ≥ xHAc ≥ 0.2) at ambient and critical conditions were examined. The potential energy surface associated with the dissociation of acetic acid molecules was calculated using a metadynamics procedure to optimize the dissociation energy of ReaxFF potential. At ambient conditions, depending on the acetic acid concentration, either acetic acid clusters or water clusters are dominant in the liquid mixture. When acetic acid is dominant (0.4 ≤ xHAc), cyclic dimers and chain structures between acetic acid molecules are present in the mixture. Both structures disappear at increased water content of the mixture. It was found by simulations that the acetic acid molecules released from these dimer and chain structures tend to stay in a dipole-dipole interaction. These structural changes are in agreement with the experimental results. When switched to critical conditions, the long-range interactions (e.g., second or fourth neighbor) disappear and the water-water and acetic acid-acetic acid structural formations become disordered. The simulated radial distribution function for water-water interactions is in agreement with experimental and computational studies. The first neighbor interactions between acetic acid and water molecules are preserved at relatively lower temperatures of the critical region. As higher temperatures are reached in the critical region, these interactions were observed to weaken. These simulations indicate that ReaxFF molecular dynamics simulations are an appropriate tool for studying supercritical water/organic acid mixtures.

Poly-3-hydroxy butyric acid interaction with the transgenic flax fibers: FT-IR and Raman spectra of the composite extracted from a GM flax

NASA Astrophysics Data System (ADS)

Wróbel-Kwiatkowska, Magdalena; Żuk, Magdalena; Szopa, Jan; Dymińska, Lucyna; Mączka, Mirosław; Hanuza, Jerzy

2009-07-01

The FT-IR and FT-Raman studies have been performed on commercial 3-hydroxy-butyric acid, commercial poly-3-hydroxy butyric acid as well as poly-3-hydroxy butyric acid (PHB) produced by bacteria. The data were compared to those obtained for poly-3-hydroxy butyric acid extracted from natural and genetically modified flax. Genetically modified flax was generated by expression of three bacterial genes coding for synthesis of poly-3-hydroxy butyric acid. Thus transgenic flaxes were enhanced with different amount of the PHB. The discussion of polymer structure and vibrational properties has been done in order to get insight into differences among these materials. The interaction between the cellulose of flax fibers and embedded poly-3-hydroxybutyric acid has been also discussed. The spectroscopic data provide evidences for structural changes in cellulose and in PHB when synthesized in fibers. Based on this data it is suggesting that cellulose and PHB interact by hydrogen and ester bonds.

Acid-base interactions and secondary structures of poly-L-lysine probed by 15N and 13C solid state NMR and Ab initio model calculations.

PubMed

Dos, Alexandra; Schimming, Volkmar; Tosoni, Sergio; Limbach, Hans-Heinrich

2008-12-11

The interactions of the 15N-labeled amino groups of dry solid poly-L-lysine (PLL) with various halogen and oxygen acids HX and the relation to the secondary structure have been studied using solid-state 15N and 13C CPMAS NMR spectroscopy (CP = cross polarization and MAS = magic angle spinning). For comparison, 15N NMR spectra of an aqueous solution of PLL were measured as a function of pH. In order to understand the effects of protonation and hydration on the 15N chemical shifts of the amino groups, DFT and chemical shielding calculations were performed on isolated methylamine-acid complexes and on periodic halide clusters of the type (CH3NH3(+)X(-))n. The combined experimental and computational results reveal low-field shifts of the amino nitrogens upon interaction with the oxygen acids HX = HF, H2SO4, CH3COOH, (CH3)2POOH, H3PO4, HNO3, and internal carbamic acid formed by reaction of the amino groups with gaseous CO2. Evidence is obtained that only hydrogen-bonded species of the type (Lys-NH2***H-X)n are formed in the absence of water. 15N chemical shifts are maximum when H is located in the hydrogen bond center and then decrease again upon full protonation, as found for aqueous solution at low pH. By contrast, halogen acids interact in a different way. They form internal salts of the type (Lys-NH3(+)X(-))n via the interaction of many acid-base pairs. This salt formation is possible only in the beta-sheet conformation. By contrast, the formation of hydrogen-bonded complexes can occur both in beta-sheet domains as well as in alpha-helical domains. The 15N chemical shifts of the protonated ammonium groups increase when the size of the interacting halogen anions is increased from chloride to iodide and when the number of the interacting anions is increased. Thus, the observed high-field 15N shift of ammonium groups upon hydration is the consequence of replacing interacting halogen atoms by oxygen atoms.

Structure-affinity relationship of the interaction between phenolic acids and their derivatives and β-lactoglobulin and effect on antioxidant activity.

PubMed

Wu, Simin; Zhang, Yunyue; Ren, Fazheng; Qin, Yinghui; Liu, Jiaxin; Liu, Jingwen; Wang, Qingyu; Zhang, Hao

2018-04-15

In this study, 71 phenolic acids and their derivatives were used to investigate the structure-affinity relationship of β-lactoglobulin binding, and the effect of this interaction on antioxidant activity. Based on a fluorescence quenching method, an improved mathematical model was adopted to calculate the binding constants, with a correction for the inner-filter effect. Hydroxylation at the 3-position increased the affinity of the phenolic acids for β-lactoglobulin, while hydroxylation at the 2- or 4-positions had a negative effect. Complete methylation of all hydroxy groups, except at the 3-position, enhanced the binding affinity. Replacing the hydroxy groups with methyl groups at the 2-position also had a positive effect. Hydrogen bonding was one of the binding forces for the interaction. The antioxidant activity of phenolic acid-β-lactoglobulin complexes was higher than that of phenolic acids alone. These findings provide an understanding of the structure-activity relationship of the interaction between β-lactoglobulin and phenolic acids. Copyright © 2017 Elsevier Ltd. All rights reserved.

Macromolecular Competition Titration Method: Accessing Thermodynamics of the Unmodified Macromolecule–Ligand Interactions Through Spectroscopic Titrations of Fluorescent Analogs

PubMed Central

Bujalowski, Wlodzimierz; Jezewska, Maria J.

2011-01-01

Analysis of thermodynamically rigorous binding isotherms provides fundamental information about the energetics of the ligand–macromolecule interactions and often an invaluable insight about the structure of the formed complexes. The Macromolecular Competition Titration (MCT) method enables one to quantitatively obtain interaction parameters of protein–nucleic acid interactions, which may not be available by other methods, particularly for the unmodified long polymer lattices and specific nucleic acid substrates, if the binding is not accompanied by adequate spectroscopic signal changes. The method can be applied using different fluorescent nucleic acids or fluorophores, although the etheno-derivatives of nucleic acid are especially suitable as they are relatively easy to prepare, have significant blue fluorescence, their excitation band lies far from the protein absorption spectrum, and the modification eliminates the possibility of base pairing with other nucleic acids. The MCT method is not limited to the specific size of the reference nucleic acid. Particularly, a simple analysis of the competition titration experiments is described in which the fluorescent, short fragment of nucleic acid, spanning the exact site-size of the protein–nucleic acid complex, and binding with only a 1:1 stoichiometry to the protein, is used as a reference macromolecule. Although the MCT method is predominantly discussed as applied to studying protein–nucleic acid interactions, it can generally be applied to any ligand–macromolecule system by monitoring the association reaction using the spectroscopic signal originating from the reference macromolecule in the presence of the competing macromolecule, whose interaction parameters with the ligand are to be determined. PMID:21195223

Unraveling the impact of hydroxylation on interactions of bile acid cationic lipids with model membranes by in-depth calorimetry studies.

PubMed

Singh, Manish; Bajaj, Avinash

2014-09-28

We used eight bile acid cationic lipids differing in the number of hydroxyl groups and performed in-depth differential scanning calorimetry studies on model membranes doped with different percentages of these cationic bile acids. These studies revealed that the number and positioning of free hydroxyl groups on bile acids modulate the phase transition and co-operativity of membranes. Lithocholic acid based cationic lipids having no free hydroxyl groups gel well with dipalmitoylphosphatidylcholine (DPPC) membranes. Chenodeoxycholic acid lipids having one free hydroxyl group at the 7'-carbon position disrupt the membranes and lower their co-operativity. Deoxycholic acid and cholic acid based cationic lipids have free hydroxyl groups at the 12'-carbon position, and at 7'- and 12'-carbon positions respectively. Doping of these lipids at high concentrations increases the co-operativity of membranes suggesting that these lipids might induce self-assembly in DPPC membranes. These different modes of interactions between cationic lipids and model membranes would help in future for exploring their use in DNA/drug delivery.

Signal enhancement in ligand-receptor interactions using dynamic polymers at quartz crystal microbalance sensors.

PubMed

Dunér, Gunnar; Anderson, Henrik; Pei, Zhichao; Ingemarsson, Björn; Aastrup, Teodor; Ramström, Olof

2016-06-20

The signal enhancement properties of QCM sensors based on dynamic, biotinylated poly(acrylic acid) brushes has been studied in interaction studies with an anti-biotin Fab fragment. The poly(acrylic acid) sensors showed a dramatic increase in signal response with more than ten times higher signal than the carboxyl-terminated self-assembled monolayer surface.

Improving protein complex classification accuracy using amino acid composition profile.

PubMed

Huang, Chien-Hung; Chou, Szu-Yu; Ng, Ka-Lok

2013-09-01

Protein complex prediction approaches are based on the assumptions that complexes have dense protein-protein interactions and high functional similarity between their subunits. We investigated those assumptions by studying the subunits' interaction topology, sequence similarity and molecular function for human and yeast protein complexes. Inclusion of amino acids' physicochemical properties can provide better understanding of protein complex properties. Principal component analysis is carried out to determine the major features. Adopting amino acid composition profile information with the SVM classifier serves as an effective post-processing step for complexes classification. Improvement is based on primary sequence information only, which is easy to obtain. Copyright © 2013 Elsevier Ltd. All rights reserved.

Influence of IL1B, IL6 and IL10 gene variants and plasma fatty acid interaction on metabolic syndrome risk in a cross-sectional population-based study.

PubMed

Maintinguer Norde, Marina; Oki, Erica; Ferreira Carioca, Antonio Augusto; Teixeira Damasceno, Nágila Raquel; Fisberg, Regina Mara; Lobo Marchioni, Dirce Maria; Rogero, Marcelo Macedo

2018-04-01

Metabolic syndrome (MetS) is a cluster of interrelated risk factors for type 2 diabetes mellitus, and cardiovascular disease, with underlying inflammatory pathophysiology. Genetic variations and diet are well-known risk factor for MetS, but the interaction between these two factors is less explored. The aim of the study was to evaluate the influence of interaction between SNP of inflammatory genes (encoding interleukin (IL)-6, IL-1β and IL-10) and plasma fatty acids on the odds of MetS, in a population-based cross-sectional study. Among participants of the Health Survey - São Paulo, 301 adults (19-59 y) from whom a blood sample was collected were included. Individuals with and without MetS were compared according to their plasma inflammatory biomarkers, fatty acid profile, and genotype frequency of the IL1B (rs16944, rs1143623, rs1143627, rs1143634 and rs1143643), IL6 (rs1800795, rs1800796 and rs1800797) and IL10 (rs1554286, rs1800871, rs1800872, rs1800890 and rs3024490) genes SNP. The influence of gene-fatty acids interaction on MetS risk was investigated. IL6 gene SNP rs1800795 G allele was associated with higher odds for MetS (OR = 1.88; p = 0.017). Gene-fatty acid interaction was found between the IL1B gene SNP rs116944 and stearic acid (p inter = 0.043), and between rs1143634 and EPA (p inter = 0.017). For the IL10 gene SNP rs1800896, an interaction was found for arachidonic acid (p inter = 0.007) and estimated D5D activity (p inter = 0.019). The IL6 gene SNP rs1800795 G allele is associated with increased odds for MetS. Plasma fatty acid profile interacts with the IL1B and IL10 gene variants to modulate the odds for MetS. This and other interactions of risk factors can account for the unexplained heritability of MetS, and their elucidation can lead to new strategies for genome-customized prevention of MetS. Copyright © 2017 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

Amino acid alphabet reduction preserves fold information contained in contact interactions in proteins.

PubMed

Solis, Armando D

2015-12-01

To reduce complexity, understand generalized rules of protein folding, and facilitate de novo protein design, the 20-letter amino acid alphabet is commonly reduced to a smaller alphabet by clustering amino acids based on some measure of similarity. In this work, we seek the optimal alphabet that preserves as much of the structural information found in long-range (contact) interactions among amino acids in natively-folded proteins. We employ the Information Maximization Device, based on information theory, to partition the amino acids into well-defined clusters. Numbering from 2 to 19 groups, these optimal clusters of amino acids, while generated automatically, embody well-known properties of amino acids such as hydrophobicity/polarity, charge, size, and aromaticity, and are demonstrated to maintain the discriminative power of long-range interactions with minimal loss of mutual information. Our measurements suggest that reduced alphabets (of less than 10) are able to capture virtually all of the information residing in native contacts and may be sufficient for fold recognition, as demonstrated by extensive threading tests. In an expansive survey of the literature, we observe that alphabets derived from various approaches-including those derived from physicochemical intuition, local structure considerations, and sequence alignments of remote homologs-fare consistently well in preserving contact interaction information, highlighting a convergence in the various factors thought to be relevant to the folding code. Moreover, we find that alphabets commonly used in experimental protein design are nearly optimal and are largely coherent with observations that have arisen in this work. © 2015 Wiley Periodicals, Inc.

Complexity in pH-Dependent Ribozyme Kinetics: Dark pKa Shifts and Wavy Rate-pH Profiles.

PubMed

Frankel, Erica A; Bevilacqua, Philip C

2018-02-06

Charged bases occur in RNA enzymes, or ribozymes, where they play key roles in catalysis. Cationic bases donate protons and perform electrostatic catalysis, while anionic bases accept protons. We previously published simulations of rate-pH profiles for ribozymes in terms of species plots for the general acid and general base that have been useful for understanding how ribozymes respond to pH. In that study, we did not consider interaction between the general acid and general base or interaction with other species on the RNA. Since that report, diverse small ribozyme classes have been discovered, many of which have charged nucleobases or metal ions in the active site that can either directly interact and participate in catalysis or indirectly interact as "influencers". Herein, we simulate experimental rate-pH profiles in terms of species plots in which reverse protonated charged nucleobases interact. These analyses uncover two surprising features of pH-dependent enzyme kinetics. (1) Cooperativity between the general acid and general base enhances population of the functional forms of a ribozyme and manifests itself as hidden or "dark" pK a shifts, real pK a shifts that accelerate the reaction but are not readily observed by standard experimental approaches, and (2) influencers favorably shift the pK a s of proton-transferring nucleobases and manifest themselves as "wavy" rate-pH profiles. We identify parallels with the protein enzyme literature, including reverse protonation and wavelike behavior, while pointing out that RNA is more prone to reverse protonation. The complexities uncovered, which arise from simple pairwise interactions, should aid deconvolution of complex rate-pH profiles for RNA and protein enzymes and suggest veiled catalytic devices for promoting catalysis that can be tested by experiment and calculation.

Anion photoelectron spectroscopy of acid-base systems, solvated molecules and MALDI matrix molecules

NASA Astrophysics Data System (ADS)

Eustis, Soren Newman

Gas phase, mass-selected, anion photoelectron spectroscopic studies were performed on a variety of molecular systems. These studies can be grouped into three main themes: acid-base interactions, solvation, and ions of analytical interest. Acid-base interactions represent some of the most fundamental processes in chemistry. The study of these processes elucidates elementary principles such as inner and outer sphere complexes, hard and soft ions, and salt formation---to name a few. Apart from their appeal from a pedagogical standpoint, the ubiquity of chemical reactions which involve acids, bases or the resulting salts makes the study of their fundamental interactions both necessary and fruitful. With this in mind, the neutral and anionic series (NH3···HX) (X= F, Cl, Br, I) were examined experimentally and theoretically. The relatively small size of these systems, combined with the advances in computational methods, allowed our experimental results to be compared with very high level ab initio theoretical results. The synergy between theory and experiment yielded an understanding of the nature of the complexes that could not be achieved with either method in isolation. The second theme present in this body or work is molecular solvation. Solvation is a phenomenon which is present in biology, chemistry and physics. Many biological molecules do not become 'active' until they are solvated by water. Thus, the study of biologically relevant species solvated by water is one step in a bottom up approach to studying the biochemical interactions in living organisms. Furthermore, the hydration of acidic molecules in the atmosphere is what drives the formation of 'free' protons or hydronium ions which are the key players in acid driven chemistry. Here are presented two unique solvation studies, Adenine(H2O)-n and C6F6(H2O)-n, these systems are very distinct, but show somewhat similar responses to hydration. The last theme presented in this work is the electronic properties of molecules relevant to analytical chemistry, or more specifically, Matrix Assisted Laser Desorption Interaction (MALDI) chemistry. For the first time electron affinities are presented for many of the common MALDI matrix compounds.

Polymorphisms of the TNF-α gene interact with plasma fatty acids on inflammatory biomarker profile: a population-based, cross-sectional study in São Paulo, Brazil.

PubMed

Oki, Erica; Norde, Marina N; Carioca, Antônio A F; Souza, José M P; Castro, Inar A; Marchioni, Dirce M L; Fisberg, Regina M; Rogero, Marcelo M

2017-06-01

The aim of the present study was to investigate the relationship of four TNF-α SNP with inflammatory biomarkers and plasma fatty acids (FA), and the interaction among them in a population-based, cross-sectional study in São Paulo, Brazil. A total of 281 subjects, aged >19 and <60 years, participated in a cross-sectional, population-based study performed in Brazil. The following SNP spanning the TNF-α gene were genotyped: -238G/A (rs361525), -308G/A (rs1800629), -857C/T (rs1799724) and -1031T/C (rs1799964). In all, eleven plasma inflammatory biomarkers and plasma FA profile were determined. To analyse the interaction between TNF-α SNP and plasma FA, a cluster analysis was performed to stratify individuals based on eleven inflammatory biomarkers into two groups used as outcome: inflammatory (INF) and non-inflammatory clusters. The -238A allele carriers had higher TNF-α (P=0·033), IL-6 (P=0·013), IL-1β (P=0·037), IL-12 (0·048) and IL-10 (P=0·010) than the GG genotype. The -308A allele carriers also had lower levels of plasma palmitoleic acid (P=0·009), oleic acid (P=0·039), total MUFA (P=0·014), stearoyl-CoA desaturase (SCD) activity index-16 (P=0·007), SCD-18 (P=0·020) and higher levels of PUFA (P=0·046) and DHA (P=0·044). Significant interactions modifying the risk of belonging to the INF cluster were observed with inflammatory cluster as outcome between -857C/T and plasma α-linolenic acid (P=0·026), and also between -308G/A and plasma stearic acid (P=0·044) and total SFA (P=0·040). Our study contributes to knowledge on TNF-α SNP and their association with inflammatory biomarker levels, plasma FA and the interaction among them, of particular interest for the Brazilian population.

Soni-removal of nucleic acids from inclusion bodies.

PubMed

Neerathilingam, Muniasamy; Mysore, Sumukh; Gandham, Sai Hari A

2014-05-23

Inclusion bodies (IBs) are commonly formed in Escherichia coli due to over expression of recombinant proteins in non-native state. Isolation, denaturation and refolding of these IBs is generally performed to obtain functional protein. However, during this process IBs tend to form non-specific interactions with sheared nucleic acids from the genome, thus getting carried over into downstream processes. This may hinder the refolding of IBs into their native state. To circumvent this, we demonstrate a methodology termed soni-removal which involves disruption of nucleic acid-inclusion body interaction using sonication; followed by solvent based separation. As opposed to conventional techniques that use enzymes and column-based separations, soni-removal is a cost effective alternative for complete elimination of buried and/or strongly bound short nucleic acid contaminants from IBs. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Supramolecular hydrogen-bonding patterns in 1:1 cocrystals of 5-fluorouracil with 4-methylbenzoic acid and 3-nitrobenzoic acid.

PubMed

Mohana, Marimuthu; Muthiah, Packianathan Thomas; McMillen, Colin D

2017-03-01

The design of a pharmaceutical cocrystal is based on the identification of specific hydrogen-bond donor and acceptor groups in active pharmaceutical ingredients (APIs) in order to choose a `complementary interacting' molecule that can act as an efficient coformer. 5-Fluorouracil (5FU) is a pyrimidine derivative with two N-H donors and C=O acceptors and shows a diversity of hydrogen-bonding motifs. Two 1:1 cocrystals of 5-fluorouracil (5FU), namely 5-fluorouracil-4-methylbenzoic acid (5FU-MBA), C 4 H 3 FN 2 O 2 ·C 8 H 8 O 2 , (I), and 5-fluorouracil-3-nitrobenzoic acid (5FU-NBA), C 4 H 3 FN 2 O 2 ·C 7 H 5 NO 4 , (II), have been prepared and characterized by single-crystal X-ray diffraction. In (I), the MBA molecules form carboxylic acid dimers [R 2 2 (8) homosynthon]. Similarly, the 5FU molecules form two types of base pair via a pair of N-H...O hydrogen bonds [R 2 2 (8) homosynthon]. In (II), 5FU interacts with the carboxylic acid group of NBA via N-H...O and O-H...O hydrogen bonds, generating an R 2 2 (8) ring motif (heterosynthon). Furthermore, the 5FU molecules form base pairs [R 2 2 (8) homosynthon] via N-H...O hydrogen bonds. Both of the crystal structures are stabilized by C-H...F interactions.

Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials

PubMed Central

Wu, Peiwen; Yu, Yang; McGhee, Claire E.; Tan, Li Huey

2014-01-01

In this review, we summarize recent progresses in the application of synchrotron-based spectroscopic techniques for nucleic acid research that takes advantage of high-flux and high-brilliance electromagnetic radiation from synchrotron sources. The first section of the review focuses on the characterization of the structure and folding processes of nucleic acids using different types of synchrotron-based spectroscopies, such as X-ray absorption spectroscopy, X-ray emission spectroscopy, X-ray photoelectron spectroscopy, synchrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering. In the second section, the characterization of nucleic acid-based nanostructures, nucleic acid-functionalized nanomaterials and nucleic acid-lipid interactions using these spectroscopic techniques is summarized. Insights gained from these studies are described and future directions of this field are also discussed. PMID:25205057

Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials

DOE PAGES

Wu, Peiwen; Yu, Yang; McGhee, Claire E.; ...

2014-09-10

In this paper, we summarize recent progress in the application of synchrotron-based spectroscopic techniques for nucleic acid research that takes advantage of high-flux and high-brilliance electromagnetic radiation from synchrotron sources. The first section of the review focuses on the characterization of the structure and folding processes of nucleic acids using different types of synchrotron-based spectroscopies, such as X-ray absorption spectroscopy, X-ray emission spectroscopy, X-ray photoelectron spectroscopy, synchrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering. In the second section, the characterization of nucleic acid-based nanostructures, nucleic acid-functionalized nanomaterials and nucleic acid-lipid interactions using these spectroscopic techniques is summarized. Insightsmore » gained from these studies are described and future directions of this field are also discussed.« less

Interactions of corn meal or molasses with a soybean-sunflower meal mix or flaxseed meal on production, milk fatty acids composition, and nutrient utilization in dairy cows fed grass hay-based diets

USDA-ARS?s Scientific Manuscript database

We investigated the interactions of molasses or corn meal [nonstructural carbohydrate (NSC) sources] with flaxseed meal or a soybean-sunflower meal protein mix [rumen-degradable protein (RDP) sources] on animal production, milk fatty acids profile, and nutrient utilization in organic Jersey cows fed...

Molecular and Cellular Mechanisms for the Interaction between Gold Nanoparticles and Neuroimmune Cells Based on Size, Shape, and Charge

DTIC Science & Technology

2014-04-25

IgG secretion. 2.3 Designing of Synthetic peptide The immunogenic peptides against the foot and mouth disease virus ( FMDV ) were designed and...synthesized based on viral protein 1 of type O FMDV . The amino acid sequence for pFMDV is NGSSKYGDTSTNNVRGDLQVLAQKAERTLC. An extra cysteine was added...peptides were synthesized based on the amino acid sequence of the VP1 coat protein of the FMDV (table 1). The peptide pFMDVD (19 amino acids in length

Fluorometric estimation of amino acids interaction with colloidal suspension of FITC functionalized graphene oxide nanoparticles

NASA Astrophysics Data System (ADS)

Dave, Kashyap; Dhayal, Marshal

2017-02-01

A hydrosol approach developed to synthesize fluorescence quenched fluorescein isothiocyanate (FITC) functionalized colloidal suspension of graphene oxide nanoparticles (GONP). UV-vis spectroscopic measurements showed characteristic peak at 236 nm and 300 nm due to pi-pi* interaction in Cdbnd C and n-pi* transition in Cdbnd O bond of GONP, respectively. Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectra showed reduced intensity of 1429 cm-1 IR band of GONP due to the electrostatic and pi-pi interactions of FITC with GONP in FITC-GONP. ATR-FTIR spectra of different amino acid co-functionalised FITC-GONP showed an increase in the FTIR band intensity at 1429 cm-1 which was significantly reduced due to electrostatic/pi-pi interactions of FITC with GONP in the absence of the amino acids. A peak at 1084 cm-1 in ATR-FTIR spectra appears which confirms the interaction between amine group of amino acids and sbnd COO- groups at GONP surface. The FITC interaction with GONP lead to fluorescence resonance energy transfers (FRET) and resulted in a liner decrease in the FITC fluorescence with an increase of GONP concentration. An increase in the reappearance of FITC fluorescence observed while the amino acid concentration was increased in co-functionalised FITC-GONP. The quantified amount of reappeared fluorescence of FITC in amino acid co-functionalised FITC-GONP depends on the concentration, polar and non-polar nature of amino acids. The reappearance of FITC from the surface of FITC-GONP with the addition of amino acid was found to be consistent with the organic substitute, size of amino acids and their functionalities. Therefore, FRET based method using FITC-GONP colloidal suspension may have potential application in determining the binding nature of biomolecules with GONP for biomedical applications.

Lipoprotein lipase variants interact with polyunsaturated fatty acids to modulate obesity traits in Puerto Ricans

USDA-ARS?s Scientific Manuscript database

Lipoprotein lipase (LPL) is a candidate gene for obesity based on its role in triglyceride hydrolysis and the partitioning of fatty acids towards storage or oxidation. Whether dietary fatty acids modify LPL associated obesity risk is unknown. We examined five single nucleotide polymorphisms (SNPs) (...

AFAL: a web service for profiling amino acids surrounding ligands in proteins

NASA Astrophysics Data System (ADS)

Arenas-Salinas, Mauricio; Ortega-Salazar, Samuel; Gonzales-Nilo, Fernando; Pohl, Ehmke; Holmes, David S.; Quatrini, Raquel

2014-11-01

With advancements in crystallographic technology and the increasing wealth of information populating structural databases, there is an increasing need for prediction tools based on spatial information that will support the characterization of proteins and protein-ligand interactions. Herein, a new web service is presented termed amino acid frequency around ligand (AFAL) for determining amino acids type and frequencies surrounding ligands within proteins deposited in the Protein Data Bank and for assessing the atoms and atom-ligand distances involved in each interaction (availability: http://structuralbio.utalca.cl/AFAL/index.html). AFAL allows the user to define a wide variety of filtering criteria (protein family, source organism, resolution, sequence redundancy and distance) in order to uncover trends and evolutionary differences in amino acid preferences that define interactions with particular ligands. Results obtained from AFAL provide valuable statistical information about amino acids that may be responsible for establishing particular ligand-protein interactions. The analysis will enable investigators to compare ligand-binding sites of different proteins and to uncover general as well as specific interaction patterns from existing data. Such patterns can be used subsequently to predict ligand binding in proteins that currently have no structural information and to refine the interpretation of existing protein models. The application of AFAL is illustrated by the analysis of proteins interacting with adenosine-5'-triphosphate.

AFAL: a web service for profiling amino acids surrounding ligands in proteins.

PubMed

Arenas-Salinas, Mauricio; Ortega-Salazar, Samuel; Gonzales-Nilo, Fernando; Pohl, Ehmke; Holmes, David S; Quatrini, Raquel

2014-11-01

With advancements in crystallographic technology and the increasing wealth of information populating structural databases, there is an increasing need for prediction tools based on spatial information that will support the characterization of proteins and protein-ligand interactions. Herein, a new web service is presented termed amino acid frequency around ligand (AFAL) for determining amino acids type and frequencies surrounding ligands within proteins deposited in the Protein Data Bank and for assessing the atoms and atom-ligand distances involved in each interaction (availability: http://structuralbio.utalca.cl/AFAL/index.html ). AFAL allows the user to define a wide variety of filtering criteria (protein family, source organism, resolution, sequence redundancy and distance) in order to uncover trends and evolutionary differences in amino acid preferences that define interactions with particular ligands. Results obtained from AFAL provide valuable statistical information about amino acids that may be responsible for establishing particular ligand-protein interactions. The analysis will enable investigators to compare ligand-binding sites of different proteins and to uncover general as well as specific interaction patterns from existing data. Such patterns can be used subsequently to predict ligand binding in proteins that currently have no structural information and to refine the interpretation of existing protein models. The application of AFAL is illustrated by the analysis of proteins interacting with adenosine-5'-triphosphate.

Exploring hydride-π interactions and their tuning by σ-hole bonds: an ab initio study

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Asadollahi, Soheila; Mousavian, Parisasadat

2018-01-01

In the present work, ab initio calculations are performed to investigate the geometry, interaction energy and bonding properties of binary complexes formed between metal-hydrides HMX (M = Be, Mg, Zn and X = H, F, CH3) and a series of π-acidic heteroaromatic rings. In all the resulting complexes, the heteroaromatic ring acts as a Lewis acid (electron acceptor), while the H atom of the HMX molecule acts as a Lewis base (electron donor). The nature of this interaction, called 'hydride-π' interaction, is explored in terms of molecular electrostatic potential, non-covalent interaction, quantum theory of atoms in molecules and natural bond orbital analyses. The results show that the interaction energies of these hydride-π interactions are between -1.24 and -2.72 kcal/mol. Furthermore, mutual influence between the hydride-π and halogen- or pnicogen-bonding interactions is studied in complexes in which these interactions coexist. For a given π-acidic ring, the formation of the pnicogen-bonding induces a larger enhancing effect on the strength of hydride-π bond than the halogen-bonding.

Complexity in Acid-Base Titrations: Multimer Formation Between Phosphoric Acids and Imines.

PubMed

Malm, Christian; Kim, Heejae; Wagner, Manfred; Hunger, Johannes

2017-08-10

Solutions of Brønsted acids with bases in aprotic solvents are not only common model systems to study the fundamentals of proton transfer pathways but are also highly relevant to Brønsted acid catalysis. Despite their importance the light nature of the proton makes characterization of acid-base aggregates challenging. Here, we track such acid-base interactions over a broad range of relative compositions between diphenyl phosphoric acid and the base quinaldine in dichloromethane, by using a combination of dielectric relaxation and NMR spectroscopy. In contrast to what one would expect for an acid-base titration, we find strong deviations from quantitative proton transfer from the acid to the base. Even for an excess of the base, multimers consisting of one base and at least two acid molecules are formed, in addition to the occurrence of proton transfer from the acid to the base and simultaneous formation of ion pairs. For equimolar mixtures such multimers constitute about one third of all intermolecular aggregates. Quantitative analysis of our results shows that the acid-base association constant is only around six times larger than that for the acid binding to an acid-base dimer, that is, to an already protonated base. Our findings have implications for the interpretation of previous studies of reactive intermediates in organocatalysis and provide a rationale for previously observed nonlinear effects in phosphoric acid catalysis. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Design of Cell-Matrix Interactions in Hyaluronic Acid Hydrogel Scaffolds

PubMed Central

Segura, Tatiana

2013-01-01

The design of hyaluronic acid-based hydrogel scaffolds to elicit highly controlled and tunable cell response and behavior is a major field of interest in developing tissue engineering and regenerative medicine applications. This review will begin with an overview of the biological context of hyaluronic acid, knowledge needed to better understand how to engineer cell-matrix interactions in the scaffolds via the incorporation of different types of signals in order to direct and control cell behavior. Specifically, recent methods of incorporating various bioactive, mechanical, and spatial signals are reviewed, as well as novel hyaluronic acid modifications and crosslinking schemes with a focus on specificity. PMID:23899481

The simulation study of protein-protein interfaces based on the 4-helix bundle structure

NASA Astrophysics Data System (ADS)

Fukuda, Masaki; Komatsu, Yu; Morikawa, Ryota; Miyakawa, Takeshi; Takasu, Masako; Akanuma, Satoshi; Yamagishi, Akihiko

2013-02-01

Docking of two protein molecules is induced by intermolecular interactions. Our purposes in this study are: designing binding interfaces on the two proteins, which specifically interact to each other; and inducing intermolecular interactions between the two proteins by mixing them. A 4-helix bundle structure was chosen as a scaffold on which binding interfaces were created. Based on this scaffold, we designed binding interfaces involving charged and nonpolar amino acid residues. We performed molecular dynamics (MD) simulation to identify suitable amino acid residues for the interfaces. We chose YciF protein as the scaffold for the protein-protein docking simulation. We observed the structure of two YciF protein molecules (I and II), and we calculated the distance between centroids (center of gravity) of the interfaces' surface planes of the molecules I and II. We found that the docking of the two protein molecules can be controlled by the number of hydrophobic and charged amino acid residues involved in the interfaces. Existence of six hydrophobic and five charged amino acid residues within an interface were most suitable for the protein-protein docking.

D-amino acids inhibit initial bacterial adhesion: thermodynamic evidence.

PubMed

Xing, Su-Fang; Sun, Xue-Fei; Taylor, Alicia A; Walker, Sharon L; Wang, Yi-Fu; Wang, Shu-Guang

2015-04-01

Bacterial biofilms are structured communities of cells enclosed in a self-produced hydrated polymeric matrix that can adhere to inert or living surfaces. D-Amino acids were previously identified as self-produced compounds that mediate biofilm disassembly by causing the release of the protein component of the polymeric matrix. However, whether exogenous D-amino acids could inhibit initial bacterial adhesion is still unknown. Here, the effect of the exogenous amino acid D-tyrosine on initial bacterial adhesion was determined by combined use of chemical analysis, force spectroscopic measurement, and theoretical predictions. The surface thermodynamic theory demonstrated that the total interaction energy increased with more D-tyrosine, and the contribution of Lewis acid-base interactions relative to the change in the total interaction energy was much greater than the overall nonspecific interactions. Finally, atomic force microscopy analysis implied that the hydrogen bond numbers and adhesion forces decreased with the increase in D-tyrosine concentrations. D-Tyrosine contributed to the repulsive nature of the cell and ultimately led to the inhibition of bacterial adhesion. This study provides a new way to regulate biofilm formation by manipulating the contents of D-amino acids in natural or engineered systems. © 2014 Wiley Periodicals, Inc.

An investigation about the structures, thermodynamics and kinetics of the formic acid involved molecular clusters

NASA Astrophysics Data System (ADS)

Zhang, Rui; Jiang, Shuai; Liu, Yi-Rong; Wen, Hui; Feng, Ya-Juan; Huang, Teng; Huang, Wei

2018-05-01

Despite the very important role of atmospheric aerosol nucleation in climate change and air quality, the detailed aerosol nucleation mechanism is still unclear. Here we investigated the formic acid (FA) involved multicomponent nucleation molecular clusters including sulfuric acid (SA), dimethylamine (DMA) and water (W) through a quantum chemical method. The thermodynamics and kinetics analysis was based on the global minima given by Basin-Hopping (BH) algorithm coupled with Density Functional Theory (DFT) and subsequent benchmarked calculations. Then the interaction analysis based on ElectroStatic Potential (ESP), Topological and Atomic Charges analysis was made to characterize the binding features of the clusters. The results show that FA binds weakly with the other molecules in the cluster while W binds more weakly. Further kinetic analysis about the time evolution of the clusters show that even though the formic acid's weak interaction with other nucleation precursors, its effect on sulfuric acid dimer steady state concentration cannot be neglected due to its high concentration in the atmosphere.

Dynamic Fluctuations of Protein-Carbohydrate Interactions Promote Protein Aggregation

PubMed Central

Voynov, Vladimir; Chennamsetty, Naresh; Kayser, Veysel; Helk, Bernhard; Forrer, Kurt; Zhang, Heidi; Fritsch, Cornelius; Heine, Holger; Trout, Bernhardt L.

2009-01-01

Protein-carbohydrate interactions are important for glycoprotein structure and function. Antibodies of the IgG class, with increasing significance as therapeutics, are glycosylated at a conserved site in the constant Fc region. We hypothesized that disruption of protein-carbohydrate interactions in the glycosylated domain of antibodies leads to the exposure of aggregation-prone motifs. Aggregation is one of the main problems in protein-based therapeutics because of immunogenicity concerns and decreased efficacy. To explore the significance of intramolecular interactions between aromatic amino acids and carbohydrates in the IgG glycosylated domain, we utilized computer simulations, fluorescence analysis, and site-directed mutagenesis. We find that the surface exposure of one aromatic amino acid increases due to dynamic fluctuations. Moreover, protein-carbohydrate interactions decrease upon stress, while protein-protein and carbohydrate-carbohydrate interactions increase. Substitution of the carbohydrate-interacting aromatic amino acids with non-aromatic residues leads to a significantly lower stability than wild type, and to compromised binding to Fc receptors. Our results support a mechanism for antibody aggregation via decreased protein-carbohydrate interactions, leading to the exposure of aggregation-prone regions, and to aggregation. PMID:20037630

Label-free amino acid detection based on nanocomposites of graphene oxide hybridized with gold nanoparticles.

PubMed

Zhang, Qian; Zhang, Diming; Lu, Yanli; Xu, Gang; Yao, Yao; Li, Shuang; Liu, Qingjun

2016-03-15

Nanocomposites of graphene oxide and gold nanoparticles (GO/GNPs) were synthesized for label-free detections of amino acids. Interactions between the composites and amino acids were investigated by both naked-eye observation and optical absorption spectroscopy. The GO/GNPs composites displayed apparent color changes and absorption spectra changes in presences of amino acids including glutamate, aspartate, and cysteine. The interaction mechanisms of the composites and amino acids were discussed and explored with sulfhydryl groups and non-α-carboxylic groups on the amino acids. Sensing properties of the composites were tested, while pure gold particles were used as the control. The results suggested that the GO/GNPs composites had better linearity and stability in dose-dependent responses to the amino acids than those of the particles, especially in detections for acidic amino acids. Therefore, the nanocomposites platform can provide a convenient and efficient approach for label-free optical detections of important molecules such as amino acids. Copyright © 2015 Elsevier B.V. All rights reserved.

Supramolecular architectures in two 1:1 cocrystals of 5-fluorouracil with 5-bromothiophene-2-carboxylic acid and thiophene-2-carboxylic acid.

PubMed

Mohana, Marimuthu; Thomas Muthiah, Packianathan; McMillen, Colin D

2017-06-01

In solid-state engineering, cocrystallization is a strategy actively pursued for pharmaceuticals. Two 1:1 cocrystals of 5-fluorouracil (5FU; systematic name: 5-fluoro-1,3-dihydropyrimidine-2,4-dione), namely 5-fluorouracil-5-bromothiophene-2-carboxylic acid (1/1), C 5 H 3 BrO 2 S·C 4 H 3 FN 2 O 2 , (I), and 5-fluorouracil-thiophene-2-carboxylic acid (1/1), C 4 H 3 FN 2 O 2 ·C 5 H 4 O 2 S, (II), have been synthesized and characterized by single-crystal X-ray diffraction studies. In both cocrystals, carboxylic acid molecules are linked through an acid-acid R 2 2 (8) homosynthon (O-H...O) to form a carboxylic acid dimer and 5FU molecules are connected through two types of base pairs [homosynthon, R 2 2 (8) motif] via a pair of N-H...O hydrogen bonds. The crystal structures are further stabilized by C-H...O interactions in (II) and C-Br...O interactions in (I). In both crystal structures, π-π stacking and C-F...π interactions are also observed.

Developing a model of plant hormone interactions

PubMed Central

Wang, Yu Hua

2011-01-01

Plant growth and development is influenced by mutual interactions among plant hormones. The five classical plant hormones are auxins, cytokinins, gibberellins, abscisic acid and ethylene. They are small diffusible molecules that easily penetrate between cells. In addition, newer classes of plant hormones have been identified such as brassinosteroids, jasmonic acid, salicylic acid and various small proteins or peptides. These hormones also play important roles in the regulation of plant growth and development. This review begins with a brief summary of the current findings on plant hormones. Based on this knowledge, a conceptual model about interactions among plant hormones is built so as to link and develop an understanding of the diverse functions of different plant hormones as a whole in plants. PMID:21406974

Exploiting Amino Acid Composition for Predicting Protein-Protein Interactions

PubMed Central

Roy, Sushmita; Martinez, Diego; Platero, Harriett; Lane, Terran; Werner-Washburne, Margaret

2009-01-01

Background Computational prediction of protein interactions typically use protein domains as classifier features because they capture conserved information of interaction surfaces. However, approaches relying on domains as features cannot be applied to proteins without any domain information. In this paper, we explore the contribution of pure amino acid composition (AAC) for protein interaction prediction. This simple feature, which is based on normalized counts of single or pairs of amino acids, is applicable to proteins from any sequenced organism and can be used to compensate for the lack of domain information. Results AAC performed at par with protein interaction prediction based on domains on three yeast protein interaction datasets. Similar behavior was obtained using different classifiers, indicating that our results are a function of features and not of classifiers. In addition to yeast datasets, AAC performed comparably on worm and fly datasets. Prediction of interactions for the entire yeast proteome identified a large number of novel interactions, the majority of which co-localized or participated in the same processes. Our high confidence interaction network included both well-studied and uncharacterized proteins. Proteins with known function were involved in actin assembly and cell budding. Uncharacterized proteins interacted with proteins involved in reproduction and cell budding, thus providing putative biological roles for the uncharacterized proteins. Conclusion AAC is a simple, yet powerful feature for predicting protein interactions, and can be used alone or in conjunction with protein domains to predict new and validate existing interactions. More importantly, AAC alone performs at par with existing, but more complex, features indicating the presence of sequence-level information that is predictive of interaction, but which is not necessarily restricted to domains. PMID:19936254

In Praise of Thiosulfate.

ERIC Educational Resources Information Center

Tykodi, R. J.

1990-01-01

The use of the thiosulfate ion in teaching the concepts of gas formation, precipitate formation, complex formation, acid-base interaction, redox interaction, time evolution of chemical processes, catalysis, and stoichiometry is discussed. Several demonstrations and activities are detailed. (CW)

Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane.

PubMed

Langner, Karol M; Kedzierski, Pawel; Sokalski, W Andrzej; Leszczynski, Jerzy

2006-05-18

On the basis of the crystallographic structures of three nucleic acid intercalation complexes involving ethidium and proflavine, we have analyzed the interaction energies between intercalator chromophores and their four nearest bases, using a hybrid variation-perturbation method at the second-order Møller-Plesset theory level (MP2) with a 6-31G(d,p) basis set. A total MP2 interaction energy minimum precisely reproduces the crystallographic position of the ethidium chromophore in the intercalation plane between UA/AU bases. The electrostatic component constitutes the same fraction of the total energy for all three studied structures. The multipole electrostatic interaction energy, calculated from cumulative atomic multipole moments (CAMMs), was found to converge only after including components above the fifth order. CAMM interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures; they exhibit additional minima in the direction of the DNA grooves, however, which also need to be examined at higher theory levels if no crystallographic data are given.

Homology-based modeling of the Erwinia amylovora type III secretion chaperone DspF used to identify amino acids required for virulence and interaction with the effector DspE.

PubMed

Triplett, Lindsay R; Wedemeyer, William J; Sundin, George W

2010-09-01

The structure of DspF, a type III secretion system (T3SS) chaperone required for virulence of the fruit tree pathogen Erwinia amylovora, was modeled based on predicted structural homology to characterized T3SS chaperones. This model guided the selection of 11 amino acid residues that were individually mutated to alanine via site-directed mutagenesis. Each mutant was assessed for its effect on virulence complementation, dimerization and interaction with the N-terminal chaperone-binding site of DspE. Four amino acid residues were identified that did not complement the virulence defect of a dspF knockout mutant, and three of these residues were required for interaction with the N-terminus of DspE. This study supports the significance of the predicted beta-sheet helix-binding groove in DspF chaperone function. Copyright 2010 Elsevier Masson SAS. All rights reserved.

Structural insights into two inorganic-organic hybrids based on chiral amino acids and polyoxomolybdates

NASA Astrophysics Data System (ADS)

Arefian, Mina; Mirzaei, Masoud; Eshtiagh-Hosseini, Hossein

2018-03-01

A new chiral inorganic-organic hybrid with the formula (L-His)2(H7CoMo6O24)·6H2O (1), based on natural amino acid and Anderson type polyoxomolybdate was synthesized through mild condition. The chiral L-histidine molecules induced chirality to the whole structure through various types of strong and unconventional hydrogen bond (HB) interactions (CH⋯O, NH⋯O and CH···π interactions), as well as bifurcated hydrogen bonds (BHBs) between L-histidine amino acid, hexamer water cluster molecules, and H7CoMo6O24·xH2O. Following, important non-covalent CH⋯O interactions is investigated in another chiral inorganic-organic hybrid structure, (L-Pro)3(PMo12O40).4.5H2O (2), in detail. The CH⋯O hydrogen bonds lead to a chiral network similar to the DNA strands affording a promising candidate to bio-inorganic studies.

The study of interaction of modified fatty acid with {sup 99m}Tc in alcoholic media

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

Skuridin, V. S.; Stasyuk, E. S.; Varlamova, N. V.

2016-08-02

The paper presents the results of laboratory research aimed at the development of methods of synthesis of new radiodiagnostic agents based on modified fatty acid labelled with technetium-99m intended for scintigraphic evaluation of myocardial metabolism. In particular, the interaction of substance with {sup 99m}Tc in alcoholic media and the use of ethanol as solvent in the synthesis of the radiopharmaceutical were studied.

Lipoprotein lipase variants interact with polyunsaturated fatty acids for obesity traits in women: replication in two populations.

PubMed

Ma, Y; Tucker, K L; Smith, C E; Lee, Y C; Huang, T; Richardson, K; Parnell, L D; Lai, C Q; Young, K L; Justice, A E; Shao, Y; North, K E; Ordovás, J M

2014-12-01

Lipoprotein lipase (LPL) is a candidate gene for obesity based on its role in triglyceride hydrolysis and the partitioning of fatty acids towards storage or oxidation. Whether dietary fatty acids modify LPL associated obesity risk is unknown. We examined five single nucleotide polymorphisms (SNPs) (rs320, rs2083637, rs17411031, rs13702, rs2197089) for potential interaction with dietary fatty acids for obesity traits in 1171 participants (333 men and 838 women, aged 45-75 y) of the Boston Puerto Rican Health Study (BPRHS). In women, SNP rs320 interacted with dietary polyunsaturated fatty acids (PUFA) for body mass index (BMI) (P = 0.002) and waist circumference (WC) (P = 0.001) respectively. Higher intake of PUFA was associated with lower BMI and WC in homozygotes of the major allele (TT) (P = 0.01 and 0.005) but not in minor allele carriers (TG and GG). These interactions were replicated in an independent population, African American women of the Atherosclerosis Risk in Communities (ARIC) study (n = 1334). Dietary PUFA modulated the association of LPL rs320 with obesity traits in two independent populations. These interactions may be relevant to the dietary management of obesity, particularly in women. Copyright © 2014. Published by Elsevier B.V.

Lipoprotein lipase variants interact with polyunsaturated fatty acids for obesity traits in women: Replication in two populations

PubMed Central

Ma, Y.; Tucker, K.L.; Smith, C.E.; Lee, Y.C.; Huang, T.; Richardson, K.; Parnell, L.D.; Lai, C.Q.; Young, K.L.; Justice, A.E.; Shao, Y.; North, K.E.; Ordovás, J.M.

2015-01-01

Background and aims Lipoprotein lipase (LPL) is a candidate gene for obesity based on its role in triglyceride hydrolysis and the partitioning of fatty acids towards storage or oxidation. Whether dietary fatty acids modify LPL associated obesity risk is unknown. Methods and results We examined five single nucleotide polymorphisms (SNPs) (rs320, rs2083637, rs17411031, rs13702, rs2197089) for potential interaction with dietary fatty acids for obesity traits in 1171 participants (333 men and 838 women, aged 45–75 y) of the Boston Puerto Rican Health Study (BPRHS). In women, SNP rs320 interacted with dietary polyunsaturated fatty acids (PUFA) for body mass index (BMI) (P = 0.002) and waist circumference (WC) (P = 0.001) respectively. Higher intake of PUFA was associated with lower BMI and WC in homozygotes of the major allele (TT) (P = 0.01 and 0.005) but not in minor allele carriers (TG and GG). These interactions were replicated in an independent population, African American women of the Atherosclerosis Risk in Communities (ARIC) study (n = 1334). Conclusion Dietary PUFA modulated the association of LPL rs320 with obesity traits in two independent populations. These interactions may be relevant to the dietary management of obesity, particularly in women. PMID:25156894

Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains.

PubMed

Makowski, Mariusz; Liwo, Adam; Sobolewski, Emil; Scheraga, Harold A

2011-05-19

A new model of side-chain-side-chain interactions for charged side-chains of amino acids, to be used in the UNRES force-field, has been developed, in which a side chain consists of a nonpolar and a charged site. The interaction energy between the nonpolar sites is composed of a Gay-Berne and a cavity term; the interaction energy between the charged sites consists of a Lennard-Jones term, a Coulombic term, a generalized-Born term, and a cavity term, while the interaction energy between the nonpolar and charged sites is composed of a Gay-Berne and a polarization term. We parametrized the energy function for the models of all six pairs of natural like-charged amino-acid side chains, namely propionate-propionate (for the aspartic acid-aspartic acid pair), butyrate-butyrate (for the glutamic acid-glutamic acid pair), propionate-butyrate (for the aspartic acid-glutamic acid pair), pentylamine cation-pentylamine cation (for the lysine-lysine pair), 1-butylguanidine cation-1-butylguanidine cation (for the arginine-arginine pair), and pentylamine cation-1-butylguanidine cation (for the lysine-arginine pair). By using umbrella-sampling molecular dynamics simulations in explicit TIP3P water, we determined the potentials of mean force of the above-mentioned pairs as functions of distance and orientation and fitted analytical expressions to them. The positions and depths of the contact minima and the positions and heights of the desolvation maxima, including their dependence on the orientation of the molecules were well represented by analytical expressions for all systems. The values of the parameters of all the energy components are physically reasonable, which justifies use of such potentials in coarse-grain protein-folding simulations. © 2011 American Chemical Society

Theoretical study of the adsorption of DNA bases on the acidic external surface of montmorillonite.

PubMed

Mignon, Pierre; Sodupe, Mariona

2012-01-14

In the present study, DFT periodic plane wave calculations, at the PBE-D level of theory, were carried out to investigate the interaction of DNA nucleobases with acidic montmorillonite. The surface model was considered in its octahedral (Osub) and tetrahedral (Tsub) substituted forms, known to have different acidic properties. The adsorption of adenine, guanine and cytosine was considered in both orthogonal and coplanar orientations with the surface, interacting with the proton via a given heteroatom. In almost all considered cases, adsorption involved the spontaneous proton transfer to the nucleobase, with a more pronounced character in the Osub structures. The binding energy is about 10 kcal mol(-1) larger for Osub than for Tsub complexes mainly due to the larger acidity in Osub surfaces and due to the better stabilization by H-bond contacts between the negatively charged surface and the protonated base. The binding energy of coplanar orientations of the base is observed to be as large as the orthogonal ones due to a balance between electrostatic and dispersion contributions. Finally the binding of guanine and adenine on the acidic surface amounts to 50 kcal mol(-1) while that of cytosine rises to 44 kcal mol(-1).

Evaluation of Drug-Drug Interaction Potential Between Sacubitril/Valsartan (LCZ696) and Statins Using a Physiologically Based Pharmacokinetic Model.

PubMed

Lin, Wen; Ji, Tao; Einolf, Heidi; Ayalasomayajula, Surya; Lin, Tsu-Han; Hanna, Imad; Heimbach, Tycho; Breen, Christopher; Jarugula, Venkateswar; He, Handan

2017-05-01

Sacubitril/valsartan (LCZ696) has been approved for the treatment of heart failure. Sacubitril is an in vitro inhibitor of organic anion-transporting polypeptides (OATPs). In clinical studies, LCZ696 increased atorvastatin C max by 1.7-fold and area under the plasma concentration-time curve by 1.3-fold, but had little or no effect on simvastatin or simvastatin acid exposure. A physiologically based pharmacokinetics modeling approach was applied to explore the underlying mechanisms behind the statin-specific LCZ696 drug interaction observations. The model incorporated OATP-mediated clearance (CL int,T ) for simvastatin and simvastatin acid to successfully describe the pharmacokinetic profiles of either analyte in the absence or presence of LCZ696. Moreover, the model successfully described the clinically observed drug effect with atorvastatin. The simulations clarified the critical parameters responsible for the observation of a low, yet clinically relevant, drug-drug interaction DDI between sacubitril and atorvastatin and the lack of effect with simvastatin acid. Atorvastatin is administered in its active form and rapidly achieves C max that coincide with the low C max of sacubitril. In contrast, simvastatin requires a hydrolysis step to the acid form and therefore is not present at the site of interactions at sacubitril concentrations that are inhibitory. Similar models were used to evaluate the drug-drug interaction risk for additional OATP-transported statins which predicted to maximally result in a 1.5-fold exposure increase. Copyright © 2017. Published by Elsevier Inc.

Apolipoprotein A2 polymorphism interacts with intakes of dairy foods to influence body weight in 2 U.S. populations

USDA-ARS?s Scientific Manuscript database

The interaction between a functional apolipoprotein A2 gene (APOA2) variant and saturated fatty acids (SFAs) for the outcome of body mass index (BMI) is among the most widely replicated gene-nutrient interactions. Whether this interaction can be extrapolated to food-based sources of SFAs, specifical...

Surface Aggregation of Candida albicans on Glass in the Absence and Presence of Adhering Streptococcus gordonii in a Parallel-Plate Flow Chamber: A Surface Thermodynamical Analysis Based on Acid-Base Interactions.

PubMed

Millsap; Bos; Busscher; van der Mei HC

1999-04-15

Adhesive interactions between yeasts and bacteria are important in the maintenance of infectious mixed biofilms on natural and biomaterial surfaces in the human body. In this study, the extended DLVO (Derjaguin-Landau-Verwey-Overbeek) approach has been applied to explain adhesive interactions between C. albicans ATCC 10261 and S. gordonii NCTC 7869 adhering on glass. Contact angles with different liquids and the zeta potentials of both the yeasts and bacteria were determined and their adhesive interactions were measured in a parallel-plate flow chamber.Streptococci were first allowed to adhere to the bottom glass plate of the flow chamber to different seeding densities, and subsequently deposition of yeasts was monitored with an image analysis system, yielding the degree of initial surface aggregation of the adhering yeasts and their spatial arrangement in a stationary end point. Irrespective of growth temperature, the yeast cells appeared uncharged in TNMC buffer, but yeasts grown at 37 degrees C were intrinsically more hydrophilic and had an increased electron-donating character than cells grown at 30 degrees C. All yeasts showed surface aggregation due to attractive Lifshitz-van der Waals forces. In addition, acid-base interactions between yeasts, yeasts and the glass substratum, and yeasts and the streptococci were attractive for yeasts grown at 30 degrees C, but yeasts grown at 37 degrees C only had favorable acid-base interactions with the bacteria, explaining the positive relationship between the surface coverage of the glass by streptococci and the surface aggregation of the yeasts. Copyright 1999 Academic Press.

Natural Indices for the Chemical Hardness/Softness of Metal Cations and Ligands

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

Xu, Huifang; Xu, David C.; Wang, Yifeng

Quantitative understanding of reactivity and stability for a chemical species is fundamental to chemistry. The concept has undergone many changes and additions throughout the history of chemistry, stemming from the ideas such as Lewis acids and bases. For a given complexing ligand (Lewis base) and a group of isovalent metal cations (Lewis acids), the stability constants of metal–ligand (ML) complexes can simply correlate to the known properties of metal ions [ionic radii (r Mn+), Gibbs free energy of formation (ΔG° f,Mn+), and solvation energy (ΔG° s,Mn+)] by 2.303RT log K ML = (α* MLΔG° f,Mn+ – β* MLr Mn+ +more » γ* MLΔG° s,Mn+ – δ* ML), where the coefficients (α* ML, β* ML, γ* ML, and intercept δ* ML) are determined by fitting the equation to the existing experimental data. Coefficients β* ML and γ* ML have the same sign and are in a linear relationship through the origin. Gibbs free energies of formation of cations (ΔG° f,Mn+) are found to be natural indices for the softness or hardness of metal cations, with positive values corresponding to soft acids and negative values to hard acids. The coefficient α* ML is an index for the softness or hardness of a complexing ligand. Proton (H +) with the softness index of zero is a unique acid that has strong interactions with both soft and hard bases. The stability energy resulting from the acid–base interactions is determined by the term α* MLΔG° f,Mn+; a positive product of α* ML and ΔG° f,Mn+ indicates that the acid–base interaction between the metal cation and the complexing ligand stabilizes the complex. The terms β* MLr Mn+ and γ* MLΔG° s,Mn+, which are related to ionic radii of metal cations, represent the steric and solvation effects of the cations. The new softness indices proposed here will help to understand the interactions of ligands (Lewis bases) with metal cations (Lewis acids) and provide guidelines for engineering materials with desired chemical reactivity and selectivity. As a result, the new correlation can also enhance our ability for predicting the speciation, mobility, and toxicity of heavy metals in the earth environments and biological systems.« less

Natural Indices for the Chemical Hardness/Softness of Metal Cations and Ligands

DOE PAGES

Xu, Huifang; Xu, David C.; Wang, Yifeng

2017-10-26

Quantitative understanding of reactivity and stability for a chemical species is fundamental to chemistry. The concept has undergone many changes and additions throughout the history of chemistry, stemming from the ideas such as Lewis acids and bases. For a given complexing ligand (Lewis base) and a group of isovalent metal cations (Lewis acids), the stability constants of metal–ligand (ML) complexes can simply correlate to the known properties of metal ions [ionic radii (r Mn+), Gibbs free energy of formation (ΔG° f,Mn+), and solvation energy (ΔG° s,Mn+)] by 2.303RT log K ML = (α* MLΔG° f,Mn+ – β* MLr Mn+ +more » γ* MLΔG° s,Mn+ – δ* ML), where the coefficients (α* ML, β* ML, γ* ML, and intercept δ* ML) are determined by fitting the equation to the existing experimental data. Coefficients β* ML and γ* ML have the same sign and are in a linear relationship through the origin. Gibbs free energies of formation of cations (ΔG° f,Mn+) are found to be natural indices for the softness or hardness of metal cations, with positive values corresponding to soft acids and negative values to hard acids. The coefficient α* ML is an index for the softness or hardness of a complexing ligand. Proton (H +) with the softness index of zero is a unique acid that has strong interactions with both soft and hard bases. The stability energy resulting from the acid–base interactions is determined by the term α* MLΔG° f,Mn+; a positive product of α* ML and ΔG° f,Mn+ indicates that the acid–base interaction between the metal cation and the complexing ligand stabilizes the complex. The terms β* MLr Mn+ and γ* MLΔG° s,Mn+, which are related to ionic radii of metal cations, represent the steric and solvation effects of the cations. The new softness indices proposed here will help to understand the interactions of ligands (Lewis bases) with metal cations (Lewis acids) and provide guidelines for engineering materials with desired chemical reactivity and selectivity. As a result, the new correlation can also enhance our ability for predicting the speciation, mobility, and toxicity of heavy metals in the earth environments and biological systems.« less

Halogen bonding based recognition processes: a world parallel to hydrogen bonding.

PubMed

Metrangolo, Pierangelo; Neukirch, Hannes; Pilati, Tullio; Resnati, Giuseppe

2005-05-01

Halogen bonding is the noncovalent interaction between halogen atoms (Lewis acids) and neutral or anionic Lewis bases. The main features of the interaction are given, and the close similarity with the hydrogen bonding will become apparent. Some heuristic principles are presented to develop a rational crystal engineering based on halogen bonding. The focus is on halogen-bonded supramolecular architectures given by halocarbons. The potential of the interaction is shown by useful applications in the field of synthetic chemistry, material science, and bioorganic chemistry.

An enrichment method based on synergistic and reversible covalent interactions for large-scale analysis of glycoproteins.

PubMed

Xiao, Haopeng; Chen, Weixuan; Smeekens, Johanna M; Wu, Ronghu

2018-04-27

Protein glycosylation is ubiquitous in biological systems and essential for cell survival. However, the heterogeneity of glycans and the low abundance of many glycoproteins complicate their global analysis. Chemical methods based on reversible covalent interactions between boronic acid and glycans have great potential to enrich glycopeptides, but the binding affinity is typically not strong enough to capture low-abundance species. Here, we develop a strategy using dendrimer-conjugated benzoboroxole to enhance the glycopeptide enrichment. We test the performance of several boronic acid derivatives, showing that benzoboroxole markedly increases glycopeptide coverage from human cell lysates. The enrichment is further improved by conjugating benzoboroxole to a dendrimer, which enables synergistic benzoboroxole-glycan interactions. This robust and simple method is highly effective for sensitive glycoproteomics analysis, especially capturing low-abundance glycopeptides. Importantly, the enriched glycopeptides remain intact, making the current method compatible with mass-spectrometry-based approaches to identify glycosylation sites and glycan structures.

A new fluorogenic sensing platform for salicylic acid derivatives based on π-π and NH-π interactions between electron-deficient and electron-rich aromatics.

PubMed

Pandith, Anup; Hazra, Giridhari; Kim, Hong-Seok

2017-05-05

A novel simple fluorescent probe was designed for the recognition of electron-rich salicylic acid derivatives (SAs). The imidazole-appended aminomethyl perylene probe 1 selectively differentiated between electron-rich amino-SAs and electron-deficient nitro-SAs in EtOH, exhibiting the highest selectivity and sensitivity toward 5-aminosalicylic acid (5-ASA) and showing strong 1:1 binding (K a =1.37×10 7 M -1 ). This high selectivity and sensitivity resulted from the synergistic multiple hydrogen bonding interactions of secondary amine and imidazole units and π-π interactions between electron-rich and electron-deficient rings, along with the unusual NH-π interactions between 5-ASA and the perylene moiety of 1. The limit of detection (LOD) for 5-ASA in EtOH was 0.012ppb. Copyright © 2017 Elsevier B.V. All rights reserved.

Adsorption and removal of phthalic acid and diethyl phthalate from water with zeolitic imidazolate and metal-organic frameworks.

PubMed

Khan, Nazmul Abedin; Jung, Beom K; Hasan, Zubair; Jhung, Sung Hwa

2015-01-23

ZIF-8 (zinc-methylimidazolate framework-8), one of the zeolitic imidazolate frameworks (ZIFs), has been used for the removal of phthalic acid (H2-PA) and diethyl phthalate (DEP) from aqueous solutions via adsorption. The adsorption capacity of the ZIF-8 for H2-PA was much higher than that of a commercial activated carbon or other typical metal-organic frameworks (MOFs). Because the surface area and pore volume of the adsorbents showed no favorable effect on the adsorption of H2-PA, the remarkable adsorption with ZIF-8 suggests a specific favorable interaction (electrostatic interaction) between the positively charged surface of ZIF-8 and the negatively charged PA anions. In addition, acid-base interactions also have a favorable contribution in the adsorption of H2-PA, based on the adsorptive performances of pristine and amino-functionalized MOFs and adsorption over ZIF-8 at acidic condition (pH=3.5). The reusability of ZIF-8 was also demonstrated after simple washing with methanol. On the other hand, ZIF-8 was not effective in adsorbing DEP probably because of little charge of DEP in a water solution. Copyright © 2014 Elsevier B.V. All rights reserved.

Design and Mechanism of Tetrahydrothiophene-Based γ-Aminobutyric Acid Aminotransferase Inactivators

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

Le, Hoang V.; Hawker, Dustin D.; Wu, Rui

Low levels of gamma-aminobutyric acid (GABA), one of two major neurotransmitters that regulate brain neuronal activity, are associated with many neurological disorders, such as epilepsy, Parkinsons disease, Alzheimers disease, Huntingtons disease, and cocaine addiction. One of the main methods to raise the GABA level in human brain is to use small molecules that cross the bloodbrain barrier and inhibit the activity of gamma-aminobutyric acid aminotransferase (GABA-AT), the enzyme that degrades GABA. We have designed a series of conformationally restricted tetrahydrothiophene-based GABA analogues with a properly positioned leaving group that could facilitate a ring-opening mechanism, leading to inactivation of GABA-AT. Onemore » compound in the series is 8 times more efficient an inactivator of GABA-AT than vigabatrin, the only FDA-approved inactivator of GABA-AT. Our mechanistic studies show that the compound inactivates GABA-AT by a new mechanism. The metabolite resulting from inactivation does not covalently bind to amino acid residues of GABA-AT but stays in the active site via H-bonding interactions with Arg-192, a pi-pi interaction with Phe-189, and a weak nonbonded (SO)-O-...=C interaction with Glu-270, thereby inactivating the enzyme.« less

Design and mechanism of tetrahydrothiophene-based γ-aminobutyric acid aminotransferase inactivators.

PubMed

Le, Hoang V; Hawker, Dustin D; Wu, Rui; Doud, Emma; Widom, Julia; Sanishvili, Ruslan; Liu, Dali; Kelleher, Neil L; Silverman, Richard B

2015-04-08

Low levels of γ-aminobutyric acid (GABA), one of two major neurotransmitters that regulate brain neuronal activity, are associated with many neurological disorders, such as epilepsy, Parkinson's disease, Alzheimer's disease, Huntington's disease, and cocaine addiction. One of the main methods to raise the GABA level in human brain is to use small molecules that cross the blood-brain barrier and inhibit the activity of γ-aminobutyric acid aminotransferase (GABA-AT), the enzyme that degrades GABA. We have designed a series of conformationally restricted tetrahydrothiophene-based GABA analogues with a properly positioned leaving group that could facilitate a ring-opening mechanism, leading to inactivation of GABA-AT. One compound in the series is 8 times more efficient an inactivator of GABA-AT than vigabatrin, the only FDA-approved inactivator of GABA-AT. Our mechanistic studies show that the compound inactivates GABA-AT by a new mechanism. The metabolite resulting from inactivation does not covalently bind to amino acid residues of GABA-AT but stays in the active site via H-bonding interactions with Arg-192, a π-π interaction with Phe-189, and a weak nonbonded S···O═C interaction with Glu-270, thereby inactivating the enzyme.

Oligomerisation status and evolutionary conservation of interfaces of protein structural domain superfamilies.

PubMed

Sukhwal, Anshul; Sowdhamini, Ramanathan

2013-07-01

Protein-protein interactions are important in carrying out many biological processes and functions. These interactions may be either permanent or of temporary nature. Several studies have employed tools like solvent accessibility and graph theory to identify these interactions, but still more studies need to be performed to quantify and validate them. Although we now have many databases available with predicted and experimental results on protein-protein interactions, we still do not have many databases which focus on providing structural details of the interacting complexes, their oligomerisation state and homologues. In this work, protein-protein interactions have been thoroughly investigated within the structural regime and quantified for their strength using calculated pseudoenergies. The PPCheck server, an in-house webserver, has been used for calculating the pseudoenergies like van der Waals, hydrogen bonds and electrostatic energy based on distances between atoms of amino acids from two interacting proteins. PPCheck can be visited at . Based on statistical data, as obtained by studying established protein-protein interacting complexes from earlier studies, we came to a conclusion that an average protein-protein interface consisted of about 51 to 150 amino acid residues and the generalized energy per residue ranged from -2 kJ mol(-1) to -6 kJ mol(-1). We found that some of the proteins have an exceptionally higher number of amino acids at the interface and it was purely because of their elaborate interface or extended topology i.e. some of their secondary structure regions or loops were either inter-mixing or running parallel to one another or they were taking part in domain swapping. Residue networks were prepared for all the amino acids of the interacting proteins involved in different types of interactions (like van der Waals, hydrogen-bonding, electrostatic or intramolecular interactions) and were analysed between the query domain-interacting partner pair and its remote homologue-interacting partner pair. We found that, in exceptional cases, homologous proteins belonging to the same superfamily, but with remote sequence similarity, can share similar interfaces.

Complexity in Acid–Base Titrations: Multimer Formation Between Phosphoric Acids and Imines

PubMed Central

Malm, Christian; Kim, Heejae; Wagner, Manfred

2017-01-01

Abstract Solutions of Brønsted acids with bases in aprotic solvents are not only common model systems to study the fundamentals of proton transfer pathways but are also highly relevant to Brønsted acid catalysis. Despite their importance the light nature of the proton makes characterization of acid–base aggregates challenging. Here, we track such acid–base interactions over a broad range of relative compositions between diphenyl phosphoric acid and the base quinaldine in dichloromethane, by using a combination of dielectric relaxation and NMR spectroscopy. In contrast to what one would expect for an acid–base titration, we find strong deviations from quantitative proton transfer from the acid to the base. Even for an excess of the base, multimers consisting of one base and at least two acid molecules are formed, in addition to the occurrence of proton transfer from the acid to the base and simultaneous formation of ion pairs. For equimolar mixtures such multimers constitute about one third of all intermolecular aggregates. Quantitative analysis of our results shows that the acid‐base association constant is only around six times larger than that for the acid binding to an acid‐base dimer, that is, to an already protonated base. Our findings have implications for the interpretation of previous studies of reactive intermediates in organocatalysis and provide a rationale for previously observed nonlinear effects in phosphoric acid catalysis. PMID:28597513

A Systems Model for Ursodeoxycholic Acid Metabolism in Healthy and Patients With Primary Biliary Cirrhosis.

PubMed

Zuo, P; Dobbins, R L; O'Connor-Semmes, R L; Young, M A

2016-08-01

A systems model was developed to describe the metabolism and disposition of ursodeoxycholic acid (UDCA) and its conjugates in healthy subjects based on pharmacokinetic (PK) data from published studies in order to study the distribution of oral UDCA and potential interactions influencing therapeutic effects upon interruption of its enterohepatic recirculation. The base model was empirically adapted to patients with primary biliary cirrhosis (PBC) based on current understanding of disease pathophysiology and clinical measurements. Simulations were performed for patients with PBC under two competing hypotheses: one for inhibition of ileal absorption of both UDCA and conjugates and the other only of conjugates. The simulations predicted distinctly different bile acid distribution patterns in plasma and bile. The UDCA model adapted to patients with PBC provides a platform to investigate a complex therapeutic drug interaction among UDCA, UDCA conjugates, and inhibition of ileal bile acid transport in this rare disease population. © 2016 The Authors CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

Evolution-Based Functional Decomposition of Proteins

PubMed Central

Rivoire, Olivier; Reynolds, Kimberly A.; Ranganathan, Rama

2016-01-01

The essential biological properties of proteins—folding, biochemical activities, and the capacity to adapt—arise from the global pattern of interactions between amino acid residues. The statistical coupling analysis (SCA) is an approach to defining this pattern that involves the study of amino acid coevolution in an ensemble of sequences comprising a protein family. This approach indicates a functional architecture within proteins in which the basic units are coupled networks of amino acids termed sectors. This evolution-based decomposition has potential for new understandings of the structural basis for protein function. To facilitate its usage, we present here the principles and practice of the SCA and introduce new methods for sector analysis in a python-based software package (pySCA). We show that the pattern of amino acid interactions within sectors is linked to the divergence of functional lineages in a multiple sequence alignment—a model for how sector properties might be differentially tuned in members of a protein family. This work provides new tools for studying proteins and for generally testing the concept of sectors as the principal units of function and adaptive variation. PMID:27254668

Interactive computer-assisted instruction in acid-base physiology for mobile computer platforms.

