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Sample records for molecular recognition scaffolds

  1. Ion and Molecular Recognition Using Aryl–Ethynyl Scaffolding

    PubMed Central

    Vonnegut, Chris L.; Tresca, Blakely W.

    2015-01-01

    The aryl–ethynyl linkage has been extensively employed in the construction of hosts for a variety of guests. Uses range from ion detection (e.g., of metal cations in the environment or industrial waste and of anions prevalent in nature), to molecular mimics for biological systems, and to applications targeting future safety issues (such as CO2 capture and indicators for the manufacture of chemical weapons). This Focus Review examines the utilization of the aryl–ethynyl linkage in engineering host molecules for a variety of different guests, and how the alkyne unit plays an integral part as both a rigid scaffolding section in host geometry design as well as a linker to allow conjugative communication between discrete π-electron systems. PMID:25586943

  2. Ion and molecular recognition using aryl-ethynyl scaffolding.

    PubMed

    Vonnegut, Chris L; Tresca, Blakely W; Johnson, Darren W; Haley, Michael M

    2015-03-01

    The aryl-ethynyl linkage has been extensively employed in the construction of hosts for a variety of guests. Uses range from ion detection (e.g., of metal cations in the environment or industrial waste and of anions prevalent in nature), to molecular mimics for biological systems, and to applications targeting future safety issues (such as CO2 capture and indicators for the manufacture of chemical weapons). This Focus Review examines the utilization of the aryl-ethynyl linkage in engineering host molecules for a variety of different guests, and how the alkyne unit plays an integral part as both a rigid scaffolding section in host geometry design as well as a linker to allow conjugative communication between discrete π-electron systems.

  3. A new generation of protein display scaffolds for molecular recognition

    PubMed Central

    Hosse, Ralf J.; Rothe, Achim; Power, Barbara E.

    2006-01-01

    Engineered antibodies and their fragments are invaluable tools for a vast range of biotechnological and pharmaceutical applications. However, they are facing increasing competition from a new generation of protein display scaffolds, specifically selected for binding virtually any target. Some of them have already entered clinical trials. Most of these nonimmunoglobulin proteins are involved in natural binding events and have amazingly diverse origins, frameworks, and functions, including even intrinsic enzyme activity. In many respects, they are superior over antibody-derived affinity molecules and offer an ever-extending arsenal of tools for, e.g., affinity purification, protein microarray technology, bioimaging, enzyme inhibition, and potential drug delivery. As excellent supporting frameworks for the presentation of polypeptide libraries, they can be subjected to powerful in vitro or in vivo selection and evolution strategies, enabling the isolation of high-affinity binding reagents. This article reviews the generation of these novel binding reagents, describing validated and advanced alternative scaffolds as well as the most recent nonimmunoglobulin libraries. Characteristics of these protein scaffolds in terms of structural stability, tolerance to multiple substitutions, ease of expression, and subsequent applications as specific targeting molecules are discussed. Furthermore, this review shows the close linkage between these novel protein tools and the constantly developing display, selection, and evolution strategies using phage display, ribosome display, mRNA display, cell surface display, or IVC (in vitro compartmentalization). Here, we predict the important role of these novel binding reagents as a toolkit for biotechnological and biomedical applications. PMID:16373474

  4. Construction of proteins with molecular recognition capabilities using α3β3 de novo protein scaffolds.

    PubMed

    Okura, Hiromichi; Mihara, Hisakazu; Takahashi, Tsuyoshi

    2013-10-01

    The molecular recognition ability of proteins is essential in biological systems, and therefore a considerable amount of effort has been devoted to constructing desired target-binding proteins using a variety of naturally occurring proteins as scaffolds. However, since generating a binding site in a native protein can often affect its structural properties, highly stable de novo protein scaffolds may be more amenable than the native proteins. We previously reported the generation of de novo proteins comprising three α-helices and three β-strands (α3β3) from a genetic library coding simplified amino acid sets. Two α3β3 de novo proteins, vTAJ13 and vTAJ36, fold into a native-like stable and molten globule-like structures, respectively, even though the proteins have similar amino acid compositions. Here, we attempted to create binding sites for the vTAJ13 and vTAJ36 proteins to prove the utility of de novo designed artificial proteins as a molecular recognition tool. Randomization of six amino acids at two linker sites of vTAJ13 and vTAJ36 followed by biopanning generated binding proteins that recognize the target molecules, fluorescein and green fluorescent protein, with affinities of 10(-7)-10(-8) M. Of note, the selected proteins from the vTAJ13-based library tended to recognize the target molecules with high specificity, probably due to the native-like stable structure of vTAJ13. Our studies provide an example of the potential of de novo protein scaffolds, which are composed of a simplified amino acid set, to recognize a variety of target compounds.

  5. The intracellular Ig fold: a robust protein scaffold for the engineering of molecular recognition.

    PubMed

    Bruning, Marc; Barsukov, Igor; Franke, Barbara; Barbieri, Sonia; Volk, Martin; Leopoldseder, Sonja; Ucurum, Zöhre; Mayans, Olga

    2012-05-01

    Protein scaffolds that support molecular recognition have multiple applications in biotechnology. Thus, protein frames with robust structural cores but adaptable surface loops are in continued demand. Recently, notable progress has been made in the characterization of Ig domains of intracellular origin--in particular, modular components of the titin myofilament. These Ig belong to the I(intermediate)-type, are remarkably stable, highly soluble and undemanding to produce in the cytoplasm of Escherichia coli. Using the Z1 domain from titin as representative, we show that the I-Ig fold tolerates the drastic diversification of its CD loop, constituting an effective peptide display system. We examine the stability of CD-loop-grafted Z1-peptide chimeras using differential scanning fluorimetry, Fourier transform infrared spectroscopy and nuclear magnetic resonance and demonstrate that the introduction of bioreactive affinity binders in this position does not compromise the structural integrity of the domain. Further, the binding efficiency of the exogenous peptide sequences in Z1 is analyzed using pull-down assays and isothermal titration calorimetry. We show that an internally grafted, affinity FLAG tag is functional within the context of the fold, interacting with the anti-FLAG M2 antibody in solution and in affinity gel. Together, these data reveal the potential of the intracellular Ig scaffold for targeted functionalization.

  6. The menagerie of human lipocalins: a natural protein scaffold for molecular recognition of physiological compounds.

    PubMed

    Schiefner, André; Skerra, Arne

    2015-04-21

    While immunoglobulins are well-known for their characteristic ability to bind macromolecular antigens (i.e., as antibodies during an immune response), the lipocalins constitute a family of proteins whose role is the complexation of small molecules for various physiological processes. In fact, a number of low-molecular-weight substances in multicellular organisms show poor solubility, are prone to chemical decomposition, or play a pathophysiological role and thus require specific binding proteins for transport through body fluids, storage, or sequestration. In many cases, lipocalins are involved in such tasks. Lipocalins are small, usually monomeric proteins with 150-180 residues and diameters of approximately 40 Å, adopting a compact fold that is dominated by a central eight-stranded up-and-down β-barrel. At the amino-terminal end, this core is flanked by a coiled polypeptide segment, while its carboxy-terminal end is followed by an α-helix that leans against the β-barrel as well as an amino acid stretch in a more-or-less extended conformation, which finally is fixed by a disulfide bond. Within the β-barrel, the antiparallel strands (designated A to H) are arranged in a (+1)7 topology and wind around a central axis in a right-handed manner such that part of strand A is hydrogen-bonded to strand H again. Whereas the lower region of the β-barrel is closed by short loops and densely packed hydrophobic side chains, including many aromatic residues, the upper end is usually open to solvent. There, four long loops, each connecting one pair of β-strands, together form the entrance to a cup-shaped cavity. Depending on the individual structure of a lipocalin, and especially on the lengths and amino acid sequences of its four loops, this pocket can accommodate chemical ligands of various sizes and shapes, including lipids, steroids, and other chemical hormones as well as secondary metabolites such as vitamins, cofactors, or odorants. While lipocalins are ubiquitous in

  7. Molecularly Imprinted Intelligent Scaffolds for Tissue Engineering Applications.

    PubMed

    Neves, Mariana I; Wechsler, Marissa E; Gomes, Manuela E; Reis, Rui L; Granja, Pedro L; Peppas, Nicholas A

    2017-02-01

    The development of molecularly imprinted polymers (MIPs) using biocompatible production methods enables the possibility to further exploit this technology for biomedical applications. Tissue engineering (TE) approaches use the knowledge of the wound healing process to design scaffolds capable of modulating cell behavior and promote tissue regeneration. Biomacromolecules bear great interest for TE, together with the established recognition of the extracellular matrix, as an important source of signals to cells, both promoting cell-cell and cell-matrix interactions during the healing process. This review focuses on exploring the potential of protein molecular imprinting to create bioactive scaffolds with molecular recognition for TE applications based on the most recent approaches in the field of molecular imprinting of macromolecules. Considerations regarding essential components of molecular imprinting technology will be addressed for TE purposes. Molecular imprinting of biocompatible hydrogels, namely based on natural polymers, is also reviewed here. Hydrogel scaffolds with molecular memory show great promise for regenerative therapies. The first molecular imprinting studies analyzing cell adhesion report promising results with potential applications for cell culture systems, or biomaterials for implantation with the capability for cell recruitment by selectively adsorbing desired molecules.

  8. Radically enhanced molecular recognition

    NASA Astrophysics Data System (ADS)

    Trabolsi, Ali; Khashab, Niveen; Fahrenbach, Albert C.; Friedman, Douglas C.; Colvin, Michael T.; Cotí, Karla K.; Benítez, Diego; Tkatchouk, Ekaterina; Olsen, John-Carl; Belowich, Matthew E.; Carmielli, Raanan; Khatib, Hussam A.; Goddard, William A.; Wasielewski, Michael R.; Stoddart, J. Fraser

    2010-01-01

    The tendency for viologen radical cations to dimerize has been harnessed to establish a recognition motif based on their ability to form extremely strong inclusion complexes with cyclobis(paraquat-p-phenylene) in its diradical dicationic redox state. This previously unreported complex involving three bipyridinium cation radicals increases the versatility of host-guest chemistry, extending its practice beyond the traditional reliance on neutral and charged guests and hosts. In particular, transporting the concept of radical dimerization into the field of mechanically interlocked molecules introduces a higher level of control within molecular switches and machines. Herein, we report that bistable and tristable [2]rotaxanes can be switched by altering electrochemical potentials. In a tristable [2]rotaxane composed of a cyclobis(paraquat-p-phenylene) ring and a dumbbell with tetrathiafulvalene, dioxynaphthalene and bipyridinium recognition sites, the position of the ring can be switched. On oxidation, it moves from the tetrathiafulvalene to the dioxynaphthalene, and on reduction, to the bipyridinium radical cation, provided the ring is also reduced simultaneously to the diradical dication.

  9. Molecular recognition of bilayer vesicles.

    PubMed

    Voskuhl, Jens; Ravoo, Bart Jan

    2009-02-01

    Vesicles have been a versatile topic of research in chemistry ever since the discovery that, besides phospholipids, synthetic amphiphiles can also form molecular bilayers enclosing a small aqueous compartment. Non-covalent interactions of receptors and ligands or hosts and guests at vesicle surfaces resemble recognition processes at biological membranes, including cell recognition, adhesion and fusion. Molecular recognition at membranes is often mediated by a multivalent instead of a monovalent interaction. This tutorial review describes the basics as well as the latest developments in biomimetic supramolecular chemistry of bilayer vesicles. We describe how molecular recognition can mediate the interaction between vesicles, and how the biomimetic supramolecular chemistry of vesicles furthers our understanding of biological membranes.

  10. Computational Exploration of Molecular Scaffolds in Medicinal Chemistry.

    PubMed

    Hu, Ye; Stumpfe, Dagmar; Bajorath, Jürgen

    2016-05-12

    The scaffold concept is widely applied in medicinal chemistry. Scaffolds are mostly used to represent core structures of bioactive compounds. Although the scaffold concept has limitations and is often viewed differently from a chemical and computational perspective, it has provided a basis for systematic investigations of molecular cores and building blocks, going far beyond the consideration of individual compound series. Over the past 2 decades, alternative scaffold definitions and organization schemes have been introduced and scaffolds have been studied in a variety of ways and increasingly on a large scale. Major applications of the scaffold concept include the generation of molecular hierarchies, structural classification, association of scaffolds with biological activities, and activity prediction. This contribution discusses computational approaches for scaffold generation and analysis, with emphasis on recent developments impacting medicinal chemistry. A variety of scaffold-based studies are discussed, and a perspective on scaffold methods is provided.

  11. Scaffolding Learning from Molecular Visualizations

    ERIC Educational Resources Information Center

    Chang, Hsin-Yi; Linn, Marcia C.

    2013-01-01

    Powerful online visualizations can make unobservable scientific phenomena visible and improve student understanding. Instead, they often confuse or mislead students. To clarify the impact of molecular visualizations for middle school students we explored three design variations implemented in a Web-based Inquiry Science Environment (WISE) unit on…

  12. Scaffolding Learning from Molecular Visualizations

    ERIC Educational Resources Information Center

    Chang, Hsin-Yi; Linn, Marcia C.

    2013-01-01

    Powerful online visualizations can make unobservable scientific phenomena visible and improve student understanding. Instead, they often confuse or mislead students. To clarify the impact of molecular visualizations for middle school students we explored three design variations implemented in a Web-based Inquiry Science Environment (WISE) unit on…

  13. Engineering of an Extremely Thermostable Alpha/Beta Barrel Scaffold to Serve as a High Affinity Molecular Recognition Element for Use in Sensor Applications

    DTIC Science & Technology

    2015-12-23

    aldehydes, ketones and carbohydrates. Directed evolution techniques were used to convert the enzyme into a simple binder of the small molecule RDX...Army Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 protein engineering, directed evolution , biomolecular recognition, RDX...dependent oxidation or reduction of alcohols, aldehydes, ketones and carbohydrates. Directed evolution techniques were used to convert the enzyme into a

  14. Analog series-based scaffolds: computational design and exploration of a new type of molecular scaffolds for medicinal chemistry.

    PubMed

    Dimova, Dilyana; Stumpfe, Dagmar; Hu, Ye; Bajorath, Jürgen

    2016-12-01

    Computational design of and systematic search for a new type of molecular scaffolds termed analog series-based scaffolds. From currently available bioactive compounds, analog series were systematically extracted, key compounds identified and new scaffolds isolated from them. Using our computational approach, more than 12,000 scaffolds were extracted from bioactive compounds. A new scaffold definition is introduced and a computational methodology developed to systematically identify such scaffolds, yielding a large freely available scaffold knowledge base.

  15. Slow Molecular Recognition by RNA.

    PubMed

    Gleitsman, Kristin R; Sengupta, Raghuvir N; Herschlag, Daniel

    2017-09-28

    Molecular recognition is central to biological processes, function, and specificity. Proteins associate with ligands with maximal rates that match the theoretical limit set by the rate of diffusional collision and with a wide range of observed values. As less is known about RNA association, we compiled association rate constants for all RNA/ligand complexes that we could find in the literature. Like proteins, RNAs exhibit a wide range of association rate constants. However, the fastest RNA association rates are considerably slower than those of the fastest protein associations and fall well below the diffusional limit. The apparently general observation of slow association with RNAs has implications for evolution and for modern-day biology. Our compilation highlights a quantitative molecular property that can contribute to biological understanding and underscores our limited physical understanding of molecular recognition events. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  16. Molecular Recognition and Ligand Association

    NASA Astrophysics Data System (ADS)

    Baron, Riccardo; McCammon, J. Andrew

    2013-04-01

    We review recent developments in our understanding of molecular recognition and ligand association, focusing on two major viewpoints: (a) studies that highlight new physical insight into the molecular recognition process and the driving forces determining thermodynamic signatures of binding and (b) recent methodological advances in applications to protein-ligand binding. In particular, we highlight the challenges posed by compensating enthalpic and entropic terms, competing solute and solvent contributions, and the relevance of complex configurational ensembles comprising multiple protein, ligand, and solvent intermediate states. As more complete physics is taken into account, computational approaches increase their ability to complement experimental measurements, by providing a microscopic, dynamic view of ensemble-averaged experimental observables. Physics-based approaches are increasingly expanding their power in pharmacology applications.

  17. Designing Electronic Components and Devices from Inorganic Molecular Scaffolds

    DTIC Science & Technology

    2012-07-04

    REPORT Designing Electronic Components and Devices from Inorganic Molecular Scaffolds 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: The synthesis of new...photo and electrical materials for molecular devices was completed comprising a signaling moiety (fluorophore), a spacer group and a guest-binding...98) Prescribed by ANSI Std. Z39.18 - 7-Mar-2012 Designing Electronic Components and Devices from Inorganic Molecular Scaffolds Report Title

  18. Molecular mobility of scaffolds' biopolymers influences cell growth.

    PubMed

    Podlipec, Rok; Gorgieva, Selestina; Jurašin, Darija; Urbančič, Iztok; Kokol, Vanja; Strancar, Janez

    2014-09-24

    Understanding biocompatibility of materials and scaffolds is one of the main challenges in the field of tissue engineering and regeneration. The complex nature of cell-biomaterial interaction requires extensive preclinical functionality testing by studying specific cell responses to different biomaterial properties, from morphology and mechanics to surface characteristics at the molecular level. Despite constant improvements, a more general picture of biocompatibility is still lacking and tailormade scaffolds are not yet available. The scope of our study was thus the investigation of the correlation of fibroblast cell growth on different gelatin scaffolds with their morphological, mechanical as well as surface molecular properties. The latter were thoroughly investigated via polymer molecular mobility studied by site-directed spin labeling and electron paramagnetic resonance spectroscopy (EPR) for the first time. Anisotropy of the rotational motion of the gelatin side chain mobility was identified as the most correlated quantity with cell growth in the first days after adhesion, while weaker correlations were found with scaffold viscoelasticity and no correlations with scaffold morphology. Namely, the scaffolds with highly mobile or unrestricted polymers identified with the cell growth being five times less efficient (N(cells) = 60 ± 25 mm(-2)) as compared to cell growth on the scaffolds with considerable part of polymers with the restricted rotational motion (N(cells) = 290 ± 25 mm(-2)). This suggests that molecular mobility of scaffold components could play an important role in cell response to medical devices, reflecting a new aspect of the biocompatibility concept.

  19. Analog series-based scaffolds: computational design and exploration of a new type of molecular scaffolds for medicinal chemistry

    PubMed Central

    Dimova, Dilyana; Stumpfe, Dagmar; Hu, Ye; Bajorath, Jürgen

    2016-01-01

    Aim: Computational design of and systematic search for a new type of molecular scaffolds termed analog series-based scaffolds. Materials & methods: From currently available bioactive compounds, analog series were systematically extracted, key compounds identified and new scaffolds isolated from them. Results: Using our computational approach, more than 12,000 scaffolds were extracted from bioactive compounds. Conclusion: A new scaffold definition is introduced and a computational methodology developed to systematically identify such scaffolds, yielding a large freely available scaffold knowledge base. PMID:28116132

  20. Characterization of molecular recognition in gas sensors

    SciTech Connect

    Hierlemann, A.; Ricco, A.J.; Bodenhoefer, K.; Goepel, W.

    1998-08-01

    Molecular recognition is an important topic when searching for new, selective coating materials for chemical sensing. Recently, the general idea of molecular recognition in the gas phase was challenged by Grate et al. However, in earlier thickness-shear mode resonator (TSMR) investigations, convincing evidence was presented for specific recognition of particular analyte target molecules. In this study, the authors systematically investigated coatings previously shown to be highly selective, such as the bucket-like cyclodextrins for chiral recognition, Ni-camphorates for the specific detection of the bases pyridine and DMMP (dimethylmethylphosphonate), and phthalocyanines to specifically detect benzene, toluene, and xylene (BTX).

  1. Plastic Antibodies: Molecular Recognition with Imprinted Polymers

    ERIC Educational Resources Information Center

    Rushton, Gregory T.; Furmanski, Brian; Shimizu, Ken D.

    2005-01-01

    Synthetic polymers are prepared and tested in a study for their molecular recognition properties of an adenine derivative, ethyl adenine-9-acetate (EA9A), within two laboratory periods. The procedure introduces undergraduate chemistry students to noncovalent molecular imprinting as well as the analytical techniques for assessing their recognition…

  2. Plastic Antibodies: Molecular Recognition with Imprinted Polymers

    ERIC Educational Resources Information Center

    Rushton, Gregory T.; Furmanski, Brian; Shimizu, Ken D.

    2005-01-01

    Synthetic polymers are prepared and tested in a study for their molecular recognition properties of an adenine derivative, ethyl adenine-9-acetate (EA9A), within two laboratory periods. The procedure introduces undergraduate chemistry students to noncovalent molecular imprinting as well as the analytical techniques for assessing their recognition…

  3. High molecular recognition: design of "Keys".

    PubMed

    Chen, Beining; Piletsky, Sergey; Turner, Anthony P F

    2002-09-01

    Molecular recognition between molecules is one of the most fundamental processes in biology and chemistry. The recognition process is largely driven by non-covalent forces such as hydrogen bonding, electrostatics, van der Waals forces, pi-pi interactions, and conformational energy. The complementarity between the receptor and substrate is very similar to the "lock and key" function, first described by Emil Fischer over 100 years ago, - the lock being the molecular receptor such as a protein or enzyme and the key being the substrate such as a drug, that is recognized to give a defined receptor-substrate complex. This review focuses on the design of specific ligand systems as "Keys" to enable the induced fit of these keys into the target macromolecules, protein/enzyme (Locks) with particular emphasis on protein recognition.

  4. Molecular recognition: The I's have it

    NASA Astrophysics Data System (ADS)

    Taylor, Mark S.

    2014-12-01

    Rotaxanes with cyclodextrin end groups have been used as a platform to investigate anion binding in water, revealing that halogen bonding can serve as the basis for molecular recognition in aqueous solvents, which may have implications in medicinal chemistry and beyond.

  5. Epigenetic molecular recognition: a biomolecular modeling perspective.

    PubMed

    Vellore, Nadeem A; Baron, Riccardo

    2014-03-01

    The abnormal regulation of epigenetic protein families is associated with the onset and progression of various human diseases. However, epigenetic processes remain relatively obscure at the molecular level, thus preventing the rational design of chemical therapeutics. An array of robust computational and modeling approaches can complement experiments to shed light on the complex mechanisms of epigenetic molecular recognition and can guide medicinal chemists in designing selective and potent drug molecules. Herein we present a review of studies focused on epigenetic molecular recognition from a biomolecular modeling viewpoint. Although the known epigenetic targets are numerous, this review focuses on the more limited protein families on which computational modeling has been successfully applied. Therefore, we review three main topics: 1) histone deacetylases, 2) histone demethylases, and 3) histone tail dynamics. A brief review of the biological background and biomedical relevance is presented for each topic, followed by a detailed discussion of the computational studies and their relevance.

  6. Studies on molecular recognition of thymidines with molecularly imprinted polymers

    NASA Astrophysics Data System (ADS)

    Chen, Zhen-He; Luo, Ai-Qin; Sun, Li-Quan

    2009-07-01

    Molecularly imprinted polymers (MIPs) with excellent molecular recognition ability have been used in chemical sensors, chromatographic separation and biochemical analyses. Thymidine is an important part of DNA for biomolecular recognition and the intermediate of many medicines. The polymers imprinted with the template of thymidine and 5'-Otosylthymidine have been prepared, using a non-proton solvent, acetonitrile as the porogen. Direct imprinting with thymidine could not form strong molecular interaction sites in this system. Relative MIPs were obtained by bulk polymerization and their adsorption capacities were investigated. The adsorption capacities of MIP (P2) and nonimprinted polymer (P20) for thymidine are 0.120 mg•g-1and 0.103 mg•g-1, respectively. The imprinting factor is 1.17. As 5'-O-tosylthymidine is more soluble than thymidine moiety in acetonitrile and give rise to more sites of molecular recognition. The results demonstrated that the imprinted polymers were able to bind and recognize thymidine moderately in acetonitrile. MIPs imprinted with 5'-O-tosylthymidine like nature enzymes displayed some recognition ability to its analogues. The insoluble derivatives in the non-proton solvent can be an effective template to prepare efficient imprinting recognition sites.

  7. Photoswitchable gel assembly based on molecular recognition

    PubMed Central

    Yamaguchi, Hiroyasu; Kobayashi, Yuichiro; Kobayashi, Ryosuke; Takashima, Yoshinori; Hashidzume, Akihito; Harada, Akira

    2012-01-01

    The formation of effective and precise linkages in bottom-up or top-down processes is important for the development of self-assembled materials. Self-assembly through molecular recognition events is a powerful tool for producing functionalized materials. Photoresponsive molecular recognition systems can permit the creation of photoregulated self-assembled macroscopic objects. Here we demonstrate that macroscopic gel assembly can be highly regulated through photoisomerization of an azobenzene moiety that interacts differently with two host molecules. A photoregulated gel assembly system is developed using polyacrylamide-based hydrogels functionalized with azobenzene (guest) or cyclodextrin (host) moieties. Reversible adhesion and dissociation of the host gel from the guest gel may be controlled by photoirradiation. The differential affinities of α-cyclodextrin or β-cyclodextrin for the trans-azobenzene and cis-azobenzene are employed in the construction of a photoswitchable gel assembly system. PMID:22215078

  8. Molecularly imprinted polymers for biomolecular recognition.

    PubMed

    Molinelli, Alexandra; Janotta, Markus; Mizaikoff, Boris

    2005-01-01

    Molecular imprinting of polymers is a concept for the synthetic formation of structurally organized materials providing binding sites with molecular selectivity. Compared to biological receptors, these polymeric recognition systems have the advantage of superior chemical and mechanical stability with potential applications in areas such as biomimetic catalysis and engineering, biomedical analysis, sensor technology, or the food industry. In particular, molecularly imprinted polymers (MIPs) providing selectivity for biorelated molecules are gaining substantial importance. In this context, a self-assembly approach for the synthesis of imprinted polymers against the flavonol quercetin is presented, which is exemplary for the biologically relevant group of flavonoid compounds. The creation of synthetic selective recognition sites for this biomolecule is demonstrated by comparing the separation capabilities of imprinted and nonimprinted polymer particles for several structurally related molecules via high-performance liquid chromatography experiments. The developed quercetin-MIP enables selective extraction of quercetin even from complex mixtures, demonstrating the potential for designing biomimetic recognition materials with improved selectivity for biomolecules with tunable functionality at a nanoscale.

  9. Scaffolded DNA origami of a DNA tetrahedron molecular container.

    PubMed

    Ke, Yonggang; Sharma, Jaswinder; Liu, Minghui; Jahn, Kasper; Liu, Yan; Yan, Hao

    2009-06-01

    We describe a strategy of scaffolded DNA origami to design and construct 3D molecular cages of tetrahedron geometry with inside volume closed by triangular faces. Each edge of the triangular face is approximately 54 nm in dimension. The estimated total external volume and the internal cavity of the triangular pyramid are about 1.8 x 10(-23) and 1.5 x 10(-23) m(3), respectively. Correct formation of the tetrahedron DNA cage was verified by gel electrophoresis, atomic force microscopy, transmission electron microscopy, and dynamic light scattering techniques.