PubMed

Longmuir, Kenneth J

2014-03-01

In this project, the traditional lecture hall presentation of acid-base physiology in the first-year medical school curriculum was replaced by interactive, computer-assisted instruction designed primarily for the iPad and other mobile computer platforms. Three learning modules were developed, each with ∼20 screens of information, on the subjects of the CO2-bicarbonate buffer system, other body buffer systems, and acid-base disorders. Five clinical case modules were also developed. For the learning modules, the interactive, active learning activities were primarily step-by-step learner control of explanations of complex physiological concepts, usually presented graphically. For the clinical cases, the active learning activities were primarily question-and-answer exercises that related clinical findings to the relevant basic science concepts. The student response was remarkably positive, with the interactive, active learning aspect of the instruction cited as the most important feature. Also, students cited the self-paced instruction, extensive use of interactive graphics, and side-by-side presentation of text and graphics as positive features. Most students reported that it took less time to study the subject matter with this online instruction compared with subject matter presented in the lecture hall. However, the approach to learning was highly examination driven, with most students delaying the study of the subject matter until a few days before the scheduled examination. Wider implementation of active learning computer-assisted instruction will require that instructors present subject matter interactively, that students fully embrace the responsibilities of independent learning, and that institutional administrations measure instructional effort by criteria other than scheduled hours of instruction.

Interaction of cinnamic acid derivatives with β-cyclodextrin in water: experimental and molecular modeling studies.

PubMed

Liu, Benguo; Zeng, Jie; Chen, Chen; Liu, Yonglan; Ma, Hanjun; Mo, Haizhen; Liang, Guizhao

2016-03-01

Cyclodextrins (CDs) can be used to improve the solubility and stability of cinnamic acid derivatives (CAs). However, there was no detailed report about understanding the effects of the substituent groups in the benzene ring on the inclusion behavior between CAs and CDs in aqueous solution. Here, the interaction of β-CD with CAs, including caffeic acid, ferulic acid, and p-coumaric acid, in water was investigated by phase-solubility method, UV, fluorescence, and (1)H NMR spectroscopy, together with ONIOM (our Own N-layer Integrated Orbital molecular Mechanics)-based QM/MM (Quantum Mechanics/Molecular Mechanics) calculations. Experimental results demonstrated that CAs could form 1:1 stoichiometric inclusion complex with β-CD by non-covalent bonds, and that the maximum apparent stability constants were found in caffeic acid (176M(-1)) followed by p-coumaric acid (160M(-1)) and ferulic acid (133M(-1)). Moreover, our calculations reasonably illustrated the binding orientations of β-CD with CAs determined by experimental observations. Copyright © 2015. Published by Elsevier Ltd.

Base pairing and base mis-pairing in nucleic acids

NASA Technical Reports Server (NTRS)

Wang, A. H. J.; Rich, A.

1986-01-01

In recent years we have learned that DNA is conformationally active. It can exist in a number of different stable conformations including both right-handed and left-handed forms. Using single crystal X-ray diffraction analysis we are able to discover not only additional conformations of the nucleic acids but also different types of hydrogen bonded base-base interactions. Although Watson-Crick base pairings are the predominant type of interaction in double helical DNA, they are not the only types. Recently, we have been able to examine mismatching of guanine-thymine base pairs in left-handed Z-DNA at atomic resolution (1A). A minimum amount of distortion of the sugar phosphate backbone is found in the G x T pairing in which the bases are held together by two hydrogen bonds in the wobble pairing interaction. Because of the high resolution of the analysis we can visualize water molecules which fill in to accommodate the other hydrogen bonding positions in the bases which are not used in the base-base interactions. Studies on other DNA oligomers have revealed that other types of non-Watson-Crick hydrogen bonding interactions can occur. In the structure of a DNA octamer with the sequence d(GCGTACGC) complexed to an antibiotic triostin A, it was found that the two central AT base pairs are held together by Hoogsteen rather than Watson-Crick base pairs. Similarly, the G x C base pairs at the ends are also Hoogsteen rather than Watson-Crick pairing. Hoogsteen base pairs make a modified helix which is distinct from the Watson-Crick double helix.

High Level ab initio Predictions of the Energetics of mCO2•(H2O)n (n = 1-3, m = 1-12) Clusters

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

Thanthiriwatte, Sahan; Duke, Jessica R.; Jackson, Virgil E.

Electronic structure calculations at the correlated molecular orbital theory and density functional theory levels have been used to generate a reliable set of clustering energies for up to three water molecules in carbon dioxide clusters up to n = 12. The structures and energetics are dominated by Lewis acid-base interactions with hydrogen bonding interactions playing a lesser energetic role. The actual binding energies are somewhat larger than might be expected. The correlated molecular orbital MP2 method and density functional theory with the ωB97X exchange-correlation functional provide good results for the energetics of the clusters but the B3LYP and ωB97X-D functionalsmore » do not. Seven CO2 molecules form the first solvent shell about a single H2O with four CO2 molecules interacting with the H2O via Lewis acid-base interactions, two CO2 interacting with the H2O by hydrogen bonds, and the seventh CO2 completing the shell. The Lewis acid-base and weak hydrogen bond interactions between the water molecules and the CO2 molecules are strong enough to disrupt the trimer ring configuration for as few as seven CO2 molecules. Calculated 13C NMR chemical shifts for mCO2•(H2O)n show little change with respect to the number of H2O or CO2 molecules in the cluster. The O-H stretching frequencies do exhibit shifts that can provide information about the interactions between water and CO2 molecules.« less

Proof of concept of a "greener" protein purification/enrichment method based on carboxylate-terminated carbosilane dendrimer-protein interactions.

PubMed

González-García, Estefanía; Maly, Marek; de la Mata, Francisco Javier; Gómez, Rafael; Marina, María Luisa; García, María Concepción

2016-11-01

Protein sample preparation is a critical and an unsustainable step since it involves the use of tedious methods that usually require high amount of solvents. The development of new materials offers additional opportunities in protein sample preparation. This work explores, for the first time, the potential application of carboxylate-terminated carbosilane dendrimers to the purification/enrichment of proteins. Studies on dendrimer binding to proteins, based on protein fluorescence intensity and emission wavelengths measurements, demonstrated the interaction between carboxylate-terminated carbosilane dendrimers and proteins at all tested pH levels. Interactions were greatly affected by the protein itself, pH, and dendrimer concentration and generation. Especially interesting was the interaction at acidic pH since it resulted in a significant protein precipitation. Dendrimer-protein interactions were modeled observing stable complexes for all proteins. Carboxylate-terminated carbosilane dendrimers at acidic pH were successfully used in the purification/enrichment of proteins extracted from a complex sample. Graphical Abstract Images showing the growing turbidity of solutions containing a mixture of proteins (lysozyme, myoglobin, and BSA) at different protein:dendrimer ratios (1:0, 1:1, 1:8, and 1:20) at acidic pH and SDS-PAGE profiles of the corresponsing supernatants. Comparison of SDS-PAGE profiles for the pellets obtained during the purification of proteins present in a complex sample using a conventional "no-clean" method based on acetone precipitation and the proposed "greener" method using carboxylate-terminated carbosilane dendrimer at a 1:20 protein:dendrimer ratio.

Design of co-crystals/salts of some Nitrogenous bases and some derivatives of thiophene carboxylic acids through a combination of hydrogen and halogen bonds.

PubMed

Jennifer, Samson Jegan; Muthiah, Packianathan Thomas

2014-01-01

The utility of N-heterocyclic bases to obtain molecular complexes with carboxylic acids is well studied. Depending on the solid state interaction between the N-heterocyclic base and a carboxylic acid a variety of neutral or ionic synthons are observed. Meanwhile, pyridines and pyrimidines have been frequently chosen in the area of crystal engineering for their multipurpose functionality. HT (hetero trimers) and LHT (linear heterotetramers) are the well known synthons that are formed in the presence of pyrimidines and carboxylic acids. Fourteen crystals involving various substituted thiophene carboxylic acid derivatives and nitrogenous bases were prepared and characterized by using single crystal X-ray diffraction. The 14 crystals can further be divided into two groups [1a-7a], [8b-14b] based on the nature of the nitrogenous base. Carboxylic acid to pyridine proton transfer has occurred in 3 compounds of each group. In addition to the commonly occurring hydrogen bond based pyridine/carboxylic acid and pyrimidine/carboxylic acid synthons which is the reason for assembly of primary motifs, various other interactions like Cl…Cl, Cl…O, C-H…Cl, C-H…S add additional support in organizing these supermolecules into extended architectures. It is also interesting to note that in all the compounds π-π stacking occurs between the pyrimidine-pyrimidine or pyridine-pyridine or acid-acid moieties rather than acid-pyrimidine/pyridine. In all the compounds (1a-14b) either neutral O-H…Npyridyl/pyrimidine or charge-assisted Npyridinium-H…Ocarboxylate hydrogen bonds are present. The HT (hetero trimers) and LHT (linear heterotetramers) are dominant in the crystal structures of the adducts containing N-heterocyclic bases with two proton acceptors (1a-7a). Similar type supramolecular ladders are observed in 5TPC44BIPY (8b), TPC44BIPY (9b), TPC44TMBP (11b). Among the seven compounds [8b-14b] the extended ligands are linear in all except for the TMBP (10b, 11b, 12b). The structure of each compound depends on the dihedral angle between the carboxyl group and the nitrogenous base. All these compounds indicate three main synthons that regularly occur, namely linear heterodimer (HD), heterotrimer (HT) and heterotetramer (LHT).

Polyelectrolyte properties of single stranded DNA measured using SAXS and single molecule FRET: beyond the wormlike chain model

PubMed Central

Meisburger, Steve P.; Sutton, Julie L.; Chen, Huimin; Pabit, Suzette A.; Kirmizialtin, Serdal; Elber, Ron; Pollack, Lois

2013-01-01

Nucleic acids are highly charged polyelectrolytes that interact strongly with salt ions. Rigid, base-paired regions are successfully described with worm like chain models, but non base-paired single stranded regions have fundamentally different polymer properties because of their greater flexibility. Recently, attention has turned to single stranded nucleic acids due to the growing recognition of their biological importance, as well as the availability of sophisticated experimental techniques sensitive to the conformation of individual molecules. We investigate polyelectrolyte properties of poly(dT), an important and widely studied model system for flexible single stranded nucleic acids, in physiologically important mixed mono- and di-valent salt. We report measurements of the form factor and interparticle interactions using SAXS, end to end distances using smFRET, and number of excess ions using ASAXS. We present a coarse-grained model that accounts for flexibility, excluded volume, and electrostatic interactions in these systems. Predictions of the model are validated against experiment. We also discuss the state of all-atom, explicit solvent Molecular Dynamics simulations of poly(dT), the next step in understanding the complexities of ion interactions with these highly charged and flexible polymers. PMID:23606337

Intramolecular interactions in aminoacyl nucleotides: Implications regarding the origin of genetic coding and protein synthesis

NASA Technical Reports Server (NTRS)

Lacey, J. C., Jr.; Mullins, D. W., Jr.; Watkins, C. L.; Hall, L. M.

1986-01-01

Cellular organisms store information as sequences of nucleotides in double stranded DNA. This information is useless unless it can be converted into the active molecular species, protein. This is done in contemporary creatures first by transcription of one strand to give a complementary strand of mRNA. The sequence of nucleotides is then translated into a specific sequence of amino acids in a protein. Translation is made possible by a genetic coding system in which a sequence of three nucleotides codes for a specific amino acid. The origin and evolution of any chemical system can be understood through elucidation of the properties of the chemical entities which make up the system. There is an underlying logic to the coding system revealed by a correlation of the hydrophobicities of amino acids and their anticodonic nucleotides (i.e., the complement of the codon). Its importance lies in the fact that every amino acid going into protein synthesis must first be activated. This is universally accomplished with ATP. Past studies have concentrated on the chemistry of the adenylates, but more recently we have found, through the use of NMR, that we can observe intramolecular interactions even at low concentrations, between amino acid side chains and nucleotide base rings in these adenylates. The use of this type of compound thus affords a novel way of elucidating the manner in which amino acids and nucleotides interact with each other. In aqueous solution, when a hydrophobic amino acid is attached to the most hydrophobic nucleotide, AMP, a hydrophobic interaction takes place between the amino acid side chain and the adenine ring. The studies to be reported concern these hydrophobic interactions.

Interference of functional monomers with polymerization efficiency of adhesives.

PubMed

Hanabusa, Masao; Yoshihara, Kumiko; Yoshida, Yasuhiro; Okihara, Takumi; Yamamoto, Takatsugu; Momoi, Yasuko; Van Meerbeek, Bart

2016-04-01

The degree of conversion (DC) of camphorquinone/amine-based adhesives is affected by acidic functional monomers as a result of inactivation of the amine co-initiator through an acid-base reaction. During bonding, functional monomers of self-etch adhesives chemically interact with hydroxyapatite (HAp). Here, we tested in how far the latter interaction of functional monomers with HAp counteracts the expected reduction in DC of camphorquinone/amine-based adhesives. The DC of three experimental adhesive formulations, containing either of the two functional monomers [10-methacryloyloxydecyl dihydrogen phosphate (10-MDP) or 4-methacryloxyethyl trimellitic acid anhydride (4-META)] or no functional monomer (no-FM; control), was measured with and without HAp powder added to the adhesive formulations. Both the variables 'functional monomer' and 'HAp' were found to be significant, with the functional monomer reducing the DC and HAp counteracting this effect. It is concluded that the functional monomers 10-MDP and 4-META interfere with the polymerization efficiency of adhesives. This interference is less prominent in the presence of HAp, which would clinically correspond to when these two functional monomers of the adhesive simultaneously interact with HAp in tooth tissue. © 2016 Eur J Oral Sci.

Crystal structures of 4-meth-oxy-benzoic acid-1,3-bis-(pyridin-4-yl)propane (2/1) and biphenyl-4,4'-di-carb-oxy-lic acid-4-meth-oxy-pyridine (1/2).

PubMed

Gotoh, Kazuma; Ishida, Hiroyuki

2017-07-01

The crystal structures of two hydrogen-bonded compounds, namely 4-meth-oxy-benzoic acid-1,3-bis-(pyridin-4-yl)propane (2/1), C 13 H 14.59 N 2 ·C 8 H 7.67 O 3 ·C 8 H 7.74 O 3 , (I), and biphenyl-4,4'-di-carb-oxy-lic acid-4-meth-oxy-pyridine (1/2), C 14 H 9.43 O 4 ·C 6 H 7.32 NO·C 6 H 7.25 NO, (II), have been determined at 93 K. In (I), the asymmetric unit consists of two crystallographically independent 4-meth-oxy-benzoic acid mol-ecules and one 1,3-bis-(pyridin-4-yl)propane mol-ecule. The asymmetric unit of (II) comprises one biphenyl-4,4'-di-carb-oxy-lic acid mol-ecule and two independent 4-meth-oxy-pyridine mol-ecules. In each crystal, the acid and base mol-ecules are linked by short O-H⋯N/N-H⋯O hydrogen bonds, in which H atoms are disordered over the acid O-atom and base N-atom sites, forming a linear hydrogen-bonded 2:1 or 1:2 unit of the acid and the base. The 2:1 units of (I) are linked via C-H⋯π, π-π and C-H⋯O inter-actions into a tape structure along [101], while the 1:2 units of (II) form a double-chain structure along [-101] through π-π and C-H⋯O inter-actions.

Chromatographic HPV-16 E6/E7 plasmid vaccine purification employing L-histidine and 1-benzyl-L-histidine affinity ligands.

PubMed

Amorim, Lúcia F A; Gaspar, Rita; Pereira, Patrícia; Černigoj, Urh; Sousa, Fani; Queiroz, João António; Sousa, Ângela

2017-11-01

Affinity chromatography based on amino acids as interacting ligands was already indicated as an alternative compared to ion exchange or hydrophobic interaction for plasmid DNA purification. Understanding the recognition mechanisms occurring between histidine-based ligands and nucleic acids enables more efficient purification of a DNA vaccine, as the binding and elution conditions can be adjusted in order to enhance the purification performance. Decreasing pH to slightly acidic conditions increases the positive charge of histidine ligand, what influences the type of interaction between chromatographic support and analytes. This was proven in this work, where hydrophobic effects established in the presence of ammonium sulfate were affected at pH 5.0 in comparison to pH 8.0, while electrostatic and cation-π interactions were intensified. Histidine ligand at pH 5.0 interacts with phosphate groups or aromatic rings of plasmid DNA. Due to different responses of RNA and pDNA on mobile phase changes, the elution order between RNA and pDNA was changed with mobile phase pH decrease from 8.0 to 5.0. The phenomenon was more evident with L-histidine ligand due to more hydrophilic character, leading to an improved selectivity of L-histidine-modified chromatographic monolith, allowing the product recovery with 99% of purity (RNA removal). With the 1-benzyl- L-histidine ligand, stronger and less selective interactions with the nucleic acids were observed due to the additional hydrophobicity associated with the phenyl aromatic ring. Optimization of sample displacement chromatography parameters (especially (NH 4 ) 2 SO 4 concentration) at slightly acidic pH enabled excellent isolation of pDNA, by the removal of RNA in a negative mode, with binding capacities above 1.5 mg pDNA per mL of chromatographic support. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular dynamics simulations on the interactions of low molecular weight natural organic acids with C60.

PubMed

Sun, Qian; Xie, Hong-Bin; Chen, Jingwen; Li, Xuehua; Wang, Zhuang; Sheng, Lianxi

2013-07-01

As an important part of dissolved organic matter (DOM), low molecular weight organic acids (LOAs) may play a key role in the process for DOM stabilizing carbon nanomaterials (e.g. C60) suspensions in aquatic environment. In addition, both LOAs and C60 have been detected in the troposphere and therefore have a chance to interact with each other in the gaseous phase. However, the mechanism for LOAs-C60 interactions and their environmental implications need further investigations. In this study, molecular dynamics (MD) simulation was employed to investigate the interactions between both neutral and ionic LOAs with C60 in vacuum and water. The results showed that the adsorptions of all LOAs on C60 in energy are favorable, and the aromatic acids have stronger interactions with C60 than the aliphatic acids in vacuum and water. The interaction energies (Eint) of the LOA anions with C60 were weaker than those of their corresponding neutral LOA molecules. The models were also developed to predict and interpret Eint based on the results from MD simulations. Dispersion, induction and hydrophobic interactions were found to be the dominating factor in Eint. These findings indicate that cost-efficient MD simulation can be employed as an important tool to predict the adsorption behavior of LOAs on carbon nanomaterials. Copyright © 2013 Elsevier Ltd. All rights reserved.

Surface acidity scales: Experimental measurements of Brønsted acidities on anatase TiO2 and comparison with coinage metal surfaces

NASA Astrophysics Data System (ADS)

Silbaugh, Trent L.; Boaventura, Jaime S.; Barteau, Mark A.

2016-08-01

The first quantitative surface acidity scale for Brønsted acids on a solid surface is presented through the use of titration-displacement and equilibrium experiments on anatase TiO2. Surface acidities of species on TiO2 correlated with gas phase acidities, as was previously observed in qualitative studies of Brønsted acid displacement on Ag(110), Cu(110) and Au(111). A 90% compression of the surface acidity scale relative to the gas phase was observed due to compensation from the covalent component of the conjugate base - surface bond. Adsorbed conjugate bases need not be completely anionic for correlations with gas phase acidities to hold. Positive and negative substituent effects, such as substituted fluorine and hydrocarbon sidechain dispersion interactions with the surface, may modify the surface acidity scale, in agreement with previous experimental and theoretical work on Au(111).

Scaleable two-component gelator from phthalic acid derivatives and primary alkyl amines: acid-base interaction in the cooperative assembly.

PubMed

Su, Ting; Hong, Kwon Ho; Zhang, Wannian; Li, Fei; Li, Qiang; Yu, Fang; Luo, Genxiang; Gao, Honghe; He, Yu-Peng

2017-06-07

A series of phthalic acid derivatives (P) with a carbon-chain tail was designed and synthesized as single-component gelators. A combination of the single-component gelator P and a non-gelling additive n-alkylamine A through acid-base interaction brought about a series of novel phase-selective two-component gelators PA. The gelation capabilities of P and PA, and the structural, morphological, thermo-dynamic and rheological properties of the corresponding gels were investigated. A molecular dynamics simulation showed that the H-bonding network in PA formed between the NH of A and the carbonyl oxygen of P altered the assembly process of gelator P. Crude PA could be synthesized through a one-step process without any purification and could selectively gel the oil phase without a typical heating-cooling process. Moreover, such a crude PA and its gelation process could be amplified to the kilogram scale with high efficiency, which offers a practical economically viable solution to marine oil-spill recovery.

Determination of kojic acid based on the interface enhancement effects of carbon nanotube/alizarin red S modified electrode.

PubMed

Liu, Jieshu; Zhou, Dazhai; Liu, Xiaopeng; Wu, Kangbing; Wan, Chidan

2009-04-01

Based on non-covalent interactions such as pi-pi stacking, van der Waals interactions and strong adsorption, alizarin red S (ARS) interacts with multi-walled carbon nanotubes (MWNT), improving the solubility of MWNT in water and resulting in a stable MWNT/ARS solution. By successive cyclic sweeps between 0.0 and 2.2V in the MWNT/ARS solution, a MWNT/ARS composite film was fabricated on an electrode surface. The electrochemical behaviors of kojic acid at the bare electrode, the ARS film-modified electrode and the MWNT/ARS film-modified electrode were investigated. It was found that the oxidation signal of kojic acid significantly increased at the MWNT/ARS film-modified electrode, which was attributed to the unique properties of MWNT such as large surface area, strong adsorptive ability and subtle electronic character. The effects of pH and cyclic number of electropolymerization were examined. A rapid, sensitive and simple electrochemical method was then developed for the determination of kojic acid. This method exhibits good linearity over the range from 4.0 x 10(-7) to 6.0 x 10(-5)mol L(-1), and the limit of detection is as low as 1.0 x 10(-7)mol L(-1). In order to validate feasibility, the MWNT/ARS film-modified electrode was used for quantitative analysis of kojic acid in food samples.

Physicochemical Profiling of α-Lipoic Acid and Related Compounds.

PubMed

Mirzahosseini, Arash; Szilvay, András; Noszál, Béla

2016-07-01

Lipoic acid, the biomolecule of vital importance following glycolysis, shows diversity in its thiol/disulfide equilibria and also in its eight different protonation forms of the reduced molecule. In this paper, lipoic acid, lipoamide, and their dihydro derivatives were studied to quantify their solubility, acid-base, and lipophilicity properties at a submolecular level. The acid-base properties are characterized in terms of six macroscopic, 12 microscopic protonation constants, and three interactivity parameters. The species-specific basicities, the pH-dependent distribution of the microspecies, and lipophilicity parameters are interpreted by various intramolecular effects, and contribute to understanding the antioxidant, chelate-forming, and enzyme cofactor behavior of the molecules observed. © 2016 Wiley-VHCA AG, Zürich.

Boronic acid-based chemical sensors for saccharides.

PubMed

Zhang, Xiao-Tai; Liu, Guang-Jian; Ning, Zhang-Wei; Xing, Guo-Wen

2017-11-27

During the past decades, the interaction between boronic acids-functionalized sensors and saccharides is of great interest in the frontier domain of the interdiscipline concerning both biology and chemistry. Various boronic acid-based sensing systems have been developed to detect saccharides and corresponding derivatives in vitro as well as in vivo, which embrace unimolecular sensors, two-component sensing ensembles, functional assemblies, and boronic acid-loaded nanomaterials or surfaces. New sensing strategies emerge in endlessly with excellent selectivity and sensitivity. In this review, several typical sensing systems were introduced and some promising examples were highlighted to enable the deep insight of saccharides sensing on the basis of boronic acids. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genome-Wide Nucleic Acid/Protein Interaction in Breast Cancer

DTIC Science & Technology

2005-04-01

Chen W, Zhang J et al: Large-scale genotyping of complex DNA. Nat Biotechnol 2003, 21(10):1233-1237. 25. Bolstad BM, Irizarry RA, Astrand M, Speed TP...2124836802660188/sup8.xls 235 Analysis of RNA-protein interactions by flow cytometry Alexander S Brodsky’*, Angus PR Johnston 2, Matt Trau 2 & Pamela A Silver1...Natl Acad Sci USA (2001) 98(23):12954-12959. genotyping using the Qbead system: A quantum dot-encoded microsphere-based assay. Nucleic Acids Res (2003

Effect of detergents, trypsin and unsaturated fatty acids on latent loquat fruit polyphenol oxidase: basis for the enzyme's activity regulation.

PubMed

Sellés-Marchart, Susana; Casado-Vela, Juan; Bru-Martínez, Roque

2007-08-15

The effects of detergents, trypsin and fatty acids on structural and functional properties of a pure loquat fruit latent polyphenol oxidase have been studied in relation to its regulation. Anionic detergents activated PPO at pH 6.0 below critical micelle concentration (cmc), but inhibited at pH 4.5 well above cmc. This behavior is due to a detergent-induced pH profile alkaline shift, accompanied by changes of intrinsic fluorescence of the protein. Gel filtration experiments demonstrate the formation of PPO-SDS mixed micelles. Partial PPO proteolysis suggest that latent PPO losses an SDS micelle-interacting region but conserves an SDS monomer-interacting site. Unsaturated fatty acids inhibit PPO at pH 4.5, the strongest being linolenic acid while the weakest was gamma-linolenic acid for both, the native and the trypsin-treated PPO. Down-regulation of PPO activity by anionic amphiphiles is discussed based on both, the pH profile shift induced upon anionic amphiphile binding and the PPO interaction with negatively charged membranes.

Syntheses, structural, computational, and thermal analysis of acid-base complexes of picric acid with N-heterocyclic bases.

PubMed

Goel, Nidhi; Singh, Udai P

2013-10-10

Four new acid-base complexes using picric acid [(OH)(NO2)3C6H2] (PA) and N-heterocyclic bases (1,10-phenanthroline (phen)/2,2';6',2"-terpyridine (terpy)/hexamethylenetetramine (hmta)/2,4,6-tri(2-pyridyl)-1,3,5-triazine (tptz)) were prepared and characterized by elemental analysis, IR, NMR and X-ray crystallography. Crystal structures provide detailed information of the noncovalent interactions present in different complexes. The optimized structures of the complexes were calculated in terms of the density functional theory. The thermolysis of these complexes was investigated by TG-DSC and ignition delay measurements. The model-free isoconversional and model-fitting kinetic approaches have been applied to isothermal TG data for kinetics investigation of thermal decomposition of these complexes.

The pH ruler: a Java applet for developing interactive exercises on acids and bases.

PubMed

Barrette-Ng, Isabelle H

2011-07-01

In introductory biochemistry courses, it is often a struggle to teach the basic concepts of acid-base chemistry in a manner that is relevant to biological systems. To help students gain a more intuitive and visual understanding of abstract acid-base concepts, a simple graphical construct called the pH ruler Java applet was developed. The applet allows students to visualize the abundance of different protonation states of diprotic and triprotic amino acids at different pH values. Using the applet, the student can drag a widget on a slider bar to change the pH and observe in real time changes in the abundance of different ionization states of this amino acid. This tool provides a means for developing more complex inquiry-based, active-learning exercises to teach more advanced topics of biochemistry, such as protein purification, protein structure and enzyme mechanism.

Ion movement in acidified, low base saturated sand soils.

Treesearch

A. Ray Harris; Douglas M. Stone

1992-01-01

Describes factors causing cation export in leachate in low base saturated forested sand soils. Reports the effects of varying acid precipitation and litter-humus treatments on ion movement and interaction.

Codes in the codons: construction of a codon/amino acid periodic table and a study of the nature of specific nucleic acid-protein interactions.

PubMed

Benyo, B; Biro, J C; Benyo, Z

2004-01-01

The theory of "codon-amino acid coevolution" was first proposed by Woese in 1967. It suggests that there is a stereochemical matching - that is, affinity - between amino acids and certain of the base triplet sequences that code for those amino acids. We have constructed a common periodic table of codons and amino acids, where the nucleic acid table showed perfect axial symmetry for codons and the corresponding amino acid table also displayed periodicity regarding the biochemical properties (charge and hydrophobicity) of the 20 amino acids and the position of the stop signals. The table indicates that the middle (2/sup nd/) amino acid in the codon has a prominent role in determining some of the structural features of the amino acids. The possibility that physical contact between codons and amino acids might exist was tested on restriction enzymes. Many recognition site-like sequences were found in the coding sequences of these enzymes and as many as 73 examples of codon-amino acid co-location were observed in the 7 known 3D structures (December 2003) of endonuclease-nucleic acid complexes. These results indicate that the smallest possible units of specific nucleic acid-protein interaction are indeed the stereochemically compatible codons and amino acids.

Contributions of separate reactions to the acid-base buffering of soils in brook floodplains (Central Forest State Reserve)

NASA Astrophysics Data System (ADS)

Sokolova, T. A.; Tolpeshta, I. I.; Rusakova, E. S.

2016-04-01

The acid-base buffering of gleyic gray-humus soils developed in brook floodplains and undisturbed southern-taiga landscapes has been characterized by the continuous potentiometric titration of soil water suspensions. During the interaction with an acid, the major amount of protons (>80%) is consumed for the displacement of exchangeable bases and the dissolution of Ca oxalates. In the O and AY horizons, Mn compounds make the major contribution (2-15%) to the acid buffering. The buffer reactions with the participation of Al compounds make up from 0.5 to 1-2% of the total buffering capacity, and the protonation of the surface OH groups of kaolinite consumes 2-3% of the total buffering capacity. The deprotonation of OH groups on the surface of Fe hydroxides (9-43%), the deprotonation of OH groups on the surface of illite crystals (3-19%), and the dissolution of unidentified aluminosilicates (9-14%) are the most significant buffer reactions whose contributions have been quantified during the interaction with a base. The contribution of the deprotonation of OH groups on the surface of kaolinite particles is lower (1-5%) because of the small specific surface area of this mineral, and that of the dissolution of Fe compounds is insignificant. In the AY horizon, the acid and base buffering of soil in the rhizosphere is higher than beyond the rhizosphere because of the higher contents of organic matter and nonsilicate Fe and Al compounds.

Enhanced dispersion of boron nitride nanosheets in aqueous media by using bile acid-based surfactants

NASA Astrophysics Data System (ADS)

Chae, Ari; Park, Soo-Jin; Min, Byunggak; In, Insik

2018-01-01

Facile noncovalent surface functionalization of hydroxylated boron nitride nanosheet (BNNS-OH) was attempted through the sonication-assisted exfoliation of h-BN in aqueous media in the presence of bile acid-based surfactants such as sodium cholic acid (SC) or sodium deoxycholic acid (SDC), resulting in SC- or SDC-BNNS-OH dispersion with high up to 2 mg ml-1 and enhanced dispersion stability due to the increased negative zeta potential. While prepared SC-BNNS-OH revealed multi-layered BNNS structures, the large lateral sizes of hundreds nanometers and clear h-BN lattice structures are very promising for the preparation and application of water-processable BNNS-based nanomaterials. It is regarded that noncovalent functionalization of BNNS-OH based on σ-π interaction between with σ-rich bile acid-based amphiphiles and π-rich BNNS is very effective to formulate multi-functional BNNS-based nanomaterials or hybrids that can be utilized in various applications where both the pristine properties of BNNS and the extra functions are simultaneously required.

Application of the fragment molecular orbital method analysis to fragment-based drug discovery of BET (bromodomain and extra-terminal proteins) inhibitors.

PubMed

Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi

2017-06-01

The molecular interactions of inhibitors of bromodomains (BRDs) were investigated. BRDs are protein interaction modules that recognizing ε-N-acetyl-lysine (εAc-Lys) motifs found in histone tails and are promising protein-protein interaction (PPI) targets. First, we analyzed a peptide ligand containing εAc-Lys to evaluate native PPIs. We then analyzed tetrahydroquinazoline-6-yl-benzensulfonamide derivatives found by fragment-based drug design (FBDD) and examined their interactions with the protein compared with the peptide ligand in terms of the inter-fragment interaction energy. In addition, we analyzed benzodiazepine derivatives that are high-affinity ligands for BRDs and examined differences in the CH/π interactions of the amino acid residues. We further surveyed changes in the charges of the amino acid residues among individual ligands, performed pair interaction energy decomposition analysis and estimated the water profile within the ligand binding site. Thus, useful insights for drug design were provided. Through these analyses and considerations, we show that the FMO method is a useful drug design tool to evaluate the process of FBDD and to explore PPI inhibitors. Copyright © 2017 Elsevier Inc. All rights reserved.

Scaling Relations for Acidity and Reactivity of Zeolites

PubMed Central

2017-01-01

Zeolites are widely applied as solid acid catalysts in various technological processes. In this work we have computationally investigated how catalytic reactivity scales with acidity for a range of zeolites with different topologies and chemical compositions. We found that straightforward correlations are limited to zeolites with the same topology. The adsorption energies of bases such as carbon monoxide (CO), acetonitrile (CH3CN), ammonia (NH3), trimethylamine (N(CH3)3), and pyridine (C5H5N) give the same trend of acid strength for FAU zeolites with varying composition. Crystal orbital Hamilton populations (COHP) analysis provides a detailed molecular orbital picture of adsorbed base molecules on the Brønsted acid sites (BAS). Bonding is dominated by strong σ donation from guest molecules to the BAS for the adsorbed CO and CH3CN complexes. An electronic descriptor of acid strength is constructed based on the bond order calculations, which is an intrinsic parameter rather than adsorption energy that contains additional contributions due to secondary effects such as van der Waals interactions with the zeolite walls. The bond order parameter derived for the CH3CN adsorption complex represents a useful descriptor for the intrinsic acid strength of FAU zeolites. For FAU zeolites the activation energy for the conversion of π-adsorbed isobutene into alkoxy species correlates well with the acid strength determined by the NH3 adsorption energies. Other zeolites such as MFI and CHA do not follow the scaling relations obtained for FAU; we ascribe this to the different van der Waals interactions and steric effects induced by zeolite framework topology. PMID:29142616

Size-Dependent Affinity of Glycine and Its Short Oligomers to Pyrite Surface: A Model for Prebiotic Accumulation of Amino Acid Oligomers on a Mineral Surface

PubMed Central

Afrin, Rehana; Ganbaatar, Narangerel; Aono, Masashi; Cleaves, H. James; Yano, Taka-aki; Hara, Masahiko

2018-01-01

The interaction strength of progressively longer oligomers of glycine, (Gly), di-Gly, tri-Gly, and penta-Gly, with a natural pyrite surface was directly measured using the force mode of an atomic force microscope (AFM). In recent years, selective activation of abiotically formed amino acids on mineral surfaces, especially that of pyrite, has been proposed as an important step in many origins of life scenarios. To investigate such notions, we used AFM-based force measurements to probe possible non-covalent interactions between pyrite and amino acids, starting from the simplest amino acid, Gly. Although Gly itself interacted with the pyrite surface only weakly, progressively larger unbinding forces and binding frequencies were obtained using oligomers from di-Gly to penta-Gly. In addition to an expected increase of the configurational entropy and size-dependent van der Waals force, the increasing number of polar peptide bonds, among others, may be responsible for this observation. The effect of chain length was also investigated by performing similar experiments using l-lysine vs. poly-l-lysine (PLL), and l-glutamic acid vs. poly-l-glutamic acid. The results suggest that longer oligomers/polymers of amino acids can be preferentially adsorbed on pyrite surfaces. PMID:29370126

Investigation into the Depth of Cure of Resin-Modified Glass-Ionomer Restorative Materials

DTIC Science & Technology

2006-08-01

al?2 studied the acid/base reaction of glass ionomer cements using Raman spectroscopy and confirmed the necessity of water availability for the acid...exchange layer." In the ion-exchange layer, Wilson et al.48 postulated the formation of an ionic bond between the polyacrylic acid and the hydroxyapatite ...investigators further detailed the interaction between the polyalkenoic acids and hydroxyapatite in a later report?’ The bonding of RMGI to dentin was

Ferrocene-Boronic Acid-Fructose Binding Based on Dual-Plate Generator-Collector Voltammetry and Square-Wave Voltammetry.

PubMed

Li, Meng; Xu, Su-Ying; Gross, Andrew J; Hammond, Jules L; Estrela, Pedro; Weber, James; Lacina, Karel; James, Tony D; Marken, Frank

2015-06-10

The interaction of ferrocene-boronic acid with fructose is investigated in aqueous 0.1 m phosphate buffer at pH 7, 8 and 9. Two voltammetric methods, based on 1) a dual-plate generator-collector micro-trench electrode (steady state) and 2) a square-wave voltammetry (transient) method, are applied and compared in terms of mechanistic resolution. A combination of experimental data is employed to obtain new insights into the binding rates and the cumulative binding constants for both the reduced ferrocene-boronic acid (pH dependent and weakly binding) and for the oxidised ferrocene-boronic acid (pH independent and strongly binding).

Evolution of acyl-ACP-thioesterases and β-ketoacyl-ACP-synthases revealed by protein-protein interactions.

PubMed

Beld, Joris; Blatti, Jillian L; Behnke, Craig; Mendez, Michael; Burkart, Michael D

2014-08-01

The fatty acid synthase (FAS) is a conserved primary metabolic enzyme complex capable of tolerating cross-species engineering of domains for the development of modified and overproduced fatty acids. In eukaryotes, acyl-acyl carrier protein thioesterases (TEs) off-load mature cargo from the acyl carrier protein (ACP), and plants have developed TEs for short/medium-chain fatty acids. We showed that engineering plant TEs into the green microalga Chlamydomonas reinhardtii does not result in the predicted shift in fatty acid profile. Since fatty acid biosynthesis relies on substrate recognition and protein-protein interactions between the ACP and its partner enzymes, we hypothesized that plant TEs and algal ACP do not functionally interact. Phylogenetic analysis revealed major evolutionary differences between FAS enzymes, including TEs and ketoacyl synthases (KSs), in which the former is present only in some species, whereas the latter is present in all, and has a common ancestor. In line with these results, TEs appeared to be selective towards their ACP partners whereas KSs showed promiscuous behavior across bacterial, plant and algal species. Based on phylogenetic analyses, in silico docking, in vitro mechanistic crosslinking and in vivo algal engineering, we propose that phylogeny can predict effective interactions between ACPs and partner enzymes.

Evolution of acyl-ACP-thioesterases and β-ketoacyl-ACP-synthases revealed by protein-protein interactions

PubMed Central

Beld, Joris; Blatti, Jillian L.; Behnke, Craig; Mendez, Michael; Burkart, Michael D.

2014-01-01

The fatty acid synthase (FAS) is a conserved primary metabolic enzyme complex capable of tolerating cross-species engineering of domains for the development of modified and overproduced fatty acids. In eukaryotes, acyl-acyl carrier protein thioesterases (TEs) off-load mature cargo from the acyl carrier protein (ACP), and plants have developed TEs for short/medium-chain fatty acids. We showed that engineering plant TEs into the green microalga Chlamydomonas reinhardtii does not result in the predicted shift in fatty acid profile. Since fatty acid biosynthesis relies on substrate recognition and protein-protein interactions between the ACP and its partner enzymes, we hypothesized that plant TEs and algal ACP do not functionally interact. Phylogenetic analysis revealed major evolutionary differences between FAS enzymes, including TEs and ketoacyl synthases (KSs), in which the former is present only in some species, whereas the latter is present in all, and has a common ancestor. In line with these results, TEs appeared to be selective towards their ACP partners whereas KSs showed promiscuous behavior across bacterial, plant and algal species. Based on phylogenetic analyses, in silico docking, in vitro mechanistic crosslinking and in vivo algal engineering, we propose that phylogeny can predict effective interactions between ACPs and partner enzymes. PMID:25110394

Biomolecular recognition and detection using gold-based nanoprobes

NASA Astrophysics Data System (ADS)

Crew, Elizabeth

The ability to control the biomolecular interactions is important for developing bioanalytical probes used in biomolecule and biomarker detections. This work aims at a fundamental understanding of the interactions and reactivities involving DNA, miRNA, and amino acids using gold-based nanoparticles as nanoprobes, which has implications for developing new strategies for the early detection of diseases, such as cancer, and controlled delivery of drugs. Surface modifications of the nanoprobes with DNA, miRNA, and amino acids and the nanoprobe directed biomolecular reactivities, such as complementary-strand binding, enzymatic cutting and amino acid interactions, have been investigated. Among various analytical techniques employed for the analysis of the biomolecule-nanoprobe interactions, surface enhanced Raman scattering spectroscopy (SERS) has been demonstrated to provide a powerful tool for real time monitoring of the DNA assembly and enzymatic cutting processes in solutions. This demonstration harnesses the "hot-spot" characteristic tuned by the interparticle biomolecular-regulated interactions and distances. The assembly of gold nanoparticles has also been exploited as sensing thin films on chemiresistor arrays for the detection of volatile organic compounds, including biomarker molecules associated with diabetes. Important findings of the nanoprobes in delivering miRNA to cells, detecting DNA hybridization kinetics, discerning chiral recognition with enantiomeric cysteines, and sensing biomarker molecules with the nanostructured thin films will be discussed, along with their implications to enhancing sensitivity, selectivity and limits of detection.

Sequentially distant but structurally similar proteins exhibit fold specific patterns based on their biophysical properties.

PubMed

Rajendran, Senthilnathan; Jothi, Arunachalam

2018-05-16

The Three-dimensional structure of a protein depends on the interaction between their amino acid residues. These interactions are in turn influenced by various biophysical properties of the amino acids. There are several examples of proteins that share the same fold but are very dissimilar at the sequence level. For proteins to share a common fold some crucial interactions should be maintained despite insignificant sequence similarity. Since the interactions are because of the biophysical properties of the amino acids, we should be able to detect descriptive patterns for folds at such a property level. In this line, the main focus of our research is to analyze such proteins and to characterize them in terms of their biophysical properties. Protein structures with sequence similarity lesser than 40% were selected for ten different subfolds from three different mainfolds (according to CATH classification) and were used for this analysis. We used the normalized values of the 49 physio-chemical, energetic and conformational properties of amino acids. We characterize the folds based on the average biophysical property values. We also observed a fold specific correlational behavior of biophysical properties despite a very low sequence similarity in our data. We further trained three different binary classification models (Naive Bayes-NB, Support Vector Machines-SVM and Bayesian Generalized Linear Model-BGLM) which could discriminate mainfold based on the biophysical properties. We also show that among the three generated models, the BGLM classifier model was able to discriminate protein sequences coming under all beta category with 81.43% accuracy and all alpha, alpha-beta proteins with 83.37% accuracy. Copyright © 2018 Elsevier Ltd. All rights reserved.

Characterization of synthetic macroporous ion-exchange resins in low-pressure cartridges and columns. Evaluation of the performance of Macro-Prep 50 S resin in the purification of anti-Klenow antibodies from goat serum.

PubMed

Dunn, L; Abouelezz, M; Cummings, L; Navvab, M; Ordunez, C; Siebert, C J; Talmadge, K W

1991-07-12

Three ion-exchange materials and one hydrophobic-interaction chromatography packing, based on a rigid macroporous polymer with large, relatively uniform pores, have been evaluated for low-pressure liquid chromatography of antibodies. These sorbents have high capacities for both small and large proteins and are mechanically, chemically, and thermally stable. Macro-Prep 50 S. CM and Q ion-exchange materials are strongly acidic, weakly acidic, and strongly basic, respectively. Protein binding and recovery, pressure-flow properties, and chemical and thermal stability were determined for each sorbent. A rapid, two-step method for the purification of anti-Klenow antibodies from goat serum was developed, based on the Macro-Prep 50 S strong-acid cation-exchange material and the Econo-Pac HIC prepacked hydrophobic-interaction cartridge.

The Acid-Base Properties and Chemical Composition of the Surface of the InSb-ZnTe System

NASA Astrophysics Data System (ADS)

Kirovskaya, I. A.; Shubenkova, E. G.; Timoshenko, O. T.; Filatova, T. N.

2008-04-01

The acid-base properties and chemical composition of the surface of solid solutions and binary components of the InSb-ZnTe system were studied by the hydrolytic adsorption, nonaqueous conductometric titration, mechanochemistry, IR spectroscopy, and mass spectrometry methods. The strength, nature, and concentration of acid centers were determined. Changes in the concentration of acid centers caused by surface exposure to CO and changes in the composition of the system were also studied. The mechanism of acid-base interactions was established. The chemical composition of the surface of system components exposed to air included adsorbed H2O molecules, OH- groups, hydrocarbon and oxocarbon compounds, and the products of surface atom oxidation. After thermal treatment in a vacuum, the composition of the surface approached the stoichiometric composition.

Adsorption of humic acids and trace metals in natural waters

NASA Technical Reports Server (NTRS)

Leung, W. H.

1982-01-01

Studies concerning the interactions between suspended hydrous iron oxide and dissolved humic acids and trace metals are reported. As a major component of dissolved organic matters and its readiness for adsorption at the solid/water interface, humic acids may play a very important role in the organometallic geochemistry of suspended sediments and in determining the fate and distribution of trace metals, pesticides and anions in natural water systems. Most of the solid phases in natural waters contain oxides and hydroxides. The most simple promising theory to describe the interactions of hydrous iron oxide interface is the surface complex formation model. In this model, the adsorptions of humic acids on hydrous iron oxide may be interpreted as complex formation of the organic bases (humic acid oxyanions) with surface Fe ions. Measurements on adsorptions were made in both fresh water and seawater. Attempts have been made to fit our data to Langmuir adsorption isotherm. Adsorption equilibrium constants were determined.

Silver ions-mediated conformational switch: facile design of structure-controllable nucleic acid probes.

PubMed

Wang, Yongxiang; Li, Jishan; Wang, Hao; Jin, Jianyu; Liu, Jinhua; Wang, Kemin; Tan, Weihong; Yang, Ronghua

2010-08-01

Conformationally constraint nucleic acid probes were usually designed by forming an intramolecular duplex based on Watson-Crick hydrogen bonds. The disadvantages of these approaches are the inflexibility and instability in complex environment of the Watson-Crick-based duplex. We report that this hydrogen bonding pattern can be replaced by metal-ligation between specific metal ions and the natural bases. To demonstrate the feasibility of this principle, two linear oligonucleotides and silver ions were examined as models for DNA hybridization assay and adenosine triphosphate detection. The both nucleic acids contain target binding sequences in the middle and cytosine (C)-rich sequences at the lateral portions. The strong interaction between Ag(+) ions and cytosines forms stable C-Ag(+)-C structures, which promises the oligonucleotides to form conformationally constraint formations. In the presence of its target, interaction between the loop sequences and the target unfolds the C-Ag(+)-C structures, and the corresponding probes unfolding can be detected by a change in their fluorescence emission. We discuss the thermodynamic and kinetic opportunities that are provided by using Ag(+) ion complexes instead of traditional Watson-Crick-based duplex. In particular, the intrinsic feature of the metal-ligation motif facilitates the design of functional nucleic acids probes by independently varying the concentration of Ag(+) ions in the medium.

Interactions between stepwise-eluted sub-fractions of fulvic acids and protons revealed by fluorescence titration combined with EEM-PARAFAC.

PubMed

Song, Fanhao; Wu, Fengchang; Guo, Fei; Wang, Hao; Feng, Weiying; Zhou, Min; Deng, Yanghui; Bai, Yingchen; Xing, Baoshan; Giesy, John P

2017-12-15

In aquatic environments, pH can control environmental behaviors of fulvic acid (FA) via regulating hydrolysis of functional groups. Sub-fractions of FA, eluted using pyrophosphate buffers with initial pHs of 3.0 (FA 3 ), 5.0 (FA 5 ), 7.0 (FA 7 ), 9.0 (FA 9 ) and 13.0 (FA 13 ), were used to explore interactions between the various, operationally defined, FA fractions and protons, by use of EEM-PARAFAC analysis. Splitting of peaks (FA 3 and FA 13 ), merging of peaks (FA 7 ), disappearance of peaks (FA 9 and FA 13 ), and red/blue-shifting of peaks were observed during fluorescence titration. Fulvic-like components were identified from FA 3 -FA 13 , and protein-like components were observed in fractions FA 9 and FA 13 . There primary compounds (carboxylic-like, phenolic-like, and protein-like chromophores) in PARAFAC components were distinguished based on acid-base properties. Dissociation constants (pK a ) for fulvic-like components with proton ranged from 2.43 to 4.13 in an acidic pH and from 9.95 to 11.27 at basic pH. These results might be due to protonation of di-carboxylate and phenolic functional groups. At basic pH, pK a values of protein-like components (9.77-10.13) were similar to those of amino acids. However, at acidic pH, pK a values of protein-like components, which ranged from 3.33 to 4.22, were 1-2units greater than those of amino acids. Results presented here, will benefit understanding of environmental behaviors of FA, as well as interactions of FA with environmental contaminants. Copyright © 2017 Elsevier B.V. All rights reserved.

Indications of hard-soft-acid-base interactions governing formation of ultra-small (r < 3 nm) digestively ripened copper oxide quantum-dots

NASA Astrophysics Data System (ADS)

Talluri, Bhusankar; Thomas, Tiju

2017-10-01

We use a soft-approach for synthesis of quasi-spherical, ultra-small, digestively-ripened, stable copper oxide QDs (radius < 3 nm). Common copper precursors (acetate, sulphite, nitrate and chloride) are explored. Triethanolamine (TEA) capping results in substantial increase of zetapotential (25 ± 5 meV); this is invariant with respect to Cu-precursor used. Relevant spectral analysis indicates that solvent and the surfactant are the most critical parameters. Hard-hard-acid-base-interaction (between CuO and TEA) based (i) mass-transfer (for pre-DR QDs) and (ii) passivation (for DR-QDs) seems to be the mechanism behind observed ceramic-DR; interestingly this is consistent with the metallic-DR-model proposed by Prasad et al. (Chem. Phys. Lett., 2012).

Kinetics of proton transfer from tetra(4-nitro-5- tert-butyl)phthalocyanine to nitrogen-containing bases in benzene

NASA Astrophysics Data System (ADS)

Petrov, O. A.; Kuzmina, E. L.; Maizlish, V. E.; Rodionov, A. V.

2014-01-01

The acid-basic interaction between tetra(4-nitro-5- tert-butyl)phthalocyanine and pyridine, 2-methylpyridine, morpholine, piperidine, n-butylamine, diethylamine, and triethylamine in benzene is studied. It is found that the intermolecular transfer of protons of NH groups from tetra(4-nitro-5- tert-butyl)phthalocyanine to morpholine and diethylamine is characterized by unusually low values of the reaction constant rates. The effect of the structure of tetra(4-nitro-5- tert-butyl)phthalocyanine and tetra(3-nitro-5- tert-butyl)phthalocyanine, and of the nature of the base on the kinetic parameters of acid-base interaction is demonstrated. A structure is proposed for complexes with the transfer of displaced phthalocyanines' protons. It is found that they undergo decomposition over time.

SURFACE MODIFICATION OF SILICA- AND CELLULOSE-BASED MICROFILTRATION MEMBRANES WITH FUNCTIONAL POLYAMINO ACIDS FOR HEAVY METAL SORPTION

EPA Science Inventory

Functionalized membranes represent a field with multiple applications. Examination of specific metal-macromolecule interactions on these surfaces presents an excellent method for characterizion of these materials. These interactions may also be exploited for heavy metal sorptio...

Characterization of humic acids by two-dimensional correlation fluorescence spectroscopy

NASA Astrophysics Data System (ADS)

Nakashima, K.; Xing, Shaoyong; Gong, Yongkuan; Miyajima, Toru

2008-07-01

We have investigated interaction between humic acids and heavy metal ions by fluorescence spectroscopy. The humic acids examined are Aldrich humic acid (AHA) and Dando humic acid (DHA), and heavy metal ions are Cu 2+ and Pb 2+. The binding constants between the humic acids and the heavy metal ions are obtained by a conventional fluorescence quenching technique. The two prominent bands in the fluorescence spectra of the humic acids give different binding constants, implying that the two bands are originated from different fluorescent species in the matrices of the humic acids. This was confirmed by two-dimensional correlation analysis based on the quenching perturbation on the fluorescence spectra. Two prominent cross peaks corresponding to the two fluorescence bands are obtained in the asynchronous maps, indicating that the two fluorescence bands belong to different species. The order of the response of the two fluorescence bands to the quenching perturbation is also elucidated based on Noda's rule.

Transport of Organic Compounds Through Porous Systems Containing Humic Acids.

PubMed

Smilek, Jiri; Sedlacek, Petr; Lastuvkova, Marcela; Kalina, Michal; Klucakova, Martina

2017-03-01

Soil pollution by the presence of different contaminants (e.g. heavy metal ions or pesticides) is one of the biggest problems worldwide. The positive affinity of natural humic acids towards these contaminants might contribute to the soil and ground water protection; therefore it is necessary to study the reactivity and barrier properties of humic acids. An original reactivity-mapping tool based on diffusion techniques designed to study the reactivity and barrier properties of polyelectrolytes was developed and tested on humic acids. The results of diffusion experiments demonstrate that the electrostatic interactions between humic acids functioning as a polyelectrolyte interpenetrated in a supporting hydrogel matrix (agarose) and cationic dye (methylene blue) as a model solute have a crucial impact on the rate of diffusion processes and on the barrier properties of hydrogels. The intensity of interactions was evaluated by fundamental diffusion parameters (effective diffusion coefficients and breakthrough time). The impact of modification of humic acids was also studied by means of diffusion experiments conducted on two types of standard humic acids (Leonardite 1S104H) and humic acids with selectively methylated carboxylic groups.

Theoretical study of interactions between cysteine and perfluoropropanoic acid in gas and aqueous phase

NASA Astrophysics Data System (ADS)

Holmes, Tiffani M.; Doskocz, Jacek; Wright, Terrance; Hill, Glake A.

The interaction of perfluoropropanoic acid (PFPA) with the amino acid cysteine was investigated using density functional theory. Previous studies suggest that the peroxisome proliferator chemical, perfluorooctanoic acid, is circulated throughout the body by way of sulfur-containing amino acids. We present conformational analysis of the interactions of PFPA, a small model of perfluorooctanoic acid, with the sulfur-containing amino acid which occur by the process of hydrogen bonding, in which the hydrogen of the sulfhydryl group interacts with the carboxyl oxygen, and the amino nitrogen forms a hydrogen bond with the hydrogen of the bond OH group of the fluorinated alkyl. We also show in our structures a recently characterized weak nonbonded interaction between divalent sulfur and a main chain carboxyl oxygen in proteins. B3LYP calculated free energies and interaction energies predict low-energy, high-interaction conformations for complex systems of perfluorinated fatty acid interactions with cysteine.

[The interaction between gamma-aminobutyric acid and other related neurotransmitters in depression].

PubMed

Li, Zhen; An, Shu-Cheng; Li, Jiang-Na

2014-06-01

Gamma-aminobutyric acid (GABA) is the major inhibitory neurotransmitter of the central nervous system (CNS) in mammalian, which involved in several mood disorders such as anxiety, depression and schizophrenia. Nowadays, there are growing evidences showed that the depression is concerned with a deficiency in brain GABA. However, there are numerous studies based on the monoamine hypothesis and glutamatergic dysfunction, while the study on GABA is relatively less and scattered. Our aim is to discuss the relationship between depression and GABA by introducing the role of GABA receptors and the interaction between GABA and 5-hydroxytryptamine, dopamine and glutamic acid. It provides new ideas for further study on the pathogenesis and therapy of depression.

Heterogeneous binary interactions of taste primaries: perceptual outcomes, physiology, and future directions.

PubMed

Wilkie, Lynn M; Capaldi Phillips, Elizabeth D

2014-11-01

Complex taste experiences arise from the combinations of five taste primaries. Here we review the literature on binary interactions of heterogeneous taste primaries, focusing on perceptual results of administering mixtures of aqueous solutions to human participants. Some interactions proved relatively consistent across tastants and experimental methods: sour acids enhanced saltiness, salts and sweeteners suppressed bitterness, sweeteners suppressed sourness, and sour acids enhanced bitterness. However, for the majority of interactions there were differential effects based on the tastants and their concentrations. Drawing conclusions about interactions with umami is currently not possible due to the low number of primary source studies investigating it and the confounding sodium ions in monosodium glutamate (MSG). Speculative physiological explanations are provided that fit the current data and suggestions for future research studies are proposed. Copyright © 2014 Elsevier Ltd. All rights reserved.

A Chemogenomic Analysis of Ionization Constants - Implications for Drug Discovery

PubMed Central

Manallack, David T.; Prankerd, Richard J.; Nassta, Gemma C.; Ursu, Oleg; Oprea, Tudor I.; Chalmers, David K.

2013-01-01

Chemogenomics methods seek to characterize the interaction between drugs and biological systems and are an important guide for the selection of screening compounds. The acid/base character of drugs has a profound influence on their affinity for the receptor, on their absorption, distribution, metabolism, excretion and toxicity (ADMET) profile and the way the drug can be formulated. In particular, the charge state of a molecule greatly influences its lipophilicity and biopharmaceutical characteristics. This study investigates the acid/base profile of human small molecule drugs, chemogenomics datasets and screening compounds including a natural products set. We estimate the ionization constants (pKa values) of these compounds and determine the identity of the ionizable functional groups in each set. We find substantial differences in acid/base profiles of the chemogenomic classes. In many cases, these differences can be linked to the nature of the target binding site and the corresponding functional groups needed for recognition of the ligand. Clear differences are also observed between the acid/base characteristics of drugs and screening compounds. For example, the proportion of drugs containing a carboxylic acid was 20%, in stark contrast to a value of 2.4% for the screening set sample. The proportion of aliphatic amines was 27% for drugs and only 3.4% for screening compounds. This suggests that there is a mismatch between commercially available screening compounds and the compounds that are likely to interact with a given chemogenomic target family. Our analysis provides a guide for the selection of screening compounds to better target specific chemogenomic families with regard to the overall balance of acids, bases and pKa distributions. PMID:23303535

Existence of both blue-shifting hydrogen bond and Lewis acid-base interaction in the complexes of carbonyls and thiocarbonyls with carbon dioxide.

PubMed

Nguyen, Tien Trung; Nguyen, Phi Hung; Tran, Thanh Hue; Minh, Tho Nguyen

2011-08-21

In this study, 16 gas phase complexes of the pairs of XCHZ and CO(2) (X = F, Cl, Br; Z = O, S) have been identified. Interaction energies calculated at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ level including both BSSE and ZPE corrections range from -5.6 to -10.5 kJ mol(-1) for XCHOCO(2) and from -5.7 to -9.1 kJ mol(-1) for XCHS···CO(2). Substitution of one H atom by one halogen in formaldehyde and thioformaldehyde reduces the interaction energy of XCHZ···CO(2), while a CH(3) substitution increases the interaction energy of both CH(3)CHO···CO(2) and CH(3)CHS···CO(2). NBO and AIM analyses also point out that the strength of Lewis acid-base interactions decreases going from >C1=S3···C6 to >C1=O3C6 and to >C1-X4···C6. This result suggests the higher capacity of solubility of thiocarbonyl compounds in scCO(2), providing an enormous potential application for designing CO(2)-philic materials based on the >C=S functional group in competition with >C=O. The Lewis acid-base interaction of the types >C=S···C, >C-Cl···C and >C-Br···C is demonstrated for the first time. The contribution of the hydrogen bonding interaction to the total interaction energy is larger for XCHS···CO(2) than for XCHO···CO(2). Upon complexation, a contraction of the C1-H2 bond length and a blue shift of its stretching frequency have been observed, as compared to the isolated monomer, indicating the existence of a blue-shifting hydrogen bond in all complexes examined. Calculated results also lend further support for the viewpoint that when acting as proton donor, a C-H bond having a weaker polarization will induce a stronger distance contraction and frequency blue shift upon complexation, and vice versa.

Biogenic and Synthetic Peptides with Oppositely Charged Amino Acids as Binding Sites for Mineralization.

PubMed

Lemloh, Marie-Louise; Altintoprak, Klara; Wege, Christina; Weiss, Ingrid M; Rothenstein, Dirk

2017-01-28

Proteins regulate diverse biological processes by the specific interaction with, e.g., nucleic acids, proteins and inorganic molecules. The generation of inorganic hybrid materials, such as shell formation in mollusks, is a protein-controlled mineralization process. Moreover, inorganic-binding peptides are attractive for the bioinspired mineralization of non-natural inorganic functional materials for technical applications. However, it is still challenging to identify mineral-binding peptide motifs from biological systems as well as for technical systems. Here, three complementary approaches were combined to analyze protein motifs consisting of alternating positively and negatively charged amino acids: (i) the screening of natural biomineralization proteins; (ii) the selection of inorganic-binding peptides derived from phage display; and (iii) the mineralization of tobacco mosaic virus (TMV)-based templates. A respective peptide motif displayed on the TMV surface had a major impact on the SiO₂ mineralization. In addition, similar motifs were found in zinc oxide- and zirconia-binding peptides indicating a general binding feature. The comparative analysis presented here raises new questions regarding whether or not there is a common design principle based on acidic and basic amino acids for peptides interacting with minerals.

Intramolecular interactions of L-phenylalanine revealed by inner shell chemical shift

NASA Astrophysics Data System (ADS)

Ganesan, Aravindhan; Wang, Feng

2009-07-01

Intramolecular interactions of the functional groups, carboxylic acid, amino, and phenyl in L-phenylalanine have been revealed through inner shell chemical shift. The chemical shift and electronic structures are studied using its derivatives, 2-phenethylamine (PEA) and 3-phenylpropionic acid (PPA), through substitutions of the functional groups on the chiral carbon Cα, i.e., carboxylic acid (-COOH) and amino (-NH2) groups. Inner shell ionization spectra of L-phenylalanine are simulated using density functional theory based B3LYP/TZVP and LB94/et-pVQZ models, which achieve excellent agreement with the most recently available synchrotron sourced x-ray photoemission spectroscopy of L-phenylalanine (Elettra, Italy). The present study reveals insight into behavior of the peptide bond (CO-NH) through chemical shift of the C1-Cα-Cβ(-Cγ) chain and intramolecular interactions with phenyl. It is found that the chemical shift of the carbonyl C1(=O) site exhibits an apparently redshift (smaller energy) when interacting with the phenyl aromatic group. Removal of the amino group (-NH2) from L-phenylalanine (which forms PPA) brings this energy on C1 close to that in L-alanine (δ <0.01 eV). Chemical environment of Cα and Cβ exhibits more significant differences in L-alanine than in the aromatic species, indicating that the phenyl group indeed affects the peptide bond in the amino acid fragment. No direct evidences are found that the carbonyl acid and amino group interact with the phenyl ring through conventional hydrogen bonds.

T:G mismatch-specific thymine-DNA glycosylase (TDG) as a coregulator of transcription interacts with SRC1 family members through a novel tyrosine repeat motif

PubMed Central

Lucey, Marie J.; Chen, Dongsheng; Lopez-Garcia, Jorge; Hart, Stephen M.; Phoenix, Fladia; Al-Jehani, Rajai; Alao, John P.; White, Roger; Kindle, Karin B.; Losson, Régine; Chambon, Pierre; Parker, Malcolm G.; Schär, Primo; Heery, David M.; Buluwela, Lakjaya; Ali, Simak

2005-01-01

Gene activation involves protein complexes with diverse enzymatic activities, some of which are involved in chromatin modification. We have shown previously that the base excision repair enzyme thymine DNA glycosylase (TDG) acts as a potent coactivator for estrogen receptor-α. To further understand how TDG acts in this context, we studied its interaction with known coactivators of nuclear receptors. We find that TDG interacts in vitro and in vivo with the p160 coactivator SRC1, with the interaction being mediated by a previously undescribed motif encoding four equally spaced tyrosine residues in TDG, each tyrosine being separated by three amino acids. This is found to interact with two motifs in SRC1 also containing tyrosine residues separated by three amino acids. Site-directed mutagenesis shows that the tyrosines encoded in these motifs are critical for the interaction. The related p160 protein TIF2 does not interact with TDG and has the altered sequence, F-X-X-X-Y, at the equivalent positions relative to SRC1. Substitution of the phenylalanines to tyrosines is sufficient to bring about interaction of TIF2 with TDG. These findings highlight a new protein–protein interaction motif based on Y-X-X-X-Y and provide new insight into the interaction of diverse proteins in coactivator complexes. PMID:16282588

Changes in properties of polyacid-modified composite resins (compomers) following storage in acidic solutions.

PubMed

Nicholson, J W; Gjorgievska, E; Bajraktarova, B; McKenzie, M A

2003-06-01

The interaction of three polyacid-modified composite resins (compomers) with various acidic storage solutions, and also water, over periods of time up to 6 months has been studied and compared with those of a glass-ionomer and a composite resin. This interaction has been shown to vary in a complex way with length of storage and nature of the acid, and citric acid was found to be the most aggressive storage medium for glass-ionomer cement, and also for the compomers. The pure composite resin, by contrast, was relatively unaffected by all of the acid solutions examined. In all acids, the compomers showed a distinct buffering effect, i.e. they increased the pH towards neutral, as did the glass-ionomer. The extent of this also varied with duration of storage and nature of the acid. The biaxial flexure strength was determined and found to be essentially unaffected by the complex chemical interactions with acidic storage solutions. Values obtained for the compomers were lower than those of the composite resin, but above those of the glass-ionomer. Fourier-transform infrared (FT-IR) spectroscopy was employed to study the changes in the compomers following storage in the aqueous media, but bands were broad and no detailed assignments could be made. There were changes in the region of the spectra associated with metal carboxylates however, and this indicates that the secondary acid-base reaction had occurred following water uptake.

Chemical Principles Revisited: Annotating Reaction Equations.

ERIC Educational Resources Information Center

Tykodi, R. J.

1987-01-01

Urges chemistry teachers to have students annotate the chemical reactions in aqueous-solutions that they see in their textbooks and witness in the laboratory. Suggests this will help students recognize the reaction type more readily. Examples are given for gas formation, precipitate formation, redox interaction, acid-base interaction, and…

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

DOE PAGES

Lin, Kuei -Han; Liao, Ben -Yang; Chang, Hao -Wei; ...

2015-12-03

Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted othermore » carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. In conclusion, our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.« less

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

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

Lin, Kuei -Han; Liao, Ben -Yang; Chang, Hao -Wei

Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted othermore » carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. In conclusion, our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.« less

Density Functional Theory (DFT) Study of Molecularly Imprinted Polymer (MIP) Methacrylic Acid (MAA) with D-Glucose

NASA Astrophysics Data System (ADS)

Wungu, T. D. K.; Marsha, S. E.; Widayani; Suprijadi

2017-07-01

In order to find an alternative biosensor material which enables to detect the glucose level, therefore in this study, the interaction between Methacrylic Acid (MAA) based Molecularly Imprinted Polymer (MIP) with D-Glucose is investigated using the Density Functional Theory (DFT). The aim of this study is to determine whether a molecule of the MAA can be functioned as a bio-sensing of glucose. In this calculation, the Gaussian 09 with B3LYP and 631+G(d) basis sets is used to calculate all electronic properties. It is found that the interaction between a molecule of MAA and a molecule of D-Glucose was observed through the shortened distance between the two molecules. The binding energy of MAA/D-glucose and the Mulliken population analysis are investigated for checking possible interaction. From analysis, the MAA based MIP can be used as a bio-sensing material.

Investigation of potent lead for acquired immunodeficiency syndrome from traditional Chinese medicine.

PubMed

Hung, Tzu-Chieh; Lee, Wen-Yuan; Chen, Kuen-Bao; Chan, Yueh-Chiu; Chen, Calvin Yu-Chian

2014-01-01

Acquired immunodeficiency syndrome (AIDS), caused by human immunodeficiency virus (HIV), has become, because of the rapid spread of the disease, a serious global problem and cannot be treated. Recent studies indicate that VIF is a protein of HIV to prevent all of human immunity to attack HIV. Molecular compounds of traditional Chinese medicine (TCM) database filtered through molecular docking and molecular dynamics simulations to inhibit VIF can protect against HIV. Glutamic acid, plantagoguanidinic acid, and Aurantiamide acetate based docking score higher with other TCM compounds selected. Molecular dynamics are useful for analysis and detection ligand interactions. According to the docking position, hydrophobic interactions, hydrogen bonding changes, and structure variation, the study try to select the efficacy of traditional Chinese medicine compound Aurantiamide acetate is better than the other for protein-ligand interactions to maintain the protein composition, based on changes in the structure.

Acid-base interactions during exocrine pancreatic secretion. Primary role for ductal bicarbonate in acinar lumen function.

PubMed

Freedman, S D; Scheele, G A

1994-03-23

The role of acid-base interactions during coordinated acinar and duct cell secretion in the exocrine pancreas is described. The sequence of acid-base events may be summarized as follows: (1) Sorting of secretory proteins and membrane components into the regulated secretory pathway of pancreatic acinar cells is triggered by acid- and calcium-induced aggregation and association mechanisms located in the trans-Golgi network. (2) Cholecystokinin-stimulated exocytosis in acinar cells releases the acidic contents of secretory granules into the acinar lumen. (3) Secretin-stimulated bicarbonate secretion from duct and duct-like cells neutralizes the acidic pH of exocytic contents, which leads to dissociation of protein aggregates and solubilization of (pro)enzymes within the acinar lumen. (4) Stimulated fluid secretion transports solubilized enzymes through the ductal system. (5) Further alkalinization of acinar lumen pH accelerates the enzymatic cleavage of the glycosyl phosphatidyl-inositol anchor associated with GP2 and thus releases the GP2/proteoglycan matrix from lumenal membranes, a process that appears to be required for vesicular retrieval of granule membranes from the apical plasma membrane and their reuse in the secretory process. We conclude that the central function of bicarbonate secretion by centroacinar and duct cells in the pancreas is to neutralize and then alkalinize the pH of the acinar lumen, sequential process that are required for (a) solubilization of secreted proteins and (b) cellular retrieval of granule membranes, respectively.

Profiling of 3696 Nuclear Receptor-Coregulator Interactions: A Resource for Biological and Clinical Discovery.

PubMed

Broekema, Marjoleine F; Hollman, Danielle A A; Koppen, Arjen; van den Ham, Henk-Jan; Melchers, Diana; Pijnenburg, Dirk; Ruijtenbeek, Rob; van Mil, Saskia W C; Houtman, René; Kalkhoven, Eric

2018-06-01

Nuclear receptors (NRs) are ligand-inducible transcription factors that play critical roles in metazoan development, reproduction, and physiology and therefore are implicated in a broad range of pathologies. The transcriptional activity of NRs critically depends on their interaction(s) with transcriptional coregulator proteins, including coactivators and corepressors. Short leucine-rich peptide motifs in these proteins (LxxLL in coactivators and LxxxIxxxL in corepressors) are essential and sufficient for NR binding. With 350 different coregulator proteins identified to date and with many coregulators containing multiple interaction motifs, an enormous combinatorial potential is present for selective NR-mediated gene regulation. However, NR-coregulator interactions have often been determined experimentally on a one-to-one basis across diverse experimental conditions. In addition, NR-coregulator interactions are difficult to predict because the molecular determinants that govern specificity are not well established. Therefore, many biologically and clinically relevant NR-coregulator interactions may remain to be discovered. Here, we present a comprehensive overview of 3696 NR-coregulator interactions by systematically characterizing the binding of 24 nuclear receptors with 154 coregulator peptides. We identified unique ligand-dependent NR-coregulator interaction profiles for each NR, confirming many well-established NR-coregulator interactions. Hierarchical clustering based on the NR-coregulator interaction profiles largely recapitulates the classification of NR subfamilies based on the primary amino acid sequences of the ligand-binding domains, indicating that amino acid sequence is an important, although not the only, molecular determinant in directing and fine-tuning NR-coregulator interactions. This NR-coregulator peptide interactome provides an open data resource for future biological and clinical discovery as well as NR-based drug design.

Modeling potential interactions of acid deposition and climate change at four watersheds in Shenandoah National Park, VA using the dynamic biogeochemical model PnET-BGC

NASA Astrophysics Data System (ADS)

Robison, A.; Scanlon, T. M.; Cosby, B. J.; Webb, J. R.; Hayhoe, K.; Galloway, J. N.

2013-12-01

The ecological threat imposed by acid deposition on watersheds in the eastern U.S. has, to a certain extent, been alleviated by the passage of the Clean Air Act and subsequent amendments. At the same time, as climate change continues to emerge as a global issue affecting temperature regimes and hydrological cycling among many other variables, new concerns are developing for these watershed ecosystems. Considering that climate change and acid deposition do not influence watersheds independently, there is an opportunity and need to examine both the potential interactions and the impacts of these two biogeochemical drivers. Long-term monitoring of four streams in Shenandoah National Park, VA has provided a favorable setting for analyzing this interaction. Deposition of both sulfur and nitrogen has significantly decreased over the past 30 years in the region. Meanwhile, all four streams have warmed significantly over the past 20-33 years at an average rate of 0.07 oC yr-1, a trend that is closely tied to atmospheric warming rather than changes in hydrology. We applied a dynamic biogeochemical model (PnET-BGC) to these four watersheds to a) investigate how climate change will affect watershed response to reduced acid deposition; b) identify the key processes through which this interaction will be manifested; and c) examine how differences in watershed characteristics (e.g. bedrock and soil properties) affect the response to these two biogeochemical drivers. Included in model application are statistically downscaled climate projections of temperature maximums and minimums, precipitation, and solar radiation. Results will be used to assess the relative impact of these climate variables in regulating stream acid-base status. This study will also provide insight into the future ecological health of these ecosystems, primarily through examination of aquatic habitat suitability based on temperature and acidity.

Interaction between MTHFR 677C>T and periconceptional folic acid supplementation in the risk of Hypospadias.

PubMed

Dokter, Elisabeth M J; van Rooij, Iris A L M; Wijers, Charlotte H W; Groothuismink, Johanne M; van der Biezen, Jan Jaap; Feitz, Wout F J; Roeleveld, Nel; van der Zanden, Loes F M

2016-04-01

Hypospadias is a congenital malformation with both environmental factors and genetic predisposition involved in the pathogenesis. The role of maternal periconceptional folic acid supplement use in the development of hypospadias is unclear. As folate levels may also be influenced by the C677T polymorphism in the methylenetetrahydrofolate reductase (MTHFR) gene, we hypothesize that a gene-environment interaction between this polymorphism and folic acid use is involved in the etiology of hypospadias. We conducted a case-control study among 855 hypospadias cases and 713 population-based controls from the AGORA data- and biobank. Folic acid supplement use was derived from maternal questionnaires and infant and maternal DNA was used to determine the MTHFR C677T polymorphism using Taqman assays. We performed separate analyses for different hypospadias phenotypes (anterior/middle/posterior). Hypospadias was neither associated with folic acid use or the MTHFR C677T polymorphism, nor with their interaction. However, we did find an association with middle hypospadias when no supplements were used (odds ratio = 1.6; 95% confidence interval, 1.1-2.4), especially in infants carrying the CT/TT genotype (odds ratio = 2.5; 95% confidence interval, 1.4-4.7). In addition, more infants with these genotypes seemed to have posterior hypospadias, regardless of folic acid use. Our study does not suggest a major role for folic acid supplements or the MTHFR C677T polymorphism in the etiology of hypospadias in general, but not using folic acid and/or carrying the MTHFR C677T polymorphism may be associated with middle and posterior hypospadias. Therefore, we stress the importance of studying gene-environment interactions preferably in stratified analyses for different hypospadias phenotypes. © 2016 Wiley Periodicals, Inc.

Insights into the structure-function relationship of brown plant hopper resistance protein, Bph14 of rice plant: a computational structural biology approach.

PubMed

Gupta, Manoj Kumar; Vadde, Ramakrishna; Donde, Ravindra; Gouda, Gayatri; Kumar, Jitendra; Nayak, Subhashree; Jena, Mayabini; Behera, Lambodar

2018-05-02

Brown plant hopper (BPH) is one of the major destructive insect pests of rice, causing severe yield loss. Thirty-two BPH resistance genes have been identified in cultivated and wild species of rice Although, molecular mechanism of rice plant resistance against BPH studied through map-based cloning, due to non-existence of NMR/crystal structures of Bph14 protein, recognition of leucine-rich repeat (LRR) domain and its interaction with different ligands are poorly understood. Thus, in the present study, in silico approach was adopted to predict three-dimensional structure of LRR domain of Bph14 using comparative modelling approach followed by interaction study with jasmonic and salicylic acids. LRR domain along with LRR-jasmonic and salicylic acid complexes were subjected to dynamic simulation using GROMACS, individually, for energy minimisation and refinement of the structure. Final binding energy of jasmonic and salicylic acid with LRR domain was calculated using MM/PBSA. Free-energy landscape analysis revealed that overall stability of LRR domain of Bph14 is not much affected after forming complex with jasmonic and salicylic acid. MM/PBSA analysis revealed that binding affinities of LRR domain towards salicylic acid is higher as compared to jasmonic acid. Interaction study of LRR domain with salicylic acid and jasmonic acid reveals that THR987 of LRR form hydrogen bond with both complexes. Thus, THR987 plays active role in the Bph14 and phytochemical interaction for inducing resistance in rice plant against BPH. In future, Bph14 gene and phytochemicals could be used in BPH management and development of novel resistant varieties for increasing rice yield.

Peroxidase-like activity of the Co3O4 nanoparticles used for biodetection and evaluation of antioxidant behavior

NASA Astrophysics Data System (ADS)

Jia, Huimin; Yang, Dongfang; Han, Xiangna; Cai, Junhui; Liu, Haiying; He, Weiwei

2016-03-01

Nanostructured enzyme mimics are of great interest as promising alternatives to artificial enzymes for biomedical and catalytic applications. Studying the chemical interactions between antioxidants and nano-enzymes may result in a better understanding of the antioxidant capability of antioxidants and may help improve the function of artificial enzymes to better mimic natural enzymes. In this study, using Co3O4 nanoparticles (NPs) as peroxidase mimics to catalyze the oxidation of chromophoric substrates by H2O2, we developed a platform that acts as a biosensor for hydrogen peroxide and glucose and that can study the inhibitory effects of natural antioxidants on peroxidase mimics. This method can be applied specifically to glucose detection in real samples. Three natural antioxidants, gallic acid (GA), tannic acid (TA), and ascorbic acid (AA), were compared for their antioxidant capabilities. We found that these three antioxidants efficiently inhibit peroxidase-like activity with concentration dependence. The antioxidants showed different efficiencies, in the following order: tannic acid > gallic acid > ascorbic acid. They also showed distinct modes of inhibition based on different interaction mechanisms. This study serves as a proof-of-concept that nano-enzyme mimics can be used to evaluate antioxidant capabilities and to screen enzyme inhibitors.Nanostructured enzyme mimics are of great interest as promising alternatives to artificial enzymes for biomedical and catalytic applications. Studying the chemical interactions between antioxidants and nano-enzymes may result in a better understanding of the antioxidant capability of antioxidants and may help improve the function of artificial enzymes to better mimic natural enzymes. In this study, using Co3O4 nanoparticles (NPs) as peroxidase mimics to catalyze the oxidation of chromophoric substrates by H2O2, we developed a platform that acts as a biosensor for hydrogen peroxide and glucose and that can study the inhibitory effects of natural antioxidants on peroxidase mimics. This method can be applied specifically to glucose detection in real samples. Three natural antioxidants, gallic acid (GA), tannic acid (TA), and ascorbic acid (AA), were compared for their antioxidant capabilities. We found that these three antioxidants efficiently inhibit peroxidase-like activity with concentration dependence. The antioxidants showed different efficiencies, in the following order: tannic acid > gallic acid > ascorbic acid. They also showed distinct modes of inhibition based on different interaction mechanisms. This study serves as a proof-of-concept that nano-enzyme mimics can be used to evaluate antioxidant capabilities and to screen enzyme inhibitors. Electronic supplementary information (ESI) available: Fig. S1-S6. See DOI: 10.1039/c6nr00860g

Seven organic salts assembled from hydrogen-bonds of N-H⋯O, O-H⋯O, and C-H⋯O between acidic compounds and bis(benzimidazole)

NASA Astrophysics Data System (ADS)

Jin, Shouwen; Liu, Hui; Gao, Xin Jun; Lin, Zhanghui; Chen, Guqing; Wang, Daqi

2014-10-01

Seven crystalline organic acid-base adducts derived from 1,4-bis(benzimidazol-2-yl)butane/1,2-bis(2-benzimidazolyl)-1,2-ethanediol and acidic components (picric acid, 2-hydroxy-5-(phenyldiazenyl)benzoic acid, 5-sulfosalicylic acid, oxalic acid, and 1,5-naphthalenedisulfonic acid) were prepared and characterized by the single crystal X-ray diffraction analysis, IR, mp, and elemental analysis. All of the seven compounds are organic salts involving proton transfer from the acidic components to the bis(benzimidazole). For the salt 3, although a competing carboxyl group is present, it has been observed that only the proton at the -SO3H group is deprotonized rather than the H at the COOH. While in the salt 7, both COOH and SO3H were ionized to exhibit a valence number of -2. For 4, the oxalic acid existed as unionized molecule, monoanion, and dianion simultaneously in one compound. All supramolecular architectures of the organic salts 1-7 involve extensive intermolecular N-H⋯O, O-H⋯O, and C-H⋯O hydrogen bonds as well as other noncovalent interactions. Since the potentially hydrogen bonding phenol group is present in the ortho position to the carboxyl group in 2, 3, and 7, it forms the more facile intramolecular O-H⋯O hydrogen bonding. The role of weak and strong noncovalent interactions in the crystal packing is ascertained. These weak interactions combined, all the complexes displayed 3D framework structure.

Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes.

PubMed

Kondo, Jiro; Westhof, Eric

2011-10-01

Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide-protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson-Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson-Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues.

Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide–protein complexes

PubMed Central

Kondo, Jiro; Westhof, Eric

2011-01-01

Nucleotide bases are recognized by amino acid residues in a variety of DNA/RNA binding and nucleotide binding proteins. In this study, a total of 446 crystal structures of nucleotide–protein complexes are analyzed manually and pseudo pairs together with single and bifurcated hydrogen bonds observed between bases and amino acids are classified and annotated. Only 5 of the 20 usual amino acid residues, Asn, Gln, Asp, Glu and Arg, are able to orient in a coplanar fashion in order to form pseudo pairs with nucleotide bases through two hydrogen bonds. The peptide backbone can also form pseudo pairs with nucleotide bases and presents a strong bias for binding to the adenine base. The Watson–Crick side of the nucleotide bases is the major interaction edge participating in such pseudo pairs. Pseudo pairs between the Watson–Crick edge of guanine and Asp are frequently observed. The Hoogsteen edge of the purine bases is a good discriminatory element in recognition of nucleotide bases by protein side chains through the pseudo pairing: the Hoogsteen edge of adenine is recognized by various amino acids while the Hoogsteen edge of guanine is only recognized by Arg. The sugar edge is rarely recognized by either the side-chain or peptide backbone of amino acid residues. PMID:21737431

Amino Acids of Epstein-Barr Virus Nuclear Antigen 3A Essential for Repression of Jκ-Mediated Transcription and Their Evolutionary Conservation

PubMed Central

Dalbiès-Tran, Rozenn; Stigger-Rosser, Evelyn; Dotson, Travis; Sample, Clare E.

2001-01-01

Epstein-Barr virus (EBV) nuclear antigen 3A (EBNA-3A) is essential for virus-mediated immortalization of B lymphocytes in vitro and is believed to regulate transcription of cellular and/or viral genes. One known mechanism of regulation is through its interaction with the cellular transcription factor Jκ. This interaction downregulates transcription mediated by EBNA-2 and Jκ. To identify the amino acids that play a role in this interaction, we have generated mutant EBNA-3A proteins. A mutant EBNA-3A protein in which alanine residues were substituted for amino acids 199, 200, and 202 no longer downregulated transcription. Surprisingly, this mutant protein remained able to coimmunoprecipitate with Jκ. Using a reporter gene assay based on the recruitment of Jκ by various regions spanning EBNA-3A, we have shown that this mutation abolished binding of Jκ to the N-proximal region (amino acids 125 to 222) and that no other region of EBNA-3A alone was sufficient to mediate an association with Jκ. To determine the biological significance of the interaction of EBNA-3A with Jκ, we have studied its conservation in the simian lymphocryptovirus herpesvirus papio (HVP) by cloning HVP-3A, the homolog of EBNA-3A encoded by this virus. This 903-amino-acid protein exhibited 37% identity with its EBV counterpart, mainly within the amino-terminal half. HVP-3A also interacted with Jκ through a region located between amino acids 127 and 223 and also repressed transcription mediated through EBNA-2 and Jκ. The evolutionary conservation of this function, in proteins that have otherwise significantly diverged, argues strongly for an important biological role in virus-mediated immortalization of B lymphocytes. PMID:11119577

Deuterium isotope effect on 13C chemical shifts of tetrabutylammonium salts of Schiff bases amino acids.

PubMed

Rozwadowski, Z

2006-09-01

Deuterium isotope effects on 13C chemical shift of tetrabutylammonium salts of Schiff bases, derivatives of amino acids (glycine, L-alanine, L-phenylalanine, L-valine, L-leucine, L-isoleucine and L-methionine) and various ortho-hydroxyaldehydes in CDCl3 have been measured. The results have shown that the tetrabutylammonium salts of the Schiff bases amino acids, being derivatives of 2-hydroxynaphthaldehyde and 3,5-dibromosalicylaldehyde, exist in the NH-form, while in the derivatives of salicylaldehyde and 5-bromosalicylaldehyde a proton transfer takes place. The interactions between COO- and NH groups stabilize the proton-transferred form through a bifurcated intramolecular hydrogen bond. Copyright (c) 2006 John Wiley & Sons, Ltd.

Gallic acid-based indanone derivative interacts synergistically with tetracycline by inhibiting efflux pump in multidrug resistant E. coli.

PubMed

Dwivedi, Gaurav Raj; Tiwari, Nimisha; Singh, Aastha; Kumar, Akhil; Roy, Sudeep; Negi, Arvind Singh; Pal, Anirban; Chanda, Debabrata; Sharma, Ashok; Darokar, Mahendra P

2016-03-01

The purpose of the present study was to study the synergy potential of gallic acid-based derivatives in combination with conventional antibiotics using multidrug resistant cultures of Escherichia coli. Gallic acid-based derivatives significantly reduced the MIC of tetracycline against multidrug resistant clinical isolate of E. coli. The best representative, 3-(3',4,'5'-trimethoxyphenyl)-4,5,6-trimethoxyindanone-1, an indanone derivative of gallic acid, was observed to inhibit ethidium bromide efflux and ATPase which was also supported by in silico docking. This derivative extended the post-antibiotic effect and decreased the mutation prevention concentration of tetracycline. This derivative in combination with TET was able to reduce the concentration of TNFα up to 18-fold in Swiss albino mice. This derivative was nontoxic and well tolerated up to 300 mg/kg dose in subacute oral toxicity study in mice. This is the first report of gallic acid-based indanone derivative as drug resistance reversal agent acting through ATP-dependent efflux pump inhibition.

Peptide array-based interaction assay of solid-bound peptides and anchorage-dependant cells and its effectiveness in cell-adhesive peptide design.

PubMed

Kato, Ryuji; Kaga, Chiaki; Kunimatsu, Mitoshi; Kobayashi, Takeshi; Honda, Hiroyuki

2006-06-01

Peptide array, the designable peptide library covalently synthesized on cellulose support, was applied to assay peptide-cell interaction, between solid-bound peptides and anchorage-dependant cells, to study objective peptide design. As a model case, cell-adhesive peptides that could enhance cell growth as tissue engineering scaffold material, was studied. On the peptide array, the relative cell-adhesion ratio of NIH/3T3 cells was 2.5-fold higher on the RGDS (Arg-Gly-Asp-Ser) peptide spot as compared to the spot with no peptide, thus indicating integrin-mediated peptide-cell interaction. Such strong cell adhesion mediated by the RGDS peptide was easily disrupted by single residue substitution on the peptide array, thus indicating that the sequence recognition accuracy of cells was strictly conserved in our optimized scheme. The observed cellular morphological extension with active actin stress-fiber on the RGD motif-containing peptide supported our strategy that peptide array-based interaction assay of solid-bound peptide and anchorage-dependant cells (PIASPAC) could provide quantitative data on biological peptide-cell interaction. The analysis of 180 peptides obtained from fibronectin type III domain (no. 1447-1629) yielded 18 novel cell-adhesive peptides without the RGD motif. Taken together with the novel candidates, representative rules of ineffective amino acid usage were obtained from non-effective candidate sequences for the effective designing of cell-adhesive peptides. On comparing the amino acid usage of the top 20 and last 20 peptides from the 180 peptides, the following four brief design rules were indicated: (i) Arg or Lys of positively charged amino acids (except His) could enhance cell adhesion, (ii) small hydrophilic amino acids are favored in cell-adhesion peptides, (iii) negatively charged amino acids and small amino acids (except Gly) could reduce cell adhesion, and (iv) Cys and Met could be excluded from the sequence combination since they have less influence on the peptide design. Such rules that are indicative of the nature of the functional peptide sequence can be obtained only by the mass comparison analysis of PIASPAC using peptide array. By following such indicative rules, numerous amino acid combinations can be effectively screened for further examination of novel peptide design.

Prediction of Ras-effector interactions using position energy matrices.

PubMed

Kiel, Christina; Serrano, Luis

2007-09-01

One of the more challenging problems in biology is to determine the cellular protein interaction network. Progress has been made to predict protein-protein interactions based on structural information, assuming that structural similar proteins interact in a similar way. In a previous publication, we have determined a genome-wide Ras-effector interaction network based on homology models, with a high accuracy of predicting binding and non-binding domains. However, for a prediction on a genome-wide scale, homology modelling is a time-consuming process. Therefore, we here successfully developed a faster method using position energy matrices, where based on different Ras-effector X-ray template structures, all amino acids in the effector binding domain are sequentially mutated to all other amino acid residues and the effect on binding energy is calculated. Those pre-calculated matrices can then be used to score for binding any Ras or effector sequences. Based on position energy matrices, the sequences of putative Ras-binding domains can be scanned quickly to calculate an energy sum value. By calibrating energy sum values using quantitative experimental binding data, thresholds can be defined and thus non-binding domains can be excluded quickly. Sequences which have energy sum values above this threshold are considered to be potential binding domains, and could be further analysed using homology modelling. This prediction method could be applied to other protein families sharing conserved interaction types, in order to determine in a fast way large scale cellular protein interaction networks. Thus, it could have an important impact on future in silico structural genomics approaches, in particular with regard to increasing structural proteomics efforts, aiming to determine all possible domain folds and interaction types. All matrices are deposited in the ADAN database (http://adan-embl.ibmc.umh.es/). Supplementary data are available at Bioinformatics online.

A study of the interaction of thioindigo dye, with several inorganic host materials

NASA Astrophysics Data System (ADS)

Ramirez, Alejandra

Maya Blue has been the focus of numerous studies and is believed to be a mixture of palygorskite clay and indigo dye.1,2 Several derivatives of this pigment have been developed with intriguing properties. For instance, the dye thioindigo reacts with the palygorskite clay to exhibit a broad range of colors from red to blue under UV-Vis excitation. Based on FT-Raman and computer simulation, previous work performed in our group could relate indigo and thioindigo interaction to the aluminum sites in the framework. 3,4 The work performed with other inorganic host materials such as, layer structures and zeolites have displayed reversible acid indicator properties, similar to the ones observed in concentrated sulfuric acid. Spectroscopic analyses and computer modeling of the above mentioned interactions have been evaluated. Results obtained by these techniques showed that in dehydrated materials a disturbance of thioindigo C=O at 1655 cm-1 to lower frequencies occurs, due to the C=O---Lewis acid sites (LAS) interaction. In the presence of water, a smaller C=O shift due to C=O---HO(H)LAS was observed. Moreover, displacement of the 001 plane in some layer materials confirmed the effect of water on the color changes displayed by UV-Vis spectroscopy. Based on these premises, it was concluded that weak electron donor-acceptor interactions took place between thioindigo functional groups (electron donors) and LAS of the aluminum silicate framework (electron acceptor). LAS (extra-framework aluminum and exchangeable cations) high hydration enthalpy made them extremely susceptible to water molecules (electron donors); generating a hydrogen bond between the two sites. The reversibility of these chromatic hybrid materials could have potential applications as water sensors and charge transfer photosensitizers in nanocrystalline TiO2-based solar cells.

Light-emitting self-assembled peptide nucleic acids exhibit both stacking interactions and Watson-Crick base pairing.

PubMed

Berger, Or; Adler-Abramovich, Lihi; Levy-Sakin, Michal; Grunwald, Assaf; Liebes-Peer, Yael; Bachar, Mor; Buzhansky, Ludmila; Mossou, Estelle; Forsyth, V Trevor; Schwartz, Tal; Ebenstein, Yuval; Frolow, Felix; Shimon, Linda J W; Patolsky, Fernando; Gazit, Ehud

2015-04-01

The two main branches of bionanotechnology involve the self-assembly of either peptides or DNA. Peptide scaffolds offer chemical versatility, architectural flexibility and structural complexity, but they lack the precise base pairing and molecular recognition available with nucleic acid assemblies. Here, inspired by the ability of aromatic dipeptides to form ordered nanostructures with unique physical properties, we explore the assembly of peptide nucleic acids (PNAs), which are short DNA mimics that have an amide backbone. All 16 combinations of the very short di-PNA building blocks were synthesized and assayed for their ability to self-associate. Only three guanine-containing di-PNAs-CG, GC and GG-could form ordered assemblies, as observed by electron microscopy, and these di-PNAs efficiently assembled into discrete architectures within a few minutes. The X-ray crystal structure of the GC di-PNA showed the occurrence of both stacking interactions and Watson-Crick base pairing. The assemblies were also found to exhibit optical properties including voltage-dependent electroluminescence and wide-range excitation-dependent fluorescence in the visible region.

Utilizing Intrinsic Properties of Polyaniline to Detect Nucleic Acid Hybridization through UV-Enhanced Electrostatic Interaction.

PubMed

Sengupta, Partha Pratim; Gloria, Jared N; Amato, Dahlia N; Amato, Douglas V; Patton, Derek L; Murali, Beddhu; Flynt, Alex S

2015-10-12

Detection of specific RNA or DNA molecules by hybridization to "probe" nucleic acids via complementary base-pairing is a powerful method for analysis of biological systems. Here we describe a strategy for transducing hybridization events through modulating intrinsic properties of the electroconductive polymer polyaniline (PANI). When DNA-based probes electrostatically interact with PANI, its fluorescence properties are increased, a phenomenon that can be enhanced by UV irradiation. Hybridization of target nucleic acids results in dissociation of probes causing PANI fluorescence to return to basal levels. By monitoring restoration of base PANI fluorescence as little as 10(-11) M (10 pM) of target oligonucleotides could be detected within 15 min of hybridization. Detection of complementary oligos was specific, with introduction of a single mismatch failing to form a target-probe duplex that would dissociate from PANI. Furthermore, this approach is robust and is capable of detecting specific RNAs in extracts from animals. This sensor system improves on previously reported strategies by transducing highly specific probe dissociation events through intrinsic properties of a conducting polymer without the need for additional labels.

Design and Mechanism of Tetrahydrothiophene-based GABA Aminotransferase Inactivators

PubMed Central

Le, Hoang V.; Hawker, Dustin D.; Wu, Rui; Doud, Emma; Widom, Julia; Sanishvili, Ruslan; Liu, Dali; Kelleher, Neil L.; Silverman, Richard B.

2015-01-01

Low levels of γ-aminobutyric acid (GABA), one of two major neurotransmitters that regulate brain neuronal activity, are associated with many neurological disorders, such as epilepsy, Parkinson’s disease, Alzheimer’s disease, Huntington’s disease, and cocaine addiction. One of the main methods to raise the GABA level in human brain is to use small molecules that cross the blood-brain barrier and inhibit the activity of γ-aminobutyric acid aminotransferase (GABA-AT), the enzyme that degrades GABA. We have designed a series of conformationally-restricted, tetrahydrothiophene-based GABA analogs with a properly-positioned leaving group that could facilitate a ring-opening mechanism, leading to inactivation of GABA-AT. One compound in the series is eight times more efficient an inactivator of GABA-AT than vigabatrin, the only FDA-approved inactivator of GABA-AT. Our mechanistic studies show that the compound inactivates GABA-AT by a new mechanism. The metabolite resulting from inactivation does not covalently bind to amino acid residues of GABA-AT but stays in the active site via H-bond interactions with Arg-192, a π-π interaction with Phe-189, and a weak nonbonded S···O=C interaction with Glu-270, thereby inactivating the enzyme. PMID:25781189

Density functional theory based probe of the affinity interaction of saccharide ligands with extra-cellular sialic acid residues.

PubMed

Patel, Anjali; Tiwari, Sanjay; Jha, Prafulla K

2018-05-10

Changes in glycosylation pattern leads to malignant transformations among the cells. In combination with upregulated actions of sialyltransferases, it ultimately leads to differential expression of sialic acid (SA) at cell surface. Given its negative charge and localization to extracellular domain, SA has been exploited for the development of targeted theranostics using approaches, such as, cationization and appending recognition saccharides on carrier surface. In this study, we have performed quantum mechanical calculations based on density functional theory (DFT) to study the interaction of saccharides with extracellular SA. Gradient-corrected DFT with the three parameter function (B3) was utilized for the calculation of Lee-Yang-Parr (LYP) correlation function. Atomic charge, vibrational frequencies and energy of the optimized structures were calculated through B3LYP. Our calculations demonstrate a stronger galactose-sialic acid interaction at tumour-relevant low pH and hyperthermic condition. These results support the application of pH responsive delivery vehicles and targeted hyperthermic chemotherapy for eradicating solid tumour deposits. These studies, conducted a priori, can guide the formulation scientists over appropriate choice of ligands and their applications in the design of 'smart' theranostic tools.

Interactions between Plant Metabolites Affect Herbivores: A Study with Pyrrolizidine Alkaloids and Chlorogenic Acid.

PubMed

Liu, Xiaojie; Vrieling, Klaas; Klinkhamer, Peter G L

2017-01-01

The high structural diversity of plant metabolites suggests that interactions among them should be common. We investigated the effects of single metabolites and combinations of plant metabolites on insect herbivores. In particular we studied the interacting effects of pyrrolizidine alkaloid (PAs), and chlorogenic acid (CGA), on a generalist herbivore, Frankliniella occidentalis. We studied both the predominantly occurring PA N -oxides and the less frequent PA free bases. We found antagonistic effects between CGA and PA free bases on thrips mortality. In contrast PA N -oxides showed synergistic interactions with CGA. PA free bases caused a higher thrips mortality than PA N -oxides while the reverse was through for PAs in combination with CGA. Our results provide an explanation for the predominate storage of PA N -oxides in plants. We propose that antagonistic interactions represent a constraint on the accumulation of plant metabolites, as we found here for Jacobaea vulgaris . The results show that the bioactivity of a given metabolite is not merely dependent upon the amount and chemical structure of that metabolite, but also on the co-occurrence metabolites in, e.g., plant cells, tissues and organs. The significance of this study is beyond the concerns of the two specific groups tested here. The current study is one of the few studies so far that experimentally support the general conception that the interactions among plant metabolites are of great importance to plant-environment interactions.

Selenium speciation in acidic environmental samples: application to acid rain-soil interaction at Mount Etna volcano.

PubMed

Floor, Geerke H; Iglesías, Mònica; Román-Ross, Gabriela; Corvini, Philippe F X; Lenz, Markus

2011-09-01

Speciation plays a crucial role in elemental mobility. However, trace level selenium (Se) speciation analyses in aqueous samples from acidic environments are hampered due to adsorption of the analytes (i.e. selenate, selenite) on precipitates. Such solid phases can form during pH adaptation up till now necessary for chromatographic separation. Thermodynamic calculations in this study predicted that a pH<4 is needed to prevent precipitation of Al and Fe phases. Therefore, a speciation method with a low pH eluent that matches the natural sample pH of acid rain-soil interaction samples from Etna volcano was developed. With a mobile phase containing 20mM ammonium citrate at pH 3, selenate and selenite could be separated in different acidic media (spiked water, rain, soil leachates) in <10 min with a LOQ of 0.2 μg L(-1) using (78)Se for detection. Applying this speciation analysis to study acid rain-soil interaction using synthetic rain based on H(2)SO(4) and soil samples collected at the flanks of Etna volcano demonstrated the dominance of selenate over selenite in leachates from samples collected close to the volcanic craters. This suggests that competitive behavior with sulfate present in acid rain might be a key factor in Se mobilization. The developed speciation method can significantly contribute to understand Se cycling in acidic, Al/Fe rich environments. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

Jin, Xin; Zhou, Pei; Zheng, Chunying

A copper complex ([Cu(py){sub 2}(L){sub 2}]·2CH{sub 3}OH){sub n} (HL=(E)-3-(3-hydroxyl-phenyl)-acrylic acid) (1) with acrylic acid ligand was synthesized and structurally analyzed by IR, elemental analysis, TGA and the single-crystal X-ray diffraction methods. It is the first time to find that phenolic hydroxyl of L coordinates to Cu(II). Complex 1 exhibits 1D chain by a double-bridge of ligands, and the 3D supramolecular framework in complex 1 is constructed by π–π stacking interactions and van der Waals Contacts among the 1D chains. The magnetic properties of complex 1 have been studied. - Graphical abstract: A copper complex based on (E)-3-(3-hydroxyl-phenyl)-acrylic acid in amore » novel coordinated way was synthesized and a ferromagnetic exchange interactions between neighboring Cu(II) ions has be achieved. - Highlights: • A new copper complex with acrylic acid ligand was synthesized and analyzed. • We find the phenolic hydroxyl of MCA ligand coordinates to metal ion firstly. • A ferromagnetic exchange interactions between Cu(II) ions has been achieved.« less

Surface properties of calcium and magnesium oxide nanopowders grafted with unsaturated carboxylic acids studied with inverse gas chromatography.

PubMed

Maciejewska, Magdalena; Krzywania-Kaliszewska, Alicja; Zaborski, Marian

2012-09-28

Inverse gas chromatography (IGC) was applied at infinite dilution to evaluate the surface properties of calcium and magnesium oxide nanoparticles and the effect of surface grafted unsaturated carboxylic acid on the nanopowder donor-acceptor characteristics. The dispersive components (γ(s)(D)) of the free energy of the nanopowders were determined by Gray's method, whereas their tendency to undergo specific interactions was estimated based on the electron donor-acceptor approach presented by Papirer. The calcium and magnesium oxide nanoparticles exhibited high surface energies (79 mJ/m² and 74 mJ/m², respectively). Modification of nanopowders with unsaturated carboxylic acids decreased their specific adsorption energy. The lowest value of γ(s)(D) was determined for nanopowders grafted with undecylenic acid, approximately 55 mJ/m². The specific interactions were characterised by the molar free energy (ΔG(A)(SP)) and molar enthalpy (ΔH(A)(SP)) of adsorption as well as the donor and acceptor interaction parameters (K(A), K(D)). Copyright © 2012 Elsevier B.V. All rights reserved.

Interactions Between Diet and Exposure to Secondhand Smoke on Metabolic Syndrome Among Children: NHANES 2007-2010.

PubMed

Moore, Brianna F; Clark, Maggie L; Bachand, Annette; Reynolds, Stephen J; Nelson, Tracy L; Peel, Jennifer L

2016-01-01

Metabolic syndrome is likely influenced by a complex interaction between exposure to secondhand smoke (SHS) and diet, but no studies have evaluated this relationship. This study aimed to investigate the interaction between diet and exposure to SHS on metabolic syndrome among 12-19 year olds. We used weighted logistic regression, adjusting for potential confounders, to examine interaction of these risk factors on the prevalence of metabolic syndrome among 12-19 year olds participating in the National Health and Nutrition Examination Survey (2007-2010). Interaction was assessed by introducing product terms between SHS (4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol, cotinine, and self-report) and the individual nutrients (dietary fiber, eicosapentaenoic acid, docosahexaenoic acid, vitamin C, and vitamin E) and nutrient patterns in separate models; the relative excess risk due to interaction was used to evaluate interaction on the additive scale. The joint effect between high exposure to SHS and low levels of certain nutrients (vitamin E and omega-3 polyunsaturated fatty acids) on metabolic syndrome risk was greater than would be expected from the effects of the individual exposures alone (for example, relative excess risk due to interaction for SHS and vitamin E = 7.5; 95% confidence interval, 2.5-17.8). Prevention strategies for metabolic syndrome aimed at reducing SHS exposures and improving diet quality may exceed the expected benefits based on targeting these risk factors separately.

Adhesion of epoxy primer to hydrotalcite conversion coated AA2024

NASA Astrophysics Data System (ADS)

Leggat, Robert Benton, III

Hydrotalcite-based (HT) conversion coatings are being developed as an environmentally benign alternative to chromate conversion coatings (CCC). Accelerated exposure tests were conducted on epoxy primed, HT-modified AA2024 to gauge service performance. HT-based conversion coatings did not perform as well as the CCC when used with an epoxy primer. The current HT chemistries are optimized for stand-alone corrosion protection, however additional research into the primer/HT interactions is necessary before they can be implemented within a coating scheme. The relative contribution of mechanical and physico-chemical interactions in controlling adhesion has been investigated in this study. Practical adhesion tests were used to assess the dry and wet bond strength of epoxy primer on HT coatings using the pull-off tensile strength (POTS) as the figure of merit. The practical adhesion of HT coated samples generally fell between that observed for the CCC and bare AA2024. Laboratory testing was done to assess the physical and chemical properties of HT coatings. Contact angle measurements were performed using powders representative of different HT chemistries to evaluate the dispersive and acid-base character of the surface. The wet POTS correlated with the electrodynamic (dipole + dispersive) parameter of the surface tension. The HT surfaces were found to be predominantly basic. Given the basicity of epoxy, these results indicate that increasing the acidic character of HT coatings may increase the adhesion performance. This was supported by electrokinetic measurements in which the dry POTS was found to increase with decreasing conversion coating iso-electric point. The correlations with the dry and wet state adhesion are interpreted as indicating that dry state adhesion is optimized by minimizing unfavorable polar interactions between the basic epoxy and HT interfaces. Wet state adhesion, where polar interactions are disrupted, is dictated by non-polar bonding. FTIR spectroscopy suggested that covalent between HT coatings and epoxy primers may occur, but could not definitively indicate so. Present results suggest that the limited chemical interactions, as governed by substrate wetting and acid-base interactions between the epoxy and HT, have minimized the possible mechanical interactions between the resin and the conversion coating.

Aqueous or solvent based surface modification: The influence of the combination solvent - organic functional group on the surface characteristics of titanium dioxide grafted with organophosphonic acids

NASA Astrophysics Data System (ADS)

Roevens, Annelore; Van Dijck, Jeroen G.; Geldof, Davy; Blockhuys, Frank; Prelot, Benedicte; Zajac, Jerzy; Meynen, Vera

2017-09-01

To alter the versatility of interactions at its surface, TiO2 is modified with organophosphonic acids (PA). A thorough understanding of the role of all synthesis conditions is necessary to achieve controlled functionalization. This study reports on the effect of using water, toluene and their mixtures when performing the modification of TiO2 with PA. Sorption and calorimetry measurements of surface interactions with various probing species clearly indicate that, by grafting PA in water, clear differences appear in the distribution of organic groups on the surface. Also the functional group of the PA determines the impact of using water as solvent. Modification in toluene results in a higher modification degree for propylphosphonic acid (3PA), as the solvent-solute interaction may hinder the grafting with phenylphosphonic acid (PhPA) in toluene. Water is preferred as solvent for PhPA modification as stabilizing π-OH interactions enhance surface grafting overcoming the competitive interaction of water at the surface as observed with 3PA. By using water in toluene mixtures for the functionalization of TiO2 with 3PA, the degree of functionalization is higher than when only water or toluene is used. Furthermore, adding small amounts of water leads to the formation of titanium propylphosphonates, next to surface grafting.

Functional Characteristics of Tumor-Associated Protein Spot14 and Interacting Proteins in Mouse Mammary Epithelial and Breast Cancer Cell Lines

DTIC Science & Technology

2009-09-01

merely qualitative, so in order to quantify the functional effect of S14 overexpression, NMR based metabolomics was used. The literature reports that...overexpression in DIP medium, even though fatty acids were significantly increased. Due to limitations of NMR based metabolomics, the chain length of the...S14 affects glucose carbon conversion directly into fatty acids. Interestingly, glucose consumption and lactate excretion was identical in either

Quantum-mechanical analysis of the energetic contributions to π stacking in nucleic acids versus rise, twist, and slide.

PubMed

Parker, Trent M; Hohenstein, Edward G; Parrish, Robert M; Hud, Nicholas V; Sherrill, C David

2013-01-30

Symmetry-adapted perturbation theory (SAPT) is applied to pairs of hydrogen-bonded nucleobases to obtain the energetic components of base stacking (electrostatic, exchange-repulsion, induction/polarization, and London dispersion interactions) and how they vary as a function of the helical parameters Rise, Twist, and Slide. Computed average values of Rise and Twist agree well with experimental data for B-form DNA from the Nucleic Acids Database, even though the model computations omitted the backbone atoms (suggesting that the backbone in B-form DNA is compatible with having the bases adopt their ideal stacking geometries). London dispersion forces are the most important attractive component in base stacking, followed by electrostatic interactions. At values of Rise typical of those in DNA (3.36 Å), the electrostatic contribution is nearly always attractive, providing further evidence for the importance of charge-penetration effects in π-π interactions (a term neglected in classical force fields). Comparison of the computed stacking energies with those from model complexes made of the "parent" nucleobases purine and 2-pyrimidone indicates that chemical substituents in DNA and RNA account for 20-40% of the base-stacking energy. A lack of correspondence between the SAPT results and experiment for Slide in RNA base-pair steps suggests that the backbone plays a larger role in determining stacking geometries in RNA than in B-form DNA. In comparisons of base-pair steps with thymine versus uracil, the thymine methyl group tends to enhance the strength of the stacking interaction through a combination of dispersion and electrosatic interactions.

Solid-phase extraction of galloyl- and caffeoylquinic acids from natural sources (Galphimia glauca and Arnicae flos) using pure zirconium silicate and bismuth citrate powders as sorbents inside micro spin columns.

PubMed

Hussain, Shah; Schönbichler, Stefan A; Güzel, Yüksel; Sonderegger, Harald; Abel, Gudrun; Rainer, Matthias; Huck, Christian W; Bonn, Günther K

2013-10-01

Galloyl- and caffeoylquinic acids are among the most important pharmacological active groups of natural compounds. This study describes a pre-step in isolation of some selected representatives of these groups from biological samples. A selective solid-phase extraction (SPE) method for these compounds may help assign classes and isomer designations within complex mixtures. Pure zirconium silicate and bismuth citrate powders (325 mesh) were employed as two new sorbents for optimized SPE of phenolic acids. These sorbents possess electrostatic interaction sites which accounts for additional interactions for carbon acid moieties as compared to hydrophilic and hydrophobic sorbents alone. Based on this principle, a selective SPE method for 1,3,4,5-tetragalloylquinic acid (an anti-HIV and anti-asthamatic agent) as a starting compound was developed and then deployed upon other phenolic acids with success. The recoveries and selectivities of both sorbents were compared to most commonly applied and commercially available sorbents by using high performance liquid chromatography. The nature of interaction between the carrier sorbent and the acidic target molecules was investigated by studying hydrophilic (silica), hydrophobic (C18), mixed-mode (ionic and hydrophobic: Oasis(®) MAX) and predominantly electrostatic (zirconium silicate) materials. The newly developed zirconium silicate and bismuth citrate stationary phases revealed promising results for the selective extraction of galloyl- and caffeoylquinic acids from natural sources. It was observed that zirconium silicate exhibited maximum recovery and selectivity for tetragalloylquinic acid (84%), chlorogenic acid (82%) and dicaffeoylquinic acid (94%) among all the tested sorbents. Copyright © 2013 Elsevier B.V. All rights reserved.

Building new discrete supramolecular assemblies through the interaction of iso-tellurazole N-oxides with Lewis acids and bases.

PubMed

Ho, Peter C; Jenkins, Hilary A; Britten, James F; Vargas-Baca, Ignacio

2017-10-13

The supramolecular macrocycles spontaneously assembled by iso-tellurazole N-oxides are stable towards Lewis bases as strong as N-heterocyclic carbenes (NHC) but readily react with Lewis acids such as BR 3 (R = Ph, F). The electron acceptor ability of the tellurium atom is greatly enhanced in the resulting O-bonded adducts, which consequently enables binding to a variety of Lewis bases that includes acetonitrile, 4-dimethylaminopyridine, 4,4'-bipyridine, triphenyl phosphine, a N-heterocyclic carbene and a second molecule of iso-tellurazole N-oxide.

Mutual Exclusion of Urea and Trimethylamine N-oxide from Amino Acids in Mixed Solvent Environment

NASA Astrophysics Data System (ADS)

Ganguly, Pritam; Hajari, Timir; Shea, Joan-Emma; van der Vegt, Nico F. A.

2015-03-01

We study the solvation thermodynamics of individual amino acids in mixed urea and trimethylamine N-oxide (TMAO) solutions using molecular dynamics simulations and the Kirkwood-Buff theory. Our results on the preferential interactions between the amino acids and the cosolvents (urea and TMAO) show a mutual exclusion of both the cosolvents from the amino acid surface in the mixed cosolvent condition which is followed by an increase in the cosolvent-cosolvent aggregation away from the amino acid surface. The effects of the mixed cosolvents on the association of the amino acids and the preferential solvation of the amino acids by water are found to be highly non-linear in terms of the effects of the individual cosolvents. A similar result has been found for the association of the protein backbone, mimicked by triglycine. Our results have been confirmed by different TMAO force-fields and the mutual exclusions of the cosolvents from the amino acids are found to be independent of the choice of the strength of the TMAO-water interactions. Based on our data, a general mechanism can potentially be proposed for the effects of the mixed cosolvents on the preferential solvations of the solutes including the case of cononsolvency.

Genotypic variability and genotype by environment interactions in oil and fatty acids in high, intermediate, and low oleic acid peanut genotypes.

PubMed

Singkham, Nattawut; Jogloy, Sanun; Kesmala, Thawan; Swatsitang, Prasan; Jaisil, Prasit; Puppala, Naveen

2010-05-26

Variability of genotype and genotype x environment (G x E) interactions for fatty acids are important to develop high-oleic types in peanut varietal improvement programs. The objective of this study was to determine the variation in fatty acid composition among peanut genotypes and G x E interactions of fatty acids in three groups of genotypes with high, intermediate, and low-oleic acid. Twenty-one genotypes were tested in three environments consisting of two rainy seasons and one dry season. The results indicated that G x E interactions were significant for biomass, pod yield, and harvest index and also for oleic, linoleic acids, and O/L ratio. G x E interactions were less important than genotypic main effect. For oleic acid, significant interactions were found in the intermediate and low-oleic groups only. Therefore, selection for high-oleic trait in peanut breeding programs should be effective.

Chlorophylls, ligands and assembly of light-harvesting complexes in chloroplasts

PubMed Central

Eggink, Laura L.; Chen, Min

2007-01-01

Chlorophyll (Chl) b serves an essential function in accumulation of light-harvesting complexes (LHCs) in plants. In this article, this role of Chl b is explored by considering the properties of Chls and the ligands with which they interact in the complexes. The overall properties of the Chls, not only their spectral features, are altered as consequences of chemical modifications on the periphery of the molecules. Important modifications are introduction of oxygen atoms at specific locations and reduction or desaturation of sidechains. These modifications influence formation of coordination bonds by which the central Mg atom, the Lewis acid, of Chl molecules interacts with amino acid sidechains, as the Lewis base, in proteins. Chl a is a versatile Lewis acid and interacts principally with imidazole groups but also with sidechain amides and water. The 7-formyl group on Chl b withdraws electron density toward the periphery of the molecule and consequently the positive Mg is less shielded by the molecular electron cloud than in Chl a. Chl b thus tends to form electrostatic bonds with Lewis bases with a fixed dipole, such as water and, in particular, peptide backbone carbonyl groups. The coordination bonds are enhanced by H-bonds between the protein and the 7-formyl group. These additional strong interactions with Chl b are necessary to achieve assembly of stable LHCs. PMID:17505910

Multi-wavelength spectrophotometric determination of acidity constant of some newly synthesized Schiff bases and their QSPR study

NASA Astrophysics Data System (ADS)

Hemmateenejad, Bahram; Emami, Leila; Sharghi, Hashem

2010-01-01

The acidity constants of some newly synthesized Schiff base derivatives were determined by hard-model based multivariate data analysis of the spectrophotometric data in the course of pH-metric titration in 50% (v/v) methanol-water binary solvent. The employed data analysis method was also able to extract the pure spectra and pH-dependent concentration profiles of the acid-base species. The molecules that possess different substituents (both electron donating and withdrawing) on the ortho-, meta- and para-positions of one of the phenyl ring showed variable acidity constants ranging from 8.77 to 11.07 whereas the parent molecule had an acidity constant of 10.25. To investigate the quantitative effects of changing of substitution pattern on the acidity constant, a quantitative structure-property relation analysis was conducted using substituent constants and molecular descriptor. Some models with high statistical quality (measured by cross-validation Q2) were obtained. It was found that the acidity constant of the studied molecules in the methanol-water mixed solvent not only is affected by electronic features of the solutes but also by the lipophilic interaction between methanol part of solvent and the deprotonated solutes.

Apolipoprotein A2 -265 T>C polymorphism interacts with dietary fatty acids intake to modulate inflammation in type 2 diabetes mellitus patients.

PubMed

Keramat, Laleh; Sadrzadeh-Yeganeh, Haleh; Sotoudeh, Gity; Zamani, Elham; Eshraghian, Mohammadreza; Mansoori, Anahita; Koohdani, Fariba

2017-05-01

Several investigations have been conducted regarding the interaction between Apolipoprotein A2 (APOA2) -265 T>C polymorphism and dietary intake of saturated fatty acids (SFAs) on obesity in healthy individuals or type 2 diabetes mellitus (T2 DM) patients. The aim of the present study is to examine the effect of this interaction on inflammatory markers in T2 DM patients. This is a comparative cross-sectional study on 180 T2 DM patients with known APOA2 genotype. Dietary intake was assessed by food-frequency questionnaire and serum levels of inflammatory markers (interleukin [IL]-18, pentraxin 3, and high-sensitivity C-reactive protein [hs-CRP]) were measured. The subjects were dichotomized into "high" and "low" categories, based on the median dietary intake of polyunsaturated fatty acids (PUFAs), monounsaturated fatty acids (MUFAs), and SFAs. The data were analyzed by analysis of covariance multivariate interaction model. In CC genotype, higher median intake of ω-3 PUFAs and MUFAs was associated with decreased serum levels of IL-18 and hs-CRP (P = 0.014 and 0.008, respectively). In T-allele carriers, higher median intake of SFAs was associated with increased serum hs-CRP level (P < 0.001). There was a significant relationship between APOA2 polymorphism and ω-3 PUFA intake on serum IL-18 level (P interaction = 0.03). Moreover, the relationship between this polymorphism and SFA and MUFA intake on serum hs-CRP level was statistically significant (P interaction = 0.03 and 0.024, respectively). In T2 DM patients, the dietary intake of antiinflammatory fatty acids, such as ω-3 PUFAs and MUFAs, could reduce the inflammatory effects associated with the CC genotype. In addition, proinflammatory fatty acids, such as SFAs, could overcome the antiinflammatory effect of the T-allele. Further studies are needed to confirm these findings. Copyright © 2016 Elsevier Inc. All rights reserved.

Density Functional Theory Study of Leaching Performance of Different Acids on Pyrochlore (100) Surface

NASA Astrophysics Data System (ADS)

Yang, Xiuli; Fang, Qing; Ouyang, Hui

2018-04-01

Pyrochlore leaching using hydrofluoric, sulfuric, and hydrochloric acids has been studied via experimental methods for years, but the interactions between niobium atoms on the pyrochlore surface and different acids have not been investigated. In this work, first-principles calculations based on density functional theory were used to elucidate the leaching performance of these three acids from the viewpoint of geometrical and electronic structures. The calculation results indicate that sulfate, chloride, and fluoride anions influence the geometric structure of pyrochlore (100) to different extents, decreasing in the order: sulfate, fluoride, chloride. Orbitals of O1 and O2 atoms of sulfate hybridized with those of surface niobium atom. Fluorine orbitals hybridized with those of surface niobium atoms. However, no obvious overlap exists between any orbitals of chlorine and surface niobium, revealing that chlorine does not interact chemically with surface niobium atoms.

Carboxylate modified porous graphitic carbon: a new class of hydrophilic interaction liquid chromatography phases.

PubMed

Wahab, M Farooq; Ibrahim, Mohammed E A; Lucy, Charles A

2013-06-18

Stationary phases for hydrophilic interaction liquid chromatography (HILIC) are predominantly based on silica and polymer supports. We present porous graphitic carbon particles with covalently attached carboxylic acid groups (carboxylate-PGC) as a new HILIC stationary phase. PGC particles were modified by adsorbing the diazonium salt of 4-aminobenzoic acid onto the PGC, followed by reduction of the adsorbed salt with sodium borohydride. The newly developed carboxylate-PGC phase exhibits different selectivity than that of 35 HPLC columns, including bare silica, zwitterionic, amine, reversed, and unmodified PGC phases. Carboxylate-PGC is stable from pH 2.0 to 12.6, yielding reproducible retention even at pH 12.6. Characterization of the new phase is presented by X-ray photoelectron spectroscopy, thermogravimetry, zeta potentials, and elemental analysis. The chromatographic performance of carboxylate-PGC as a HILIC phase is illustrated by separations of carboxylic acids, nucleotides, phenols, and amino acids.

Density Functional Theory Study of Leaching Performance of Different Acids on Pyrochlore (100) Surface

NASA Astrophysics Data System (ADS)

Yang, Xiuli; Fang, Qing; Ouyang, Hui

2018-06-01

Pyrochlore leaching using hydrofluoric, sulfuric, and hydrochloric acids has been studied via experimental methods for years, but the interactions between niobium atoms on the pyrochlore surface and different acids have not been investigated. In this work, first-principles calculations based on density functional theory were used to elucidate the leaching performance of these three acids from the viewpoint of geometrical and electronic structures. The calculation results indicate that sulfate, chloride, and fluoride anions influence the geometric structure of pyrochlore (100) to different extents, decreasing in the order: sulfate, fluoride, chloride. Orbitals of O1 and O2 atoms of sulfate hybridized with those of surface niobium atom. Fluorine orbitals hybridized with those of surface niobium atoms. However, no obvious overlap exists between any orbitals of chlorine and surface niobium, revealing that chlorine does not interact chemically with surface niobium atoms.

Quantitative single molecule measurements on the interaction forces of poly(L-glutamic acid) with calcite crystals.

PubMed

Sonnenberg, Lars; Luo, Yufei; Schlaad, Helmut; Seitz, Markus; Cölfen, Helmut; Gaub, Hermann E

2007-12-12

The interaction between poly(L-glutamic acid) (PLE) and calcite crystals was studied with AFM-based single molecule force spectroscopy. Block copolymers of poly(ethylene oxide) (PEO) and PLE were synthesized and covalently attached to the tip of an AFM cantilever. In desorption measurements the molecules were allowed to adsorb on the calcite crystal faces and afterward successively desorbed. The corresponding desorption forces were detected with high precision, showing for example a force transition between the two blocks. Because of its importance in the crystallization process in biominerals, the PLE-calcite interaction was investigated as a function of the pH as well as the calcium concentration of the aqueous solution. The sensitivity of the technique was underlined by resolving different interaction forces for calcite (104) and calcite (100).

Spectroscopic studies on the interaction of cinnamic acid and its hydroxyl derivatives with human serum albumin

NASA Astrophysics Data System (ADS)

Min, Jiang; Meng-Xia, Xie; Dong, Zheng; Yuan, Liu; Xiao-Yu, Li; Xing, Chen

2004-04-01

Cinnamic acid and its derivatives possess various biological effects in remedy of many diseases. Interaction of cinnamic acid and its hydroxyl derivatives, p-coumaric acid and caffeic acid, with human serum albumin (HSA), and concomitant changes in its conformation were studied using fluorescence and Fourier transform infrared spectroscopic methods. Fluorescence data revealed the presence of one binding site on HSA for cinnamic acid and its hydroxyl derivatives, and their binding constants ( KA) are caffeic acid> p-coumaric acid> cinnamic acid when Cdrug/ CHSA ranging from 1 to 10. The changes of the secondary structure of HSA after interacting with the three drugs are estimated, respectively by combining the curve-fitting results of amid I and amid III bands. The α-helix structure has a decrease of ≈9, 5 and 3% after HSA interacted with caffeic acid, p-coumaric acid and cinnamic acid, respectively. It was found that the hydroxyls substituted on aromatic ring of the drugs play an important role in the changes of protein's secondary structure. Combining the result of fluorescence quenching and the changes of secondary structure of HSA after interaction with the three drugs, the drug-HSA interaction mode was discussed.

Embryo-Specific Gene Expression in Microspore-Derived Embryos of Brassica napus. An Interaction between Abscisic Acid and Jasmonic Acid1, 2

PubMed Central

Hays, Dirk B.; Wilen, Ronald W.; Sheng, Chuxing; Moloney, Maurice M.; Pharis, Richard P.

1999-01-01

The induction of napin and oleosin gene expression in Brassica napus microspore-derived embryos (MDEs) was studied to assess the possible interaction between abscisic acid (ABA) and jasmonic acid (JA). Napin and oleosin transcripts were detected sooner following treatment with ABA than JA. Treatment of MDEs with ABA plus JA gave an additive accumulation of both napin and oleosin mRNA, the absolute amount being dependent on the concentration of each hormone. Endogenous ABA levels were reduced by 10-fold after treatment with JA, negating the possibility that the observed additive interaction was due to JA-induced ABA biosynthesis. Also, JA did not significantly increase the uptake of [3H-ABA] from the medium into MDEs. This suggests that the additive interaction was not due to an enhanced carrier-mediated ABA uptake by JA. Finally, when JA was added to MDEs that had been treated with the ABA biosynthesis inhibitor fluridone, napin mRNA did not increase. Based on these results with the MDE system, it is possible that embryos of B. napus use endogenous JA to modulate ABA effects on expression of both napin and oleosin. In addition, JA could play a causal role in the reduction of ABA that occurs during late stages of seed development. PMID:10069845

The basic amino acids in the coiled-coil domain of CIN85 regulate its interaction with c-Cbl and phosphatidic acid during epidermal growth factor receptor (EGFR) endocytosis.

PubMed

Zheng, Xiudan; Zhang, Jing; Liao, Kan

2014-07-08

During EGFR internalization CIN85 bridges EGFR-Cbl complex, endocytic machinery and fusible membrane through the interactions of CIN85 with c-Cbl, endophilins and phosphatidic acid. These protein-protein and protein-lipid interactions are mediated or regulated by the positively charged C-terminal coiled-coil domain of CIN85. However, the details of CIN85-lipid interaction remain unknown. The present study suggested a possible electric interaction between the negative charge of phosphatidic acid and the positive charge of basic amino acids in coiled-coil domain. Mutations of the basic amino acids in the coiled-coil domain, especially K645, K646, R648 and R650, into neutral amino acid alanine completely blocked the interaction of CIN85 with c-Cbl or phosphatidic acid. However, they did not affect CIN85-endophilin interaction. In addition, CIN85 was found to associate with the internalized EGFR endosomes. It interacted with several ESCRT (Endosomal Sorting Complex Required for Transport) component proteins for ESCRT assembly on endosomal membrane. Mutations in the coiled-coil domain (deletion of the coiled-coil domain or point mutations of the basic amino acids) dissociated CIN85 from endosomes. These mutants bound the ESCRT components in cytoplasm to prevent them from assembly on endosomal membrane and inhibited EGFR sorting for degradation. As an adaptor protein, CIN85 interacts with variety of partners through several domains. The positive charges of basic amino acids in the coiled-coil domain are not only involved in the interaction with phosphatidic acid, but also regulate the interaction of CIN85 with c-Cbl. CIN85 also interacts with ESCRT components for protein sorting in endosomes. These CIN85-protein and CIN85-lipid interactions enable CIN85 to link EGFR-Cbl endocytic complex with fusible membrane during EGFR endocytosis and subsequently to facilitate ESCRT formation on endosomal membrane for EGFR sorting and degradation.

Interactive effects of photoperiod and light intensity on blood physiological and biochemical reactions of broilers grown to heavy weights

USDA-ARS?s Scientific Manuscript database

The effects of photoperiod, light intensity, and their interaction on blood acid-base balance, metabolites, and electrolytes in broiler chickens under environmentally controlled conditions were examined in 2 trials. The experiment was consisted of a factorial arrangement of treatments in a randomize...

Corrosion Control through a Better Understanding of the Metallic Substrate/Organic Coating Interface

DTIC Science & Technology

1990-03-16

electrically coupling steel electrodes in different pH solutions. Anodic and cathodic sites beneath a coating are known to produce acidic and alkaline...9,16]. Lead-steel couples were used to model the interactions between metallic lead and steel. Both acidic and alkaline solutions were used because the...acetate solution can be altered by the addition of acid or base without precipitation of the anion. Other anions such as chlorides and sulfates are

Choline-Based Amino Acid ILs-Collagen Interaction: Enunciating Its Role in Stabilization/Destabilization Phenomena.

PubMed

Tarannum, Aafiya; Rao, J Raghava; Fathima, N Nishad

2018-01-25

Given the potential of productive interaction between choline-based amino acid ionic liquids (CAAILs) and collagen, we investigated the role of four CAAILs, viz., choline serinate, threoninate, lysinate, and phenylalaninate, and the changes mediated by them in the structure of collagen at different hierarchical orderings, that is, at molecular and fibrillar levels. The rheological, dielectric behavior and the secondary structural changes signify the alteration in the triple helical structure of collagen at higher concentrations of CAAILs. A marginal swelling and slight decrease in the thermal stability of rat tail tendon collagen fibers were observed for choline serinate and threoninate, albeit distortions in banding patterns were noticed for choline lysinate and phenylalaninate, suggesting chaotropicity of the ions at the fibrillar level. This signifies the changes in the hydrogen-bonding environment of collagen with increasing concentrations of CAAILs, which could be due to competitive hydrogen bonding between the carbonyl group of amino acid ionic liquids and the hydroxyl groups of collagen.

Amino acid-functionalized multi-walled carbon nanotubes for improving compatibility with chiral poly(amide-ester-imide) containing L-phenylalanine and L-tyrosine linkages

NASA Astrophysics Data System (ADS)

Abdolmaleki, Amir; Mallakpour, Shadpour; Borandeh, Sedigheh

2013-12-01

Amino acid functionalized multi-walled carbon nanotubes (f-MWCNTs)/poly(amide-ester-imide) (PAEI) composites were fabricated by solution mixing method. Proper functionalization and mixing strategy of MWCNTs provides the best opportunity for better distribution and bonding of nanoparticles to the polymer matrix. MWCNTs have been chemically modified with L-phenylalanine to improve their compatibility with L-phenylalanine based PAEI. Field emission scanning electron microscopy micrographs of composite revealed that f-MWCNTs made a good interaction with polymer chains by wrapping the polymer around them, and transmission electron microscopy results confirmed well dispersion with nano size of f-MWCNTs in the polymer matrix. In addition, thermal analysis showed good enhancement in thermal properties of composites compared to pure polymer. Thermal stability of the composites containing f-MWCNTs was enhanced due to their good dispersion and improved interfacial interaction between the amino acid based PAEI matrix and f-MWCNTs.

Flavylium network of chemical reactions in confined media: modulation of 3',4',7-trihydroxyflavilium reactions by host-guest interactions with cucurbit[7]uril.

PubMed

Basílio, Nuno; Pina, Fernando

2014-08-04

In moderately acidic aqueous solutions, flavylium compounds undergo a pH-, and in some cases, light-dependent array of reversible chemical reactions. This network can be described as a single acid-base reaction involving a flavylium cation (acidic form) and a mixture of basic forms (quinoidal base, hemiketal and cis and trans chalcones). The apparent pK'a of the system and the relative mole fractions of the basic forms can be modulated by the interaction with cucurbit[7]uril. The system is studied by using (1) H NMR spectroscopy, UV/Vis spectroscopy, flash photolysis, and steady-state irradiation. Of all the network species, the flavylium cation possesses the highest affinity for cucurbit[7]uril. The rate of interconversion between flavylium cation and the basic species (where trans-chalcone is dominant) is approximately nine times lower inside the cucurbit[7]uril. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Bile Acid Receptor TGR5 Does Not Interact with β-Arrestins or Traffic to Endosomes but Transmits Sustained Signals from Plasma Membrane Rafts*

PubMed Central

Jensen, Dane D.; Godfrey, Cody B.; Niklas, Christian; Canals, Meritxell; Kocan, Martina; Poole, Daniel P.; Murphy, Jane E.; Alemi, Farzad; Cottrell, Graeme S.; Korbmacher, Christoph; Lambert, Nevin A.; Bunnett, Nigel W.; Corvera, Carlos U.

2013-01-01

TGR5 is a G protein-coupled receptor that mediates bile acid (BA) effects on energy balance, inflammation, digestion, and sensation. The mechanisms and spatiotemporal control of TGR5 signaling are poorly understood. We investigated TGR5 signaling and trafficking in transfected HEK293 cells and colonocytes (NCM460) that endogenously express TGR5. BAs (deoxycholic acid (DCA), taurolithocholic acid) and the selective agonists oleanolic acid and 3-(2-chlorophenyl)-N-(4-chlorophenyl)-N, 5-dimethylisoxazole-4-carboxamide stimulated cAMP formation but did not induce TGR5 endocytosis or recruitment of β-arrestins, as assessed by confocal microscopy. DCA, taurolithocholic acid, and oleanolic acid did not stimulate TGR5 association with β-arrestin 1/2 or G protein-coupled receptor kinase (GRK) 2/5/6, as determined by bioluminescence resonance energy transfer. 3-(2-chlorophenyl)-N-(4-chlorophenyl)-N, 5-dimethylisoxazole-4-carboxamide stimulated a low level of TGR5 interaction with β-arrestin 2 and GRK2. DCA induced cAMP formation at the plasma membrane and cytosol, as determined using exchange factor directly regulated by cAMP (Epac2)-based reporters, but cAMP signals did not desensitize. AG1478, an inhibitor of epidermal growth factor receptor tyrosine kinase, the metalloprotease inhibitor batimastat, and methyl-β-cyclodextrin and filipin, which block lipid raft formation, prevented DCA stimulation of ERK1/2. Bioluminescence resonance energy transfer analysis revealed TGR5 and EGFR interactions that were blocked by disruption of lipid rafts. DCA stimulated TGR5 redistribution to plasma membrane microdomains, as localized by immunogold electron microscopy. Thus, TGR5 does not interact with β-arrestins, desensitize, or traffic to endosomes. TGR5 signals from plasma membrane rafts that facilitate EGFR interaction and transactivation. An understanding of the spatiotemporal control of TGR5 signaling provides insights into the actions of BAs and therapeutic TGR5 agonists/antagonists. PMID:23818521

Multispectroscopic investigation of the interaction of BSA and DNA with the anticancer drug, N-(6-ferrocenyl-2-naphthoyl)-gamma-amino butyric acid methyl ester

NASA Astrophysics Data System (ADS)

Rajina, S. R.; Sudhi, Geethu; Austin, P.; Praveen, S. G.; Xavier, T. S.; Kenny, Peter T. M.; Binoy, J.

2018-05-01

The interaction of a drug with DNA and BSA play a great role in studying anti cancer activity and drug transport properties, which can be effectively, investigated using vibrational spectroscopy, UV visible spectroscopy and Fluorescence spectroscopy. The present work reports the structural features of N-(6-ferrocenyl-2-naphthoyl)-gamma-amino butyric acid Methyl ester (FNGABME) based on FTIR and FTRaman spectroscopy. The absorption and fluorescence spectroscopic methods were used to study the efficiency of the interaction of the compound FNGABME with BSA and DNA and also molecular docking were performed computationally to validate the results which shows that the title compound may exhibit inhibitory activity against the cancer cells.

Role of Metal Oxides in Chemical Evolution: Interaction of Ribose Nucleotides with Alumina

NASA Astrophysics Data System (ADS)

Arora, Avnish Kumar; Kamaluddin

2009-03-01

Interaction of ribonucleotides—namely, 5‧-AMP, 5‧-GMP, 5‧-CMP, and 5‧-UMP—with acidic, neutral, and basic alumina has been studied. Purine nucleotides showed higher adsorption on alumina in comparison with pyrimidine nucleotides under acidic conditions. Adsorption data obtained followed Langmuir adsorption isotherm, and Xm and KL values were calculated. On the basis of infrared spectral studies of ribonucleotides, alumina, and ribonucleotide-alumina adducts, we propose that the nitrogen base and phosphate moiety of the ribonucleotides interact with the positive charge surface of alumina. Results of the present study may indicate the importance of alumina in concentrating organic molecules from dilute aqueous solutions in primeval seas in the course of chemical evolution on Earth.

Influence of toll-like receptor 4 gene variants and plasma fatty acid profile on systemic inflammation: A population-based cross-sectional study.

PubMed

Norde, Marina Maintinguer; Oki, Erica; Carioca, Antonio A F; Castro, Inar A; Souza, José M P; Marchioni, Dirce M L; Fisberg, Regina M; Rogero, Marcelo M

2017-03-01

The aim of this study was to investigate the interaction of toll-like receptor 4 (TLR4) gene single nucleotide polymorphism (SNP) and plasma fatty acid (FA) profile in modulating risk for systemic inflammation. In all, 262 adult (19-59 y) participants of the Health Survey of São Paulo met the inclusion criteria. Anthropometric parameters, blood pressure, plasma inflammatory biomarker concentration, and fatty acid profile were measured and four SNPs of the TLR4 gene (rs4986790, rs4986791, rs11536889, and rs5030728) were genotyped. Multivariate cluster analysis was performed to stratify individuals based on levels of 11 plasma inflammatory biomarkers into two groups: inflammatory (INF) and noninflammatory (NINF). No association was found between any of the SNPs studied and systemic inflammation. The INF cluster had higher palmitic acid levels (P = 0.039) and estimated stearoyl coenzyme A desaturase activity (P = 0.045) and lower polyunsaturated fatty acid (P = 0.011), ω-6 fatty acid (P = 0.018), arachidonic acid (P = 0.002) levels, and estimated δ-5 desaturase activity (P = 0.025) compared with the NINF cluster. Statistically significant interaction between rs11536889 and arachidonic acid/eicosapentaenoic acid (AA/EPA) ratio (P = 0.034) was found to increase the odds of belonging to the INF cluster when individuals had the variant allele C and were at the higher percentile of AA/EPA plasma ratio. Plasma fatty acid profile modulated the odds of belonging to the INF cluster depending on genotypes of TRL4 gene polymorphisms. Copyright © 2016 Elsevier Inc. All rights reserved.

Fragment-based discovery of novel pentacyclic triterpenoid derivatives as cholesteryl ester transfer protein inhibitors.

PubMed

Chang, Yongzhi; Zhou, Shuxi; Li, Enqin; Zhao, Wenfeng; Ji, Yanpeng; Wen, Xiaoan; Sun, Hongbin; Yuan, Haoliang

2017-01-27

Cholesteryl Ester Transfer Protein (CETP) is an important therapeutic target for the treatment of atherosclerotic cardiovascular disease. Our molecular modeling study revealed that pentacyclic triterpenoid compounds could mimic the protein-ligand interactions of the endogenous ligand cholesteryl ester (CE) by occupying its binding site. Alignment of the docking conformations of oleanolic acid (OA), ursolic acid (UA) and the crystal conformations of known CETP inhibitor Torcetrapib in the active site proposed the applicability of fragment-based drug design (FBDD) approaches in this study. Accordingly, a series of pentacyclic triterpenoid derivatives have been designed and synthesized as novel CETP inhibitors. The most potent compound 12e (IC 50 :0.28 μM) validated our strategy for molecular design. Molecular dynamics simulations illustrated that the more stable hydrogen bond interaction of the UA derivative 12e with Ser191 and stronger hydrophobic interactions with Val198, Phe463 than those of OA derivative 12b mainly led to their significantly different CETP inhibitory activity. These novel potent CETP inhibitors based on ursane-type scaffold should deserve further investigation. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Analysis of acid-base interactions at Al2O3 (11-20) interfaces by means of single molecule force spectroscopy

NASA Astrophysics Data System (ADS)

Mosebach, Bastian; Ozkaya, Berkem; Giner, Ignacio; Keller, Adrian; Grundmeier, Guido

2017-10-01

Single molecule force spectroscopy (SMFS) was employed to investigate the interaction forces between aliphatic amino, hydroxyl and ether groups and aluminum oxide single crystal surfaces in an aqueous electrolyte at pH = 6. The force studies were based on the variation of the terminal group of polyethylene glycol which was bound via a Ssbnd Au bond to the gold coated AFM tip. X-ray Photoelectron Spectroscopy (XPS) was performed to characterize the surface chemistry of the substrate. Force distance curves were measured between the PEG-NH2, sbnd OH and sbnd OCH3 functionalized atomic force microscope (AFM) tip and the non-polar single crystalline Al2O3(11-20) surface. The experimental results exhibit non-equilibrium desorption events which hint at acid-base interactions of the electron donating hydroxyl and amino groups with Al-ions in the surface of the oxide. The observed desorption forces for the sbnd NH2, sbnd OH/Al2O3(11-20) were in the range of 100-200 pN.

DNA Encoding Training Using 3D Gesture Interaction.

PubMed

Nicola, Stelian; Handrea, Flavia-Laura; Crişan-Vida, Mihaela; Stoicu-Tivadar, Lăcrămioara

2017-01-01

The work described in this paper summarizes the development process and presents the results of a human genetics training application, studying the 20 amino acids formed by the combination of the 3 nucleotides of DNA targeting mainly medical and bioinformatics students. Currently, the domain applications using recognized human gestures of the Leap Motion sensor are used in molecules controlling and learning from Mendeleev table or in visualizing the animated reactions of specific molecules with water. The novelty in the current application consists in using the Leap Motion sensor creating new gestures for the application control and creating a tag based algorithm corresponding to each amino acid, depending on the position in the 3D virtual space of the 4 nucleotides of DNA and their type. The team proposes a 3D application based on Unity editor and on Leap Motion sensor where the user has the liberty of forming different combinations of the 20 amino acids. The results confirm that this new type of study of medicine/biochemistry using the Leap Motion sensor for handling amino acids is suitable for students. The application is original and interactive and the users can create their own amino acid structures in a 3D-like environment which they could not do otherwise using traditional pen-and-paper.

Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids

NASA Astrophysics Data System (ADS)

Zhukhlistova, N. E.; Balaev, V. V.; Lyashenko, A. V.; Lashkov, A. A.

2012-05-01

Endonucleases (EC 3.1) are enzymes of the hydrolase class that catalyze the hydrolytic cleavage of deoxyribonucleic and ribonucleic acids at any region of the polynucleotide chain. Endonucleases are widely used both in biotechnological processes and in veterinary medicine as antiviral agents. Medical applications of endonucleases in human cancer therapy hold promise. The results of X-ray diffraction studies of the spatial organization of endonucleases and their complexes and the mechanism of their action are analyzed and generalized. An analysis of the structural studies of this class of enzymes showed that the specific binding of enzymes to nucleic acids is characterized by interactions with nitrogen bases and the nucleotide backbone, whereas the nonspecific binding of enzymes is generally characterized by interactions only with the nucleic-acid backbone. It should be taken into account that the specificity can be modulated by metal ions and certain low-molecular-weight organic compounds. To test the hypotheses about specific and nonspecific nucleic-acid-binding proteins, it is necessary to perform additional studies of atomic-resolution three-dimensional structures of enzyme-nucleic-acid complexes by methods of structural biology.

Designed Synthesis of Mesoporous Solid-Supported Lewis Acid-Base Pairs and Their CO2 Adsorption Behaviors.