  10. Applications of Systematic Molecular Scaffold Enumeration to Enrich Structure-Activity Relationship Information.

    PubMed

    Mok, N Yi; Brown, Nathan

    2017-01-23

    Establishing structure-activity relationships (SARs) in hit identification during early stage drug discovery is important in accelerating hit confirmation and expansion. We describe the development of EnCore, a systematic molecular scaffold enumeration protocol using single atom mutations, to enhance the application of objective scaffold definitions and to enrich SAR information from analysis of high-throughput screening output. A list of 43 literature medicinal chemistry compound series, each containing a minimum of 100 compounds, published in the Journal of Medicinal Chemistry was collated to validate the protocol. Analysis using the top representative Level 1 scaffolds this list of literature compound series demonstrated that EnCore could mimic the scaffold exploration conducted when establishing SAR. When EnCore was applied to analyze an HTS library containing over 200 000 compounds, we observed that over 70% of the molecular scaffolds matched extant scaffolds within the library after enumeration. In particular, over 60% of the singleton scaffolds with only one representative compound were found to have structurally related compounds after enumeration. These results illustrate the potential of EnCore to enrich SAR information. A case study using literature cyclooxygenase-2 inhibitors further demonstrates the advantage of EnCore application in establishing SAR from structurally related scaffolds. EnCore complements literature enumeration methods in enabling changes to the physicochemical properties of molecular scaffolds and structural modifications to aliphatic rings and linkers. The enumerated scaffold clusters generated would constitute a comprehensive collection of scaffolds for scaffold morphing and hopping.

  11. Fibronectin adsorption on functionalized electrospun polycaprolactone scaffolds: experimental and molecular dynamics studies.

    PubMed

    Regis, Shawn; Youssefian, Sina; Jassal, Manisha; Phaneuf, Matthew D; Rahbar, Nima; Bhowmick, Sankha

    2014-06-01

    Designing scaffolds to modulate protein adsorption is a key to building advanced scaffolds for tissue regeneration. Protein adsorption to tissue engineering scaffolds is critical in early cell attachment, survival, and eventual proliferation. The goal of this study is to examine the effect of functionalization on fibronectin adsorption to electrospun polycaprolactone (PCL) scaffolds through experimentation using fluorescently labeled fibronectin and to couple this experimental data with analysis of interaction energies obtained through molecular dynamics (MD) simulations to develop a better understanding of the adsorption process. This study is the first to analyze and compare experimental and MD simulation results of fibronectin adsorption on functionalized electrospun PCL scaffolds. Electrospun nanofiber PCL scaffolds were treated with either 1 N NaOH (hydrolyzed) or 46% hexamethylenediamine (HMD) (aminated) solution to be compared with untreated (control) scaffolds. We found that aminated PCL scaffolds experimentally adsorbed more fibronectin than control scaffolds, whereas hydrolyzed scaffolds showed decreased adsorption. MD simulations carried out with NVT ensemble at a temperature of 310 K indicated a higher work of adhesion for both functionalized scaffolds over control. Also, the simulations revealed different conformations of fibronectin on each scaffold type after adsorption, with the arginine-glycine-aspartic acid sequence appearing most accessible on the aminated scaffolds. This suggests that functionalization affects not only the quantity of protein that will adsorb on a scaffold but how it attaches as well, which could affect subsequent cell attachment.

  12. Protein-targeted corona phase molecular recognition.

    PubMed

    Bisker, Gili; Dong, Juyao; Park, Hoyoung D; Iverson, Nicole M; Ahn, Jiyoung; Nelson, Justin T; Landry, Markita P; Kruss, Sebastian; Strano, Michael S

    2016-01-08

    Corona phase molecular recognition (CoPhMoRe) uses a heteropolymer adsorbed onto and templated by a nanoparticle surface to recognize a specific target analyte. This method has not yet been extended to macromolecular analytes, including proteins. Herein we develop a variant of a CoPhMoRe screening procedure of single-walled carbon nanotubes (SWCNT) and use it against a panel of human blood proteins, revealing a specific corona phase that recognizes fibrinogen with high selectivity. In response to fibrinogen binding, SWCNT fluorescence decreases by >80% at saturation. Sequential binding of the three fibrinogen nodules is suggested by selective fluorescence quenching by isolated sub-domains and validated by the quenching kinetics. The fibrinogen recognition also occurs in serum environment, at the clinically relevant fibrinogen concentrations in the human blood. These results open new avenues for synthetic, non-biological antibody analogues that recognize biological macromolecules, and hold great promise for medical and clinical applications.

  13. Protein-targeted corona phase molecular recognition

    NASA Astrophysics Data System (ADS)

    Bisker, Gili; Dong, Juyao; Park, Hoyoung D.; Iverson, Nicole M.; Ahn, Jiyoung; Nelson, Justin T.; Landry, Markita P.; Kruss, Sebastian; Strano, Michael S.

    2016-01-01

    Corona phase molecular recognition (CoPhMoRe) uses a heteropolymer adsorbed onto and templated by a nanoparticle surface to recognize a specific target analyte. This method has not yet been extended to macromolecular analytes, including proteins. Herein we develop a variant of a CoPhMoRe screening procedure of single-walled carbon nanotubes (SWCNT) and use it against a panel of human blood proteins, revealing a specific corona phase that recognizes fibrinogen with high selectivity. In response to fibrinogen binding, SWCNT fluorescence decreases by >80% at saturation. Sequential binding of the three fibrinogen nodules is suggested by selective fluorescence quenching by isolated sub-domains and validated by the quenching kinetics. The fibrinogen recognition also occurs in serum environment, at the clinically relevant fibrinogen concentrations in the human blood. These results open new avenues for synthetic, non-biological antibody analogues that recognize biological macromolecules, and hold great promise for medical and clinical applications.

  14. Protein-targeted corona phase molecular recognition

    PubMed Central

    Bisker, Gili; Dong, Juyao; Park, Hoyoung D.; Iverson, Nicole M.; Ahn, Jiyoung; Nelson, Justin T.; Landry, Markita P.; Kruss, Sebastian; Strano, Michael S.

    2016-01-01

    Corona phase molecular recognition (CoPhMoRe) uses a heteropolymer adsorbed onto and templated by a nanoparticle surface to recognize a specific target analyte. This method has not yet been extended to macromolecular analytes, including proteins. Herein we develop a variant of a CoPhMoRe screening procedure of single-walled carbon nanotubes (SWCNT) and use it against a panel of human blood proteins, revealing a specific corona phase that recognizes fibrinogen with high selectivity. In response to fibrinogen binding, SWCNT fluorescence decreases by >80% at saturation. Sequential binding of the three fibrinogen nodules is suggested by selective fluorescence quenching by isolated sub-domains and validated by the quenching kinetics. The fibrinogen recognition also occurs in serum environment, at the clinically relevant fibrinogen concentrations in the human blood. These results open new avenues for synthetic, non-biological antibody analogues that recognize biological macromolecules, and hold great promise for medical and clinical applications. PMID:26742890

  15. Molecular Recognition in the Colloidal World.

    PubMed

    Elacqua, Elizabeth; Zheng, Xiaolong; Shillingford, Cicely; Liu, Mingzhu; Weck, Marcus

    2017-10-06

    Colloidal self-assembly is a bottom-up technique to fabricate functional nanomaterials, with paramount interest stemming from programmable assembly of smaller building blocks into dynamic crystalline domains and photonic materials. Multiple established colloidal platforms feature diverse shapes and bonding interactions, while achieving specific orientations along with short- and long-range order. A major impediment to their universal use as building blocks for predesigned architectures is the inability to precisely dictate and control particle functionalization and concomitant reversible self-assembly. Progress in colloidal self-assembly necessitates the development of strategies that endow bonding specificity and directionality within assemblies. Methodologies that emulate molecular and polymeric three-dimensional (3D) architectures feature elements of covalent bonding, while high-fidelity molecular recognition events have been installed to realize responsive reconfigurable assemblies. The emergence of anisotropic 'colloidal molecules', coupled with the ability to site-specifically decorate particle surfaces with supramolecular recognition motifs, has facilitated the formation of superstructures via directional interactions and shape recognition. In this Account, we describe supramolecular assembly routes to drive colloidal particles into precisely assembled architectures or crystalline lattices via directional noncovalent molecular interactions. The design principles are based upon the fabrication of colloidal particles bearing surface-exposed functional groups that can undergo programmable conjugation to install recognition motifs with high fidelity. Modular and versatile by design, our strategy allows for the introduction and integration of molecular recognition principles into the colloidal world. We define noncovalent molecular interactions as site-specific forces that are predictable (i.e., feature selective and controllable complementary bonding partners

  16. Synthesis and Characterization of Two-Dimensional Molecular Recognition Interfaces

    DTIC Science & Technology

    1993-11-23

    Molecular Recognition Interfaces" 6. AUTHOR(S) R. M. Crooks, 0. Chailapakul, C. B. Ross, L. Sun, and J. K. Schoer 7. PERFORMING ORGANIZATION NAME(S) AND...We have used self-assembly chemistry to synthesize monolayer assemblies that function as molecular recognition interfaces. In the first part of this... Molecular Recognition Interfaces by Richard M. Crooks, Orawon Chailapakul, Claudia B. Ross, Li Sun, and Jonathan K. Schoer Prepared for Publication in

  17. Carbon nanodots as molecular scaffolds for development of antimicrobial agents.

    PubMed

    Ngu-Schwemlein, Maria; Chin, Suk Fun; Hileman, Ryan; Drozdowski, Chris; Upchurch, Clint; Hargrove, April

    2016-04-01

    We report the potential of carbon nanodots (CNDs) as a molecular scaffold for enhancing the antimicrobial activities of small dendritic poly(amidoamines) (PAMAM). Carbon nanodots prepared from sago starch are readily functionalized with PAMAM by using N-ethyl-N'-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS). Electron microscopy images of these polyaminated CNDs show that they are approximately 30-60nm in diameter. Infrared and fluorescence spectroscopy analyses of the water-soluble material established the presence of the polyamidoaminated moiety and the intrinsic fluorescence of the nanodots. The polyaminated nanodots (CND-PAM1 and CND-PAM2) exhibit in vitro antimicrobial properties, not only to non-multidrug resistant bacteria but also to the corresponding Gram-negative multidrug bacteria. Their minimum inhibitory concentration (MIC) ranges from 8 to 64μg/mL, which is much lower than that of PAMAM G1 or the non-active PAMAM G0 and CNDs. Additionally, they show synergistic effect in combination with tetracycline or colistin. These preliminary results imply that CNDs can serve as a promising scaffold for facilitating the rational design of antimicrobial materials for combating the ever-increasing threat of antibiotic resistance. Moreover, their fluorescence could be pertinent to unraveling their mode of action for imaging or diagnostic applications.

  18. Developments in Molecular Recognition and Sensing at Interfaces

    PubMed Central

    Ariga, Katsuhiko; Hill, Jonathan P.; Endo, Hiroshi

    2007-01-01

    In biological systems, molecular recognition events occur mostly within interfacial environments such as at membrane surfaces, enzyme reaction sites, or at the interior of the DNA double helix. Investigation of molecular recognition at model interfaces provides great insights into biological phenomena. Molecular recognition at interfaces not only has relevance to biological systems but is also important for modern applications such as high sensitivity sensors. Selective binding of guest molecules in solution to host molecules located at solid surfaces is crucial for electronic or photonic detection of analyte substances. In response to these demands, molecular recognition at interfaces has been investigated extensively during the past two decades using Langmuir monolayers, self-assembled monolayers, and lipid assemblies as recognition media. In this review, advances of molecular recognition at interfaces are briefly summarized.

  19. Molecular recognition: from solution science to nano/materials technology.

    PubMed

    Ariga, Katsuhiko; Ito, Hiroshi; Hill, Jonathan P; Tsukube, Hiroshi

    2012-09-07

    In the 25 years since its Nobel Prize in chemistry, supramolecular chemistry based on molecular recognition has been paid much attention in scientific and technological fields. Nanotechnology and the related areas seek breakthrough methods of nanofabrication based on rational organization through assembly of constituent molecules. Advanced biochemistry, medical applications, and environmental and energy technologies also depend on the importance of specific interactions between molecules. In those current fields, molecular recognition is now being re-evaluated. In this review, we re-examine current trends in molecular recognition from the viewpoint of the surrounding media, that is (i) the solution phase for development of basic science and molecular design advances; (ii) at nano/materials interfaces for emerging technologies and applications. The first section of this review includes molecular recognition frontiers, receptor design based on combinatorial approaches, organic capsule receptors, metallo-capsule receptors, helical receptors, dendrimer receptors, and the future design of receptor architectures. The following section summarizes topics related to molecular recognition at interfaces including fundamentals of molecular recognition, sensing and detection, structure formation, molecular machines, molecular recognition involving polymers and related materials, and molecular recognition processes in nanostructured materials.

  20. Molecular Recognition in the Digital Radio Domain

    NASA Astrophysics Data System (ADS)

    William D. Hunt,; Peter J. Edmonson,; Desmond D. Stubbs,; Sang-Hun Lee,

    2010-07-01

    In this paper we discuss the theoretical and experimental constructs which together point the way towards the transduction of biomolecular recognition events into a palpable set of electrical signals. This combines the applied physics of surface perturbations on acoustic wave device surfaces and the biochemistry of the interactions between an immobilized biomolecule (e.g., an antibody) and a target molecule which is flowing past the sensor surface (e.g., an antigen). We will first provide the theoretical basis for our contention that we can extract information about both molecular recognition and conformational change from the electrical signal and will then confirm this assertion with experimental results relating to induced conformational changes in DNA on a quartz crystal microbalance (QCM) surface. Next we will discuss our digital radio technique whereby the real time measurements using antibody coated surface acoustic wave (SAW) devices in the vapor phase allow us to differentiate between close chemical analogs of nitro-based molecules (e.g., tri-nitro toluene vs musk oil) by virtue of the cross-reactivity of the antibody-antigen interaction. In immunochemistry this is referred to as antibody promiscuity. Finally, we present two- and three-dimensional plots illustrating our technique which derives much from in-phase and quadrature phase (IQ) mapping. The end result is a powerful technique which allows one to differentiate between target molecules and chemically similar interferrents.

  1. Molecular Recognition and Specific Interactions for Biosensing Applications

    PubMed Central

    Kim, Dong Chung; Kang, Dae Joon

    2008-01-01

    Molecular recognition and specific interactions are reliable and versatile routes for site-specific and well-oriented immobilization of functional biomolecules on surfaces. The control of surface properties via the molecular recognition and specific interactions at the nanoscale is a key element for the nanofabrication of biosensors with high sensitivity and specificity. This review intends to provide a comprehensive understanding of the molecular recognition- and specific interaction-mediated biosensor fabrication routes that leads to biosensors with well-ordered and controlled structures on both nanopatterned surfaces and nanomaterials. Herein self-assembly of the biomolecules via the molecular recognition and specific interactions on nanoscaled surfaces as well as nanofabrication techniques of the biomolecules for biosensor architecture are discussed. We also describe the detection of molecular recognition- and specific interaction-mediated molecular binding as well as advantages of nanoscale detection. PMID:27873889

  2. Method for Systematic Assessment of Chemical Changes in Molecular Scaffolds with Conserved Topology and Application to the Analysis of Scaffold-Activity Relationships.

    PubMed

    Hu, Ye; Zhang, Bijun; Bajorath, Jürgen

    2015-08-01

    Sets of scaffolds with conserved molecular topology are abundant among drugs and bioactive compounds. Core structure topology is one of the determinants of biological activity. Heteroatom replacements and/or bond order variation render topologically equivalent scaffolds chemically distinct and also contribute to differences in the biological activity of compounds containing these scaffolds. Relationships between core structure topology, chemical modifications, and observed activity profiles are difficult to analyze. A computational method is introduced to consistently assess chemical transformations that distinguish scaffolds with conserved topology. The methodology is applied to quantify chemical differences in conserved topological environments and systematically relate chemical changes in topologically equivalent scaffolds to associated activity profiles.

  3. Homotypic dimerization of a maltose kinase for molecular scaffolding

    PubMed Central

    Li, Jun; Guan, Xiaotao; Shaw, Neil; Chen, Weimin; Dong, Yu; Xu, Xiaoling; Li, Xuemei; Rao, Zihe

    2014-01-01

    Mycobacterium tuberculosis (Mtb) uses maltose-1-phosphate to synthesize α-glucans that make up the major component of its outer capsular layer. Maltose kinase (MaK) catalyzes phosphorylation of maltose. The molecular basis for this phosphorylation is currently not understood. Here, we describe the first crystal structure of MtbMaK refined to 2.4 Å resolution. The bi-modular architecture of MtbMaK reveals a remarkably unique N-lobe. An extended sheet protrudes into ligand binding pocket of an adjacent monomer and contributes residues critical for kinase activity. Structure of the complex of MtbMaK bound with maltose reveals that maltose binds in a shallow cavity of the C-lobe. Structural constraints permit phosphorylation of α-maltose only. Surprisingly, instead of a Gly-rich loop, MtbMaK employs ‘EQS’ loop to tether ATP. Notably, this loop is conserved across all MaK homologues. Structures of MtbMaK presented here unveil features that are markedly different from other kinases and support the scaffolding role proposed for this kinase. PMID:25245657

  4. Homotypic dimerization of a maltose kinase for molecular scaffolding.

    PubMed

    Li, Jun; Guan, Xiaotao; Shaw, Neil; Chen, Weimin; Dong, Yu; Xu, Xiaoling; Li, Xuemei; Rao, Zihe

    2014-09-23

    Mycobacterium tuberculosis (Mtb) uses maltose-1-phosphate to synthesize α-glucans that make up the major component of its outer capsular layer. Maltose kinase (MaK) catalyzes phosphorylation of maltose. The molecular basis for this phosphorylation is currently not understood. Here, we describe the first crystal structure of MtbMaK refined to 2.4 Å resolution. The bi-modular architecture of MtbMaK reveals a remarkably unique N-lobe. An extended sheet protrudes into ligand binding pocket of an adjacent monomer and contributes residues critical for kinase activity. Structure of the complex of MtbMaK bound with maltose reveals that maltose binds in a shallow cavity of the C-lobe. Structural constraints permit phosphorylation of α-maltose only. Surprisingly, instead of a Gly-rich loop, MtbMaK employs 'EQS' loop to tether ATP. Notably, this loop is conserved across all MaK homologues. Structures of MtbMaK presented here unveil features that are markedly different from other kinases and support the scaffolding role proposed for this kinase.

  5. Molecular Recognition: Detection of Colorless Compounds Based on Color Change

    ERIC Educational Resources Information Center

    Khalafi, Lida; Kashani, Samira; Karimi, Javad

    2016-01-01

    A laboratory experiment is described in which students measure the amount of cetirizine in allergy-treatment tablets based on molecular recognition. The basis of recognition is competition of cetirizine with phenolphthalein to form an inclusion complex with ß-cyclodextrin. Phenolphthalein is pinkish under basic condition, whereas it's complex form…

  6. Molecular Recognition: Detection of Colorless Compounds Based on Color Change

    ERIC Educational Resources Information Center

    Khalafi, Lida; Kashani, Samira; Karimi, Javad

    2016-01-01

    A laboratory experiment is described in which students measure the amount of cetirizine in allergy-treatment tablets based on molecular recognition. The basis of recognition is competition of cetirizine with phenolphthalein to form an inclusion complex with ß-cyclodextrin. Phenolphthalein is pinkish under basic condition, whereas it's complex form…

  7. Relating pore size variation of poly (ɛ-caprolactone) scaffolds to molecular weight of porogen and evaluation of scaffold properties after degradation.

    PubMed

    Columbus, Soumya; Krishnan, Lissy K; Kalliyana Krishnan, V

    2014-05-01

    The major challenge in designing a scaffold for fabricating tissue engineered blood vessels is optimization of its microstructure for supporting uniform cellular in-growth with good mechanical integrity and degradation kinetics suitable for long-term implantation. In this study, we have investigated the feasibility of varying the pore size of poly(ɛ-caprolactone) (PCL) scaffold by altering the molecular weight of porogen and studied the effect of degradation on morphological characteristics and mechanical properties of scaffolds by correlating to the extent of degradation. Scaffolds with two different pore sizes were prepared by solvent casting and particulate leaching where poly(ethylene glycol) (PEG) porogens having two molecular weights (3400 and 8000) were used and subjected to in vitro degradation in phosphate buffered saline (PBS) upto six months. Microcomputed tomography studies of scaffolds revealed narrower pore size distribution when PEG-3400 was used as porogen and had 78% pores in the 12-24 µ range, whereas incorporation of PEG-8000 resulted in broader distribution with only 65% pores in the same range. Degradation resulted in scaffolds with narrower pore size distribution to have better retention of morphological and mechanical characteristics compared to scaffolds with broader distribution. Gravimetric and molecular weight studies also showed that scaffold degradation in both cases was only in initial stages after 6 months and PCL scaffolds had potential to be recommended for vascular tissue engineering applications. Copyright © 2013 Wiley Periodicals, Inc.

  8. Molecular Recognition in a Lattice Model: An Enumeration Study

    NASA Astrophysics Data System (ADS)

    Bogner, Thorsten; Degenhard, Andreas; Schmid, Friederike

    2004-12-01

    We investigate the mechanisms underlying selective molecular recognition of single heteropolymers at chemically structured planar surfaces. To this end, we study systems with two-letter (HP) lattice heteropolymers by exact enumeration techniques. Selectivity for a particular surface is defined by an adsorption energy criterion. We analyze the distributions of selective sequences and the role of mutations. A particularly important factor for molecular recognition is the small-scale structure on the polymers.

  9. Gamma Peptide Nucleic Acids: As Orthogonal Nucleic Acid Recognition Codes for Organizing Molecular Self-Assembly.

    PubMed

    Sacui, Iulia; Hsieh, Wei-Che; Manna, Arunava; Sahu, Bichismita; Ly, Danith H

    2015-07-08

    Nucleic acids are an attractive platform for organizing molecular self-assembly because of their specific nucleobase interactions and defined length scale. Routinely employed in the organization and assembly of materials in vitro, however, they have rarely been exploited in vivo, due to the concerns for enzymatic degradation and cross-hybridization with the host's genetic materials. Herein we report the development of a tight-binding, orthogonal, synthetically versatile, and informationally interfaced nucleic acid platform for programming molecular interactions, with implications for in vivo molecular assembly and computing. The system consists of three molecular entities: the right-handed and left-handed conformers and a nonhelical domain. The first two are orthogonal to each other in recognition, while the third is capable of binding to both, providing a means for interfacing the two conformers as well as the natural nucleic acid biopolymers (i.e., DNA and RNA). The three molecular entities are prepared from the same monomeric chemical scaffold, with the exception of the stereochemistry or lack thereof at the γ-backbone that determines if the corresponding oligo adopts a right-handed or left-handed helix, or a nonhelical motif. These conformers hybridize to each other with exquisite affinity, sequence selectivity, and level of orthogonality. Recognition modules as short as five nucleotides in length are capable of organizing molecular assembly.

  10. Molecular Recognition Involving Anthraquinone Derivatives and Molecular Clips

    NASA Astrophysics Data System (ADS)

    Alaparthi, Madhubabu

    In the past, we have demonstrated that 1,8-anthraquinone-18-crown-5 (1) and its heterocyclic derivatives act as luminescent hosts for a variety of cations of environmental and clinical concern. We report here a series of heteroatom-substituted macrocycles containing an anthraquinone moiety as a fluorescent signaling unit and a cyclic polyheteroether chain as the receptor. Sulfur, selenium, and tellurium derivatives of 1,8-anthraquinone-18-crown-5 (1) were synthesized by reacting sodium sulfide (Na2S), sodium selenide (Na2Se) and sodium telluride (Na2Te) with 1,8-bis(2-bromoethylethyleneoxy)anthracene - 9,10-dione in a 1:1 ratio (2,3, and 6). These sensors bind metal ions in a 1:1 ratio (7 and 8), and the optical properties of the new complexes were examined and the sulfur and selenium analogues show that selectivity for Pb(II) is markedly improved as compared to the oxygen analogue 1 which was competitive for Ca(II) ion. Selective reduction of 1 yields secondary alcohols where either one or both of the anthraquinone carbonyl groups has been reduced ( 15 and 9). A new mechanism for the fluorescence detection of metal cations in solution is introduced involving a unique keto-enol tautomerization. Reduction of 1 yields the doubly reduced secondary alcohol, 9. 9 acts as a chemodosimeter for Al(III) ion producing a strong blue emission due to the formation of the anthracene fluorophore, 10, via dehydration of the internal secondary alcohol in DMSO/aqueous solution. The enol form is not the most thermodynamically stable form under these conditions however, and slowly converts to the keto form 11.. Currently we are focusing on cucurbituril derivatives, also described as molecular clips due to their folded geometry used as molecular recognition hosts. We first investigated the synthesis and characterization of aromatic methoxy/catechol terminated cucurbituril units that act as hosts for small solvent molecules, such as CH2Cl2, CH3CN, DMF, and MeOH, through dual pi...H-C T

  11. Nucleic Acid Conjugated Nanomaterials for Enhanced Molecular Recognition

    PubMed Central

    Wang, Hao; Yang, Ronghua; Yang, Liu; Tan, Weihong

    2009-01-01

    Nucleic acids, whether designed or selected in vitro, play important roles in biosensing, medical diagnostics and therapy. Specifically, the conjugation of functional nucleic acid-based probe molecules and nanomaterials has resulted in an unprecedented improvement in the field of molecular recognition. With their unique physical and chemical properties, nanomaterials facilitate the sensing process and amplify the signal of recognition events. Thus, the coupling of nucleic acids with various nanomaterials opens up a promising future for molecular recognition. The literature offers a broad spectrum of recent advances in biosensing by employing different nano-platforms with designed nucleic acids, especially gold nanoparticles, carbon nanotubes, silica nanoparticles and quantum dots. The advantages of these novel combinations are discussed from the perspective of molecular recognition in chemistry, biology and medicine, along with the problems confronting future applications. PMID:19658387

  12. Chiral recognition applications of molecularly imprinted polymers: a critical review.

    PubMed

    Maier, Norbert M; Lindner, Wolfgang

    2007-09-01

    Molecular imprinting technology offers the unique opportunity to tailor chiral stationary phases with predefined chiral recognition properties by employing the enantiomers of interest as binding-site-forming templates. Added advantages, such as ease of preparation, chemical robustness, low-cost production, and the possibility of shaping molecularly imprinted polymers (MIPs) in various self-supporting formats, render them attractive materials for a broad range of chiral recognition applications. In this review a critical overview on recent developments in the field of MIP-based chiral recognition applications is given, focusing on separation techniques and molecular sensing. Inherent limitations associated with the use of enantioselective MIP materials in high-performance separation techniques are outlined, including binding site heterogeneity and slow mass transfer characteristics. The prospects of MIP materials as versatile recognition elements for the design of enantioselective sensor systems are highlighted.