PubMed

Zakharova, Maria V; Masoumifard, Nima; Hu, Yimu; Han, Jongho; Kleitz, Freddy; Fontaine, Frédéric-Georges

2018-04-18

Conventional amines and phosphines, such as diethylenetriamine, diphenylpropylphosphine, triethylamine, and tetramethylpiperidine, were grafted or impregnated on the surface of metalated SBA-15 materials, such as Ti-, Al-, and Zr-SBA-15, to generate air-stable solid-supported Lewis acid-base pairs. The Lewis acidity of the metalated materials before and after the introduction of Lewis bases was verified by means of pyridine adsorption-Fourier transform infrared spectroscopy. Detailed characterization of the materials was achieved by solid-state 13 C and 31 P MAS NMR spectroscopy, low-temperature N 2 physisorption, X-ray photoelectron spectroscopy, and energy-dispersive X-ray mapping analyses. Study of their potential interactions with CO 2 was performed using CO 2 adsorption isotherm experiments, which provided new insights into their applicability as solid CO 2 adsorbents. A correlation between solid-supported Lewis acid-base pair strength and the resulting affinity to CO 2 is discussed based on the calculation of isosteric enthalpy of adsorption.

Understanding interactions in the adsorption of gaseous organic compounds to indoor materials.

PubMed

Ongwandee, Maneerat; Chatsuvan, Thabtim; Suksawas Na Ayudhya, Wichitsawat; Morris, John

2017-02-01

We studied adsorption of organic compounds to a wide range of indoor materials, including plastics, gypsum board, carpet, and many others, under various relative humidity conditions by applying a conceptual model of the free energy of interfacial interactions of both van der Waals and Lewis acid-base (e-donor/acceptor) types. Data used for the analyses were partitioning coefficients of adsorbates between surface and gas phase obtained from three sources: our sorption experiments and two other published studies. Target organic compounds included apolars, monopolars, and bipolars. We established correlations of partitioning coefficients of adsorbates for a considered surface with the corresponding hexadecane/air partitioning coefficients of the adsorbates which are used as representative of a van der Waals descriptor instead of vapor pressure. The logarithmic adsorption coefficients of the apolars and weak bases, e.g., aliphatics and aromatics, to indoor materials linearly correlates well with the logarithmic hexadecane/air partitioning coefficients regardless of the surface polarity. The surface polarity in terms of e-donor/acceptor interactions becomes important for adsorption of the strong bases and bipolars, e.g., amines, phenols, and alcohols, to unpainted gypsum board. Under dry or humid conditions, the adsorption to flat plastic materials still linearly correlates well with the van der Waals interactions of the adsorbates, but no correlations were observed for the adsorption to fleecy or plush materials, e.g., carpet. Adsorption of highly bipolar compounds, e.g., phenol and isopropanol, is strongly affected by humidity, attributed to Lewis acid-base interactions with modified surfaces.

Hard and soft acids and bases: atoms and atomic ions.

PubMed

Reed, James L

2008-07-07

The structural origin of hard-soft behavior in atomic acids and bases has been explored using a simple orbital model. The Pearson principle of hard and soft acids and bases has been taken to be the defining statement about hard-soft behavior and as a definition of chemical hardness. There are a number of conditions that are imposed on any candidate structure and associated property by the Pearson principle, which have been exploited. The Pearson principle itself has been used to generate a thermodynamically based scale of relative hardness and softness for acids and bases (operational chemical hardness), and a modified Slater model has been used to discern the electronic origin of hard-soft behavior. Whereas chemical hardness is a chemical property of an acid or base and the operational chemical hardness is an experimental measure of it, the absolute hardness is a physical property of an atom or molecule. A critical examination of chemical hardness, which has been based on a more rigorous application of the Pearson principle and the availability of quantitative measures of chemical hardness, suggests that the origin of hard-soft behavior for both acids and bases resides in the relaxation of the electrons not undergoing transfer during the acid-base interaction. Furthermore, the results suggest that the absolute hardness should not be taken as synonymous with chemical hardness but that the relationship is somewhat more complex. Finally, this work provides additional groundwork for a better understanding of chemical hardness that will inform the understanding of hardness in molecules.

An In Vivo Photo-Cross-Linking Approach Reveals a Homodimerization Domain of Aha1 in S. cerevisiae

PubMed Central

Berg, Michael; Michalowski, Annette; Palzer, Silke; Rupp, Steffen; Sohn, Kai

2014-01-01

Protein-protein interactions play an essential role in almost any biological processes. Therefore, there is a particular need for methods which describe the interactions of a defined target protein in its physiological context. Here we report a method to photo-cross-link interacting proteins in S. cerevisiae by using the non-canonical amino acid p-azido-L-phenylalanine (pAzpa). Based on the expanded genetic code the photoreactive non-canonical amino acid pAzpa was site-specifically incorporated at eight positions into a domain of Aha1 that was previously described to bind Hsp90 in vitro to function as a cochaperone of Hsp90 and activates its ATPase activity. In vivo photo-cross-linking to the cognate binding partner of Aha1 was carried out by irradiation of mutant strains with UV light (365 nm) to induce covalent intermolecular bonds. Surprisingly, an interaction between Aha1 and Hsp90 was not detected, although, we could confirm binding of suppressed pAzpa containing Aha1 to Hsp90 by native co-immunoprecipitation. However, a homodimer consisting of two covalently crosslinked Aha1 monomers was identified by mass spectrometry. This homodimer could also be confirmed using p-benzoyl-L-phenylalanine, another photoreactive non-canonical amino acid. Crosslinking was highly specific as it was dependent on irradiation using UV light, the exact position of the non-canonical amino acid in the protein sequence as well as on the addition of the non-canonical amino acid to the growth medium. Therefore it seems possible that an interaction of Aha1 with Hsp90 takes place at different positions than previously described in vitro highlighting the importance of in vivo techniques to study protein-protein interactions. Accordingly, the expanded genetic code can easily be applied to other S. cerevisiae proteins to study their interaction under physiological relevant conditions in vivo. PMID:24614167

NMR studies of protein-nucleic acid interactions.

PubMed

Varani, Gabriele; Chen, Yu; Leeper, Thomas C

2004-01-01

Protein-DNA and protein-RNA complexes play key functional roles in every living organism. Therefore, the elucidation of their structure and dynamics is an important goal of structural and molecular biology. Nuclear magnetic resonance (NMR) studies of protein and nucleic acid complexes have common features with studies of protein-protein complexes: the interaction surfaces between the molecules must be carefully delineated, the relative orientation of the two species needs to be accurately and precisely determined, and close intermolecular contacts defined by nuclear Overhauser effects (NOEs) must be obtained. However, differences in NMR properties (e.g., chemical shifts) and biosynthetic pathways for sample productions generate important differences. Chemical shift differences between the protein and nucleic acid resonances can aid the NMR structure determination process; however, the relatively limited dispersion of the RNA ribose resonances makes the process of assigning intermolecular NOEs more difficult. The analysis of the resulting structures requires computational tools unique to nucleic acid interactions. This chapter summarizes the most important elements of the structure determination by NMR of protein-nucleic acid complexes and their analysis. The main emphasis is on recent developments (e.g., residual dipolar couplings and new Web-based analysis tools) that have facilitated NMR studies of these complexes and expanded the type of biological problems to which NMR techniques of structural elucidation can now be applied.

Counting the ions surrounding nucleic acids

PubMed Central

2017-01-01

Abstract Nucleic acids are strongly negatively charged, and thus electrostatic interactions—screened by ions in solution—play an important role in governing their ability to fold and participate in biomolecular interactions. The negative charge creates a region, known as the ion atmosphere, in which cation and anion concentrations are perturbed from their bulk values. Ion counting experiments quantify the ion atmosphere by measuring the preferential ion interaction coefficient: the net total number of excess ions above, or below, the number expected due to the bulk concentration. The results of such studies provide important constraints on theories, which typically predict the full three-dimensional distribution of the screening cloud. This article reviews the state of nucleic acid ion counting measurements and critically analyzes their ability to test both analytical and simulation-based models. PMID:28034959

Boronic acid recognition of non-interacting carbohydrates for biomedical applications: increasing fluorescence signals of minimally interacting aldoses and sucralose.

PubMed

Resendez, Angel; Halim, Md Abdul; Singh, Jasmeet; Webb, Dominic-Luc; Singaram, Bakthan

2017-11-22

To address carbohydrates that are commonly used in biomedical applications with low binding affinities for boronic acid based detection systems, two chemical modification methods were utilized to increase sensitivity. Modified carbohydrates were analyzed using a two component fluorescent probe based on boronic acid-appended viologen-HPTS (4,4'-o-BBV). Carbohydrates normally giving poor signals (fucose, l-rhamnose, xylose) were subjected to sodium borohydride (NaBH 4 ) reduction in ambient conditions for 1 h yielding the corresponding sugar alcohols from fucose, l-rhamnose and xylose in essentially quantitative yields. Compared to original aldoses, apparent binding affinities were increased 4-25-fold. The chlorinated sweetener and colon permeability marker sucralose (Splenda), otherwise undetectable by boronic acids, was dechlorinated to a detectable derivative by reactive oxygen and hydroxide intermediates by the Fenton reaction or by H 2 O 2 and UV light. This method is specific to sucralose as other common sugars, such as sucrose, do not contain any carbon-chlorine bonds. Significant fluorescence response was obtained for chemically modified sucralose with the 4,4'-o-BBV-HPTS probe system. This proof of principle can be applied to biomedical applications, such as gut permeability, malabsorption, etc.

Impacts of low-molecular-weight organic acids on aquatic behavior of graphene nanoplatelets and their induced algal toxicity and antioxidant capacity.

PubMed

Wang, Zhuang; Gao, Yucheng; Wang, Se; Fang, Hao; Xu, Defu; Zhang, Fan

2016-06-01

Knowledge of the interaction between graphene-based materials and low-molecular-weight organic acids (LOAs) is essential to understand fate and effects of graphene-based materials in the aquatic environment, but this interaction remains poorly elucidated. In this study, the effects of LOAs on the physicochemical properties of graphene nanoplatelets (GNPs) in an aqueous medium and on the GNP toxicity to algae were studied. The unicellular green alga Scenedesmus obliquus was exposed to GNP suspensions in the presence of benzoic acid or gallic acid at various concentrations. The GNPs had smaller hydrodynamic sizes and the GNP suspensions were more stable and had higher or lower surface zeta potentials in the presence of LOAs than when LOAs were not present. The toxic effects in S. obliquus cultures incubated with GNP suspensions containing LOAs were related to the LOA concentration, and the presence of LOAs caused three effects: stimulation, alleviation, and synergistic inhibition. The intensities of the effects mainly correlated with the LOA concentration, the extent of agglomeration, and particle-induced oxidative stress. The results indicate that the environmental fates and toxicities of GNPs are strongly affected by the binding of GNPs to LOAs.

Effect of metal ions on the reactions of the cumyloxyl radical with hydrogen atom donors. Fine control on hydrogen abstraction reactivity determined by Lewis acid-base interactions.

PubMed

Salamone, Michela; Mangiacapra, Livia; DiLabio, Gino A; Bietti, Massimo

2013-01-09

A time-resolved kinetic study on the effect of metal ions (M(n+)) on hydrogen abstraction reactions from C-H donor substrates by the cumyloxyl radical (CumO(•)) was carried out in acetonitrile. Metal salt addition was observed to increase the CumO(•) β-scission rate constant in the order Li(+) > Mg(2+) > Na(+). These effects were explained in terms of the stabilization of the β-scission transition state determined by Lewis acid-base interactions between M(n+) and the radical. When hydrogen abstraction from 1,4-cyclohexadiene was studied in the presence of LiClO(4) and Mg(ClO(4))(2), a slight increase in rate constant (k(H)) was observed indicating that interaction between M(n+) and CumO(•) can also influence, although to a limited extent, the hydrogen abstraction reactivity of alkoxyl radicals. With Lewis basic C-H donors such as THF and tertiary amines, a decrease in k(H) with increasing Lewis acidity of M(n+) was observed (k(H)(MeCN) > k(H)(Li(+)) > k(H)(Mg(2+))). This behavior was explained in terms of the stronger Lewis acid-base interaction of M(n+) with the substrate as compared to the radical. This interaction reduces the degree of overlap between the α-C-H σ* orbital and a heteroatom lone-pair, increasing the C-H BDE and destabilizing the carbon centered radical formed after abstraction. With tertiary amines, a >2-order of magnitude decrease in k(H) was measured after Mg(ClO(4))(2) addition up to a 1.5:1 amine/Mg(ClO(4))(2) ratio. At higher amine concentrations, very similar k(H) values were measured with and without Mg(ClO(4))(2). These results clearly show that with strong Lewis basic substrates variations in the nature and concentration of M(n+) can dramatically influence k(H), allowing for a fine control of the substrate hydrogen atom donor ability, thus providing a convenient method for C-H deactivation. The implications and generality of these findings are discussed.

Density functional theory calculations of biomolecules adsorption on phosphorene for biomedical applications

NASA Astrophysics Data System (ADS)

Rubio-Pereda, Pamela; H. Cocoletzi, Gregorio

2018-01-01

Recent experimental studies have found that phosphorene, the two-dimensional counterpart of black phosphorus, is more biological-friendly, in comparison with graphene, for the design of bio-integrated electronics based devices for biomedical applications. Following this research line, we theoretically investigate by first principle calculations, accounting for van der Waals effects, the interactions between phosphorene and typical amino acids (nonpolar, aromatic, positively charged and negatively charged). Testing different possible molecular orientations adsorption calculations have been done. Structural analysis, Löwdin electron population analysis and the study of the hydrophobic effect upon adsorption orientation were carried out in order to reveal the nature of the composite system interactions. Results show that amino acid molecules physisorb, mediated by an electron transfer process, on the phosphorene surface with a minimum disruption of their structure. Furthermore, the hydrophilic nature of phosphorene dictates the more energetically preferred adsorbed amino acid orientation. Ultimately, the nature of these interactions manifests the biological-friendly characteristic of phosphorene and its potential to be used as part of bioinorganic interfaces.

NMR studies reveal the role of biomembranes in modulating ligand binding and release by intracellular bile acid binding proteins.

PubMed

Pedò, Massimo; Löhr, Frank; D'Onofrio, Mariapina; Assfalg, Michael; Dötsch, Volker; Molinari, Henriette

2009-12-18

Bile acid molecules are transferred vectorially between basolateral and apical membranes of hepatocytes and enterocytes in the context of the enterohepatic circulation, a process regulating whole body lipid homeostasis. This work addresses the role of the cytosolic lipid binding proteins in the intracellular transfer of bile acids between different membrane compartments. We present nuclear magnetic resonance (NMR) data describing the ternary system composed of the bile acid binding protein, bile acids, and membrane mimetic systems, such as anionic liposomes. This work provides evidence that the investigated liver bile acid binding protein undergoes association with the anionic membrane and binding-induced partial unfolding. The addition of the physiological ligand to the protein-liposome mixture is capable of modulating this interaction, shifting the equilibrium towards the free folded holo protein. An ensemble of NMR titration experiments, based on nitrogen-15 protein and ligand observation, confirm that the membrane and the ligand establish competing binding equilibria, modulating the cytoplasmic permeability of bile acids. These results support a mechanism of ligand binding and release controlled by the onset of a bile salt concentration gradient within the polarized cell. The location of a specific protein region interacting with liposomes is highlighted.

Born energy, acid-base equilibrium, structure and interactions of end-grafted weak polyelectrolyte layers.

PubMed

Nap, R J; Tagliazucchi, M; Szleifer, I

2014-01-14

This work addresses the effect of the Born self-energy contribution in the modeling of the structural and thermodynamical properties of weak polyelectrolytes confined to planar and curved surfaces. The theoretical framework is based on a theory that explicitly includes the conformations, size, shape, and charge distribution of all molecular species and considers the acid-base equilibrium of the weak polyelectrolyte. Namely, the degree of charge in the polymers is not imposed but it is a local varying property that results from the minimization of the total free energy. Inclusion of the dielectric properties of the polyelectrolyte is important as the environment of a polymer layer is very different from that in the adjacent aqueous solution. The main effect of the Born energy contribution on the molecular organization of an end-grafted weak polyacid layer is uncharging the weak acid (or basic) groups and consequently decreasing the concentration of mobile ions within the layer. The magnitude of the effect increases with polymer density and, in the case of the average degree of charge, it is qualitatively equivalent to a small shift in the equilibrium constant for the acid-base equilibrium of the weak polyelectrolyte monomers. The degree of charge is established by the competition between electrostatic interactions, the polymer conformational entropy, the excluded volume interactions, the translational entropy of the counterions and the acid-base chemical equilibrium. Consideration of the Born energy introduces an additional energetic penalty to the presence of charged groups in the polyelectrolyte layer, whose effect is mitigated by down-regulating the amount of charge, i.e., by shifting the local-acid base equilibrium towards its uncharged state. Shifting of the local acid-base equilibrium and its effect on the properties of the polyelectrolyte layer, without considering the Born energy, have been theoretically predicted previously. Account of the Born energy leads to systematic, but in general small, corrections to earlier theoretical predictions describing the behavior of weak polyelectrolyte layers. However, polyelectrolyte uncharging results in a decrease in the concentration of counterions and inclusion of the Born Energy can result in a substantial decrease of the counterion concentration. The effect of considering the Born energy contribution is explored for end-grafted weak polyelectrolyte layers by calculating experimental observables which are known to depend on the presence of charges within the polyelectrolyte layer: inclusion of the Born energy contribution leads to a decrease in the capacitance of polyelectrolyte-modified electrodes, a decrease of conductivity of polyelectrolyte-modified nanopores and an increase in the repulsion exerted by a planar polyelectrolyte layer confined by an opposing wall.

Lewis acid-base interactions in weakly bound formaldehyde complexes with CO2, HCN, and FCN: considerations on the cooperative H-bonding effects.

PubMed

Rivelino, Roberto

2008-01-17

Ab initio quantum chemistry calculations reveal that HCN and mainly FCN can form Lewis acid-base complexes with formaldehyde associated with cooperative H bonds, as first noticed by Wallen et al. (Blatchford, M. A.; Raveendran, P.; Wallen, S. L. J. Am. Chem. Soc. 2002, 124, 14818-14819) for CO2-philic materials under supercritical conditions. The present results, obtained with MP2(Full)/aug-cc-pVDZ calculations, show that the degeneracy of the nu(2) mode in free HCN or FCN is removed upon complexation in the same fashion as that of CO2. The splitting of these bands along with the electron structure analysis provides substantial evidence of the interaction of electron lone pairs of the carbonyl oxygen with the electron-deficient carbon atom of the cyanides. Also, this work investigates the role of H bonds acting as additional stabilizing interactions in the complexes by performing the energetic and geometric characterization.

A molecular rotor based ratiometric sensor for basic amino acids

NASA Astrophysics Data System (ADS)

Pettiwala, Aafrin M.; Singh, Prabhat K.

2018-01-01

The inevitable importance of basic amino acids, arginine and lysine, in human health and metabolism demands construction of efficient sensor systems for them. However, there are only limited reports on the 'ratiometric' detection of basic amino acids which is further restricted by the use of chemically complex sensor molecules, which impedes their prospect for practical applications. Herein, we report a ratiometric sensor system build on simple mechanism of disassociation of novel emissive Thioflavin-T H-aggregates from heparin surface, when subjected to interaction with basic amino acids. The strong and selective electrostatic and hydrogen bonding interaction of basic amino acids with heparin leads to large alteration in photophysical attributes of heparin bound Thioflavin-T, which forms a highly sensitive sensor platform for detection of basic amino acids in aqueous solution. These selective interactions between basic amino acids and heparin allow our sensor system to discriminate arginine and lysine from other amino acids. This unique mechanism of dissociation of Thioflavin-T aggregates from heparin surface provides ratiometric response on both fluorimetric and colorimetric outputs for detection of arginine and lysine, and thus it holds a significant advantage over other developed sensor systems which are restricted to single wavelength detection. Apart from the sensitivity and selectivity, our system also provides the advantage of simplicity, dual mode of sensing, and more importantly, it employs an inexpensive commercially available probe molecule, which is a significant advantage over other developed sensor systems that uses tedious synthesis protocol for the employed probe in the detection scheme, an impediment for practical applications. Additionally, our sensor system also shows response in complex biological media of serum samples.

Nanostructure-Directed Chemical Sensing: The IHSAB Principle and the Effect of Nitrogen and Sulfur Functionalization on Metal Oxide Decorated Interface Response

PubMed Central

Laminack, William I.; Gole, James L.

2013-01-01

The response matrix, as metal oxide nanostructure decorated n-type semiconductor interfaces are modified in situ through direct amination and through treatment with organic sulfides and thiols, is demonstrated. Nanostructured TiO2, SnOx, NiO and CuxO (x = 1,2), in order of decreasing Lewis acidity, are deposited to a porous silicon interface to direct a dominant electron transduction process for reversible chemical sensing in the absence of significant chemical bond formation. The metal oxide sensing sites can be modified to decrease their Lewis acidity in a process appearing to substitute nitrogen or sulfur, providing a weak interaction to form the oxynitrides and oxysulfides. Treatment with triethylamine and diethyl sulfide decreases the Lewis acidity of the metal oxide sites. Treatment with acidic ethane thiol modifies the sensor response in an opposite sense, suggesting that there are thiol (SH) groups present on the surface that provide a Brønsted acidity to the surface. The in situ modification of the metal oxides deposited to the interface changes the reversible interaction with the analytes, NH3 and NO. The observed change for either the more basic oxynitrides or oxysulfides or the apparent Brønsted acid sites produced from the interaction of the thiols do not represent a simple increase in surface basicity or acidity, but appear to involve a change in molecular electronic structure, which is well explained using the recently developed inverse hard and soft acids and bases (IHSAB) model. PMID:28348345

[Study on THz spectra and vibrational modes of benzoic acid and sodium Benzoate].

PubMed

Zheng, Zhuan-Ping; Fan, Wen-Hui; Yan, Hui; Liu, Jia; Xu, Li-Min

2013-03-01

Terahertz time-domain spectroscopy was employed to measure the terahertz absorption spectra of benzoic acid and sodium benzoate at room temperature. The origins of the measured features of benzoic acid were summarized based on previous study. Density functional theory was used to compute and analyze the molecular structure and vibrational modes of sodium benzoate in monomer. Based on the obtained results, the authors found that the THz spectral features can be used to distinguish benzoic acid and sodium benzoate totally; the essential reason for the THz spectral difference between benzoic acid and sodium benzoate is that the electrovalent bond of sodium benzoate affects the values of covalent bond lengths and bond angles, as well as the molecular interactions and arrangement in unit cell; the measured features of benzoic acid and sodium benzoate come from the collective vibrations except the peaks located at 107 cm-1 of benzoic acid and 54 cm-1 of sodium benzoate.

Transcriptome-Based Characterization of Interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in Lactose-Grown Chemostat Cocultures

PubMed Central

Mendes, Filipa; Sieuwerts, Sander; de Hulster, Erik; Almering, Marinka J. H.; Luttik, Marijke A. H.; Pronk, Jack T.; Smid, Eddy J.; Bron, Peter A.

2013-01-01

Mixed populations of Saccharomyces cerevisiae yeasts and lactic acid bacteria occur in many dairy, food, and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir fermentations, were studied during anaerobic growth on lactose. By combining physiological and transcriptome analysis of the two strains in the cocultures, five mechanisms of interaction were identified. (i) Lb. delbrueckii subsp. bulgaricus hydrolyzes lactose, which cannot be metabolized by S. cerevisiae, to galactose and glucose. Subsequently, galactose, which cannot be metabolized by Lb. delbrueckii subsp. bulgaricus, is excreted and provides a carbon source for yeast. (ii) In pure cultures, Lb. delbrueckii subsp. bulgaricus grows only in the presence of increased CO2 concentrations. In anaerobic mixed cultures, the yeast provides this CO2 via alcoholic fermentation. (iii) Analysis of amino acid consumption from the defined medium indicated that S. cerevisiae supplied alanine to the bacterium. (iv) A mild but significant low-iron response in the yeast transcriptome, identified by DNA microarray analysis, was consistent with the chelation of iron by the lactate produced by Lb. delbrueckii subsp. bulgaricus. (v) Transcriptome analysis of Lb. delbrueckii subsp. bulgaricus in mixed cultures showed an overrepresentation of transcripts involved in lipid metabolism, suggesting either a competition of the two microorganisms for fatty acids or a response to the ethanol produced by S. cerevisiae. This study demonstrates that chemostat-based transcriptome analysis is a powerful tool to investigate microbial interactions in mixed populations. PMID:23872557

Transcriptome-based characterization of interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in lactose-grown chemostat cocultures.

PubMed

Mendes, Filipa; Sieuwerts, Sander; de Hulster, Erik; Almering, Marinka J H; Luttik, Marijke A H; Pronk, Jack T; Smid, Eddy J; Bron, Peter A; Daran-Lapujade, Pascale

2013-10-01

Mixed populations of Saccharomyces cerevisiae yeasts and lactic acid bacteria occur in many dairy, food, and beverage fermentations, but knowledge about their interactions is incomplete. In the present study, interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus, two microorganisms that co-occur in kefir fermentations, were studied during anaerobic growth on lactose. By combining physiological and transcriptome analysis of the two strains in the cocultures, five mechanisms of interaction were identified. (i) Lb. delbrueckii subsp. bulgaricus hydrolyzes lactose, which cannot be metabolized by S. cerevisiae, to galactose and glucose. Subsequently, galactose, which cannot be metabolized by Lb. delbrueckii subsp. bulgaricus, is excreted and provides a carbon source for yeast. (ii) In pure cultures, Lb. delbrueckii subsp. bulgaricus grows only in the presence of increased CO2 concentrations. In anaerobic mixed cultures, the yeast provides this CO2 via alcoholic fermentation. (iii) Analysis of amino acid consumption from the defined medium indicated that S. cerevisiae supplied alanine to the bacterium. (iv) A mild but significant low-iron response in the yeast transcriptome, identified by DNA microarray analysis, was consistent with the chelation of iron by the lactate produced by Lb. delbrueckii subsp. bulgaricus. (v) Transcriptome analysis of Lb. delbrueckii subsp. bulgaricus in mixed cultures showed an overrepresentation of transcripts involved in lipid metabolism, suggesting either a competition of the two microorganisms for fatty acids or a response to the ethanol produced by S. cerevisiae. This study demonstrates that chemostat-based transcriptome analysis is a powerful tool to investigate microbial interactions in mixed populations.

Nanostructure-directed chemical sensing: The IHSAB principle and the dynamics of acid/base-interface interaction

PubMed Central

Laminack, William

2013-01-01

Summary Nanostructure-decorated n-type semiconductor interfaces are studied in order to develop chemical sensing with nanostructured materials. We couple the tenets of acid/base chemistry with the majority charge carriers of an extrinsic semiconductor. Nanostructured islands are deposited in a process that does not require self-assembly in order to direct a dominant electron-transduction process that forms the basis for reversible chemical sensing in the absence of chemical-bond formation. Gaseous analyte interactions on a metal-oxide-decorated n-type porous silicon interface show a dynamic electron transduction to and from the interface depending upon the relative strength of the gas and metal oxides. The dynamic interaction of NO with TiO2, SnO2, NiO, CuxO, and AuxO (x >> 1), in order of decreasing acidity, demonstrates this effect. Interactions with the metal-oxide-decorated interface can be modified by the in situ nitridation of the oxide nanoparticles, enhancing the basicity of the decorated interface. This process changes the interaction of the interface with the analyte. The observed change to the more basic oxinitrides does not represent a simple increase in surface basicity but appears to involve a change in molecular electronic structure, which is well explained by using the recently developed IHSAB model. The optical pumping of a TiO2 and TiO2− xNx decorated interface demonstrates a significant enhancement in the ability to sense NH3 and NO2. Comparisons to traditional metal-oxide sensors are also discussed. PMID:23400337

Chromatographic resolution of a salt into its parent acid and base constituents.

PubMed

Davankov, Vadim; Tsyurupa, Maria

2006-12-08

Based on the results of the earlier proposed process of separation of mixtures of mineral electrolytes by size-exclusion chromatography (SEC), it has been suggested that a mineral salt must spontaneously resolve, at least partially, into its parent acid and base constituents, provided that the separating media discriminates the anion and cation of the salt according to their size. Indeed, migration of a zone of an aqueous salt solution through a bed of neutral nanoporous hypercrosslinked polystyrene-type packing was shown to result in the generation of acidic and alkaline effluent fractions. The principle of spontaneous salt resolution has been extended to other types of discriminating interactions between the stationary phase and the two ions of the salt. The idea was exemplified by the resolution of ammonium acetate, due to hydrophobic retention of the acetate, into fractions enriched in ammoniac and then acetic acid.

Conformational Switching of a Foldamer in a Multicomponent System by pH-Filtered Selection between Competing Noncovalent Interactions

PubMed Central

2015-01-01

Biomolecular systems are able to respond to their chemical environment through reversible, selective, noncovalent intermolecular interactions. Typically, these interactions induce conformational changes that initiate a signaling cascade, allowing the regulation of biochemical pathways. In this work, we describe an artificial molecular system that mimics this ability to translate selective noncovalent interactions into reversible conformational changes. An achiral but helical foldamer carrying a basic binding site interacts selectively with the most acidic member of a suite of chiral ligands. As a consequence of this noncovalent interaction, a global absolute screw sense preference, detectable by 13C NMR, is induced in the foldamer. Addition of base, or acid, to the mixture of ligands competitively modulates their interaction with the binding site, and reversibly switches the foldamer chain between its left and right-handed conformations. As a result, the foldamer–ligand mixture behaves as a biomimetic chemical system with emergent properties, functioning as a “proton-counting” molecular device capable of providing a tunable, pH-dependent conformational response to its environment. PMID:25915163

Structure-property relationships in halogenbenzoic acids: Thermodynamics of sublimation, fusion, vaporization and solubility.

PubMed

Zherikova, Kseniya V; Svetlov, Aleksey A; Kuratieva, Natalia V; Verevkin, Sergey P

2016-10-01

Temperature dependences of vapor pressures for 2-, 3-, and 4-bromobenzoic acid, as well as for five isomeric bromo-methylbenzoic acids were studied by the transpiration method. Melting temperatures and enthalpies of fusion for all isomeric bromo-methylbenzoic acids and 4-bromobenzoic acid were measured with a DSC. The molar enthalpies of sublimation and vaporization were derived. These data together with results available in the literature were collected and checked for internal consistency using a group-additivity procedure and results from X-ray structural diffraction studies. Specific (hydrogen bonding) interactions in the liquid and in the crystal phase of halogenbenzoic acids were quantified based on experimental values of vaporization and sublimation enthalpies. Structure-property correlations of solubilities of halogenobenzoic acids with sublimation pressures and sublimation enthalpies were developed and solubilities of bromo-benzoic acids were estimated. These new results resolve much of the ambiguity in the available thermochemical and solubility data on bromobenzoic acids. The approach based on structure property correlations can be applied for the assessment of water solubility of sparingly soluble drugs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Application of nanoparticle tracking analysis for characterising the fate of engineered nanoparticles in sediment-water systems.

PubMed

Luo, Ping; Roca, Alejandro; Tiede, Karen; Privett, Katie; Jiang, Jiachao; Pinkstone, John; Ma, Guibin; Veinot, Jonathan; Boxall, Alisatair

2018-02-01

Novel applications of nanotechnology may lead to the release of engineered nanoparticles (ENPs), which result in concerns over their potential environmental hazardous impact. It is essential for the research workers to be able to quantitatively characterise ENPs in the environment and subsequently to assist the risk assessment of the ENPs. This study hence explored the application of nanoparticle tracking system (NTA) to quantitatively describe the behaviour of the ENPs in natural sediment-water systems. The NTA allows the measurement of both particle number concentration (PNC) and particle size distribution (PSD) of the ENPs. The developed NTA method was applied to a range of gold and magnetite ENPs with a selection of surface properties. The results showed that the positively-charged ENPs interacted more strongly with the sediment than neutral and negatively-charged ENPs. It was also found that the citrate coated Au ENPs had a higher distribution percentage (53%) than 11-mercaptoundecanoic acid coated Au ENPs (20%) and citrate coated magnetite ENPs (21%). The principles of the electrostatic interactions between hard (and soft) acids and bases (HSAB) are used to explain such behaviours; the hard base coating (i.e. citrate ions) will interact more strongly with hard acid (i.e. magnetite) than soft acid (i.e. gold). The results indicate that NTA is a complementary method to existing approaches to characterise the fate and behaviour of ENPs in natural sediment. Copyright © 2017. Published by Elsevier B.V.

The basic amino acids in the coiled-coil domain of CIN85 regulate its interaction with c-Cbl and phosphatidic acid during epidermal growth factor receptor (EGFR) endocytosis

PubMed Central

2014-01-01

Background During EGFR internalization CIN85 bridges EGFR-Cbl complex, endocytic machinery and fusible membrane through the interactions of CIN85 with c-Cbl, endophilins and phosphatidic acid. These protein-protein and protein-lipid interactions are mediated or regulated by the positively charged C-terminal coiled-coil domain of CIN85. However, the details of CIN85-lipid interaction remain unknown. The present study suggested a possible electric interaction between the negative charge of phosphatidic acid and the positive charge of basic amino acids in coiled-coil domain. Results Mutations of the basic amino acids in the coiled-coil domain, especially K645, K646, R648 and R650, into neutral amino acid alanine completely blocked the interaction of CIN85 with c-Cbl or phosphatidic acid. However, they did not affect CIN85-endophilin interaction. In addition, CIN85 was found to associate with the internalized EGFR endosomes. It interacted with several ESCRT (Endosomal Sorting Complex Required for Transport) component proteins for ESCRT assembly on endosomal membrane. Mutations in the coiled-coil domain (deletion of the coiled-coil domain or point mutations of the basic amino acids) dissociated CIN85 from endosomes. These mutants bound the ESCRT components in cytoplasm to prevent them from assembly on endosomal membrane and inhibited EGFR sorting for degradation. Conclusions As an adaptor protein, CIN85 interacts with variety of partners through several domains. The positive charges of basic amino acids in the coiled-coil domain are not only involved in the interaction with phosphatidic acid, but also regulate the interaction of CIN85 with c-Cbl. CIN85 also interacts with ESCRT components for protein sorting in endosomes. These CIN85-protein and CIN85-lipid interactions enable CIN85 to link EGFR-Cbl endocytic complex with fusible membrane during EGFR endocytosis and subsequently to facilitate ESCRT formation on endosomal membrane for EGFR sorting and degradation. PMID:25005938

Fatty acids bind tightly to the N-terminal domain of angiopoietin-like protein 4 and modulate its interaction with lipoprotein lipase.

PubMed

Robal, Terje; Larsson, Mikael; Martin, Miina; Olivecrona, Gunilla; Lookene, Aivar

2012-08-24

Angiopoietin-like protein 4 (Angptl4), a potent regulator of plasma triglyceride metabolism, binds to lipoprotein lipase (LPL) through its N-terminal coiled-coil domain (ccd-Angptl4) inducing dissociation of the dimeric enzyme to inactive monomers. In this study, we demonstrate that fatty acids reduce the inactivation of LPL by Angptl4. This was the case both with ccd-Angptl4 and full-length Angptl4, and the effect was seen in human plasma or in the presence of albumin. The effect decreased in the sequence oleic acid > palmitic acid > myristic acid > linoleic acid > linolenic acid. Surface plasmon resonance, isothermal titration calorimetry, fluorescence, and chromatography measurements revealed that fatty acids bind with high affinity to ccd-Angptl4. The interactions were characterized by fast association and slow dissociation rates, indicating formation of stable complexes. The highest affinity for ccd-Angptl4 was detected for oleic acid with a subnanomolar equilibrium dissociation constant (K(d)). The K(d) values for palmitic and myristic acid were in the nanomolar range. Linoleic and linolenic acid bound with much lower affinity. On binding of fatty acids, ccd-Angptl4 underwent conformational changes resulting in a decreased helical content, weakened structural stability, dissociation of oligomers, and altered fluorescence properties of the Trp-38 residue that is located close to the putative LPL-binding region. Based on these results, we propose that fatty acids play an important role in modulating the effects of Angptl4.

Identification of acidic and aromatic residues in the Zta activation domain essential for Epstein-Barr virus reactivation.

PubMed

Deng, Z; Chen, C J; Zerby, D; Delecluse, H J; Lieberman, P M

2001-11-01

Epstein-Barr virus (EBV) lytic cycle transcription and DNA replication require the transcriptional activation function of the viral immediate-early protein Zta. We describe a series of alanine substitution mutations in the Zta activation domain that reveal two functional motifs based on amino acid composition. Alanine substitution of single or paired hydrophobic aromatic amino acid residues resulted in modest transcription activation defects, while combining four substitutions of aromatic residues (F22/F26/W74/F75) led to more severe transcription defects. Substitution of acidic amino acid residue E27, D35, or E54 caused severe transcription defects on most viral promoters. Promoter- and cell-specific defects were observed for some substitution mutants. Aromatic residues were required for Zta interaction with TFIIA-TFIID and the CREB-binding protein (CBP) and for stimulation of CBP histone acetyltransferase activity in vitro. In contrast, acidic amino acid substitution mutants interacted with TFIIA-TFIID and CBP indistinguishably from the wild type. The nuclear domain 10 (ND10) protein SP100 was dispersed by most Zta mutants, but acidic residue mutations led to reduced, while aromatic substitution mutants led to increased SP100 nuclear staining. Acidic residue substitution mutants had more pronounced defects in transcription activation of endogenous viral genes in latently infected cells and for viral replication, as measured by the production of infectious virus. One mutant, K12/F13, was incapable of stimulating EBV lytic replication but had only modest transcription defects. These results indicate that Zta stimulates viral reactivation through two nonredundant structural motifs, one of which interacts with general transcription factors and coactivators, and the other has an essential but as yet not understood function in lytic transcription.

Interaction of SNP in the CRP gene and plasma fatty acid profile in inflammatory pattern: A cross-sectional population-based study.

PubMed

Oki, Erica; Norde, Marina M; Carioca, Antônio A F; Ikeda, Renata E; Souza, José M P; Castro, Inar A; Marchioni, Dirce M L; Fisberg, Regina M; Rogero, Marcelo M

2016-01-01

To assess the interaction of three single nucleotide polymorphisms in the C-reactive protein (CRP) gene and plasma fatty acid (FA) levels in modulating inflammatory profile. A total of 262 subjects, aged >19 y and <60 y, participated in a cross-sectional, population-based study performed in Brazil. Three single nucleotide polymorphisms (rs1205, rs1417938, and rs2808630) spanning the CRP gene were genotyped. Eleven plasma inflammatory biomarkers and plasma FA profile were determined. Cluster analysis was performed to stratify individuals based on eleven inflammatory biomarkers into two groups: an inflammatory (INF) and a noninflammatory group. The INF cluster had higher age, waist circumference, systolic blood pressure, and diastolic blood pressure; higher levels of triacylglycerol, high-sensitivity CRP, tumor necrosis factor-α, interleukin (IL)-8, IL-6, IL-1β, IL-12, IL-10, soluble monocyte chemoattractant protein-1, soluble intercellular adhesion molecule-1, C16:0, polyunsaturated fatty acid, and omega (n)-6 polyunsaturated fatty acid; and greater C20:4n-6, C18:1/18:0, and C20:4/20:3 ratios than the noninflammatory group. Statistically significant gene-plasma C16:1n-7 interaction was detected for rs1417938 (P = 0.047). Those with a dominant homozygous rs2808630 had a lower risk of belonging to the INF group with the upper 50th percentile of C20:4n-6, n-3 highly unsaturated FA, and C20:4/20:3 ratio. Regarding rs1205, A allele carriers had lower risk of being in the INF group when C20:5n-3 and n-3 highly unsaturated FA levels were greater than the median. The INF group exhibited changes in metabolic parameters that predispose this group to chronic disease, where polymorphisms in the CRP gene modulated the risk of being in the INF group depending on individual plasma fatty acid and lipid profile. Copyright © 2016 Elsevier Inc. All rights reserved.

Alteration of intersubunit acid–base pair interactions at the quasi-threefold axis of symmetry of Cucumber mosaic virus disrupts aphid vector transmission

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

Bricault, Christine A.; Perry, Keith L., E-mail: KLP3@cornell.edu

2013-06-05

In the atomic model of Cucumber mosaic virus (CMV), six amino acid residues form stabilizing salt bridges between subunits of the asymmetric unit at the quasi-threefold axis of symmetry. To evaluate the effects of these positions on virion stability and aphid vector transmissibility, six charged amino acid residues were individually mutated to alanine. All of the six engineered viruses were viable and exhibited near wild type levels of virion stability in the presence of urea. Aphid vector transmissibility was nearly or completely eliminated in the case of four of the mutants; two mutants demonstrated intermediate aphid transmissibility. For the majoritymore » of the engineered mutants, second-site mutations were observed following aphid transmission and/or mechanical passaging, and one restored transmission rates to that of the wild type. CMV capsids tolerate disruption of acid–base pairing interactions at the quasi-threefold axis of symmetry, but these interactions are essential for maintaining aphid vector transmissibility. - Highlights: ► Amino acids between structural subunits of Cucumber mosaic virus affect vector transmission. ► Mutant structural stability was retained, while aphid vector transmissibility was disrupted. ► Spontaneous, second-site mutations restored aphid vector transmissibility.« less

Nanotoxicity of graphene oxide: Assessing the influence of oxidation debris in the presence of humic acid.

PubMed

Clemente, Zaira; Castro, Vera Lúcia S S; Franqui, Lidiane S; Silva, Cristiane A; Martinez, Diego Stéfani T

2017-06-01

This study sought to evaluate the toxicological effects of graphene oxide (GO) through tests with Danio rerio (zebrafish) embryos, considering the influence of the base washing treatment and the interaction with natural organic matter (i.e., humic acid, HA). A commercial sample of GO was refluxed with NaOH to remove oxidation debris (OD) byproducts, which resulted in a base washed GO sample (bw-GO). This process decreased the total oxygenated groups in bw-GO and its stability in water compared to GO. When tested in the presence of HA, both GO and bw-GO stabilities were enhanced in water. Although the embryo exposure showed no acute toxicity or malformation, the larvae exposed to GO showed a reduction in their overall length and acetylcholinesterase activity. In the presence of HA, GO also inhibited acid phosphatase activity. Our findings indicate a mitigation of material toxicity after OD removal. The difference in the biological effects may be related to the materials' bioavailability and biophysicochemical interactions. This study reports for the first time the critical influence of OD on the GO material biological reactivity and HA interaction, providing new data for nanomaterial environmental risk assessment and sustainable nanotechnology. Copyright © 2017 Elsevier Ltd. All rights reserved.

An additional role for the Brønsted acid-base catalysts of mandelate racemase in transition state stabilization.

PubMed

Nagar, Mitesh; Bearne, Stephen L

2015-11-10

Mandelate racemase (MR) catalyzes the interconversion of the enantiomers of mandelate and serves as a paradigm for understanding the enzyme-catalyzed abstraction of an α-proton from a carbon acid substrate with a high pKa. The enzyme utilizes a two-base mechanism with Lys 166 and His 297 acting as Brønsted acid and base catalysts, respectively, in the R → S reaction direction. In the S → R reaction direction, their roles are reversed. Using isothermal titration calorimetry (ITC), MR is shown to bind the intermediate/transition state (TS) analogue inhibitor benzohydroxamate (BzH) in an entropy-driven process with a value of ΔCp equal to -358 ± 3 cal mol(-1) K(-1), consistent with an increased number of hydrophobic interactions. However, MR binds BzH with an affinity that is ∼2 orders of magnitude greater than that predicted solely on the basis of hydrophobic interactions [St. Maurice, M., and Bearne, S. L. (2004) Biochemistry 43, 2524], suggesting that additional specific interactions contribute to binding. To test the hypothesis that cation-π/NH-π interactions between the side chains of Lys 166 and His 297 and the aromatic ring and/or the hydroxamate/hydroximate moiety of BzH contribute to the binding of BzH, site-directed mutagenesis was used to generate the MR variants K166M, K166C, H297N, and K166M/H297N and their binding affinity for various ligands determined using ITC. Comparison of the binding affinities of these MR variants with the intermediate/TS analogues BzH and cyclohexanecarbohydroxamate revealed that cation-π/NH-π interactions between His 297 and the hydroxamate/hydroximate moiety and the phenyl ring of BzH contribute approximately 0.26 and 0.91 kcal/mol to binding, respectively, while interactions with Lys 166 contribute approximately 1.74 and 1.74 kcal/mol, respectively. Similarly, comparison of the binding affinities of these mutants with substrate analogues revealed that Lys 166 contributes >2.93 kcal/mol to the binding of (R)-atrolactate, and His 297 contributes 2.46 kcal/mol to the binding of (S)-atrolactate. These results are consistent with Lys 166 and His 297 playing dual roles in catalysis: they act as Brønsted acid-base catalysts, and they stabilize both the enolate moiety and phenyl ring of the altered substrate in the TS.

A calix[4]arene derivative and its selective interaction with drugs (clofibric acid, diclofenac and aspirin).

PubMed

Danil de Namor, Angela F; Al Nuaim, Maan; Villanueva Salas, Jose A; Bryant, Sophie; Howlin, Brendan

2017-03-30

The synthesis and characterisation of a partially substituted calix[4]arene, namely, 5,11,17,23-tetra-tert-butyl,25,27-bis[aminoethoxy] 26,28-dihydroxycalix[4]arene are reported. Its interaction with commonly used pharmaceuticals (clofibric acid, diclofenac and aspirin) was investigated by spectroscopic ( 1 H NMR and UV), electrochemical (conductance measurements) and thermal (titration calorimetry) techniques. It is concluded on the basis of the experimental work and molecular simulation studies that the receptor interacts selectively with these drugs. Preliminary studies on the selective extraction of these pharmaceuticals from water by the calix receptor are reported and the potential for a carrier mediated sensor based on this ligand for 'on site' monitoring of pharmaceuticals is discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Plasmonics-Based Detection of Virus Using Sialic Acid Functionalized Gold Nanoparticles.

PubMed

Lee, Changwon; Wang, Peng; Gaston, Marsha A; Weiss, Alison A; Zhang, Peng

2017-01-01

Biosensor for the detection of virus was developed by utilizing plasmonic peak shift phenomenon of the gold nanoparticles and viral infection mechanism of hemagglutinin on virus and sialic acid on animal cells. The plasmonic peak of the colloidal gold nanoparticles changes with the aggregation of the particles due to the plasmonic interaction between nearby particles and the color of the colloidal nanoparticle solution changes from wine red to purple. Sialic acid reduced and stabilized colloidal gold nanoparticle aggregation is induced by the addition of viral particles in the solution due to the hemagglutinin-sialic acid interaction. In this work, sialic acid reduced and stabilized gold nanoparticles (d = 20.1 ± 1.8 nm) were synthesized by a simple one-pot, green method without chemically modifying sialic acid. The gold nanoparticles showed target-specific aggregation with viral particles via hemagglutinin-sialic acid binding. A linear correlation was observed between the change in optical density and dilution of chemically inactivated influenza B virus species. The detection limit of the virus dilution (hemagglutinination assay titer, 512) was shown to be 0.156 vol% and the upper limit of the linearity can be extended with the use of more sialic acid-gold nanoparticles.

Reduction of CO 2 to methanol using aluminum ester FLPs

DOE PAGES

Smythe, Nathan C.; Dixon, David A.; Garner, III, Edward B.; ...

2015-10-09

Herein we report the synthesis of Al-based esters containing halogenated benzene rings. These Lewis acids were paired with phosphines to form frustrated Lewis pairs (FLPs) which could subsequently bind CO 2. While these FLPs were not sufficiently water-stable to catalyze the reduction of CO 2 to MeOH using NH 3BH 3 as the reductant, we examine the effect of varying Lewis acid strength. Frustrated Lewis pairs (FLPs) are combinations of Lewis acids and Lewis bases where the acid and base are either sterically or geometrically restricted from interacting as strongly as their electronic structures would allow. This effect leads tomore » enhanced reactivity towards small molecules and, consequently, interest in their potential as metal-free catalysts [1], [2], [3], [4] and [5]. Furthermore, to-date, the biggest success has been based around the ability of a myriad of systems to heterolytically cleave H 2 and perform catalytic hydrogenations [2] and [3].« less

Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria

NASA Astrophysics Data System (ADS)

Amin, S. A.; Hmelo, L. R.; van Tol, H. M.; Durham, B. P.; Carlson, L. T.; Heal, K. R.; Morales, R. L.; Berthiaume, C. T.; Parker, M. S.; Djunaedi, B.; Ingalls, A. E.; Parsek, M. R.; Moran, M. A.; Armbrust, E. V.

2015-06-01

Interactions between primary producers and bacteria impact the physiology of both partners, alter the chemistry of their environment, and shape ecosystem diversity. In marine ecosystems, these interactions are difficult to study partly because the major photosynthetic organisms are microscopic, unicellular phytoplankton. Coastal phytoplankton communities are dominated by diatoms, which generate approximately 40% of marine primary production and form the base of many marine food webs. Diatoms co-occur with specific bacterial taxa, but the mechanisms of potential interactions are mostly unknown. Here we tease apart a bacterial consortium associated with a globally distributed diatom and find that a Sulfitobacter species promotes diatom cell division via secretion of the hormone indole-3-acetic acid, synthesized by the bacterium using both diatom-secreted and endogenous tryptophan. Indole-3-acetic acid and tryptophan serve as signalling molecules that are part of a complex exchange of nutrients, including diatom-excreted organosulfur molecules and bacterial-excreted ammonia. The potential prevalence of this mode of signalling in the oceans is corroborated by metabolite and metatranscriptome analyses that show widespread indole-3-acetic acid production by Sulfitobacter-related bacteria, particularly in coastal environments. Our study expands on the emerging recognition that marine microbial communities are part of tightly connected networks by providing evidence that these interactions are mediated through production and exchange of infochemicals.

Alignment-Annotator web server: rendering and annotating sequence alignments.

PubMed

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Electronic structure and acid-base properties of Kojic acid and its dimers. A DFT and quantum topology study

NASA Astrophysics Data System (ADS)

Aziz, Saadullah G.; Alyoubi, Abdulrahman O.; Elroby, Shaaban A.; Hilal, Rifaat H.

2017-10-01

Kojic acid is a polyfunctional heterocyclic compound, with several important reaction centres; it has a wide range of applications in the cosmetic, medicine, food, agriculture and chemical industries. The present study aims at better insight into its electronic structure and bonding characteristics. Thus, density functional theory at the M06-2x /6-311++G** level of theory is used to investigate its ground state electronic and acid-base properties. Protonation and deprotonation enthalpies are computed and analysed. The ability of Kojic acid to form both water complexes and dimers is explored. Several different complexes and dimer structures were examined. Natural bond order and quantum topology features of the charge density were analysed. The origin of the stability of the studied complexes and dimer structures can be traced to hydrogen bonding, π-conjugative and non-covalent dispersive interactions.

Interaction of silicene with amino acid analogues—from physical to chemical adsorption in gas and solvated phases

NASA Astrophysics Data System (ADS)

Jagvaral, Yesukhei; He, Haiying; Pandey, Ravindra

2018-01-01

Silicene is an emerging 2D material, and an understanding of its interaction with amino acids, the basic building blocks of protein, is of fundamental importance. In this paper, we investigate the nature of adsorption of amino-acid analogues on silicene employing density functional theory and an implicit solvation model. Amino acid analogues are defined as CH3-R molecules, where R is the functional group of the amino acid side chain. The calculated results find three distinct groups within the amino-acid analogues considered: (i) group I, which includes MeCH3 and MeSH, interacts with silicene via the van der Waals dispersive terms leading to physisorbed configurations; (ii) group II strongly interacts with silicene forming Si-O/N chemical bonds in the chemisorbed configurations; and (iii) group III, which consists of the phenyl group, interacts with silicene via π-π interactions leading to physisorbed configurations. The results show that the lateral chains of the amino acids intrinsically determine the interactions between protein and silicene at the interface under the given physiological conditions.

NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation.

PubMed

Giollo, Manuel; Martin, Alberto J M; Walsh, Ian; Ferrari, Carlo; Tosatto, Silvio C E

2014-01-01

The rapid growth of un-annotated missense variants poses challenges requiring novel strategies for their interpretation. From the thermodynamic point of view, amino acid changes can lead to a change in the internal energy of a protein and induce structural rearrangements. This is of great relevance for the study of diseases and protein design, justifying the development of prediction methods for variant-induced stability changes. Here we propose NeEMO, a tool for the evaluation of stability changes using an effective representation of proteins based on residue interaction networks (RINs). RINs are used to extract useful features describing interactions of the mutant amino acid with its structural environment. Benchmarking shows NeEMO to be very effective, allowing reliable predictions in different parts of the protein such as β-strands and buried residues. Validation on a previously published independent dataset shows that NeEMO has a Pearson correlation coefficient of 0.77 and a standard error of 1 Kcal/mol, outperforming nine recent methods. The NeEMO web server can be freely accessed from URL: http://protein.bio.unipd.it/neemo/. NeEMO offers an innovative and reliable tool for the annotation of amino acid changes. A key contribution are RINs, which can be used for modeling proteins and their interactions effectively. Interestingly, the approach is very general, and can motivate the development of a new family of RIN-based protein structure analyzers. NeEMO may suggest innovative strategies for bioinformatics tools beyond protein stability prediction.

Study of nucleic acid-gold nanorod interactions and detecting nucleic acid hybridization using gold nanorod solutions in the presence of sodium citrate.

PubMed

Kanjanawarut, Roejarek; Su, Xiaodi

2010-09-01

In this study, the authors report that sodium citrate can aggregate hexadecyl-trimethyl-ammonium ion(+)-coated gold nanorods (AuNRs), and nucleic acids of different charge and structure properties, i.e., single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), single-stranded peptide nucleic acid (PNA), and PNA-DNA complex, can bind to the AuNRs and therefore retard the sodium citrate-induced aggregation to different extents. The discovery that hybridized dsDNA (and the PNA-DNA complex) has a more pronounced protection effect than ssDNA (and PNA) allows the authors to develop a homogeneous phase AuNRs-based UV-visible (UV-vis) spectral assay for detecting specific sequences of oligonucleotides (20 mer) with a single-base-mismatch selectivity and a limit of detection of 5 nM. This assay involves no tedious bioconjugation and on-particle hybridization. The simple "set and test" format allows for a highly efficient hybridization in a homogeneous phase and a rapid display of the results in less than a minute. By measuring the degree of reduction in AuNR aggregation in the presence of different nucleic acid samples, one can assess how different nucleic acids interact with the AuNRs to complement the knowledge of spherical gold nanoparticles. Besides UV-vis characterization, transmission electron microscopy and zeta potential measurements were conduced to provide visual evidence of the particle aggregation and to support the discussion of the assay principle.

A charge transfer amplified fluorescent Hg2+ complex for detection of picric acid and construction of logic functions.

PubMed

Kumar, Manoj; Reja, Shahi Imam; Bhalla, Vandana

2012-12-07

A chemosensor 3 based on the N,N-dimethylaminocinnamaldehyde has been synthesized which shows fluorescence turn-on response with Hg(2+) ions, and the in situ prepared 3-Hg(2+) complex has been used for detection of picric acid via electrostatic interaction and construction of a combinatorial logic circuit with NOR and INHIBIT logic functions.

Amino acid substitutions affecting aspartic acid 605 and valine 606 decrease the interaction strength between the influenza virus RNA polymerase PB2 '627' domain and the viral nucleoprotein.

PubMed

Hsia, Ho-Pan; Yang, Yin-Hua; Szeto, Wun-Chung; Nilsson, Benjamin E; Lo, Chun-Yeung; Ng, Andy Ka-Leung; Fodor, Ervin; Shaw, Pang-Chui

2018-01-01

The influenza virus RNA genome is transcribed and replicated in the context of the viral ribonucleoprotein (vRNP) complex by the viral RNA polymerase. The nucleoprotein (NP) is the structural component of the vRNP providing a scaffold for the viral RNA. In the vRNP as well as during transcription and replication the viral polymerase interacts with NP but it is unclear which parts of the polymerase and NP mediate these interactions. Previously the C-terminal '627' domain (amino acids 538-693) of PB2 was shown to interact with NP. Here we report that a fragment encompassing amino acids 146-185 of NP is sufficient to mediate this interaction. Using NMR chemical shift perturbation assays we show that amino acid region 601 to 607 of the PB2 '627' domain interacts with this fragment of NP. Substitutions of these PB2 amino acids resulted in diminished RNP activity and surface plasmon resonance assays showed that amino acids D605 was essential for the interaction with NP and V606 may also play a partial role in the interaction. Collectively these results reveal a possible interaction surface between NP and the PB2 subunit of the RNA polymerase complex.

Study of pyrolysed acid and based treated coconut coir as green photocatalyst substrate

NASA Astrophysics Data System (ADS)

Asim, Nilofar; Emdadi, Zeynab; Abdullah, N. A.; Mohammad, Masita; Badiei, Marzieh; Sopian, Kamaruzzaman

2017-12-01

This study investigates the possible contribution to sustainable development by utilizing agriculture waste materials to prepare a substrate for photo-catalysis application. The photocatalytic performance of impregnated TiO2 on acid and base- treated coconut coir (CC) and their pyrolysed form have been studied. The photocatalytic performance of impregnated TiO2 on acid treated CC improved compared to bare TiO2. However, the pyrolysed samples showed higher thermal stability and porosity compared to only treated CC, their catalytic performance was decreased. It seems that impregnated TiO2 undergo interaction with treated CC during pyrolysis. More investigations to reveal exact reason of this behavior is in progress.

Sialic Acid-Responsive Polymeric Interface Material: From Molecular Recognition to Macroscopic Property Switching

NASA Astrophysics Data System (ADS)

Xiong, Yuting; Jiang, Ge; Li, Minmin; Qing, Guangyan; Li, Xiuling; Liang, Xinmiao; Sun, Taolei

2017-01-01

Biological systems that utilize multiple weak non-covalent interactions and hierarchical assemblies to achieve various bio-functions bring much inspiration for the design of artificial biomaterials. However, it remains a big challenge to correlate underlying biomolecule interactions with macroscopic level of materials, for example, recognizing such weak interaction, further transforming it into regulating material’s macroscopic property and contributing to some new bio-applications. Here we designed a novel smart polymer based on polyacrylamide (PAM) grafted with lactose units (PAM-g-lactose0.11), and reported carbohydrate-carbohydrate interaction (CCI)-promoted macroscopic properties switching on this smart polymer surface. Detailed investigations indicated that the binding of sialic acid molecules with the grafted lactose units via the CCIs induced conformational transformation of the polymer chains, further resulted in remarkable and reversible switching in surface topography, wettability and stiffness. With these excellent recognition and response capacities towards sialic acid, the PAM-g-lactose0.11 further facilitated good selectivity, strong anti-interference and high adsorption capacity in the capture of sialylated glycopeptides (important biomarkers for cancers). This work provides some enlightenment for the development of biointerface materials with tunable property, as well as high-performance glycopeptide enrichment materials.

Identification of continuous interaction sites in PLA(2)-based protein complexes by peptide arrays.

PubMed

Fortes-Dias, Consuelo Latorre; Santos, Roberta Márcia Marques dos; Magro, Angelo José; Fontes, Marcos Roberto de Mattos; Chávez-Olórtegui, Carlos; Granier, Claude

2009-01-01

Crotoxin (CA.CB) is a beta-neurotoxin from Crotalus durissus terrificus snake venom that is responsible for main envenomation effects upon biting by this snake. It is a heterodimer of an acidic protein (CA) devoid of any biological activity per se and a basic, enzymatically active, PLA(2) counterpart (CB). Both lethal and enzymatic activities of crotoxin have been shown to be inhibited by CNF, a protein from the blood of C. d. terrificus snakes. CNF replaces CA in the CA.CB complex, forming a stable, non-toxic complex CNF.CB. The molecular sites involved in the tight interfacial protein-protein interactions in these PLA(2)-based complexes have not been clearly determined. To help address this question, we used the peptide arrays approach to map possible interfacial interaction sites in CA.CB and CNF.CB. Amino acid stretches putatively involved in these interactions were firstly identified in the primary structure of CB. Further analysis of the interfacial availability of these stretches in the presumed biologically active structure of CB, suggested two interaction main sites, located at the amino-terminus and beta-wing regions. Peptide segments at the carboxyl-terminus of CB were also suggested to play a secondary role in the binding of both CA and CNF.

Amino Acid Interaction (INTAA) web server.

PubMed

Galgonek, Jakub; Vymetal, Jirí; Jakubec, David; Vondrášek, Jirí

2017-07-03

Large biomolecules-proteins and nucleic acids-are composed of building blocks which define their identity, properties and binding capabilities. In order to shed light on the energetic side of interactions of amino acids between themselves and with deoxyribonucleotides, we present the Amino Acid Interaction web server (http://bioinfo.uochb.cas.cz/INTAA/). INTAA offers the calculation of the residue Interaction Energy Matrix for any protein structure (deposited in Protein Data Bank or submitted by the user) and a comprehensive analysis of the interfaces in protein-DNA complexes. The Interaction Energy Matrix web application aims to identify key residues within protein structures which contribute significantly to the stability of the protein. The application provides an interactive user interface enhanced by 3D structure viewer for efficient visualization of pairwise and net interaction energies of individual amino acids, side chains and backbones. The protein-DNA interaction analysis part of the web server allows the user to view the relative abundance of various configurations of amino acid-deoxyribonucleotide pairs found at the protein-DNA interface and the interaction energies corresponding to these configurations calculated using a molecular mechanical force field. The effects of the sugar-phosphate moiety and of the dielectric properties of the solvent on the interaction energies can be studied for the various configurations. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

[Molecular Dynamics of N- and C-terminal Interactions during Autoinhibition and Activation of Formin mDial].

PubMed

Orshanskiy, I A; Popinako, A V; Volokh, O I; Shaitan, K V; Sokolova, O S

2015-01-01

With the method of molecular dynamics, pairs of amino acid residues have been identified on the surface of the interacting formin mDial domains: DID-DAD, which are responsible for the autoinhibition of formin, and the GTPase Rho-DID domain, and control activation. It was found that the most stable interactions are ionic interactions between Glu178 residue and Arg248 residue, as well as hydrophobic interactions between Thr175 and Phe247. The strongest interactions proved to be between the DID domain with Rho-GTPase. These interactions are mediated by specific triple ionic interactions between positively charged amino acid in Rho, and a triplet of amino acids in DID, consisting of two negatively charged amino acids, separated by one uncharged. Binding sites for Rho-GTPase and DAD partially overlap, but various amino acids on the DID participate in interactions with different domains. We discuss the possible conformational changes in formin domains during activation and inactivation.

Somnambulism due to probable interaction of valproic acid and zolpidem.

PubMed

Sattar, S Pirzada; Ramaswamy, Sriram; Bhatia, Subhash C; Petty, Frederick

2003-10-01

To report a case of somnambulism due to a probable interaction between valproic acid and zolpidem in a patient with no prior personal or family history of somnambulism. A 47-year-old white man with a history of bipolar disorder was being maintained on citalopram 40 mg once daily and zolpidem 5 mg at bedtime. During treatment, he developed manic symptoms and was started on adjunctive valproic acid therapy. Soon after this, he developed episodes of somnambulism, which stopped when valproic acid was discontinued. On rechallenge with valproic acid, somnambulism returned. To our knowledge, this is the first report in the literature describing a probable interaction between valproic acid and zolpidem leading to somnambulism. Even though valproic acid has been associated with sleep changes, there are no published reports of somnambulism with this agent. Zolpidem has been associated with somnambulism, but our patient did not experience this when he was on zolpidem monotherapy. However, within 2 days of starting adjunctive valproic acid, sleepwalking occurred. It stopped after valproic acid was withdrawn. On rechallenge with valproic acid, sleepwalking recurred. However, when zolpidem was discontinued and valproic acid was continued, somnambulism did not occur. An assessment on the Naranjo probability scale suggests probable pharmacokinetic or pharmacodynamic interactions between the 2 medications. Valproic acid and zolpidem are generally safe medications that are commonly prescribed and often used together. No interactions have been previously reported with combined use of valproic acid and zolpidem. This case suggests a probable interaction between these 2 agents that can have a serious consequence, somnambulism. This could be frightening to patients and put them in danger. Recognition of such interactions that place patients at risk for potentially serious adverse events is imperative for appropriate care.

Optimization of o-phtaldialdehyde/2-mercaptoethanol postcolumn reaction for the hydrophilic interaction liquid chromatography determination of memantine utilizing a silica hydride stationary phase.

PubMed

Douša, Michal; Pivoňková, Veronika; Sýkora, David

2016-08-01

A rapid procedure for the determination of memantine based on hydrophilic interaction chromatography with fluorescence detection was developed. Fluorescence detection after postcolumn derivatization with o-phtaldialdehyde/2-mercaptoethanol was performed at excitation and emission wavelengths of 345 and 450 nm, respectively. The postcolumn reaction conditions such as reaction temperature, derivatization reagent flow rate, and reagents concentration were studied due to steric hindrance of amino group of memantine. The derivatization reaction was applied for the hydrophilic interaction liquid chromatography method which was based on Cogent Silica-C stationary phase with a mobile phase consisting of a mixture of 10 mmol/L citric acid and 10 mmol/L o-phosphoric acid (pH 6.0) with acetonitrile using an isocratic composition of 2:8 v/v. The benefit of the reported approach consists in a simple sample pretreatment and a quick and sensitive hydrophilic interaction chromatography method. The developed method was validated in terms of linearity, accuracy, precision, and selectivity according to the International Conference on Harmonisation guidelines. The developed method was successfully applied for the analysis of commercial memantine tablets. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A method for generating reliable atomistic models of amorphous polymers based on a random search of energy minima

NASA Astrophysics Data System (ADS)

Curcó, David; Casanovas, Jordi; Roca, Marc; Alemán, Carlos

2005-07-01

A method for generating atomistic models of dense amorphous polymers is presented. The method is organized in a two-steps procedure. First, structures are generated using an algorithm that minimizes the torsional strain. After this, a relaxation algorithm is applied to minimize the non-bonding interactions. Two alternative relaxation methods, which are based simple minimization and Concerted Rotation techniques, have been implemented. The performance of the method has been checked by simulating polyethylene, polypropylene, nylon 6, poly(L,D-lactic acid) and polyglycolic acid.

The role of the acidity of N-heteroaryl sulfonamides as inhibitors of bcl-2 family protein-protein interactions.

PubMed

Touré, B Barry; Miller-Moslin, Karen; Yusuff, Naeem; Perez, Lawrence; Doré, Michael; Joud, Carol; Michael, Walter; DiPietro, Lucian; van der Plas, Simon; McEwan, Michael; Lenoir, Francois; Hoe, Madelene; Karki, Rajesh; Springer, Clayton; Sullivan, John; Levine, Kymberly; Fiorilla, Catherine; Xie, Xiaoling; Kulathila, Raviraj; Herlihy, Kara; Porter, Dale; Visser, Michael

2013-02-14

Overexpression of the antiapoptotic members of the Bcl-2 family of proteins is commonly associated with cancer cell survival and resistance to chemotherapeutics. Here, we describe the structure-based optimization of a series of N-heteroaryl sulfonamides that demonstrate potent mechanism-based cell death. The role of the acidic nature of the sulfonamide moiety as it relates to potency, solubility, and clearance is examined. This has led to the discovery of novel heterocyclic replacements for the acylsulfonamide core of ABT-737 and ABT-263.

Mixed micelles of 7,12-dioxolithocholic acid and selected hydrophobic bile acids: interaction parameter, partition coefficient of nitrazepam and mixed micelles haemolytic potential.

PubMed

Poša, Mihalj; Tepavčević, Vesna

2011-09-01

The formation of mixed micelles built of 7,12-dioxolithocholic and the following hydrophobic bile acids was examined by conductometric method: cholic (C), deoxycholic (D), chenodeoxycholic (CD), 12-oxolithocholic (12-oxoL), 7-oxolithocholic (7-oxoL), ursodeoxycholic (UD) and hiodeoxycholic (HD). Interaction parameter (β) in the studied binary mixed micelles had negative value, suggesting synergism between micelle building units. Based on β value, the hydrophobic bile acids formed two groups: group I (C, D and CD) and group II (12-oxoL, 7-oxoL, UD and HD). Bile acids from group II had more negative β values than bile acids from group I. Also, bile acids from group II formed intermolecular hydrogen bonds in aggregates with both smaller (2) and higher (4) aggregation numbers, according to the analysis of their stereochemical (conformational) structures and possible structures of mixed micelles built of these bile acids and 7,12-dioxolithocholic acid. Haemolytic potential and partition coefficient of nitrazepam were higher in mixed micelles built of the more hydrophobic bile acids (C, D, CD) and 7,12-dioxolithocholic acid than in micelles built only of 7,12-dioxolithocholic acid. On the other hand, these mixed micelles still had lower values of haemolytic potential than micelles built of C, D or CD. The mixed micelles that included bile acids: 12-oxoL, 7-oxoL, UD or HD did not significantly differ from the micelles of 7,12-dioxolithocholic acid, observing the values of their haemolytic potential. Copyright © 2011 Elsevier B.V. All rights reserved.

Study of mixed Ca-Zn hydroxyapatite surface modified by lactic acid

NASA Astrophysics Data System (ADS)

Turki, Thouraya; Aissa, Abdallah; Bac, Christophe Goze; Rachdi, Férid; Debbabi, Mongi

2012-07-01

The new hybrid inorganic-organic composites, Ca(10-x)Znx(PO4)6(OH)2-lactic acid, at different amounts of zinc and lactic acid were prepared by dissolution of the organic compound in an hydroxyapatite suspension. They were characterized by XRD, IR, MAS NMR (13C and 1H) and chemical analysis. The crystallinity was slightly affected by the presence of organic fragments. IR and (13C and 1H) MAS NMR measurements indicate that the carboxylic groups of the acid interact with calcium and zinc ions of hydroxyapatite surface. Chemical analysis displays that zinc promotes the acid grafting. A mechanism of surface modification is proposed based on the obtained results.

Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids

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

Zhukhlistova, N. E.; Balaev, V. V.; Lyashenko, A. V.

2012-05-15

Endonucleases (EC 3.1) are enzymes of the hydrolase class that catalyze the hydrolytic cleavage of deoxyribonucleic and ribonucleic acids at any region of the polynucleotide chain. Endonucleases are widely used both in biotechnological processes and in veterinary medicine as antiviral agents. Medical applications of endonucleases in human cancer therapy hold promise. The results of X-ray diffraction studies of the spatial organization of endonucleases and their complexes and the mechanism of their action are analyzed and generalized. An analysis of the structural studies of this class of enzymes showed that the specific binding of enzymes to nucleic acids is characterized bymore » interactions with nitrogen bases and the nucleotide backbone, whereas the nonspecific binding of enzymes is generally characterized by interactions only with the nucleic-acid backbone. It should be taken into account that the specificity can be modulated by metal ions and certain low-molecular-weight organic compounds. To test the hypotheses about specific and nonspecific nucleic-acid-binding proteins, it is necessary to perform additional studies of atomic-resolution three-dimensional structures of enzyme-nucleic-acid complexes by methods of structural biology.« less

Crystal engineering of novel cocrystals of a triazole drug with 1,4-dicarboxylic acids.

PubMed

Remenar, Julius F; Morissette, Sherry L; Peterson, Matthew L; Moulton, Brian; MacPhee, J Michael; Guzmán, Héctor R; Almarsson, Orn

2003-07-16

Cocrystals of the poorly soluble antifungal drug cis-itraconazole (1) with 1,4-dicarboxylic acids have been prepared. The crystal structure of the succinic acid cocrystal with 1 was determined to be a trimer by single-crystal X-ray. The trimer is comprised of two molecules of 1 oriented in antiparallel fashion to form a pocket with a triazole at either end. The extended succinic acid molecule fills the pocket, bridging the triazole groups through hydrogen-bonding interactions rather than interacting with the more basic piperazine nitrogens. The solubility and dissolution rate of some of the cocrystals are approximately the same as those of the amorphous drug in the commercial formulation and are much higher than those for the crystalline free base. The results suggest that cocrystals of drug molecules have the possibility of achieving the higher oral bioavailability common for amorphous forms of water-insoluble drugs while maintaining the long-term chemical and physical stability that crystal forms provide.

A molecular rotor based ratiometric sensor for basic amino acids.

PubMed

Pettiwala, Aafrin M; Singh, Prabhat K

2018-01-05

The inevitable importance of basic amino acids, arginine and lysine, in human health and metabolism demands construction of efficient sensor systems for them. However, there are only limited reports on the 'ratiometric' detection of basic amino acids which is further restricted by the use of chemically complex sensor molecules, which impedes their prospect for practical applications. Herein, we report a ratiometric sensor system build on simple mechanism of disassociation of novel emissive Thioflavin-T H-aggregates from heparin surface, when subjected to interaction with basic amino acids. The strong and selective electrostatic and hydrogen bonding interaction of basic amino acids with heparin leads to large alteration in photophysical attributes of heparin bound Thioflavin-T, which forms a highly sensitive sensor platform for detection of basic amino acids in aqueous solution. These selective interactions between basic amino acids and heparin allow our sensor system to discriminate arginine and lysine from other amino acids. This unique mechanism of dissociation of Thioflavin-T aggregates from heparin surface provides ratiometric response on both fluorimetric and colorimetric outputs for detection of arginine and lysine, and thus it holds a significant advantage over other developed sensor systems which are restricted to single wavelength detection. Apart from the sensitivity and selectivity, our system also provides the advantage of simplicity, dual mode of sensing, and more importantly, it employs an inexpensive commercially available probe molecule, which is a significant advantage over other developed sensor systems that uses tedious synthesis protocol for the employed probe in the detection scheme, an impediment for practical applications. Additionally, our sensor system also shows response in complex biological media of serum samples. Copyright © 2017 Elsevier B.V. All rights reserved.

A hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS) based metabolomics study on colour stability of ovine meat.

PubMed

Subbaraj, Arvind K; Kim, Yuan H Brad; Fraser, Karl; Farouk, Mustafa M

2016-07-01

Meat colour is one of the cues available to the consumer to gauge overall meat quality and wholesomeness. Colour stability of meat is determined by several factors both inherent to the animal and post-slaughter conditions, including ageing, storage/packaging and display times. A hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS) based metabolomics study was undertaken to identify and compare polar metabolites between ovine meat samples that were exposed to different durations of ageing, storage conditions, and display times. Primary metabolites comprising amino acids, sugars, nucleotides, nucleosides, organic acids and their breakdown products were mainly identified as discriminating factors. For the first time, boron complexes of sugar and malic acid were also tentatively identified. As expected, most compounds identified were related to myoglobin chemistry, and compounds with antioxidant properties were found in higher levels in colour stable samples. Supplementary studies identifying semi-polar, non-polar and volatile compounds will provide a holistic understanding of the chemical basis of colour stability in ovine meat. Copyright © 2016 Elsevier Ltd. All rights reserved.

Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis

PubMed Central

Jakubec, David; Laskowski, Roman A.; Vondrasek, Jiri

2016-01-01

Decades of intensive experimental studies of the recognition of DNA sequences by proteins have provided us with a view of a diverse and complicated world in which few to no features are shared between individual DNA-binding protein families. The originally conceived direct readout of DNA residue sequences by amino acid side chains offers very limited capacity for sequence recognition, while the effects of the dynamic properties of the interacting partners remain difficult to quantify and almost impossible to generalise. In this work we investigated the energetic characteristics of all DNA residue—amino acid side chain combinations in the conformations found at the interaction interface in a very large set of protein—DNA complexes by the means of empirical potential-based calculations. General specificity-defining criteria were derived and utilised to look beyond the binding motifs considered in previous studies. Linking energetic favourability to the observed geometrical preferences, our approach reveals several additional amino acid motifs which can distinguish between individual DNA bases. Our results remained valid in environments with various dielectric properties. PMID:27384774

Arginine 26 and aspartic acid 69 of the regulatory subunit are key residues of subunits interaction of acetohydroxyacid synthase isozyme III from E. coli.

PubMed

Zhao, Yuefang; Wen, Xin; Niu, Congwei; Xi, Zhen

2012-11-05

Acetohydroxyacid synthase (AHAS), which catalyzes the first step in the biosynthesis of branched-chain amino acids, is composed of catalytic and regulatory subunits. The enzyme exhibits full activity only when the regulatory subunit (RSU) binds to the catalytic subunit (CSU). However, the crystal structure of the holoenzyme has not been reported yet, and the molecular interaction between the CSU and RSU is also unknown. Herein, we introduced a global-surface, site-directed labeling scanning method to determine the potential interaction region of the RSU. This approach relies on the insertion of a bulky fluorescent probe at the designated site on the surface of the RSU to cause a dramatic change in holoenzyme activity by perturbing subunit interaction. Then, the key amino acid residues in the potential interaction regions were identified by site-directed mutagenesis. Compared to the wild-type, the single-point mutants R26A and D69A showed 54 and 64 % activity, respectively, whereas the double mutant (R26A+D69A) gave 14 %, thus suggesting that residues Arg26 and Asp69 are the key residues of subunit interaction with cooperative action. Additionally, the results of GST pull-down assays and pH-dependence experiments suggested that polar interaction is the main force for subunits interaction. A plausible protein-protein interaction model of the holoenzyme of Escherichia coli AHAS III is proposed, based on the mutagenesis and protein docking studies. The protocol established here should be useful for the identification of the molecular interactions between proteins. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure-based conformational preferences of amino acids

PubMed Central

Koehl, Patrice; Levitt, Michael

1999-01-01

Proteins can be very tolerant to amino acid substitution, even within their core. Understanding the factors responsible for this behavior is of critical importance for protein engineering and design. Mutations in proteins have been quantified in terms of the changes in stability they induce. For example, guest residues in specific secondary structures have been used as probes of conformational preferences of amino acids, yielding propensity scales. Predicting these amino acid propensities would be a good test of any new potential energy functions used to mimic protein stability. We have recently developed a protein design procedure that optimizes whole sequences for a given target conformation based on the knowledge of the template backbone and on a semiempirical potential energy function. This energy function is purely physical, including steric interactions based on a Lennard-Jones potential, electrostatics based on a Coulomb potential, and hydrophobicity in the form of an environment free energy based on accessible surface area and interatomic contact areas. Sequences designed by this procedure for 10 different proteins were analyzed to extract conformational preferences for amino acids. The resulting structure-based propensity scales show significant agreements with experimental propensity scale values, both for α-helices and β-sheets. These results indicate that amino acid conformational preferences are a natural consequence of the potential energy we use. This confirms the accuracy of our potential and indicates that such preferences should not be added as a design criterion. PMID:10535955

Ligand-functionalized degradable polyplexes formed by cationic poly(aspartic acid)-grafted chitosan-cyclodextrin conjugates

NASA Astrophysics Data System (ADS)

Song, Hai-Qing; Li, Rui-Quan; Duan, Shun; Yu, Bingran; Zhao, Hong; Chen, Da-Fu; Xu, Fu-Jian

2015-03-01

Polypeptide-based degradable polyplexes attracted considerable attention in drug delivery systems. Polysaccharides including cyclodextrin (CD), dextran, and chitosan (CS) were readily grafted with cationic poly(aspartic acid)s (PAsps). To further enhance the transfection performances of PAsp-based polyplexes, herein, different types of ligand (folic acid, FA)-functionalized degradable polyplexes were proposed based on the PAsp-grafted chitosan-cyclodextrin conjugate (CCPE), where multiple β-CDs were tied on a CS chain. The FA-functionalized CCPE (i.e., CCPE-FA) was obtained via a host-guest interaction between the CD units of CCPE and the adamantane (Ad) species of Ad-modified FA (Ad-FA). The resulting CCPE/pDNA, CCPE-FA/pDNA, and ternary CCPE-FA/CCPE/pDNA (prepared by layer-by-layer assembly) polyplexes were investigated in detail using different cell lines. The CCPE-based polyplexes displayed much higher transfection efficiencies than the CS-based polyplexes reported earlier by us. The ternary polyplexes of CCPE-FA/CCPE/pDNA produced excellent gene transfection abilities in the folate receptor (FR)-positive tumor cells. This work would provide a promising means to produce highly efficient polyplexes for future gene therapy applications.Polypeptide-based degradable polyplexes attracted considerable attention in drug delivery systems. Polysaccharides including cyclodextrin (CD), dextran, and chitosan (CS) were readily grafted with cationic poly(aspartic acid)s (PAsps). To further enhance the transfection performances of PAsp-based polyplexes, herein, different types of ligand (folic acid, FA)-functionalized degradable polyplexes were proposed based on the PAsp-grafted chitosan-cyclodextrin conjugate (CCPE), where multiple β-CDs were tied on a CS chain. The FA-functionalized CCPE (i.e., CCPE-FA) was obtained via a host-guest interaction between the CD units of CCPE and the adamantane (Ad) species of Ad-modified FA (Ad-FA). The resulting CCPE/pDNA, CCPE-FA/pDNA, and ternary CCPE-FA/CCPE/pDNA (prepared by layer-by-layer assembly) polyplexes were investigated in detail using different cell lines. The CCPE-based polyplexes displayed much higher transfection efficiencies than the CS-based polyplexes reported earlier by us. The ternary polyplexes of CCPE-FA/CCPE/pDNA produced excellent gene transfection abilities in the folate receptor (FR)-positive tumor cells. This work would provide a promising means to produce highly efficient polyplexes for future gene therapy applications. Electronic supplementary information (ESI) available: 1H NMR assay, synthetic route of Ad-FA, AFM images and cellular internalization rate can be found in ESI. See DOI: 10.1039/c4nr07515c

Variable Temperature Infrared Spectroscopy Investigation of Benzoic Acid Interactions with Montmorillonite Clay Interlayer Water.

PubMed

Nickels, Tara M; Ingram, Audrey L; Maraoulaite, Dalia K; White, Robert L

2015-07-01

Molecular interactions between benzoic acid and cations and water contained in montmorillonite clay interlayer spaces are characterized by using variable temperature diffuse reflection infrared Fourier transform spectroscopy (VT-DRIFTS). Using sample perturbation and difference spectroscopy, infrared spectral changes resulting from removal of interlayer water and associated changes in local benzoic acid environments are identified. Difference spectra features can be correlated with changes in specific molecular vibrations that are characteristic of benzoic acid molecular orientation. Results suggest that the carboxylic acid functionality of benzoic acid interacts with interlayer cations through a bridging water molecule and that this interaction is affected by the nature of the cation present in the clay interlayer space.

The cytosolic domain of T-cell receptor ζ associates with membranes in a dynamic equilibrium and deeply penetrates the bilayer.

PubMed

Zimmermann, Kerstin; Eells, Rebecca; Heinrich, Frank; Rintoul, Stefanie; Josey, Brian; Shekhar, Prabhanshu; Lösche, Mathias; Stern, Lawrence J

2017-10-27

Interactions between lipid bilayers and the membrane-proximal regions of membrane-associated proteins play important roles in regulating membrane protein structure and function. The T-cell antigen receptor is an assembly of eight single-pass membrane-spanning subunits on the surface of T lymphocytes that initiates cytosolic signaling cascades upon binding antigens presented by MHC-family proteins on antigen-presenting cells. Its ζ-subunit contains multiple cytosolic immunoreceptor tyrosine-based activation motifs involved in signal transduction, and this subunit by itself is sufficient to couple extracellular stimuli to intracellular signaling events. Interactions of the cytosolic domain of ζ (ζ cyt ) with acidic lipids have been implicated in the initiation and regulation of transmembrane signaling. ζ cyt is unstructured in solution. Interaction with acidic phospholipids induces structure, but its disposition when bound to lipid bilayers is controversial. Here, using surface plasmon resonance and neutron reflection, we characterized the interaction of ζ cyt with planar lipid bilayers containing mixtures of acidic and neutral lipids. We observed two binding modes of ζ cyt to the bilayers in dynamic equilibrium: one in which ζ cyt is peripherally associated with lipid headgroups and one in which it penetrates deeply into the bilayer. Such an equilibrium between the peripherally bound and embedded forms of ζ cyt apparently controls accessibility of the immunoreceptor tyrosine-based activation signal transduction pathway. Our results reconcile conflicting findings of the ζ structure reported in previous studies and provide a framework for understanding how lipid interactions regulate motifs to tyrosine kinases and may regulate the T-cell antigen receptor biological activities for this cell-surface receptor system.

Lewis base activation of Lewis acids: catalytic, enantioselective addition of silyl ketene acetals to aldehydes.

PubMed

Denmark, Scott E; Beutner, Gregory L; Wynn, Thomas; Eastgate, Martin D

2005-03-23

The concept of Lewis base activation of Lewis acids has been reduced to practice for catalysis of the aldol reaction of silyl ketene acetals and silyl dienol ethers with aldehydes. The weakly acidic species, silicon tetrachloride (SiCl4), can be activated by binding of a strongly Lewis basic chiral phosphoramide, leading to in situ formation of a chiral Lewis acid. This species has proven to be a competent catalyst for the aldol addition of acetate-, propanoate-, and isobutyrate-derived silyl ketene acetals to conjugated and nonconjugated aldehydes. Furthermore, vinylogous aldol reactions of silyl dienol ethers are also demonstrated. The high levels of regio-, anti diastereo-, and enantioselectivity observed in these reactions can be rationalized through consideration of an open transition structure where steric interactions between the silyl cation complex and the approaching nucleophile are dominant.

Acid-Base Electronic Properties in the Gas Phase: Permanent Electric Dipole Moments of a Photoacidic Substrate.

NASA Astrophysics Data System (ADS)

Fleisher, Adam J.; Morgan, Philip J.; Pratt, David W.

2009-06-01

The permanent electric dipole moments of two conformers of 2-naphthol (2HN) in their ground and electronically excited states have been experimentally determined by Stark-effect measurements in a molecular beam. When in solution, 2HN is a weak base in the S{_0} state and a strong acid in the S{_1} state. Using sequential solvation of the cis-2HN photoacid with the base ammonia, we have begun to approach condensed phase acid-base interactions with gas phase rotational resolution. Our study, void of bulk solvent perturbations, is of importance to the larger community currently describing aromatic biomolecule and "super" photoacid behavior via theoretical modeling and condensed phase solvatochromism. [2] A. Weller. Prog. React. Kinet. 5, 273 (1970). [3] D. F. Plusquellic, X. -Q. Tan, and D. W. Pratt. J. Chem. Phys. 96, 8026 (1992).

Use of Synthetic Antibodies Targeted to the Jak/Stat Pathway in Breast Cancer

DTIC Science & Technology

2011-03-01

substance P ( SP ), an 11 amino acid neuropeptide that is rapidly internalized through specific interaction...no. 27 11011–11015 BI O CH EM IS TR Y Results Engineering a Delivery Vehicle Based on Substance P . Substance P ( SP ) is an 11 amino acid... substance P variant for receptor-mediated delivery of synthetic antibodies into tumor cells, Proc Natl Acad Sci USA. 106:11011- 5 , 2009.

Unexpected Solubility Enhancement of Drug Bases in the Presence of a Dimethylaminoethyl Methacrylate Copolymer.

PubMed

Saal, Wiebke; Ross, Alfred; Wyttenbach, Nicole; Alsenz, Jochem; Kuentz, Martin

2018-01-02

The methacrylate copolymer Eudragit EPO (EPO) has previously shown to greatly enhance solubilization of acidic drugs via ionic interactions and by multiple hydrophobic contacts with polymeric side chains. The latter type of interaction could also play a role for solubilization of other compounds than acids. The aim of this study was therefore to investigate the solubility of six poorly soluble bases in presence and absence of EPO by quantitative ultrapressure liquid chromatography with concomitant X-ray powder diffraction analysis of the solid state. For a better mechanistic understanding, spectra and diffusion data were obtained by 1 H nuclear magnetic resonance (NMR) spectroscopy. Unexpected high solubility enhancement (up to 360-fold) was evidenced in the presence of EPO despite the fact that bases and polymer were both carrying positive charges. This exceptional and unexpected solubilization was not due to a change in the crystalline solid state. NMR spectra and measured diffusion coefficients indicated both strong drug-polymer interactions in the bulk solution, and diffusion data suggested conformational changes of the polymer in solution. Such conformational changes may have increased the accessibility and extent of hydrophobic contacts thereby leading to increased overall molecular interactions. These initially surprising solubilization results demonstrate that excipient selection should not be based solely on simple considerations of, for example, opposite charges of drug and excipient, but it requires a more refined molecular view. Different solution NMR techniques are especially promising tools to gain such mechanistic insights.

The pH dependence of silicon-iron interaction in rats.

PubMed

Jia, X; Emerick, R J; Kayongo-Male, H

1997-01-01

A 2 x 2 x 3 factorial experiment was conducted to study the pH dependence of a silicon-iron interaction in vivo. The dietary treatments used in the factorial design were the following (mg/kg of diet): silicon, 0 and 500; iron, 35 and 187; acid-base, ammonium chloride as 0.5% of total diet (acidic), sodium bicarbonate as 1.0% of total diet (basic), or no supplementation of acid or base (control). The supplementation of 500 mg silicon/kg of diet increased plasma-iron concentration in rats fed the acidic or control diets, but not in rats fed the basic diet. A high dietary-iron level suppressed copper absorption and utilization and subsequently imposed a negative effect on its own utilization. An increase in the plasma total-cholesterol concentration caused by high dietary-iron level was likely a consequence of the antagonistic effect of iron on copper absorption and utilization. The use of cupric sulfate pentahydrate as the dietary-copper source in this study resulted in plasma copper concentrations that were approximately twice those obtained in a related study using cupric carbonate. Also, a 42% coefficient of variation (C.V.) for plasma-copper concentrations of rats fed cupric sulfate in this study was greatly reduced from the C.V. = 108% previously associated with the dietary cupric carbonate.

Boronic acid recognition of non-interacting carbohydrates for biomedical applications: increasing fluorescence signals of minimally interacting aldoses and sucralose†

PubMed Central

Resendez, Angel; Halim, Md Abdul; Singh, Jasmeet; Webb, Dominic-Luc

2017-01-01

To address carbohydrates that are commonly used in biomedical applications with low binding affinities for boronic acid based detection systems, two chemical modification methods were utilized to increase sensitivity. Modified carbohydrates were analyzed using a two component fluorescent probe based on boronic acid-appended viologen–HPTS (4,4′-o-BBV). Carbohydrates normally giving poor signals (fucose, l-rhamnose, xylose) were subjected to sodium borohydride (NaBH4) reduction in ambient conditions for 1 h yielding the corresponding sugar alcohols from fucose, l-rhamnose and xylose in essentially quantitative yields. Compared to original aldoses, apparent binding affinities were increased 4–25-fold. The chlorinated sweetener and colon permeability marker sucralose (Splenda), otherwise undetectable by boronic acids, was dechlorinated to a detectable derivative by reactive oxygen and hydroxide intermediates by the Fenton reaction or by H2O2 and UV light. This method is specific to sucralose as other common sugars, such as sucrose, do not contain any carbon-chlorine bonds. Significant fluorescence response was obtained for chemically modified sucralose with the 4,4′-o-BBV–HPTS probe system. This proof of principle can be applied to biomedical applications, such as gut permeability, malabsorption, etc. PMID:29130464

Zwitterionic chiral stationary phases based on cinchona and chiral sulfonic acids for the direct stereoselective separation of amino acids and other amphoteric compounds.

PubMed

Zhang, Tong; Holder, Emilie; Franco, Pilar; Lindner, Wolfgang

2014-06-01

An extensive series of free amino acids and analogs were directly resolved into enantiomers (and stereoisomers where appropriate) by HPLC on zwitterionic chiral stationary phases (Chiralpak ZWIX(+) and Chiralpak ZWIX(-)). The interaction and chiral recognition mechanisms were based on the synergistic double ion-paring process between the analyte and the chiral selectors. The chiral separation and elution order were found to be predictable for primary α-amino acids with apolar aliphatic side chains. A systematic investigation was undertaken to gain an insight into the influence of the structural features on the enantiorecognition. The presence of polar and/or aromatic groups in the analyte structure is believed to tune the double ion-paring equilibrium by the involvement of the secondary interaction forces such as hydrogen bonding, Van der Waals forces and π-π stacking in concert with steric parameters. The ZWIX chiral columns were able to separate enantiomers and stereoisomers of various amphoteric compounds with no need for precolumn derivatization. Column switching between ZWIX(+) and ZWIX(-) is believed to be an instrumental tool to reverse or control the enantiomers elution order, due to the complementarity of the applied chiral selectors. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An overview of poly(lactic-co-glycolic) acid (PLGA)-based biomaterials for bone tissue engineering.

PubMed

Gentile, Piergiorgio; Chiono, Valeria; Carmagnola, Irene; Hatton, Paul V

2014-02-28

Poly(lactic-co-glycolic) acid (PLGA) has attracted considerable interest as a base material for biomedical applications due to its: (i) biocompatibility; (ii) tailored biodegradation rate (depending on the molecular weight and copolymer ratio); (iii) approval for clinical use in humans by the U.S. Food and Drug Administration (FDA); (iv) potential to modify surface properties to provide better interaction with biological materials; and (v) suitability for export to countries and cultures where implantation of animal-derived products is unpopular. This paper critically reviews the scientific challenge of manufacturing PLGA-based materials with suitable properties and shapes for specific biomedical applications, with special emphasis on bone tissue engineering. The analysis of the state of the art in the field reveals the presence of current innovative techniques for scaffolds and material manufacturing that are currently opening the way to prepare biomimetic PLGA substrates able to modulate cell interaction for improved substitution, restoration, or enhancement of bone tissue function.

Predicting protein instability in sustained protein delivery systems using spectral-phase interference.

PubMed

Seidel, Nina; Sitterberg, Johannes; Vornholt, Wolfgang; Bakowsky, Udo; Keusgen, Michael; Kissel, Thomas

2012-02-01

Biodegradable and non-biodegradable polymers represent promising materials for sustained protein delivery systems. However, structural protein instabilities due to interactions with the polymer surface are often observed. Aim of the present study was to analyze and predict these instabilities by determination of adsorption pattern and extent via biomolecular interaction analysis. A new optical method based on spectral-phase interference successfully demonstrated its suitability for this new application scope. It was characterized in terms of sensitivity, reproducibility and dynamic range using bovine serum albumin (BSA) as model compound. For protein-polymer interaction studies, materials with different wettabilities and zeta potential were selected and successfully applied on the sensor chip: Glass, poly(styrene), poly(lactic acid), poly(lactic-co-glycolic acid), and poly(ethylene carbonate). Concentration dependent adsorption curves revealed two principal adsorption patterns based on the connection between BSA spreading and supply rate. This connection was stronger influenced by polymer hydrophobicity than surface charge. Association, dissociation and binding rate constants in the range from 0.15 to 34.19 × 10(-6) M were obtained. Atomic force microscopy images of the films before and after adsorption confirmed the previous elaborated model. Poly(ethylene carbonate) emerged as highly promising biomaterial for protein delivery due to its favorable adsorption behavior based on low polymer-protein interactions. Copyright © 2011 Elsevier Ltd. All rights reserved.

A novel TPR-BEN domain interaction mediates PICH-BEND3 association.

PubMed

Pitchai, Ganesha P; Kaulich, Manuel; Bizard, Anna H; Mesa, Pablo; Yao, Qi; Sarlos, Kata; Streicher, Werner W; Nigg, Erich A; Montoya, Guillermo; Hickson, Ian D

2017-11-02

PICH is a DNA translocase required for the maintenance of chromosome stability in human cells. Recent data indicate that PICH co-operates with topoisomerase IIα to suppress pathological chromosome missegregation through promoting the resolution of ultra-fine anaphase bridges (UFBs). Here, we identify the BEN domain-containing protein 3 (BEND3) as an interaction partner of PICH in human cells in mitosis. We have purified full length PICH and BEND3 and shown that they exhibit a functional biochemical interaction in vitro. We demonstrate that the PICH-BEND3 interaction occurs via a novel interface between a TPR domain in PICH and a BEN domain in BEND3, and have determined the crystal structure of this TPR-BEN complex at 2.2 Å resolution. Based on the structure, we identified amino acids important for the TPR-BEN domain interaction, and for the functional interaction of the full-length proteins. Our data reveal a proposed new function for BEND3 in association with PICH, and the first example of a specific protein-protein interaction mediated by a BEN domain. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Interaction between Wine Phenolic Acids and Salivary Proteins by Saturation-Transfer Difference Nuclear Magnetic Resonance Spectroscopy (STD-NMR) and Molecular Dynamics Simulations.

PubMed

Ferrer-Gallego, Raúl; Hernández-Hierro, José Miguel; Brás, Natércia F; Vale, Nuno; Gomes, Paula; Mateus, Nuno; de Freitas, Victor; Heredia, Francisco J; Escribano-Bailón, María Teresa

2017-08-09

The interaction between phenolic compounds and salivary proteins is highly related to the astringency perception. Recently, it has been proven the existence of synergisms on the perceived astringency when phenolic acids were tested as mixtures in comparison to individual compounds, maintaining constant the total amount of the stimulus. The interactions between wine phenolic acids and the peptide fragment IB7 12 have been studied by saturation-transfer difference (STD) NMR spectroscopy. This technique provided the dissociation constants and the percentage of interaction between both individual and mixtures of hydroxybenzoic and hydroxycinnamic acids and the model peptide. It is noteworthy that hydroxybenzoic acids showed higher affinity for the peptide than hydroxycinnamic acids. To obtain further insights into the mechanisms of interaction, molecular dynamics simulations have been performed. Results obtained not only showed the ability of these compounds to interact with salivary proteins but also may justify the synergistic effect observed in previous sensory studies.

Design of a photoswitchable hollow microcapsular drug delivery system by using a supramolecular drug-loading approach.

PubMed

Xiao, Wang; Chen, Wei-Hai; Zhang, Jing; Li, Cao; Zhuo, Ren-Xi; Zhang, Xian-Zheng

2011-11-24

In this study, photoswitchable microcapsules were fabricated based on host-guest interactions between α-cyclodextrin (α-CD) and azobenzene (Azo). Carboxymethyl dextran-graft-α-CD (CMD-g-α-CD) and poly(acrylic acid) N-aminododecane p-azobenzeneaminosuccinic acid (PAA-C(12)-Azo) were assembled layer by layer on CaCO(3) particles. α-CD-rhodamine B (α-CD-RhB), used as a model drug, was loaded on PAA-C(12)-Azo layers by host-guest interaction. After removal of CaCO(3) particles by ethylenediaminetetraacetic acid (EDTA), hollow microcapsules loaded with α-CD-RhB were obtained. Since the interactions between α-CD and Azo were photosensitive, the capsules could be dissociated with the irradiation of UV light, followed by the release of the model drug, α-CD-RhB. Compared with traditional drug-loading approaches such as chemical bonding and physical adsorption, our supramolecular drug-loading system has a facile loading process, ideal bonding strength, and photoswitchable behavior. These photosensitive microcapsules exhibit great potential in biomedical applications. © 2011 American Chemical Society

Proteomic strategy for the identification of critical actors in reorganization of the post-meiotic male genome.

PubMed

Govin, Jerome; Gaucher, Jonathan; Ferro, Myriam; Debernardi, Alexandra; Garin, Jerome; Khochbin, Saadi; Rousseaux, Sophie

2012-01-01

After meiosis, during the final stages of spermatogenesis, the haploid male genome undergoes major structural changes, resulting in a shift from a nucleosome-based genome organization to the sperm-specific, highly compacted nucleoprotamine structure. Recent data support the idea that region-specific programming of the haploid male genome is of high importance for the post-fertilization events and for successful embryo development. Although these events constitute a unique and essential step in reproduction, the mechanisms by which they occur have remained completely obscure and the factors involved have mostly remained uncharacterized. Here, we sought a strategy to significantly increase our understanding of proteins controlling the haploid male genome reprogramming, based on the identification of proteins in two specific pools: those with the potential to bind nucleic acids (basic proteins) and proteins capable of binding basic proteins (acidic proteins). For the identification of acidic proteins, we developed an approach involving a transition-protein (TP)-based chromatography, which has the advantage of retaining not only acidic proteins due to the charge interactions, but also potential TP-interacting factors. A second strategy, based on an in-depth bioinformatic analysis of the identified proteins, was then applied to pinpoint within the lists obtained, male germ cells expressed factors relevant to the post-meiotic genome organization. This approach reveals a functional network of DNA-packaging proteins and their putative chaperones and sheds a new light on the way the critical transitions in genome organizations could take place. This work also points to a new area of research in male infertility and sperm quality assessments.

Theoretical evidence of charge transfer interaction between SO₂ and deep eutectic solvents formed by choline chloride and glycerol.

PubMed

Li, Hongping; Chang, Yonghui; Zhu, Wenshuai; Wang, Changwei; Wang, Chao; Yin, Sheng; Zhang, Ming; Li, Huaming

2015-11-21

The nature of the interaction between deep eutectic solvents (DESs), formed by ChCl and glycerol, and SO2 has been systematically investigated using the M06-2X density functional combined with cluster models. Block-localized wave function energy decomposition (BLW-ED) analysis shows that the interaction between SO2 and DESs is dominated by a charge transfer interaction. After this interaction, the SO2 molecule becomes negatively charged, whereas the ChCl-glycerol molecule is positively charged, which is the result of Lewis acid-base interaction. The current result affords a theoretical proof that it is highly useful and efficient to manipulate the Lewis acidity of absorbents for SO2 capture. Moreover, hydrogen bonding as well as electrostatic interactions may also contribute to the stability of the complex. Structure analysis shows that solvent molecules will adjust their geometries to interact with SO2. In addition, the structure of SO2 is barely changed after interaction. The interaction energy between different cluster models and SO2 ranges from -6.8 to -14.4 kcal mol(-1). It is found that the interaction energy is very sensitive to the solvent structure. The moderate interaction between ChCl-glycerol and SO2 is consistent with the concept that highly efficient solvents for SO2 absorption should not only be solvable but also regenerable.

Tuning of acyl-ACP thioesterase activity directed for tailored fatty acid synthesis.

PubMed

Feng, Yanbin; Zhang, Yunxiu; Wang, Yayue; Liu, Jiao; Liu, Yinghui; Cao, Xupeng; Xue, Song

2018-04-01

Medium-chain fatty acids have attracted significant attention as sources of biofuels in recent years. Acyl-ACP thioesterase, which is considered as the key enzyme to determine the carbon chain length, catalyzes the termination of de novo fatty acid synthesis. Although recombinant medium-chain acyl-ACP thioesterase (TE) affects the fatty acid profile in heterologous cells, tailoring of the fatty acid composition merely by engineering a specific TE is still intractable. In this study, the activity of a C8-C10-specific thioesterase FatB2 from Cuphea hookeriana on C10-ACP was quantified twice as high as that on C8-ACP based on a synthetic C8-C16 acyl-ACP pool in vitro. Whereas in vivo, it was demonstrated that ChFatB2 preferred to accumulate C8 fatty acids with 84.9% composition in the ChFatB2-engineered E. coli strain. To achieve C10 fatty acid production, ChFatB2 was rationally tuned based on structural investigation and enzymatic analysis. An I198E mutant was identified to redistribute the C8-ACP flow, resulting in C10 fatty acid being produced as the principal component at 57.6% of total fatty acids in vivo. It was demonstrated that the activity of TE relative to β-ketoacyl-ACP synthases (KAS) directly determined the fatty acid composition. Our results provide a prospective strategy in tailoring fatty acid synthesis by tuning of TE activities based on TE-ACP interaction.

Coxsackievirus and adenovirus receptor (CAR) mediates trafficking of acid sensing ion channel 3 (ASIC3) via PSD-95.

PubMed

Excoffon, Katherine J D A; Kolawole, Abimbola O; Kusama, Nobuyoshi; Gansemer, Nicholas D; Sharma, Priyanka; Hruska-Hageman, Alesia M; Petroff, Elena; Benson, Christopher J

2012-08-17

We have previously shown that the Coxsackievirus and adenovirus receptor (CAR) can interact with post-synaptic density 95 (PSD-95) and localize PSD-95 to cell-cell junctions. We have also shown that activity of the acid sensing ion channel (ASIC3), a H(+)-gated cation channel that plays a role in mechanosensation and pain signaling, is negatively modulated by PSD-95 through a PDZ-based interaction. We asked whether CAR and ASIC3 simultaneously interact with PSD-95, and if so, whether co-expression of these proteins alters their cellular distribution and localization. Results indicate that CAR and ASIC3 co-immunoprecipitate only when co-expressed with PSD-95. CAR also brings both PSD-95 and ASIC3 to the junctions of heterologous cells. Moreover, CAR rescues PSD-95-mediated inhibition of ASIC3 currents. These data suggest that, in addition to activity as a viral receptor and adhesion molecule, CAR can play a role in trafficking proteins, including ion channels, in a PDZ-based scaffolding complex. Copyright © 2012 Elsevier Inc. All rights reserved.

The sensory interactions of organic acids and various flavors in ramen soup systems.

PubMed

Kang, M-W; Chung, S-J; Lee, H-S; Kim, Y; Kim, K-O

2007-11-01

This study was conducted to investigate the sensory interactions between various organic acids and flavorants in 3 types of ramen soup ('beef,' seafood, and 'kimchi') when types and levels of organic acids (citric, malic, and lactic) varied. For 'beef' and seafood ramen soup, weak suprathreshold levels of acids (0.0039% to 0.0071%) were applied to the system and medium suprathreshold of acids (0.0128% to 0.0299%) were applied to the kimchi ramen soup. The amount of acid applied to each system was chosen based on the equiweight level. Descriptive analyses were performed separately for each ramen soup system using 8 trained panelists. A total of 11, 13, and 12 flavor descriptors were generated for 'beef,' seafood, and 'kimchi' soup, respectively. Analysis of variance was conducted to evaluate the effect of organic acid on the sensory characteristics of ramen soup. Principal component analysis was conducted to summarize the relationship between the soup samples and attributes. The effect of organic acids on the flavor attributes of ramen soup was dependent on the soup system as well as adding levels of acid. Addition of lactic acid power (at 0.0066%) in 'beef'ramen soup showed enhancement effect on the sour, salty, beefy, 'mushroom' flavor, and fermented soybean paste soup flavor, whereas lactic acid powder (at 0.0071%) showed enhancement effect only on the sour and fermented soybean paste soup flavor in seafood ramen soup due to the strong 'hot' flavor characteristics of the soup. In kimchi ramen soup, flavor attributes congruent to sourness were enhanced by the addition of organic acids to the system.

Computer Series, 13.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1981-01-01

Provides short descriptions of chemists' applications of computers in instruction: an interactive instructional program for Instrumental-Qualitative Organic Analysis; question-and-answer exercises in organic chemistry; computerized organic nomenclature drills; integration of theoretical and descriptive materials; acid-base titration simulation;…

Sensitive detection of strong acidic condition by a novel rhodamine-based fluorescent pH chemosensor.

PubMed

Tan, Jia-Lian; Yang, Ting-Ting; Liu, Yu; Zhang, Xue; Cheng, Shu-Jin; Zuo, Hua; He, Huawei

2016-05-01

A novel rhodamine-based fluorescent pH probe responding to extremely low pH values has been synthesized and characterized. This probe showed an excellent photophysical response to pH on the basis that the colorless spirocyclic structure under basic conditions opened to a colored and highly fluorescent form under extreme acidity. The quantitative relationship between fluorescence intensity and pH value (1.75-2.62) was consistent with the equilibrium equation pH = pKa + log[(Imax - I)/(I - Imin)]. This sensitive pH probe was also characterized with good reversibility and no interaction with interfering metal ions, and was successfully applied to image Escherichia coli under strong acidity. Copyright © 2015 John Wiley & Sons, Ltd.

Nucleic acid aptamers: research tools in disease diagnostics and therapeutics.

PubMed

Santosh, Baby; Yadava, Pramod K

2014-01-01

Aptamers are short sequences of nucleic acid (DNA or RNA) or peptide molecules which adopt a conformation and bind cognate ligands with high affinity and specificity in a manner akin to antibody-antigen interactions. It has been globally acknowledged that aptamers promise a plethora of diagnostic and therapeutic applications. Although use of nucleic acid aptamers as targeted therapeutics or mediators of targeted drug delivery is a relatively new avenue of research, one aptamer-based drug "Macugen" is FDA approved and a series of aptamer-based drugs are in clinical pipelines. The present review discusses the aspects of design, unique properties, applications, and development of different aptamers to aid in cancer diagnosis, prevention, and/or treatment under defined conditions.

INTERACTION OF AQUEOUS SOLUTIONS OF CHLORINE WITH MALIC ACID, TARTARIC ACID, AND VARIOUS FRUIT JUICES, A SOURCE OF MUTAGENS

EPA Science Inventory

The interactions of aqueous solutions of chlorine with some fruit acids (citric acid, DL-malic acid, and L-tartaric acid) at different pH values were studied. iethyl ether extraction followed by GC/MS analysis indicated that a number of mutagens (certain chlorinated propanones an...

Computational studies of molecular charge transfer complexes of heterocyclic 4-methylepyridine-2-azomethine-p-benzene derivatives with picric acid and m-dinitrobenzene.

PubMed

Al-Harbi, L M; El-Mossalamy, E H; Obaid, A Y; Al-Jedaani, A H

2014-01-01

Charge transfer complexes of substituted aryl Schiff bases as donors with picric acid and m-dinitrobenzene as acceptors were investigated by using computational analysis calculated by Configuration Interaction Singles Hartree-Fock (CIS-HF) at standard 6-31G∗ basis set and Time-Dependent Density-Functional Theory (TD-DFT) levels of theory at standard 6-31G∗∗ basis set, infrared spectra, visible and nuclear magnetic resonance spectra are investigated. The optimized geometries and vibrational frequencies were evaluated. The energy and oscillator strength were calculated by Configuration Interaction Singles Hartree-Fock method (CIS-HF) and the Time-Dependent Density-Functional Theory (TD-DFT) results. Electronic properties, such as HOMO and LUMO energies and band gaps of CTCs set, were studied by the Time-Dependent density functional theory with Becke-Lee-Young-Parr (B3LYP) composite exchange correlation functional and by Configuration Interaction Singles Hartree-Fock method (CIS-HF). The ionization potential Ip and electron affinity EA were calculated by PM3, HF and DFT methods. The columbic force was calculated theoretically by using (CIS-HF and TD-DFT) methods. This study confirms that the theoretical calculation of vibrational frequencies for (aryl Schiff bases--(m-dinitrobenzene and picric acid)) complexes are quite useful for the vibrational assignment and for predicting new vibrational frequencies. Copyright © 2013 Elsevier B.V. All rights reserved.

Structural basis of DNA bending and oriented heterodimer binding by the basic leucine zipper domains of Fos and Jun.

PubMed

Leonard, D A; Rajaram, N; Kerppola, T K

1997-05-13

Interactions among transcription factors that bind to separate sequence elements require bending of the intervening DNA and juxtaposition of interacting molecular surfaces in an appropriate orientation. Here, we examine the effects of single amino acid substitutions adjacent to the basic regions of Fos and Jun as well as changes in sequences flanking the AP-1 site on DNA bending. Substitution of charged amino acid residues at positions adjacent to the basic DNA-binding domains of Fos and Jun altered DNA bending. The change in DNA bending was directly proportional to the change in net charge for all heterodimeric combinations between these proteins. Fos and Jun induced distinct DNA bends at different binding sites. Exchange of a single base pair outside of the region contacted in the x-ray crystal structure altered DNA bending. Substitution of base pairs flanking the AP-1 site had converse effects on the opposite directions of DNA bending induced by homodimers and heterodimers. These results suggest that Fos and Jun induce DNA bending in part through electrostatic interactions between amino acid residues adjacent to the basic region and base pairs flanking the AP-1 site. DNA bending by Fos and Jun at inverted binding sites indicated that heterodimers bind to the AP-1 site in a preferred orientation. Mutation of a conserved arginine within the basic regions of Fos and transversion of the central C:G base pair in the AP-1 site to G:C had complementary effects on the orientation of heterodimer binding and DNA bending. The conformational variability of the Fos-Jun-AP-1 complex may contribute to its functional versatility at different promoters.

Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks.

PubMed

Babaei, Sepideh; Geranmayeh, Amir; Seyyedsalehi, Seyyed Ali

2010-12-01

The supervised learning of recurrent neural networks well-suited for prediction of protein secondary structures from the underlying amino acids sequence is studied. Modular reciprocal recurrent neural networks (MRR-NN) are proposed to model the strong correlations between adjacent secondary structure elements. Besides, a multilayer bidirectional recurrent neural network (MBR-NN) is introduced to capture the long-range intramolecular interactions between amino acids in formation of the secondary structure. The final modular prediction system is devised based on the interactive integration of the MRR-NN and the MBR-NN structures to arbitrarily engage the neighboring effects of the secondary structure types concurrent with memorizing the sequential dependencies of amino acids along the protein chain. The advanced combined network augments the percentage accuracy (Q₃) to 79.36% and boosts the segment overlap (SOV) up to 70.09% when tested on the PSIPRED dataset in three-fold cross-validation. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

STD-NMR-Based Protein Engineering of the Unique Arylpropionate-Racemase AMDase G74C.

PubMed

Gaßmeyer, Sarah Katharina; Yoshikawa, Hiroyuki; Enoki, Junichi; Hülsemann, Nadine; Stoll, Raphael; Miyamoto, Kenji; Kourist, Robert

2015-06-23

Structure-guided protein engineering achieved a variant of the unique racemase AMDase G74C, with 40-fold increased activity in the racemisation of several arylaliphatic carboxylic acids. Substrate binding during catalysis was investigated by saturation-transfer-difference NMR (STD-NMR) spectroscopy. All atoms of the substrate showed interactions with the enzyme. STD-NMR measurements revealed distinct nuclear Overhauser effects in experiments with and without molecular conversion. The spectroscopic analysis led to the identification of several amino acid residues whose substitutions increased the activity of G74C. Single amino acid exchanges increased the activity moderately; structure-guided saturation mutagenesis yielded a quadruple mutant with a 40 times higher reaction rate. This study presents STD-NMR as versatile tool for the analysis of enzyme-substrate interactions in catalytically competent systems and for the guidance of protein engineering. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Selective Metal-Ion-Mediated Vesicle Adhesion Based on Dynamic Self-Organization of a Pyrene-Appended Glutamic Acid.

PubMed

Xing, Pengyao; Wang, Yajie; Yang, Minmin; Zhang, Yimeng; Wang, Bo; Hao, Aiyou

2016-07-13

Vesicles with dynamic membranes provide an ideal model system for investigating biological membrane activities, whereby vesicle aggregation behaviors including adhesion, fusion, fission, and membrane contraction/extension have attracted much attention. In this work we utilize an aromatic amino acid (pyrene-appended glutamic acid, PGlu) to prepare nanovesicles that aggregate to form vesicle clusters selectively induced by Fe(3+) or Cu(2+), and the vesicles transform into irregular nano-objects when interacting with Al(3+). Vesicle clusters have better stability than pristine vesicles, which hinders the spontaneous morphological transformation from vesicles into lamellar nanosheets with long incubation period. The difference between complexation of Fe(3+) and Al(3+) with vesicles was studied by various techniques. On the basis of metal ion-vesicle interactions, this self-assembled nanovesicle system also behaves as an effective fluorescent sensor for Fe(3+) and Al(3+), which cause fluorescence quenching and enhanced excimer emission, respectively.

Microwave-assisted preparation of nitrogen-doped biochars by ammonium acetate activation for adsorption of acid red 18

NASA Astrophysics Data System (ADS)

Wang, Li; Yan, Wei; He, Chi; Wen, Hang; Cai, Zhang; Wang, Zixuan; Chen, Zhengzheng; Liu, Weifeng

2018-03-01

Nitrogen-doped biochars derived from Phragmites australis (PA) were prepared using ammonium chloride (AC) and ammonium acetate (AA) as nitrogen sources by phosphoric acid activation via microwave assisted treatment. Their physicochemical properties, acid red 18 (AR18) adsorption performance and possible mechanisms were systematically evaluated. Nitrogen was successfully doped onto the biochar's surface in the formation of pyrrole-N, pyridine-N and oxidized-N with pyridine-N being the major component (64%). The pHiep and basic foundational groups of the biochars increased consequently however their surface areas slightly decreased. The adsorption kinetic data were best fit to the pseudo-second order model and the equilibrium data were well simulated by Freundlich model for all biochars, indicating the important role of chemical interactions. The maximum AR18 adsorption capacities of PAB-AA and PAB-AC were 1.41 and 1.18 times higher compared with the non N-doped biochar, which were mainly attributed to the π-π EDA interaction between the pyridine-N and AR18 as revealed by the comparison of XPS analyses before and after AR18 adsorption. Meanwhile, other mechanisms such as pore filling effect, Lewis acid-base interaction, electrostatic attraction and hydrogen bonding also existed as demonstrated by BET, XPS and FTIR analyses.

Sulfamide-Lattice Restructuring To Form Dimensionally Controlled Molecular Arrays and Gel-Forming Systems.

PubMed

Raghava, Saripalli V; Gopinath, Pushparathinam; Srivastava, Bhartendu K; Ramkumar, Venkatachalam; Muraleedharan, Kannoth M

2017-03-13

A design approach that incorporates structural requirements for the formation of a 1D assembly, fibril stability, and fibril-fibril interactions for gelation was attempted by using amino acid-based sulfamides with the general structure Aa-NH-SO 2 -NH-Aa (Aa=amino acid). A preference for 1D assembly alone was not a sufficient condition for gelation, which became evident from studies involving sulfamide esters 1-5. Reducing the crystallization tendency without hindering unidirectional growth was executed through diacids of the sulfamide precursors with various amines that form an envelope around the sulfamide core through salt bridges. This strategy was fruitful, and gels of a wide variety of solvents could be formed by varying the acid and amine components. The use of dodecylamine or benzylamine, which could stabilize the molecular layers through alkyl-chain segregation or π-π interactions improved the gelation tendency, whereas the nature of the amino acid side chain, especially the rotational freedom and hydrophobicity, had a direct role in dictating the solvent preference. Crystallographic studies of these two-component systems gave molecular-level insight into the assembly and showed the importance of anisotropy in the distribution of secondary interactions in gelation. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Prebiotic Chemistry Experiment on the Adsorption of Nucleic Acids Bases onto a Natural Zeolite.

PubMed

Anizelli, Pedro R; Baú, João Paulo T; Gomes, Frederico P; da Costa, Antonio Carlos S; Carneiro, Cristine E A; Zaia, Cássia Thaïs B V; Zaia, Dimas A M

2015-09-01

There are currently few mechanisms that can explain how nucleic acid bases were synthesized, concentrated from dilute solutions, and/or protected against degradation by UV radiation or hydrolysis on the prebiotic Earth. A natural zeolite exhibited the potential to adsorb adenine, cytosine, thymine, and uracil over a range of pH, with greater adsorption of adenine and cytosine at acidic pH. Adsorption of all nucleic acid bases was decreased in artificial seawater compared to water, likely due to cation complexation. Furthermore, adsorption of adenine appeared to protect natural zeolite from thermal degradation. The C=O groups from thymine, cytosine and uracil appeared to assist the dissolution of the mineral while the NH2 group from adenine had no effect. As shown by FT-IR spectroscopy, adenine interacted with a natural zeolite through the NH2 group, and cytosine through the C=O group. A pseudo-second-order model best described the kinetics of adenine adsorption, which occurred faster in artificial seawaters.

Complexes of polyadenylic acid and the methyl esters of amino acids

NASA Technical Reports Server (NTRS)

Khaled, M. A.; Mulins, D. W., Jr.; Swindle, M.; Lacey, J. C., Jr.

1983-01-01

A study of amino acid methyl esters binding to polyadenylic acid supports the theory that the genetic code originated through weak but selective affinities between amino acids and nucleotides. NMR, insoluble complex analysis, and ultraviolet spectroscopy are used to illustrate a correlation between the hydrophybicities of A amino acids and their binding constants, which, beginning with the largest, are in the order of Phe (having nominally a hydrophobic AAA anticodon), Ile, Leu, Val and Gly (having a hydrophilic anticodon with no A). In general, the binding constants are twice the values by Reuben and Polk (1980) for monomeric AMP, which suggests that polymer amino acids are interacting with only one base. No real differences are found betwen poly A binding for free Phe, Phe methyl ester or Phe amide, except that the amide value is slightly lower.

Synthesis, physicochemical studies, embryos toxicity and DNA interaction of some new Iron(II) Schiff base amino acid complexes

NASA Astrophysics Data System (ADS)

Abdel-Rahman, Laila H.; El-Khatib, Rafat M.; Nassr, Lobna A. E.; Abu-Dief, Ahmed M.

2013-05-01

New Fe(II) Schiff base amino acid complexes derived from the condensation of o-hydroxynaphthaldehyde with L-alanine, L-phenylalanine, L-aspartic acid, L-histidine and L-arginine were synthesized and characterized by elemental analysis, IR, electronic spectra, and conductance measurements. The stoichiometry and the stability constants of the complexes were determined spectrophotometrically. The investigated Schiff bases exhibited tridentate coordination mode with the general formulae [Fe(HL)2]·nH2O for all amino acids except L-histidine. But in case of L-histidine, the ligand acts as tetradentate ([FeL(H2O)2]·2H2O), where HL = mono anion and L = dianion of the ligand. The structure of the prepared complexes is suggested to be octahedral. The prepared complexes were tested for their toxicity on chick embryos and found to be safe until a concentration of 100 μg/egg with full embryos formation. The interaction between CT-DNA and the investigated complexes were followed by spectrophotometry and viscosity measurements. It was found that, the prepared complexes bind to DNA via classical intercalative mode and showed a different DNA cleavage activity with the sequence: nhi > nari > nali > nasi > nphali. The thermodynamic Profile of the binding of nphali complex and CT-DNA was constructed by analyzing the experimental data of absorption titration and UV melting studies with the McGhee equation, van't Hoff's equation, and the Gibbs-Helmholtz equation.

Differential Proteomic Analysis of Lactic Acid Bacteria-Escherichia coli O157:H7 Interaction and Its Contribution to Bioprotection Strategies in Meat.

PubMed

Orihuel, Alejandra; Terán, Lucrecia; Renaut, Jenny; Vignolo, Graciela M; De Almeida, André M; Saavedra, María L; Fadda, Silvina

2018-01-01

Human infection by Enterohemorrhagic Escherichia (E.) coli (EHEC) occurs through the ingestion of contaminated foods such as milk, vegetable products, water-based drinks, and particularly minced meats. Indeed EHEC is a pathogen that threatens public health and meat industry. The potential of different Lactic Acid Bacteria (LAB) strains to control EHEC in a meat-based medium was evaluated by using a simple and rapid method and by analyzing the growth kinetics of co-cultures (LAB-EHEC) in a meat-based medium. The activity of LAB toward EHEC in co-cultures showed variable inhibitory effect. Although, LAB were able to control EHEC, neither the produced acid nor bacteriocins were responsible of the inhibition. The bacteriocinogenic Enteroccus (Ent.) mundtii CRL35 presented one of the highest inhibition activities. A proteomic approach was used to evaluate bacterial interaction and antagonistic mechanisms between Ent. mundtii and EHEC. Physiological observations, such as growth kinetics, acidification ability and EHEC inhibitory potential were supported by the proteomic results, demonstrating significant differences in protein expression in LAB: (i) due to the presence of the pathogen and (ii) according to the growth phase analyzed. Most of the identified proteins belonged to carbohydrate/amino acid metabolism, energy production, transcription/translation, and cell division. These results contribute to the knowledge of competition strategies used by Ent. mundtii during its co-culture with EHEC setting new perspectives for the use of LAB to control this pathogen in meat.

Interaction of milk whey protein with common phenolic acids

NASA Astrophysics Data System (ADS)

Zhang, Hao; Yu, Dandan; Sun, Jing; Guo, Huiyuan; Ding, Qingbo; Liu, Ruihai; Ren, Fazheng

2014-01-01

Phenolics-rich foods such as fruit juices and coffee are often consumed with milk. In this study, the interactions of α-lactalbumin and β-lactoglobulin with the phenolic acids (chlorogenic acid, caffeic acid, ferulic acid, and coumalic acid) were examined. Fluorescence, CD, and FTIR spectroscopies were used to analyze the binding modes, binding constants, and the effects of complexation on the conformation of whey protein. The results showed that binding constants of each whey protein-phenolic acid interaction ranged from 4 × 105 to 7 × 106 M-n and the number of binding sites n ranged from 1.28 ± 0.13 to 1.54 ± 0.34. Because of these interactions, the conformation of whey protein was altered, with a significant reduction in the amount of α-helix and an increase in the amounts of β-sheet and turn structures.

Preparation, chromatographic evaluation and application of adenosine 5'-monophosphate modified ZrO2/SiO2 stationary phase in hydrophilic interaction chromatography.

PubMed

Wang, Qing; Luo, Zhi-Yuan; Ye, Mao; Wang, Yu-Zhuo; Xu, Li; Shi, Zhi-Guo; Xu, Lanying

2015-02-27

The zirconia-coated silica (ZrO2/SiO2) material was obtained by coupling layer-by-layer (LbL) self-assembly method and sol-gel technology, to take dual advantages of the suitable porous structure of SiO2 and basic resistance of ZrO2. Adenosine 5'-monophosphate (5'-AMP) was then self-assembled onto ZrO2/SiO2 via Lewis acid-base interaction, generating 5'-AMP-ZrO2/SiO2. The chromatographic properties of 5'-AMP-ZrO2/SiO2 were systemically studied by evaluating the effect of acetonitrile content, pH and buffer concentration in the mobile phase. The results demonstrated that the 5'-AMP-ZrO2/SiO2 possessed hydrophilic interaction chromatographic (HILIC) property comprising hydrophilic, hydrogen-bonding, electrostatic and ion-exchange interactions. For basic analytes, the column efficiency of ZrO2/SiO2 and 5'-AMP-ZrO2/SiO2 was superior to the bare ZrO2, and different selectivity was obtained after the introduction of 5'-AMP. For acidic analytes, good resolution was obtained on 5'-AMP-ZrO2/SiO2 while the analysis failed on the bare ZrO2 column owing to strong adsorption. Hence, the proposed 5'-AMP-ZrO2/SiO2 had great potential in analyzing acidic compounds in HILIC mode. It was an extended application of ZrO2 based SP. Copyright © 2015 Elsevier B.V. All rights reserved.

Hard and soft acids and bases: structure and process.

PubMed

Reed, James L

2012-07-05

Under investigation is the structure and process that gives rise to hard-soft behavior in simple anionic atomic bases. That for simple atomic bases the chemical hardness is expected to be the only extrinsic component of acid-base strength, has been substantiated in the current study. A thermochemically based operational scale of chemical hardness was used to identify the structure within anionic atomic bases that is responsible for chemical hardness. The base's responding electrons have been identified as the structure, and the relaxation that occurs during charge transfer has been identified as the process giving rise to hard-soft behavior. This is in contrast the commonly accepted explanations that attribute hard-soft behavior to varying degrees of electrostatic and covalent contributions to the acid-base interaction. The ability of the atomic ion's responding electrons to cause hard-soft behavior has been assessed by examining the correlation of the estimated relaxation energies of the responding electrons with the operational chemical hardness. It has been demonstrated that the responding electrons are able to give rise to hard-soft behavior in simple anionic bases.

Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment.

PubMed

Sponer, Jiří; Sponer, Judit E; Mládek, Arnošt; Jurečka, Petr; Banáš, Pavel; Otyepka, Michal

2013-12-01

Base stacking is a major interaction shaping up and stabilizing nucleic acids. During the last decades, base stacking has been extensively studied by experimental and theoretical methods. Advanced quantum-chemical calculations clarified that base stacking is a common interaction, which in the first approximation can be described as combination of the three most basic contributions to molecular interactions, namely, electrostatic interaction, London dispersion attraction and short-range repulsion. There is not any specific π-π energy term associated with the delocalized π electrons of the aromatic rings that cannot be described by the mentioned contributions. The base stacking can be rather reasonably approximated by simple molecular simulation methods based on well-calibrated common force fields although the force fields do not include nonadditivity of stacking, anisotropy of dispersion interactions, and some other effects. However, description of stacking association in condensed phase and understanding of the stacking role in biomolecules remain a difficult problem, as the net base stacking forces always act in a complex and context-specific environment. Moreover, the stacking forces are balanced with many other energy contributions. Differences in definition of stacking in experimental and theoretical studies are explained. Copyright © 2013 Wiley Periodicals, Inc.

Interactions of carbon dioxide with model organic molecules: A comparative theoretical study

NASA Astrophysics Data System (ADS)

Trung, Nguyen Tien; Nguyen, Minh Tho

2013-08-01

Interaction energies obtained using CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ computations including both ZPE and BSSE corrections range from -2.9 to -14.2 kJ mol-1. While formic acid forms the most stable complex with CO2, formaldehyde yields the least stable complex. Lewis acid-base interaction such as C-N⋯C(CO2), Cdbnd O⋯C(CO2), which overcomes C-H⋯O blue-shifting hydrogen bond, plays a significant role in stabilizing most complexes. However, the strength of (HCOOH, CO2) is mainly determined by O-H⋯O red-shifting hydrogen bond. The C-H⋯O blue-shifting hydrogen bond is revealed upon complexation of CH3OH, HCHO, HCOOH, CH3COCH3 and HCOOCH3 with CO2. Remarkably, existence of weak hydrogen bonded C-H⋯O interaction is not found in the (CH3OCH3, CO2) and (CH3NH2, CO2) pairs.

Interaction of fructose with other medium components to affect bioproduction of docosahexaenoic acid (DHA) by Aurantiochytrium sp. SW1

NASA Astrophysics Data System (ADS)

Manikan, Vidyah; Kalil, Mohd. Sahaid; Shuib, Shuwahida; Hamid, Aidil Abdul

2018-04-01

Thraustochytrids are a group of marine fungus-like microheterotrophs of which some can accumulate considerable amounts of the high valued omega-3 oil, docosahexaenoic acid (DHA). In this study, a local thraustochytrid isolate, Aurantiochytrium sp. SW1, was cultivated in a medium containing fructose as the major carbon source. The effects of this carbon source in interaction with yeast extract, monosodium glutamate (MSG) and sea salt were studied using a software-based two level full factorial design. Results showed that fructose as a single factor, has significant positive effect on the volumetric DHA content of SW1. Similarly, its interaction with yeast extract has profound positive effect. However, interactions of fructose with MSG and sea salt were significant negative effects. These results indicate that manipulation of the concentration of fructose in the culture medium may serve as a simple and useful strategy to help achieve preferred amount of DHA.

Surfactant protein B: lipid interactions of synthetic peptides representing the amino-terminal amphipathic domain.

PubMed Central

Bruni, R; Taeusch, H W; Waring, A J

1991-01-01

The mechanisms by which pulmonary surfactant protein B (SP-B) affects the surface activity of surfactant lipids are unclear. We have studied the peptide/lipid interactions of the amino-terminal amphipathic domain of SP-B by comparing the secondary conformations and surface activities of a family of synthetic peptides based on the native human SP-B sequence, modified by site-specific amino acid substitutions. Circular dichroism measurements show an alpha-helical structure correlating with the ability of the peptides to interact with lipids and with the surface activity of peptide/lipid dispersions. Amino acid substitutions altering either the charge or the hydrophobicity of the residues lowered the helical content and reduced the association of the aminoterminal segment with lipid dispersions. Surface activity of peptide/lipid mixtures was maximally altered by reversal of charge in synthetic peptides. These observations indicate that electrostatic interactions and hydrophobicity are important factors in determining optimal structure and function of surfactant peptides in lipid dispersions. Images PMID:1871144

Structure based classification for bile salt export pump (BSEP) inhibitors using comparative structural modeling of human BSEP

NASA Astrophysics Data System (ADS)

Jain, Sankalp; Grandits, Melanie; Richter, Lars; Ecker, Gerhard F.

2017-06-01

The bile salt export pump (BSEP) actively transports conjugated monovalent bile acids from the hepatocytes into the bile. This facilitates the formation of micelles and promotes digestion and absorption of dietary fat. Inhibition of BSEP leads to decreased bile flow and accumulation of cytotoxic bile salts in the liver. A number of compounds have been identified to interact with BSEP, which results in drug-induced cholestasis or liver injury. Therefore, in silico approaches for flagging compounds as potential BSEP inhibitors would be of high value in the early stage of the drug discovery pipeline. Up to now, due to the lack of a high-resolution X-ray structure of BSEP, in silico based identification of BSEP inhibitors focused on ligand-based approaches. In this study, we provide a homology model for BSEP, developed using the corrected mouse P-glycoprotein structure (PDB ID: 4M1M). Subsequently, the model was used for docking-based classification of a set of 1212 compounds (405 BSEP inhibitors, 807 non-inhibitors). Using the scoring function ChemScore, a prediction accuracy of 81% on the training set and 73% on two external test sets could be obtained. In addition, the applicability domain of the models was assessed based on Euclidean distance. Further, analysis of the protein-ligand interaction fingerprints revealed certain functional group-amino acid residue interactions that could play a key role for ligand binding. Though ligand-based models, due to their high speed and accuracy, remain the method of choice for classification of BSEP inhibitors, structure-assisted docking models demonstrate reasonably good prediction accuracies while additionally providing information about putative protein-ligand interactions.

A polarizable dipole-dipole interaction model for evaluation of the interaction energies for N-H···O=C and C-H···O=C hydrogen-bonded complexes.

PubMed

Li, Shu-Shi; Huang, Cui-Ying; Hao, Jiao-Jiao; Wang, Chang-Sheng

2014-03-05

In this article, a polarizable dipole-dipole interaction model is established to estimate the equilibrium hydrogen bond distances and the interaction energies for hydrogen-bonded complexes containing peptide amides and nucleic acid bases. We regard the chemical bonds N-H, C=O, and C-H as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. We apply this polarizable dipole-dipole interaction model to a series of hydrogen-bonded complexes containing the N-H···O=C and C-H···O=C hydrogen bonds, such as simple amide-amide dimers, base-base dimers, peptide-base dimers, and β-sheet models. We find that a simple two-term function, only containing the permanent dipole-dipole interactions and the van der Waals interactions, can produce the equilibrium hydrogen bond distances compared favorably with those produced by the MP2/6-31G(d) method, whereas the high-quality counterpoise-corrected (CP-corrected) MP2/aug-cc-pVTZ interaction energies for the hydrogen-bonded complexes can be well-reproduced by a four-term function which involves the permanent dipole-dipole interactions, the van der Waals interactions, the polarization contributions, and a corrected term. Based on the calculation results obtained from this polarizable dipole-dipole interaction model, the natures of the hydrogen bonding interactions in these hydrogen-bonded complexes are further discussed. Copyright © 2013 Wiley Periodicals, Inc.

Protein-membrane interaction and fatty acid transfer from intestinal fatty acid-binding protein to membranes. Support for a multistep process.

PubMed

Falomir-Lockhart, Lisandro J; Laborde, Lisandro; Kahn, Peter C; Storch, Judith; Córsico, Betina

2006-05-19

Fatty acid transfer from intestinal fatty acid-binding protein (IFABP) to phospholipid membranes occurs during protein-membrane collisions. Electrostatic interactions involving the alpha-helical "portal" region of the protein have been shown to be of great importance. In the present study, the role of specific lysine residues in the alpha-helical region of IFABP was directly examined. A series of point mutants in rat IFABP was engineered in which the lysine positive charges in this domain were eliminated or reversed. Using a fluorescence resonance energy transfer assay, we analyzed the rates and mechanism of fatty acid transfer from wild type and mutant proteins to acceptor membranes. Most of the alpha-helical domain mutants showed slower absolute fatty acid transfer rates to zwitterionic membranes, with substitution of one of the lysines of the alpha2 helix, Lys27, resulting in a particularly dramatic decrease in the fatty acid transfer rate. Sensitivity to negatively charged phospholipid membranes was also reduced, with charge reversal mutants in the alpha2 helix the most affected. The results support the hypothesis that the portal region undergoes a conformational change during protein-membrane interaction, which leads to release of the bound fatty acid to the membrane and that the alpha2 segment is of particular importance in the establishment of charge-charge interactions between IFABP and membranes. Cross-linking experiments with a phospholipid-photoactivable reagent underscored the importance of charge-charge interactions, showing that the physical interaction between wild-type intestinal fatty acid-binding protein and phospholipid membranes is enhanced by electrostatic interactions. Protein-membrane interactions were also found to be enhanced by the presence of ligand, suggesting different collisional complex structures for holo- and apo-IFABP.

Abscisic acid does not disrupt either the Arabidopsis FCA-FY interaction or its rice counterpart in vitro.

PubMed

Jang, Yun Hee; Lee, Jeong Hwan; Kim, Jeong-Kook

2008-12-01

We examined the effect of (+)-ABA on the in vitro interaction of rice FCA and FY homologs, OsFCA and OsFY. From this analysis, we found no disruption of the OsFCA-OsFY complexes by ABA treatment. This result prompted us to examine the effect of ABA on the FCA-FY interaction. In these experiments, we could not reproduce the inhibitory effect of (+)-ABA on the interaction between FCA and FY. Based on these combined results, we believe that the inhibitory effect of (+)-ABA on the FCA-FY interaction should be cautiously reconsidered.

The Interactions between L-Tyrosine Based Nanoparticles Decorated with Folic Acid and Cervical Cancer Cells Under Physiological Flow

PubMed Central

Ditto, Andrew J.; Shah, Kush N.; Robishaw, Nikki K.; Panzner, Matthew J.; Youngs, Wiley J.; Yun, Yang H.

2012-01-01

Many anticancer drugs have been established clinically, but their efficacy can be compromised by nonspecific toxicity and an inability to reach the desired cancerous intracellular spaces. In order to address these issues, researchers have explored the use of folic acid as a targeted moiety to increase specificity of chemotherapeutic drugs. To expand upon such research, we have conjugated folic acid to functionalized poly(ethylene glycol) and subsequently decorated the surface of L-tyrosine polyphosphate (LTP) nanoparticles. These nanoparticles possess the appropriate size (100–500 nm) for internalization as shown by scanning electron microscopy and dynamic light scattering. Under simulated physiological flow, LTP nanoparticles decorated with folic acid (targeted nanoparticles) show a 10-fold greater attachment to HeLa, a cervical cancer cell line, compared to control nanoparticles and to human dermal fibroblasts. The attachment of these targeted nanoparticles progresses at a linear rate, and the strength of this nanoparticle attachment is shown to withstand shear stresses of 3.0 dynes/cm2. These interactions of the targeted nanoparticles to HeLa are likely a result of a receptor-ligand binding, as a competition study with free folic acid inhibits the nanoparticle attachment. Finally, the targeted nanoparticles encapsulated with a silver based drug show increased efficacy in comparison to non-decorated (plain) nanoparticles and drug alone against HeLa cells. Thus, targeted nanoparticles are a promising delivery platform for developing anticancer therapies that over-express the folate receptors (FRs). PMID:22957928

Interaction between Al3+ and acrylic acid and polyacrylic acid in acidic aqueous solution: a model experiment for the behavior of Al3+ in acidified soil solution.

PubMed

Etou, Mayumi; Masaki, Yuka; Tsuji, Yutaka; Saito, Tomoyuki; Bai, Shuqin; Nishida, Ikuko; Okaue, Yoshihiro; Yokoyama, Takushi

2011-01-01

From the viewpoint of the phytotoxicity and mobility of Al(3+) released from soil minerals due to soil acidification, the interaction between Al(3+) and acrylic acid (AA) and polyacrylic acid (PAA) as a model compound of fulvic acid was investigated. The interaction was examined at pH 3 so as to avoid the hydrolysis of Al(3+). The interaction between Al(3+) and AA was weak. However, the interaction between Al(3+) and PAA was strong and depended on the initial (COOH in PAA)/Al molar ratio (R(P)) of the solution. For the range of 1/R(P), the interaction between Al(3+) and PAA can be divided into three categories: (1) 1:1 Al-PAA-complex (an Al(3+) combines to a carboxyl group), (2) intermolecular Al-PAA-complex (an Al(3+) combines to more than 2 carboxyl groups of other Al-PAA-complexes) in addition to the 1:1 Al-PAA-complex and (3) precipitation of intermolecular complexes. In conclusion, R(P) is an important factor affecting the behavior of Al(3+) in acidic soil solution.

Influence of Poly(ethylenimine) on the Monolayer of Oleic Acid at the Air/Water Interface.

PubMed

Hwan Ha, Tai; Kyu Kim, Dai; Choi, Myung-Un; Kim, Kwan

2000-06-01

The effect of poly(ethylenimine) (PEI) dissolved in water on the surface pressure-area isotherm of oleic acid (OA) at the air/water interface was investigated. On a concentrated PEI solution, the isotherm of the OA monolayers exhibited a noticeable difference as a function of subphase pH. PEI caused the collapse pressure of the OA monolayer to increase up to 45 mN/m, due to a stronger acid-base-type interaction occurring between the amine group of the PEI and the carboxyl group of OA; on a pure water subphase, the collapse pressure was;28 mN/m. On the other hand, owing to a stronger OA-PEI interaction, the OA monolayers favored a liquid-expanded state more on the PEI-containing water subphase than on the pure water. From the QCM measurement, each OA molecule appeared to interact, on average, with 4.3-5.8 ethylenimine repeating units at basic pHs. We also found that OA multilayers could be assembled on a hydrophilic substrate by a Z-type Langmuir-Blodgett (LB) deposition in a PEI-containing subphase at basic pHs. The ATR-IR spectral data revealed that, in a Z-type LB film, the headgroup of OA was mostly present as carboxylate, interacting in an ionic state with the protonated amine groups of PEI. In acidic conditions, neither a Y-type nor a Z-type deposition was really accomplished. Nonetheless, the ATR-IR spectral data suggested that OA molecules should exist in a monomeric state in a LB film assembled at acidic pHs without PEI while they would form intermolecular hydrogen bridges and/or dimers in the presence of PEI. Copyright 2000 Academic Press.

The Role of the Acidity of N-Heteroaryl Sulfonamides as Inhibitors of Bcl-2 Family Protein–Protein Interactions

PubMed Central

2013-01-01

Overexpression of the antiapoptotic members of the Bcl-2 family of proteins is commonly associated with cancer cell survival and resistance to chemotherapeutics. Here, we describe the structure-based optimization of a series of N-heteroaryl sulfonamides that demonstrate potent mechanism-based cell death. The role of the acidic nature of the sulfonamide moiety as it relates to potency, solubility, and clearance is examined. This has led to the discovery of novel heterocyclic replacements for the acylsulfonamide core of ABT-737 and ABT-263. PMID:24900652

HIV-1 Nef binds with human GCC185 protein and regulates mannose 6 phosphate receptor recycling

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

Kumar, Manjeet; Kaur, Supinder; Nazir, Aamir

HIV-1 Nef modulates cellular function that enhances viral replication in vivo which culminate into AIDS pathogenesis. With no enzymatic activity, Nef regulates cellular function through host protein interaction. Interestingly, trans-cellular introduction of recombinant Nef protein in Caenorhabditis elegans results in AIDS like pathogenesis which might share common pathophysiology because the gene sequence of C. elegans and humans share considerable homology. Therefore employing C. elegans based initial screen complemented with sequence based homology search we identified GCC185 as novel host protein interacting with HIV-1 Nef. The detailed molecular characterization revealed N-terminal EEEE{sub 65} acidic domain of Nef as key region for interaction. GCC185 ismore » a tethering protein that binds with Rab9 transport vesicles. Our results show that Nef-GCC185 interaction disrupts Rab9 interaction resulting in delocalization of CI-MPR (cation independent Mannose 6 phosphate receptor) resulting in elevated secretion of hexosaminidase. In agreement with this, our studies identified novel host GCC185 protein that interacts with Nef EEEE65 acidic domain interfering GCC185-Rab9 vesicle membrane fusion responsible for retrograde vesicular transport of CI-MPR from late endosomes to TGN. In light of existing report suggesting critical role of Nef-GCC185 interaction reveals valuable mechanistic insights affecting specific protein transport pathway in docking of late endosome derived Rab9 bearing transport vesicle at TGN elucidating role of Nef during viral pathogenesis. -- Highlights: •Nef, an accessory protein of HIV-1 interacts with host factor and culminates into AIDS pathogenesis. •Using Caenorhabditis elegans based screen system, novel Nef interacting cellular protein GCC185 was identified. •Molecular characterization of Nef and human protein GCC185 revealed Nef EEEE{sub 65} key region interacted with full length GCC185. •Nef impeded the GCC185-Rab 9 interaction and perturb the mannose 6 phosphate receptor recycling. •Our study identified novel Nef interacting human GCC185 protein and their role regulation of M6P receptor recycling.« less

Thermodynamics of antibody-antigen interaction revealed by mutation analysis of antibody variable regions.