  13. Molecular recognition by gold, silver and copper nanoparticles

    PubMed Central

    Tauran, Yannick; Brioude, Arnaud; Coleman, Anthony W; Rhimi, Moez; Kim, Beonjoom

    2013-01-01

    The intrinsic physical properties of the noble metal nanoparticles, which are highly sensitive to the nature of their local molecular environment, make such systems ideal for the detection of molecular recognition events. The current review describes the state of the art concerning molecular recognition of Noble metal nanoparticles. In the first part the preparation of such nanoparticles is discussed along with methods of capping and stabilization. A brief discussion of the three common methods of functionalization: Electrostatic adsorption; Chemisorption; Affinity-based coordination is given. In the second section a discussion of the optical and electrical properties of nanoparticles is given to aid the reader in understanding the use of such properties in molecular recognition. In the main section the various types of capping agents for molecular recognition; nucleic acid coatings, protein coatings and molecules from the family of supramolecular chemistry are described along with their numerous applications. Emphasis for the nucleic acids is on complementary oligonucleotide and aptamer recognition. For the proteins the recognition properties of antibodies form the core of the section. With respect to the supramolecular systems the cyclodextrins, calix[n]arenes, dendrimers, crown ethers and the cucurbitales are treated in depth. Finally a short section deals with the possible toxicity of the nanoparticles, a concern in public health. PMID:23977421

  14. Polymer side-chains as arms for molecular recognition

    NASA Astrophysics Data System (ADS)

    South, Clinton Ray

    This thesis describes research based on synthetic protocols, methodologies, and applications of polymers containing side-chain molecular recognition elements. The motivation for the thesis lies in the belief among many in the field that a strict covalent paradigm for polymer chemistry is reaching its limit. The use of molecular recognition, in lieu of covalent chemistry, potentially presents a path through the current limits of polymer science. The work described in the following chapters of this thesis is, at least in part, a testament to this proposal. The first two chapters present a basic introduction and survey of the fundamental noncovalent interactions that are ubiquitous in the research of supramolecular polymers and molecular recognition. A hierarchy of noncovalent interactions, molecular recognition, and self-assembly is outlined and discussed. Chapter 2 lays the foundation for the remaining chapters of this thesis by presenting several examples of prior work related specifically to the use of molecular recognition on the side-chains of polymers. The next two chapters present research focused on advancing the functionalization of polymers through molecular recognition. The goal of this research is primarily to develop a general polymer backbone that both site-specifically and strongly associates noncovalently with small molecular substrates. These chapters demonstrate that both architecturally controlled block copolymers and random terpolymers can accept a full load of different substrates without interference among distinct molecular recognition elements along the polymer backbone. Chapters 5 and 6 present a unique application of polymers containing molecular recognition elements, templated synthesis. Chapter 5 first discusses lessons learned from small molecule based templated synthesis in which a template and a substrate are held together by metal coordination and a subsequent bond forming reaction occurs. Ultimately, the results of this chapter

  15. Molecular Recognition of Alpha-Neurotoxins

    DTIC Science & Technology

    1990-11-30

    representing each of the Bgt loops (11,12). In these investigations, we have developed a new approach for studying the details of protein - protein ...recognition. Each of the active peptides of one protein Is allowed to Interact with each of the active peptides of the other protein . Based on relative...described (12) Bgt and its synthetic peptides were labeled with iodine-125 using the chloramine -T method (114). Radioiodinated materi~ls were used

  16. Molecular scaffold analysis of natural products databases in the public domain.

    PubMed

    Yongye, Austin B; Waddell, Jacob; Medina-Franco, José L

    2012-11-01

    Natural products represent important sources of bioactive compounds in drug discovery efforts. In this work, we compiled five natural products databases available in the public domain and performed a comprehensive chemoinformatic analysis focused on the content and diversity of the scaffolds with an overview of the diversity based on molecular fingerprints. The natural products databases were compared with each other and with a set of molecules obtained from in-house combinatorial libraries, and with a general screening commercial library. It was found that publicly available natural products databases have different scaffold diversity. In contrast to the common concept that larger libraries have the largest scaffold diversity, the largest natural products collection analyzed in this work was not the most diverse. The general screening library showed, overall, the highest scaffold diversity. However, considering the most frequent scaffolds, the general reference library was the least diverse. In general, natural products databases in the public domain showed low molecule overlap. In addition to benzene and acyclic compounds, flavones, coumarins, and flavanones were identified as the most frequent molecular scaffolds across the different natural products collections. The results of this work have direct implications in the computational and experimental screening of natural product databases for drug discovery. © 2012 John Wiley & Sons A/S.

  17. Molecular Basis for Bcl-2 Homology 3 Domain Recognition in the Bcl-2 Protein Family

    PubMed Central

    Moroy, Gautier; Martin, Elyette; Dejaegere, Annick; Stote, Roland H.

    2009-01-01

    The proteins of the Bcl-2 family are important regulators of apoptosis, or programmed cell death. These proteins regulate this fundamental biological process via the formation of heterodimers involving both pro- and anti-apoptotic family members. Disruption of the balance between anti- and pro-apoptotic Bcl-2 proteins is the cause of numerous pathologies. Bcl-xl, an anti-apoptotic protein of this family, is known to form heterodimers with multiple pro-apoptotic proteins, such as Bad, Bim, Bak, and Bid. To elucidate the molecular basis of this recognition process, we used molecular dynamics simulations coupled with the Molecular Mechanics/Poisson-Boltzmann Surface Area approach to identify the amino acids that make significant energetic contributions to the binding free energy of four complexes formed between Bcl-xl and pro-apoptotic Bcl-2 homology 3 peptides. A fifth protein-peptide complex composed of another anti-apoptotic protein, Bcl-w, in complex with the peptide from Bim was also studied. The results identified amino acids of both the anti-apoptotic proteins as well as the Bcl-2 homology 3 (BH3) domains of the pro-apoptotic proteins that make strong, recurrent interactions in the protein complexes. The calculations show that the two anti-apoptotic proteins, Bcl-xl and Bcl-w, share a similar recognition mechanism. Our results provide insight into the molecular basis for the promiscuous nature of this molecular recognition process by members of the Bcl-2 protein family. These amino acids could be targeted in the design of new mimetics that serve as scaffolds for new antitumoral molecules. PMID:19293158

  18. Creating molecular macrocycles for anion recognition

    PubMed Central

    2016-01-01

    Summary The creation and functionality of new classes of macrocycles that are shape persistent and can bind anions is described. The genesis of triazolophane macrocycles emerges out of activity surrounding 1,2,3-triazoles made using click chemistry; and the same triazoles are responsible for anion capture. Mistakes made and lessons learnt in anion recognition provide deeper understanding that, together with theory, now provides for computer-aided receptor design. The lessons are acted upon in the creation of two new macrocycles. First, cyanostars are larger and like to capture large anions. Second is tricarb, which also favors large anions but shows a propensity to self-assemble in an orderly and stable manner, laying a foundation for future designs of hierarchical nanostructures. PMID:27340452

  19. Molecular Handshake: Recognition through Weak Noncovalent Interactions

    ERIC Educational Resources Information Center

    Murthy, Parvathi S.

    2006-01-01

    The weak noncovalent interactions between substances, the handshake in the form of electrostatic interactions, van der Waals' interactions or hydrogen bonding is universal to all living and nonliving matter. They significantly influence the molecular and bulk properties and behavior of matter. Their transient nature affects chemical reactions and…

  20. Molecular Handshake: Recognition through Weak Noncovalent Interactions

    ERIC Educational Resources Information Center

    Murthy, Parvathi S.

    2006-01-01

    The weak noncovalent interactions between substances, the handshake in the form of electrostatic interactions, van der Waals' interactions or hydrogen bonding is universal to all living and nonliving matter. They significantly influence the molecular and bulk properties and behavior of matter. Their transient nature affects chemical reactions and…

  1. Associative Pattern Recognition Through Macro-molecular Self-Assembly

    NASA Astrophysics Data System (ADS)

    Zhong, Weishun; Schwab, David J.; Murugan, Arvind

    2017-05-01

    We show that macro-molecular self-assembly can recognize and classify high-dimensional patterns in the concentrations of N distinct molecular species. Similar to associative neural networks, the recognition here leverages dynamical attractors to recognize and reconstruct partially corrupted patterns. Traditional parameters of pattern recognition theory, such as sparsity, fidelity, and capacity are related to physical parameters, such as nucleation barriers, interaction range, and non-equilibrium assembly forces. Notably, we find that self-assembly bears greater similarity to continuous attractor neural networks, such as place cell networks that store spatial memories, rather than discrete memory networks. This relationship suggests that features and trade-offs seen here are not tied to details of self-assembly or neural network models but are instead intrinsic to associative pattern recognition carried out through short-ranged interactions.

  2. Molecular Recognition Directed Self-Assembly of Supramolecular Polymers

    DTIC Science & Technology

    1994-06-30

    SUPRAMOLECULAR POLYMERS by V. Percec, J. Heck, G. Johansson, D. Tomazos, M. Kawasumi and G. Ungar Published in the J. Macromol. SOi: Part A: Pure...W.asetaqIom OC JOS0l 4 TITE AN SUBITLES. FUNDING NUMBERS Molecular Recognition Directed Self-Assembly of Suprainolecular Polymers N00014-89--J-1828 6. AUTHOR(S...comparison between various supramolecular (generated via H-bonding, iions) and molecular " polymer backbones" will be made. The present limitations

  3. Virtual screening and scaffold hopping based on GRID molecular interaction fields.

    PubMed

    Ahlström, Marie M; Ridderström, Marianne; Luthman, Kristina; Zamora, Ismael

    2005-01-01

    In this study, a set of strategies for structure-based design using GRID molecular interaction fields (MIFs) to derive a pharmacophoric representation of a protein is reported. Thrombin, one of the key enzymes involved in the blood coagulation cascade, was chosen as the model system since abundant published experimental data are available related to both crystal structures and structurally diverse sets of inhibitors. First, a virtual screening methodology was developed either using a pharmacophore representation of the protein based on GRID MIFs or using GRID MIFs from the 3D structure of a set of chosen thrombin inhibitors. The search was done in a 3D multiconformation version of the Available Chemical Directory (ACD) database, which had been spiked with 262 known thrombin inhibitors (multiple conformers available per compound). The model managed to find 80% of the known thrombin inhibitors among the 74,291 conformers in the ACD by only searching 5% of the database; hence, a 15-fold enrichment of the library was achieved. Second, a scaffold hopping methodology was developed using GRID MIFs, giving the scaffold interaction pattern and the shape of the scaffold, together with the distance between the anchor points. The scaffolds reported by Dolle in the Journal of Combinatorial Chemistry summaries (2000 and 2001) and scaffolds built or derived from ligands cocomplexed with the thrombin enzyme were parameterized using a new set of descriptors and saved into a searchable database. The scaffold representation from the database was then compared to a template scaffold (from a thrombin crystal structure), and the thrombin-derived scaffolds included in the database were found among the top solutions. To validate the usefulness of the methodology to replace the template scaffold, the entire molecule was built (scaffold and side chains) and the resulting compounds were docked into the active site of thrombin. The docking solutions showed the same binding pattern as the

  4. Molecular recognition of agonist ligands by RXRs.

    PubMed

    Egea, Pascal F; Mitschler, André; Moras, Dino

    2002-05-01

    The nuclear receptor RXR is an obligate partner in many signal transduction pathways. We report the high-resolution structures of two complexes of the human RXRalpha ligand-binding domain specifically bound to two different and chemically unrelated agonist compounds: docosa hexaenoic acid, a natural derivative of eicosanoic acid, present in mammalian cells and recently identified as a potential endogenous RXR ligand in the mouse brain, and the synthetic ligand BMS 649. In both structures the RXR-ligand-binding domain forms homodimers and exhibits the active conformation previously observed with 9-cis-RA. Analysis of the differences in ligand-protein contacts (predominantly van der Waals forces) and binding cavity geometries and volumes for the several agonist-bound RXR structures clarifies the structural features important for ligand recognition. The L-shaped ligand-binding pocket adapts to the diverse ligands, especially at the level of residue N306, which might thus constitute a new target for drug-design. Despite its highest affinity 9-cis-RA displays the lowest number of ligand-protein contacts. These structural results support the idea that docosa hexaenoic acid and related fatty acids could be natural agonists of RXRs and question the real nature of the endogenous ligand(s) in mammalian cells.

  5. Molecular Engineering of Supramolecular Scaffold Coatings that Can Reduce Static Platelet Adhesion

    PubMed Central

    Kumar, Aryavarta M. S.; Sivakova, Sona; Fox, Justin D.; Green, Jennifer E.; Marchant, Roger E.; Rowan, Stuart J.

    2008-01-01

    Novel supramolecular coatings that make use of low molecular weight ditopic monomers with guanine end groups are studied using fluid tapping AFM. These molecules assemble on highly oriented pyrolytic graphite (HOPG) from aqueous solutions to form nano-sized banding structures whose sizes can be systematically tuned at the nano-scale by tailoring the molecular structure of the monomers. The nature of the self-assembly in these systems has been studied through a combination of the self-assembly of structural derivatives and molecular modeling. Furthermore, we introduce the concept of using these molecular assemblies as scaffolds to organize functional groups on the surface. As a first demonstrationof this concept, scaffold monomers that contain a monomethyl triethyleneglycol branch were used to organize these “functional” units on a HOPG surface. These supramolecular grafted assemblies have been shown to be stable in biologically-relevant environments and even have the ability to significantly reduce static platelet adhesion. PMID:18177047

  6. A unified lead-oriented synthesis of over fifty molecular scaffolds.

    PubMed

    Doveston, Richard G; Tosatti, Paolo; Dow, Mark; Foley, Daniel J; Li, Ho Yin; Campbell, Amanda J; House, David; Churcher, Ian; Marsden, Stephen P; Nelson, Adam

    2015-01-21

    Controlling the properties of lead molecules is critical in drug discovery, but sourcing large numbers of lead-like compounds for screening collections is a major challenge. A unified synthetic approach is described that enabled the synthesis of 52 diverse lead-like molecular scaffolds from a minimal set of 13 precursors. The divergent approach exploited a suite of robust, functional group-tolerant transformations. Crucially, after derivatisation, these scaffolds would target significant lead-like chemical space, and complement commercially-available compounds.

  7. Monolithic molecularly imprinted cryogel for lysozyme recognition.

    PubMed

    Rabieizadeh, Mohammadmahdi; Kashefimofrad, Seyed Mohammadreza; Naeimpoor, Fereshteh

    2014-10-01

    The application of molecularly imprinted polymers in the selective adsorption of macromolecules such as proteins by monolithic protein-imprinted columns requires a macroporous structure, which can be provided by cryogelation at low temperature in which the formation of ice crystals gives a porous structure to the molecularly imprinted polymer. In this study, we applied this technique to synthesize lysozyme-imprinted polyacrylamide cryogels containing 8% w/v of total monomers and 0.3% w/v of lysozyme. The synthesized cryogel was sponge-like and elastic with very fast swelling and reshaping properties, showing a swelling ratio of 24.5 ± 3 and gel fraction yield of about 72%. It showed an imprinting effect of 1.58 and a separation factor of 1.37 for cytochrome c as the competing protein. Adsorption studies on the cryogel revealed that it follows the Langmuir isotherm, with a maximum theoretical adsorption capacity of 36.3 mg lysozyme per gram of cryogel. Additionally, it was shown that a salt-free rebinding solution at low flow rate and pH = 7.0 is favorable for lysozyme rebinding. This kind of monolithic column promises a wide range of application in separation of various biomolecules due to its preparation simplicity, good rebinding characteristics, and macroporosity.

  8. Molecular Recognition Effects in Atomistic Models of Imprinted Polymers

    PubMed Central

    Dourado, Eduardo M. A.; Herdes, Carmelo; van Tassel, Paul R.; Sarkisov, Lev

    2011-01-01

    In this article we present a model for molecularly imprinted polymers, which considers both complexation processes in the pre-polymerization mixture and adsorption in the imprinted structures within a single consistent framework. As a case study we investigate MAA/EGDMA polymers imprinted with pyrazine and pyrimidine. A polymer imprinted with pyrazine shows substantial selectivity towards pyrazine over pyrimidine, thus exhibiting molecular recognition, whereas the pyrimidine imprinted structure shows no preferential adsorption of the template. Binding sites responsible for the molecular recognition of pyrazine involve one MAA molecule and one EGDMA molecule, forming associations with the two functional groups of the pyrazine molecule. Presence of these specific sites in the pyrazine imprinted system and lack of the analogous sites in the pyrimidine imprinted system is directly linked to the complexation processes in the pre-polymerization solution. These processes are quite different for pyrazine and pyrimidine as a result of both enthalpic and entropic effects. PMID:21954325

  9. Molecular recognition effects in atomistic models of imprinted polymers.

    PubMed

    Dourado, Eduardo M A; Herdes, Carmelo; van Tassel, Paul R; Sarkisov, Lev

    2011-01-01

    In this article we present a model for molecularly imprinted polymers, which considers both complexation processes in the pre-polymerization mixture and adsorption in the imprinted structures within a single consistent framework. As a case study we investigate MAA/EGDMA polymers imprinted with pyrazine and pyrimidine. A polymer imprinted with pyrazine shows substantial selectivity towards pyrazine over pyrimidine, thus exhibiting molecular recognition, whereas the pyrimidine imprinted structure shows no preferential adsorption of the template. Binding sites responsible for the molecular recognition of pyrazine involve one MAA molecule and one EGDMA molecule, forming associations with the two functional groups of the pyrazine molecule. Presence of these specific sites in the pyrazine imprinted system and lack of the analogous sites in the pyrimidine imprinted system is directly linked to the complexation processes in the pre-polymerization solution. These processes are quite different for pyrazine and pyrimidine as a result of both enthalpic and entropic effects.

  10. Modulating mechanical behaviour of 3D-printed cartilage-mimetic PCL scaffolds: influence of molecular weight and pore geometry.

    PubMed

    Olubamiji, Adeola D; Izadifar, Zohreh; Si, Jennifer L; Cooper, David M L; Eames, B Frank; Chen, Daniel X B

    2016-06-22

    Three-dimensional (3D)-printed poly(ε)-caprolactone (PCL)-based scaffolds are increasingly being explored for cartilage tissue engineering (CTE) applications. However, ensuring that the mechanical properties of these PCL-based constructs are comparable to that of articular cartilage that they are meant to regenerate is an area that has been under-explored. This paper presents the effects of PCL's molecular weight (MW) and scaffold's pore geometric configurations; strand size (SZ), strand spacing (SS), and strand orientation (SO), on mechanical properties of 3D-printed PCL scaffolds. The results illustrate that MW has significant effect on compressive moduli and yield strength of 3D-printed PCL scaffolds. Specifically, PCL with MW of 45 K was a more feasible choice for fabrication of visco-elastic, flexible and load-bearing PCL scaffolds. Furthermore, pore geometric configurations; SZ, SS, and SO, all significantly affect on tensile moduli of scaffolds. However, only SZ and SS have statistically significant effects on compressive moduli and porosity of these scaffolds. That said, inverse linear relationship was observed between porosity and mechanical properties of 3D-printed PCL scaffolds in Pearson's correlation test. Altogether, this study illustrates that modulating MW of PCL and pore geometrical configurations of the scaffolds enabled design and fabrication of PCL scaffolds with mechanical and biomimetic properties that better mimic mechanical behaviour of human articular cartilage. Thus, the modulated PCL scaffold proposed in this study is a framework that offers great potentials for CTE applications.

  11. A Molecular Mechanics Analysis of Molecular Recognition by Cyclodextrin Mimics of Alpha-Chymotrypsin

    DTIC Science & Technology

    1989-05-26

    Recognition By Cyclodextrin Mimics of Alpha-Chymotrypsin i by C.A. Venanzi. P.M. Canzius, Z. Zhang, and J.D. Bunce LT IC To Be Published in CLECTE JUN 0 51...Clasification) A Molecular Mechanics Analysis of Molecular Recognition By Cyclodextrin Mimics of Alpha-Chymotrypsin. 12. PERSONAL AUTHOR(S) C.A. Venanzil... CYCLODEXTRIN MIMICS OF 0( -CHYMOTRYPSIN Carol A. Venanzi1 , Preston M. Canzius, Zhifeng Zhang, and Jeffrey D. Bunce Department of Chemical Engineering

  12. Recent Progress in Molecular Recognition Imaging Using Atomic Force Microscopy.

    PubMed

    Senapati, Subhadip; Lindsay, Stuart

    2016-03-15

    Atomic force microscopy (AFM) is an extremely powerful tool in the field of bionanotechnology because of its ability to image single molecules and make measurements of molecular interaction forces with piconewton sensitivity. It works in aqueous media, enabling studies of molecular phenomenon taking place under physiological conditions. Samples can be imaged in their near-native state without any further modifications such as staining or tagging. The combination of AFM imaging with the force measurement added a new feature to the AFM technique, that is, molecular recognition imaging. Molecular recognition imaging enables mapping of specific interactions between two molecules (one attached to the AFM tip and the other to the imaging substrate) by generating simultaneous topography and recognition images (TREC). Since its discovery, the recognition imaging technique has been successfully applied to different systems such as antibody-protein, aptamer-protein, peptide-protein, chromatin, antigen-antibody, cells, and so forth. Because the technique is based on specific binding between the ligand and receptor, it has the ability to detect a particular protein in a mixture of proteins or monitor a biological phenomenon in the native physiological state. One key step for recognition imaging technique is the functionalization of the AFM tips (generally, silicon, silicon nitrides, gold, etc.). Several different functionalization methods have been reported in the literature depending on the molecules of interest and the material of the tip. Polyethylene glycol is routinely used to provide flexibility needed for proper binding as a part of the linker that carries the affinity molecule. Recently, a heterofunctional triarm linker has been synthesized and successfully attached with two different affinity molecules. This novel linker, when attached to AFM tip, helped to detect two different proteins simultaneously from a mixture of proteins using a so-called "two

  13. Molecularly imprinted polymers immobilized on 3D printed scaffolds as novel solid phase extraction sorbent for metergoline.

    PubMed

    De Middeleer, Gilke; Dubruel, Peter; De Saeger, Sarah

    2017-09-15

    In the present work, a novel solid phase extraction (SPE) sorbent was developed based on molecularly imprinted polymers (MIPs) immobilized on 3D-printed scaffolds using polymer networks as MIP-immobilizing layer. MIPs were produced by precipitation polymerization in acetonitrile (ACN) using methacrylic acid (MAA) as functional monomer, trimethylolpropane trimethacrylate (TRIM) as crosslinker and metergoline as model template which allows final recognition of ergot alkaloid mycotoxins. Scanning electron microscopy (SEM) and dynamic light scattering (DLS) analyses showed an average MIP particle size of 457 ± 145 nm. Functional MIP analysis revealed dissociation constants (KD) of 0.29 and 38.90 μM for high and low affinity binding sites respectively. Subsequently, crosslinking of polymer network building blocks was applied as MIP immobilization method on poly-ε-caprolactone (PCL) which was selected as polymer model. Methodology optimization and subsequent evaluation were first realized on 2D PCL surfaces. Based on analyses such as optical evaluation of MIP availability after immobilization through SEM and depth profilometry, an optimal polymer network building block concentration of 7.5 w/w% was selected. In a final part, transfer of MIP immobilization to 3D PCL scaffolds was successfully realized. Functional analysis showed that the newly developed SPE sorbents were able to rebind 44.87 ± 8.30% of a 1 μM metergoline solution. In conclusion, a new type of SPE sorbent was developed for the detection of metergoline by the use of MIP-functionalized polymer scaffolds. The applied technology opens up future possibilities for the extraction of a broad range of components such as other mycotoxins. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Tailoring the morphology of high molecular weight PLLA scaffolds through bioglass addition.

    PubMed

    Barroca, N; Daniel-da-Silva, A L; Vilarinho, P M; Fernandes, M H V

    2010-09-01

    Thermally induced phase separation (TIPS) has proven to be a suitable method for the preparation of porous structures for tissue engineering applications, and particular attention has been paid to increasing the pore size without the use of possible toxic surfactants. Within this context, an alternative method to control the porosity of polymeric scaffolds via the combination with a bioglass is proposed in this work. The addition of a bioactive glass from the 3CaO x P2O5-MgO-SiO2 system enables the porous structure of high molecular weight poly(l-lactic) acid (PLLA) scaffolds prepared by TIPS to be tailored. Bioglass acts as a nucleating catalyst agent of the PLLA matrix, promoting its crystallization, and the glass solubility controls the pore size. A significant increase in the pore size is observed as the bioglass content increases and scaffolds with large pore size (approximately 150 microm) can be prepared. In addition, the bioactive character of the scaffolds is proved by in vitro tests in synthetic plasma. The importance of this approach resides on the combination of the ability to tailor the porosity of polymeric scaffolds via the tunable solubility of bioglasses, without the use of toxic surfactants, leading to a composite structure with suitable properties for bone tissue engineering applications.

  15. Characterization of Monobody Scaffold Interactions with Ligand via Force Spectroscopy and Steered Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Cheung, Luthur Siu-Lun; Shea, Daniel J.; Nicholes, Nathan; Date, Amol; Ostermeier, Marc; Konstantopoulos, Konstantinos

    2015-02-01

    Monobodies are antibody alternatives derived from fibronectin that are thermodynamically stable, small in size, and can be produced in bacterial systems. Monobodies have been engineered to bind a wide variety of target proteins with high affinity and specificity. Using alanine-scanning mutagenesis simulations, we identified two scaffold residues that are critical to the binding interaction between the monobody YS1 and its ligand, maltose-binding protein (MBP). Steered molecular dynamics (SMD) simulations predicted that the E47A and R33A mutations in the YS1 scaffold substantially destabilize the YS1-MBP interface by reducing the bond rupture force and the lifetime of single hydrogen bonds. SMD simulations further indicated that the R33A mutation weakens the hydrogen binding between all scaffold residues and MBP and not just between R33 and MBP. We validated the simulation data and characterized the effects of mutations on YS1-MBP binding by using single-molecule force spectroscopy and surface plasmon resonance. We propose that interfacial stability resulting from R33 of YS1 stacking with R344 of MBP synergistically stabilizes both its own bond and the interacting scaffold residues of YS1. Our integrated approach improves our understanding of the monobody scaffold interactions with a target, thus providing guidance for the improved engineering of monobodies.

  16. Assessment of scaffold hopping efficiency by use of molecular interaction fingerprints.

    PubMed

    Venhorst, Jennifer; Núñez, Sara; Terpstra, Jan Willem; Kruse, Chris G

    2008-06-12

    A novel scoring algorithm based on molecular interaction fingerprints (IFPs) was comparatively evaluated in its scaffold hopping efficiency against four virtual screening standards (GlideXP, Gold, ROCS, and a Bayesian classifier). Decoy databases for the two targets under examination, adenosine deaminase and retinoid X receptor alpha, were obtained from the Directory of Useful Decoys and were further enriched with approximately 5% of active ligands. Structure and ligand-based methods were used to generate the ligand poses, and a Tanimoto metric was chosen for the calculation of the similarity interaction fingerprint between the reference ligand and the screening database. Database enrichments were found to strongly depend on the pose generator algorithm. In spite of these dependencies, enrichments using molecular IFPs were comparable to those obtained with GlideXP, Gold, ROCS, and the Bayesian classifier. More interestingly, the molecular IFP scoring algorithm outperformed these methods at scaffold hopping enrichment, regardless of the pose generator algorithm.

  17. Molecular threading and tunable molecular recognition on DNA origami nanostructures.

    PubMed

    Wu, Na; Czajkowsky, Daniel M; Zhang, Jinjin; Qu, Jianxun; Ye, Ming; Zeng, Dongdong; Zhou, Xingfei; Hu, Jun; Shao, Zhifeng; Li, Bin; Fan, Chunhai

    2013-08-21

    The DNA origami technology holds great promise for the assembly of nanoscopic technological devices and studies of biochemical reactions at the single-molecule level. For these, it is essential to establish well controlled attachment of functional materials to predefined sites on the DNA origami nanostructures for reliable measurements and versatile applications. However, the two-sided nature of the origami scaffold has shown limitations in this regard. We hypothesized that holes of the commonly used two-dimensional DNA origami designs are large enough for the passage of single-stranded (ss)-DNA. Sufficiently long ssDNA initially located on one side of the origami should thus be able to "thread" to the other side through the holes in the origami sheet. By using an origami sheet attached with patterned biotinylated ssDNA spacers and monitoring streptavidin binding with atomic force microscopic (AFM) imaging, we provide unambiguous evidence that the biotin ligands positioned on one side have indeed threaded through to the other side. Our finding reveals a previously overlooked critical design feature that should provide new interpretations to previous experiments and new opportunities for the construction of origami structures with new functional capabilities.

  18. The tachykinin tale: molecular recognition in a historical perspective.

    PubMed

    Werge, Thomas

    2007-01-01

    Crystallography, mutational mapping and crosslinking are but a few of the experimental techniques that have helped to elucidate the underlying principles of molecular recognition between macromolecules and to improve our understanding of the evolution of the structure-activity relationship (SAR). While this development has been particularly successful for small and rigid ligands and substrates that bind to larger hydrophilic biomolecules, our understanding of membrane-embedded proteins is still rather limited. This review uses the example of the neuropeptide family of tachykinins and their G-protein coupled receptors (GPCR) to present how complementary experimental strategies over the past decades have nourished and modified conceptual models of the structural requisites of molecular recognition and function. Given the little we know, the pertinent question is how we proceed from here.