PubMed

Akiba, Hiroki; Tsumoto, Kouhei

2015-07-01

Antibodies (immunoglobulins) bind specific molecules (i.e. antigens) with high affinity and specificity. In order to understand their mechanisms of recognition, interaction analysis based on thermodynamic and kinetic parameters, as well as structure determination is crucial. In this review, we focus on mutational analysis which gives information about the role of each amino acid residue in antibody-antigen interaction. Taking anti-hen egg lysozyme antibodies and several anti-small molecule antibodies, the energetic contribution of hot-spot and non-hot-spot residues is discussed in terms of thermodynamics. Here, thermodynamics of the contribution from aromatic, charged and hydrogen bond-forming amino acids are discussed, and their different characteristics have been elucidated. The information gives fundamental understanding of the antibody-antigen interaction. Furthermore, the consequences of antibody engineering are analysed from thermodynamic viewpoints: humanization to reduce immunogenicity and rational design to improve affinity. Amino acid residues outside hot-spots in the interface play important roles in these cases, and thus thermodynamic and kinetic parameters give much information about the antigen recognition. Thermodynamic analysis of mutant antibodies thus should lead to advanced strategies to design and select antibodies with high affinity. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

A new viscosupplement based on partially hydrophobic hyaluronic acid: a comparative study.

PubMed

Finelli, Ivana; Chiessi, Ester; Galesso, Devis; Renier, Davide; Paradossi, Gaio

2011-01-01

A novel partially hydrophobized derivative of hyaluronic acid (HYADD® 4), containing a low number of C16 side-chains per polysaccharide backbone, provides injectable hydrogels stabilized by side-chain hydrophobic interactions. The rheological properties of Hymovis®, a physical hydrogel based on the hyaluronic acid derivative HYADD® 4, were evaluated using as reference a solution of the parent natural polysaccharide, hyaluronic acid. The rheological measurements were performed both in flow and oscillation regimes at the physiological frequency values of the knee, typically spanning the range from 0.5 Hz (walking frequency) to 3 Hz (running frequency). Moreover, the viscoelastic features of Hymovis® were compared with the market-available viscosupplementation products in view of its use in joint diseases.The different behavior of the investigated materials in crossover frequency measurements and in structure recovery experiments can be explained on the basis of the structural and dynamic properties of the polymeric systems.

Mechanism of cinnamic acid-induced trypsin inhibition: A multi-technique approach

NASA Astrophysics Data System (ADS)

Zhang, Hongmei; Zhou, Qiuhua; Cao, Jian; Wang, Yanqing

2013-12-01

In order to investigate the association of the protease trypsin with cinnamic acid, the interaction was characterized by using fluorescence, UV-vis absorption spectroscopy, molecular modeling and an enzymatic inhibition assay. The binding process may be outlined as follows: cinnamic acid can interact with trypsin with one binding site to form cinnamic acid-trypsin complex, resulting in inhibition of trypsin activity; the spectroscopic data show that the interaction is a spontaneous process with the estimated enthalpy and entropy changes being -8.95 kJ mol-1 and 50.70 J mol-1 K-1, respectively. Noncovalent interactions make the main contribution to stabilize the trypsin-cinnamic acid complex; cinnamic acid can enter into the primary substrate-binding pocket and alter the environment around Trp and Tyr residues.

Effect of molecular parameters on the binding of phenoxyacetic acid derivatives to albumins.

PubMed

Cserháti, T; Forgács, E; Deyl, Z; Miksík, I

2001-03-25

The interaction of 12 phenoxyacetic acid derivatives with human and serum albumin as well as with egg albumin was studied by charge-transfer reversed-phase (RP) thin-layer chromatography (TLC) and the relative strength of interaction was calculated. Each phenoxyacetic acid derivative interacted with human and bovine serum albumins whereas no interaction was observed with egg albumin. Stepwise regression analysis proved that the lipophilicity of the derivatives exert a significant impact on their capacity to bind to serum albumins. This result supports the hypothesis that the binding of phenoxyacetic acid derivatives to albumins may involve hydrophobic forces occurring between the corresponding apolar substructures of these derivatives and the amino acid side chains.

Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein’s structural organization

PubMed Central

2012-01-01

Background The three-dimensional structure of a protein can be described as a graph where nodes represent residues and the strength of non-covalent interactions between them are edges. These protein contact networks can be separated into long and short-range interactions networks depending on the positions of amino acids in primary structure. Long-range interactions play a distinct role in determining the tertiary structure of a protein while short-range interactions could largely contribute to the secondary structure formations. In addition, physico chemical properties and the linear arrangement of amino acids of the primary structure of a protein determines its three dimensional structure. Here, we present an extensive analysis of protein contact subnetworks based on the London van der Waals interactions of amino acids at different length scales. We further subdivided those networks in hydrophobic, hydrophilic and charged residues networks and have tried to correlate their influence in the overall topology and organization of a protein. Results The largest connected component (LCC) of long (LRN)-, short (SRN)- and all-range (ARN) networks within proteins exhibit a transition behaviour when plotted against different interaction strengths of edges among amino acid nodes. While short-range networks having chain like structures exhibit highly cooperative transition; long- and all-range networks, which are more similar to each other, have non-chain like structures and show less cooperativity. Further, the hydrophobic residues subnetworks in long- and all-range networks have similar transition behaviours with all residues all-range networks, but the hydrophilic and charged residues networks don’t. While the nature of transitions of LCC’s sizes is same in SRNs for thermophiles and mesophiles, there exists a clear difference in LRNs. The presence of larger size of interconnected long-range interactions in thermophiles than mesophiles, even at higher interaction strength between amino acids, give extra stability to the tertiary structure of the thermophiles. All the subnetworks at different length scales (ARNs, LRNs and SRNs) show assortativity mixing property of their participating amino acids. While there exists a significant higher percentage of hydrophobic subclusters over others in ARNs and LRNs; we do not find the assortative mixing behaviour of any the subclusters in SRNs. The clustering coefficient of hydrophobic subclusters in long-range network is the highest among types of subnetworks. There exist highly cliquish hydrophobic nodes followed by charged nodes in LRNs and ARNs; on the other hand, we observe the highest dominance of charged residues cliques in short-range networks. Studies on the perimeter of the cliques also show higher occurrences of hydrophobic and charged residues’ cliques. Conclusions The simple framework of protein contact networks and their subnetworks based on London van der Waals force is able to capture several known properties of protein structure as well as can unravel several new features. The thermophiles do not only have the higher number of long-range interactions; they also have larger cluster of connected residues at higher interaction strengths among amino acids, than their mesophilic counterparts. It can reestablish the significant role of long-range hydrophobic clusters in protein folding and stabilization; at the same time, it shed light on the higher communication ability of hydrophobic subnetworks over the others. The results give an indication of the controlling role of hydrophobic subclusters in determining protein’s folding rate. The occurrences of higher perimeters of hydrophobic and charged cliques imply the role of charged residues as well as hydrophobic residues in stabilizing the distant part of primary structure of a protein through London van der Waals interaction. PMID:22720789

Spectroscopic and microcalorimetric studies on the molecular binding of food colorant acid red 27 with deoxyribonucleic acid.

PubMed

Basu, Anirban; Kumar, Gopinatha Suresh

2016-08-01

Interaction of the food colorant acid red 27 with double stranded DNA was investigated using spectroscopic and calorimetric methods. Absorbance and fluorescence studies suggested an intimate binding interaction between the dye and DNA. The quantum efficiency value testified an effective energy transfer from the DNA base pairs to the dye molecules. Minor groove displacement assay with Hoechst 33258 revealed that the binding occurs in the minor groove of DNA. Circular dichroism studies revealed that acid red 27 induces moderate conformational perturbations in DNA. Results of calorimetric studies suggested that the complexation process was driven largely by positive entropic contribution with a smaller favorable enthalpy contribution. The equilibrium constant of the binding was calculated to be (3.04 ± 0.09) × 10(4)  M(-1) at 298.15 K. Negative heat capacity value along with the enthalpy-entropy compensation phenomenon established the involvement of dominant hydrophobic forces in the binding process. Differential scanning calorimetry studies presented evidence for an increased thermal stability of DNA on binding of acid red 27. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Metformin interferes with bile acid homeostasis through AMPK-FXR crosstalk

PubMed Central

Lien, Fleur; Berthier, Alexandre; Bouchaert, Emmanuel; Gheeraert, Céline; Alexandre, Jeremy; Porez, Geoffrey; Prawitt, Janne; Dehondt, Hélène; Ploton, Maheul; Colin, Sophie; Lucas, Anthony; Patrice, Alexandre; Pattou, François; Diemer, Hélène; Van Dorsselaer, Alain; Rachez, Christophe; Kamilic, Jelena; Groen, Albert K.; Staels, Bart; Lefebvre, Philippe

2014-01-01

The nuclear bile acid receptor farnesoid X receptor (FXR) is an important transcriptional regulator of bile acid, lipid, and glucose metabolism. FXR is highly expressed in the liver and intestine and controls the synthesis and enterohepatic circulation of bile acids. However, little is known about FXR-associated proteins that contribute to metabolic regulation. Here, we performed a mass spectrometry–based search for FXR-interacting proteins in human hepatoma cells and identified AMPK as a coregulator of FXR. FXR interacted with the nutrient-sensitive kinase AMPK in the cytoplasm of target cells and was phosphorylated in its hinge domain. In cultured human and murine hepatocytes and enterocytes, pharmacological activation of AMPK inhibited FXR transcriptional activity and prevented FXR coactivator recruitment to promoters of FXR-regulated genes. Furthermore, treatment with AMPK activators, including the antidiabetic biguanide metformin, inhibited FXR agonist induction of FXR target genes in mouse liver and intestine. In a mouse model of intrahepatic cholestasis, metformin treatment induced FXR phosphorylation, perturbed bile acid homeostasis, and worsened liver injury. Together, our data indicate that AMPK directly phosphorylates and regulates FXR transcriptional activity to precipitate liver injury under conditions favoring cholestasis. PMID:24531544

CSF/plasma ratios of amino acids: reference data and transports in children.

PubMed

Akiyama, Tomoyuki; Kobayashi, Katsuhiro; Higashikage, Akihito; Sato, Junko; Yoshinaga, Harumi

2014-01-01

We intended to investigate the effects of age, gender, and medications on amino acid cerebrospinal fluid (CSF)/plasma ratios in children, and to determine whether amino acid transports across the blood-CSF barrier in children differ from those in adults. Amino acid concentrations measured by ion-exchange high-performance liquid chromatography were used (CSF from 99 children, simultaneously collected plasma from 76 children). Influence of age, gender, and medications on the amino acid CSF concentrations and CSF/plasma ratios were analyzed by linear multiple regression. Interactions of amino acid transports were analyzed by correlation analysis of CSF/plasma ratios. CSF/plasma ratios of serine, valine, histidine, and arginine were higher in younger children. The glutamate CSF/plasma ratio was higher in older children. Serine, alanine, threonine, valine, and histidine CSF/plasma ratios were lower in females. Glutamine, methionine, tyrosine, and phenylalanine CSF/plasma ratios were elevated with valproate therapy. Serine, threonine, valine, leucine, and tyrosine CSF/plasma ratios were lower with clobazam therapy. The asparagine CSF/plasma ratio was elevated with pyridoxal phosphate therapy. Transports of most essential neutral amino acids interacted with each other, as did neutral amino acids with low molecular weights. Cationic amino acids interacted with each other and some essential neutral amino acids. Acidic amino acids had no interactions with other amino acids. Age, gender, and anti-epileptic drugs affect amino acid CSF/plasma ratios in children. Transport interactions between amino acids in children showed no remarkable difference from those of adults and generally followed the substrate specificities of multiple amino acid transport systems. Copyright © 2012 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.

Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of Gallic acid imprinted polymers

NASA Astrophysics Data System (ADS)

Pardeshi, Sushma; Dhodapkar, Rita; Kumar, Anupama

2013-12-01

Gallic acid (GA) is known by its antioxidant, anticarcinogenic properties and scavenger activity against several types of harmful free radicals. Molecularly imprinted polymers (MIPs) are used in separation of a pure compound from complex matrices. A stable template-monomer complex generates the MIPs with the highest affinity and selectivity for the template. The quantum chemical computations based on density functional theory (DFT) was used on the template Gallic acid (GA), monomer acrylic acid (AA) and GA-AA complex to study the nature of interactions involved in the GA-AA complex. B3LYP/6-31+G(2d,2p) model chemistry was used to optimize their structures and frequency calculations. The effect of porogen acetonitrile (ACN) on complex formation was included by using polarizable continuum model (PCM). The results demonstrated the formation of a stable GA-AA complex through the intermolecular hydrogen bonding between carboxylic acid groups of GA and AA. The Mulliken atomic charge analysis and simulated vibrational spectra also supported the stable hydrogen bonding interaction between the carboxylic acid groups of GA and AA with minimal interference of porogen ACN. Further, simulations on GA-AA mole ratio revealed that 1:4 GA-AA was optimum for synthesis of MIP for GA.

Measuring protein-protein and protein-nucleic Acid interactions by biolayer interferometry.

PubMed

Sultana, Azmiri; Lee, Jeffrey E

2015-02-02

Biolayer interferometry (BLI) is a simple, optical dip-and-read system useful for measuring interactions between proteins, peptides, nucleic acids, small molecules, and/or lipids in real time. In BLI, a biomolecular bait is immobilized on a matrix at the tip of a fiber-optic sensor. The binding between the immobilized ligand and another molecule in an analyte solution produces a change in optical thickness at the tip and results in a wavelength shift proportional to binding. BLI provides direct binding affinities and rates of association and dissociation. This unit describes an efficient approach using streptavidin-based BLI to analyze DNA-protein and protein-protein interactions. A quantitative set of equilibrium binding affinities (K(d)) and rates of association and dissociation (k(a)/k(d)) can be measured in minutes using nanomole quantities of sample. Copyright © 2015 John Wiley & Sons, Inc.

Interaction of anticancer drug methotrexate with nucleic acids analyzed by multi-spectroscopic method

NASA Astrophysics Data System (ADS)

Cai, Changqun; Chen, Xiaoming; Gong, Hang

2009-02-01

Methotrexate (MTX) as an antifolate, which is widely used as chemotherapeutic drugs. A high-dose MTX therapy has a direct toxicity influence on the non-germinal cells, especially the liver cells. It is known that the inject dose for adults is 10-30 mg and is half for children for routine use, while our experiments showed that the optimum dosage of MTX which enhanced the RLS intensities to the maximum is 4.54 ng ml -1. The interaction of methotrexate (MTX) with nucleic acids in aqueous solution in the presence of cetyltrimethylammonium bromide (CTMAB), a kind of cationic surfactant similar to the Human cells, were investigated based on the measurements of resonance light scattering (RLS), UV-vis, fluorescence and NMR spectra, etc. The interaction has been proved to give a ternary complex of MTX-CTMAB-DNA in BR buffer (pH 9.30), which exhibits strong enhanced RLS signals at 339.5 nm.

Quantitative structure activity relationship studies of mushroom tyrosinase inhibitors

NASA Astrophysics Data System (ADS)

Xue, Chao-Bin; Luo, Wan-Chun; Ding, Qi; Liu, Shou-Zhu; Gao, Xing-Xiang

2008-05-01

Here, we report our results from quantitative structure-activity relationship studies on tyrosinase inhibitors. Interactions between benzoic acid derivatives and tyrosinase active sites were also studied using a molecular docking method. These studies indicated that one possible mechanism for the interaction between benzoic acid derivatives and the tyrosinase active site is the formation of a hydrogen-bond between the hydroxyl (aOH) and carbonyl oxygen atoms of Tyr98, which stabilized the position of Tyr98 and prevented Tyr98 from participating in the interaction between tyrosinase and ORF378. Tyrosinase, also known as phenoloxidase, is a key enzyme in animals, plants and insects that is responsible for catalyzing the hydroxylation of tyrosine into o-diphenols and the oxidation of o-diphenols into o-quinones. In the present study, the bioactivities of 48 derivatives of benzaldehyde, benzoic acid, and cinnamic acid compounds were used to construct three-dimensional quantitative structure-activity relationship (3D-QSAR) models using comparative molecular field (CoMFA) and comparative molecular similarity indices (CoMSIA) analyses. After superimposition using common substructure-based alignments, robust and predictive 3D-QSAR models were obtained from CoMFA ( q 2 = 0.855, r 2 = 0.978) and CoMSIA ( q 2 = 0.841, r 2 = 0.946), with 6 optimum components. Chemical descriptors, including electronic (Hammett σ), hydrophobic (π), and steric (MR) parameters, hydrogen bond acceptor (H-acc), and indicator variable ( I), were used to construct a 2D-QSAR model. The results of this QSAR indicated that π, MR, and H-acc account for 34.9, 31.6, and 26.7% of the calculated biological variance, respectively. The molecular interactions between ligand and target were studied using a flexible docking method (FlexX). The best scored candidates were docked flexibly, and the interaction between the benzoic acid derivatives and the tyrosinase active site was elucidated in detail. We believe that the QSAR models built here provide important information necessary for the design of novel tyrosinase inhibitors.

Polyunsaturated fatty acid interactions and breast cancer incidence: a population-based case-control study on Long Island, New York.

PubMed

Khankari, Nikhil K; Bradshaw, Patrick T; Steck, Susan E; He, Ka; Olshan, Andrew F; Shen, Jing; Ahn, Jiyoung; Chen, Yu; Ahsan, Habibul; Terry, Mary Beth; Teitelbaum, Susan L; Neugut, Alfred I; Santella, Regina M; Gammon, Marilie D

2015-12-01

Experimental studies demonstrate that ω-3 polyunsaturated fatty acids (PUFAs) inhibit inflammatory eicosanoids generated by ω-6 PUFAs. Epidemiologic studies on dietary ω-3 PUFA intake show consistent inverse associations with breast cancer incidence among Asian populations, where ω-3, relative to ω-6, intake is high. In contrast, associations are inconsistent among Western populations, where intake of ω-3, relative to ω-6, is low. We hypothesized that examining interactions between ω-3 and ω-6 would help elucidate the PUFA-breast cancer association in the United States. In a Long Island, New York, population-based study of 1463 breast cancer cases and 1500 controls, we estimated multivariable-adjusted odds ratios (ORs) and 95% confidence intervals (CIs) using unconditional logistic regression to examine interactions between ω-3 and ω-6 intake. We observed a super-additive interaction (relative excess risk due to interaction = 0.41; 95% confidence interval = 0.06-0.76) between ω-3 and ω-6 intake in association with breast cancer incidence, although the CIs for the joint exposure of low ω-3/high ω-6 compared to high ω-3/low ω-6 intake were wide (odds ratio = 1.20; 95% confidence interval = 0.85-1.69). Breast cancer risk reduction may be possible for U.S. women with dietary consumption of higher ω-3, which has anti-inflammatory properties, in concert with lower ω-6, which induces inflammation. Replication from future U.S.-based investigations is needed. Copyright © 2015 Elsevier Inc. All rights reserved.

Disrupting the Acyl Carrier Protein/SpoT Interaction In Vivo: Identification of ACP Residues Involved in the Interaction and Consequence on Growth

PubMed Central

Angelini, Sandra; My, Laetitia; Bouveret, Emmanuelle

2012-01-01

In bacteria, Acyl Carrier Protein (ACP) is the central cofactor for fatty acid biosynthesis. It carries the acyl chain in elongation and must therefore interact successively with all the enzymes of this pathway. Yet, ACP also interacts with proteins of diverse unrelated function. Among them, the interaction with SpoT has been proposed to be involved in regulating ppGpp levels in the cell in response to fatty acid synthesis inhibition. In order to better understand this mechanism, we screened for ACP mutants unable to interact with SpoT in vivo by bacterial two-hybrid, but still functional for fatty acid synthesis. The position of the selected mutations indicated that the helix II of ACP is responsible for the interaction with SpoT. This suggested a mechanism of recognition similar to one used for the enzymes of fatty acid synthesis. Consistently, the interactions tested by bacterial two-hybrid of ACP with fatty acid synthesis enzymes were also affected by the mutations that prevented the interaction with SpoT. Yet, interestingly, the corresponding mutant strains were viable, and the phenotypes of one mutant suggested a defect in growth regulation. PMID:22558350

Controlled Interactions between Two Dimensional Layered Inorganic Nanosheets and Polymers

DTIC Science & Technology

2016-06-15

transition metal and non- pair electrons of amine allows us to develop scalable, stable and uniform composite films with numerous combinations of TMD...modification of TMDs sheets with amine-terminated polymers is introduced and the strong Lewis acid-base interaction between transition metal and non- pair ...can be readily entangled with other chains of the matrix polymer, thereby ensuring homogeneous PNC formation. The solvent medium offers an extra

Arginine homopeptides for plasmid DNA purification using monolithic supports.

PubMed

Cardoso, Sara; Sousa, Ângela; Queiroz, João A; Azzoni, Adriano R; Sousa, Fani

2018-06-15

Purification of plasmid DNA targeting therapeutic applications still presents many challenges, namely on supports and specific ligand development. Monolithic supports have emerged as interesting approaches for purifying pDNA due to its excellent mass transfer properties and higher binding capacity values. Moreover, arginine ligands were already described to establish specific and preferential interactions with pDNA. Additionally, some studies revealed the ability of arginine based cationic peptides to condense plasmid DNA, which increased lengthening can result in strongest interactions with higher binding capacities for chromatographic purposes of large molecules such as pDNA. In this work, arginine homopeptides were immobilized in monolithic supports and their performance was evaluated and compared with a single arginine monolithic column regarding supercoiled (sc) plasmid DNA purification. Specific interactions of arginine based peptides with several nucleic acids present in a clarified Escherichia coli lysate sample showed potential for the sc pDNA purification. Effectively, the immobilization of the arginine homopeptides became more functional compared with the single arginine amino acid, showing higher binding capacities, which was also reflected in the intensity of the interactions. The combination of structural versatilities of monoliths with the specificity of arginine peptides raised as a promising strategy for sc pDNA purification. Copyright © 2018 Elsevier B.V. All rights reserved.

Metal-mediated aminocatalysis provides mild conditions: Enantioselective Michael addition mediated by primary amino catalysts and alkali-metal ions

PubMed Central

Leven, Matthias; Neudörfl, Jörg M

2013-01-01

Summary Four catalysts based on new amides of chiral 1,2-diamines and 2-sulfobenzoic acid have been developed. The alkali-metal salts of these betaine-like amides are able to form imines with enones, which are activated by Lewis acid interaction for nucleophilic attack by 4-hydroxycoumarin. The addition of 4-hydroxycoumarin to enones gives ee’s up to 83% and almost quantitative yields in many cases. This novel type of catalysis provides an effective alternative to conventional primary amino catalysis were strong acid additives are essential components. PMID:23400419

Explicit ions/implicit water generalized Born model for nucleic acids

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

Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

Ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model, and utilizes a non-standard approach to defining the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes – disconnected dielectric boundary around the solute-ion or ion-ion pairs. Fully analytical description of all energymore » components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force (PMF) for Na+-Cl− ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within kBT. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of DNA duplex; these differences in the counterion binding patters were shown earlier to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with homopolymeric poly(dA·dT) DNA duplex with modified (de-methylated) and native Thymine bases are used to explore the physics behind CoHex-Thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-Thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range, and may be important to consider in the context of methylation effects on DNA condensation.« less

Explicit ions/implicit water generalized Born model for nucleic acids

NASA Astrophysics Data System (ADS)

Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

2018-05-01

The ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure, and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model and utilizes a non-standard approach to define the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes—disconnected dielectric boundary around the solute-ion or ion-ion pairs. A fully analytical description of all energy components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force for Na+-Cl- ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within kBT. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of the RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of the DNA duplex; these differences in the counterion binding patters were earlier shown to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with the homopolymeric poly(dA.dT) DNA duplex with modified (de-methylated) and native thymine bases are used to explore the physics behind CoHex-thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range and may be important to consider in the context of methylation effects on DNA condensation.

A multiprotein binding interface in an intrinsically disordered region of the tumor suppressor protein interferon regulatory factor-1.

PubMed

Narayan, Vikram; Halada, Petr; Hernychová, Lenka; Chong, Yuh Ping; Žáková, Jitka; Hupp, Ted R; Vojtesek, Borivoj; Ball, Kathryn L

2011-04-22

The interferon-regulated transcription factor and tumor suppressor protein IRF-1 is predicted to be largely disordered outside of the DNA-binding domain. One of the advantages of intrinsically disordered protein domains is thought to be their ability to take part in multiple, specific but low affinity protein interactions; however, relatively few IRF-1-interacting proteins have been described. The recent identification of a functional binding interface for the E3-ubiquitin ligase CHIP within the major disordered domain of IRF-1 led us to ask whether this region might be employed more widely by regulators of IRF-1 function. Here we describe the use of peptide aptamer-based affinity chromatography coupled with mass spectrometry to define a multiprotein binding interface on IRF-1 (Mf2 domain; amino acids 106-140) and to identify Mf2-binding proteins from A375 cells. Based on their function as known transcriptional regulators, a selection of the Mf2 domain-binding proteins (NPM1, TRIM28, and YB-1) have been validated using in vitro and cell-based assays. Interestingly, although NPM1, TRIM28, and YB-1 all bind to the Mf2 domain, they have differing amino acid specificities, demonstrating the degree of combinatorial diversity and specificity available through linear interaction motifs.

Experimental investigation of halogen-bond hard-soft acid-base complementarity.

PubMed

Riel, Asia Marie S; Jessop, Morly J; Decato, Daniel A; Massena, Casey J; Nascimento, Vinicius R; Berryman, Orion B

2017-04-01

The halogen bond (XB) is a topical noncovalent interaction of rapidly increasing importance. The XB employs a `soft' donor atom in comparison to the `hard' proton of the hydrogen bond (HB). This difference has led to the hypothesis that XBs can form more favorable interactions with `soft' bases than HBs. While computational studies have supported this suggestion, solution and solid-state data are lacking. Here, XB soft-soft complementarity is investigated with a bidentate receptor that shows similar associations with neutral carbonyls and heavy chalcogen analogs. The solution speciation and XB soft-soft complementarity is supported by four crystal structures containing neutral and anionic soft Lewis bases.

Spectroscopic characterisation of interaction of ferulic acid with aldehyde dehydrogenase (ALDH).

PubMed

Kolawole, Ayodele O; Agaba, Ruth J; Oluwole, Matthew O

2017-05-01

Interaction of a pharmacological important phenolic, ferulic acid, with Aldehyde dehydrogenase (ALDH) at the simulative pH condition, was studied using spectroscopic approach. Ferulic acid caused a decrease in the fluorescence intensity formed from ALDH-ferulic acid complex resulting in mixed inhibition of ALDH activity (IC 50 =30.65μM). The intrinsic quenching was dynamic and induced altered conformation of ALDH and made the protein less compact but might not unfold it. ALDH has two binding sites for ferulic acid at saturating concentrations having association constant of 1.35×10 3 Lmol -1 and a dissociation constant of 9.7×10 7 Lmol -1 at 25°C indicating ALDH-ferulic acid complex formation is more favourable than its dissociation. The interaction was not spontaneous and endothermic and suggests the involvement of hydrophobic interactions with a FRET binding distance of 4.49nm. Change in pH near and far from isoelectric points of ferulic acid did not affect the bonding interaction. Using trehalose as viscosogen, the result from Stoke-Einstein hypothesis showed that ferulic acid-ALDH binding and dissociation equilibrium was diffusion controlled. These results clearly suggest the unique binding properties and lipophilicity influence of ferulic acid. Copyright © 2017 Elsevier B.V. All rights reserved.

Surface radical chain-transfer reaction in deep eutectic solvents for preparation of silica-grafted stationary phases in hydrophilic interaction chromatography.

PubMed

Yang, Beibei; Cai, Tianpei; Li, Zhan; Guan, Ming; Qiu, Hongdeng

2017-12-01

In this paper, deep eutectic solvents (DESs) were firstly used as new and green solvents for the preparation of polymer-grafted silica stationary phases. 1-Vinylimidazole and acrylic acid were homopolymerized and copolymerized on silica via surface radical chain-transfer reaction in the DESs. Three stationary phases including poly(1-vinylimidazole)-, poly(acrylic acid)-, poly(1-vinylimidazole-co-acrylic acid)-grafted silica were obtained and characterized by elemental analysis and Fourier transform infrared spectroscopy. Their hydrophilic interaction chromatographic properties were investigated for separation of nucleosides, nucleobases, saccharides and amino acids. The retention changes of nucleosides and nucleobases on these columns were investigated under different chromatographic conditions including acetonitrile content, salt concentration, pH of mobile phase and column temperature. The repeatability of these columns was also investigated. The results demonstrate that DESs can be used as new media for the synthesis of silica-based stationary phases by homopolymerization and copolymerization on the surface of porous silica particles. Copyright © 2017 Elsevier B.V. All rights reserved.

Effect of Backbone Design on Hybridization Thermodynamics of Oligo-nucleic Acids: A Coarse-Grained Molecular Dynamics Simulation Study

NASA Astrophysics Data System (ADS)

Ghobadi, Ahmadreza F.; Jayaraman, Arthi

DNA hybridization is the basis of various bio-nano technologies, such as DNA origami and assembly of DNA-functionalized nanoparticles. A hybridized double stranded (ds) DNA is formed when complementary nucleobases on hybridizing strands exhibit specific and directional hydrogen bonds through canonical Watson-Crick base-pairing interactions. In recent years, the need for cheaper alternatives and significant synthetic advances have driven design of DNA mimics with new backbone chemistries. However, a fundamental understanding of how these backbone modifications in the oligo-nucleic acids impact the hybridization and melting behavior of the duplex is still lacking. In this talk, we present our recent findings on impact of varying backbone chemistry on hybridization of oligo-nucleic acid duplexes. We use coarse-grained molecular dynamics simulations to isolate the effect of strand flexibility, electrostatic interactions and nucleobase spacing on the melting curves for duplexes with various strand sequences and concentrations. Since conjugation of oligo-nucleic acids with polymers serve as building blocks for thermo-responsive polymer networks and gels, we also present the effect of such conjugation on hybridization thermodynamics and polymer conformation.

Impact of US Brown Swiss genetics on milk quality from low-input herds in Switzerland: Interactions with season.

PubMed

Stergiadis, Sokratis; Bieber, Anna; Chatzidimitriou, Eleni; Franceschin, Enrica; Isensee, Anne; Rempelos, Leonidas; Baranski, Marcin; Maurer, Veronika; Cozzi, Giulio; Bapst, Beat; Butler, Gillian; Leifert, Carlo

2018-06-15

This study investigated the effect of, and interactions between, US Brown Swiss (BS) genetics and season on milk yield, basic composition and fatty acid profiles, from cows on low-input farms in Switzerland. Milk samples (n = 1,976) were collected from 1,220 crossbreed cows with differing proportions of BS, Braunvieh and Original Braunvieh genetics on 40 farms during winter-housing and summer-grazing. Cows with more BS genetics produced more milk in winter but not in summer, possibly because of underfeeding potentially high-yielding cows on low-input pasture-based diets. Cows with more Original Braunvieh genetics produced milk with more (i) nutritionally desirable eicosapentaenoic and docosapentaenoic acids, throughout the year, and (ii) vaccenic and α-linolenic acids, total omega-3 fatty acid concentrations and a higher omega-3/omega-6 ratio only during summer-grazing. This suggests that overall milk quality could be improved by re-focussing breeding strategies on cows' ability to respond to local dietary environments and seasonal dietary changes. Copyright © 2018 Elsevier Ltd. All rights reserved.

Quest for steroidomimetics: Amino acids derived steroidal and nonsteroidal architectures.

PubMed

Shagufta; Ahmad, Irshad; Panda, Gautam

2017-06-16

The chiral pool amino acids have been utilized for the construction of steroidal and non-steroidal architectures in the quest for steroidomimetics. Chirality derived from amino acid-based architectures provides new and easy to incorporate chiral chemical space, which is otherwise very difficult to introduce and comprised of several synthetic steps for asymmetric steroids. The different and exciting ligand-receptor interactions may arise from the use of each amino acid enantiomer that was introduced into the chiral steroidal backbone. The A and D rings of steroidal architectures can be mimicked by the phenyl group of the amino acid tyrosine. The Mitsunobu reaction, nucleophilic substitution and elimination, etc. were utilized for constructing diverse tri- and tetracyclic steroidal skeletons as well as benzofused seco-steroids from amino acids. These benzofused, amino acid-derived steroidal and nonsteroidal molecules had promising biological activity in hormonal related disorders. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

The μ3 model of acids and bases: extending the Lewis theory to intermetallics.

PubMed

Stacey, Timothy E; Fredrickson, Daniel C

2012-04-02

A central challenge in the design of new metallic materials is the elucidation of the chemical factors underlying the structures of intermetallic compounds. Analogies to molecular bonding phenomena, such as the Zintl concept, have proven very productive in approaching this goal. In this Article, we extend a foundational concept of molecular chemistry to intermetallics: the Lewis theory of acids and bases. The connection is developed through the method of moments, as applied to DFT-calibrated Hückel calculations. We begin by illustrating that the third and fourth moments (μ(3) and μ(4)) of the electronic density of states (DOS) distribution tune the properties of a pseudogap. μ(3) controls the balance of states above and below the DOS minimum, with μ(4) then determining the minimum's depth. In this way, μ(3) predicts an ideal occupancy for the DOS distribution. The μ(3)-ideal electron count is used to forge a link between the reactivity of transition metals toward intermetallic phase formation, and that of Lewis acids and bases toward adduct formation. This is accomplished through a moments-based definition of acidity which classifies systems that are electron-poor relative to the μ(3)-ideal as μ(3)-acidic, and those that are electron-rich as μ(3)-basic. The reaction of μ(3) acids and bases, whether in the formation of a Lewis acid/base adduct or an intermetallic phase, tends to neutralize the μ(3) acidity or basicity of the reactants. This μ(3)-neutralization is traced to the influence of electronegativity differences at heteroatomic contacts on the projected DOS curves of the atoms involved. The role of μ(3)-acid/base interactions in intermetallic phases is demonstrated through the examination of 23 binary phases forming between 3d metals, the stability range of the CsCl type, and structural trends within the Ti-Ni system.

Poly(acrylic acid) to induce competitive crystallization of a theophylline/oxalic acid cocrystal and a theophylline polymorph

NASA Astrophysics Data System (ADS)

Jang, Jisun; Kim, Il Won

2016-01-01

Polymeric additives to induce competitive crystallization of pharmaceutical compounds were explored. A cocrystal of theophylline and oxalic acid was used as a model system, and poly(acrylic acid), poly(caprolactone), and poly(ethylene glycol) were the additives. The cocrystal formation was selectively hindered with addition of poly(acrylic acid). First the size of the cocrystals were reduced, and eventually the cocrystallization was inhibited to generate neat theophylline crystals. The theophylline crystals were of a distinctively different crystal structure from known polymorphs, based on powder X-ray diffraction. They were also obtained in nanoscale size, when millimeter-scale crystals formed without poly(acrylic acid). Polymeric additives that could form specific interactions with crystallizing compounds seem to be useful tools for the phase and size control of pharmaceutical crystals.

Exploring the Sequence-based Prediction of Folding Initiation Sites in Proteins.

PubMed

Raimondi, Daniele; Orlando, Gabriele; Pancsa, Rita; Khan, Taushif; Vranken, Wim F

2017-08-18

Protein folding is a complex process that can lead to disease when it fails. Especially poorly understood are the very early stages of protein folding, which are likely defined by intrinsic local interactions between amino acids close to each other in the protein sequence. We here present EFoldMine, a method that predicts, from the primary amino acid sequence of a protein, which amino acids are likely involved in early folding events. The method is based on early folding data from hydrogen deuterium exchange (HDX) data from NMR pulsed labelling experiments, and uses backbone and sidechain dynamics as well as secondary structure propensities as features. The EFoldMine predictions give insights into the folding process, as illustrated by a qualitative comparison with independent experimental observations. Furthermore, on a quantitative proteome scale, the predicted early folding residues tend to become the residues that interact the most in the folded structure, and they are often residues that display evolutionary covariation. The connection of the EFoldMine predictions with both folding pathway data and the folded protein structure suggests that the initial statistical behavior of the protein chain with respect to local structure formation has a lasting effect on its subsequent states.

Adsorption Behavior of High Stable Zr-Based MOFs for the Removal of Acid Organic Dye from Water

PubMed Central

Zhang, Ke-Deng; Tsai, Fang-Chang; Ma, Ning; Xia, Yue; Liu, Huan-Li; Zhan, Xue-Qing; Yu, Xiao-Yan; Zeng, Xiang-Zhe; Jiang, Tao; Shi, Dean; Chang, Chang-Jung

2017-01-01

Zirconium based metal organic frameworks (Zr-MOFs) have become popular in engineering studies due to their high mechanical stability, thermostability and chemical stability. In our work, by using a theoretical kinetic adsorption isotherm, we can exert MOFs to an acid dye adsorption process, experimentally exploring the adsorption of MOFs, their external behavior and internal mechanism. The results indicate their spontaneous and endothermic nature, and the maximum adsorption capacity of this material for acid orange 7 (AO7) could be up to 358 mg·g−1 at 318 K, estimated by the Langmuir isotherm model. This is ascribed to the presence of an open active metal site that significantly intensified the adsorption, by majorly increasing the interaction strength with the adsorbates. Additionally, the enhanced π delocalization and suitable pore size of UiO-66 gave rise to the highest host–guest interaction, which further improves both the adsorption capacity and separation selectivity at low concentrations. Furthermore, the stability of UiO-66 was actually verified for the first time, through comparing the structure of the samples before and after adsorption mainly by Powder X-ray diffraction and thermal gravimetric analysis. PMID:28772564

New stationary phase for hydrophilic interaction chromatography to separate chito-oligosaccharides with degree of polymerization 2-6.

PubMed

Zhai, Xingchen; Zhao, Haitian; Zhang, Min; Yang, Xin; Sun, Jingming; She, Yongxin; Dong, Aijun; Zhang, Hua; Yao, Lei; Wang, Jing

2018-04-01

A new 3‑aminophenylboronic acid-functionalized stationary phase based on silica for hydrophilic interaction liquid chromatography (HILIC) was developed and showed great HILIC characteristics on separation for chito‑oligosaccharides. The material was synthesized by grafting 3‑aminophenylboronic acid group to silica, and it was characterized by scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FT-IR), elemental analysis and thermal gravimetric analysis (TGA). Nucleobases and nucleosides were used to evaluate the retention property and to investigate retention mechanism by the models designed for description of partitioning and surface adsorption through adjusting ratio of water in the mobile phase. Parameters affecting chromatography behavior such as ionic strength, buffer pH and column temperature were also investigated. Results have indicated that the retention mechanism was a combination of partitioning and surface adsorption, and the hydrogen bond seemed to be the main force for the retention behavior. Finally, the new 3‑aminophenylboronic acid-functionalized based on silica stationary phase was applied to separate chito-oligosaccharide samples with optimized mobile phase conditions and showed acceptable chromatograms. Copyright © 2018 Elsevier B.V. All rights reserved.

Prediction of valid acidity in intact apples with Fourier transform near infrared spectroscopy.

PubMed

Liu, Yan-De; Ying, Yi-Bin; Fu, Xia-Ping

2005-03-01

To develop nondestructive acidity prediction for intact Fuji apples, the potential of Fourier transform near infrared (FT-NIR) method with fiber optics in interactance mode was investigated. Interactance in the 800 nm to 2619 nm region was measured for intact apples, harvested from early to late maturity stages. Spectral data were analyzed by two multivariate calibration techniques including partial least squares (PLS) and principal component regression (PCR) methods. A total of 120 Fuji apples were tested and 80 of them were used to form a calibration data set. The influences of different data preprocessing and spectra treatments were also quantified. Calibration models based on smoothing spectra were slightly worse than that based on derivative spectra, and the best result was obtained when the segment length was 5 nm and the gap size was 10 points. Depending on data preprocessing and PLS method, the best prediction model yielded correlation coefficient of determination (r2) of 0.759, low root mean square error of prediction (RMSEP) of 0.0677, low root mean square error of calibration (RMSEC) of 0.0562. The results indicated the feasibility of FT-NIR spectral analysis for predicting apple valid acidity in a nondestructive way.

Prediction of valid acidity in intact apples with Fourier transform near infrared spectroscopy*

PubMed Central

Liu, Yan-de; Ying, Yi-bin; Fu, Xia-ping

2005-01-01

To develop nondestructive acidity prediction for intact Fuji apples, the potential of Fourier transform near infrared (FT-NIR) method with fiber optics in interactance mode was investigated. Interactance in the 800 nm to 2619 nm region was measured for intact apples, harvested from early to late maturity stages. Spectral data were analyzed by two multivariate calibration techniques including partial least squares (PLS) and principal component regression (PCR) methods. A total of 120 Fuji apples were tested and 80 of them were used to form a calibration data set. The influences of different data preprocessing and spectra treatments were also quantified. Calibration models based on smoothing spectra were slightly worse than that based on derivative spectra, and the best result was obtained when the segment length was 5 nm and the gap size was 10 points. Depending on data preprocessing and PLS method, the best prediction model yielded correlation coefficient of determination (r 2) of 0.759, low root mean square error of prediction (RMSEP) of 0.0677, low root mean square error of calibration (RMSEC) of 0.0562. The results indicated the feasibility of FT-NIR spectral analysis for predicting apple valid acidity in a nondestructive way. PMID:15682498

Symposium: Ionic and Respiratory Interaction in Aquatic Animals

ERIC Educational Resources Information Center

Physiologist, 1976

1976-01-01

Presented are eight abstracts of a symposium held in conjunction with the American Physiological Society (APS) and the American Society of Zoologists (ASZ). Fish gill structure and function, renal function, acid-base balance and ionic sensitivity are topics discussed. (EB)

Mechanism of cinnamic acid-induced trypsin inhibition: a multi-technique approach.

PubMed

Zhang, Hongmei; Zhou, Qiuhua; Cao, Jian; Wang, Yanqing

2013-12-01

In order to investigate the association of the protease trypsin with cinnamic acid, the interaction was characterized by using fluorescence, UV-vis absorption spectroscopy, molecular modeling and an enzymatic inhibition assay. The binding process may be outlined as follows: cinnamic acid can interact with trypsin with one binding site to form cinnamic acid-trypsin complex, resulting in inhibition of trypsin activity; the spectroscopic data show that the interaction is a spontaneous process with the estimated enthalpy and entropy changes being -8.95 kJ mol(-1) and 50.70 J mol(-1) K(-1), respectively. Noncovalent interactions make the main contribution to stabilize the trypsin-cinnamic acid complex; cinnamic acid can enter into the primary substrate-binding pocket and alter the environment around Trp and Tyr residues. Copyright © 2013 Elsevier B.V. All rights reserved.

The Citrus transcription factor, CitERF13, regulates citric acid accumulation via a protein-protein interaction with the vacuolar proton pump, CitVHA-c4.

PubMed

Li, Shao-jia; Yin, Xue-ren; Xie, Xiu-lan; Allan, Andrew C; Ge, Hang; Shen, Shu-ling; Chen, Kun-song

2016-02-03

Organic acids are essential to fruit flavor. The vacuolar H(+) transporting adenosine triphosphatase (V-ATPase) plays an important role in organic acid transport and accumulation. However, less is known of V-ATPase interacting proteins and their relationship with organic acid accumulation. The relationship between V-ATPase and citric acid was investigated, using the citrus tangerine varieties 'Ordinary Ponkan (OPK)' and an early maturing mutant 'Zaoshu Ponkan (ZPK)'. Five V-ATPase genes (CitVHA) were predicted as important to citric acid accumulation. Among the genes, CitVHA-c4 was observed, using a yeast two-hybrid screen, to interact at the protein level with an ethylene response factor, CitERF13. This was verified using bimolecular fluorescence complementation assays. A similar interaction was also observed between Arabidopsis AtERF017 (a CitERF13 homolog) and AtVHA-c4 (a CitVHA-c4 homolog). A synergistic effect on citric acid levels was observed between V-ATPase proteins and interacting ERFs when analyzed using transient over-expression in tobacco and Arabidopsis mutants. Furthermore, the transcript abundance of CitERF13 was concomitant with CitVHA-c4. CitERF13 or AtERF017 over-expression leads to significant citric acid accumulation. This accumulation was abolished in an AtVHA-c4 mutant background. ERF-VHA interactions appear to be involved in citric acid accumulation, which was observed in both citrus and Arabidopsis.

Potential for food-drug interactions by dietary phenolic acids on human organic anion transporters 1 (SLC22A6), 3 (SLC22A8), and 4 (SLC22A11).

PubMed

Wang, Li; Sweet, Douglas H

2012-10-15

Phenolic acids exert beneficial health effects such as anti-oxidant, anti-carcinogenic, and anti-inflammatory activities and show systemic exposure after consumption of common fruits, vegetables, and beverages. However, knowledge regarding which components convey therapeutic benefits and the mechanism(s) by which they cross cell membranes is extremely limited. Therefore, we determined the inhibitory effects of nine food-derived phenolic acids, p-coumaric acid, ferulic acid, gallic acid, gentisic acid, 4-hydroxybenzoic acid, protocatechuic acid, sinapinic acid, syringic acid, and vanillic acid, on human organic anion transporter 1 (hOAT1), hOAT3, and hOAT4. In the present study, inhibition of OAT-mediated transport of prototypical substrates (1 μM) by phenolic acids (100 μM) was examined in stably expressing cell lines. All compounds significantly inhibited hOAT3 transport, while just ferulic, gallic, protocatechuic, sinapinic, and vanillic acid significantly blocked hOAT1 activity. Only sinapinic acid inhibited hOAT4 (~35%). For compounds exhibiting inhibition > ~60%, known clinical plasma concentration levels and plasma protein binding in humans were examined to select compounds to evaluate further with dose-response curves (IC(50) values) and drug-drug interaction (DDI) index determinations. IC(50) values ranged from 1.24 to 18.08 μM for hOAT1 and from 7.35 to 87.36 μM for hOAT3. Maximum DDI indices for gallic and gentisic acid (≫0.1) indicated a very strong potential for DDIs on hOAT1 and/or hOAT3. This study indicates that gallic acid from foods or supplements, or gentisic acid from salicylate-based drug metabolism, may significantly alter the pharmacokinetics (efficacy and toxicity) of concomitant therapeutics that are hOAT1 and/or hOAT3 substrates. Copyright © 2012 Elsevier Inc. All rights reserved.

Reaction-based Indicator displacement Assay (RIA) for the selective colorimetric and fluorometric detection of peroxynitrite.

PubMed

Sun, Xiaolong; Lacina, Karel; Ramsamy, Elena C; Flower, Stephen E; Fossey, John S; Qian, Xuhong; Anslyn, Eric V; Bull, Steven D; James, Tony D

2015-05-01

Using the self-assembly of aromatic boronic acids with Alizarin Red S (ARS), we developed a new chemosensor for the selective detection of peroxynitrite. Phenylboronic acid (PBA), benzoboroxole (BBA) and 2-( N , N -dimethylaminomethyl)phenylboronic acid (NBA) were employed to bind with ARS to form the complex probes. In particular, the ARS-NBA system with a high binding affinity can preferably react with peroxynitrite over hydrogen peroxide and other ROS/RNS due to the protection of the boron via the solvent-insertion B-N interaction. Our simple system produces a visible colorimetric change and on-off fluorescence response towards peroxynitrite. By coupling a chemical reaction that leads to an indicator displacement, we have developed a new sensing strategy, referred to herein as RIA (Reaction-based Indicator displacement Assay).

Changes in monosaccharides, organic acids and amino acids during Cabernet Sauvignon wine ageing based on a simultaneous analysis using gas chromatography-mass spectrometry.

PubMed

Zhang, Xin-Ke; Lan, Yi-Bin; Zhu, Bao-Qing; Xiang, Xiao-Feng; Duan, Chang-Qing; Shi, Ying

2018-01-01

Monosaccharides, organic acids and amino acids are the important flavour-related components in wines. The aim of this article is to develop and validate a method that could simultaneously analyse these compounds in wine based on silylation derivatisation and gas chromatography-mass spectrometry (GC-MS), and apply this method to the investigation of the changes of these compounds and speculate upon their related influences on Cabernet Sauvignon wine flavour during wine ageing. This work presented a new approach for wine analysis and provided more information concerning red wine ageing. This method could simultaneously quantitatively analyse 2 monosaccharides, 8 organic acids and 13 amino acids in wine. A validation experiment showed good linearity, sensitivity, reproducibility and recovery. Multiple derivatives of five amino acids have been found but their effects on quantitative analysis were negligible, except for methionine. The evolution pattern of each category was different, and we speculated that the corresponding mechanisms involving microorganism activities, physical interactions and chemical reactions had a great correlation with red wine flavours during ageing. Simultaneously quantitative analysis of monosaccharides, organic acids and amino acids in wine was feasible and reliable and this method has extensive application prospects. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Leishmania donovani Utilize Sialic Acids for Binding and Phagocytosis in the Macrophages through Selective Utilization of Siglecs and Impair the Innate Immune Arm.

PubMed

Roy, Saptarshi; Mandal, Chitra

2016-08-01

Leishmania donovani, belonging to a unicellular protozoan parasite, display the differential level of linkage-specific sialic acids on their surface. Sialic acids binding immunoglobulin-like lectins (siglecs) are a class of membrane-bound receptors present in the haematopoetic cell lineages interact with the linkage-specific sialic acids. Here we aimed to explore the utilization of sialic acids by Leishmania donovani for siglec-mediated binding, phagocytosis, modulation of innate immune response and signaling pathways for establishment of successful infection in the host. We have found enhanced binding of high sialic acids containing virulent strains (AG83+Sias) with siglec-1 and siglec-5 present on macrophages compared to sialidase treated AG83+Sias (AG83-Sias) and low sialic acids-containing avirulent strain (UR6) by flow cytometry. This specific receptor-ligand interaction between sialic acids and siglecs were further confirmed by confocal microscopy. Sialic acids-siglec-1-mediated interaction of AG83+Sias with macrophages induced enhanced phagocytosis. Additionally, sialic acids-siglec-5 interaction demonstrated reduced ROS, NO generation and Th2 dominant cytokine response upon infection with AG83+Sias in contrast to AG83-Sias and UR6. Sialic acids-siglecs binding also facilitated multiplication of intracellular amastigotes. Moreover, AG83+Sias induced sialic acids-siglec-5-mediated upregulation of host phosphatase SHP-1. Such sialic acids-siglec interaction was responsible for further downregulation of MAPKs (p38, ERK and JNK) and PI3K/Akt pathways followed by the reduced translocation of p65 subunit of NF-κβ to the nucleus from cytosol in the downstream signaling pathways. This sequence of events was reversed in AG83-Sias and UR6-infected macrophages. Besides, siglec-knockdown macrophages also showed the reversal of AG83+Sias infection-induced effector functions and downstream signaling events. Taken together, this study demonstrated that virulent parasite (AG83+Sias) establish a unique sialic acids-mediated binding and subsequent phagocytosis in the host cell through the selective exploitation of siglec-1. Additionally, sialic acids-siglec-5 interaction altered the downstream signaling pathways which contributed impairment of immune effector functions of macrophages. To the best of our knowledge, this is a comprehensive report describing sialic acids-siglec interactions and their role in facilitating uptake of the virulent parasite within the host.

Raman spectroscopy study and first-principles calculations of the interaction between nucleic acid bases and carbon nanotubes.

PubMed

Stepanian, Stepan G; Karachevtsev, Maksym V; Glamazda, Alexander Yu; Karachevtsev, Victor A; Adamowicz, L

2009-04-16

In this work, we have used Raman spectroscopy and quantum chemical methods (MP2 and DFT) to study the interactions between nucleic acid bases (NABs) and single-walled carbon nanotubes (SWCNT). We found that the appearance of the interaction between the nanotubes and the NABs is accompanied by a spectral shift of the high-frequency component of the SWCNT G band in the Raman spectrum to a lower frequency region. The value of this shift varies from 0.7 to 1.3 cm(-1) for the metallic nanotubes and from 2.1 to 3.2 cm(-1) for the semiconducting nanotubes. Calculations of the interaction energies between the NABs and a fragment of the zigzag(10,0) carbon nanotube performed at the MP2/6-31++G(d,p)[NABs atoms]|6-31G(d)[nanotube atoms] level of theory while accounting for the basis set superposition error during geometry optimization allowed us to order the NABs according to the increasing interaction energy value. The order is: guanine (-67.1 kJ mol(-1)) > adenine (-59.0 kJ mol(-1)) > cytosine (-50.3 kJ mol(-1)) approximately = thymine (-50.2 kJ mol(-1)) > uracil (-44.2 kJ mol(-1)). The MP2 equilibrium structures and the interaction energies were used as reference points in the evaluation of the ability of various functionals in the DFT method to predict those structures and energies. We showed that the M05, MPWB1K, and MPW1B95 density functionals are capable of correctly predicting the SWCNT-NAB geometries but not the interaction energies, while the M05-2X functional is capable of correctly predicting both the geometries and the interaction energies.

Influences of the chemical structure of entrainers on the activity coefficients in presence of biodiesel

NASA Astrophysics Data System (ADS)

Mäder, A.; Fleischmann, A.; Fang, Ye; Ruck, W.; Krahl, J.

2012-05-01

In this work we analyzed the strength of the intermolecular forces between biodiesel and the entrainer and their influence on the entrainer's ability to interact with biodiesel. Furthermore we investigated the influence of the chemical structure of an entrainer to the interaction with biodiesel. For this purpose the activity coefficients γ∞ at infinite dilution of acids, aldehydes, ketones and alcohols in biodiesel were measured with the method of headspace gas chromatography (HSGC). Short-chained acids showed the highest interaction of the analyzed entrainers caused by their ability to build hydrogen bonds with biodiesel. Increased chain length of the acids cause reduced interaction with biodiesel, which is mainly due to the higher obstruction of the acid molecule and therefore the reduced ability to build hydrogen bonds with biodiesel. Aldehydes, ketones and alcohols showed lower interaction with biodiesel compared to the acids. Longer-chained alcohols showed increased interaction with biodiesel due to the raised London Forces and an inductive +I effect of the molecule chain.

Tetracoordinate Imidazole-Based Boron Complexes for the Selective Detection of Picric Acid.

PubMed

Dhanunjayarao, Kunchala; Mukundam, Vanga; Venkatasubbaiah, Krishnan

2016-11-07

N,N-Dimethylamine and N,N-diphenylamine-decorated highly fluorescent imidazole borates have been synthesized and investigated as new fluorophores for the selective detection of trinitrophenol/picric acid (PA). Structural studies of a probe 1 and PA (1·PA) complex revealed that the adduct formed by the deprotonation of PA by the -NMe 2 group along with weak interactions is responsible for the selective detection of PA over other polynitrated organic compounds.

Layered double hydroxide intercalated with aromatic acid anions for the efficient capture of aniline from aqueous solution.

PubMed

Yu, Shujun; Wang, Xiangxue; Chen, Zhongshan; Wang, Jian; Wang, Suhua; Hayat, Tasawar; Wang, Xiangke

2017-01-05

Aniline is toxic and hard to be degraded, and thereby causes the environmental pollution seriously. Herein, a practical and green hydrothermal method was applied to fabricate terephthalic acid and pyromellitic acid intercalated layered double hydroxides (LDH) (named as TAL and PAL) for aniline efficient removal. The sorption of aniline on LDH-based materials were investigated at different experimental conditions, and the results indicated that aniline sorption on LDH, TAL and PAL were strongly dependent on pH and independent of ionic strength. The maximum sorption capacities of aniline on TAL and PAL at pH 5.0 and 293K were 90.4 and 130.0mg/g, respectively, which were significantly higher than that of aniline on LDH (52.6mg/g). Based on the BET, FTIR and XPS analysis, the higher sorption capacities of TAL and PAL were mainly due to high surface area and basal spacing as well as the abundant functional groups (e.g. -COO - ). The interactions of aniline with TAL and PAL were mainly dominated by hydrogen bonds and electrostatic interactions. Such a facile synthesis method, efficient removal performance and superior reusability indicated that the aromatic acid modified LDH materials had potential application for efficient treatment of organic pollutants in environmental pollution cleanup. Copyright © 2016 Elsevier B.V. All rights reserved.

Effects of Lewis acidity of metal oxide promoters on the activity and selectivity of Co-based Fischer–Tropsch synthesis catalysts

DOE PAGES

Johnson, Gregory R.; Bell, Alexis T.

2016-03-31

Metal oxides of Ce, Gd, La, Mn, and Zr were investigated as promoters for improving the activity and selectivity of Co-based FTS catalysts. The extent to which these promoters decrease the selectivity toward CH 4 and increase the selectivity toward C 5+ hydrocarbons was found to depend on both the loading and the composition of the oxide promoter. Elemental mapping by STEM-EDS revealed that the propensity for a given metal oxide to associate with Co affects the sensitivity of the product distribution to changes in promoter loading. For all promoters, a sufficiently high loading resulted in the product distributions becomingmore » insensitive to further increases in promoter loading, very likely due to the formation of a half monolayer of promoter oxide over the Co surface. Simulations suggest that the fraction of Co active sites that are adjacent to the promoter moieties approaches unity at this degree of coverage. The oxidation state of the promoter metal cation under reaction conditions, determined by in situ XANES measurements, was used to calculate relative Lewis acidity of the promoter metal cation. We found a strong positive correlation between the C 5+ product selectivity and the Lewis acidity of the promoter metal cations, suggesting that the promotional effects are a consequence of Lewis acid-base interactions between the reaction intermediates and the promoter metal cations. Rate data obtained at different pressures were used to estimate the apparent rate coefficient and the CO adsorption constant appearing in the Langmuir-Hinshelwood expression that describes the CO consumption kinetics for both unpromoted and the metal oxide-promoted catalysts. Both parameters exhibited positive correlations with the promoter Lewis acidity. Our results are consistent with the hypothesis that the metal cations of the promoter act as Lewis acids that interact with the O atom of adsorbed CO to facilitate CO adsorption and dissociation.« less

Carboxylate ligands induced structural diversity of zinc(II) coordination polymers based on 3,6-bis(imidazol-1-yl)carbazole: Syntheses, structures and photocatalytic properties

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

Cheng, Hong-Jian, E-mail: hjcheng@cslg.cn; Tang, Hui-Xiang; Shen, Ya-Li

2015-12-15

Solvothermal reactions of Zn(NO{sub 3}){sub 2}·6H{sub 2}O with 3,6-bis(1-imidazolyl)carbazole (3,6-bmcz) and 1,4-benzenedicarboxylic acid (1,4-H{sub 2}bdc), p-phenylenediacetic acid (p-H{sub 2}pda), benzophenone-4,4-dicarboxylic acid (H{sub 2}bpda) afforded three coordination polymers [Zn(1,4-bdc)(3,6-bmcz)]{sub n} (1), {[Zn(p-pda)(3,6-bmcz)]·1.5H_2O}{sub n} (2) and {[Zn(bpda)(3,6-bmcz)]·0.25H_2O}{sub n} (3). Complexes 1–3 were characterized by elemental analysis, IR, powder X-ray diffraction, and single-crystal X-ray diffraction. Complex 1 shows 3D structure with 2D nets inclined polycatenation. Complexes 2 and 3 possess an extended 3D supramolecular architecture based on their respective 2D layers through hydrogen-bonding interactions and the π···π stacking interactions. The solid state luminescent and optical properties of 1–3 at ambient temperature were alsomore » investigated. A comparative study on their photocatalytic activity toward the degradation of methylene blue in polluted water was explored. - Graphical abstract: Reactions of Zn(NO{sub 3}){sub 2} and 3,6-(1-imidazolyl)carbazole with 1,4-benzenedicarboxylic acid, p-phenylenediacetic acid or benzophenone-4,4-dicarboxylic acid afforded three coordination polymers with different topologies and photocatalytic activity. - Highlights: • Reactions of 1,4-H{sub 2}bdc, p-H{sub 2}pda or H{sub 2}bpda with 3,6-bmcz and Zn(II) gave three CPs. • Complex 1 is a 3D entanglement. • Complex 2 or 3 is a 3D supramolecular structure based on different 2D layers. • Complex 2 exhibited good catalytic activity of methylene blue photodegradation.« less

Probing hydrogen and halogen-oxo interactions in uranyl coordination polymers: a combined crystallographic and computational study

DOE PAGES

Carter, Korey P.; Kalaj, Mark; Kerridge, Andrew; ...

2018-01-01

Four uranyl compounds containing either benzoic acid ( 1 ), m -chlorobenzoic acid ( 2 ), m -bromobenzoic acid ( 3 ), or m -iodobenzoic acid ( 4 ) are described, and the latter two compounds are used to probe non-covalent interaction strengths via structural, vibrational, and computational means.

Modeled effects of soil acidification on long-term ecological and economic outcomes for managed forests in the Adirondack region (USA).

PubMed

Caputo, Jesse; Beier, Colin M; Sullivan, Timothy J; Lawrence, Gregory B

2016-09-15

Sugar maple (Acer saccharum) is among the most ecologically and economically important tree species in North America, and its growth and regeneration is often the focus of silvicultural practices in northern hardwood forests. A key stressor for sugar maple (SM) is acid rain, which depletes base cations from poorly-buffered forest soils and has been associated with much lower SM vigor, growth, and recruitment. However, the potential interactions between forest management and soil acidification - and their implications for the sustainability of SM and its economic and cultural benefits - have not been investigated. In this study, we simulated the development of 50 extant SM stands in the western Adirondack region of NY (USA) for 100years under different soil chemical conditions and silvicultural prescriptions. We found that interactions between management prescription and soil base saturation will strongly shape the ability to maintain SM in managed forests. Below 12% base saturation, SM did not regenerate sufficiently after harvest and was replaced mainly by red maple (Acer rubrum) and American beech (Fagus grandifolia). Loss of SM on acid-impaired sites was predicted regardless of whether the shelterwood or diameter-limit prescriptions were used. On soils with sufficient base saturation, models predicted that SM will regenerate after harvest and be sustained for future rotations. We then estimated how these different post-harvest outcomes, mediated by acid impairment of forest soils, would affect the potential monetary value of ecosystem services provided by SM forests. Model simulations indicated that a management strategy focused on syrup production - although not feasible across the vast areas where acid impairment has occurred - may generate the greatest economic return. Although pollution from acid rain is declining, its long-term legacy in forest soils will shape future options for sustainable forestry and ecosystem stewardship in the northern hardwood forests of North America. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Modeled effects of soil acidification on long-term ecological and economic outcomes for managed forests in the Adirondack region (USA)

USGS Publications Warehouse

Caputo, Jesse PhD.; Beier, Colin M.; Sullivan, Timothy J.; Lawrence, Gregory B.

2016-01-01

Sugar maple (Acer saccharum) is among the most ecologically and economically important tree species in North America, and its growth and regeneration is often the focus of silvicultural practices in northern hardwood forests. A key stressor for sugar maple (SM) is acid rain, which depletes base cations from poorly-buffered forest soils and has been associated with much lower SM vigor, growth, and recruitment. However, the potential interactions between forest management and soil acidification – and their implications for the sustainability of SM and its economic and cultural benefits – have not been investigated. In this study, we simulated the development of 50 extant SM stands in the western Adirondack region of NY (USA) for 100 years under different soil chemical conditions and silvicultural prescriptions. We found that interactions between management prescription and soil base saturation will strongly shape the ability to maintain SM in managed forests. Below 12% base saturation, SM did not regenerate sufficiently after harvest and was replaced mainly by red maple (Acer rubrum) and American beech (Fagus grandifolia). Loss of SM on acid-impaired sites was predicted regardless of whether the shelterwood or diameter-limit prescriptions were used. On soils with sufficient base saturation, models predicted that SM will regenerate after harvest and be sustained for future rotations. We then estimated how these different post-harvest outcomes, mediated by acid impairment of forest soils, would affect the potential monetary value of ecosystem services provided by SM forests. Model simulations indicated that a management strategy focused on syrup production – although not feasible across the vast areas where acid impairment has occurred – may generate the greatest economic return. Although pollution from acid rain is declining, its long-term legacy in forest soils will shape future options for sustainable forestry and ecosystem stewardship in the northern hardwood forests of North America.

BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE.

PubMed

Rao, Archana N; Grainger, David W

2014-04-01

Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.

Design of stereoelectronically promoted super lewis acids and unprecedented chemistry of their complexes.

PubMed

Foroutan-Nejad, Cina; Vicha, Jan; Marek, Radek

2014-09-01

A new family of stereoelectronically promoted aluminum and scandium super Lewis acids is introduced on the basis of state-of-the-art computations. Structures of these molecules are designed to minimize resonance electron donation to central metal atoms in the Lewis acids. Acidity of these species is evaluated on the basis of their fluoride-ion affinities relative to the antimony pentafluoride reference system. It is demonstrated that introduced changes in the stereochemistry of the designed ligands increase acidity considerably relative to Al and Sc complexes with analogous monodentate ligands. The high stability of fluoride complexes of these species makes them ideal candidates to be used as weakly coordinating anions in combination with highly reactive cations instead of conventional Lewis acid-fluoride complexes. Further, the interaction of all designed molecules with methane is investigated. All studied acids form stable pentavalent-carbon complexes with methane. In addition, interactions of the strongest acid of this family with very weak bases, namely, H2, N2, carbon oxides, and noble gases were investigated; it is demonstrated that this compound can form considerably stable complexes with the aforementioned molecules. To the best of our knowledge, carbonyl and nitrogen complexes of this species are the first hypothetical four-coordinated carbonyl and nitrogen complexes of aluminum. The nature of bonding in these systems is studied in detail by various bonding analysis approaches. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE

PubMed Central

Rao, Archana N.; Grainger, David W.

2014-01-01

Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA’s persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools. PMID:24765522

Investigation of the chemical interface in the soybean–aphid and rice–bacteria interactions using MALDI-mass spectrometry imaging

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

Klein, Adam T.; Yagnik, Gargey B.; Hohenstein, Jessica D.

Mass spectrometry imaging (MSI) is an emerging technology for high-resolution plant biology. It has been utilized to study plant–pest interactions, but limited to the surface interfaces. Here we expand the technology to explore the chemical interactions occurring inside the plant tissues. Two sample preparation methods, imprinting and fracturing, were developed and applied, for the first time, to visualize internal metabolites of leaves in matrix-assisted laser desorption ionization (MALDI)-MSI. This is also the first time nanoparticle-based ionization was implemented to ionize diterpenoid phytochemicals that were difficult to analyze with traditional organic matrices. The interactions between rice–bacterium and soybean–aphid were investigated asmore » two model systems to demonstrate the capability of high-resolution MSI based on MALDI. Localized molecular information on various plant- or pest-derived chemicals provided valuable insight for the molecular processes occurring during the plant–pest interactions. Basically, salicylic acid and isoflavone based resistance was visualized in the soybean–aphid system and antibiotic diterpenoids in rice–bacterium interactions.« less

Investigation of the chemical interface in the soybean–aphid and rice–bacteria interactions using MALDI-mass spectrometry imaging

DOE PAGES

Klein, Adam T.; Yagnik, Gargey B.; Hohenstein, Jessica D.; ...

2015-04-27

Mass spectrometry imaging (MSI) is an emerging technology for high-resolution plant biology. It has been utilized to study plant–pest interactions, but limited to the surface interfaces. Here we expand the technology to explore the chemical interactions occurring inside the plant tissues. Two sample preparation methods, imprinting and fracturing, were developed and applied, for the first time, to visualize internal metabolites of leaves in matrix-assisted laser desorption ionization (MALDI)-MSI. This is also the first time nanoparticle-based ionization was implemented to ionize diterpenoid phytochemicals that were difficult to analyze with traditional organic matrices. The interactions between rice–bacterium and soybean–aphid were investigated asmore » two model systems to demonstrate the capability of high-resolution MSI based on MALDI. Localized molecular information on various plant- or pest-derived chemicals provided valuable insight for the molecular processes occurring during the plant–pest interactions. Basically, salicylic acid and isoflavone based resistance was visualized in the soybean–aphid system and antibiotic diterpenoids in rice–bacterium interactions.« less

Relationships between acid deposition, watershed characteristics, and stream chemistry in Maryland's coastal plain. Final report. Volume 1. Text. Report for May 1984-June 1985

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

Campbell, S.; Bartoshesky, J.; Heimbuch, D.

1987-06-01

Precipitation and stream-water chemistry data were collected from three watersheds in the Coastal Plain region of Maryland during the period May 1984 through June 1985 in an attempt to determine the potential effects of acidic deposition on the chemistry of these streams. The study streams included Lyons Creek, Morgan Creek, and Granny Finley Branch; these streams were chosen based on their differential responses to storm events observed in a survey of Coastal Plain streams in the spring of 1983. Lyons Creek typically exhibited lower pH, acid-neutralizing capacity, and concentrations of base cations than observed in the other streams. Sulfate massmore » balances suggest that the soils in the Lyons Creek watershed also have less affinity for sulfur retention than do soils of the other watersheds. Acidic pulses were observed in all three streams during the spring months; however, the magnitude of these pulses was less than that observed in 1983. Modeling of the relationships between precipitation chemistry, watershed interactions, and stream chemistry suggests that precipitation acidity can influence stream-water acidity, depending upon hydrological conditions and availabiility of acid-neutralizing materials in the watersheds.« less

Urinary metabolic insights into host-gut microbial interactions in healthy and IBD children

PubMed Central

Martin, Francois-Pierre; Su, Ming-Ming; Xie, Guo-Xiang; Guiraud, Seu Ping; Kussmann, Martin; Godin, Jean-Philippe; Jia, Wei; Nydegger, Andreas

2017-01-01

AIM To identify metabolic signatures in urine samples from healthy and inflammatory bowel disease (IBD) children. METHODS We applied liquid chromatography and gas chromatography coupled to targeted mass spectrometry (MS)-based metabolite profiling to identify and quantify bile acids and host-gut microbial metabolites in urine samples collected from 21 pediatric IBD patients monitored three times over one year (baseline, 6 and 12 mo), and 27 age- and gender-matched healthy children. RESULTS urinary metabolic profiles of IBD children differ significantly from healthy controls. Such metabolic differences encompass central energy metabolism, amino acids, bile acids and gut microbial metabolites. In particular, levels of pyroglutamic acid, glutamic acid, glycine and cysteine, were significantly higher in IBD children in the course of the study. This suggests that glutathione cannot be optimally synthesized and replenished. Whilst alterations of the enterohepatic circulation of bile acids in pediatric IBD patients is known, we show here that non-invasive urinary bile acid profiling can assess those altered hepatic and intestinal barrier dysfunctions. CONCLUSION The present study shows how non-invasive sampling of urine followed by targeted MS-based metabonomic analysis can elucidate and monitor the metabolic status of children with different GI health/disease status. PMID:28611517

Electrophilic fluorination of pyroglutamic acid derivatives: application of substrate-dependent reactivity and diastereoselectivity to the synthesis of optically active 4-fluoroglutamic acids.

PubMed

Konas, D W; Coward, J K

2001-12-28

Electrophilic fluorination of enantiomerically pure 2-pyrrolidinones (4) derived from (L)-glutamic acid has been investigated as a method for the synthesis of single stereoisomers of 4-fluorinated glutamic acids. Reaction of the lactam enolate derived from 9 with NFSi results in a completely diastereoselective monofluorination reaction to yield the monocyclic trans-substituted alpha-fluoro lactam product 21. Unfortunately, a decreased kinetic acidity in 21 and other structurally related monofluorinated products renders them resistant to a second fluorination. In contrast, the bicyclic lactam 12 is readily difluorinated under the standard conditions described to yield the alpha,alpha-difluoro lactam 24. The difference in reactivity between the two types of related lactams is attributed mainly to the presence or lack of a steric interaction between the base used for deprotonation and the protecting group present in the pyrrolidinone substrates. This conclusion was reached based on analysis of the X-ray crystal structure of 21, molecular modeling, and experimental evidence. The key intermediates 21 and 24 are converted to (2S,4R)-4-fluoroglutamic acid and (2S)-4,4-difluoroglutamic acid, respectively.

tRNA acceptor-stem and anticodon bases embed separate features of amino acid chemistry

PubMed Central

Carter, Charles W.; Wolfenden, Richard

2016-01-01

abstract The universal genetic code is a translation table by which nucleic acid sequences can be interpreted as polypeptides with a wide range of biological functions. That information is used by aminoacyl-tRNA synthetases to translate the code. Moreover, amino acid properties dictate protein folding. We recently reported that digital correlation techniques could identify patterns in tRNA identity elements that govern recognition by synthetases. Our analysis, and the functionality of truncated synthetases that cannot recognize the tRNA anticodon, support the conclusion that the tRNA acceptor stem houses an independent code for the same 20 amino acids that likely functioned earlier in the emergence of genetics. The acceptor-stem code, related to amino acid size, is distinct from a code in the anticodon that is related to amino acid polarity. Details of the acceptor-stem code suggest that it was useful in preserving key properties of stereochemically-encoded peptides that had developed the capacity to interact catalytically with RNA. The quantitative embedding of the chemical properties of amino acids into tRNA bases has implications for the origins of molecular biology. PMID:26595350

[Development and application of electroanalytical methods in biomedical fields].