  19. Programmable molecular recognition based on the geometry of DNA nanostructures

    NASA Astrophysics Data System (ADS)

    Woo, Sungwook; Rothemund, Paul W. K.

    2011-08-01

    From ligand-receptor binding to DNA hybridization, molecular recognition plays a central role in biology. Over the past several decades, chemists have successfully reproduced the exquisite specificity of biomolecular interactions. However, engineering multiple specific interactions in synthetic systems remains difficult. DNA retains its position as the best medium with which to create orthogonal, isoenergetic interactions, based on the complementarity of Watson-Crick binding. Here we show that DNA can be used to create diverse bonds using an entirely different principle: the geometric arrangement of blunt-end stacking interactions. We show that both binary codes and shape complementarity can serve as a basis for such stacking bonds, and explore their specificity, thermodynamics and binding rules. Orthogonal stacking bonds were used to connect five distinct DNA origami. This work, which demonstrates how a single attractive interaction can be developed to create diverse bonds, may guide strategies for molecular recognition in systems beyond DNA nanostructures.

  20. Method of assembly of molecular-sized nets and scaffolding

    DOEpatents

    Michl, Josef; Magnera, Thomas F.; David, Donald E.; Harrison, Robin M.

    1999-01-01

    The present invention relates to methods and starting materials for forming molecular-sized grids or nets, or other structures based on such grids and nets, by creating molecular links between elementary molecular modules constrained to move in only two directions on an interface or surface by adhesion or bonding to that interface or surface. In the methods of this invention, monomers are employed as the building blocks of grids and more complex structures. Monomers are introduced onto and allowed to adhere or bond to an interface. The connector groups of adjacent adhered monomers are then polymerized with each other to form a regular grid in two dimensions above the interface. Modules that are not bound or adhered to the interface are removed prior to reaction of the connector groups to avoid undesired three-dimensional cross-linking and the formation of non-grid structures. Grids formed by the methods of this invention are useful in a variety of applications, including among others, for separations technology, as masks for forming regular surface structures (i.e., metal deposition) and as templates for three-dimensional molecular-sized structures.

  1. Method of assembly of molecular-sized nets and scaffolding

    DOEpatents

    Michl, J.; Magnera, T.F.; David, D.E.; Harrison, R.M.

    1999-03-02

    The present invention relates to methods and starting materials for forming molecular-sized grids or nets, or other structures based on such grids and nets, by creating molecular links between elementary molecular modules constrained to move in only two directions on an interface or surface by adhesion or bonding to that interface or surface. In the methods of this invention, monomers are employed as the building blocks of grids and more complex structures. Monomers are introduced onto and allowed to adhere or bond to an interface. The connector groups of adjacent adhered monomers are then polymerized with each other to form a regular grid in two dimensions above the interface. Modules that are not bound or adhered to the interface are removed prior to reaction of the connector groups to avoid undesired three-dimensional cross-linking and the formation of non-grid structures. Grids formed by the methods of this invention are useful in a variety of applications, including among others, for separations technology, as masks for forming regular surface structures (i.e., metal deposition) and as templates for three-dimensional molecular-sized structures. 9 figs.

  2. Molecularly imprinted polymers for histamine recognition in aqueous environment.

    PubMed

    Trikka, Foteini A; Yoshimatsu, Keiichi; Ye, Lei; Kyriakidis, Dimitrios A

    2012-11-01

    Molecularly imprinted polymers (MIP) for histamine using methacrylic acid were developed and recognition mechanisms were thoroughly characterized for the first time in this study. The binding affinity of imprinted polymer with structurally related compounds was studied in organic and aqueous media, at various conditions. In organic media, MIP was found to bind histamine two and six times more than ranitidine and fluoxetine, respectively, whereas higher selectivity was observed in the case of dimentidene or disodium cromoglycate. The specific binding sites of MIP recognized histamine over L-histidine in aqueous conditions, while higher affinity for histamine compared to ranitidine, disodium cromoglycate, putrescine and to a putrescine analogue was observed. A combination of NMR and UV spectroscopy analyses for investigation of imprinting and recognition properties revealed that strong specific interactions between the functional monomer and histamine in the prepolymerization and in the aqueous solutions were probably responsible for histamine recognition. The preparation of histamine MIPs and elucidation of imprinting and recognition mechanism may serve as useful insight for future application of MIPs.

  3. Molecular recognition of HER-1 in whole-blood samples.

    PubMed

    Moldoveanu, Iuliana; Stanciu Gavan, Camelia; Stefan-van Staden, Raluca-Ioana

    2014-11-01

    Multimode sensing was proposed for molecular screening and recognition of HER-1 in whole blood. The tools used for molecular recognition were platforms based on nanostructured materials such as the complex of Mn(III) with meso-tetra (4-carboxyphenyl) porphyrin, and maltodextrin (dextrose equivalence between 4 and 7), immobilized in diamond paste, graphite paste or C60 fullerene paste. The identification of HER-1 in whole-blood samples, at molecular level, is performed using stochastic mode and is followed by the quantification of it using stochastic and differential pulse voltammetry modes. HER-1 can be identified in the concentration range between 280 fg/ml and 4.86 ng/ml using stochastic mode, this making possible the early detection of cancers such as gastrointestinal, pancreatic and lung cancers. The recovery tests performed using whole-blood samples proved that the platforms can be used for identification and quantification of HER-1 with high sensitivity and reliability in such samples, these making them good molecular screening tools. Copyright © 2014 John Wiley & Sons, Ltd.

  4. Orchestration of Molecular Information through Higher Order Chemical Recognition

    NASA Astrophysics Data System (ADS)

    Frezza, Brian M.

    Broadly defined, higher order chemical recognition is the process whereby discrete chemical building blocks capable of specifically binding to cognate moieties are covalently linked into oligomeric chains. These chains, or sequences, are then able to recognize and bind to their cognate sequences with a high degree of cooperativity. Principally speaking, DNA and RNA are the most readily obtained examples of this chemical phenomenon, and function via Watson-Crick cognate pairing: guanine pairs with cytosine and adenine with thymine (DNA) or uracil (RNA), in an anti-parallel manner. While the theoretical principles, techniques, and equations derived herein apply generally to any higher-order chemical recognition system, in practice we utilize DNA oligomers as a model-building material to experimentally investigate and validate our hypotheses. Historically, general purpose information processing has been a task limited to semiconductor electronics. Molecular computing on the other hand has been limited to ad hoc approaches designed to solve highly specific and unique computation problems, often involving components or techniques that cannot be applied generally in a manner suitable for precise and predictable engineering. Herein, we provide a fundamental framework for harnessing high-order recognition in a modular and programmable fashion to synthesize molecular information process networks of arbitrary construction and complexity. This document provides a solid foundation for routinely embedding computational capability into chemical and biological systems where semiconductor electronics are unsuitable for practical application.

  5. Magnetic molecularly imprinted polymer for aspirin recognition and controlled release

    NASA Astrophysics Data System (ADS)

    Kan, Xianwen; Geng, Zhirong; Zhao, Yao; Wang, Zhilin; Zhu, Jun-Jie

    2009-04-01

    Core-shell structural magnetic molecularly imprinted polymers (magnetic MIPs) with combined properties of molecular recognition and controlled release were prepared and characterized. Magnetic MIPs were synthesized by the co-polymerization of methacrylic acid (MAA) and trimethylolpropane trimethacrylate (TRIM) around aspirin (ASP) at the surface of double-bond-functionalized Fe3O4 nanoparticles in chloroform. The obtained spherical magnetic MIPs with diameters of about 500 nm had obvious superparamagnetism and could be separated quickly by an external magnetic field. Binding experiments were carried out to evaluate the properties of magnetic MIPs and magnetic non-molecularly imprinted polymers (magnetic NIPs). The results demonstrated that the magnetic MIPs had high adsorption capacity and selectivity to ASP. Moreover, release profiles and release rate of ASP from the ASP-loaded magnetic MIPs indicated that the magnetic MIPs also had potential applications in drug controlled release.

  6. Water mediation in protein folding and molecular recognition.

    PubMed

    Levy, Yaakov; Onuchic, José N

    2006-01-01

    Water is essential for life in many ways, and without it biomolecules might no longer truly be biomolecules. In particular, water is important to the structure, stability, dynamics, and function of biological macromolecules. In protein folding, water mediates the collapse of the chain and the search for the native topology through a funneled energy landscape. Water actively participates in molecular recognition by mediating the interactions between binding partners and contributes to either enthalpic or entropic stabilization. Accordingly, water must be included in recognition and structure prediction codes to capture specificity. Thus water should not be treated as an inert environment, but rather as an integral and active component of biomolecular systems, where it has both dynamic and structural roles. Focusing on water sheds light on the physics and function of biological machinery and self-assembly and may advance our understanding of the natural design of proteins and nucleic acids.

  7. A molecular mechanism of chaperone-client recognition

    PubMed Central

    He, Lichun; Sharpe, Timothy; Mazur, Adam; Hiller, Sebastian

    2016-01-01

    Molecular chaperones are essential in aiding client proteins to fold into their native structure and in maintaining cellular protein homeostasis. However, mechanistic aspects of chaperone function are still not well understood at the atomic level. We use nuclear magnetic resonance spectroscopy to elucidate the mechanism underlying client recognition by the adenosine triphosphate-independent chaperone Spy at the atomic level and derive a structural model for the chaperone-client complex. Spy interacts with its partially folded client Im7 by selective recognition of flexible, locally frustrated regions in a dynamic fashion. The interaction with Spy destabilizes a partially folded client but spatially compacts an unfolded client conformational ensemble. By increasing client backbone dynamics, the chaperone facilitates the search for the native structure. A comparison of the interaction of Im7 with two other chaperones suggests that the underlying principle of recognizing frustrated segments is of a fundamental nature. PMID:28138538

  8. Molecular basis for peptidoglycan recognition by a bactericidal lectin.

    PubMed

    Lehotzky, Rebecca E; Partch, Carrie L; Mukherjee, Sohini; Cash, Heather L; Goldman, William E; Gardner, Kevin H; Hooper, Lora V

    2010-04-27

    RegIII proteins are secreted C-type lectins that kill Gram-positive bacteria and play a vital role in antimicrobial protection of the mammalian gut. RegIII proteins bind their bacterial targets via interactions with cell wall peptidoglycan but lack the canonical sequences that support calcium-dependent carbohydrate binding in other C-type lectins. Here, we use NMR spectroscopy to determine the molecular basis for peptidoglycan recognition by HIP/PAP, a human RegIII lectin. We show that HIP/PAP recognizes the peptidoglycan carbohydrate backbone in a calcium-independent manner via a conserved "EPN" motif that is critical for bacterial killing. While EPN sequences govern calcium-dependent carbohydrate recognition in other C-type lectins, the unusual location and calcium-independent functionality of the HIP/PAP EPN motif suggest that this sequence is a versatile functional module that can support both calcium-dependent and calcium-independent carbohydrate binding. Further, we show HIP/PAP binding affinity for carbohydrate ligands depends on carbohydrate chain length, supporting a binding model in which HIP/PAP molecules "bind and jump" along the extended polysaccharide chains of peptidoglycan, reducing dissociation rates and increasing binding affinity. We propose that dynamic recognition of highly clustered carbohydrate epitopes in native peptidoglycan is an essential mechanism governing high-affinity interactions between HIP/PAP and the bacterial cell wall.

  9. Molecular basis for peptidoglycan recognition by a bactericidal lectin

    PubMed Central

    Lehotzky, Rebecca E.; Partch, Carrie L.; Mukherjee, Sohini; Cash, Heather L.; Goldman, William E.; Gardner, Kevin H.; Hooper, Lora V.

    2010-01-01

    RegIII proteins are secreted C-type lectins that kill Gram-positive bacteria and play a vital role in antimicrobial protection of the mammalian gut. RegIII proteins bind their bacterial targets via interactions with cell wall peptidoglycan but lack the canonical sequences that support calcium-dependent carbohydrate binding in other C-type lectins. Here, we use NMR spectroscopy to determine the molecular basis for peptidoglycan recognition by HIP/PAP, a human RegIII lectin. We show that HIP/PAP recognizes the peptidoglycan carbohydrate backbone in a calcium-independent manner via a conserved “EPN” motif that is critical for bacterial killing. While EPN sequences govern calcium-dependent carbohydrate recognition in other C-type lectins, the unusual location and calcium-independent functionality of the HIP/PAP EPN motif suggest that this sequence is a versatile functional module that can support both calcium-dependent and calcium-independent carbohydrate binding. Further, we show HIP/PAP binding affinity for carbohydrate ligands depends on carbohydrate chain length, supporting a binding model in which HIP/PAP molecules “bind and jump” along the extended polysaccharide chains of peptidoglycan, reducing dissociation rates and increasing binding affinity. We propose that dynamic recognition of highly clustered carbohydrate epitopes in native peptidoglycan is an essential mechanism governing high-affinity interactions between HIP/PAP and the bacterial cell wall. PMID:20382864

  10. Plant systems for recognition of pathogen-associated molecular patterns.

    PubMed

    Postel, Sandra; Kemmerling, Birgit

    2009-12-01

    Research of the last decade has revealed that plant immunity consists of different layers of defense that have evolved by the co-evolutional battle of plants with its pathogens. Particular light has been shed on PAMP- (pathogen-associated molecular pattern) triggered immunity (PTI) mediated by pattern recognition receptors. Striking similarities exist between the plant and animal innate immune system that point for a common optimized mechanism that has evolved independently in both kingdoms. Pattern recognition receptors (PRRs) from both kingdoms consist of leucine-rich repeat receptor complexes that allow recognition of invading pathogens at the cell surface. In plants, PRRs like FLS2 and EFR are controlled by a co-receptor SERK3/BAK1, also a leucine-rich repeat receptor that dimerizes with the PRRs to support their function. Pathogens can inject effector proteins into the plant cells to suppress the immune responses initiated after perception of PAMPs by PRRs via inhibition or degradation of the receptors. Plants have acquired the ability to recognize the presence of some of these effector proteins which leads to a quick and hypersensitive response to arrest and terminate pathogen growth.

  11. Synthetic Peptide templates for molecular recognition: recent advances and applications.

    PubMed

    Singh, Yashveer; Dolphin, Gunnar T; Razkin, Jesus; Dumy, Pascal

    2006-09-01

    The creation of molecular systems that can mimic some of the properties of natural macromolecules is one of the major endeavors in contemporary protein chemistry. However, the construction of artificial proteins with predetermined structure and function is difficult on account of complex folding pathways. The use of topological peptide templates has been suggested to induce and stabilize defined secondary and tertiary structures. This is because the recent advances in the chemistry of coupling reagents, protecting groups, and solid-phase synthesis have made the chemical synthesis of peptides with conformationally controlled and complex structures feasible. Besides their use as structure-inducing devices, these peptide templates can also be utilized to construct novel structures with tailor-made functions. Herein, we present recent advances in the field of peptide-template-based approaches with particular emphasis on the demonstrated utility of this approach in molecular recognition, along with related applications.

  12. Affinity sensor based on immobilized molecular imprinted synthetic recognition elements.

    PubMed

    Lenain, Pieterjan; De Saeger, Sarah; Mattiasson, Bo; Hedström, Martin

    2015-07-15

    An affinity sensor based on capacitive transduction was developed to detect a model compound, metergoline, in a continuous flow system. This system simulates the monitoring of low-molecular weight organic compounds in natural flowing waters, i.e. rivers and streams. During operation in such scenarios, control of the experimental parameters is not possible, which poses a true analytical challenge. A two-step approach was used to produce a sensor for metergoline. Submicron spherical molecularly imprinted polymers, used as recognition elements, were obtained through emulsion polymerization and subsequently coupled to the sensor surface by electropolymerization. This way, a robust and reusable sensor was obtained that regenerated spontaneously under the natural conditions in a river. Small organic compounds could be analyzed in water without manipulating the binding or regeneration conditions, thereby offering a viable tool for on-site application.

  13. Fundamental insight into the effect of carbodiimide crosslinking on cellular recognition of collagen-based scaffolds.

    PubMed

    Bax, Daniel V; Davidenko, Natalia; Gullberg, Donald; Hamaia, Samir W; Farndale, Richard W; Best, Serena M; Cameron, Ruth E

    2017-02-01

    Research on the development of collagen constructs is extremely important in the field of tissue engineering. Collagen scaffolds for numerous tissue engineering applications are frequently crosslinked with 1-ethyl-3-(3-dimethylaminopropyl-carbodiimide hydrochloride (EDC) in the presence of N-hydroxy-succinimide (NHS). Despite producing scaffolds with good biocompatibility and low cellular toxicity the influence of EDC/NHS crosslinking on the cell interactive properties of collagen has been overlooked. Here we have extensively studied the interaction of model cell lines with collagen I-based materials after crosslinking with different ratios of EDC in relation to the number of carboxylic acid residues on collagen. Divalent cation-dependent cell adhesion, via integrins α1β1, α2β1, α10β1 and α11β1, were sensitive to EDC crosslinking. With increasing EDC concentration, this was replaced with cation-independent adhesion. These results were replicated using purified recombinant I domains derived from integrin α1 and α2 subunits. Integrin α2β1-mediated cell spreading, apoptosis and proliferation were all heavily influenced by EDC crosslinking of collagen. Data from this rigorous study provides an exciting new insight that EDC/NHS crosslinking is utilising the same carboxylic side chain chemistry that is vital for native-like integrin-mediated cell interactions. Due to the ubiquitous usage of EDC/NHS crosslinked collagen for biomaterials fabrication this data is essential to have a full understanding in order to ensure optimized collagen-based material performance.

  14. Protein flexibility and ligand recognition: challenges for molecular modeling.

    PubMed

    Spyrakis, Francesca; BidonChanal, Axel; Barril, Xavier; Luque, F Javier

    2011-01-01

    The intrinsic dynamics of macromolecules is an essential property to relate the structure of biomolecular systems with their function in the cell. In the field of ligand-receptor recognition, numerous evidences have revealed the limitations of the lock-and-key theory, and the need to elaborate models that take into account the inherent plasticity of biomolecules, such as the induced-fit model or the existence of an ensemble of pre-equilibrated conformations. Depending on the nature of the target system, ligand binding can be associated with small local adjustments in side chains or even the backbone to large-scale motions of structural fragments, domains or even subunits. Reproducing the inherent flexibility of biomolecules has thus become one of the most challenging issues in molecular modeling and simulation studies, as it has direct implications in our understanding of the structure-function relationships, but even in areas such as virtual screening and structure-based drug discovery. Given the intrinsic limitation of conventional simulation tools, only events occurring in short time scales can be reproduced at a high accuracy level through all-atom techniques such as Molecular Dynamics simulations. However, larger structural rearrangements demand the use of enhanced sampling methods relying on modified descriptions of the biomolecular system or the potential surface. This review illustrates the crucial role that structural plasticity plays in mediating ligand recognition through representative examples. In addition, it discusses some of the most powerful computational tools developed to characterize the conformational flexibility in ligand-receptor complexes.

  15. Deciphering Epigenetic Cytosine Modifications by Direct Molecular Recognition.

    PubMed

    Kubik, Grzegorz; Summerer, Daniel

    2015-07-17

    Epigenetic modification at the 5-position of cytosine is a key regulatory element of mammalian gene expression with important roles in genome stability, development, and disease. The repertoire of cytosine modifications has long been confined to only 5-methylcytosine (mC) but has recently been expanded by the discovery of 5-hydroxymethyl-, 5-formyl-, and 5-carboxylcytosine. These are key intermediates of active mC demethylation but may additionally represent new epigenetic marks with distinct biological roles. This leap in chemical complexity of epigenetic cytosine modifications has not only created a pressing need for analytical approaches that enable unraveling of their functions, it has also created new challenges for such analyses with respect to sensitivity and selectivity. The crucial step of any such approach that defines its analytic potential is the strategy used for the actual differentiation of the cytosine 5-modifications from one another, and this selectivity can in principle be provided either by chemoselective conversions or by selective, molecular recognition events. While the former strategy has been particularly successful for accurate genomic profiling of cytosine modifications in vitro, the latter strategy provides interesting perspectives for simplified profiling of natural, untreated DNA, as well as for emerging applications such as single cell analysis and the monitoring of cytosine modification in vivo. We here review analytical techniques for the deciphering of epigenetic cytosine modifications with an emphasis on approaches that are based on the direct molecular recognition of these modifications in DNA.

  16. Molecularly imprinted polymers as recognition materials for electronic tongues.

    PubMed

    Huynh, Tan-Phat; Kutner, Wlodzimierz

    2015-12-15

    For over three decades now, molecularly imprinted polymers (MIPs) have successfully been used for selective chemical sensing because the shape and size of their imprinted molecular cavities perfectly matched those of the target analyte molecules. Moreover, orientation of recognizing sites of these cavities corresponded to those of the binding sites of the template molecules. In contrast, electronic tongue (e-tongue) is usually an array of low-affinity recognition units. Its selectivity is based on recognition pattern or multivariate analysis. Merging these two sensing devices led to a synergetic hybrid sensor, an MIP based e-tongue. Fabrication of these e-tongues permitted simultaneous sensing and discriminating several analytes in complex solutions of many components so that these arrays compensated for limitation in cross-reactivity of MIPs. Apparently, analytical signals generated by MIP-based e-tongues, compared to those of ordinary sensor arrays, were more reliable where a unique pattern or 'fingerprint' for each analyte was generated. Additionally, several transduction platforms (from spectroscopic to electrochemical) engaged in constructing MIP-based e-tongues, found their broad and flexible applications. The present review critically evaluates achievements in recent developments of the MIP based e-tongues for chemosensing. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA

    PubMed Central

    Wieczór, Miłosz; Tobiszewski, Adrian; Wityk, Paweł; Tomiczek, Bartłomiej; Czub, Jacek

    2014-01-01

    Telomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1 and TRF2. These two homologous proteins are therefore essential for the formation and normal function of telomeres. Indeed, TRF1 and TRF2 are implicated in a plethora of different cellular functions and their depletion leads to telomere dysfunction with chromosomal fusions, followed by apoptotic cell death. More specifically, it was found that TRF1 acts as a negative regulator of telomere length, and TRF2 is involved in stabilizing the loop structure. Consequently, these proteins are of great interest, not only because of their key role in telomere maintenance and stability, but also as potential drug targets. In the current study, we investigated the molecular basis of telomeric sequence recognition by TRF1 and TRF2 and their DNA binding mechanism. We used molecular dynamics (MD) to calculate the free energy profiles for binding of TRFs to telomeric DNA. We found that the predicted binding free energies were in good agreement with experimental data. Further, different molecular determinants of binding, such as binding enthalpies and entropies, the hydrogen bonding pattern and changes in surface area, were analyzed to decompose and examine the overall binding free energies at the structural level. With this approach, we were able to draw conclusions regarding the consecutive stages of sequence-specific association, and propose a novel aspartate-dependent mechanism of sequence recognition. Finally, our work demonstrates the applicability of computational MD-based methods to studying protein-DNA interactions. PMID:24586793

  18. Quantum origins of molecular recognition and olfaction in drosophila

    NASA Astrophysics Data System (ADS)

    Bittner, Eric R.; Madalan, Adrian; Czader, Arkadiusz; Roman, Gregg

    2012-12-01

    The standard model for molecular recognition of an odorant is that receptor sites discriminate by molecular geometry as evidenced that two chiral molecules may smell very differently. However, recent studies of isotopically labeled olfactants indicate that there may be a molecular vibration-sensing component to olfactory reception, specifically in the spectral region around 2300 cm-1. Here, we present a donor-bridge-acceptor model for olfaction which attempts to explain this effect. Our model, based upon accurate quantum chemical calculations of the olfactant (bridge) in its neutral and ionized states, posits that internal modes of the olfactant are excited impulsively during hole transfer from a donor to acceptor site on the receptor, specifically those modes that are resonant with the tunneling gap. By projecting the impulsive force onto the internal modes, we can determine which modes are excited at a given value of the donor-acceptor tunneling gap. Only those modes resonant with the tunneling gap and are impulsively excited will give a significant contribution to the inelastic transfer rate. Using acetophenone as a test case, our model and experiments on D. melanogaster suggest that isotopomers of a given olfactant give rise to different odorant qualities. These results support the notion that inelastic scattering effects may play a role in discriminating between isotopomers but that this is not a general spectroscopic effect.

  19. Investigation of synthetic molecular recognition for biosensing applications

    NASA Astrophysics Data System (ADS)

    Stratis-Cullum, Dimitra N.; McMasters, Sun; Sooter, Letha J.; Pellegrino, Paul M.

    2007-04-01

    A fundamental understanding of the factors which influence binding performance is critical to any technology or methodology relying on molecular recognition of a specific target species. For the Army, there is a growing need for a basic understanding of these interactions with traditional recognition elements (e.g., antibodies) in non-traditional environmental conditions, such as with new and emerging threats. There is a similar need for building a base of knowledge on non-traditional affinity ligands that are biomimetic or biosynthetic in nature. In this paper, specific research at the Army Research Laboratory towards the development, evaluation and use of synthetic affinity ligands for sensing applications is discussed. This includes the results of our investigations of aptamer-based affinity ligands targeting Campylobacter jejuni. Using capillary electrophoretic techniques, the relative binding affinities of the aptamer ligands towards the target pathogen as well as the degree of cross-reactivity with other food borne-pathogens (i.e., Escherichia coli O157:H7 and Salmonella typhimurium) were evaluated. Current progress towards the development of synthetic affinity ligands for sensing applications will also be discussed.

  20. The Molecular Recognition Paradigm of Environmental Chemicals with Biomacromolecules.

    PubMed

    Zhang, Wenjing; Pan, Liumeng; Wang, Haifei; Lv, Xuan; Ding, Keke

    2017-01-01

    The interactions of ligands with biomacromolecules play a fundamental role in almost all bioprocesses occuring in living organisms. The binding of ligands can cause the conformational changes of biomacromolecules, possibly affecting their physiological functions. The interactions of ligands with biomacromolecules are thus becoming a research hotspot. However, till now, there still lacks a systematic compilation of review with the focus on the interactions between environmental chemicals and biomacromolecules. In this review, we focus on the molecular recognition paradigm of environmental chemicals with biomacromolecules and chemical basis for driving the complex formation. The state-of-the-art review on in vitro and in silico studies on interaction of organic chemicals with transport proteins, nuclear receptors and CYP450 enzymes was provided, and the enantioselective interactions of chiral environmental chemicals was also mentioned.

  1. Consequences of Morphology on Molecularly Imprinted Polymer-Ligand Recognition

    PubMed Central

    Rosengren, Annika M.; Karlsson, Björn C. G.; Nicholls, Ian A.

    2013-01-01

    The relationship between molecularly imprinted polymer (MIP) morphology and template-rebinding over a series of warfarin-imprinted methacrylic acid co(ethylene dimethacrylate) polymers has been explored. Detailed investigations of the nature of template recognition revealed that an optimal template binding was obtained with polymers possessing a narrow population of pores (~3–4 nm) in the mesopore size range. Importantly, the warfarin-polymer rebinding analyses suggest strategies for regulating ligand binding capacity and specificity through variation of the degree of cross-linking, where polymers prepared with a lower degree of cross-linking afford higher capacity though non-specific in character. In contrast, the co-existence of specific and non-specific binding was found in conjunction with higher degrees of cross-linking and resultant mesoand macropore size distributions. PMID:23303280

  2. Using photo-initiated polymerization reactions to detect molecular recognition.

    PubMed

    Kaastrup, K; Sikes, H D

    2016-02-07

    Widely used medical diagnostic devices and assays that sense the presence of a particular molecule in a bodily fluid often rely on either a nanoparticle label or an enzymatic reaction to generate a signal that is easily detectable. In many cases, it is desirable if the magnitude of the signal correlates with the concentration of the molecule of interest. Photo-initiated polymerization reactions are an alternative means of generating amplified signals that can be used to quantify biological molecules in complex fluids. In this case, the formation of a polymer, typically a cross-linked hydrogel, signifies the presence of the molecule of interest. This tutorial review explains how photo-initiated polymerization reactions have been used in a conditional manner to detect and quantify molecular recognition events. We weigh the advantages and disadvantages of using photo-initiated reactions in comparison with other approaches and highlight exciting directions and opportunities in this area.

  3. Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification.

    PubMed

    Ballester, Pedro J; Mangold, Martina; Howard, Nigel I; Robinson, Richard L Marchese; Abell, Chris; Blumberger, Jochen; Mitchell, John B O

    2012-12-07

    One of the initial steps of modern drug discovery is the identification of small organic molecules able to inhibit a target macromolecule of therapeutic interest. A small proportion of these hits are further developed into lead compounds, which in turn may ultimately lead to a marketed drug. A commonly used screening protocol used for this task is high-throughput screening (HTS). However, the performance of HTS against antibacterial targets has generally been unsatisfactory, with high costs and low rates of hit identification. Here, we present a novel computational methodology that is able to identify a high proportion of structurally diverse inhibitors by searching unusually large molecular databases in a time-, cost- and resource-efficient manner. This virtual screening methodology was tested prospectively on two versions of an antibacterial target (type II dehydroquinase from Mycobacterium tuberculosis and Streptomyces coelicolor), for which HTS has not provided satisfactory results and consequently practically all known inhibitors are derivatives of the same core scaffold. Overall, our protocols identified 100 new inhibitors, with calculated K(i) ranging from 4 to 250 μM (confirmed hit rates are 60% and 62% against each version of the target). Most importantly, over 50 new active molecular scaffolds were discovered that underscore the benefits that a wide application of prospectively validated in silico screening tools is likely to bring to antibacterial hit identification.

  4. X-ray and molecular modelling in fragment-based design of three small quinoline scaffolds for HIV integrase inhibitors.

    PubMed

    Majerz-Maniecka, Katarzyna; Musiol, Robert; Skórska-Stania, Agnieszka; Tabak, Dominik; Mazur, Pawel; Oleksyn, Barbara J; Polanski, Jaroslaw

    2011-03-01

    Crystal structures of three small molecular scaffolds based on quinoline, 2-methylquinoline-5,8-dione, 5-hydroxy-quinaldine-6-carboxylic acid and 8-hydroxy-quinaldine-7-carboxylic acid, were characterised. 5-Hydroxy-quinaldine-6-carboxylic acid was co-crystallized with cobalt(II) chloride to form a model of divalent metal cation-ligand interactions for potential HIV integrase inhibitors. Molecular docking into active site of HIV IN was also performed on 1WKN PDB file. Selected ligand-protein interactions have been found specific for active compounds. Studied structures can be used as scaffolds in fragment-based design of new potent drugs.

  5. TEM-1 beta-lactamase as a scaffold for protein recognition and assay.

    PubMed

    Legendre, Daniel; Vucic, Bénédicte; Hougardy, Vincent; Girboux, Anne-Lise; Henrioul, Christophe; Van Haute, Julien; Soumillion, Patrice; Fastrez, Jacques

    2002-06-01

    A large number of different proteins or protein domains have been investigated as possible scaffolds to engineer antibody-like molecules. We have previously shown that the TEM-1 beta-lactamase can accommodate insertions of random sequences in two loops surrounding its active site without compromising its activity. From the libraries that were generated, active enzymes binding with high affinities to monoclonal antibodies raised against prostate-specific antigen, a protein unrelated to beta-lactamase, could be isolated. Antibody binding was shown to affect markedly the enzyme activity. As a consequence, these enzymes have the potential to be used as signaling molecules in direct or competitive homogeneous immunoassay. Preliminary results showed that beta-lactamase clones binding to streptavidin could also be isolated, indicating that some enzymes in the libraries have the ability to recognize proteins other than antibodies. In this paper, we show that, in addition to beta-lactamases binding to streptavidin, beta-lactamase clones binding to horse spleen ferritin and beta-galactosidase could be isolated. Affinity maturation of a clone binding to ferritin allowed obtaining beta-lactamases with affinities comprised between 10 and 20 nM (Kd) for the protein. Contrary to what was observed for beta-lactamases issued from selections on antibodies, enzyme complexation induced only a modest effect on enzyme activity, in the three cases studied. This kind of enzyme could prove useful in replacement of enzyme-conjugated antibodies in enzyme-linked immunosorbant assays (ELISA) or in other applications that use antibodies conjugated to an enzyme.

  6. Molecular recognition between pancreatic lipase and natural and synthetic inhibitors.

    PubMed

    Bello, Martiniano; Basilio-Antonio, Lucia; Fragoso-Vázquez, Jonathan; Avalos-Soriano, Anaguiven; Correa-Basurto, José

    2017-05-01

    Pancreatic lipase (PL) is a primary lipase critical for triacylglyceride digestion in humans and is considered as a promising target for the treatment of obesity. Although the current synthetic drugs available for treating obesity have been demonstrated to be effective in inhibiting PL, their prolonged usage results in severe side effects. Based on this argument, in this study, we evaluated the structural and energetic features linked to molecular recognition between two well-known PL inhibitors, orlistat (ORL, synthetic inhibitor) and (-)-epigallocatechin gallate (EGCG, natural inhibitor) and PL through molecular dynamics simulations and free energy calculations of ORL and EGCG at the PL binding site when it is isolated (PL) from the heterodimer complex, forming the heterodimer complex with colipase (PLCL) and lacking structural calcium. Our study showed that the binding free energy of ORL and EGCG to the target correlates with their experimental affinity tendency. The presence of the heterodimer PLCL state, the presence of structural calcium and the type of inhibitor resulted in differences in structural stability and in the map of protein-ligand and protein-protein interactions. Overall, our results suggest that the heterodimer complex and structural calcium are linked to the binding properties of PL.

  7. Molecular Recognition at the Protein-Hydroxyapatite Interface

    SciTech Connect

    Stayton, Partick S.; Drobny, G. P.; Shaw, Wendy J.; Long, Joanna R.; Gilbert, Michelle R.

    2003-09-01

    Proteins found in mineralized tissues act as nature's crystal engineers, where they play a key role in promoting or inhibiting the growth of minerals, such as hydroxyapitite (bones/teeth) and calcium oxalate (kidney stones). Despite their importance in hard-tissue formation and remodeling, and in pathological processes such as stone formation and arterial calcification, there is little known of the protein structure-function relationships that govern hard-tissue engineering. Here we review early studies that have utilized solid-state NMR (ssNMR) techniques to provide in situ secondary-structure determination of statherin and statherin peptides on their biologically relevant hydroxyapatite (HAP) surfaces. In addition to direct structural study, molecular dynamics studies have provided considerable insight into the protein-binding footprint on hydroxyapatite. The molecular insight provided by these studies has also led to the design of biomimetic fusion peptides that utilize nature's crystal-recognition mechanism to display accessible and dynamic bioactive sequences from the HAP surface. These peptides selectively engage adhesion receptors and direct specific outside-in signaling pathway activation in osteoblast-like cells.

  8. Molecular Genetics of Mating Recognition in Basidiomycete Fungi

    PubMed Central

    Casselton, Lorna A.; Olesnicky, Natalie S.

    1998-01-01

    The recognition of compatible mating partners in the basidiomycete fungi requires the coordinated activities of two gene complexes defined as the mating-type genes. One complex encodes members of the homeobox family of transcription factors, which heterodimerize on mating to generate an active transcription regulator. The other complex encodes peptide pheromones and 7-transmembrane receptors that permit intercellular signalling. Remarkably, a single species may have many thousands of cross-compatible mating types because the mating-type genes are multiallelic. Different alleles of both sets of genes are necessary for mating compatibility, and they trigger the initial stages of sexual development—the formation of a specialized filamentous mycelium termed the dikaryon, in which the haploid nuclei remain closely associated in each cell but do not fuse. Three species have been taken as models to describe the molecular structure and organization of the mating-type loci and the genes sequestered within them: the pathogenic smut fungus Ustilago maydis and the mushrooms Coprinus cinereus and Schizophyllum commune. Topics addressed in this review are the roles of the mating-type gene products in regulating sexual development, the molecular basis for multiple mating types, and the molecular interactions that permit different allelic products of the mating type genes to be discriminated. Attention is drawn to the remarkable conservation in the mechanisms that regulate sexual development in basidiomycetes and unicellular ascomycete yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe, a theme which is developed in the general conclusion to include the filamentous ascomycetes Neurospora crassa and Podospora anserina. PMID:9529887

  9. Recent advances in molecular recognition based on nanoengineered platforms.

    PubMed

    Mu, Bin; Zhang, Jingqing; McNicholas, Thomas P; Reuel, Nigel F; Kruss, Sebastian; Strano, Michael S

    2014-04-15

    Nanoparticles and nanoengineered platforms have great potential for technologies involving biomoleuclar detection or cell-related biosensing, and have provided effective chemical interfaces for molecular recognition. Typically, chemists work on the modification of synthetic polymers or macromolecules, which they link to the nanoparticles by covalent or noncovalent approaches. The motivation for chemical modification is to enhance the selectivity and sensitivity, and to improve the biocompatibility for the in vivo applications. In this Account, we present recent advances in the development and application of chemical interfaces for molecular recognition for nanoparticles and nanoengineered platforms, in particular single-walled carbon nanotubes (SWNTs). We discuss emerging approaches for recognizing small molecules, glycosylated proteins, and serum biomarkers. For example, we compare and discuss detection methods for ATP, NO, H2O2, and monosaccharides for recent nanomaterials. Fluorometric detection appears to have great potential for quantifying concentration gradients and determining their location in living cells. For macromolecular detection, new methods for glycoprofiling using such interfaces appear promising, and benefit specifically from the potential elimination of cumbersome labeling and liberation steps during conventional analysis of glycans, augmenting the currently used mass spectrometry (MS), capillary electrophoresis (CE), and liquid chromatography (LC) methods. In particular, we demonstrated the great potential of fluorescent SWNTs for glycan-lectin interactions sensing. In this case, SWNTs are noncovalently functionalized to introduce a chelated nickel group. This group provides a docking site for the His-tagged lectin and acts as the signal modulator. As the nickel proximity to the SWNT surface changes, the fluorescent signal is increased or attenuated. When a free glycan or glycosylated probe interacts with the lectin, the signal increases and

  10. The DBHS proteins SFPQ, NONO and PSPC1: a multipurpose molecular scaffold.

    PubMed

    Knott, Gavin J; Bond, Charles S; Fox, Archa H

    2016-05-19

    Nuclear proteins are often given a concise title that captures their function, such as 'transcription factor,' 'polymerase' or 'nuclear-receptor.' However, for members of the Drosophila behavior/human splicing (DBHS) protein family, no such clean-cut title exists. DBHS proteins are frequently identified engaging in almost every step of gene regulation, including but not limited to, transcriptional regulation, RNA processing and transport, and DNA repair. Herein, we present a coherent picture of DBHS proteins, integrating recent structural insights on dimerization, nucleic acid binding modalities and oligomerization propensity with biological function. The emerging paradigm describes a family of dynamic proteins mediating a wide range of protein-protein and protein-nucleic acid interactions, on the whole acting as a multipurpose molecular scaffold. Overall, significant steps toward appreciating the role of DBHS proteins have been made, but we are only beginning to understand the complexity and broader importance of this family in cellular biology.

  11. Biological Activities of Natural and Engineered Cyclotides, a Novel Molecular Scaffold for Peptide-Based Therapeutics

    PubMed Central

    Garcia, Angie E.; Camarero, Julio A.

    2012-01-01

    Cyclotides are a growing family of large plant-derived backbone-cyclized polypeptides (≈30 amino acids long) that share a disulfide-stabilized core characterized by an unusual knotted structure. Their unique circular backbone topology and knotted arrangement of three disulfide bonds makes them exceptionally stable to thermal, chemical, and enzymatic degradation compared to other peptides of similar size. Currently more than 100 sequences of different cyclotides have been characterized and the number is expected to increase dramatically in the coming years. Considering their stability, biological activities and ability to cross the cell membrane, cyclotides can be exploited to develop new peptide-based drugs with high potential for success. The cyclotide scaffold can be engineered or evolved using molecular evolution to inhibit protein-protein interactions implicated in cancer and other human diseases, or design new antimicrobial. The present review reports the biological diversity and therapeutic potential of natural and engineered cyclotides. PMID:20858197

  12. Hamming Distance as a Concept in DNA Molecular Recognition.

    PubMed

    Mohammadi-Kambs, Mina; Hölz, Kathrin; Somoza, Mark M; Ott, Albrecht

    2017-04-30

    DNA microarrays constitute an in vitro example system of a highly crowded molecular recognition environment. Although they are widely applied in many biological applications, some of the basic mechanisms of the hybridization processes of DNA remain poorly understood. On a microarray, cross-hybridization arises from similarities of sequences that may introduce errors during the transmission of information. Experimentally, we determine an appropriate distance, called minimum Hamming distance, in which the sequences of a set differ. By applying an algorithm based on a graph-theoretical method, we find large orthogonal sets of sequences that are sufficiently different not to exhibit any cross-hybridization. To create such a set, we first derive an analytical solution for the number of sequences that include at least four guanines in a row for a given sequence length and eliminate them from the list of candidate sequences. We experimentally confirm the orthogonality of the largest possible set with a size of 23 for the length of 7. We anticipate our work to be a starting point toward the study of signal propagation in highly competitive environments, besides its obvious application in DNA high throughput experiments.

  13. Advanced Molecular Probes for Sequence-Specific DNA Recognition

    NASA Astrophysics Data System (ADS)

    Bertucci, Alessandro; Manicardi, Alex; Corradini, Roberto

    DNA detection can be achieved using the Watson-Crick base pairing with oligonucleotides or oligonucleotide analogs, followed by generation of a physical or chemical signal coupled with a transducer device. The nature of the probe is an essential feature which determines the performances of the sensing device. Many synthetic processes are presently available for "molecular engineering" of DNA probes, enabling label-free and PCR-free detection to be performed. Furthermore, many DNA analogs with improved performances are available and are under development; locked nucleic acids (LNA), peptide nucleic acids (PNA) and their analogs, morpholino oligonucleotides (MO) and other modified probes have shown improved properties of affinity and selectivity in target recognition compared to those of simple DNA probes. The performances of these probes in sensing devices, and the requirements for detection of unamplified DNA will be discussed in this chapter. Chemistry and architectures for conjugation of probes to reporter units, surfaces and nanostructures will also be discussed. Examples of probes used in ultrasensitive detection of unamplified DNA are listed.

  14. Molecularly imprinted silica-silver nanowires for tryptophan recognition

    NASA Astrophysics Data System (ADS)

    Díaz-Faes López, T.; Díaz-García, M. E.; Badía-Laíño, R.

    2014-10-01

    We report on silver nanowires (AgNWs) coated with molecularly imprinted silica (MIP SiO2) for recognition of tryptophan (Trp). The use of AgNWs as a template confers an imprinted material with adequate mechanical strength and with a capability of recognizing Trp due to its nanomorphology when compared to spherical microparticles with a similar surface-to-volume ratio. Studies on adsorption isotherms showed the MIP-SiO2-AgNWs to exhibit homogeneous affinity sites with narrow affinity distribution. This suggests that the synthesized material behaves as a 1D nanomaterial with a large area and small thickness with very similar affinity sites. Trp release from MIP-SiO2-AgNWs was demonstrated to be dominated by the diffusion rate of Trp as controlled by the specific interactions with the imprinted silica shell. Considering these results and the lack of toxicity of silica sol-gel materials, the material offers potential in the field of drug or pharmaceutical controlled delivery, but also in optoelectronic devices, electrodes and sensors.

  15. Aptamers: versatile molecular recognition probes for cancer detection

    PubMed Central

    Sun, Hongguang; Tan, Weihong; Zu, Youli

    2015-01-01

    In the past two decades, aptamers have emerged as a novel class of molecular recognition probes comprising uniquely-folded short RNA or single-stranded DNA oligonucleotides that bind to their cognate targets with high specificity and affinity. Aptamers, often referred to as “chemical antibodies”, possess several highly desirable features for clinical use. They can be chemically synthesized and are easily conjugated to a wide range of reporters for different applications, and are able to rapidly penetrate tissues. These advantages significantly enhance their clinical applicability, and render them excellent alternatives to antibody-based probes in cancer diagnostics and therapeutics. Aptamer probes based on fluorescence, colorimetry, magnetism, electrochemistry, and in conjunction with nanomaterials (e.g., nanoparticles, quantum dots, single-walled carbon nanotubes, and magnetic nanoparticles) have provided novel ultrasensitive cancer diagnostic strategies and assays. Furthermore, promising aptamer targeted-multimodal tumor imaging probes have been recently developed in conjunction with fluorescence, positron emission tomography (PET), single-photon emission computed tomography (SPECT), and magnetic resonance imaging (MRI). The capabilities of the aptamer-based platforms described herein underscore the great potential they hold for the future of cancer detection. In this review, we highlight the most prominent recent developments in this rapidly advancing field. PMID:26618445

  16. Early stage P22 viral capsid self-assembly mediated by scaffolding protein: atom-resolved model and molecular dynamics simulation.

    PubMed

    Jiang, Jiajian; Yang, Jing; Sereda, Yuriy V; Ortoleva, Peter J

    2015-04-23

    Molecular dynamics simulation of an atom-resolved bacteriophage P22 capsid model is used to delineate the underlying mechanism of early stage P22 self-assembly. A dimer formed by the C-terminal fragment of scaffolding protein with a new conformation is demonstrated to catalyze capsomer (hexamer and pentamer) aggregation efficiently. Effects of scaffolding protein/coat protein binding patterns and scaffolding protein concentration on efficiency, fidelity, and capsid curvature of P22 self-assembly are identified.

  17. Towards a universal polymer backbone: design and synthesis of polymeric scaffolds containing terminal hydrogen-bonding recognition motifs at each repeating unit.

    PubMed

    Stubbs, Ludger P; Weck, Marcus

    2003-02-17

    Polymers containing terminal hydrogen-bonding recognition motifs based on diaminotriazine and diaminopyridine groups in their side chains for the self-assembly of appropriate receptors have been prepared by ring-opening metathesis polymerization (ROMP) of norbornenes. A new synthetic method for the preparation of norbornene monomers based on pure alkyl spacers is introduced. These monomers show unprecedented high reactivity using ROMP. To suppress self-association of diaminotriazine-based polymers, polymerizations were run in presence of N-butylthymine. The butylthymine acts as a protecting group via self-assembly onto the hydrogen-bonding sites of the polymeric scaffold, thereby solubilizing the polymer. Diaminopyridine monomers do not require the presence of a protecting group due to their low propensity to dimerize. In addition, they exhibit a high affinity for hydrogen-bonded receptors on both monomeric and polymeric level. These polymers present our first building blocks towards the design and synthesis of a "universal polymer scaffold".

  18. Novel thiol-based histone deacetylase inhibitors bearing 3-phenyl-1H-pyrazole-5-carboxamide scaffold as surface recognition motif: Design, synthesis and SAR study.

    PubMed

    Wen, Jiachen; Niu, Qun; Liu, Jiang; Bao, Yu; Yang, Jinyu; Luan, Shenglin; Fan, Yinbo; Liu, Dan; Zhao, Linxiang

    2016-01-15

    A series of novel thiol-based histone deacetylase (HDAC) inhibitors bearing 3-phenyl-1H-pyrazole-5-carboxamide scaffold as surface recognition motif was designed, synthesized, and evaluated for their HDAC inhibition activity. Among them, 15j (IC50=0.08μM) was identified as a better inhibitor than Vorinostat (IC50=0.25μM) against total HDACs. In addition, Structure-activity relationships (SAR) analyses indicated that (i) compounds with different substituents on pyrazole N-1 position exhibited superior activities than those on pyrazole N-2 position, (ii) variation of functional groups on N-1'-alkyl chain terminus followed the trends of carboxyl group>hydroxyl group≫alkyl group, and (iii) methylation on pyrazole C-4 position diminished the HDAC inhibition activity. The SAR will guide us to further refine compounds bearing 3-phenyl-1H-pyrazole-5-carboxamide scaffold to achieve better HDAC inhibitors.

  19. Carbon Nanomaterials and DNA: from Molecular Recognition to Applications.

    PubMed

    Sun, Hanjun; Ren, Jinsong; Qu, Xiaogang

    2016-03-15

    DNA is polymorphic. Increasing evidence has indicated that many biologically important processes are related to DNA's conformational transition and assembly states. In particular, noncanonical DNA structures, such as the right-handed A-form, the left-handed Z-form, the triplex, the G-quadruplex, the i-motif, and so forth, have been specific targets for the diagnosis and therapy of human diseases. Meanwhile, they have been widely used in the construction of smart DNA nanomaterials and nanoarchitectures. As rising stars in materials science, the family of carbon nanomaterials (CNMs), including two-dimensional graphene, one-dimensional carbon nanotubes (CNTs), and zero-dimensional graphene or carbon quantum dots (GQDs or CQDs), interact with DNA and are able to regulate the conformational transitions of DNA. The interaction of DNA with CNMs not only opens new opportunities for specific molecular recognition, but it also expands the promising applications of CNMs from materials science to biotechnology and biomedicine. In this Account, we focus on our contributions to the field of interactions between CNMs and DNA in which we have explored their promising applications in nanodevices, sensing, materials synthesis, and biomedicine. For one-dimensional CNTs, two-dimensional graphene, and zero-dimensional GQDs and CQDs, the basic principles, binding modes, and applications of the interactions between CNMs and DNA are reviewed. We aim to give prominence to the important status of CNMs in the field of molecular recognition for DNA. First, we summarized our discovery of the interactions between single-walled carbon nanotubes (SWNTs) with duplex, triplex, and human telomeric i-motif DNA and their interesting applications. For example, SWNTs are the first chemical agents that can selectively stabilize human telomeric i-motif DNA and induce its formation under physiological conditions. On the basis of this principle, two types of nanodevices were designed. One was used for

  20. Molecularly Imprinted Polymers: Thermodynamic and Kinetic Considerations on the Specific Sorption and Molecular Recognition.

    PubMed

    Li, Songjun; Huang, Xing; Zheng, Mingxia; Li, Wuke; Tong, Kejun

    2008-04-23

    This article presents a work aiming at thermodynamically and kinetically interpreting the specific sorption and recognition by a molecularly imprinted polymer. Using Boc-L-Phe-OH as a template, the imprinted material was prepared. The result indicates that the prepared polymer can well discriminate the imprint species from its analogue (Boc-D-Phe-OH), so as to adsorb more for the former but less for the latter. Kinetic analysis indicates that this specific sorption, in nature, can be a result of a preferential promotion. The imprint within the polymer causes a larger adsorption rate for the template than for the analogue. Thermodynamic study also implies that the molecular induction from the specific imprint to the template is larger than to the analogue, which thus makes the polymer capable of preferentially alluring the template to bind.

  1. Gating-like Motions and Wall Porosity in a DNA Nanopore Scaffold Revealed by Molecular Simulations.

    PubMed

    Maingi, Vishal; Lelimousin, Mickaël; Howorka, Stefan; Sansom, Mark S P

    2015-11-24

    Recently developed synthetic membrane pores composed of folded DNA enrich the current range of natural and engineered protein pores and of nonbiogenic channels. Here we report all-atom molecular dynamics simulations of a DNA nanotube (DNT) pore scaffold to gain fundamental insight into its atomic structure, dynamics, and interactions with ions and water. Our multiple simulations of models of DNTs that are composed of a six-duplex bundle lead to a coherent description. The central tube lumen adopts a cylindrical shape while the mouth regions at the two DNT openings undergo gating-like motions which provide a possible molecular explanation of a lower conductance state observed in our previous experimental study on a membrane-spanning version of the DNT (ACS Nano 2015, 9, 1117-26). Similarly, the central nanotube lumen is filled with water and ions characterized by bulk diffusion coefficients while the gating regions exhibit temporal fluctuations in their aqueous volume. We furthermore observe that the porous nature of the walls allows lateral leakage of ions and water. This study will benefit rational design of DNA nanopores of enhanced stability of relevance for sensing applications, of nanodevices with tunable gating properties that mimic gated ion channels, or of nanopores featuring defined permeation behavior.

  2. Mito-DCA: a mitochondria targeted molecular scaffold for efficacious delivery of metabolic modulator dichloroacetate.

    PubMed

    Pathak, Rakesh K; Marrache, Sean; Harn, Donald A; Dhar, Shanta

    2014-05-16

    Tumor growth is fueled by the use of glycolysis, which normal cells use only in the scarcity of oxygen. Glycolysis makes tumor cells resistant to normal death processes. Targeting this unique tumor metabolism can provide an alternative strategy to selectively destroy the tumor, leaving normal tissue unharmed. The orphan drug dichloroacetate (DCA) is a mitochondrial kinase inhibitor that has the ability to show such characteristics. However, its molecular form shows poor uptake and bioavailability and limited ability to reach its target mitochondria. Here, we describe a targeted molecular scaffold for construction of a multiple DCA loaded compound, Mito-DCA, with three orders of magnitude enhanced potency and cancer cell specificity compared to DCA. Incorporation of a lipophilic triphenylphosphonium cation through a biodegradable linker in Mito-DCA allowed for mitochondria targeting. Mito-DCA did not show any significant metabolic effects toward normal cells but tumor cells with dysfunctional mitochondria were affected by Mito-DCA, which caused a switch from glycolysis to glucose oxidation and subsequent cell death via apoptosis. Effective delivery of DCA to the mitochondria resulted in significant reduction in lactate levels and played important roles in modulating dendritic cell (DC) phenotype evidenced by secretion of interleukin-12 from DCs upon activation with tumor antigens from Mito-DCA treated cancer cells. Targeting mitochondrial metabolic inhibitors to the mitochondria could lead to induction of an efficient antitumor immune response, thus introducing the concept of combining glycolysis inhibition with immune system to destroy tumor.

  3. Molecular Recognition of Biomolecules by Chiral CdSe Quantum Dots

    NASA Astrophysics Data System (ADS)

    Mukhina, Maria V.; Korsakov, Ivan V.; Maslov, Vladimir G.; Purcell-Milton, Finn; Govan, Joseph; Baranov, Alexander V.; Fedorov, Anatoly V.; Gun’Ko, Yurii K.

    2016-04-01

    Molecular recognition is one of the most important phenomena in Chemistry and Biology. Here we present a new way of enantiomeric molecular recognition using intrinsically chiral semiconductor nanocrystals as assays. Real-time confocal microscopy studies supported by circular dichroism spectroscopy data and theoretical modelling indicate an ability of left-handed molecules of cysteine and, to a smaller extent, histidine and arginine to discriminate between surfaces of left- and right-handed nanocrystals.

  4. Molecular Recognition of Biomolecules by Chiral CdSe Quantum Dots

    PubMed Central

    Mukhina, Maria V.; Korsakov, Ivan V.; Maslov, Vladimir G.; Purcell-Milton, Finn; Govan, Joseph; Baranov, Alexander V.; Fedorov, Anatoly V.; Gun’ko, Yurii K.