PubMed

Kusu, Fumiyo

2015-01-01

To summarize our electroanalytical research in the biomedical field over the past 43 years, this review describes studies on specular reflection measurement, redox potential determination, amperometric acid sensing, HPLC with electrochemical detection, and potential oscillation across a liquid membrane. The specular reflection method was used for clarifying the adsorption of neurotransmitters and their related drugs onto a gold electrode and the interaction between dental alloys and compound iodine glycerin. A voltammetric screening test using a redox potential for the antioxidative effect of flavonoids was proposed. Amperometric acid sensing based on the measurement of the reduction prepeak current of 2-methyl-1,4-naphthoquinone (VK3) or 3,5-di-tert-buty1-1,2-benzoquinone (DBBQ) was applied to determine acid values of fats and oils, titrable acidity of coffee, and enzyme activity of lipase, free fatty acids (FFAs) in serum, short-chain fatty acids in feces, etc. The electrode reactions of phenothiazines, catechins, and cholesterol were applied to biomedical analysis using HPLC with electrochemical detection. A three-channel electrochemical detection system was utilized for the sensitive determination of redox compounds in Chinese herbal medicines. The behavior of barbituric acid derivatives was examined based on potential oscillation measurements.

Response surface methodology for the determination of the design space of enantiomeric separations on cinchona-based zwitterionic chiral stationary phases by high performance liquid chromatography.

PubMed

Hanafi, Rasha Sayed; Lämmerhofer, Michael

2018-01-26

Quality-by-Design approach for enantioselective HPLC method development surpasses Quality-by-Testing in offering the optimal separation conditions with the least number of experiments and in its ability to describe the method's Design Space visually which helps to determine enantiorecognition to a significant extent. Although some schemes exist for enantiomeric separations on Cinchona-based zwitterionic stationary phases, the exact design space and the weights by which each of the chromatographic parameters influences the separation have not yet been statistically studied. In the current work, a screening design followed by a Response Surface Methodology optimization design were adopted for enantioseparation optimization of 3 model drugs namely the acidic Fmoc leucine, the amphoteric tryptophan and the basic salbutamol. The screening design proved that the acid/base additives are of utmost importance for the 3 chiral drugs, and that among 3 different pairs of acids and bases, acetic acid and diethylamine is the couple able to provide acceptable resolution at variable conditions. Visualization of the response surface of the retention factor, separation factor and resolution helped describe accurately the magnitude by which each chromatographic factor (% MeOH, concentration and ratio of acid base modifiers) affects the separation while interacting with other parameters. The global optima compromising highest enantioresolution with the least run time for the 3 chiral model drugs varied extremely, where it was best to set low % methanol with equal ratio of acid-base modifiers for the acidic drug, very high % methanol and 10-fold higher concentration of the acid for the amphoteric drug while 20 folds of the base modifier with moderate %methanol were needed for the basic drug. Considering the selected drugs as models for many series of structurally related compounds, the design space defined and the optimum conditions computed are the key for method development on cinchona-based chiral stationary phases. Copyright © 2017 Elsevier B.V. All rights reserved.

Agent-based model of fecal microbial transplant effect on bile acid metabolism on suppressing Clostridium difficile infection: an example of agent-based modeling of intestinal bacterial infection.

PubMed

Peer, Xavier; An, Gary

2014-10-01

Agent-based modeling is a computational modeling method that represents system-level behavior as arising from multiple interactions between the multiple components that make up a system. Biological systems are thus readily described using agent-based models (ABMs), as multi-cellular organisms can be viewed as populations of interacting cells, and microbial systems manifest as colonies of individual microbes. Intersections between these two domains underlie an increasing number of pathophysiological processes, and the intestinal tract represents one of the most significant locations for these inter-domain interactions, so much so that it can be considered an internal ecology of varying robustness and function. Intestinal infections represent significant disturbances of this internal ecology, and one of the most clinically relevant intestinal infections is Clostridium difficile infection (CDI). CDI is precipitated by the use of broad-spectrum antibiotics, involves the depletion of commensal microbiota, and alterations in bile acid composition in the intestinal lumen. We present an example ABM of CDI (the C. difficile Infection ABM, or CDIABM) to examine fundamental dynamics of the pathogenesis of CDI and its response to treatment with anti-CDI antibiotics and a newer treatment therapy, fecal microbial transplant. The CDIABM focuses on one specific mechanism of potential CDI suppression: commensal modulation of bile acid composition. Even given its abstraction, the CDIABM reproduces essential dynamics of CDI and its response to therapy, and identifies a paradoxical zone of behavior that provides insight into the role of intestinal nutritional status and the efficacy of anti-CDI therapies. It is hoped that this use case example of the CDIABM can demonstrate the usefulness of both agent-based modeling and the application of abstract functional representation as the biomedical community seeks to address the challenges of increasingly complex diseases with the goal of personalized medicine.

Agent-based model of Fecal Microbial Transplant effect on Bile Acid Metabolism on suppressing Clostridium difficile infection: an example of agent-based modeling of intestinal bacterial infection

PubMed Central

Peer, Xavier; An, Gary

2014-01-01

Agent-based modeling is a computational modeling method that represents system-level behavior as arising from multiple interactions between the multiple components that make up a system. Biological systems are thus readily described using agent-based models (ABMs), as multi-cellular organisms can be viewed as populations of interacting cells, and microbial systems manifest as colonies of individual microbes. Intersections between these two domains underlie an increasing number of pathophysiological processes, and the intestinal tract represents one of the most significant locations for these inter-domain interactions, so much so that it can be considered an internal ecology of varying robustness and function. Intestinal infections represent significant disturbances of this internal ecology, and one of the most clinically relevant intestinal infections is Clostridium difficile infection (CDI). CDI is precipitated by the use of broad-spectrum antibiotics, involves the depletion of commensal microbiota, and alterations in bile acid composition in the intestinal lumen. We present an example ABM of CDI (the Clostridium difficile Infection ABM, or CDIABM) to examine fundamental dynamics of the pathogenesis of CDI and its response to treatment with anti-CDI antibiotics and a newer treatment therapy, Fecal Microbial Transplant (FMT). The CDIABM focuses on one specific mechanism of potential CDI suppression: commensal modulation of bile acid composition. Even given its abstraction, the CDIABM reproduces essential dynamics of CDI and its response to therapy, and identifies a paradoxical zone of behavior that provides insight into the role of intestinal nutritional status and the efficacy of anti-CDI therapies. It is hoped that this use case example of the CDIABM can demonstrate the usefulness of both agent-based modeling and the application of abstract functional representation as the biomedical community seeks to address the challenges of increasingly complex diseases with the goal of personalized medicine. PMID:25168489

Unraveling the role of photons and electrons upon their chemical interaction with photoresist during EUV exposure

NASA Astrophysics Data System (ADS)

Pollentier, Ivan; Vesters, Yannick; Petersen, John S.; Vanelderen, Pieter; Rathore, Atish; de Simone, Danilo; Vandenberghe, Geert

2018-03-01

The interaction of 91.6 eV EUV photons with photoresist - in particular chemically amplified resist (CAR) - is different than exposure at 193 nm and 248 nm wavelengths. The latter is understood well and it is known that photons interact with electrons in the resist's molecular valence orbitals (for chemically amplified resist (CAR) the photon interacts with the photo acid generator (PAG), which leads to a deprotection reaction on a polymer after a thermal catalytic reaction during a post-exposure-bake.). At EUV however, more steps are involved in the radiolysis process between the absorption of the photon and the final chemical modification. These are related to the generation of primary electrons and their decay to lower energy secondary electrons, and most of this steps are not well understood. In this paper, the reaction products from EUV and low energy electron exposure are examined using Residual Gas Analysis (RGA), which measures and analyzes the outgassing products related to the ongoing reactions. This investigation is applied firstly on a model CAR where details of the resist chemical constituents were known prior to testing. The measurement not only resolved information on the expected acid related reactions from the PAG and protection groups, but also exhibited direct scission reactions of the polymer, where some of them lead to polymerization reactions. Moreover, the measurement quantifies the balance between the different ongoing reactions, which were confirmed by contrast curve measurements. Based on learnings on the model resist, applied the measurement technique to commercial resists, where actual resist chemistry composition is not known. Despite that, it was found that information could be deduced to distinguish between acid related ongoing reactions and direct scission of reaction on the base polymer and quantify their relation. Moreover, different generations of commercial resists based on similar chemistry platform were investigated, which revealed that improvements in printing performance could be explained by PAG reaction yield increase.

Architecture effects on multivalent interactions by polypeptide-based multivalent ligands

NASA Astrophysics Data System (ADS)

Liu, Shuang

Multivalent interactions are characterized by the simultaneous binding between multiple ligands and multiple binding sites, either in solutions or at interfaces. In biological systems, most multivalent interactions occur between protein receptors and carbohydrate ligands through hydrogen-bonding and hydrophobic interactions. Compared with weak affinity binding between one ligand and one binding site, i.e. monovalent interaction, multivalent interactioins provide greater avidity and specificity, and therefore play unique roles in a broad range of biological activities. Moreover, the studies of multivalent interactions are also essential for producing effective inhibitors and effectors of biological processes that could have important therapeutic applications. Synthetic multivalent ligands have been designed to mimic the biological functions of natural multivalent interactions, and various types of scaffolds have been used to display multiple ligands, including small molecules, linear polymers, dendrimers, nanoparticle surfaces, monolayer surfaces and liposomes. Studies have shown that multivalent interactions can be highly affected by various architectural parameters of these multivalent ligands, including ligand identities, valencies, spacing, ligand densities, nature of linker arms, scaffold length and scaffold conformation. Most of these multivalent ligands are chemically synthesized and have limitations of controlling over sequence and conformation, which is a barrier for mimicking ordered and controlled natural biological systems. Therefore, multivalent ligands with precisely controlled architecture are required for improved structure-function relationship studies. Protein engineering methods with subsequent chemical coupling of ligands provide significant advantages of controlling over backbone conformation and functional group placement, and therefore have been used to synthesize recombinant protein-based materials with desired properties similar to natural protein materials, including structural as well as functional proteins. Therefore, polypeptide-based multivalent scaffolds are used to display ligands to assess the contribution of different architectural parameters to the multivalent binding events. In this work, a family of alanine-rich alpha-helical glycopolypeptides was designed and synthesized by a combination of protein engineering and chemical coupling, to display two types of saccharide ligands for two different multivalent binding systems. The valencies, chain length and spacing between adjacent ligands of these multivalent ligands were designed in order to study architecture effects on multivalent interactions. The polypeptides and their glycoconjugates were characterized via various methods, including SDS-PAGE, NMR, HPLC, amino acid analysis (AAA), MALDI, circular dichroism (CD) and GPC. In the first multivalent binding system, cholera toxin B pentamer (CT B5) was chosen to be the protein receptor due to its well-characterized structure, lack of significant steric interference of binding to multiple binding sites, and requirement of only simple monosaccharide as ligands. Galactopyranoside was incorporated into polypeptide scaffolds through amine-carboxylic acid coupling to the side chains of glutamic acid residues. The inhibition and binding to CT B5 of these glycopolypeptide ligands were evaluated by direct enzyme-linked assay (DELA). As a complement method, weak affinity chromatography (WAC) was also used to evaluate glycopolypeptides binding to a CT B5 immobilized column. The architecture effects on CT B 5 inhibition are discussed. In the second system, cell surface receptor L-selectin was targeted by polypeptide-based multivalent ligands containing disulfated galactopyranoside ligands, due to its important roles in various immunological activities. The effects of glycopolypeptide architectural variables L-selectin shedding were evaluated via ELISA-based assays. These polypeptide-based multivalent ligands are suggested to be useful for elucidating architecture effects on multivalent interactions, manipulating multivalent interactions and the subsequent cellular responses in different systems. These materials have great potential applications in therapeutics and could also provide guidelines for design of multivalent ligands for other protein receptors.

Molecular mechanics and dynamics studies on the interaction of gallic acid with collagen-like peptides

NASA Astrophysics Data System (ADS)

Madhan, B.; Thanikaivelan, P.; Subramanian, V.; Raghava Rao, J.; Unni Nair, Balachandran; Ramasami, T.

2001-10-01

Molecular modelling approaches have been used to understand the interaction of collagen-like peptides with gallic acid, which mimic vegetable tanning processes involved in protein stabilization. Several interaction sites have been identified and the binding energies of the complexes have been calculated. The calculated binding energies for various geometries are in the range 6-13 kcal/mol. It is found that some complexes exhibit hydrogen bonding, and electrostatic interaction plays a dominant role in the stabilization of the peptide by gallic acid. The π-OH type of interaction is also observed in the peptide stabilization. Molecular dynamics (MD) simulation for 600 ps revealed the possibility of hydrogen bonding between the collagen-like peptide and gallic acid.

Co-assembly of Peptide Amphiphiles and Lipids into Supramolecular Nanostructures Driven by Anion-π Interactions

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

Yu, Zhilin; Erbas, Aykut; Tantakitti, Faifan

Co-assembly of binary systems driven by specific non-covalent interactions can greatly expand the structural and functional space of supramolecular nanostructures. We report here on the self-assembly of peptide amphiphiles and fatty acids driven primarily by anion-π interactions. The peptide sequences investigated were functionalized with a perfluorinated phenylalanine residue to promote anion-π interactions with carboxylate headgroups in fatty acids. These interactions were verified here by NMR and circular dichroism experiments as well as investigated using atomistic simulations. Positioning the aromatic units close to the N-terminus of the peptide backbone near the hydrophobic core of cylindrical nanofibers leads to strong anion-π interactionsmore » between both components. With a low content of dodecanoic acid in this position, the cylindrical morphology is preserved. However, as the aromatic units are moved along the peptide backbone away from the hydrophobic core, the interactions with dodecanoic acid transform the cylindrical supramolecular morphology into ribbon-like structures. Increasing the ratio of dodecanoic acid to PA leads to either the formation of large vesicles in the binary systems where the anion-π interactions are strong, or a heterogeneous mixture of assemblies when the peptide amphiphiles associate weakly with dodecanoic acid. Our findings reveal how co-assembly involving designed specific interactions can drastically change supramolecular morphology and even cross from nano to micro scales.« less

A High Content Drug Screen Identifies Ursolic Acid as an Inhibitor of Amyloid β Protein Interactions with Its Receptor CD36*

PubMed Central

Wilkinson, Kim; Boyd, Justin D.; Glicksman, Marcie; Moore, Kathryn J.; El Khoury, Joseph

2011-01-01

A pathological hallmark of Alzheimer disease (AD) is deposition of amyloid β (Aβ) in the brain. Aβ binds to microglia via a receptor complex that includes CD36 leading to production of proinflammatory cytokines and neurotoxic reactive oxygen species and subsequent neurodegeneration. Interruption of Aβ binding to CD36 is a potential therapeutic strategy for AD. To identify pharmacologic inhibitors of Aβ binding to CD36, we developed a 384-well plate assay for binding of fluorescently labeled Aβ to Chinese hamster ovary cells stably expressing human CD36 (CHO-CD36) and screened an Food and Drug Administration-approved compound library. The assay was optimized based on the cells' tolerance to dimethyl sulfoxide, Aβ concentration, time required for Aβ binding, reproducibility, and signal-to-background ratio. Using this assay, we identified four compounds as potential inhibitors of Aβ binding to CD36. These compounds were ursolic acid, ellipticine, zoxazolamine, and homomoschatoline. Of these compounds, only ursolic acid, a naturally occurring pentacyclic triterpenoid, successfully inhibited binding of Aβ to CHO-CD36 cells in a dose-dependent manner. The ursolic acid effect reached a plateau at ∼20 μm, with a maximal inhibition of 64%. Ursolic acid also blocked binding of Aβ to microglial cells and subsequent ROS production. Our data indicate that cell-based high-content screening of small molecule libraries for their ability to block binding of Aβ to its receptors is a useful tool to identify novel inhibitors of receptors involved in AD pathogenesis. Our data also suggest that ursolic acid is a potential therapeutic agent for AD via its ability to block Aβ-CD36 interactions. PMID:21835916

The phagocytic capacity and immunological potency of human dendritic cells is improved by α2,6‐sialic acid deficiency

PubMed Central

Cabral, M. Guadalupe; Silva, Zélia; Ligeiro, Dário; Seixas, Elsa; Crespo, Hélio; Carrascal, Mylène A.; Silva, Mariana; Piteira, Ana R.; Paixão, Paulo; Lau, Joseph T.; Videira, Paula A.

2013-01-01

Summary Dendritic cells (DCs) play an essential role in immunity against bacteria by phagocytosis and by eliciting adaptive immune responses. Previously, we demonstrated that human monocyte‐derived DCs (MDDCs) express a high content of cell surface α2,6‐sialylated glycans. However, the relative role of these sialylated structures in phagocytosis of bacteria has not been reported. Here, we show that treatment with a sialidase significantly improved the capacity of both immature and mature MDDCs to phagocytose Escherichia coli. Desialylated MDDCs had a significantly more mature phenotype, with higher expression of MHC molecules and interleukin (IL)‐12, tumour necrosis factor‐α, IL‐6 and IL‐10 cytokines, and nuclear factor‐κB activation. T lymphocytes primed by desialylated MDDCs expressed more interferon‐γ when compared with priming by sialylated MDDCs. Improved phagocytosis required E. coli sialic acids, indicating a mechanism of host–pathogen interaction dependent on sialic acid moieties. The DCs harvested from mice deficient in the ST6Gal.1 sialyltransferase showed improved phagocytosis capacity, demonstrating that the observed sialidase effect was a result of the removal of α2,6‐sialic acid. The phagocytosis of different pathogenic E. coli isolates was also enhanced by sialidase, which suggests that modifications on MDDC sialic acids may be considered in the development of MDDC‐based antibacterial therapies. Physiologically, our findings shed new light on mechanisms that modulate the function of both immature and mature MDDCs, in the context of host–bacteria interaction. Hence, with particular relevance to DC‐based therapies, the engineering of α2,6‐sialic acid cell surface is a novel possibility to fine tune DC phagocytosis and immunological potency. PMID:23113614

Essential amino acids interacting with flavonoids: A theoretical approach

NASA Astrophysics Data System (ADS)

Codorniu-Hernández, Edelsys; Mesa-Ibirico, Ariel; Hernández-Santiesteban, Richel; Montero-Cabrera, Luis A.; Martínez-Luzardo, Francisco; Santana-Romero, Jorge L.; Borrmann, Tobias; Stohrer, Wolf-D.

The interaction of two flavonoid species (resorcinolic and fluoroglucinolic) with the 20 essential amino acids was studied by the multiple minima hypersurface (MMH) procedures, through the AM1 and PM3 semiempirical methods. Remarkable thermodynamic data related to the properties of the molecular association of these compounds were obtained, which will be of great utility for future investigations concerning the interaction of flavonoids with proteins. These results are compared with experimental and classical force field results reported in the available literature, and new evidences and criteria are shown. The hydrophilic amino acids demonstrated high affinity in the interaction with flavonoid molecules; the complexes with lysine are especially extremely stable. An affinity order for the interaction of both flavonoid species with the essential amino acids is suggested. Our theoretical results are compared with experimental evidence on flavonoid interactions with proteins of biomedical interest.

Acid-base characteristics of the Grass Pond watershed in the Adirondack Mountains of New York State, USA: interactions among soil, vegetation and surface waters

NASA Astrophysics Data System (ADS)

McEathron, K. M.; Mitchell, M. J.; Zhang, L.

2013-07-01

Grass Pond watershed is located within the southwestern Adirondack Mountain region of New York State, USA. This region receives some of the highest rates of acidic deposition in North America and is particularly sensitive to acidic inputs due to many of its soils having shallow depths and being generally base poor. Differences in soil chemistry and tree species between seven subwatersheds were examined in relation to acid-base characteristics of the seven major streams that drain into Grass Pond. Mineral soil pH, stream water BCS (base-cation surplus) and pH exhibited a positive correlation with sugar maple basal area (p = 0.055; 0.48 and 0.39, respectively). Black cherry basal area was inversely correlated with stream water BCS, ANC (acid neutralizing capacity)c and NO3- (p = 0.23; 0.24 and 0.20, respectively). Sugar maple basal areas were positively associated with watershed characteristics associated with the neutralization of atmospheric acidic inputs while in contrast, black cherry basal areas showed opposite relationships to these same watershed characteristics. Canonical correspondence analysis indicated that black cherry had a distinctive relationship with forest floor chemistry apart from the other tree species, specifically a strong positive association with forest floor NH4, while sugar maple had a distinctive relationship with stream chemistry variables, specifically a strong positive association with stream water ANCc, BCS and pH. Our results provide evidence that sugar maple is acid-intolerant or calciphilic tree species and also demonstrate that black cherry is likely an acid-tolerant tree species.

Engaging the Terminal: Promoting Halogen Bonding Interactions with Uranyl Oxo Atoms.

PubMed

Carter, Korey P; Kalaj, Mark; Surbella, Robert G; Ducati, Lucas C; Autschbach, Jochen; Cahill, Christopher L

2017-11-02

Engaging the nominally terminal oxo atoms of the linear uranyl (UO 2 2+ ) cation in non-covalent interactions represents both a significant challenge and opportunity within the field of actinide hybrid materials. An approach has been developed for promoting oxo atom participation in a range of non-covalent interactions, through judicious choice of electron donating equatorial ligands and appropriately polarizable halogen-donor atoms. As such, a family of uranyl hybrid materials was generated based on a combination of 2,5-dihalobenzoic acid and aromatic, chelating N-donor ligands. Delineation of criteria for oxo participation in halogen bonding interactions has been achieved by preparing materials containing 2,5-dichloro- (25diClBA) and 2,5-dibromobenzoic acid (25diBrBA) coupled with 2,2'-bipyridine (bipy) (1 and 2), 1,10-phenanthroline (phen) (3-5), 2,2':6',2''-terpyridine (terpy) (6-8), or 4'-chloro-2,2':6',2''-terpyridine (Cl-terpy) (9-10), which have been characterized through single crystal X-ray diffraction, Raman, Infrared (IR), and luminescence spectroscopy, as well as through density functional calculations of electrostatic potentials. Looking comprehensively, these results are compared with recently published analogues featuring 2,5-diiodobenzoic acid which indicate that although inclusion of a capping ligand in the uranyl first coordination sphere is important, it is the polarizability of the selected halogen atom that ultimately drives halogen bonding interactions with the uranyl oxo atoms. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

De-repression of RaRF-mediated RAR repression by adenovirus E1A in the nucleolus.

PubMed

Um, Soo-Jong; Youn, Hye Sook; Kim, Eun-Joo

2014-02-21

Transcriptional activity of the retinoic acid receptor (RAR) is regulated by diverse binding partners, including classical corepressors and coactivators, in response to its ligand retinoic acid (RA). Recently, we identified a novel corepressor of RAR called the retinoic acid resistance factor (RaRF) (manuscript submitted). Here, we report how adenovirus E1A stimulates RAR activity by associating with RaRF. Based on immunoprecipitation (IP) assays, E1A interacts with RaRF through the conserved region 2 (CR2), which is also responsible for pRb binding. The first coiled-coil domain of RaRF was sufficient for this interaction. An in vitro glutathione-S-transferase (GST) pull-down assay was used to confirm the direct interaction between E1A and RaRF. Further fluorescence microscopy indicated that E1A and RaRF were located in the nucleoplasm and nucleolus, respectively. However, RaRF overexpression promoted nucleolar translocation of E1A from the nucleoplasm. Both the RA-dependent interaction of RAR with RaRF and RAR translocation to the nucleolus were disrupted by E1A. RaRF-mediated RAR repression was impaired by wild-type E1A, but not by the RaRF binding-defective E1A mutant. Taken together, our data suggest that E1A is sequestered to the nucleolus by RaRF through a specific interaction, thereby leaving RAR in the nucleoplasm for transcriptional activation. Copyright © 2014 Elsevier Inc. All rights reserved.

pH-responsive ion transport in polyelectrolyte multilayers of poly(diallyldimethylammonium chloride) (PDADMAC) and poly(4-styrenesulfonic acid-co-maleic acid) (PSS-MA) bearing strong- and weak anionic groups.

PubMed

Maza, Eliana; Tuninetti, Jimena S; Politakos, Nikolaos; Knoll, Wolfgang; Moya, Sergio; Azzaroni, Omar

2015-11-28

The layer-by-layer construction of interfacial architectures displaying stimuli-responsive control of mass transport is attracting increasing interest in materials science. In this work, we describe the creation of interfacial architectures displaying pH-dependent ionic transport properties which until now have not been observed in polyelectrolyte multilayers. We describe a novel approach to create pH-controlled ion-rectifying systems employing polyelectrolyte multilayers assembled from a copolymer containing both weakly and strongly charged pendant groups, poly(4-styrenesulfonic acid-co-maleic acid) (PSS-MA), alternately deposited with poly(diallyldimethylammonium chloride) (PDADMAC). The conceptual framework is based on the very contrasting and differential interactions of PSS and MA units with PDADMAC. In our setting, sulfonate groups play a structural role by conferring stability to the multilayer due to the strong electrostatic interactions with the polycations, while the weakly interacting MA groups remain "silent" within the film and then act as on-demand pH-responsive units. When these multilayers are combined with a strong cationic capping layer that repels the passage of cationic probes, a pH-gateable rectified transport of anions is observed. Concomitantly, we also observed that these functional properties are significantly affected when multilayers are subjected to extensive pH cycling as a consequence of irreversible morphological changes taking place in the film. We envision that the synergy derived from combining weak and strong interactions within the same multilayer will play a key role in the construction of new interfacial architectures displaying tailorable ion transport properties.

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations.

PubMed

Černý, Jiří; Schneider, Bohdan; Biedermannová, Lada

2017-07-14

Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures. The crystal-derived data include 3D maps of water distribution around amino-acids and probability of occurrence of each of the identified hydration sites. The quantum mechanics calculations validate and extend this primary description by optimizing the water position for each hydration site, by providing hydrogen atom positions and by quantifying the interaction energy that stabilizes the water molecule at the particular hydration site position. The calculations show that the majority of experimentally derived hydration sites are positioned near local energy minima for water, and the calculated interaction energies help to assess the preference of water for the individual hydration sites. We propose that the atlas can be used to validate water placement in electron density maps in crystallographic refinement, to locate water molecules mediating protein-ligand interactions in drug design, and to prepare and evaluate molecular dynamics simulations. WatAA: Atlas of Protein Hydration is freely available without login at .

Role of Amine Functionality for CO2 Chemisorption on Silica.

PubMed

Hahn, Maximilian W; Jelic, Jelena; Berger, Edith; Reuter, Karsten; Jentys, Andreas; Lercher, Johannes A

2016-03-03

The mechanism of CO2 adsorption on primary, secondary, and bibasic aminosilanes synthetically functionalized in porous SiO2 was qualitatively and quantitatively investigated by a combination of IR spectroscopy, thermogravimetry, and quantum mechanical modeling. The mode of CO2 adsorption depends particularly on the nature of the amine group and the spacing between the aminosilanes. Primary amines bonded CO2 preferentially through the formation of intermolecular ammonium carbamates, whereas CO2 was predominantly stabilized as carbamic acid, when interacting with secondary amines. Ammonium carbamate formation requires the transfer of the carbamic acid proton to a second primary amine group to form the ammonium ion and hence two (primary) amine groups are required to bind one CO2 molecule. The higher base strength of secondary amines enables the stabilization of carbamic acid, which is thereby hindered to interact further with nearby amine functions, because their association with Si-OH groups (either protonation or hydrogen bonding) does not allow further stabilization of carbamic acid as carbamate. Steric hindrance of the formation of intermolecular ammonium carbamates leads to higher uptake capacities for secondary amines functionalized in porous SiO2 at higher amine densities. In aminosilanes possessing a primary and a secondary amine group, the secondary amine group tends to be protonated by Si-OH groups and therefore does not substantially interact with CO2.

Effect of exogenous enzymes in maize-based diets varying in nutrient density for young broilers: growth performance and digestibility of energy, minerals and amino acids.

PubMed

Cowieson, A J; Ravindran, V

2008-01-01

1. A total of 192 male broilers (Cobb 500) were used in a growth and digestibility assay, involving a 2 x 2 factorial arrangement of treatments, to assess the effects of an enzyme cocktail of xylanase, amylase and protease in maize-based diets. 2. The following two diets were formulated: a positive control diet containing adequate nutrient concentrations for broiler starters as per breeder recommendations and a negative control diet to contain approximately 0.63 MJ/kg apparent metabolisable energy (AME) and 3% amino acids less than the positive control. 3. A further two dietary treatments were developed by supplementing each control diet with an enzyme product containing xylanase, amylase and protease. 4. Birds fed on the negative control diet had poorer weight gain and feed efficiency than those given the positive control diet. There was no effect of diet or enzyme on feed intake. The digestibility of nitrogen, calcium, phosphorus and most amino acids were unaffected by dietary nutrient density. 5. Supplementation of both the positive and negative control diets with the enzyme improved weight gain and feed efficiency compared with the unsupplemented diets. In the case of the negative control, supplemental enzyme improved performance to that of the unsupplemented positive control diet. There was no interaction between diet and enzyme for either weight gain or FCR, suggesting similar beneficial responses regardless of the nutrient density of the diet. 6. In both diets, enzyme supplementation improved AME by an average of 3% (0.35 MJ/kg DM) and nitrogen retention by an average of 11.7% (26 g/kg DM intake vs 29 g/kg DM intake). There was no interaction between diet and enzyme for AME or nitrogen retention. 7. Ileal digestibilities of calcium and phosphorus were not influenced by supplemental enzyme, whereas the digestibility of nitrogen and most amino acids was improved by enzyme addition compared with the unsupplemented control diets. There was no interaction between diet and enzyme for the ileal digestibility of nitrogen and amino acids. 8. These data demonstrate that it is possible to improve the nutritional value of a maize/soy-based diet for broiler starters through the use of exogenous enzymes. The nutrient density of the diet does not appear markedly to influence the response to enzyme, offering flexibility in the use of enzymes for maize-based diets. 9. It is concluded that the energy and amino acid values of maize-based diets for broilers can be enhanced by supplementation with an enzyme cocktail of xylanase, amylase and protease, offering potential economic benefits to producers.

Structure-activity relationships and mechanism of action of Eph-ephrin antagonists: interaction of cholanic acid with the EphA2 receptor

PubMed Central

Tognolini, Massimiliano; Incerti, Matteo; Mohamed, Iftiin Hassan; Giorgio, Carmine; Russo, Simonetta; Bruni, Renato; Lelli, Barbara; Bracci, Luisa; Noberini, Roberta; Pasquale, Elena B.; Barocelli, Elisabetta; Vicini, Paola; Mor, Marco

2012-01-01

The Eph–ephrin system, including the EphA2 receptor and the ephrin-A1 ligand, plays a critical role in tumor and vascular functions during carcinogenesis. We previously identified (3α,5β)-3-hydroxycholan-24-oic acid (lithocholic acid) as an Eph-ephrin antagonist able to inhibit EphA2 receptor activation and therefore potentially useful as a novel EphA2 receptor targeting agent. Here, we explore the structure-activity relationships of a focused set of lithocholic acid derivatives, based on molecular modelling investigation and displacement binding assays. Our exploration shows that while the 3-α-hydroxyl group of lithocholic acid has a negligible role in the recognition of the EphA2 receptor, its carboxylate group is critical for disrupting the binding of ephrin-A1 to the EphA2. As a result of our investigation, we identified (5β)-cholan-24-oic acid (cholanic acid) as a novel compound that competitively inhibits EphA2-ephrin-A1 interaction with higher potency than lithocholic acid. Surface plasmon resonance analysis indicates that cholanic acid binds specifically and reversibly to the ligand-binding domain of EphA2, with a steady-state dissociation constant (KD) in the low micromolar range. Furthermore, cholanic acid blocks the phosphorylation of EphA2 and cell retraction and rounding in PC3 prostate cancer cells, two effects that depend on EphA2 activation by the ephrin-A1 ligand. These findings suggest that cholanic acid can be used as a template structure to design effective EphA2 antagonists, with potential impact in the elucidation of the role played by this receptor in pathological conditions. PMID:22529030

Interactions between the PDZ domains of Bazooka (Par-3) and phosphatidic acid: in vitro characterization and role in epithelial development.

PubMed

Yu, Cao Guo; Harris, Tony J C

2012-09-01

Bazooka (Par-3) is a conserved polarity regulator that organizes molecular networks in a wide range of cell types. In epithelia, it functions as a plasma membrane landmark to organize the apical domain. Bazooka is a scaffold protein that interacts with proteins through its three PDZ (postsynaptic density 95, discs large, zonula occludens-1) domains and other regions. In addition, Bazooka has been shown to interact with phosphoinositides. Here we show that the Bazooka PDZ domains interact with the negatively charged phospholipid phosphatidic acid immobilized on solid substrates or in liposomes. The interaction requires multiple PDZ domains, and conserved patches of positively charged amino acid residues appear to mediate the interaction. Increasing or decreasing levels of diacylglycerol kinase or phospholipase D-enzymes that produce phosphatidic acid-reveal a role for phosphatidic acid in Bazooka embryonic epithelial activity but not its localization. Mutating residues implicated in phosphatidic acid binding revealed a possible role in Bazooka localization and function. These data implicate a closer connection between Bazooka and membrane lipids than previously recognized. Bazooka polarity landmarks may be conglomerates of proteins and plasma membrane lipids that modify each other's activities for an integrated effect on cell polarity.

Cu+ association to some Ph-X (X = OH, NH2, CHO, COOH, CF3) phenyl derivatives.: A comparison with Li+ complexes

NASA Astrophysics Data System (ADS)

Corral, Ines; Mo, Otilia; Yanez, Manuel

2006-09-01

The complexes of Cu+ with phenol, aniline, benzaldehyde, benzoic acid, and trifluromethyl-benzene were investigated through the use of MP2 and density functional theory (DFT) methods. Both harmonic vibrational frequencies and optimized geometries were obtained at the B3LYP/6-311G(d,p) and MP2(full)/6-311G(d,p) levels of theory. Final energies were obtained through single point B3LYP/6-311+G(3df,2p)//B3LYP/6-311G(d,p) calculations. The interactions of Cu+ with these aromatic compounds have a non-negligible covalent character, which clearly differentiate Cu+-complexes from the corresponding Li+-complexes. These dissimilarities are reflected in the geometries, binding energies and infrared spectra of the most stable adducts. For Li+ only conventional [pi]-complexes should be expected when interacting with aniline, while Cu+ attaches preferentially to the para carbon atom. For phenol, besides the conventional [pi]-complexes, a 12% of oxygen attached species are expected to be found upon Li+ association. Conversely, no oxygen attached species should be formed in reactions of phenol with Cu+. For benzoic acid and benzaldehyde, Li+ aligns with the dipole moment of the base, interacting exclusively with the carbonyl oxygen in the plane of the molecule. This is also the case in Cu+-benzoic acid complex, while in the Cu+-benzaldehyde complex the metal ion also interacts with the aromatic [pi]-system. Cu+ binding enthalpies (BEs) are systematically larger (about 1.3 times) than Li+ BEs. The covalent character of Cu+ interactions is associated with electron donations from bonding ([pi]) orbitals or lone-pairs of the base toward the 4s empty orbital of the metal and with back-donations from the occupied d orbitals of the metal toward antibonding ([pi]*) empty orbitals of the base. This non-negligible covalent character is also reflected in a rough correlation between the calculated Cu+ BEs and the available experimental proton affinities that does not exist for Li+ BEs.

dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

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

Liu, Ling; Xiong, Yi; Gao, Hongyun

Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acidmore » complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.« less

pH dependence of the properties of waterborne pressure-sensitive adhesives containing acrylic acid.

PubMed

Wang, Tao; Canetta, Elisabetta; Weerakkody, Tecla G; Keddie, Joseph L; Rivas, Urko

2009-03-01

Polymer colloids are often copolymerized with acrylic acid monomers in order to impart colloidal stability. Here, the effects of the pH on the nanoscale and macroscopic adhesive properties of waterborne poly(butyl acrylate-co-acrylic acid) films are reported. In films cast from acidic colloidal dispersions, hydrogen bonding between carboxylic acid groups dominates the particle-particle interactions, whereas ionic dipolar interactions are dominant in films cast from basic dispersions. Force spectroscopy using an atomic force microscope and macroscale mechanical measurements show that latex films with hydrogen-bonding interactions have lower elastic moduli and are more deformable. They yield higher adhesion energies. On the other hand, in basic latex, ionic dipolar interactions increase the moduli of the dried films. These materials are stiffer and less deformable and, consequently, exhibit lower adhesion energies. The rate of water loss from acidic latex is slower, perhaps because of hydrogen bonding with the water. Therefore, although acid latex offers greater adhesion, there is a limitation in the film formation.

dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

DOE PAGES

Liu, Ling; Xiong, Yi; Gao, Hongyun; ...

2018-04-02

Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acidmore » complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.« less

Dietary fat and gut microbiota interactions determine diet-induced obesity in mice.

PubMed

Kübeck, Raphaela; Bonet-Ripoll, Catalina; Hoffmann, Christina; Walker, Alesia; Müller, Veronika Maria; Schüppel, Valentina Luise; Lagkouvardos, Ilias; Scholz, Birgit; Engel, Karl-Heinz; Daniel, Hannelore; Schmitt-Kopplin, Philippe; Haller, Dirk; Clavel, Thomas; Klingenspor, Martin

2016-12-01

Gut microbiota may promote positive energy balance; however, germfree mice can be either resistant or susceptible to diet-induced obesity (DIO) depending on the type of dietary intervention. We here sought to identify the dietary constituents that determine the susceptibility to body fat accretion in germfree (GF) mice. GF and specific pathogen free (SPF) male C57BL/6N mice were fed high-fat diets either based on lard or palm oil for 4 wks. Mice were metabolically characterized at the end of the feeding trial. FT-ICR-MS and UPLC-TOF-MS were used for cecal as well as hepatic metabolite profiling and cecal bile acids quantification, respectively. Hepatic gene expression was examined by qRT-PCR and cecal gut microbiota of SPF mice was analyzed by high-throughput 16S rRNA gene sequencing. GF mice, but not SPF mice, were completely DIO resistant when fed a cholesterol-rich lard-based high-fat diet, whereas on a cholesterol-free palm oil-based high-fat diet, DIO was independent of gut microbiota. In GF lard-fed mice, DIO resistance was conveyed by increased energy expenditure, preferential carbohydrate oxidation, and increased fecal fat and energy excretion. Cecal metabolite profiling revealed a shift in bile acid and steroid metabolites in these lean mice, with a significant rise in 17β-estradiol, which is known to stimulate energy expenditure and interfere with bile acid metabolism. Decreased cecal bile acid levels were associated with decreased hepatic expression of genes involved in bile acid synthesis. These metabolic adaptations were largely attenuated in GF mice fed the palm-oil based high-fat diet. We propose that an interaction of gut microbiota and cholesterol metabolism is essential for fat accretion in normal SPF mice fed cholesterol-rich lard as the main dietary fat source. This is supported by a positive correlation between bile acid levels and specific bacteria of the order Clostridiales (phylum Firmicutes ) as a characteristic feature of normal SPF mice fed lard. In conclusion, our study identified dietary cholesterol as a candidate ingredient affecting the crosstalk between gut microbiota and host metabolism.

Phthalic acid chemical probes synthesized for protein-protein interaction analysis.

PubMed

Liang, Shih-Shin; Liao, Wei-Ting; Kuo, Chao-Jen; Chou, Chi-Hsien; Wu, Chin-Jen; Wang, Hui-Min

2013-06-24

Plasticizers are additives that are used to increase the flexibility of plastic during manufacturing. However, in injection molding processes, plasticizers cannot be generated with monomers because they can peel off from the plastics into the surrounding environment, water, or food, or become attached to skin. Among the various plasticizers that are used, 1,2-benzenedicarboxylic acid (phthalic acid) is a typical precursor to generate phthalates. In addition, phthalic acid is a metabolite of diethylhexyl phthalate (DEHP). According to Gene_Ontology gene/protein database, phthalates can cause genital diseases, cardiotoxicity, hepatotoxicity, nephrotoxicity, etc. In this study, a silanized linker (3-aminopropyl triethoxyslane, APTES) was deposited on silicon dioxides (SiO2) particles and phthalate chemical probes were manufactured from phthalic acid and APTES-SiO2. These probes could be used for detecting proteins that targeted phthalic acid and for protein-protein interactions. The phthalic acid chemical probes we produced were incubated with epithelioid cell lysates of normal rat kidney (NRK-52E cells) to detect the interactions between phthalic acid and NRK-52E extracted proteins. These chemical probes interacted with a number of chaperones such as protein disulfide-isomerase A6, heat shock proteins, and Serpin H1. Ingenuity Pathways Analysis (IPA) software showed that these chemical probes were a practical technique for protein-protein interaction analysis.

Interactions of calcium and fulvic acid at the goethite-water interface

NASA Astrophysics Data System (ADS)

Weng, Li Ping; Koopal, Luuk K.; Hiemstra, Tjisse; Meeussen, Johannes C. L.; Van Riemsdijk, Willem H.

2005-01-01

Interactions of calcium and fulvic acid (Strichen ) with the surface of goethite were studied with batch and titration experiments. The mutual influence of the interactions on the adsorption of fulvic acid, calcium ions and protons were examined. Adsorption of the fulvic acid to goethite decreased with increase in pH (pH range 3-11). Addition of Ca (1.0 mM) at intermediate and high pH significantly enhanced the adsorption of fulvic acid. Compared to the adsorption to pure goethite, the presence of fulvic acid enhanced the adsorption of Ca significantly. In comparison to the simple linear sum of Ca bound to fulvic acid and goethite, the interactions between goethite and fulvic acid led to a reduced adsorption of Ca at low pH and an enhanced adsorption at high pH. With the adsorption of fulvic acid, protons were released at low pH and coadsorbed at high pH. When Ca was added, fewer protons were released at low pH and fewer coadsorbed at high pH. The experimental results can be adequately described using a surface complexation model, the Ligand and Charge Distribution (LCD) model, in which the CD-MUSIC model for ion adsorption to mineral oxides and the NICA model for ion binding to humics are integrated. In the model calculations, adequate descriptions of the ternary system data (Ca-fulvic acid-goethite) were obtained with parameters derived from three binary systems (fulvic acid-goethite, Ca-goethite and Ca-fulvic acid) without further adjustment. The model calculations suggest that the interactions between Ca and fulvic acid at the surface of goethite are mainly due to the electrostatic effects.

Molecular spectroscopic studies on the interaction of ferulic acid with calf thymus DNA

NASA Astrophysics Data System (ADS)

Zhang, Shufang; Sun, Xuejun; Qu, Fengli; Kong, Rongmei

2013-08-01

The interaction between ferulic acid and calf thymus deoxyribonucleic acid (ctDNA) under physiological conditions (Tris-HCl buffer solutions, pH 7.4) was investigated by UV-Vis spectroscopy, fluorescence spectroscopy, DNA melting techniques, and viscosity measurements. Results indicated that a complex of ferulic acid with ctDNA was formed with a binding constant of K290K = 7.60 × 104 L mol-1 and K310K = 4.90 × 104 L mol-1. The thermodynamic parameters enthalpy change (ΔH°), entropy change (ΔS°) and Gibbs free energy (ΔG°) were calculated to be -1.69 × 104 J mol-1, 35.36 J K-1 mol-1 and -2.79 × 104 J mol-1 at 310 K, respectively. The acting forces between ferulic acid and DNA mainly included hydrophobic interaction and hydrogen bonds. Acridine orange displacement studies revealed that ferulic acid can substitute for AO probe in the AO-DNA complex which was indicative of intercalation binding. Thermal denaturation study suggested that the interaction of ferulic acid with DNA could result in the increase of the denaturation temperature, which indicated that the stabilization of the DNA helix was increased in the presence of ferulic acid. Spectroscopic techniques together with melting techniques and viscosity determination provided evidences of intercalation mode of binding for the interaction between ferulic acid and ctDNA.

Microwave-assisted acid and base hydrolysis of intact proteins containing disulfide bonds for protein sequence analysis by mass spectrometry.

PubMed

Reiz, Bela; Li, Liang

2010-09-01

Controlled hydrolysis of proteins to generate peptide ladders combined with mass spectrometric analysis of the resultant peptides can be used for protein sequencing. In this paper, two methods of improving the microwave-assisted protein hydrolysis process are described to enable rapid sequencing of proteins containing disulfide bonds and increase sequence coverage, respectively. It was demonstrated that proteins containing disulfide bonds could be sequenced by MS analysis by first performing hydrolysis for less than 2 min, followed by 1 h of reduction to release the peptides originally linked by disulfide bonds. It was shown that a strong base could be used as a catalyst for microwave-assisted protein hydrolysis, producing complementary sequence information to that generated by microwave-assisted acid hydrolysis. However, using either acid or base hydrolysis, amide bond breakages in small regions of the polypeptide chains of the model proteins (e.g., cytochrome c and lysozyme) were not detected. Dynamic light scattering measurement of the proteins solubilized in an acid or base indicated that protein-protein interaction or aggregation was not the cause of the failure to hydrolyze certain amide bonds. It was speculated that there were some unknown local structures that might play a role in preventing an acid or base from reacting with the peptide bonds therein. 2010 American Society for Mass Spectrometry. Published by 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.

Natural Phenolic Inhibitors of Trichothecene Biosynthesis by the Wheat Fungal Pathogen Fusarium culmorum: A Computational Insight into the Structure-Activity Relationship

PubMed Central

Pani, Giovanna; Dessì, Alessandro; Dallocchio, Roberto; Scherm, Barbara; Azara, Emanuela; Delogu, Giovanna

2016-01-01

A model of the trichodiene synthase (TRI5) of the wheat fungal pathogen and type-B trichothecene producer Fusarium culmorum was developed based on homology modelling with the crystallized protein of F. sporotrichioides. Eight phenolic molecules, namely ferulic acid 1, apocynin 2, propyl gallate 3, eugenol 4, Me-dehydrozingerone 5, eugenol dimer 6, magnolol 7, and ellagic acid 8, were selected for their ability to inhibit trichothecene production and/or fungal vegetative growth in F. culmorum. The chemical structures of phenols were constructed and partially optimised based on Molecular Mechanics (MM) studies and energy minimisation by Density Functional Theory (DFT). Docking analysis of the phenolic molecules was run on the 3D model of F. culmorum TRI5. Experimental biological activity, molecular descriptors and interacting-structures obtained from computational analysis were compared. Besides the catalytic domain, three privileged sites in the interaction with the inhibitory molecules were identified on the protein surface. The TRI5-ligand interactions highlighted in this study represent a powerful tool to the identification of new Fusarium-targeted molecules with potential as trichothecene inhibitors. PMID:27294666

Comparative study of single/combination use of Huang-Lian-Jie-Du decoction and berberine on their protection on sepsis induced acute liver injury by NMR metabolic profiling.

PubMed

Lv, Yan; Wang, Junsong; Xu, Dingqiao; Liao, Shanting; Li, Pei; Zhang, Qian; Yang, Minghua; Kong, Lingyi

2017-10-25

Sepsis is a serious clinical disease with a high mortality rate all around the world. Liver organ dysfunction is an important sign for the severity and outcome of sepsis in patients. In this study, 1 H NMR-based metabolomics approach and biochemical assays were applied to investigate the metabolic profiling for cecal ligation and puncture (CLP) induced acute liver injury, the therapeutical effect of single/combination use of Huang-Lian-Jie-Du decoction (HLJDD) and berberine, and the interaction of them. Metabolomics analysis revealed significant perturbations in livers of septic rats, which could be ameliorated by HLJDD, berberine and their combination treatment. Berberine could better rectified glycolysis and nucleic acid metabolism in the liver. HLJDD had exceptional better anti-inflammatory, antibacterial and antioxidative effects than berberine. The interaction of berberine and HLJDD could further strengthen the anti-inflammation and anti-oxidation, but with poor effect on amino acids metabolism. These findings highlighted the feasibility of the integrated NMR based metabolomics approach to understand the pathogenesis of diseases, the action mechanisms of therapy and the herb-drug interaction. Copyright © 2017 Elsevier B.V. All rights reserved.

A comparative study based on docking and molecular dynamics simulations over HDAC-tubulin dual inhibitors.

PubMed

Hassanzadeh, Malihe; Bagherzadeh, Kowsar; Amanlou, Massoud

2016-11-01

Nowadays the ability to prediction of complex behavior rationally based on the computational approaches has been a successful technique in drug discovery. In the present study interactions of a new series of hybrids, which were made by linking colchicine as a tubulin inhibitor and suberoylanilide hydroxamic acid (SAHA) as a HDAC inhibitor, with HDAC8 and HDAC1 were investigated and compared. This research has been facilitated by the availability of experimental information besides employing docking methodology as well as classical molecular dynamics simulations and binding free energy calculation were performed. The obtained findings indicate different modes of interactions and inhibition strengths of the studied inhibitors for HDAC8 and HDAC1. HDAC8 binding free energies (-34.35 to -26.27kcal/mol) revealed higher binding affinity to HDAC8 compared to HDAC1 (-33.17 to -7.99kcal/mol). The binding energy contribution of each residue with the hybrid compounds 4a-4e within the active site of HDAC1 and HDAC8 was analyzed and the results confirmed the rule of key amino acids in interaction with the hybrid compounds. Copyright © 2016 Elsevier Inc. All rights reserved.

Prohibitin/annexin 2 interaction regulates fatty acid transport in adipose tissue

PubMed Central

Salameh, Ahmad; Daquinag, Alexes C.; Staquicini, Daniela I.; An, Zhiqiang; Pasqualini, Renata; Kolonin, Mikhail G.

2016-01-01

We have previously identified prohibitin (PHB) and annexin A2 (ANX2) as proteins interacting on the surface of vascular endothelial cells in white adipose tissue (WAT) of humans and mice. Here, we demonstrate that ANX2 and PHB also interact in adipocytes. Mice lacking ANX2 have normal WAT vascularization, adipogenesis, and glucose metabolism but display WAT hypotrophy due to reduced fatty acid uptake by WAT endothelium and adipocytes. By using cell culture systems in which ANX2/PHB binding is disrupted either genetically or through treatment with a blocking peptide, we show that fatty acid transport efficiency relies on this protein complex. We also provide evidence that the interaction between ANX2 and PHB mediates fatty acid transport from the endothelium into adipocytes. Moreover, we demonstrate that ANX2 and PHB form a complex with the fatty acid transporter CD36. Finally, we show that the colocalization of PHB and CD36 on adipocyte surface is induced by extracellular fatty acids. Together, our results suggest that an unrecognized biochemical interaction between ANX2 and PHB regulates CD36-mediated fatty acid transport in WAT, thus revealing a new potential pathway for intervention in metabolic diseases. PMID:27468426

The Citrus transcription factor, CitERF13, regulates citric acid accumulation via a protein-protein interaction with the vacuolar proton pump, CitVHA-c4

PubMed Central

Li, Shao-jia; Yin, Xue-ren; Xie, Xiu-lan; Allan, Andrew C.; Ge, Hang; Shen, Shu-ling; Chen, Kun-song

2016-01-01

Organic acids are essential to fruit flavor. The vacuolar H+ transporting adenosine triphosphatase (V-ATPase) plays an important role in organic acid transport and accumulation. However, less is known of V-ATPase interacting proteins and their relationship with organic acid accumulation. The relationship between V-ATPase and citric acid was investigated, using the citrus tangerine varieties ‘Ordinary Ponkan (OPK)’ and an early maturing mutant ‘Zaoshu Ponkan (ZPK)’. Five V-ATPase genes (CitVHA) were predicted as important to citric acid accumulation. Among the genes, CitVHA-c4 was observed, using a yeast two-hybrid screen, to interact at the protein level with an ethylene response factor, CitERF13. This was verified using bimolecular fluorescence complementation assays. A similar interaction was also observed between Arabidopsis AtERF017 (a CitERF13 homolog) and AtVHA-c4 (a CitVHA-c4 homolog). A synergistic effect on citric acid levels was observed between V-ATPase proteins and interacting ERFs when analyzed using transient over-expression in tobacco and Arabidopsis mutants. Furthermore, the transcript abundance of CitERF13 was concomitant with CitVHA-c4. CitERF13 or AtERF017 over-expression leads to significant citric acid accumulation. This accumulation was abolished in an AtVHA-c4 mutant background. ERF-VHA interactions appear to be involved in citric acid accumulation, which was observed in both citrus and Arabidopsis. PMID:26837571

Modulation of trichloroethylene in vitro metabolism by different drugs in human.

PubMed

Cheikh Rouhou, Mouna; Haddad, Sami

2014-08-01

Toxicological interactions with drugs have the potential to modulate the toxicity of trichloroethylene (TCE). Our objective is to identify metabolic interactions between TCE and 14 widely used drugs in human suspended hepatocytes and characterize the strongest using microsomal assays. Changes in concentrations of TCE and its metabolites were measured by headspace GC-MS. Results with hepatocytes show that amoxicillin, cimetidine, ibuprofen, mefenamic acid and ranitidine caused no significant interactions. Naproxen and salicylic acid showed to increase both TCE metabolites levels, whereas acetaminophen, carbamazepine and erythromycin rather decreased them. Finally, diclofenac, gliclazide, sulphasalazine and valproic acid had an impact on the levels of only one metabolite. Among the 14 tested drugs, 5 presented the most potent interactions and were selected for confirmation with microsomes, namely naproxen, salicylic acid, acetaminophen, carbamazepine and valproic acid. Characterization in human microsomes confirmed interaction with naproxen by competitively inhibiting trichloroethanol (TCOH) glucuronidation (Ki=2.329 mM). Inhibition of TCOH formation was also confirmed for carbamazepine (partial non-competitive with Ki=70 μM). Interactions with human microsomes were not observed with salicylic acid and acetaminophen, similar to prior results in rat material. For valproic acid, interactions with microsomes were observed in rat but not in human. Inhibition patterns were shown to be similar in human and rat hepatocytes, but some differences in mechanisms were noted in microsomal material between species. Next research efforts will focus on determining the adequacy between in vitro observations and the in vivo situation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Thermodynamics of Nucleic Acid ‘Shape Readout’ by an Aminosugar†

PubMed Central

Xi, Hongjuan; Davis, Erik; Ranjan, Nihar; Xue, Liang; Hyde-Volpe, David; Arya, Dev P.

2012-01-01

Recognition of nucleic acids is important for our understanding of nucleic acid structure as well as for our understanding of nucleic acid-protein interactions. In addition to the direct readout mechanisms of nucleic acids such as H-bonding, shape recognition of nucleic acids is being increasingly recognized to play an equally important role in DNA recognition. Competition Dialysis, UV, Flourescent Intercalator displacement (FID), Computational Docking, and calorimetry studies were conducted to study the interaction of neomycin with a variety of nucleic acid conformations (shapes). At pH 5.5, these results suggest: (1) Neomycin binds three RNA structures (16S A site rRNA, poly(rA)•poly(rA), and poly(rA)•poly(rU)) with high affinities, Ka~107M−1. (2) The binding of neomycin to A-form GC-rich oligomer d(A2G15C15T2)2 has comparable affinity to RNA structures. (3) The binding of neomycin to DNA•RNA hybrids shows a three-fold variance attributable to their structural differences (poly(dA) •poly(rU), Ka=9.4×106M−1 and poly(rA)•poly(dT), Ka=3.1×106M−1). (4) The interaction of neomycin with DNA triplex poly(dA)•2poly(dT) yields a binding affinity of Ka=2.4×105M−1. (5) Poly(dA-dT)2 showed the lowest association constant for all nucleic acids studied (Ka=<105). (6) Neomycin binds to G-quadruplexes with Ka~104-105M−1. (7) Computational studies show that the decrease in major groove width in the B to A transition correlates with increasing neomycin affinity. Neomycin’s affinity for various nucleic acid structures can be ranked as follows, RNAs and GC-rich d(A2G15C15T2)2 structures > poly(dA)•poly(rU) > poly(rA)•poly(dT) > T•A-T triplex , G-quadruplexes, B-form AT-rich or GC-rich DNA sequences. The results illustrate the first example of a small molecule based ‘shape readout’ of different nucleic acid conformations. PMID:21863895

Supramolecular Assembly of Uridine Monophosphate (UMP) and Thymidine Monophosphate (TMP) with a Dinuclear Copper(II) Receptor.

PubMed

Rhaman, Md Mhahabubur; Powell, Douglas R; Hossain, Md Alamgir

2017-11-30

Understanding the intermolecular interactions between nucleotides and artificial receptors is crucial to understanding the role of nucleic acids in living systems. However, direct structural evidence showing precise interactions and bonding features of a nucleoside monophosphate (NMP) with a macrocycle-based synthetic molecule has not been provided so far. Herein, we present two novel crystal structures of uridine monophosphate (UMP) and thymidine monophosphate (TMP) complexes with a macrocycle-based dinuclear receptor. Structural characterization of these complexes reveals that the receptor recognizes UMP through coordinate-covalent interactions with phosphates and π-π stackings with nucleobases and TMP through coordinate-covalent interactions with phosphate groups. Furthermore, the receptor has been shown to effectively bind nucleoside monophosphates in the order of GMP > AMP > UMP > TMP > CMP in water at physiological pH, as investigated by an indicator displacement assay.

Liquid droplet sensing using twisted optical fiber couplers fabricated by hydrofluoric acid flow etching

NASA Astrophysics Data System (ADS)

Son, Gyeongho; Jung, Youngho; Yu, Kyoungsik

2017-04-01

We report a directional-coupler-based refractive index sensor and its cost-effective fabrication method using hydrofluoric acid droplet wet-etching and surface-tension-driven liquid flows. The proposed fiber sensor consists of a pair of twisted tapered optical fibers with low excess losses. The fiber cores in the etched microfiber region are exposed to the surrounding medium for efficient interaction with the guided light. We observe that the etching-based low-loss fiber-optic sensors can measure the water droplet volume by detecting the refractive index changes of the surrounding medium around the etched fiber core region.

Acid-free co-operative self-assembly of graphene-ZnO nanocomposites and its defect mediated visible light photocatalytic activities

NASA Astrophysics Data System (ADS)

Parameshwari, R.; Jothivenkatachalam, K.; Banks, Craig E.; Jeganathan, K.

2017-02-01

We propose an acid-free and environmental friendly surfactant based approach to anchor zinc oxide (ZnO) nanoparticles on graphene. Herein, liquid-phase exfoliated graphene in water by ultrasonic waves has been used to prepare graphene-ZnO (G-ZnO) nanocomposites that circumvent the use of various toxic acids and chemicals which are generally used in the preparation of graphene-based nanocomposites. Oxygen vacancy related defect peaks observed by Raman and photoluminescence confirm the formation of C-O-Zn bond due to the synergistic interaction of carbon and zinc via oxygen atoms in G-ZnO nanocomposites. The enhanced photocatalytic behavior of G-ZnO under visible light as evaluated using the dye Rhodamine B holds its genesis from the intrinsic oxygen defects in G-ZnO. Furthermore, graphene acts as electron sink for accumulation of charges from defect levels of ZnO, which controls recombination of charge carriers. It is envisaged that the acid-free and facile strategy can be a potential route for the preparation of graphene-based hybrid materials using liquid-phase exfoliation methodology.

Fast preconcentration of trace rare earth elements from environmental samples by di(2-ethylhexyl)phosphoric acid grafted magnetic nanoparticles followed by inductively coupled plasma mass spectrometry detection

NASA Astrophysics Data System (ADS)

Yan, Ping; He, Man; Chen, Beibei; Hu, Bin

2017-10-01

In this work, di(2-ethylhexyl)phosphoric acid (P204) grafted magnetic nanoparticles were synthesized by fabricating P204 onto Fe3O4@TiO2 nanoparticles based on Lewis acid-base interaction between Ti and phosphate group under weakly acidic condition. The prepared Fe3O4@TiO2@P204 nanoparticles exhibited excellent selectivity for rare earth elements, and good anti-interference ability. Based on it, a method of magnetic solid phase extraction (MSPE) combined with inductively coupled plasma mass spectrometry (ICP-MS) was developed for fast preconcentration and determination of trace rare earth elements in environmental samples. Under the optimal conditions, the detection limits of rare earth elements were in the range of 0.01 (Tm)-0.12 (Nd) ng L- 1 with an enrichment factor of 100-fold, and the relative standard deviations ranged from 4.9 (Pr) to 10.7% (Er). The proposed method was successfully applied to the determination of rare earth elements in environmental samples, including river water, lake water, seawater and sediment.

Sialic Acids in the Brain: Gangliosides and Polysialic Acid in Nervous System Development, Stability, Disease, and Regeneration

PubMed Central

Gerardy-Schahn, Rita; Hildebrandt, Herbert

2014-01-01

Every cell in nature carries a rich surface coat of glycans, its glycocalyx, which constitutes the cell's interface with its environment. In eukaryotes, the glycocalyx is composed of glycolipids, glycoproteins, and proteoglycans, the compositions of which vary among different tissues and cell types. Many of the linear and branched glycans on cell surface glycoproteins and glycolipids of vertebrates are terminated with sialic acids, nine-carbon sugars with a carboxylic acid, a glycerol side-chain, and an N-acyl group that, along with their display at the outmost end of cell surface glycans, provide for varied molecular interactions. Among their functions, sialic acids regulate cell-cell interactions, modulate the activities of their glycoprotein and glycolipid scaffolds as well as other cell surface molecules, and are receptors for pathogens and toxins. In the brain, two families of sialoglycans are of particular interest: gangliosides and polysialic acid. Gangliosides, sialylated glycosphingolipids, are the most abundant sialoglycans of nerve cells. Mouse genetic studies and human disorders of ganglioside metabolism implicate gangliosides in axon-myelin interactions, axon stability, axon regeneration, and the modulation of nerve cell excitability. Polysialic acid is a unique homopolymer that reaches >90 sialic acid residues attached to select glycoproteins, especially the neural cell adhesion molecule in the brain. Molecular, cellular, and genetic studies implicate polysialic acid in the control of cell-cell and cell-matrix interactions, intermolecular interactions at cell surfaces, and interactions with other molecules in the cellular environment. Polysialic acid is essential for appropriate brain development, and polymorphisms in the human genes responsible for polysialic acid biosynthesis are associated with psychiatric disorders including schizophrenia, autism, and bipolar disorder. Polysialic acid also appears to play a role in adult brain plasticity, including regeneration. Together, vertebrate brain sialoglycans are key regulatory components that contribute to proper development, maintenance, and health of the nervous system. PMID:24692354

UHV AFM based colloidal probe studies of adhesive properties of VAlN hard coatings

NASA Astrophysics Data System (ADS)

Wiesing, M.; de los Arcos, T.; Grundmeier, G.

2018-01-01

The adhesion of polystyrene (PS) on V0.27Al0.29N0.44 and the related influence of the oxidation states of both surfaces was investigated using X-Ray Photoelectron Spectroscopy (XPS) and Colloidal Force Spectroscopy (CFS) in Ultra-High Vacuum (UHV). Complementary, the intimate relation between the adhesion force, the chemical structure and surface polarizability was investigated by XPS valence band spectroscopy and the calculation of non-retarded Hamaker coefficients using Lifshitz theory based on optical data as derived from Reflection Electron Energy Loss Spectroscopy (REELS) spectra. The combined electron and force spectroscopic analysis of the interaction forces disclosed quantitatively the separation of the adhesion force in van der Waals and Lewis acid-base contributions. Further, the surface polarizability of VAlN was shown to be unaffected by oxygen incorporation due to the formation of an only gradually oxidized surface comprising a range of vanadium oxidation states. In contrast, the adhesion force analysis revealed additional Lewis acid-base interactions between the oxidized and non-oxidized VAlN surfaces and carboxyl groups present in the surface of PS after an oxidative oxygen beam treatment.

Graphene symmetry-breaking with molecular adsorbates: modeling and experiment

NASA Astrophysics Data System (ADS)

Groce, M. A.; Hawkins, M. K.; Wang, Y. L.; Cullen, W. G.; Einstein, T. L.

2012-02-01

Graphene's structure and electronic properties provide a framework for understanding molecule-substrate interactions and developing techniques for band gap engineering. Controlled deposition of molecular adsorbates can create superlattices which break the degeneracy of graphene's two-atom unit cell, opening a band gap. We simulate scanning tunneling microscopy and spectroscopy measurements for a variety of organic molecule/graphene systems, including pyridine, trimesic acid, and isonicotinic acid, based on density functional theory calculations using VASP. We also compare our simulations to ultra-high vacuum STM and STS results.

Double stranded nucleic acid biochips

DOEpatents

Chernov, Boris; Golova, Julia

2006-05-23

This invention describes a new method of constructing double-stranded DNA (dsDNA) microarrays based on the use of pre-synthesized or natural DNA duplexes without a stem-loop structure. The complementary oligonucleotide chains are bonded together by a novel connector that includes a linker for immobilization on a matrix. A non-enzymatic method for synthesizing double-stranded nucleic acids with this novel connector enables the construction of inexpensive and robust dsDNA/dsRNA microarrays. DNA-DNA and DNA-protein interactions are investigated using the microarrays.

Probing Lewis Acid-Base Interactions with Born-Oppenheimer Molecular Dynamics: The Electronic Absorption Spectrum of p-Nitroaniline in Supercritical CO2.

PubMed

Cabral, Benedito J Costa; Rivelino, Roberto; Coutinho, Kaline; Canuto, Sylvio

2015-07-02

The structure and dynamics of p-nitroaniline (PNA) in supercritical CO2 (scCO2) at T = 315 K and ρ = 0.81 g cm(-3) are investigated by carrying out Born-Oppenheimer molecular dynamics, and the electronic absorption spectrum in scCO2 is determined by time dependent density functional theory. The structure of the PNA-scCO2 solution illustrates the role played by Lewis acid-base (LA-LB) interactions. In comparison with isolated PNA, the ν(N-O) symmetric and asymmetric stretching modes of PNA in scCO2 are red-shifted by -17 and -29 cm(-1), respectively. The maximum of the charge transfer (CT) absorption band of PNA in scSCO2 is at 3.9 eV, and the predicted red-shift of the π → π* electronic transition relative to the isolated gas-phase PNA molecule reproduces the experimental value of -0.35 eV. An analysis of the relationship between geometry distortions and excitation energies of PNA in scCO2 shows that the π → π* CT transition is very sensitive to changes of the N-O bond distance, strongly indicating a correlation between vibrational and electronic solvatochromism driven by LA-LB interactions. Despite the importance of LA-LB interactions to explain the solvation of PNA in scCO2, the red-shift of the CT band is mainly determined by electrostatic interactions.

Metal-chelating active packaging film enhances lysozyme inhibition of Listeria monocytogenes.

PubMed

Roman, Maxine J; Decker, Eric A; Goddard, Julie M

2014-07-01

Several studies have demonstrated that metal chelators enhance the antimicrobial activity of lysozyme. This study examined the effect of metal-chelating active packaging film on the antimicrobial activity of lysozyme against Listeria monocytogenes. Polypropylene films were surface modified by photoinitiated graft polymerization of acrylic acid (PP-g-PAA) from the food contact surface of the films to impart chelating activity based on electrostatic interactions. PP-g-PAA exhibited a carboxylic acid density of 113 ± 5.4 nmol cm(-2) and an iron chelating activity of 53.7 ± 9.8 nmol cm(-2). The antimicrobial interaction of lysozyme and PP-g-PAA depended on growth media composition. PP-g-PAA hindered lysozyme activity at low ionic strength (2.48-log increase at 64.4 mM total ionic strength) and enhanced lysozyme activity at moderate ionic strength (5.22-log reduction at 120 mM total ionic strength). These data support the hypothesis that at neutral pH, synergy between carboxylate metal-chelating films (pKa(bulk) 6.45) and lysozyme (pI 11.35) is optimal in solutions of moderate to high ionic strength to minimize undesirable charge interactions, such as lysozyme absorption onto film. These findings suggest that active packaging, which chelates metal ions based on ligand-specific interactions, in contrast to electrostatic interactions, may improve antimicrobial synergy. This work demonstrates the potential application of metal-chelating active packaging films to enhance the antimicrobial activity of membrane-disrupting antimicrobials, such as lysozyme.

Halogen bonding from a hard and soft acids and bases perspective: investigation by using density functional theory reactivity indices.

PubMed

Pinter, Balazs; Nagels, Nick; Herrebout, Wouter A; De Proft, Frank

2013-01-07

Halogen bonds between the trifluoromethyl halides CF(3)Cl, CF(3)Br and CF(3)I, and dimethyl ether, dimethyl sulfide, trimethylamine and trimethyl phosphine were investigated using Pearson's hard and soft acids and bases (HSAB) concept with conceptual DFT reactivity indices, the Ziegler-Rauk-type energy-decomposition analysis, the natural orbital for chemical valence (NOCV) framework and the non-covalent interaction (NCI) index. It is found that the relative importance of electrostatic and orbital (charge transfer) interactions varies as a function of both the donor and acceptor molecules. Hard and soft interactions were distinguished and characterised by atomic charges, electrophilicity and local softness indices. Dual-descriptor plots indicate an orbital σ hole on the halogen similar to the electrostatic σ hole manifested in the molecular electrostatic potential. The predicted high halogen-bond-acceptor affinity of N-heterocyclic carbenes was evidenced in the highest complexation energy for the hitherto unknown CF(3) I·NHC complex. The dominant NOCV orbital represents an electron-density deformation according to a n→σ*-type interaction. The characteristic signal found in the reduced density gradient versus electron-density diagram corresponds to the non-covalent interaction between contact atoms in the NCI plots, which is the manifestation of halogen bonding within the NCI theory. The unexpected C-X bond strengthening observed in several cases was rationalised within the molecular orbital framework. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multipolar Electrostatic Energy Prediction for all 20 Natural Amino Acids Using Kriging Machine Learning.

PubMed

Fletcher, Timothy L; Popelier, Paul L A

2016-06-14

A machine learning method called kriging is applied to the set of all 20 naturally occurring amino acids. Kriging models are built that predict electrostatic multipole moments for all topological atoms in any amino acid based on molecular geometry only. These models then predict molecular electrostatic interaction energies. On the basis of 200 unseen test geometries for each amino acid, no amino acid shows a mean prediction error above 5.3 kJ mol(-1), while the lowest error observed is 2.8 kJ mol(-1). The mean error across the entire set is only 4.2 kJ mol(-1) (or 1 kcal mol(-1)). Charged systems are created by protonating or deprotonating selected amino acids, and these show no significant deviation in prediction error over their neutral counterparts. Similarly, the proposed methodology can also handle amino acids with aromatic side chains, without the need for modification. Thus, we present a generic method capable of accurately capturing multipolar polarizable electrostatics in amino acids.

Properties investigation of sulfonated poly(ether ether ketone)/polyacrylonitrile acid-base blend membrane for vanadium redox flow battery application.

PubMed

Li, Zhaohua; Dai, Wenjing; Yu, Lihong; Liu, Le; Xi, Jingyu; Qiu, Xinping; Chen, Liquan

2014-11-12

Acid-base blend membrane prepared from sulfonated poly(ether ether ketone) (SPEEK) and polyacrylonitrile (PAN) was detailedly evaluated for vanadium redox flow battery (VRFB) application. SPEEK/PAN blend membrane exhibited dense and homogeneous cross-section morphology as scanning electron microscopy and energy-dispersive X-ray spectroscopy images show. The acid-base interaction of ionic cross-linking and hydrogen bonding between SPEEK and PAN could effectively reduce water uptake, swelling ratio, and vanadium ion permeability, and improve the performance and stability of blend membrane. Because of the good balance of proton conductivity and vanadium ion permeability, blend membrane with 20 wt % PAN (S/PAN-20%) showed higher Coulombic efficiency (96.2% vs 91.1%) and energy efficiency (83.5% vs 78.4%) than Nafion 117 membrane at current density of 80 mA cm(-2) when they were used in VRFB single cell. Besides, S/PAN-20% membrane kept a stable performance during 150 cycles at current density of 80 mA cm(-2) in the cycle life test. Hence the SPEEK/PAN acid-base blend membrane could be used as promising candidate for VRFB application.

Weights in the balance: jasmonic acid and salicylic acid signaling in root-biotroph interactions.

PubMed

Gutjahr, Caroline; Paszkowski, Uta

2009-07-01

Work on the interaction of aerial plant parts with pathogens has identified the signaling molecules jasmonic acid (JA) and salicylic acid (SA) as important players in induced defense of the plant against invading organisms. Much less is known about the role of JA and SA signaling in root infection. Recent progress has been made in research on plant interactions with biotrophic mutualists and parasites that exclusively associate with roots, namely arbuscular mycorrhizal and rhizobial symbioses on one hand and nematode and parasitic plant interactions on the other hand. Here, we review these recent advances relating JA and SA signaling to specific stages of root colonization and discuss how both signaling molecules contribute to a balance between compatibility and defense in mutualistic as well as parasitic biotroph-root interactions.

Hierarchical CaCO3 chromatography: a stationary phase based on biominerals.

PubMed

Sato, Kosuke; Oaki, Yuya; Takahashi, Daisuke; Toshima, Kazunobu; Imai, Hiroaki

2015-03-23

In biomineralization, acidic macromolecules play important roles for the growth control of crystals through a specific interaction. Inspired by this interaction, we report on an application of the hierarchical structures in CaCO3 biominerals to a stationary phase of chromatography. The separation and purification of acidic small organic molecules are achieved by thin-layer chromatography and flash chromatography using the powder of biominerals as the stationary phase. The unit nanocrystals and their oriented assembly, the hierarchical structure, are suitable for the adsorption site of the target organic molecules and the flow path of the elution solvents, respectively. The separation mode is ascribed to the specific adsorption of the acidic molecules on the crystal face and the coordination of the functional groups to the calcium ions. The results imply that a new family of stationary phase of chromatography can be developed by the fine tuning of hierarchical structures in CaCO3 materials. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cross-linked sulfonated poly(ether ether ketone) by using diamino-organosilicon for proton exchange fuel cells.

PubMed

Kayser, Marie J; Reinholdt, Marc X; Kaliaguine, Serge

2011-03-31

Fuel cells are at the battlefront to find alternate sources of energy to the highly polluting, economically and environmentally constraining fossil fuels. This work uses an organosilicon molecule presenting two amine functions, bis(3-aminopropyl)-tetramethyldisiloxane (APTMDS) with the aim of preparing cross-linked sulfonated poly(ether ether ketone) (SPEEK) based membranes. The hybrid membranes obtained at varying APTMDS loadings are characterized for their acid, proton conductivity, water uptake, and swelling properties. APTMDS may be considered as an extreme case of silica nanoparticle and is therefore most advantageously distributed within the polymeric matrix. The two amine groups can interact, via electrostatic interactions, with the sulfonic acid groups of SPEEK, resulting in a double anchoring of the molecule. The addition of a small amount of APTMDS is enhancing the mechanical and hydrolytic properties of the membranes and allows some unfolding of the polymer chains, rendering some acid sites accessible to water molecules and thus available for proton transport.

Proton-conducting ionic liquid-based Proton Exchange Membrane Fuel Cell membranes: The key role of ionomer-ionic liquid interaction

NASA Astrophysics Data System (ADS)

Martinez, Mathieu; Molmeret, Yannick; Cointeaux, Laure; Iojoiu, Cristina; Leprêtre, Jean-Claude; El Kissi, Nadia; Judeinstein, Patrick; Sanchez, Jean-Yves

The paper deals with the synthesis and characterisation of proton-conducting ionic liquids (PCILs) and their polymer electrolytes obtained by blending modified Nafion membranes with different concentrations of PCILs. The PCILs are obtained by the neutralization of triethylamine with different organic acids. The first part of the paper studies the influence of acidity and acid structure on PCIL thermal and electrochemical performance, while the second part examines membrane conductivity and reveals it to depend more on PCIL structure than on its intrinsic conductivity. At 130 °C, conductivities exceeding 10 mS cm -1 were obtained in fully anhydrous conditions.

Learning Stoichiometry: A Comparison of Text and Multimedia Formats

ERIC Educational Resources Information Center

Evans, Karen L.; Yaron, David; Leinhardt, Gaea

2008-01-01

Even after repeated instruction, first year college chemistry students are often unable to apply stoichiometry knowledge to equilibrium and acid-base chemistry problems. The dynamic and interactive capabilities of online technology may facilitate stoichiometry instruction that promotes more meaningful learning. This study compares a…

Novel beta-cyclodextrin derivative functionalized polymethacrylate-based monolithic columns for enantioselective separation of ibuprofen and naproxen enantiomers in capillary electrochromatography.

PubMed

Tian, Yun; Zhong, Cheng; Fu, Enqin; Zeng, Zhaorui

2009-02-06

A novel enantioselective polymethacrylate-based monolithic column for capillary electrochromatography was prepared by ring-opening reaction of epoxy groups from poly(glycidyl methacrylate-co-ethylene dimethacrylate) monolith with a novel beta-cyclodextrin derivative bearing 4-dimethylamino-1,8-naphthalimide functionalities. Conditions for the ring-opening reaction with respect to different reaction parameters were thoroughly optimized to obtain high electroosmotic flow, separation efficiency and enantioselectivity for the analytes. The nonaqueous mobile phase composition regarding acetonitrile-methanol ratio and the concentration of electrolyte were examined to manipulate the hydrophobic inclusion and anion-exchange interaction between the analytes and chiral stationary phase. It was observed that in addition to beta-cyclodextrin cavity, the electrostatic interaction exhibited pronounced influence on the enantioseparation of acidic analytes. Acidic enantiomers (ibuprofen and naproxen) could be separated with separation factor (alpha) values up to 1.08 and a maximum separation efficiency of 86000 plates/m could be achieved.

Prediction of protein-protein interactions based on PseAA composition and hybrid feature selection.

PubMed

Liu, Liang; Cai, Yudong; Lu, Wencong; Feng, Kaiyan; Peng, Chunrong; Niu, Bing

2009-03-06

Based on pseudo amino acid (PseAA) composition and a novel hybrid feature selection frame, this paper presents a computational system to predict the PPIs (protein-protein interactions) using 8796 protein pairs. These pairs are coded by PseAA composition, resulting in 114 features. A hybrid feature selection system, mRMR-KNNs-wrapper, is applied to obtain an optimized feature set by excluding poor-performed and/or redundant features, resulting in 103 remaining features. Using the optimized 103-feature subset, a prediction model is trained and tested in the k-nearest neighbors (KNNs) learning system. This prediction model achieves an overall accurate prediction rate of 76.18%, evaluated by 10-fold cross-validation test, which is 1.46% higher than using the initial 114 features and is 6.51% higher than the 20 features, coded by amino acid compositions. The PPIs predictor, developed for this research, is available for public use at http://chemdata.shu.edu.cn/ppi.

Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations

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

Nawrocki, Grzegorz; Cieplak, Marek

2014-03-07

The growing usage of nanoparticles of zinc sulfide as quantum dots and biosensors calls for a theoretical assessment of interactions of ZnS with biomolecules. We employ the molecular-dynamics-based umbrella sampling method to determine potentials of mean force for 20 single amino acids near the ZnS (110) surface in aqueous solutions. We find that five amino acids do not bind at all and the binding energy of the remaining amino acids does not exceed 4.3 kJ/mol. Such energies are comparable to those found for ZnO (and to hydrogen bonds in proteins) but the nature of the specificity is different. Cysteine canmore » bind with ZnS in a covalent way, e.g., by forming the disulfide bond with S in the solid. If this effect is included within a model incorporating the Morse potential, then the potential well becomes much deeper—the binding energy is close to 98 kJ/mol. We then consider tryptophan cage, a protein of 20 residues, and characterize its events of adsorption to ZnS. We demonstrate the relevance of interactions between the amino acids in the selection of optimal adsorbed conformations and recognize the key role of cysteine in generation of lasting adsorption. We show that ZnS is more hydrophobic than ZnO and that the density profile of water is quite different than that forming near ZnO—it has only a minor articulation into layers. Furthermore, the first layer of water is disordered and mobile.« less

Metabolic mechanisms of drug-nutrient interactions.

PubMed

Hathcock, J N

1985-01-01

Metabolic mechanisms of nutrition and drug interactions include 1) the effects of diet on drug metabolism and action and 2) the effects of drugs on nutritional processes. The type, amount, and timing of foods consumed influence drug dissolution, absorption, distribution, metabolism, and excretion. High-fat meals enhance the absorption of griseofulvin and some other drugs. Milk and other sources of calcium inhibit absorption of tetracycline. High-fat meals increase plasma concentrations of free fatty acids and thereby displace many drugs from binding sites on plasma albumin. High-protein diets increase the activity of the mixed-function oxidase system and enhance the metabolism of numerous drugs. High-electrolyte intakes increase excretion of lithium and also diminish the action of diuretic agents. Bile acid sequestrants and some laxatives decrease lipid digestion and absorption, as well as absorption of the fat-soluble vitamins. Numerous drugs, including tetracycline and cholestyramine, bind iron and decrease its absorption. Coumarins inhibit the function of vitamin K. Phenobarbital and other anticonvulsants are inducers of cytochrome P-450 and the mixed-function oxidase system. Long-term treatment with these inducers can cause excessive metabolism and deficiency of vitamin D. Prooxidant drugs such as chloroquine, drugs detoxified by conjugation with glutathione, and alcohol can deplete reduced glutathione with consequent effects on amino acid transport and the redox status of cells. Acid-forming foods acidify the urine and increase the loss of alkaline drugs such as the amphetamines. Base-forming drugs increase the loss of acidic drugs such as barbiturates. The range of metabolic interactions of drugs and nutrients includes the full scope of physiological processes to which drugs and nutrients are subject.

Energy and structure of bonds in the interaction of organic anions with layered double hydroxide nanosheets: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Tsukanov, A. A.; Psakhie, S. G.

2016-01-01

The application of hybrid and hierarchical nanomaterials based on layered hydroxides and oxyhydroxides of metals is a swiftly progressing field in biomedicine. Layered double hydroxides (LDH) possess a large specific surface area, significant surface electric charge and biocompatibility. Their physical and structural properties enable them to adsorb various kinds of anionic species and to transport them into cells. However, possible side effects resulting from the interaction of LDH with anions of the intercellular and intracellular medium need to be considered, since such interaction can potentially disrupt ion transport, signaling processes, apoptosis, nutrition and proliferation of living cells. In the present paper molecular dynamics is used to determine the energies of interaction of organic anions (aspartic acid, glutamic acid and bicarbonate) with a fragment of layered double hydroxide Mg/Al-LDH. The average number of hydrogen bonds between the anions and the hydroxide surface and characteristic binding configurations are determined. Possible effects of LDH on the cell resulting from binding of protein fragments and replacement of native intracellular anions with delivered anions are considered.

Protein-Carbohydrate Interactions Studied by NMR: From Molecular Recognition to Drug Design

PubMed Central

Fernández-Alonso, María del Carmen; Díaz, Dolores; Berbis, Manuel Álvaro; Marcelo, Filipa; Cañada, Javier; Jiménez-Barbero, Jesús

2012-01-01

Diseases that result from infection are, in general, a consequence of specific interactions between a pathogenic organism and the cells. The study of host-pathogen interactions has provided insights for the design of drugs with therapeutic properties. One area that has proved to be promising for such studies is the constituted by carbohydrates which participate in biological processes of paramount importance. On the one hand, carbohydrates have shown to be information carriers with similar, if not higher, importance than traditionally considered carriers as amino acids and nucleic acids. On the other hand, the knowledge on molecular recognition of sugars by lectins and other carbohydrate-binding proteins has been employed for the development of new biomedical strategies. Biophysical techniques such as X-Ray crystallography and NMR spectroscopy lead currently the investigation on this field. In this review, a description of traditional and novel NMR methodologies employed in the study of sugar-protein interactions is briefly presented in combination with a palette of NMR-based studies related to biologically and/or pharmaceutically relevant applications. PMID:23305367

A series of coordination polymers constructed from R-isophthalic acid (R=–SO{sub 3}H, –NO{sub 2}, and –OH) and N-donor ligands: Syntheses, structures and fluorescence properties

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

Zhou, Yong-Hong, E-mail: zhou21921@sina.com; Zhou, Xu-Wan; Zhou, Su-Rong

Six novel Zn(II), Cd(II), and Cu(II) mixed-ligand coordination complexes, namely, [Zn{sub 2}Na(sip){sub 2}(bpp){sub 3}(Hbpp)(H{sub 2}O){sub 2}]·8H{sub 2}O (1), [Cd{sub 3}(sip){sub 2}(nbi){sub 6}(H{sub 2}O){sub 2}]·7H{sub 2}O (2), [Zn(sip)(nbi){sub 2}(H{sub 2}O)]·Hnbi·3H{sub 2}O (3), [Cd(hip)(nbi){sub 2}(H{sub 2}O)]·nbi·5H{sub 2}O (4), [Cd{sub 2}(nip){sub 2}(nbi){sub 2}(H{sub 2}O){sub 2}]·DMF (5), and [Cu(nip)(nbi)(H{sub 2}O){sub 2}]·H{sub 2}O (6) (H{sub 3}sip=5-sulfoisophthalic acid, H{sub 2}hip=5-hydroxylisophthalic acid, H{sub 2}nip=5-nitroisophthalic acid, bpp=1,3-bis(4-pyridyl)propane, and nbi=6-nitrobenzimidazole) have been synthesized hydrothermally by the self-assembly of R-isophthalic acid (R=–SO{sub 3}H, –NO{sub 2}, and –OH) and N-donor ligands. Single crystal X-ray analyses reveal that two Zn(II) ions and one Na(I) ion of complex 1 are linked through Omore » atoms to generate a 1D linear chain. Then the 2D supramolecular architectures are constructed via intermolecular interactions. In complex 2, the Cd1 ions are connected by bridging carboxyl groups from sip{sup 3−} anions to form 1D double chain, which are further connected by Cd2 ions to afford 2D layer structure. The adjacent 2D layers are further linked via hydrogen-bonding interactions to give 3D supramolecular network. Compounds 3–5 show 1D chain structures, which are assembled into 2D or 3D supramolecular frameworks via weak interactions. In compound 6, the Cu(II) ions are bridged by the nip{sup 2−} ligands to form 48-membered ring, which is assembled into 1Dchain via the π-π stacking interaction. In addition, the thermal stabilities and fluorescence properties of these compounds have also been studied. - Graphical abstract: A series of Cd(II)/Zn(II)/ Cu(II) coordination polymers based on R-isophthalic acid (R=–SO{sub 3}H, –NO{sub 2}, and –OH) and N-donor ligands have been synthesized under hydrothermal conditions and structurally characterized. Photoluminescent properties have been discussed. - Highlights: • Six coordination polymers were synthesized based on mixed-ligand strategy. • The polycarboxylate acids play a crucial role in determining the final structures. • Each complex shows diverse structures and different supramolecular interactions.« less

A 1H NMR Investigation of the Interaction between Phenolic Acids Found in Mango (Manguifera indica cv Ataulfo) and Papaya (Carica papaya cv Maradol) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) Free Radicals

PubMed Central

López-Martínez, Luis M.; Santacruz-Ortega, Hisila; Navarro, Rosa-Elena; Sotelo-Mundo, Rogerio R.; González-Aguilar, Gustavo A.

2015-01-01

The benefits of phenolic acids on human health are very often ascribed to their potential to counteract free radicals to provide antioxidant protection. This potential has been attributed to their acidic chemical structure, which possesses hydroxyl groups in different positions. Phenolic acids can interact between themselves and exhibit an additive, antagonistic or synergistic effect. In this paper, we used 1H NMR to analyze the interactions and mechanisms that are present in major phenolic acids found in mango (gallic, protocatechuic, chlorogenic and vanillic acids) and papaya (caffeic, ferulic and p-coumaric acids), and the DPPH radical was used to evaluate the effect of the antioxidant mixtures. The interactions were found to occur via hydrogen bonds between the -OH and -COOH groups. Moreover, the phenolic acids exhibit two types of mechanisms for the neutralization of the DPPH radical. According to the results, these two mechanisms are Hydrogen Atom Transfer (HAT) and Single Electron Transfer (SET). The ability of the phenolic acid to neutralize the DPPH radical decreases in the following order in mango: gallic > chlorogenic > protocatechuic > vanillic. Moreover, within the acids found in papaya, the order was as follows: caffeic > p-coumaric > ferulic. PMID:26559189

A ¹H NMR Investigation of the Interaction between Phenolic Acids Found in Mango (Manguifera indica cv Ataulfo) and Papaya (Carica papaya cv Maradol) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) Free Radicals.

PubMed

López-Martínez, Luis M; Santacruz-Ortega, Hisila; Navarro, Rosa-Elena; Sotelo-Mundo, Rogerio R; González-Aguilar, Gustavo A

2015-01-01

The benefits of phenolic acids on human health are very often ascribed to their potential to counteract free radicals to provide antioxidant protection. This potential has been attributed to their acidic chemical structure, which possesses hydroxyl groups in different positions. Phenolic acids can interact between themselves and exhibit an additive, antagonistic or synergistic effect. In this paper, we used 1H NMR to analyze the interactions and mechanisms that are present in major phenolic acids found in mango (gallic, protocatechuic, chlorogenic and vanillic acids) and papaya (caffeic, ferulic and p-coumaric acids), and the DPPH radical was used to evaluate the effect of the antioxidant mixtures. The interactions were found to occur via hydrogen bonds between the -OH and -COOH groups. Moreover, the phenolic acids exhibit two types of mechanisms for the neutralization of the DPPH radical. According to the results, these two mechanisms are Hydrogen Atom Transfer (HAT) and Single Electron Transfer (SET). The ability of the phenolic acid to neutralize the DPPH radical decreases in the following order in mango: gallic > chlorogenic > protocatechuic > vanillic. Moreover, within the acids found in papaya, the order was as follows: caffeic > p-coumaric > ferulic.

Specific interactions between mycobacterial FtsZ protein and curcumin derivatives: Molecular docking and ab initio molecular simulations

NASA Astrophysics Data System (ADS)

Fujimori, Mitsuki; Sogawa, Haruki; Ota, Shintaro; Karpov, Pavel; Shulga, Sergey; Blume, Yaroslav; Kurita, Noriyuki

2018-01-01

Filamentous temperature-sensitive Z (FtsZ) protein plays essential role in bacteria cell division, and its inhibition prevents Mycobacteria reproduction. Here we adopted curcumin derivatives as candidates of novel inhibitors and investigated their specific interactions with FtsZ, using ab initio molecular simulations based on protein-ligand docking, classical molecular mechanics and ab initio fragment molecular orbital (FMO) calculations. Based on FMO calculations, we specified the most preferable site of curcumin binding to FtsZ and highlighted the key amino acid residues for curcumin binding at an electronic level. The result will be useful for proposing novel inhibitors against FtsZ based on curcumin derivatives.

Technological applications arising from the interactions of DNA bases with metal ions.

PubMed

Park, Ki Soo; Park, Hyun Gyu

2014-08-01

An intense interest has grown in the unique interactions of nucleic acids with metal ions, which lead to the formation of metal-base pairs and the generation of fluorescent nanomaterials. In this review, different types of metal-base pairs, especially those formed from naturally occurring nucleosides, are described with emphasis also being given to recent advances made in employing these complexes to govern enzymatic reactions. The review also contains a comprehensive description of DNA-templated inorganic nanomaterials such as silver nanoclusters which possess excellent fluorescence properties. Finally, a summary is given about how these materials have led to recent advances in the field of nanobiotechnology. Copyright © 2013 Elsevier Ltd. All rights reserved.

Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors.

PubMed

Xu, Fengqi; Tanaka, Shigenori; Watanabe, Hirofumi; Shimane, Yasuhiro; Iwasawa, Misako; Ohishi, Kazue; Maruyama, Tadashi

2018-05-03

Measles virus (MV) causes an acute and highly devastating contagious disease in humans. Employing the crystal structures of three human receptors, signaling lymphocyte-activation molecule (SLAM), CD46, and Nectin-4, in complex with the measles virus hemagglutinin (MVH), we elucidated computationally the details of binding energies between the amino acid residues of MVH and those of the receptors with an ab initio fragment molecular orbital (FMO) method. The calculated inter-fragment interaction energies (IFIEs) revealed a number of significantly interacting amino acid residues of MVH that played essential roles in binding to the receptors. As predicted from previously reported experiments, some important amino-acid residues of MVH were shown to be common but others were specific to interactions with the three receptors. Particularly, some of the (non-polar) hydrophobic residues of MVH were found to be attractively interacting with multiple receptors, thus indicating the importance of the hydrophobic pocket for intermolecular interactions (especially in the case of Nectin-4). In contrast, the electrostatic interactions tended to be used for specific molecular recognition. Furthermore, we carried out FMO calculations for in silico experiments of amino acid mutations, finding reasonable agreements with virological experiments concerning the substitution effect of residues. Thus, the present study demonstrates that the electron-correlated FMO method is a powerful tool to search exhaustively for amino acid residues that contribute to interactions with receptor molecules. It is also applicable for designing inhibitors of MVH and engineered MVs for cancer therapy.

Reductive transformation of dioxins: An assessment of the contribution of dissolved organic matter to dechlorination reactions

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

Fu, Q.S.; Barkovskii, A.L.; Adriaens, P.

1999-11-01

The susceptibility of dioxins to dissolved organic carbon (DOC)-mediated dechlorination reactions was investigated using 1,2,3,4,6,7,9-heptachlorodibenzo-p-dioxin (HpCDD), Aldrich humic acid (AHA), and polymaleic acid (PMA) as model compounds. The dechlorination yields were on the order of 4--20% which, when normalized to phenolic acidity, was comparable to yields observed in the presence of the humic constituents catechol and resorcinol. Based on the ratio of dechlorination yields as a function of phenolic acidity and electron transfer capacity, differences in electron transfer efficiency to dioxins are likely combined effects of specific interactions with the functional groups and nonspecific hydrophobic interactions. Hexa- and pentaCDD homologuesmore » were dominant in all incubations, and diCDD constituted the final product of dechlorination. The rates of appearance of lesser chlorinated products were similar to those observed in sediment systems and followed thermodynamic considerations as they decreased with a decrease in level of chlorination. Generally, both absolute and phenolic acidity-normalized rate constants for AHA-mediated reactions were up to 2-fold higher than those effected by PMA. These results indicate that the electron shuttling capacity of sediment DOC may significantly affect the fate of dioxins, in part through dechlorination reactions.« less

[Studies on interaction of acid-treated nanotube titanic acid and amino acids].

PubMed

Zhang, Huqin; Chen, Xuemei; Jin, Zhensheng; Liao, Guangxi; Wu, Xiaoming; Du, Jianqiang; Cao, Xiang

2010-06-01

Nanotube titanic acid (NTA) has distinct optical and electrical character, and has photocatalysis character. In accordance with these qualities, NTA was treated with acid so as to enhance its surface activity. Surface structures and surface groups of acid-treated NTA were characterized and analyzed by Transmission Electron Microscope (TEM) and Fourier Transform Infrared Spectrometry (FT-IR). The interaction between acid-treated NTA and amino acids was investigated. Analysis results showed that the lengths of acid-treated NTA became obviously shorter. The diameters of nanotube bundles did not change obviously with acid-treating. Meanwhile, the surface of acid-treated NTA was cross-linked with carboxyl or esterfunction. In addition, acid-treated NTA can catch amino acid residues easily, and then form close combination.

Structure-wise discrimination of adenine and guanine by proteins on the basis of their nonbonded interactions.

PubMed

Usha, S; Selvaraj, S

2015-01-01

We have analyzed the nonbonded interactions of the structurally similar moieties, adenine and guanine forming complexes with proteins. The results comprise (a) the amino acid-ligand atom preferences, (b) solvent accessibility of ligand atoms before and after complex formation with proteins, and (c) preferred amino acid residue atoms involved in the interactions. We have observed that the amino acid preferences involved in the hydrogen bonding interactions vary for adenine and guanine. The structural variation between the purine atoms is clearly reflected by their burial tendency in the solvent environment. Correlation of the mean amino acid preference values show the variation that exists between adenine and guanine preferences of all the amino acid residues. All our observations provide evidence for the discriminating nature of the proteins in recognizing adenine and guanine.

Interaction of amino acids with the Au(111) surface: adsorption free energies from molecular dynamics simulations.

PubMed

Hoefling, Martin; Iori, Francesco; Corni, Stefano; Gottschalk, Kay-Eberhard

2010-06-01

Interactions of proteins with inorganic surfaces are of high importance in biological events and in modern biotechnological applications. Therefore, peptides have been engineered to recognize inorganic surfaces with high specificity. However, the underlying interactions are still not well understood. Here, we investigated the adsorption of amino acids as protein building blocks onto a Au(111) surface. In particular, using molecular dynamics simulations, we calculated the potential of mean force between all the 20 amino acids and the gold surface. We found a strong dependence of the binding affinities on the chemical character of the amino acids. Additionally, the interaction free energy is correlated with the propensity of amino acids to form beta-sheets, hinting at design principles for gold binding peptides and induction of beta-sheet formation near surfaces.

A strategy for the study of the interactions between metal-dyes and proteins with QM/MM approaches: the case of iron-gall dye.

PubMed

Jurinovich, Sandro; Degano, Ilaria; Mennucci, Benedetta

2012-11-15

Historical textiles dyed with tannins usually show more extended degradation than fabrics dyed with other coloring materials. In order to shed light on this phenomenon we investigated the molecular interactions between tannin dyes and protein-based textiles using quantum-mechanical tools. In particular, we focused on the iron-gall complex with a fragment of α-helix wool keratin. We developed a step by step protocol which moves from the simplest ternary complexes with free amino acids (all treated quantum mechanically) to the more realistic system of the polypeptide fragment (treated at QM/MM level), passing through an intermediate model of interacting sites to evaluate the local environmental effects. The analysis of the interactions between the iron-gall complexes and free amino acids allowed us to identify possible coordination modes as well as determining their relative geometries. However, we also showed that only with the addition of the proteic environment a detailed picture of the interaction sites and binding modes can be achieved. An important role is in fact played by the microenvironment which can favor specific coordinations with respect to others due to both structural and electronic changes in the possible interaction sites.

Influence of biopolymers on the solubility of branched-chain amino acids and stability of their solutions.

PubMed

Hong, Chi Rac; Lee, Gyu Whan; Paik, Hyun-Dong; Chang, Pahn-Shick; Choi, Seung Jun

2018-01-15

This study confirmed the possibility of biopolymer-type stabilizers to increase the saturation concentration of branched-chain amino acids by preventing their crystallization/precipitation. Although microfluidization increased the initial solubility, it failed to increase the saturation concentration of the branched-chain amino acids. The saturation concentration of the branched-chain amino acids increased from 3.81% to 4.42% and 4.85% after the incorporation of food hydrocolloids and proteins, respectively. However, the branched-chain amino acids:stabilizer ratio did not affect the solubility. In the case of food hydrocolloid-based solutions, crystal formation and growth of branched-chain amino acids occurred during storage, resulting in the precipitation of branched-chain amino acid crystals. However, food proteins effectively increased the stability of the solubilized branched-chain amino acids. The improved solubility and stability of the solubilized branched-chain amino acids could be attributed to interactions between the functional groups (carboxyl, amine, sulfate, aliphatic, aromatic, etc.) of the stabilizer and the branched-chain amino acid molecules. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ada protein-RNA polymerase sigma subunit interaction and alpha subunit-promoter DNA interaction are necessary at different steps in transcription initiation at the Escherichia coli Ada and aidB promoters.

PubMed

Landini, P; Bown, J A; Volkert, M R; Busby, S J

1998-05-22

The methylated form of the Ada protein (meAda) binds the ada and aidB promoters between 60 and 40 base pairs upstream from the transcription start and activates transcription of the Escherichia coli ada and aidB genes. This region is also a binding site for the alpha subunit of RNA polymerase and resembles the rrnB P1 UP element in A/T content and location relative to the core promoter. In this report, we show that deletion of the C-terminal domain of the alpha subunit severely decreases meAda-independent binding of RNA polymerase to ada and aidB, affecting transcription initiation at these promoters. We provide evidence that meAda activates transcription by direct interaction with the C-terminal domain of RNA polymerase sigma70 subunit (amino acids 574-613). Several negatively charged residues in the sigma70 C-terminal domain are important for transcription activation by meAda; in particular, a glutamic acid to valine substitution at position 575 has a dramatic effect on meAda-dependent transcription. Based on these observations, we propose that the role of the alpha subunit at ada and aidB is to allow initial binding of RNA polymerase to the promoters. However, transcription initiation is dependent on meAda-sigma70 interaction.

A common bacterial metabolite elicits prion-based bypass of glucose repression

PubMed Central

Garcia, David M; Dietrich, David; Clardy, Jon; Jarosz, Daniel F

2016-01-01

Robust preference for fermentative glucose metabolism has motivated domestication of the budding yeast Saccharomyces cerevisiae. This program can be circumvented by a protein-based genetic element, the [GAR+] prion, permitting simultaneous metabolism of glucose and other carbon sources. Diverse bacteria can elicit yeast cells to acquire [GAR+], although the molecular details of this interaction remain unknown. Here we identify the common bacterial metabolite lactic acid as a strong [GAR+] inducer. Transient exposure to lactic acid caused yeast cells to heritably circumvent glucose repression. This trait had the defining genetic properties of [GAR+], and did not require utilization of lactic acid as a carbon source. Lactic acid also induced [GAR+]-like epigenetic states in fungi that diverged from S. cerevisiae ~200 million years ago, and in which glucose repression evolved independently. To our knowledge, this is the first study to uncover a bacterial metabolite with the capacity to potently induce a prion. DOI: http://dx.doi.org/10.7554/eLife.17978.001 PMID:27906649

Complexation of Nickel Ions by Boric Acid or (Poly)borates.

PubMed

Graff, Anais; Barrez, Etienne; Baranek, Philippe; Bachet, Martin; Bénézeth, Pascale

2017-01-01

An experiment based on electrochemical reactions and pH monitoring was performed in which nickel ions were gradually formed by oxidation of a nickel metal electrode in a solution of boric acid. Based on the experimental results and aqueous speciation modeling, the evolution of pH showed the existence of significant nickel-boron complexation. A triborate nickel complex was postulated at high boric acid concentrations when polyborates are present, and the equilibrium constants were determined at 25, 50 and 70 °C. The calculated enthalpy and entropy at 25 °C for the formation of the complex from boric acid and Ni 2+ ions are respectively equal to (65.6 ± 3.1) kJ·mol -1 and (0.5 ± 11.1) J·K -1 ·mol -1 . The results of this study suggest that complexation of nickel ions by borates can significantly enhance the solubility of nickel metal and nickel oxide depending on the concentration of boric acid and pH. First principles calculations were investigated and tend to show that the complex is thermodynamically stable and the nickel cation in solution should interact more strongly with the [Formula: see text] than with boric acid.

Influence of cations on noncovalent interactions between 6-propionyl-2-dimethylaminonaphthalene (PRODAN) and dissolved fulvic and humic acids.

PubMed

Gadad, Praveen; Nanny, Mark A

2008-12-01

The influence of cations (Na(+), Ca(2+) and Mg(2+)) on noncovalent interactions between 6-propionyl-2-dimethylaminonaphthalene (PRODAN) and dissolved fulvic acids (FAs) (Norman landfill leachate fulvic acid (NLFA) and Suwannee River fulvic acid (SRFA)) and dissolved humic acids (HAs) (Suwannee River humic acid (SRHA) and Leonardite humic acid (LHA)) was examined using steady-state fluorescence spectroscopy at pH 4, 7 and 10 as a function of cation concentration (up to 25-100mM). Regardless of pH and cation concentration, PRODAN quenching by FA was unaffected by cations. However, interactions between PRODAN and HA decreased in the presence of cations at pH 7 and 10. Cation concentrations below the HA charge density resulted in the greatest decrease of PRODAN quenching, while very little additional decrease in PRODAN quenching occurred at cation concentrations above the HA charge density. This suggests that as the HA carboxylic acid functional groups form inner sphere complexes with divalent cations, intramolecular interactions result in a contraction of the HA molecular structure, thereby preventing PRODAN from associating with the condensed aromatic, electron accepting moieties inherent within HA molecules and responsible for PRODAN quenching. However, once the HA carboxylic acid functional groups are fully titrated with divalent cations, PRODAN quenching is no longer significantly influenced by the further addition of cations, even though these additional cations facilitate intermolecular interactions between the HA molecules to form supramolecular HA aggregates that can continue to increase in size. Regardless of FA and HA type, pH, cation type and concentration, the lack of blue-shifted fluorescence emission spectra indicated that micelle-like hydrophobic regions, amenable to PRODAN partitioning, were not formed by intra- and intermolecular interactions of FA and HA.

Catalysis in human hypoxanthine-guanine phosphoribosyltransferase: Asp 137 acts as a general acid/base.

PubMed

Xu, Y; Grubmeyer, C

1998-03-24

Hypoxanthine-guanine phosphoribosyltransferase (HGPRTase) catalyzes the reversible formation of IMP and GMP from their respective bases hypoxanthine (Hx) and guanine (Gua) and the phosphoribosyl donor 5-phosphoribosyl-1-pyrophosphate (PRPP). The net formation and cleavage of the nucleosidic bond requires removal/addition of a proton at the purine moiety, allowing enzymic catalysis to reduce the energy barrier associated with the reaction. The pH profile of kcat for IMP pyrophosphorolysis revealed an essential acidic group with pKa of 7.9 whereas those for IMP or GMP formation indicated involvement of essential basic groups. Based on the crystal structure of human HGPRTase, protonation/deprotonation is likely to occur at N7 of the purine ring, and Lys 165 or Asp 137 are each candidates for the general base/acid. We have constructed, purified, and kinetically characterized two mutant HGPRTases to test this hypothesis. D137N displayed an 18-fold decrease in kcat for nucleotide formation with Hx as substrate, a 275-fold decrease in kcat with Gua, and a 500-fold decrease in kcat for IMP pyrophosphorolysis. D137N also showed lower KD values for nucleotides and PRPP. The pH profiles of kcat for D137N were severely altered. In contrast to D137N, the kcat for K165Q was decreased only 2-fold in the forward reaction and was slightly increased in the reverse reaction. The Km and KD values showed that K165Q interacts with substrates more weakly than does the wild-type enzyme. Pre-steady-state experiments with K165Q indicated that the phosphoribosyl transfer step was fast in the forward reaction, as observed with the wild type. In contrast, D137N showed slower phosphoribosyl transfer chemistry, although guanine (3000-fold reduction) was affected much more than hypoxanthine (32-fold reduction). In conclusion, Asp137 acts as a general catalytic acid/base for HGPRTase and Lys165 makes ground-state interactions with substrates.

Molecular spectroscopic studies on the interaction of ferulic acid with calf thymus DNA.

PubMed

Zhang, Shufang; Sun, Xuejun; Qu, Fengli; Kong, Rongmei

2013-08-01

The interaction between ferulic acid and calf thymus deoxyribonucleic acid (ctDNA) under physiological conditions (Tris-HCl buffer solutions, pH 7.4) was investigated by UV-Vis spectroscopy, fluorescence spectroscopy, DNA melting techniques, and viscosity measurements. Results indicated that a complex of ferulic acid with ctDNA was formed with a binding constant of K(290K)=7.60×10(4) L mol(-1) and K(310K)=4.90×10(4) L mol(-1). The thermodynamic parameters enthalpy change (ΔH°), entropy change (ΔS°) and Gibbs free energy (ΔG°) were calculated to be -1.69×10(4) J mol(-1), 35.36 J K(-1) mol(-1) and -2.79×10(4) J mol(-1) at 310 K, respectively. The acting forces between ferulic acid and DNA mainly included hydrophobic interaction and hydrogen bonds. Acridine orange displacement studies revealed that ferulic acid can substitute for AO probe in the AO-DNA complex which was indicative of intercalation binding. Thermal denaturation study suggested that the interaction of ferulic acid with DNA could result in the increase of the denaturation temperature, which indicated that the stabilization of the DNA helix was increased in the presence of ferulic acid. Spectroscopic techniques together with melting techniques and viscosity determination provided evidences of intercalation mode of binding for the interaction between ferulic acid and ctDNA. Copyright © 2013 Elsevier B.V. All rights reserved.

Effects of lipid sources, lysophospholipids and organic acids in maize-based broiler diets on nutrient balance, liver concentration of fat-soluble vitamins, jejunal microbiota and performance.

PubMed

Polycarpo, G V; Burbarelli, M F C; CarÃo, A C P; Merseguel, C E B; Dadalt, J C; Maganha, S R L; Sousa, R L M; Cruz-Polycarpo, V C; Albuquerque, R

2016-12-01

Three experiments with a 2 × 2 × 2 factorial arrangement were conducted to evaluate maize-based diets for broilers containing different lipid sources [soybean oil (S) or beef tallow (T)] supplemented with or without lysophospholipids and organic acids on nutrient balance (Experiment I, evaluation period of 10-14 d), on liver concentration of fat-soluble vitamins, on jejunal microbiota (Experiment II, sampling at d 14) and on performance (Experiment III, accumulated periods of 1-14, 1-21 and 1-42 d). A total of 1344 male chicks were used. In each experiment, the birds were allotted in a completely randomised design with 8 replications. The lysophospholipids were mainly composed of lysolecithins and the organic acids blend was constituted by lactic (40%), acetic (7%) and butyric acids (1%). An interaction between lipid sources and lysophospholipids was observed on faecal apparent digestibility of lipid (ADL), which improved with lysophospholipids addition in T diets. Broilers fed on S had higher ADL and faecal apparent digestibility of nitrogen-corrected gross energy (ADGE N ). It was not possible to demonstrate a significant treatment effect on the liver concentration of vitamins A and E, even with the differences in fatty acid profile between S and T. Enterobacteria values were below the detection threshold. Lysophospholipid supplementation reduced gram-positive cocci in T-fed birds. S diets promoted lower total anaerobe counts compared with T diets, independent of additives. S diets increased BW gain and feed:gain ratio in all evaluation periods. Lysophospholipids and organic acids improved feed:gain ratio at 1-21 d in T diets. Furthermore, main effects were observed for lysophospholipids and organic acids at 1-42 d, which increased BW gain and improved feed:gain ratio, respectively. No positive interactions between additives were found.

Fatty acids and small organic compounds bind to mineralo-organic nanoparticles derived from human body fluids as revealed by metabolomic analysis

NASA Astrophysics Data System (ADS)

Martel, Jan; Wu, Cheng-Yeu; Hung, Cheng-Yu; Wong, Tsui-Yin; Cheng, Ann-Joy; Cheng, Mei-Ling; Shiao, Ming-Shi; Young, John D.

2016-03-01

Nanoparticles entering the human body instantly become coated with a ``protein corona'' that influences the effects and distribution of the particles in vivo. Yet, whether nanoparticles may bind to other organic compounds remains unclear. Here we use an untargeted metabolomic approach based on ultra-performance liquid chromatography and quadruple time-of-flight mass spectrometry to identify the organic compounds that bind to mineral nanoparticles formed in human body fluids (serum, plasma, saliva, and urine). A wide range of organic compounds is identified, including fatty acids, glycerophospholipids, amino acids, sugars, and amides. Our results reveal that, in addition to the proteins identified previously, nanoparticles harbor an ``organic corona'' containing several fatty acids which may affect particle-cell interactions in vivo. This study provides a platform to study the organic corona of biological and synthetic nanoparticles found in the human body.Nanoparticles entering the human body instantly become coated with a ``protein corona'' that influences the effects and distribution of the particles in vivo. Yet, whether nanoparticles may bind to other organic compounds remains unclear. Here we use an untargeted metabolomic approach based on ultra-performance liquid chromatography and quadruple time-of-flight mass spectrometry to identify the organic compounds that bind to mineral nanoparticles formed in human body fluids (serum, plasma, saliva, and urine). A wide range of organic compounds is identified, including fatty acids, glycerophospholipids, amino acids, sugars, and amides. Our results reveal that, in addition to the proteins identified previously, nanoparticles harbor an ``organic corona'' containing several fatty acids which may affect particle-cell interactions in vivo. This study provides a platform to study the organic corona of biological and synthetic nanoparticles found in the human body. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08116e

A new protein-protein interaction sensor based on tripartite split-GFP association.

PubMed

Cabantous, Stéphanie; Nguyen, Hau B; Pedelacq, Jean-Denis; Koraïchi, Faten; Chaudhary, Anu; Ganguly, Kumkum; Lockard, Meghan A; Favre, Gilles; Terwilliger, Thomas C; Waldo, Geoffrey S

2013-10-04

Monitoring protein-protein interactions in living cells is key to unraveling their roles in numerous cellular processes and various diseases. Previously described split-GFP based sensors suffer from poor folding and/or self-assembly background fluorescence. Here, we have engineered a micro-tagging system to monitor protein-protein interactions in vivo and in vitro. The assay is based on tripartite association between two twenty amino-acids long GFP tags, GFP10 and GFP11, fused to interacting protein partners, and the complementary GFP1-9 detector. When proteins interact, GFP10 and GFP11 self-associate with GFP1-9 to reconstitute a functional GFP. Using coiled-coils and FRB/FKBP12 model systems we characterize the sensor in vitro and in Escherichia coli. We extend the studies to mammalian cells and examine the FK-506 inhibition of the rapamycin-induced association of FRB/FKBP12. The small size of these tags and their minimal effect on fusion protein behavior and solubility should enable new experiments for monitoring protein-protein association by fluorescence.

A New Protein-Protein Interaction Sensor Based on Tripartite Split-GFP Association

PubMed Central

Cabantous, Stéphanie; Nguyen, Hau B.; Pedelacq, Jean-Denis; Koraïchi, Faten; Chaudhary, Anu; Ganguly, Kumkum; Lockard, Meghan A.; Favre, Gilles; Terwilliger, Thomas C.; Waldo, Geoffrey S.

2013-01-01

Monitoring protein-protein interactions in living cells is key to unraveling their roles in numerous cellular processes and various diseases. Previously described split-GFP based sensors suffer from poor folding and/or self-assembly background fluorescence. Here, we have engineered a micro-tagging system to monitor protein-protein interactions in vivo and in vitro. The assay is based on tripartite association between two twenty amino-acids long GFP tags, GFP10 and GFP11, fused to interacting protein partners, and the complementary GFP1-9 detector. When proteins interact, GFP10 and GFP11 self-associate with GFP1-9 to reconstitute a functional GFP. Using coiled-coils and FRB/FKBP12 model systems we characterize the sensor in vitro and in Escherichia coli. We extend the studies to mammalian cells and examine the FK-506 inhibition of the rapamycin-induced association of FRB/FKBP12. The small size of these tags and their minimal effect on fusion protein behavior and solubility should enable new experiments for monitoring protein-protein association by fluorescence. PMID:24092409

A preference for edgewise interactions between aromatic rings and carboxylate anions: the biological relevance of anion-quadrupole interactions.

PubMed

Jackson, Michael R; Beahm, Robert; Duvvuru, Suman; Narasimhan, Chandrasegara; Wu, Jun; Wang, Hsin-Neng; Philip, Vivek M; Hinde, Robert J; Howell, Elizabeth E

2007-07-19

Noncovalent interactions are quite important in biological structure-function relationships. To study the pairwise interaction of aromatic amino acids (phenylalanine, tyrosine, tryptophan) with anionic amino acids (aspartic and glutamic acids), small molecule mimics (benzene, phenol or indole interacting with formate) were used at the MP2 level of theory. The overall energy associated with an anion-quadrupole interaction is substantial (-9.5 kcal/mol for a benzene-formate planar dimer at van der Waals contact distance), indicating the electropositive ring edge of an aromatic group can interact with an anion. Deconvolution of the long-range coplanar interaction energy into fractional contributions from charge-quadrupole interactions, higher-order electrostatic interactions, and polarization terms was achieved. The charge-quadrupole term contributes between 30 to 45% of the total MP2 benzene-formate interaction; most of the rest of the interaction arises from polarization contributions. Additional studies of the Protein Data Bank (PDB Select) show that nearly planar aromatic-anionic amino acid pairs occur more often than expected from a random angular distribution, while axial aromatic-anionic pairs occur less often than expected; this demonstrates the biological relevance of the anion-quadrupole interaction. While water may mitigate the strength of these interactions, they may be numerous in a typical protein structure, so their cumulative effect could be substantial.

Structural and spectral comparisons between isomeric benzisothiazole and benzothiazole based aromatic heterocyclic dyes

NASA Astrophysics Data System (ADS)

Wang, Yin-Ge; Wang, Yue-Hua; Tao, Tao; Qian, Hui-Fen; Huang, Wei

2015-09-01

A pair of isomeric heterocyclic compounds, namely 3-amino-5-nitro-[2,1]-benzisothiazole and 2-amino-6-nitrobenzothiazole, are used as the diazonium components to couple with two N-substituted 4-aminobenzene derivatives. As a result, two pairs of isomeric aromatic heterocyclic azo dyes have been produced and they are structurally and spectrally characterized and compared including single-crystal structures, electronic spectra, solvatochromism and reversible acid-base discoloration, thermal stability and theoretically calculations. It is concluded that both benzisothiazole and benzothiazole based dyes show planar molecular structures and offset π-π stacking interactions, solvatochromism and reversible acid-base discoloration. Furthermore, benzisothiazole based aromatic heterocyclic dyes exhibit higher thermal stability, larger solvatochromic effects and maximum absorption wavelengths than corresponding benzothiazole based ones, which can be explained successfully by the differences of their calculated isomerization energy, dipole moment and molecular band gaps.

A Multiprotein Binding Interface in an Intrinsically Disordered Region of the Tumor Suppressor Protein Interferon Regulatory Factor-1*

PubMed Central

Narayan, Vikram; Halada, Petr; Hernychová, Lenka; Chong, Yuh Ping; Žáková, Jitka; Hupp, Ted R.; Vojtesek, Borivoj; Ball, Kathryn L.

2011-01-01

The interferon-regulated transcription factor and tumor suppressor protein IRF-1 is predicted to be largely disordered outside of the DNA-binding domain. One of the advantages of intrinsically disordered protein domains is thought to be their ability to take part in multiple, specific but low affinity protein interactions; however, relatively few IRF-1-interacting proteins have been described. The recent identification of a functional binding interface for the E3-ubiquitin ligase CHIP within the major disordered domain of IRF-1 led us to ask whether this region might be employed more widely by regulators of IRF-1 function. Here we describe the use of peptide aptamer-based affinity chromatography coupled with mass spectrometry to define a multiprotein binding interface on IRF-1 (Mf2 domain; amino acids 106–140) and to identify Mf2-binding proteins from A375 cells. Based on their function as known transcriptional regulators, a selection of the Mf2 domain-binding proteins (NPM1, TRIM28, and YB-1) have been validated using in vitro and cell-based assays. Interestingly, although NPM1, TRIM28, and YB-1 all bind to the Mf2 domain, they have differing amino acid specificities, demonstrating the degree of combinatorial diversity and specificity available through linear interaction motifs. PMID:21245151

European Science Notes, Volume 40, Number 7.

DTIC Science & Technology

1986-07-01

for example, University of i.e., the details of protein-protein, Gbttingen--have departments of biochem- protein-nucleic acid , and nucleic acid ...istry but do not award degrees in bio- nucleic acid interactions and their reg- chemistry.) The Institute for Biochem- ulation is still to be resolved. A...tertiary structure acids structure and function; protein/ of the 5S rRNA molecule--the folding of nucleic- acid interactions; molecular the entire molecule of

Interactions of zinc octacarboxyphthalocyanine with selected amino acids and with albumin

NASA Astrophysics Data System (ADS)

Kliber, Marta; Broda, Małgorzata A.; Nackiewicz, Joanna

2016-02-01

Effect of selected amino acids (glycine, L-histidine, L-cysteine, L-serine, L-tryptophan) and albumin on the spectroscopic properties and photostability of zinc octacarboxyphthalocyanine (ZnPcOC) was explored in the phosphate buffer at a pH of 7.0. The photodegradation of ZnPcOC alone and in the presence of amino acids or albumin has been investigated in aqueous phase using UV-366 nm and daylight irradiation. Kinetic analysis showed that the interaction with amino acids or albumin enhances the photostability of ZnPcOC. To answer the question of how zinc phthalocyanine interacts with amino acids extensive DFT calculations were performed. Analysis of the optimized geometry features of ZnPcOC: amino acids complexes in the gas phase and in water environment as well as the BSSE corrected interaction energies indicates that the more likely is the formation of equatorial complexes in which H-bonds are formed between the COOH groups of the phthalocyanine and carboxyl or amino groups of amino acids. UV-Vis spectra calculated by employing time dependent density functional theory (TD-DFT) are also consistent with this conclusion.

Molecular dynamics simulation studies of the interactions between ionic liquids and amino acids in aqueous solution.

PubMed

Tomé, Luciana I N; Jorge, Miguel; Gomes, José R B; Coutinho, João A P

2012-02-16

Although the understanding of the influence of ionic liquids (ILs) on the solubility behavior of biomolecules in aqueous solutions is relevant for the design and optimization of novel biotechnological processes, the underlying molecular-level mechanisms are not yet consensual or clearly elucidated. In order to contribute to the understanding of the molecular interactions established between amino acids and ILs in aqueous media, classical molecular dynamics (MD) simulations were performed for aqueous solutions of five amino acids with different structural characteristics (glycine, alanine, valine, isoleucine, and glutamic acid) in the presence of 1-butyl-3-methylimidazolium bis(trifluoromethyl)sulfonyl imide. The results from MD simulations enable to relate the properties of the amino acids, namely their hydrophobicity, to the type and strength of their interactions with ILs in aqueous solutions and provide an explanation for the direction and magnitude of the solubility phenomena observed in [IL + amino acid + water] systems by a mechanism governed by a balance between competitive interactions of the IL cation, IL anion, and water with the amino acids.

Spectroscopic and thermodynamic studies on ferulic acid - Alpha-2-macroglobulin interaction

NASA Astrophysics Data System (ADS)

Rehman, Ahmed Abdur; Sarwar, Tarique; Arif, Hussain; Ali, Syed Saqib; Ahsan, Haseeb; Tabish, Mohammad; Khan, Fahim Halim

2017-09-01

Ferulic acid is a major phenolic acid found in numerous plant species in conjugated form. It binds to enzymes and oligomeric proteins and modifies their structure and function. This study was designed to examine the interaction of ferulic acid, an active ingredient of some important medicines, with α2M, a key serum proteinase, under physiological conditions. The mechanism of interaction was studied by spectroscopic techniques such as, UV-visible absorption, fluorescence spectroscopy, circular dichroism along with isothermal titration calorimetry. Fluorescence quenching of α2M by ferulic acid demonstrated the formation of α2M-ferulic acid complex by static quenching mechanism. Binding parameters calculated by Stern-Volmer method showed that ferulic acid binds to α2M with moderate affinity of the order of ∼104 M-1. The thermodynamic signatures reveal that binding was enthalpy driven and hydrogen bonding played a major role in ferulic acid-α2M binding. CD spectra analysis suggests very little conformational changes in α2M on ferulic acid binding.

Conformational landscape of isolated capped amino acids: on the nature of non-covalent interactions*

NASA Astrophysics Data System (ADS)

González, Jorge; Martínez, Rodrigo; Fernández, José A.; Millan, Judith

2017-08-01

The intramolecular interactions for isolated capped amino acids were investigated computationally by characterizing the conformers for selected amino acids with charged (arginine), polar (asparagine and glutamine), non-polar (alanine, valine and isoleucine), and aromatic (phenylalanine, tryptophan and tyrosine) side chains. The computational method applied combined a molecular mechanics conformational search (with an MMFFs forced field) followed by structural and vibrational density-functional calculations (M06-2X with a triple- ζ Pople's basis set). The intramolecular forces in each amino acid were analyzed with the Non-Covalent Interactions (NCI) analysis. The results for the 15 most stable conformers studied showed that the structure of isolated capped amino acids resembles those found in proteins. In particular, the two most stable conformers of the nine amino acids investigated exhibit γ L and β L conformations with 7- and 5-membered rings, respectively, as a result of the balance between non-covalent interactions (hydrogen bonds and van der Waals).

Effect of the structure of gallic acid and its derivatives on their interaction with plant ferritin.

PubMed

Wang, Qunqun; Zhou, Kai; Ning, Yong; Zhao, Guanghua

2016-12-15

Gallic acid and its derivatives co-exist with protein components in foodstuffs, but there is few report on their interaction with proteins. On the other hand, plant ferritin represents not only a novel class of iron supplement, but also a new nanocarrier for encapsulation of bioactive nutrients. However, plant ferritin is easy to be degraded by pepsin in the stomach, thereby limiting its application. Herein, we investigated the interaction of gallic acid and its derivatives with recombinant soybean seed H-2 ferritin (rH-2). We found that these phenolic acids interacted with rH-2 in a structure-dependent manner; namely, gallic acid (GA), methyl gallate (MEGA) and propyl gallate (PG) having three HO groups can bind to rH-2, while their analogues with two HO groups cannot. Consequently, such binding largely inhibited ferritin degradation by pepsin. These findings advance our understanding of the relationship between the structure and function of phenolic acids. Copyright © 2016 Elsevier Ltd. All rights reserved.

A simple and efficient method for predicting protein-protein interaction sites.

PubMed

Higa, R H; Tozzi, C L

2008-09-23

Computational methods for predicting protein-protein interaction sites based on structural data are characterized by an accuracy between 70 and 80%. Some experimental studies indicate that only a fraction of the residues, forming clusters in the center of the interaction site, are energetically important for binding. In addition, the analysis of amino acid composition has shown that residues located in the center of the interaction site can be better discriminated from the residues in other parts of the protein surface. In the present study, we implement a simple method to predict interaction site residues exploiting this fact and show that it achieves a very competitive performance compared to other methods using the same dataset and criteria for performance evaluation (success rate of 82.1%).

A dual wavelength-activatable gold nanorod complex for synergistic cancer treatment

NASA Astrophysics Data System (ADS)

Pacardo, Dennis B.; Neupane, Bhanu; Rikard, S. Michaela; Lu, Yue; Mo, Ran; Mishra, Sumeet R.; Tracy, Joseph B.; Wang, Gufeng; Ligler, Frances S.; Gu, Zhen

2015-07-01

A multifunctional gold nanorod (AuNR) complex is described with potential utility for theranostic anticancer treatment. The AuNR was functionalized with cyclodextrin for encapsulation of doxorubicin, with folic acid for targeting, and with a photo-responsive dextran-azo compound for intracellular controlled drug release. The interaction of a AuNR complex with HeLa cells was facilitated via a folic acid targeting ligand as displayed in the dark-field images of cells. Enhanced anticancer efficacy was demonstrated through the synergistic combination of promoted drug release upon ultraviolet (UV) light irradiation and photothermal therapy upon infrared (IR) irradiation. This multifunctional AuNR-based system represents a novel theranostic strategy for spatiotemporal delivery of anticancer therapeutics.A multifunctional gold nanorod (AuNR) complex is described with potential utility for theranostic anticancer treatment. The AuNR was functionalized with cyclodextrin for encapsulation of doxorubicin, with folic acid for targeting, and with a photo-responsive dextran-azo compound for intracellular controlled drug release. The interaction of a AuNR complex with HeLa cells was facilitated via a folic acid targeting ligand as displayed in the dark-field images of cells. Enhanced anticancer efficacy was demonstrated through the synergistic combination of promoted drug release upon ultraviolet (UV) light irradiation and photothermal therapy upon infrared (IR) irradiation. This multifunctional AuNR-based system represents a novel theranostic strategy for spatiotemporal delivery of anticancer therapeutics. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr01568e

Weak interactions and cooperativity effects on disiloxane: a look at the building block of silicones

NASA Astrophysics Data System (ADS)

Martín-Fernández, Carlos; Montero-Campillo, M. Merced; Alkorta, Ibon; Elguero, José

2018-06-01

The behaviour of disiloxane 1 towards a set of Lewis acids (LA) and Lewis bases (LB) forming complexes through its oxygen and silicon atoms, respectively, was studied at the MP2/aug‧-cc-pVTZ level of theory, exploring a wide variety of non-covalent interactions. Disiloxane is a moderate electron acceptor and a good electron donor, exhibiting in the latter case binding energies up to almost -100 kJ/mol with BeCl2. Cooperativity effects were also analysed by looking at ternary 1:LA:LB complexes. Shorter intermolecular distances than in the corresponding binary complexes and a negative contribution of the three-body term to the binding energy indicate that the non-covalent interactions allowed by disiloxane through its acid and basic centres cooperate between them to reinforce both donor-acceptor pairs. These effects are particularly strong in complexes involving beryllium and triel bonds, but are also relevant for complexes containing hydrogen bonds.

Improving protein-protein interaction prediction using evolutionary information from low-quality MSAs.

PubMed

Várnai, Csilla; Burkoff, Nikolas S; Wild, David L

2017-01-01

Evolutionary information stored in multiple sequence alignments (MSAs) has been used to identify the interaction interface of protein complexes, by measuring either co-conservation or co-mutation of amino acid residues across the interface. Recently, maximum entropy related correlated mutation measures (CMMs) such as direct information, decoupling direct from indirect interactions, have been developed to identify residue pairs interacting across the protein complex interface. These studies have focussed on carefully selected protein complexes with large, good-quality MSAs. In this work, we study protein complexes with a more typical MSA consisting of fewer than 400 sequences, using a set of 79 intramolecular protein complexes. Using a maximum entropy based CMM at the residue level, we develop an interface level CMM score to be used in re-ranking docking decoys. We demonstrate that our interface level CMM score compares favourably to the complementarity trace score, an evolutionary information-based score measuring co-conservation, when combined with the number of interface residues, a knowledge-based potential and the variability score of individual amino acid sites. We also demonstrate, that, since co-mutation and co-complementarity in the MSA contain orthogonal information, the best prediction performance using evolutionary information can be achieved by combining the co-mutation information of the CMM with co-conservation information of a complementarity trace score, predicting a near-native structure as the top prediction for 41% of the dataset. The method presented is not restricted to small MSAs, and will likely improve interface prediction also for complexes with large and good-quality MSAs.

Identification of Amino Acids in the Human Tetherin Transmembrane Domain Responsible for HIV-1 Vpu Interaction and Susceptibility▿ †

PubMed Central

Kobayashi, Tomoko; Ode, Hirotaka; Yoshida, Takeshi; Sato, Kei; Gee, Peter; Yamamoto, Seiji P.; Ebina, Hirotaka; Strebel, Klaus; Sato, Hironori; Koyanagi, Yoshio

2011-01-01

Tetherin, also known as BST-2/CD317/HM1.24, is an antiviral cellular protein that inhibits the release of HIV-1 particles from infected cells. HIV-1 viral protein U (Vpu) is a specific antagonist of human tetherin that might contribute to the high virulence of HIV-1. In this study, we show that three amino acid residues (I34, L37, and L41) in the transmembrane (TM) domain of human tetherin are critical for the interaction with Vpu by using a live cell-based assay. We also found that the conservation of an additional amino acid at position 45 and two residues downstream of position 22, which are absent from monkey tetherins, are required for the antagonism by Vpu. Moreover, computer-assisted structural modeling and mutagenesis studies suggest that an alignment of these four amino acid residues (I34, L37, L41, and T45) on the same helical face in the TM domain is crucial for the Vpu-mediated antagonism of human tetherin. These results contribute to the molecular understanding of human tetherin-specific antagonism by HIV-1 Vpu. PMID:21068238

Thz Spectroscopy and DFT Modeling of Intermolecular Vibrations in Hydrophobic Amino Acids

NASA Astrophysics Data System (ADS)

Williams, michael R. C.; Aschaffenburg, Daniel J.; Schmuttenmaer, Charles A.

2013-06-01

Vibrations that involve intermolecular displacements occur in molecular crystals at frequencies in the 0.5-5 THz range (˜15-165 cm^{-1}), and these motions are direct indicators of the interaction potential between the molecules. The intermolecular potential energy surface of crystalline hydrophobic amino acids is inherently interesting simply because of the wide variety of forces (electrostatic, dipole-dipole, hydrogen-bonding, van der Waals) that are present. Furthermore, an understanding of these particular interactions is immediately relevant to important topics like protein conformation and pharmaceutical polymorphism. We measured the low-frequency absorption spectra of several polycrystalline hydrophobic amino acids using THz time-domain spectroscopy, and in addition we carried out DFT calculations using periodic boundary conditions and an exchange-correlation functional that accounts for van der Waals dispersion forces. We chose to investigate a series of similar amino acids with closely analogous unit cells (leucine, isoleucine, and allo-isoleucine, in racemic or pseudo-racemic mixtures). This allows us to consider trends in the vibrational spectra as a function of small changes in molecular arrangement and/or crystal geometry. In this way, we gain confidence that peak assignments are not based on serendipitous similarities between calculated and observed features.

Multivalent interaction based carbohydrate biosensors for signal amplification

PubMed Central

Wang, Yanyan; Chalagalla, Srinivas; Li, Tiehai; Sun, Xue-long; Zhao, Wei; Wang, Peng; Zeng, Xiangqun

2010-01-01

Multivalent interaction between boronic acids immobilized on Quartz Crystal Microbalance (QCM) sensor surface and the carbohydrates modified Au - nanoparticle (AuNP) has been demonstrated for the development of a sensitive carbohydrate biosensor. Briefly, a boronic acid - containing polymer (boropolymer) as multivalent carbohydrate receptor was oriented immobilized on the cysteamine coated electrode through isourea bond formation. Carbohydrates were conjugated to AuNPs to generate a multivalent carbohydrates moiety to amplify the response signal. Thus, the binding of the carbohydrate conjugated AuNPs to the boropolymer surface are multivalent which could simultaneously increase the binding affinity and specificity. We systematically studied the binding between five carbohydrate conjugated AuNPs and the boropolymer. Our studies show that the associate constant (Ka) was in the order of fucose < glucose < mannose < galactose < maltose. A linear response in the range from 23 µM to 3.83 mM was observed for mannose conjugated AuNPs and the boropolymer recognition elements, with the lower detection limit of 1.5 µM for the carbohydrate analytes. Furthermore, the multivalent binding between carbohydrates and boronic acids are reversible and allow the regeneration of boropolymer surface by using 1M acetic acid so as to sequentially capture and release the carbohydrate analytes. PMID:20863680

Identification of amino acids in the human tetherin transmembrane domain responsible for HIV-1 Vpu interaction and susceptibility.

PubMed

Kobayashi, Tomoko; Ode, Hirotaka; Yoshida, Takeshi; Sato, Kei; Gee, Peter; Yamamoto, Seiji P; Ebina, Hirotaka; Strebel, Klaus; Sato, Hironori; Koyanagi, Yoshio

2011-01-01

Tetherin, also known as BST-2/CD317/HM1.24, is an antiviral cellular protein that inhibits the release of HIV-1 particles from infected cells. HIV-1 viral protein U (Vpu) is a specific antagonist of human tetherin that might contribute to the high virulence of HIV-1. In this study, we show that three amino acid residues (I34, L37, and L41) in the transmembrane (TM) domain of human tetherin are critical for the interaction with Vpu by using a live cell-based assay. We also found that the conservation of an additional amino acid at position 45 and two residues downstream of position 22, which are absent from monkey tetherins, are required for the antagonism by Vpu. Moreover, computer-assisted structural modeling and mutagenesis studies suggest that an alignment of these four amino acid residues (I34, L37, L41, and T45) on the same helical face in the TM domain is crucial for the Vpu-mediated antagonism of human tetherin. These results contribute to the molecular understanding of human tetherin-specific antagonism by HIV-1 Vpu.

DFT study of the energetic and noncovalent interactions between imidazolium ionic liquids and hydrofluoric acid.

PubMed

Velarde, Marco V; Gallo, Marco; Alonso, P A; Miranda, A D; Dominguez, J M

2015-04-16

In this work, we evaluated the energetic interactions between imidazolium ionic liquids (ILs) and hydrofluoric acid, as well as the cation-anion interactions in ILs. We used DFT calculations that include dispersion corrections employing the PBE and M06 functionals. We tested 22 ILs, including [C4MIM][PF6], [C4MIM][NTf2], and [C4MIM][CH3COO], obtaining interaction energies in the range of -27 to -13 kcal/mol with the PBE functional. The NCI (noncovalent interaction) index developed by Yang and collaborators ( J. Am. Chem. Soc. 2010 , 132 , 6498 - 6506 ; J. Chem. Theory Comput. 2011 , 7 , 625 - 632 ) also was used for mapping the key noncovalent interactions (hydrogen bonds, van der Waals, and steric repulsions) between the anions and cations of ILs and also for interactions of ILs with hydrofluoric acid (HF). The results obtained show that the anions have a stronger effect with respect to cations in their capacity for interacting with hydrofluoric acid, and the strongest interaction energies occur in systems where the key noncovalent interactions are mainly hydrogen bonds. The [C4MIM][PF6], [C4MIM][NTf2], and [C4MIM][BF4] ionic liquids displayed the weakest cation-anion interactions.

Natural deep eutectic solvents: cytotoxic profile.

PubMed

Hayyan, Maan; Mbous, Yves Paul; Looi, Chung Yeng; Wong, Won Fen; Hayyan, Adeeb; Salleh, Zulhaziman; Mohd-Ali, Ozair

2016-01-01

The purpose of this study was to investigate the cytotoxic profiles of different ternary natural deep eutectic solvents (NADESs) containing water. For this purpose, five different NADESs were prepared using choline chloride as a salt, alongside five hydrogen bond donors (HBD) namely glucose, fructose, sucrose, glycerol, and malonic acid. Water was added as a tertiary component during the eutectics preparation, except for the malonic acid-based mixture. Coincidentally, the latter was found to be more toxic than any of the water-based NADESs. A trend was observed between the cellular requirements of cancer cells, the viscosity of the NADESs, and their cytotoxicity. This study also highlights the first time application of the conductor-like screening model for real solvent (COSMO-RS) software for the analysis of the cytotoxic mechanism of NADESs. COSMO-RS simulation of the interactions between NADESs and cellular membranes' phospholipids suggested that NADESs strongly interacted with cell surfaces and that their accumulation and aggregation possibly defined their cytotoxicity. This reinforced the idea that careful selection of NADESs components is necessary, as it becomes evident that organic acids as HBD highly contribute to the increasing toxicity of these neoteric mixtures. Nevertheless, NADESs in general seem to possess relatively less acute toxicity profiles than their DESs parents. This opens the door for future large scale utilization of these mixtures.

Quantitative structure-cytotoxicity relationship of piperic acid amides.

PubMed

Shimada, Chiyako; Uesawa, Yoshihiro; Ishihara, Mariko; Kagaya, Hajime; Kanamoto, Taisei; Terakubo, Shigemi; Nakashima, Hideki; Takao, Koichi; Miyashiro, Takaki; Sugita, Yoshiaki; Sakagami, Hiroshi

2014-09-01

A total of 12 piperic acid amides, including piperine, were subjected to quantitative structure-activity relationship (QSAR) analysis, based on their cytotoxicity, tumor selectivity and anti-HIV activity, in order to find new biological activities. Cytotoxicity against four human oral squamous cell carcinoma (OSCC) cell lines and three human oral normal cells was determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method. Tumor selectivity was evaluated by the ratio of the mean 50% cytotoxic concentration (CC50) against normal oral cells to that against OSCC cell lines. Anti-HIV activity was evaluated by the ratio of the CC50 to 50% HIV infection-cytoprotective concentration (EC50). Physicochemical, structural, and quantum-chemical parameters were calculated based on the conformations optimized by LowModeMD method followed by density functional theory method. All compounds showed low-to-moderate tumor selectivity, but no anti-HIV activity. N-Piperoyldopamine ( 8: ) which has a catechol moiety, showed the highest tumor selectivity, possibly due to its unique molecular shape and electrostatic interaction, especially its largest partial equalization of orbital electronegativities and vsurf descriptors. The present study suggests that molecular shape and ability for electrostatic interaction are useful parameters for estimating the tumor selectivity of piperic acid amides. Copyright© 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Charge characteristics of humic and fulvic acids: comparative analysis by colloid titration and potentiometric titration with continuous pK-distribution function model.

PubMed

Bratskaya, S; Golikov, A; Lutsenko, T; Nesterova, O; Dudarchik, V

2008-09-01

Charge characteristics of humic and fulvic acids of a different origin (inshore soils, peat, marine sediments, and soil (lysimetric) waters) were evaluated by means of two alternative methods - colloid titration and potentiometric titration. In order to elucidate possible limitations of the colloid titration as an express method of analysis of low content of humic substances we monitored changes in acid-base properties and charge densities of humic substances with soil depth, fractionation, and origin. We have shown that both factors - strength of acidic groups and molecular weight distribution in humic and fulvic acids - can affect the reliability of colloid titration. Due to deviations from 1:1 stoichiometry in interactions of humic substances with polymeric cationic titrant, the colloid titration can underestimate total acidity (charge density) of humic substances with domination of weak acidic functional groups (pK>6) and high content of the fractions with molecular weight below 1kDa.

Study on the interaction between cinnamic acid and lysozyme

NASA Astrophysics Data System (ADS)

Zhang, Hong-Mei; Chen, Jian; Zhou, Qiu-Hua; Shi, Yue-Qin; Wang, Yan-Qing

2011-02-01

The interaction between lysozyme and cinnamic acid was investigated systematically by ultraviolet-vis absorbance, circular dichroism, fluorescence, synchronous fluorescence, and three-dimensional fluorescence spectra techniques at pH 7.40. The binding constants, quenching mechanism, and the number of binding sites were determined by the quenching of lysozyme fluorescence in presence of cinnamic acid. The results showed that the fluorescence quenching of lysozyme by cinnamic acid was a result of the formation of cinnamic acid-lysozyme complex. The hydrophobic and electrostatic interactions played major roles in stabilizing the complex; the distance r between donor and acceptor was obtained to be 2.07 nm according to Förster's theory; the effect of cinnamic acid on the conformation of lysozyme was analyzed using synchronous fluorescence, circular dichroism and three-dimensional fluorescence spectra.

Phenylboronate chromatography selectively separates glycoproteins through the manipulation of electrostatic, charge transfer, and cis-diol interactions.

PubMed

Carvalho, Rimenys J; Woo, James; Aires-Barros, M Raquel; Cramer, Steven M; Azevedo, Ana M

2014-10-01

Phenylboronate chromatography (PBC) has been applied for several years, however details regarding the mechanisms of interactions between the ligand and biomolecules are still scarce. The goal of this work is to investigate the various chemical interactions between proteins and their ligands, using a protein library containing both glycosylated and nonglycosylated proteins. Differences in the adsorption of these proteins over a pH range from 4 to 9 were related to two main properties: charge and presence of glycans. Acidic or neutral proteins were strongly adsorbed below pH 8 although the uncharged trigonal form of phenylboronate (PB) is less susceptible to forming electrostatic and cis-diol interactions with proteins. The glycosylated proteins were only adsorbed above pH 8 when the electrostatic repulsion between the boronate anion and the protein surface was mitigated (at 200 mM NaCl). All basic proteins were highly adsorbed above pH 8 with PB also acting as a cation-exchanger with binding occurring through electrostatic interactions. Batch adsorption performed at acidic conditions in the presence of Lewis base showed that charge-transfer interactions are critical for protein retention. This study demonstrates the multimodal interaction of PBC, which can be a selective tool for separation of different classes of proteins. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.