    2016-01-01

    Molecular recognition is one of the most important phenomena in Chemistry and Biology. Here we present a new way of enantiomeric molecular recognition using intrinsically chiral semiconductor nanocrystals as assays. Real-time confocal microscopy studies supported by circular dichroism spectroscopy data and theoretical modelling indicate an ability of left-handed molecules of cysteine and, to a smaller extent, histidine and arginine to discriminate between surfaces of left- and right-handed nanocrystals. PMID:27063962

  5. Effect of buffer at nanoscale molecular recognition interfaces - electrostatic binding of biological polyanions.

    PubMed

    Rodrigo, Ana C; Laurini, Erik; Vieira, Vânia M P; Pricl, Sabrina; Smith, David K

    2017-10-09

    We investigate the impact of an over-looked component on molecular recognition in water-buffer. The binding of a cationic dye to biological polyanion heparin is shown by isothermal calorimetry to depend on buffer (Tris-HCl > HEPES > PBS). The heparin binding of self-assembled multivalent (SAMul) cationic micelles is even more buffer dependent. Multivalent electrostatic molecular recognition is buffer dependent as a result of competitive interactions between the cationic binding interface and anions present in the buffer.

  6. Molecular recognition-based detoxification of aluminum in human plasma.

    PubMed

    Demircelik, Ahmet H; Andac, Muge; Andac, Cenk A; Say, Ridvan; Denizli, Adil

    2009-01-01

    Molecular recognition-based Al(3+)-imprinted poly(hydroxyethyl methacrylate-N-methacryloyl-L-glutamic acid) (PHEMAGA-Al(3+)) beads were prepared to be used in selective removal of Al(3+) out of human plasma overdosed with Al(3+) cations. The PHEMAGA-Al(3+) beads were synthesized by suspension polymerization in the presence of a template-monomer complex (MAGA-Al(3+)). The specific surface area of PHEMAGA-Al(3+) beads was found to be 55.6 m(2)/g on the average. The MAGA content in the PHEMAGA-Al(3+) beads were found to be 640 micgomol/g polymer. The template Al(3+) cations could be reversibly detached from the matrix to form PHEMAGA-Al(3+) using a 50 mM solution of EDTA. The Al(3+)-free PHEMAGA-Al(3+) beads were then exposed to a selective separation procedure of Al(3+) out of human plasma, which was implemented in a continuous system by packing the beads into a separation column (10 cm long with an inner diameter of 0.9 cm) equipped with a water jacket to control the temperature. The Al(3+) adsorption capacity of the PHEMAGA-Al(3+) beads decreased drastically from 0.76 mg/g polymer to 0.22 mg/g polymer as the flow rate was increased from 0.3 ml/min to 1.5 ml/min. The relative selectivity coefficients of the PHEMAGA-Al(3+) beads for Al(3+)/Fe(3+), Al(3+)/Cu(2+) and Al(3+)/Zn(2+) were found to be 4.49, 8.95 and 32.44 times greater than those of the non-imprinted PHEMAGA beads, respectively. FT-IR analyses on the synthesized PHEMAGA-Al(3+) beads reveals monodentate and bidentate binding modes of Al(3+) in complex with the carboxylate groups of the glutamate residues. Density functional theory computations at the B3LYP/6-31G(d,p) basis set suggests that structured water molecules play essential role in the stability of the monodentate binding mode in 1:1 PHEMAGA-Al(3+) complexes. The PHEMAGA-Al(3+) beads were recovered and reused many times, with no significant decrease in their adsorption capacities.

  7. The integration of 3-D cell printing and mesoscopic fluorescence molecular tomography of vascular constructs within thick hydrogel scaffolds.

    PubMed

    Zhao, Lingling; Lee, Vivian K; Yoo, Seung-Schik; Dai, Guohao; Intes, Xavier

    2012-07-01

    Developing methods that provide adequate vascular perfusion is an important step toward engineering large functional tissues. Meanwhile, an imaging modality to assess the three-dimensional (3-D) structures and functions of the vascular channels is lacking for thick matrices (>2 ≈ 3 mm). Herein, we report on an original approach to construct and image 3-D dynamically perfused vascular structures in thick hydrogel scaffolds. In this work, we integrated a robotic 3-D cell printing technology with a mesoscopic fluorescence molecular tomography imaging system, and demonstrated the capability of the platform to construct perfused collagen scaffolds with endothelial lining and to image both the fluid flow and fluorescent-labeled living endothelial cells at high-frame rates, with high sensitivity and accuracy. These results establish the potential of integrating both 3-D cell printing and fluorescence mesoscopic imaging for functional and molecular studies in complex tissue-engineered tissues.

  8. The Integration of 3-D Cell-Printing and Mesoscopic Fluorescence Molecular Tomography of Vascular Constructs within Thick Hydrogel Scaffolds

    PubMed Central

    Zhao, Lingling; Lee, Vivian K.; Yoo, Seung-Schik; Dai, Guohao; Intes, Xavier

    2012-01-01

    Developing methods that provide adequate vascular perfusion is an important step toward engineering large functional tissues. Meanwhile, an imaging modality to assess the three-dimensional (3-D) structures and functions of the vascular channels is lacking for thick matrices (>2~3mm). Herein, we report on an original approach to construct and image 3-D dynamically perfused vascular structures in thick hydrogel scaffolds. In this work, we integrated a robotic 3-D cell-printing technology with a mesoscopic fluorescence molecular tomography imaging system, and demonstrated the capability of the platform to construct perfused collagen scaffolds with endothelial lining and to image both the fluid flow and fluorescent-labeled living endothelial cells at high-frame rates, with high sensitivity and accuracy. These results establish the potential of integrating both 3-D cell-printing and fluorescence mesoscopic imaging for functional and molecular studies in complex tissue engineered tissues. PMID:22531221

  9. The DBHS proteins SFPQ, NONO and PSPC1: a multipurpose molecular scaffold

    PubMed Central

    Knott, Gavin J.; Bond, Charles S.; Fox, Archa H.

    2016-01-01

    Nuclear proteins are often given a concise title that captures their function, such as ‘transcription factor,’ ‘polymerase’ or ‘nuclear-receptor.’ However, for members of the Drosophila behavior/human splicing (DBHS) protein family, no such clean-cut title exists. DBHS proteins are frequently identified engaging in almost every step of gene regulation, including but not limited to, transcriptional regulation, RNA processing and transport, and DNA repair. Herein, we present a coherent picture of DBHS proteins, integrating recent structural insights on dimerization, nucleic acid binding modalities and oligomerization propensity with biological function. The emerging paradigm describes a family of dynamic proteins mediating a wide range of protein–protein and protein–nucleic acid interactions, on the whole acting as a multipurpose molecular scaffold. Overall, significant steps toward appreciating the role of DBHS proteins have been made, but we are only beginning to understand the complexity and broader importance of this family in cellular biology. PMID:27084935

  10. Scaffolding Students' Online Critiquing of Expert- and Peer-generated Molecular Models of Chemical Reactions

    NASA Astrophysics Data System (ADS)

    Chang, Hsin-Yi; Chang, Hsiang-Chi

    2013-08-01

    In this study, we developed online critiquing activities using an open-source computer learning environment. We investigated how well the activities scaffolded students to critique molecular models of chemical reactions made by scientists, peers, and a fictitious peer, and whether the activities enhanced the students' understanding of science models and chemical reactions. The activities were implemented in an eighth-grade class with 28 students in a public junior high school in southern Taiwan. The study employed mixed research methods. Data collected included pre- and post-instructional assessments, post-instructional interviews, and students' electronic written responses and oral discussions during the critiquing activities. The results indicated that these activities guided the students to produce overall quality critiques. Also, the students developed a more sophisticated understanding of chemical reactions and scientific models as a result of the intervention. Design considerations for effective model critiquing activities are discussed based on observational results, including the use of peer-generated artefacts for critiquing to promote motivation and collaboration, coupled with critiques of scientific models to enhance students' epistemological understanding of model purpose and communication.

  11. Syntheses of steroid-based molecularly imprinted polymers and their molecular recognition study with spectrometric detection

    NASA Astrophysics Data System (ADS)

    Dong, He; Tong, Ai-jun; Li, Long-di

    2003-01-01

    Recognition of five steroid compounds, β-estradiol, ethynylestradiol, estradiolbenzoate, testosterone and methyltestosterone were studied using a synthesized molecularly imprinted polymer (MIP). When β-estradiol was used as the template molecule, the polymer was synthesized with methacrylic acid (MAA) as the functional monomer and ethylene glycol dimethacrylate (EGDMA) as the cross linking agent through non-covalent interactions. It is found that the kind of porogen solvent and the polymerization conditions greatly affected the binding ability of a MIP to a certain molecule. Releasing of the template was performed by continuous extraction with methanol containing 10% acetic acid in a Soxhlet extractor. Our results indicated that such carefully synthesized MIP showed specific affinity toward β-estradiol in the adsorption process.

  12. Characteristics of high-molecular-weight hyaluronic acid as a brain-derived neurotrophic factor scaffold in periodontal tissue regeneration.

    PubMed

    Takeda, Katsuhiro; Sakai, Noriyuki; Shiba, Hideki; Nagahara, Takayoshi; Fujita, Tsuyoshi; Kajiya, Mikihito; Iwata, Tomoyuki; Matsuda, Shinji; Kawahara, Kazuko; Kawaguchi, Hiroyuki; Kurihara, Hidemi

    2011-04-01

    Brain-derived neurotrophic factor (BDNF), for which bovine collagen-derived atelocollagen is used as a scaffold, enhances periodontal tissue regeneration. However, a scaffold that does not contain unknown ingredients is preferable. Since the synthesized high-molecular-weight (HMW)-hyaluronic acid (HA) is safe and inexpensive, we evaluated the efficacy of HMW-HA as a BDNF scaffold. CD44, a major receptor of HA, was expressed in cultures of human periodontal ligament cells, and HMW-HA promoted the adhesion and proliferation of human periodontal ligament cells, although it did not influence the mRNA expression of bone (cementum)-related proteins. The in vitro release kinetics of BDNF from HMW-HA showed that BDNF release was sustained for 14 days. Subsequently, we examined the effect of BDNF/HMW-HA complex on periodontal tissue regeneration in dogs. A greater volume of newly formed alveolar bone and a longer newly formed cementum were observed in the BDNF/HMW-HA group than in the HMW-HA group, suggesting that HMW-HA assists the regenerative capacity of BDNF, although HMW-HA itself does not enhance periodontal tissue regeneration. Neither the poly (lactic-co-glycolic acid) group nor the BDNF/poly (lactic-co-glycolic acid) group enhanced periodontal tissue regeneration. In conclusion, HMW-HA is an adequate scaffold for the clinical application of BDNF.

  13. Corona Phase Molecular Recognition (CoPhMoRe) to Enable New Nanosensor Interfaces

    NASA Astrophysics Data System (ADS)

    Strano, Michael

    2015-03-01

    Our lab at MIT has been interested in how the 1D and 2D electronic structures of carbon nanotubes and graphene respectively can be utilized to advance new concepts in molecular detection. We introduce CoPhMoRe or corona phase molecular recognition as a method of discovering synthetic antibodies, or nanotube-templated recognition sites from a heteropolymer library. We show that certain synthetic heteropolymers, once constrained onto a single-walled carbon nanotube by chemical adsorption, also form a new corona phase that exhibits highly selective recognition for specific molecules. To prove the generality of this phenomenon, we report three examples of heteropolymers-nanotube recognition complexes for riboflavin, L-thyroxine and estradiol. The platform opens new opportunities to create synthetic recognition sites for molecular detection. We have also extended this molecular recognition technique to neurotransmitters, producing the first fluorescent sensor for dopamine. Another area of advancement in biosensor development is the use of near infrared fluorescent carbon nanotube sensors for in-vivo detection. Here, we show that PEG-ligated d(AAAT)7 DNA wrapped SWNT are selective for nitric oxide, a vasodilator of blood vessels, and can be tail vein injected into mice and localized within the viable mouse liver. We use an SJL mouse model to study liver inflammation in vivo using the spatially and spectrally resolved nIR signature of the localized SWNT sensors.

  14. 3D-QSAR, molecular docking, and molecular dynamic simulations for prediction of new Hsp90 inhibitors based on isoxazole scaffold.

    PubMed

    Abbasi, Maryam; Sadeghi-Aliabadi, Hojjat; Amanlou, Massoud

    2017-05-24

    Heat shock protein 90(Hsp90), as a molecular chaperone, play a crucial role in folding and proper function of many proteins. Hsp90 inhibitors containing isoxazole scaffold are currently being used in the treatment of cancer as tumor suppressers. Here in the present studies, new compounds based on isoxazole scaffold were predicted using a combination of molecular modeling techniques including three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamic (MD) simulations. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were also done. The steric and electrostatic contour map of CoMFA and CoMSIA were created. Hydrophobic, hydrogen bond donor and acceptor of CoMSIA model also were generated, and new compounds were predicted by CoMFA and CoMSIA contour maps. To investigate the binding modes of the predicted compounds in the active site of Hsp90, a molecular docking simulation was carried out. MD simulations were also conducted to evaluate the obtained results on the best predicted compound and the best reported Hsp90 inhibitors in the 3D-QSAR model. Findings indicate that the predicted ligands were stable in the active site of Hsp90.

  15. pH response and molecular recognition in a low molecular weight peptide hydrogel.

    PubMed

    Lange, Stefanie C; Unsleber, Jan; Drücker, Patrick; Galla, Hans-Joachim; Waller, Mark P; Ravoo, Bart Jan

    2015-01-14

    In this article we report the preparation and characterization of a peptide-based hydrogel, which possesses characteristic rheological properties, is pH responsive and can be functionalized at its thiol function. The tripeptide N-(fluorenyl-9-methoxycarbonyl)-L-Cys(acetamidomethyl)-L-His-L-Cys-OH 1 forms stable supramolecular aggregates in water leading to hydrogels above 1.5 wt%. Rheological analysis of the hydrogel revealed visco-elastic and shear thinning properties of samples containing 1.5 wt% of peptide 1. The hydrogel reversibly responds to pH changes. Below and above pH 6, electrostatic repulsion of the peptide results in a weakening of the three-dimensional gel network. Based on atomic force microscopy, small angle X-ray scattering and molecular dynamics simulations, it is proposed that the peptide assembles into nanostructures that tend to entangle at higher concentrations in water. The development of functional materials based on the peptide assemblies was possible via thiol-ene-click chemistry of the free thiol function at the C-terminal cysteine unit. As a proof of concept, the functionalization with adamantyl units to give 1-Ad was shown by molecular recognition of β-cyclodextrin vesicles. These vesicles were used as supramolecular cross-linkers of the assemblies of peptide 1 mixed with peptide 1-Ad leading to gel networks at a reduced peptide concentration.

  16. Supramolecular Scaffold for Tailoring the Two-Dimensional Assembly of Functional Molecular Units into Organic Thin Films.

    PubMed

    Leung, Franco King-Chi; Ishiwari, Fumitaka; Kajitani, Takashi; Shoji, Yoshiaki; Hikima, Takaaki; Takata, Masaki; Saeki, Akinori; Seki, Shu; Yamada, Yoichi M A; Fukushima, Takanori

    2016-09-14

    Tailoring structurally anisotropic molecular assemblies while controlling their orientation on solid substrates is an important subject for advanced technologies that use organic thin films. Here we report a supramolecular scaffold based on tripodal triptycene assemblies, which enables functional molecular units to assemble into a highly oriented, multilayered two-dimensional (2D) structure on solid substrates. The triptycene building block carries an ethynyl group and three flexible side chains at the 10- and 1,8,13-positions, respectively. These bridgehead-substituted tripodal triptycenes self-assembled on solid substrates to form a well-defined "2D hexagonal + 1D lamellar" structure, which developed parallel to the surface of the substrates. Remarkably, the assembling properties of the triptycene building blocks, particularly for a derivative with tri(oxyethylene)-containing side chains, were not impaired when the alkyne terminal was functionalized with a large molecular unit such as C60, which is comparable in diameter to the triptycene framework. Consequently, thin films with a multilayered 2D assembly of the C60 unit were obtained. Flash-photolysis time-resolved microwave conductivity (FP-TRMC) measurements revealed that the C60 film exhibits highly anisotropic charge-transport properties. Bridgehead-substituted tripodal triptycenes may provide a versatile supramolecular scaffold for tailoring the 2D assembly of molecular units into a highly oriented thin film, and in turn for exploiting the full potential of anisotropic molecular functions.

  17. Protected amine labels: a versatile molecular scaffold for multiplexed nominal mass and sub-Da isotopologue quantitative proteomic reagents.

    PubMed

    Ficarro, Scott B; Biagi, Jessica M; Wang, Jinhua; Scotcher, Jenna; Koleva, Rositsa I; Card, Joseph D; Adelmant, Guillaume; He, Huan; Askenazi, Manor; Marshall, Alan G; Young, Nicolas L; Gray, Nathanael S; Marto, Jarrod A

    2014-04-01

    We assemble a versatile molecular scaffold from simple building blocks to create binary and multiplexed stable isotope reagents for quantitative mass spectrometry. Termed Protected Amine Labels (PAL), these reagents offer multiple analytical figures of merit including, (1) robust targeting of peptide N-termini and lysyl side chains, (2) optimal mass spectrometry ionization efficiency through regeneration of primary amines on labeled peptides, (3) an amino acid-based mass tag that incorporates heavy isotopes of carbon, nitrogen, and oxygen to ensure matched physicochemical and MS/MS fragmentation behavior among labeled peptides, and (4) a molecularly efficient architecture, in which the majority of hetero-atom centers can be used to synthesize a variety of nominal mass and sub-Da isotopologue stable isotope reagents. We demonstrate the performance of these reagents in well-established strategies whereby up to four channels of peptide isotopomers, each separated by 4 Da, are quantified in MS-level scans with accuracies comparable to current commercial reagents. In addition, we utilize the PAL scaffold to create isotopologue reagents in which labeled peptide analogs differ in mass based on the binding energy in carbon and nitrogen nuclei, thereby allowing quantification based on MS or MS/MS spectra. We demonstrate accurate quantification for reagents that support 6-plex labeling and propose extension of this scheme to 9-channels based on a similar PAL scaffold. Finally, we provide exemplar data that extend the application of isotopologe-based quantification reagents to medium resolution, quadrupole time-of-flight mass spectrometers.

  18. Intersectin (ITSN) Family of Scaffolds Function as Molecular Hubs in Protein Interaction Networks

    PubMed Central

    Wong, Katy A.; Wilson, Jessica; Russo, Angela; Wang, Li; Okur, Mustafa Nazir; Wang, Xuerong; Martin, Negin P.; Scappini, Erica; Carnegie, Graeme K.; O'Bryan, John P.

    2012-01-01

    Members of the intersectin (ITSN) family of scaffold proteins consist of multiple modular domains, each with distinct ligand preferences. Although ITSNs were initially implicated in the regulation of endocytosis, subsequent studies have revealed a more complex role for these scaffold proteins in regulation of additional biochemical pathways. In this study, we performed a high throughput yeast two-hybrid screen to identify additional pathways regulated by these scaffolds. Although several known ITSN binding partners were identified, we isolated more than 100 new targets for the two mammalian ITSN proteins, ITSN1 and ITSN2. We present the characterization of several of these new targets which implicate ITSNs in the regulation of the Rab and Arf GTPase pathways as well as regulation of the disrupted in schizophrenia 1 (DISC1) interactome. In addition, we demonstrate that ITSN proteins form homomeric and heteromeric complexes with each other revealing an added level of complexity in the function of these evolutionarily conserved scaffolds. PMID:22558309

  19. Molecular Recognition of Insulin by a Synthetic Receptor

    SciTech Connect

    Chinai, Jordan M.; Taylor, Alexander B.; Ryno, Lisa M.; Hargreaves, Nicholas D.; Morris, Christopher A.; Hart, P. John; Urbach, Adam R.

    2011-08-29

    The discovery of molecules that bind tightly and selectively to desired proteins continues to drive innovation at the interface of chemistry and biology. This paper describes the binding of human insulin by the synthetic receptor cucurbit[7]uril (Q7) in vitro. Isothermal titration calorimetry and fluorescence spectroscopy experiments show that Q7 binds to insulin with an equilibrium association constant of 1.5 x 10{sup 6} M{sup -1} and with 50-100-fold selectivity versus proteins that are much larger but lack an N-terminal aromatic residue, and with >1000-fold selectivity versus an insulin variant lacking the N-terminal phenylalanine (Phe) residue. The crystal structure of the Q7{center_dot}insulin complex shows that binding occurs at the N-terminal Phe residue and that the N-terminus unfolds to enable binding. These findings suggest that site-selective recognition is based on the properties inherent to a protein terminus, including the unique chemical epitope presented by the terminal residue and the greater freedom of the terminus to unfold, like the end of a ball of string, to accommodate binding. Insulin recognition was predicted accurately from studies on short peptides and exemplifies an approach to protein recognition by targeting the terminus.

  20. Molecular imprinting of proteins emerging as a tool for protein recognition.

    PubMed

    Takeuchi, Toshifumi; Hishiya, Takayuki

    2008-07-21

    This article gives the recent developments in molecular imprinting for proteins. Currently bio-macromolecules such as antibodies and enzymes are mainly employed for protein recognition purposes. However, such bio-macromolecules are sometimes difficult to find and/or produce, therefore, receptor-like synthetic materials such as protein-imprinted polymers have been intensively studied as substitutes for natural receptors. Recent advances in protein imprinting shown here demonstrate the possibility of this technique as a future technology of protein recognition.

  1. Molecular recognition of human ephrinB2 cell surface receptor by an emergent African henipavirus.

    PubMed

    Lee, Benhur; Pernet, Olivier; Ahmed, Asim A; Zeltina, Antra; Beaty, Shannon M; Bowden, Thomas A

    2015-04-28

    The discovery of African henipaviruses (HNVs) related to pathogenic Hendra virus (HeV) and Nipah virus (NiV) from Southeast Asia and Australia presents an open-ended health risk. Cell receptor use by emerging African HNVs at the stage of host-cell entry is a key parameter when considering the potential for spillover and infection of human populations. The attachment glycoprotein from a Ghanaian bat isolate (GhV-G) exhibits <30% sequence identity with Asiatic NiV-G/HeV-G. Here, through functional and structural analysis of GhV-G, we show how this African HNV targets the same human cell-surface receptor (ephrinB2) as the Asiatic HNVs. We first characterized this virus-receptor interaction crystallographically. Compared with extant HNV-G-ephrinB2 structures, there was significant structural variation in the six-bladed β-propeller scaffold of the GhV-G receptor-binding domain, but not the Greek key fold of the bound ephrinB2. Analysis revealed a surprisingly conserved mode of ephrinB2 interaction that reflects an ongoing evolutionary constraint among geographically distal and phylogenetically divergent HNVs to maintain the functionality of ephrinB2 recognition during virus-host entry. Interestingly, unlike NiV-G/HeV-G, we could not detect binding of GhV-G to ephrinB3. Comparative structure-function analysis further revealed several distinguishing features of HNV-G function: a secondary ephrinB2 interaction site that contributes to more efficient ephrinB2-mediated entry in NiV-G relative to GhV-G and cognate residues at the very C terminus of GhV-G (absent in Asiatic HNV-Gs) that are vital for efficient receptor-induced fusion, but not receptor binding per se. These data provide molecular-level details for evaluating the likelihood of African HNVs to spill over into human populations.

  2. Molecular recognition of human ephrinB2 cell surface receptor by an emergent African henipavirus

    PubMed Central

    Lee, Benhur; Pernet, Olivier; Ahmed, Asim A.; Zeltina, Antra; Beaty, Shannon M.; Bowden, Thomas A.

    2015-01-01

    The discovery of African henipaviruses (HNVs) related to pathogenic Hendra virus (HeV) and Nipah virus (NiV) from Southeast Asia and Australia presents an open-ended health risk. Cell receptor use by emerging African HNVs at the stage of host-cell entry is a key parameter when considering the potential for spillover and infection of human populations. The attachment glycoprotein from a Ghanaian bat isolate (GhV-G) exhibits <30% sequence identity with Asiatic NiV-G/HeV-G. Here, through functional and structural analysis of GhV-G, we show how this African HNV targets the same human cell-surface receptor (ephrinB2) as the Asiatic HNVs. We first characterized this virus−receptor interaction crystallographically. Compared with extant HNV-G–ephrinB2 structures, there was significant structural variation in the six-bladed β-propeller scaffold of the GhV-G receptor-binding domain, but not the Greek key fold of the bound ephrinB2. Analysis revealed a surprisingly conserved mode of ephrinB2 interaction that reflects an ongoing evolutionary constraint among geographically distal and phylogenetically divergent HNVs to maintain the functionality of ephrinB2 recognition during virus–host entry. Interestingly, unlike NiV-G/HeV-G, we could not detect binding of GhV-G to ephrinB3. Comparative structure–function analysis further revealed several distinguishing features of HNV-G function: a secondary ephrinB2 interaction site that contributes to more efficient ephrinB2-mediated entry in NiV-G relative to GhV-G and cognate residues at the very C terminus of GhV-G (absent in Asiatic HNV-Gs) that are vital for efficient receptor-induced fusion, but not receptor binding per se. These data provide molecular-level details for evaluating the likelihood of African HNVs to spill over into human populations. PMID:25825759

  3. Molecular recognition of organic ammonium ions in solution using synthetic receptors

    PubMed Central

    Späth, Andreas

    2010-01-01

    Summary Ammonium ions are ubiquitous in chemistry and molecular biology. Considerable efforts have been undertaken to develop synthetic receptors for their selective molecular recognition. The type of host compounds for organic ammonium ion binding span a wide range from crown ethers to calixarenes to metal complexes. Typical intermolecular interactions are hydrogen bonds, electrostatic and cation–π interactions, hydrophobic interactions or reversible covalent bond formation. In this review we discuss the different classes of synthetic receptors for organic ammonium ion recognition and illustrate the scope and limitations of each class with selected examples from the recent literature. The molecular recognition of ammonium ions in amino acids is included and the enantioselective binding of chiral ammonium ions by synthetic receptors is also covered. In our conclusion we compare the strengths and weaknesses of the different types of ammonium ion receptors which may help to select the best approach for specific applications. PMID:20502608

  4. [Study on molecular recognition technology in active constituents extracted and isolated from Aconitum pendulum].

    PubMed

    Ma, Xue-Qin; Li, Guo-Shan; Fu, Xue-Yan; Ma, Jing-Zu

    2011-03-01

    To investigate CD molecular recognition technology applied in active constituents extracted and isolated from traditional Chinese medicine--Aconitum pendulum. The inclusion constant and form probability of the inclusion complex of Aconitum pendulum with p-CD was calculated by UV spectra method. The active constituents of Aconitum pendulum were extracted and isolated by molecular recognition technology. The inclusion complex was identified by UV. The chemical constituents of Aconitum pendulum and inclusion complex was determined by HPLC. The analgesic effects of inclusion complex was investigated by experiment of intraperitoneal injection of acetic acid in rats. The inclusion complex was identified and confirmed by UV spectra method, the chemical components of inclusion complex were simple, and the content of active constituents increased significantly, the analgesic effects of inclusion complex was well. The molecular recognition technology can be used for extracting and isolating active constituents of Aconitum pendulum, and the effects are obvious.

  5. Molecular Recognition-Mediated Transformation of Single-Chain Polymer Nanoparticles into Crosslinked Polymer Films.

    PubMed

    Mahon, Clare S; McGurk, Christopher J; Watson, Scott M D; Fascione, Martin A; Sakonsinsiri, Chadamas; Turnbull, W Bruce; Fulton, David A

    2017-08-14

    We describe single-chain polymer nanoparticles (SCNPs) possessing intramolecular dynamic covalent crosslinks that can transform into polymer films through a molecular recognition-mediated crosslinking process. The SCNPs utilise molecular recognition with surface-immobilised proteins to concentrate upon a substrate, bringing the SCNPs into close spatial proximity with one another and allowing their dynamic covalent crosslinkers to undergo intra- to interpolymer chain crosslinking leading to the formation of polymeric film. SCNPs must possess both the capacity for specific molecular recognition and a dynamic nature to their intramolecular crosslinkers to form polymer films, and an investigation of the initial phase of film formation indicates it proceeds from features which form upon the surface then grow predominantly in the xy directions. This approach to polymer film formation presents a potential method to "wrap" surfaces displaying molecular recognition motifs-which could potentially include viral, cellular and bacterial surfaces or artificial surfaces displaying multivalent recognition motifs-within a layer of polymer film. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  6. Molecular Recognition Directed Self-Assembly of Supramolecular Liquid Crystals

    DTIC Science & Technology

    1994-06-30

    supramolecular (generated via H-bonding, ionic and electrostatic interactions) and molecular " polymer backbones" will be made. The formation of columnar hexagonal...electrostatic interactions) and molecular " polymer backbones" will be made. The formation of columnar hexagonal (0h), nematic and re-entrant isotropic phases by...trihydroxybenzoate with either bromoalkanes or with alkoxybenzyloxybenzyl chloride. Variants of these taper shaped side groups were attached to polymer

  7. Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles

    NASA Astrophysics Data System (ADS)

    Edwardson, Thomas G. W.; Lau, Kai Lin; Bousmail, Danny; Serpell, Christopher J.; Sleiman, Hanadi F.

    2016-02-01

    DNA nanotechnology offers unparalleled precision and programmability for the bottom-up organization of materials. This approach relies on pre-assembling a DNA scaffold, typically containing hundreds of different strands, and using it to position functional components. A particularly attractive strategy is to employ DNA nanostructures not as permanent scaffolds, but as transient, reusable templates to transfer essential information to other materials. To our knowledge, this approach, akin to top-down lithography, has not been examined. Here we report a molecular printing strategy that chemically transfers a discrete pattern of DNA strands from a three-dimensional DNA structure to a gold nanoparticle. We show that the particles inherit the DNA sequence configuration encoded in the parent template with high fidelity. This provides control over the number of DNA strands and their relative placement, directionality and sequence asymmetry. Importantly, the nanoparticles produced exhibit the site-specific addressability of DNA nanostructures, and are promising components for energy, information and biomedical applications.

  8. The Molecular Basis of N-End Rule Recognition

    SciTech Connect

    Wang, K.H.; Roman-Hernandez, G.; Grant, R.A.; Sauer, R.T.; Baker, T.A.

    2009-03-27

    The N-end rule targets specific proteins for destruction in prokaryotes and eukaryotes. Here, we report a crystal structure of a bacterial N-end rule adaptor, ClpS, bound to a peptide mimic of an N-end rule substrate. This structure, which was solved at a resolution of 1.15 {angstrom}, reveals specific recognition of the peptide {alpha}-amino group via hydrogen bonding and shows that the peptide's N-terminal tyrosine side chain is buried in a deep hydrophobic cleft that pre-exists on the surface of ClpS. The adaptor side chains that contact the peptide's N-terminal residue are highly conserved in orthologs and in E3 ubiquitin ligases that mediate eukaryotic N-end rule recognition. We show that mutation of critical ClpS contact residues abrogates substrate delivery to and degradation by the AAA+ protease ClpAP, demonstrate that modification of the hydrophobic pocket results in altered N-end rule specificity, and discuss functional implications for the mechanism of substrate delivery.

  9. Multipoint molecular recognition within a calix[6]arene funnel complex

    PubMed Central

    Coquière, David; de la Lande, Aurélien; Martí, Sergio; Parisel, Olivier; Prangé, Thierry; Reinaud, Olivia

    2009-01-01

    A multipoint recognition system based on a calix[6]arene is described. The calixarene core is decorated on alternating aromatic subunits by 3 imidazole arms at the small rim and 3 aniline groups at the large rim. This substitution pattern projects the aniline nitrogens toward each other when Zn(II) binds at the Tris-imidazole site or when a proton binds at an aniline. The XRD structure of the monoprotonated complex having an acetonitrile molecule bound to Zn(II) in the cavity revealed a constrained geometry at the metal center reminiscent of an entatic state. Computer modeling suggests that the aniline groups behave as a tritopic monobasic site in which only 1 aniline unit is protonated and interacts with the other 2 through strong hydrogen bonding. The metal complex selectively binds a monoprotonated diamine vs. a monoamine through multipoint recognition: coordination to the metal ion at the small rim, hydrogen bonding to the calix-oxygen core, CH/π interaction within the cavity's aromatic walls, and H-bonding to the anilines at the large rim. PMID:19237564

  10. Strategy for molecular beacon binding readout: separating molecular recognition element and signal reporter.

    PubMed

    Wang, Yongxiang; Li, Jishan; Jin, Jianyu; Wang, Hao; Tang, Hongxing; Yang, Ronghua; Wang, Kemin

    2009-12-01

    A new strategy for molecular beacon binding readout is proposed by using separation of the molecular recognition element and signal reporter. The signal transduction of the target binding event is based on displacing interaction between the target DNA and a competitor, the signal transducer. The target-free capture DNA is first interacted with the competitor, forming an assembled complex. In the presence of a target DNA that the affinity is stronger than that of the competitor, hybridization between capture DNA and the target disassembles the assembled complex and releases the free competitor to change the readout of the signal reporter. To demonstrate the feasibility of the design, a thymine-rich oligonucleotide was examined as a model system. Hg2+ was selected as the competitor, and mercaptoacetic acid-coated CdTe/ZnS quantum dots served as the fluorescent reporter. Selective binding of Hg2+ between the two thymine bases of the capture DNA forms a hairpin-structure. Hybridization between the capture DNA and target DNA destroys the hairpin-structure, releasing Hg2+ ions to quench the quantum dots fluorescence. Under the optimal conditions, fluorescence intensity of the quantum dots against the concentration of perfect cDNA was linear over the concentration range of 0.1-1.6 microM, with a limit of detection of 25 nM. This new assay method is simple in design, avoiding any oligonucleotide labeling. Furthermore, this strategy is generalizable since any target binding can in principle release the signal transducer and be detected with separated signal reporter.

  11. Effects of substitution groups of glutamide-derived molecular gels on molecular shape recognition.

    PubMed

    Noguchi, Hiroki; Charoenraks, Tiraporn; Takafuji, Makoto; Ihara, Hirotaka

    2015-05-01

    We have reported that self-assembling glutamide lipid-grafted porous silica particles show high selectivity towards polycyclic aromatic hydrocarbons (PAHs) and bio-molecules. This enhancement of molecular recognition is brought about by the formation of a highly ordered structure in the glutamide lipid through intermolecular hydrogen bonding. To utilise, for selective separations, the highly oriented structure of glutamide lipids on the silica surface, in this study, we synthesised four glutamide lipids with different substitution groups and studied the separation behaviours of the glutamide lipid-grafted porous silica particles as reversed phase high-performance liquid chromatography (RP-HPLC) stationary phases. According to the HPLC studies, the functional group substitutions and the spacer group connecting the glutamide moiety and silica surface had a noticeable effect on the retention behaviours. Particularly, glutamide lipids with a long spacer group (C10) showed a higher selectivity towards positional (o-/m-/p-terphenyl) and geometrical (cis-/trans-stilbene) isomers. Differential scanning calorimetric and Fourier transform infrared spectroscopic studies suggested that the long spacer group induced the assembled structure of the glutamide lipid on the silica surface. Interestingly, the glutamide lipids with dodecyl groups and benzyl groups showed reverse elution orders towards the length to breadth ratio of PAHs.

  12. Utilization of Molecular Dynamics Simulation Coupled with Experimental Assays to Optimize Biocompatibility of an Electrospun PCL/PVA Scaffold.

    PubMed

    Sarmadi, Morteza; Shamloo, Amir; Mohseni, Mina

    2017-01-01

    The main focus of this study is to address the possibility of using molecular dynamics (MD) simulation, as a computational framework, coupled with experimental assays, to optimize composite structures of a particular electrospun scaffold. To this aim, first, MD simulations were performed to obtain an initial theoretical insight into the capability of heterogeneous surfaces for protein adsorption. The surfaces were composed of six different blends of PVA (polyvinyl alcohol) and PCL (polycaprolactone) with completely unlike hydrophobicity. Next, MTT assay was performed on the electrospun scaffolds made from the same percentages of polymers as in MD models to gain an understanding of the correlation between protein adsorption on the composite surfaces and their capability for cell proliferation. To perform simulations, two ECM (extracellular matrix) protein fragments, namely, collagen type I and fibronectin, two essential proteins for initial cell attachment and eventual cell proliferation, were considered. To evaluate the strength of protein adsorption, adhesion energy and final conformations of proteins were studied. For MTT analysis, different blends of PCL/PVA electrospun scaffolds were prepared, on which endothelial cells were cultured for one week. Theoretical results indicated that the samples with more than 50% of PCL significantly represented stronger protein adsorption. In agreement with simulation results, experimental analysis also demonstrated that the more hydrophobic the surface became, the better initial cell attachment and cell proliferation could be achieved, which was particularly better observed in samples with more than 70% of PCL.

  13. Utilization of Molecular Dynamics Simulation Coupled with Experimental Assays to Optimize Biocompatibility of an Electrospun PCL/PVA Scaffold

    PubMed Central

    Sarmadi, Morteza; Shamloo, Amir; Mohseni, Mina

    2017-01-01

    The main focus of this study is to address the possibility of using molecular dynamics (MD) simulation, as a computational framework, coupled with experimental assays, to optimize composite structures of a particular electrospun scaffold. To this aim, first, MD simulations were performed to obtain an initial theoretical insight into the capability of heterogeneous surfaces for protein adsorption. The surfaces were composed of six different blends of PVA (polyvinyl alcohol) and PCL (polycaprolactone) with completely unlike hydrophobicity. Next, MTT assay was performed on the electrospun scaffolds made from the same percentages of polymers as in MD models to gain an understanding of the correlation between protein adsorption on the composite surfaces and their capability for cell proliferation. To perform simulations, two ECM (extracellular matrix) protein fragments, namely, collagen type I and fibronectin, two essential proteins for initial cell attachment and eventual cell proliferation, were considered. To evaluate the strength of protein adsorption, adhesion energy and final conformations of proteins were studied. For MTT analysis, different blends of PCL/PVA electrospun scaffolds were prepared, on which endothelial cells were cultured for one week. Theoretical results indicated that the samples with more than 50% of PCL significantly represented stronger protein adsorption. In agreement with simulation results, experimental analysis also demonstrated that the more hydrophobic the surface became, the better initial cell attachment and cell proliferation could be achieved, which was particularly better observed in samples with more than 70% of PCL. PMID:28118371

  14. Molecular Recognition and Structural Influences on Function in Bio-nanosystems of Nucleic Acids and Proteins

    NASA Astrophysics Data System (ADS)

    Sethaphong, Latsavongsakda

    This work examines smart material properties of rational self-assembly and molecular recognition found in nano-biosystems. Exploiting the sequence and structural information encoded within nucleic acids and proteins will permit programmed synthesis of nanomaterials and help create molecular machines that may carry out new roles involving chemical catalysis and bioenergy. Responsive to different ionic environments thru self-reorgnization, nucleic acids (NA) are nature's signature smart material; organisms such as viruses and bacteria use features of NAs to react to their environment and orchestrate their lifecycle. Furthermore, nucleic acid systems (both RNA and DNA) are currently exploited as scaffolds; recent applications have been showcased to build bioelectronics and biotemplated nanostructures via directed assembly of multidimensional nanoelectronic devices 1. Since the most stable and rudimentary structure of nucleic acids is the helical duplex, these were modeled in order to examine the influence of the microenvironment, sequence, and cation-dependent perturbations of their canonical forms. Due to their negatively charged phosphate backbone, NA's rely on counterions to overcome the inherent repulsive forces that arise from the assembly of two complementary strands. As a realistic model system, we chose the HIV-TAR helix (PDB ID: 397D) to study specific sequence motifs on cation sequestration. At physiologically relevant concentrations of sodium and potassium ions, we observed sequence based effects where purine stretches were adept in retaining high residency cations. The transitional space between adenine and guanosine nucleotides (ApG step) in a sequence proved the most favorable. This work was the first to directly show these subtle interactions of sequence based cationic sequestration and may be useful for controlling metallization of nucleic acids in conductive nanowires. Extending the study further, we explored the degree to which the structure of NA

  15. Protein dynamics and conformational disorder in molecular recognition.

    PubMed

    Mittag, Tanja; Kay, Lewis E; Forman-Kay, Julie D

    2010-01-01

    Recognition requires protein flexibility because it facilitates conformational rearrangements and induced-fit mechanisms upon target binding. Intrinsic disorder is an extreme on the continuous spectrum of possible protein dynamics and its role in recognition may seem counterintuitive. However, conformational disorder is widely found in many eukaryotic regulatory proteins involved in processes such as signal transduction and transcription. Disordered protein regions may in fact confer advantages over folded proteins in binding. Rapidly interconverting and diverse conformers may create mean electrostatic fields instead of presenting discrete charges. The resultant "polyelectrostatic" interactions allow for the utilization of post-translational modifications as a means to change the net charge and thereby modify the electrostatic interaction of a disordered region. Plasticity of disordered protein states enables steric advantages over folded proteins and allows for unique binding configurations. Disorder may also have evolutionary advantages, as it facilitates alternative splicing, domain shuffling and protein modularity. As proteins exist in a continuous spectrum of disorder, so do their complexes. Indeed, disordered regions in complexes may control the degree of motion between domains, mask binding sites, be targets of post-translational modifications, permit overlapping binding motifs, and enable transient binding of different binding partners, making them excellent candidates for signal integrators and explaining their prevalence in eukaryotic signaling pathways. "Dynamic" complexes arise if more than two transient protein interfaces are involved in complex formation of two binding partners in a dynamic equilibrium. "Disordered" complexes, in contrast, do not involve significant ordering of interacting protein segments but rely exclusively on transient contacts. The nature of these interactions is not well understood yet but advancements in the structural

  16. Molecular recognition of the Thomsen-Friedenreich antigen-threonine conjugate by adhesion/growth regulatory galectin-3: nuclear magnetic resonance studies and molecular dynamics simulations.

    PubMed

    Yongye, Austin B; Calle, Luis; Ardá, Ana; Jiménez-Barbero, Jesús; André, Sabine; Gabius, Hans-Joachim; Martínez-Mayorga, Karina; Cudic, Mare

    2012-09-18

    Nuclear magnetic resonance (NMR) spectroscopy and molecular modeling methods have been strategically combined to elucidate the molecular recognition features of the binding of threonine O-linked Thomsen-Friedenreich (TF) antigen to chimera-type avian galectin-3 (CG-3). Saturation transfer difference (STD) NMR experiments revealed the highest intensities for the H4 protons of both the β-D-Galp and α-D-GalpNAc moieties, with 100 and 71% of relative STD, respectively. The methyl protons of the threonine residue exhibited a small STD effect, <15%, indicating that the interaction of the amino acid with the protein is rather transient. Two-dimensional transferred nuclear Overhauser effect spectroscopy NMR experiments and molecular modeling suggested some differences in conformer populations between the free and bound states. A dynamic binding mode for the TF antigen-CG-3 complex consisting of two poses has been deduced. In one pose, intermolecular interactions were formed between the terminal threonine residue and the receptor. In the second pose, intermolecular interactions involved the internal GalpNAc. The difference in the trend of some shifts in the heteronuclear single-quantum coherence titration spectra indicates some disparities in the binding interactions of CG-3 with lactose and TF antigen. The results obtained from this model of the avian orthologue of human galectin-3 will allow detailed interspecies comparison to give sequence deviations in phylogeny a structural and functional meaning. Moreover, the results indicate that the peptide scaffold presenting TF antigen could be relevant for binding and thus provides a possible route for the design of galectin-3 inhibitors with improved affinity and selectivity.

  17. Molecular Recognition Directed Self-Assembly of Supramolecular Architectures

    DTIC Science & Technology

    1994-06-30

    chemistry. The ability of these supramolecular architectures to form liquid crystalline phases is determined by the shape of the self-assembled...be discussed. In the case of TMV-like supramolecular architectures a comparison between various supramolecdr (generated via H-bonding, ionic and...molecular, macromolecular and supramolecular chemistry. The ability of these supramolecular architectures to form liquid crystalline phases is determined

  18. Structural insights for engineering binding proteins based on non-antibody scaffolds.

    PubMed

    Gilbreth, Ryan N; Koide, Shohei

    2012-08-01

    Engineered binding proteins derived from non-antibody scaffolds constitute an increasingly prominent class of reagents in both research and therapeutic applications. The growing number of crystal structures of these 'alternative' scaffold-based binding proteins in complex with their targets illustrate the mechanisms of molecular recognition that are common among these systems and those unique to each. This information is useful for critically assessing and improving/expanding engineering strategies. Furthermore, the structural features of these synthetic proteins produced under tightly controlled, directed evolution deepen our understanding of the underlying principles governing molecular recognition.

  19. All-organic microelectromechanical systems integrating specific molecular recognition--a new generation of chemical sensors.

    PubMed

    Ayela, Cédric; Dubourg, Georges; Pellet, Claude; Haupt, Karsten

    2014-09-03

    Cantilever-type all-organic microelectromechanical systems based on molecularly imprinted polymers for specific analyte recognition are used as chemical sensors. They are produced by a simple spray-coating-shadow-masking process. Analyte binding to the cantilever generates a measurable change in its resonance frequency. This allows label-free detection by direct mass sensing of low-molecular-weight analytes at nanomolar concentrations.

  20. Molecular recognition properties of tartrates and metal-tartrates in solution and gas phase.

    PubMed

    Wijeratne, Aruna B; Schug, Kevin A

    2009-05-01

    Solution phase and gas phase chiral molecular recognition properties of tartrates (salts or esters of tartaric acid) and metal tartrates (binuclear tartrato(4-)-metal-bridged complexes) are reviewed in conjunction with their applications in enantiomeric separation science and their mass spectrometric chiral discrimination properties.

  1. Molecular recognition of nitrated fatty acids by PPAR[gamma

    SciTech Connect

    Li, Yong; Zhang, Jifeng; Schopfer, Francisco J.; Martynowski, Dariusz; Garcia-Barrio, Minerva T.; Kovach, Amanda; Suino-Powell, Kelly; Baker, Paul R.S.; Freeman, Bruce A.; Chen, Y. Eugene; Xu, H. Eric

    2010-03-08

    Peroxisome proliferator activated receptor-{gamma} (PPAR{gamma}) regulates metabolic homeostasis and adipocyte differentiation, and it is activated by oxidized and nitrated fatty acids. Here we report the crystal structure of the PPAR{gamma} ligand binding domain bound to nitrated linoleic acid, a potent endogenous ligand of PPAR{gamma}. Structural and functional studies of receptor-ligand interactions reveal the molecular basis of PPAR{gamma} discrimination of various naturally occurring fatty acid derivatives.

  2. Molecular recognition directed self-assembly of supramolecular architectures

    NASA Astrophysics Data System (ADS)

    Percec, C.; Heck, J.; Johansson, G.; Tomazos, D.; Kawasumi, M.

    1994-06-01

    This paper reviews some of our research on three classes of supramolecular architectures which are generated via various combinations of molecular, macromolecular and supramolecular chemistry. The ability of these supramolecular architectures to form liquid crystalline phases is determined by the shape of the self-assembled architecture and will be used to visualize it via various characterization techniques. The molecular design of selected examples of structural units containing taper shaped exo-receptors and crown-ether, oligooxyethylenic, and H-bonding based endo-receptors which self-assemble into cylindrical channel-like architectures via principles resembling those of tobacco mosaic virus (TMV), of macrocyclics which self-assemble into a willow-like architecture will be discussed. In the case of TMV-like supramolecular architectures a comparison between various supramolecular (generated via H-bonding, ionic and electrostatic interactions) and molecular 'polymer backbones' will be made. The present state of the art of the engineering of these supramolecular architectures and some possible novel material functions derived from them will be briefly mentioned.

  3. Molecular mechanism underlying promiscuous polyamine recognition by spermidine acetyltransferase.

    PubMed

    Sugiyama, Shigeru; Ishikawa, Sae; Tomitori, Hideyuki; Niiyama, Mayumi; Hirose, Mika; Miyazaki, Yuma; Higashi, Kyohei; Murata, Michio; Adachi, Hiroaki; Takano, Kazufumi; Murakami, Satoshi; Inoue, Tsuyoshi; Mori, Yusuke; Kashiwagi, Keiko; Igarashi, Kazuei; Matsumura, Hiroyoshi

    2016-07-01

    Spermidine acetyltransferase (SAT) from Escherichia coli, which catalyses the transfer of acetyl groups from acetyl-CoA to spermidine, is a key enzyme in controlling polyamine levels in prokaryotic cells. In this study, we determined the crystal structure of SAT in complex with spermidine (SPD) and CoA at 2.5Å resolution. SAT is a dodecamer organized as a hexamer of dimers. The secondary structural element and folding topology of the SAT dimer resemble those of spermidine/spermine N(1)-acetyltransferase (SSAT), suggesting an evolutionary link between SAT and SSAT. However, the polyamine specificity of SAT is distinct from that of SSAT and is promiscuous. The SPD molecule is also located at the inter-dimer interface. The distance between SPD and CoA molecules is 13Å. A deep, highly acidic, water-filled cavity encompasses the SPD and CoA binding sites. Structure-based mutagenesis and in-vitro assays identified SPD-bound residues, and the acidic residues lining the walls of the cavity are mostly essential for enzymatic activities. Based on mutagenesis and structural data, we propose an acetylation mechanism underlying promiscuous polyamine recognition for SAT. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Design, synthesis, and molecular recognition of phosphazene materials

    NASA Astrophysics Data System (ADS)

    Sunderland, Nicolas Jean

    2000-08-01

    This thesis represents several innovative approaches in the modification of polymers and solid-state hosts in order to obtain novel microstructures and properties. The first approach involves the use of cyclotriphosphazenes, a versatile class of hosts that generate tunnel clathrate adducts. Tris(o-phenylenedioxy)cyclotriphosphazene was found to form hexagonal host-guest inclusion adducts (clathrates) with the polymers: cis-1,4-polybutadiene, trans-1,4-polyisoprene, polyethylene, poly(ethylene oxide) and polytetrahydrofuran. Single crystal X-ray diffraction studies of both the polyethylene and poly(ethylene oxide) inclusion adduct revealed the presence of individual polymer chains extended along tunnel-like voids within the host lattice. Tris(o-phenylenedioxy)cyclotriphosphazene can entrap and separate various polymers and small molecules within its tunnels based on their microstructure, molecular weight, and end-group functionality. Inclusion adducts with various polymers show a preferential inclusion for the polymer that will best stabilize the hexagonal structure of the host. Separations based on end-groups show preferential inclusion of the species with the more hydrophobic end-groups. Polymers and small molecule hydrocarbons with higher molecular weights are preferentially included within the tunnel compared to analogues with lower molecular weights. The synthesis and inclusion properties of a new clathration host, tris(3,6-dimethylphenylenedioxy)cyclotriphosphazene, is described. The guest-free structure has a triclinic unit cell. The dioxane inclusion adduct crystallizes in a monoclinic system. The guest occupies a cage-like void located between the phosphazene rings. The poly(tetramethylene oxide) adduct crystallizes in a hexagonal system, with the guest located in tunnels created along the c-axis. Adduct formation also with tetrahydrofuran, methylene chloride, polyethylene and cis-polybutadiene. Modification of polymer properties is investigated by using a

  5. Protected Amine Labels: A Versatile Molecular Scaffold for Multiplexed Nominal Mass and Sub-Da Isotopologue Quantitative Proteomic Reagents

    PubMed Central

    Ficarro, Scott B.; Biagi, Jessica M.; Wang, Jinhua; Scotcher, Jenna; Koleva, Rositsa I.; Card, Joseph D.; Adelmant, Guillaume; He, Huan; Askenazi, Manor; Marshall, Alan G.; Young, Nicolas L.; Gray, Nathanael S.; Marto, Jarrod A.

    2014-01-01

    We assemble a versatile molecular scaffold from simple building blocks to create binary and multiplexed stable isotope reagents for quantitative mass spectrometry. Termed Protected Amine Labels (PAL), these reagents offer multiple analytical figures of merit including, (i) robust targeting of peptide N-termini and lysyl side chains, (ii) optimal mass spectrometry ionization efficiency through regeneration of primary amines on labeled peptides, (iii) an amino acid-based mass tag that incorporates heavy isotopes of carbon, nitrogen, and oxygen to ensure matched physicochemical and MS/MS fragmentation behavior among labeled peptides, and (iv) a molecularly efficient architecture, in which the majority of hetero-atom centers can be used to synthesize a variety of nominal mass and sub-Da isotopologue stable isotope reagents. We demonstrate the performance of these reagents in well-established strategies whereby up to four channels of peptide isotopomers, each separated by 4 Da are quantified in MS-level scans with accuracies comparable to current commercial reagents. In addition we utilize the PAL scaffold to create isotopologue reagents in which labeled peptide analogs differ in mass based on the binding energy in carbon and nitrogen nuclei, thereby allowing quantification based on MS or MS/MS spectra. We demonstrate accurate quantification for reagents that support 6-plex labeling and propose extension of this scheme to 9-channels based on a similar PAL scaffold. Finally we provide exemplar data that extends the application of isotopologe-based quantification reagents to medium resolution, quadrupole time-of-flight mass spectrometers. PMID:24496597

  6. Characterization of molecular recognition of STAT3 SH2 domain inhibitors through molecular simulation.

    PubMed

    Park, In-Hee; Li, Chenglong

    2011-01-01

    Signal transducer and activator of transcription 3 (STAT3) is an anti-cancer target protein due to its over-activation in tumor cells. The Tyr705-phosphorylated (pTyr) STAT3 binds to the pTyr-recognition site of its Src Homology 2 (SH2) domain of another STAT3 monomer to form a homo-dimer, which then causes cellular anti-apoptosis, proliferation, and tumor invasion. Recently, many STAT3 SH2 dimerization inhibitors have been discovered via both computational and experimental methods. To systematically assess their binding affinities and specificities, for eight representative inhibitors, we utilized molecular docking, molecular dynamics simulation, and ensuing energetic analysis to compare their binding characteristics. The inhibitors' binding free energies were calculated via MMPB(GB)SA, and the STAT3 SH2 binding "hot spots" were evaluated through binding energy decomposition and hydrogen bond (H-bond) distribution analysis. Several conclusions can be drawn: (1) the overall enthalpy-entropy compensation paradigm is preserved for the STAT3 SH2/ligand binding thermodynamics; (2) at one end of the binding spectrum, two compounds bind to SH2 due to their minimum entropic penalties that result from their relative rigidities and increased dynamics of SH2 upon their binding; at the other end of the binding spectrum, one compound shows a typical weak binder behavior due to its loose binding in the SH2's strongest enthalpy-contributing binding subsite; (3) hydrogen bonding seems a strong indicator to evaluate the SH2/ligand binding potency, which echoes a finding that CH/π non-classical H-bond is responsible for some pTyr peptides binding to their corresponding SH2 domains; (4) STAT3 SH2 domain possesses three binding "hot spots": pTyr705-binding pocket with polar residues and contributing the largest binding enthalpy (two-thirds); Leu706 subsite which is the most dynamic and hardest to target; a hydrophobic side pocket which is unique to STAT3 and very targetable, which

  7. ERK Signals: Scaffolding Scaffolds?

    PubMed Central

    Casar, Berta; Crespo, Piero

    2016-01-01

    ERK1/2 MAP Kinases become activated in response to multiple intra- and extra-cellular stimuli through a signaling module composed of sequential tiers of cytoplasmic kinases. Scaffold proteins regulate ERK signals by connecting the different components of the module into a multi-enzymatic complex by which signal amplitude and duration are fine-tuned, and also provide signal fidelity by isolating this complex from external interferences. In addition, scaffold proteins play a central role as spatial regulators of ERKs signals. In this respect, depending on the subcellular localization from which the activating signals emanate, defined scaffolds specify which substrates are amenable to be phosphorylated. Recent evidence has unveiled direct interactions among different scaffold protein species. These scaffold-scaffold macro-complexes could constitute an additional level of regulation for ERK signals and may serve as nodes for the integration of incoming signals and the subsequent diversification of the outgoing signals with respect to substrate engagement. PMID:27303664

  8. Imprinting of Molecular Recognition Sites on Nanostructures and Its Applications in Chemosensors.

    PubMed

    Guan, Guijian; Liu, Bianhua; Wang, Zhenyang; Zhang, Zhongping

    2008-12-15

    Biological receptors including enzymes, antibodies and active proteins have been widely used as the detection platform in a variety of chemo/biosensors and bioassays. However, the use of artificial host materials in chemical/biological detections has become increasingly attractive, because the synthetic recognition systems such as molecularly imprinted polymers (MIPs) usually have lower costs, higher physical/chemical stability, easier preparation and better engineering possibility than biological receptors. Molecular imprinting is one of the most efficient strategies to offer a synthetic route to artificial recognition systems by a template polymerization technique, and has attracted considerable efforts due to its importance in separation, chemo/biosensors, catalysis and biomedicine. Despite the fact that MIPs have molecular recognition ability similar to that of biological receptors, traditional bulky MIP materials usually exhibit a low binding capacity and slow binding kinetics to the target species. Moreover, the MIP materials lack the signal-output response to analyte binding events when used as recognition elements in chemo/biosensors or bioassays. Recently, various explorations have demonstrated that molecular imprinting nanotechniques may provide a potential solution to these difficulties. Many successful examples of the development of MIP-based sensors have also been reported during the past several decades. This review will begin with a brief introduction to the principle of molecular imprinting nanotechnology, and then mainly summarize various synthesis methodologies and recognition properties of MIP nanomaterials and their applications in MIP-based chemosensors. Finally, the future perspectives and efforts in MIP nanomaterials and MIP-based sensors are given.

  9. Imprinting of Molecular Recognition Sites on Nanostructures and Its Applications in Chemosensors

    PubMed Central

    Guan, Guijian; Liu, Bianhua; Wang, Zhenyang; Zhang, Zhongping

    2008-01-01

    Biological receptors including enzymes, antibodies and active proteins have been widely used as the detection platform in a variety of chemo/biosensors and bioassays. However, the use of artificial host materials in chemical/biological detections has become increasingly attractive, because the synthetic recognition systems such as molecularly imprinted polymers (MIPs) usually have lower costs, higher physical/chemical stability, easier preparation and better engineering possibility than biological receptors. Molecular imprinting is one of the most efficient strategies to offer a synthetic route to artificial recognition systems by a template polymerization technique, and has attracted considerable efforts due to its importance in separation, chemo/biosensors, catalysis and biomedicine. Despite the fact that MIPs have molecular recognition ability similar to that of biological receptors, traditional bulky MIP materials usually exhibit a low binding capacity and slow binding kinetics to the target species. Moreover, the MIP materials lack the signal-output response to analyte binding events when used as recognition elements in chemo/biosensors or bioassays. Recently, various explorations have demonstrated that molecular imprinting nanotechniques may provide a potential solution to these difficulties. Many successful examples of the development of MIP-based sensors have also been reported during the past several decades. This review will begin with a brief introduction to the principle of molecular imprinting nanotechnology, and then mainly summarize various synthesis methodologies and recognition properties of MIP nanomaterials and their applications in MIP-based chemosensors. Finally, the future perspectives and efforts in MIP nanomaterials and MIP-based sensors are given. PMID:27873989

  10. Molecular Recognition at Purine and Pyrimidine Nucleotide (P2) Receptors

    PubMed Central

    Jacobson, Kenneth A.; Constanzi, Stefano; Ohno, Michihiro; Joshi, Bhalchandra V.; Besada, Pedro; Xu, Bin; Tchilibon, Susanna

    2015-01-01

    In comparison to other classes of cell surface receptors, the medicinal chemistry at P2X (ligand-gated ion channels) and P2Y (G protein-coupled) nucleotide receptors has been relatively slow to develop. Recent effort to design selective agonists and antagonists based on a combination of library screening, empirical modification of known ligands, and rational design have led to the introduction of potent antagonists of the P2X1 (derivatives of pyridoxal phosphates and suramin), P2X3 (A-317491), P2X7 (derivatives of the isoquinoline KN-62), P2Y1 (nucleotide analogues MRS 2179 and MRS 2279), P2Y2 (thiouracil derivatives such as AR-C126313), and P2Y12 (nucleotide/nucleoside analogues AR-C69931X and AZD6140) receptors. A variety of native agonist ligands (ATP, ADP, UTP, UDP, and UDP-glucose) are currently the subject of structural modification efforts to improve selectivity. MRS2365 is a selective agonist for P2Y1 receptors. The dinucleotide INS 37217 potently activates the P2Y2 receptor. UTP-γ-S and UDP-β-S are selective agonists for P2Y2/P2Y4 and P2Y6 receptors, respectively. The current knowledge of the structures of P2X and P2Y receptors, is derived mainly from mutagenesis studies. Site-directed mutagenesis has shown that ligand recognition in the human P2Y1 receptor involves individual residues of both the TMs (3, 5, 6, and 7), as well as EL 2 and 3. The binding of the negatively-charged phosphate moiety is dependent on positively charged lysine and arginine residues near the exofacial side of TMs 3 and 7. PMID:15078212

  11. Autophagic clearance of bacterial pathogens: molecular recognition of intracellular microorganisms.

    PubMed

    Pareja, Maria Eugenia Mansilla; Colombo, Maria I

    2013-01-01

    Autophagy is involved in several physiological and pathological processes. One of the key roles of the autophagic pathway is to participate in the first line of defense against the invasion of pathogens, as part of the innate immune response. Targeting of intracellular bacteria by the autophagic machinery, either in the cytoplasm or within vacuolar compartments, helps to control bacterial proliferation in the host cell, controlling also the spreading of the infection. In this review we will describe the means used by diverse bacterial pathogens to survive intracellularly and how they are recognized by the autophagic molecular machinery, as well as the mechanisms used to avoid autophagic clearance.

  12. Autophagic clearance of bacterial pathogens: molecular recognition of intracellular microorganisms

    PubMed Central

    Mansilla Pareja, Maria Eugenia; Colombo, Maria I.

    2013-01-01

    Autophagy is involved in several physiological and pathological processes. One of the key roles of the autophagic pathway is to participate in the first line of defense against the invasion of pathogens, as part of the innate immune response. Targeting of intracellular bacteria by the autophagic machinery, either in the cytoplasm or within vacuolar compartments, helps to control bacterial proliferation in the host cell, controlling also the spreading of the infection. In this review we will describe the means used by diverse bacterial pathogens to survive intracellularly and how they are recognized by the autophagic molecular machinery, as well as the mechanisms used to avoid autophagic clearance. PMID:24137567

  13. How hydrophobic drying forces impact the kinetics of molecular recognition.

    PubMed

    Mondal, Jagannath; Morrone, Joseph A; Berne, B J

    2013-08-13

    A model of protein-ligand binding kinetics, in which slow solvent dynamics results from hydrophobic drying transitions, is investigated. Molecular dynamics simulations show that solvent in the receptor pocket can fluctuate between wet and dry states with lifetimes in each state that are long enough for the extraction of a separable potential of mean force and wet-to-dry transitions. We present a diffusive surface hopping model that is represented by a 2D Markovian master equation. One dimension is the standard reaction coordinate, the ligand-pocket separation, and the other is the solvent state in the region between ligand and binding pocket which specifies whether it is wet or dry. In our model, the ligand diffuses on a dynamic free-energy surface which undergoes kinetic transitions between the wet and dry states. The model yields good agreement with results from explicit solvent molecular dynamics simulation and an improved description of the kinetics of hydrophobic assembly. Furthermore, it is consistent with a "non-Markovian Brownian theory" for the ligand-pocket separation coordinate alone.

  14. Design, synthesis and decoration of molecular scaffolds for exploitation in the production of alkaloid-like libraries.

    PubMed

    Craven, Philip; Aimon, Anthony; Dow, Mark; Fleury-Bregeot, Nicolas; Guilleux, Rachel; Morgentin, Remy; Roche, Didier; Kalliokoski, Tuomo; Foster, Richard; Marsden, Stephen P; Nelson, Adam

    2015-06-01

    The design, synthesis and decoration of six small molecule libraries is described. Each library was inspired by structures embedded in the framework of specific alkaloid natural products. The development of optimised syntheses of the required molecular scaffolds is described, in which reactions including Pd-catalysed aminoarylation and diplolar cycloadditions have been exploited as key steps. The synthesis of selected exemplar screening compounds is also described. In five cases, libraries were subsequently nominated for production on the basis of the scope and limitations of the validation work, as well as predicted molecular properties. In total, the research has led to the successful synthesis of >2500 novel alkaloid-like compounds for addition to the screening collection (the Joint European Compound Library, JECL) of the European Lead Factory. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Emergence of molecular recognition phenomena in a simple model of imprinted porous materials

    NASA Astrophysics Data System (ADS)

    Dourado, Eduardo M. A.; Sarkisov, Lev

    2009-06-01

    Polymerization in the presence of templates, followed by their consequent removal, leads to structures with cavities capable of molecular recognition. This molecular imprinting technology has been employed to create porous polymers with tailored selectivity for adsorption, chromatographic separations, sensing, and other applications. Performance of these materials crucially depends on the availability of highly selective binding sites. This parameter is a function of a large number of processing conditions and is difficult to control. Furthermore, the nature of molecular recognition processes in these materials is poorly understood to allow a more systematic design. In this work we propose a simple model of molecularly imprinted polymers mimicking the actual process of their formation. We demonstrate that a range of molecular recognition effects emerge in this model and that they are consistent with the experimental observations. The model also provides a wealth of information on how binding sites form and function in the imprinted structures. It demonstrates the capability to assess the role of various processing conditions in the final properties of imprinted materials, and therefore it can be used to provide some qualitative insights on the optimal values of processing parameters.

  16. Substrate recognition by norovirus polymerase: microsecond molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Maláč, Kamil; Barvík, Ivan

    2013-04-01

    Molecular dynamics simulations of complexes between Norwalk virus RNA dependent RNA polymerase and its natural CTP and 2dCTP (both containing the O5'-C5'-C4'-O4' sequence of atoms bridging the triphosphate and sugar moiety) or modified coCTP ( C5' -O5'-C4'-O4'), cocCTP ( C5' -O5'-C4'- C4'') substrates were produced by means of CUDA programmable graphical processing units and the ACEMD software package. It enabled us to gain microsecond MD trajectories clearly showing that similar nucleoside triphosphates can bind surprisingly differently into the active site of the Norwalk virus RNA dependent RNA polymerase. It corresponds to their different modes of action (CTP—substrate, 2dCTP—poor substrate, coCTP—chain terminator, cocCTP—inhibitor). Moreover, extremely rare events—as repetitive pervasion of Arg182 into a potentially reaction promoting arrangement—were captured.

  17. Modeling of enhanced catalysis in multienzyme nanostructures: effect of molecular scaffolds, spatial organization, and concentration.

    PubMed

    Roberts, Christopher C; Chang, Chia-en A

    2015-01-13

    Colocalized multistep enzymatic reaction pathways within biological catabolic and metabolic processes occur with high yield and specificity. Spatial organization on membranes or surfaces may be associated with increased efficiency of intermediate substrate transfer. Using a new Brownian dynamics package, GeomBD, we explored the geometric features of a surface-anchored enzyme system by parallel coarse-grained Brownian dynamics simulations of substrate diffusion over microsecond (μs) to millisecond (ms) time scales. We focused on a recently developed glucose oxidase (GOx), horseradish peroxidase (HRP), and DNA origami-scaffold enzyme system, where the H2O2 substrate of HRP is produced by GOx. The results revealed and explained a significant advantage in catalytic enhancement by optimizing interenzyme distance and orientation in the presence of the scaffold model. The planar scaffold colocalized the enzymes and provided a diffusive barrier that enhanced substrate transfer probability, becoming more relevant with increasing interenzyme distance. The results highlight the importance of protein geometry in the proper assessment of distance and orientation dependence on the probability of substrate transfer. They shed light on strategies for engineering multienzyme complexes and further investigation of enhanced catalytic efficiency for substrate diffusion between membrane-anchoring proteins.

  18. Toxocara canis: Molecular basis of immune recognition and evasion

    PubMed Central

    Maizels, Rick M.

    2013-01-01

    Toxocara canis has extraordinary abilities to survive for many years in the tissues of diverse vertebrate species, as well as to develop to maturity in the intestinal tract of its definitive canid host. Human disease is caused by larval stages invading musculature, brain and the eye, and immune mechanisms appear to be ineffective at eliminating the infection. Survival of T. canis larvae can be attributed to two molecular strategies evolved by the parasite. Firstly, it releases quantities of ‘excretory–secretory’ products which include lectins, mucins and enzymes that interact with and modulate host immunity. For example, one lectin (CTL-1) is very similar to mammalian lectins, required for tissue inflammation, suggesting that T. canis may interfere with leucocyte extravasation into infected sites. The second strategy is the elaboration of a specialised mucin-rich surface coat; this is loosely attached to the parasite epicuticle in a fashion that permits rapid escape when host antibodies and cells adhere, resulting in an inflammatory reaction around a newly vacated focus. The mucins have been characterised as bearing multiple glycan side-chains, consisting of a blood-group-like trisaccharide with one or two O-methylation modifications. Both the lectins and these trisaccharides are targeted by host antibodies, with anti-lectin antibodies showing particular diagnostic promise. Antibodies to the mono-methylated trisaccharide appear to be T. canis-specific, as this epitope is not found in the closely related Toxocara cati, but all other antigenic determinants are very similar between the two species. This distinction may be important in designing new and more accurate diagnostic tests. Further tools to control toxocariasis could also arise from understanding the molecular cues and steps involved in larval development. In vitro-cultivated larvae express high levels of four mRNAs that are translationally silenced, as the proteins they encode are not detectable in

  19. Multivalency in Recognition and Antagonism of HIV TAR RNA – TAT Assembly using an Aminoglycoside Benzimidazole Scaffold

    PubMed Central

    Kumar, Sunil; Ranjan, Nihar; Kellish, Patrick; Gong, Changjun; Watkins, Derrick; Arya, Dev P.

    2016-01-01

    Recognition of RNA by high-affinity binding small molecules is crucial for expanding existing approaches in RNA recognition, and for the development of novel RNA binding drugs. A novel neomycin dimer benzimidazole conjugate 5 (DPA 83) was synthesized by conjugating a neomycin-dimer with benzimidazole alkyne using click chemistry to target multiple binding sites on HIV TAR RNA. Ligand 5 significantly enhances the thermal stability of HIV TAR RNA and interacts stoichiometrically with HIV TAR RNA with a low nanomolar affinity. 5 displayed enhanced binding than its individual building blocks including neomycin dimer azide and benzimidazole alkyne. In essence, a high affinity multivalent ligand was designed and synthesized to target HIV TAR RNA. PMID:26765486

  20. Multivalency in the recognition and antagonism of a HIV TAR RNA-TAT assembly using an aminoglycoside benzimidazole scaffold.

    PubMed

    Kumar, Sunil; Ranjan, Nihar; Kellish, Patrick; Gong, Changjun; Watkins, Derrick; Arya, Dev P

    2016-02-14

    Recognition of RNA by high-affinity binding small molecules is crucial for expanding existing approaches in RNA recognition, and for the development of novel RNA binding drugs. A novel neomycin dimer benzimidazole conjugate 5 (DPA 83) was synthesized by conjugating a neomycin-dimer with a benzimidazole alkyne using click chemistry to target multiple binding sites on HIV TAR RNA. Ligand 5 significantly enhances the thermal stability of HIV TAR RNA and interacts stoichiometrically with HIV TAR RNA with a low nanomolar affinity. 5 displayed enhanced binding compared to its individual building blocks including the neomycin dimer azide and benzimidazole alkyne. In essence, a high affinity multivalent ligand was designed and synthesized to target HIV TAR RNA.

  1. Synthesis of molecularly imprinted polymer with 7-chloroethyl-theophylline-immobilized silica gel as template and its molecular recognition function

    NASA Astrophysics Data System (ADS)

    Zhang, Yuhui; Tong, Aijun; Li, Longdi

    2004-01-01

    By reaction of 7-chloroethyl-theophylline with aminopropylsilanized silica gel we synthesized a 7-chloroethyl-theophylline-immobilized silica gel as template molecule and prepared a molecularly imprinted polymer (MIP-Si), which had special recognition sites to 7-chloroethyl-theophylline. A conventional molecularly imprinted polymer (MIP) using 7-chloroethyl-theophylline as template was also prepared for comparison. Binding abilities to 7-chloroethyl-theophylline and its structural analogs revealed that the MIP-Si shows much higher binding speed and much more binding capacity than the MIP does.

  2. Molecular basis for substrate recognition by lysine methyltransferases and demethylases.

    PubMed

    Del Rizzo, Paul A; Trievel, Raymond C

    2014-12-01

    Lysine methylation has emerged as a prominent covalent modification in histones and non-histone proteins. This modification has been implicated in numerous genomic processes, including heterochromatinization, cell cycle progression, DNA damage response, DNA replication, genome stability, and epigenetic gene regulation that underpins developmental programs defining cell identity and fate. The site and degree of lysine methylation is dynamically modulated through the enzymatic activities of protein lysine methyltransferases (KMTs) and protein lysine demethylases (KDMs). These enzymes display distinct substrate specificities that in part define their biological functions. This review explores recent progress in elucidating the molecular basis of these specificities, highlighting structural and functional studies of the methyltransferases SUV4-20H1 (KMT5B), SUV4-20H2 (KMT5C), and ATXR5, and the demethylases UTX (KDM6A), JMJD3 (KDM6B), and JMJD2D (KDM4D). We conclude by examining these findings in the context of related KMTs and KDMs and by exploring unresolved questions regarding the specificities and functions of these enzymes. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Brittle cornea syndrome: recognition, molecular diagnosis and management

    PubMed Central

    2013-01-01

    Brittle cornea syndrome (BCS) is an autosomal recessive disorder characterised by extreme corneal thinning and fragility. Corneal rupture can therefore occur either spontaneously or following minimal trauma in affected patients. Two genes, ZNF469 and PRDM5, have now been identified, in which causative pathogenic mutations collectively account for the condition in nearly all patients with BCS ascertained to date. Therefore, effective molecular diagnosis is now available for affected patients, and those at risk of being heterozygous carriers for BCS. We have previously identified mutations in ZNF469 in 14 families (in addition to 6 reported by others in the literature), and in PRDM5 in 8 families (with 1 further family now published by others). Clinical features include extreme corneal thinning with rupture, high myopia, blue sclerae, deafness of mixed aetiology with hypercompliant tympanic membranes, and variable skeletal manifestations. Corneal rupture may be the presenting feature of BCS, and it is possible that this may be incorrectly attributed to non-accidental injury. Mainstays of management include the prevention of ocular rupture by provision of protective polycarbonate spectacles, careful monitoring of visual and auditory function, and assessment for skeletal complications such as developmental dysplasia of the hip. Effective management depends upon appropriate identification of affected individuals, which may be challenging given the phenotypic overlap of BCS with other connective tissue disorders. PMID:23642083

  4. Brittle cornea syndrome: recognition, molecular diagnosis and management.

    PubMed

    Burkitt Wright, Emma M M; Porter, Louise F; Spencer, Helen L; Clayton-Smith, Jill; Au, Leon; Munier, Francis L; Smithson, Sarah; Suri, Mohnish; Rohrbach, Marianne; Manson, Forbes D C; Black, Graeme C M

    2013-05-04

    Brittle cornea syndrome (BCS) is an autosomal recessive disorder characterised by extreme corneal thinning and fragility. Corneal rupture can therefore occur either spontaneously or following minimal trauma in affected patients. Two genes, ZNF469 and PRDM5, have now been identified, in which causative pathogenic mutations collectively account for the condition in nearly all patients with BCS ascertained to date. Therefore, effective molecular diagnosis is now available for affected patients, and those at risk of being heterozygous carriers for BCS. We have previously identified mutations in ZNF469 in 14 families (in addition to 6 reported by others in the literature), and in PRDM5 in 8 families (with 1 further family now published by others). Clinical features include extreme corneal thinning with rupture, high myopia, blue sclerae, deafness of mixed aetiology with hypercompliant tympanic membranes, and variable skeletal manifestations. Corneal rupture may be the presenting feature of BCS, and it is possible that this may be incorrectly attributed to non-accidental injury. Mainstays of management include the prevention of ocular rupture by provision of protective polycarbonate spectacles, careful monitoring of visual and auditory function, and assessment for skeletal complications such as developmental dysplasia of the hip. Effective management depends upon appropriate identification of affected individuals, which may be challenging given the phenotypic overlap of BCS with other connective tissue disorders.

  5. Molecular Recognition: Use of Metal-Containing Molecular Clefts for Supramolecular Self-Assembly and Host-Guest Formation

    SciTech Connect

    Crowley, James D.; Bosnich, Brice

    2008-10-03

    Molecular clefts consisting of a rigid spacer linked to two parallel cofacially disposed terpy-M-X (M = Pd{sup 2+}, Pt{sup 2+}) units, which can vary in separation from 6.6 to 7.2 {angstrom}, have been used as molecular receptors and for self-assembly with linear and triangular linkers to produce rectangles and trigonal prisms, respectively. Aromatic molecules form multiple host-guest adducts with the molecular cleft receptors and with the rectangles and trigonal prisms. Planar complexes of Pt{sup 2+} also form host-guest adducts. The forces that control this molecular recognition, namely, {pi}-{pi} interactions, charge-induced dipole interactions, charge-charge forces, weak metal-metal interactions and solvation effects, are discussed and assigned to the various adducts.

  6. Functional Proteomic And Structural Insights Into Molecular Recognition in the Nitrilase Family Enzymes

    SciTech Connect

    Barglow, K.T.; Saikatendu, K.; Bracey, M.H.; Huey, R.; Morris, G.M.; Olson, A.J.; Stevens, R.C.; Cravatt, B.F.

    2009-05-11

    Nitrilases are a large and diverse family of nonpeptidic C-N hydrolases. The mammalian genome encodes eight nitrilase enzymes, several of which remain poorly characterized. Prominent among these are nitrilase-1 (Nit1) and nitrilase-2 (Nit2), which, despite having been shown to exert effects on cell growth and possibly serving as tumor suppressor genes, are without known substrates or selective inhibitors. In previous studies, we identified several nitrilases, including Nit1 and Nit2, as targets for dipeptide-chloroacetamide activity-based proteomics probes. Here, we have used these probes, in combination with high-resolution crystallography and molecular modeling, to systematically map the active site of Nit2 and identify residues involved in molecular recognition. We report the 1.4 {angstrom} crystal structure of mouse Nit2 and use this structure to identify residues that discriminate probe labeling between the Nit1 and Nit2 enzymes. Interestingly, some of these residues are conserved across all vertebrate Nit2 enzymes and, conversely, not found in any vertebrate Nit1 enzymes, suggesting that they are key discriminators of molecular recognition between these otherwise highly homologous enzymes. Our findings thus point to a limited set of active site residues that establish distinct patterns of molecular recognition among nitrilases and provide chemical probes to selectively perturb the function of these enzymes in biological systems.

  7. Molecular Recognition of CXCR4 by a Dual Tropic HIV-1 gp120 V3 Loop

    PubMed Central

    Tamamis, Phanourios; Floudas, Christodoulos A.

    2013-01-01

    HIV-1 cell entry is initiated by the interaction of the viral envelope glycoprotein gp120 with CD4, and chemokine coreceptors CXCR4 and CCR5. The molecular recognition of CXCR4 or CCR5 by the HIV-1 gp120 is mediated through the V3 loop, a fragment of gp120. The binding of the V3 loop to CXCR4 or CCR5 determines the cell tropism of HIV-1 and constitutes a key step before HIV-1 cell entry. Thus, elucidating the molecular recognition of CXCR4 by the V3 loop is important for understanding HIV-1 viral infectivity and tropism, and for the design of HIV-1 inhibitors. We employed a comprehensive set of computational tools, predominantly based on free energy calculations and molecular-dynamics simulations, to investigate the molecular recognition of CXCR4 by a dual tropic V3 loop. We report what is, to our knowledge, the first HIV-1 gp120 V3 loop:CXCR4 complex structure. The computationally derived structure reveals an abundance of polar and nonpolar intermolecular interactions contributing to the HIV-1 gp120:CXCR4 binding. Our results are in remarkable agreement with previous experimental findings. Therefore, this work sheds light on the functional role of HIV-1 gp120 V3 loop and CXCR4 residues associated with HIV-1 coreceptor activity. PMID:24048002

  8. Quantification of Extracellular Matrix Proteins from a Rat Lung Scaffold to Provide a Molecular Readout for Tissue Engineering*

    PubMed Central

    Hill, Ryan C.; Calle, Elizabeth A.; Dzieciatkowska, Monika; Niklason, Laura E.; Hansen, Kirk C.

    2015-01-01

    The use of extracellular matrix (ECM)1 scaffolds, derived from decellularized tissues for engineered organ generation, holds enormous potential in the field of regenerative medicine. To support organ engineering efforts, we developed a targeted proteomics method to extract and quantify extracellular matrix components from tissues. Our method provides more complete and accurate protein characterization than traditional approaches. This is accomplished through the analysis of both the chaotrope-soluble and -insoluble protein fractions and using recombinantly generated stable isotope labeled peptides for endogenous protein quantification. Using this approach, we have generated 74 peptides, representing 56 proteins to quantify protein in native (nondecellularized) and decellularized lung matrices. We have focused on proteins of the ECM and additional intracellular proteins that are challenging to remove during the decellularization procedure. Results indicate that the acellular lung scaffold is predominantly composed of structural collagens, with the majority of these proteins found in the insoluble ECM, a fraction that is often discarded using widely accepted proteomic methods. The decellularization procedure removes over 98% of intracellular proteins evaluated and retains, to varying degrees, proteoglycans and glycoproteins of the ECM. Accurate characterization of ECM proteins from tissue samples will help advance organ engineering efforts by generating a molecular readout that can be correlated with functional outcome to drive the next generation of engineered organs. PMID:25660013

  9. High-Efficiency Perovskite Solar Cell Based on Poly(3-Hexylthiophene): Influence of Molecular Weight and Mesoscopic Scaffold Layer.

    PubMed

    Nia, Narges Yaghoobi; Matteocci, Fabio; Cina, Lucio; Di Carlo, Aldo

    2017-05-28

    Here, we investigated the effect of the molecular weight (MW) of poly 3-hexylthiophene (P3HT) hole-transport material on the performance of perovskite solar cells (PSCs). We found that by increasing the MW the photovoltaic performances of the cells are enhanced leading to an improvement of the overall efficiency. P3HT-based PSCs with a MW of 124 kDa can achieve an overall average efficiency of 16.2 %, double with respect to the ones with a MW of 44 kDa. Opposite to spiro-OMeTAD-based PSCs, the photovoltaic parameters of the P3HT-based devices are enhanced by increasing the mesoporous TiO2 layer thickness from 250 to 500 nm. Moreover, for a titania scaffold layer thickness of 500 nm, the efficiency of P3HT-based PSCs with high MW is larger than the spiro-OMeTAD based PSCs with the same scaffold layer thickness. Recombination reactions of the devices were also investigated by voltage decay and electrochemical impedance spectroscopy. We found that the relationship between P3HT MW and cell performance is related to the reduction of charge recombination and to the increase of the P3HT light absorption by increasing the MW. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Molecular recognition using corona phase complexes made of synthetic polymers adsorbed on carbon nanotubes.

    PubMed

    Zhang, Jingqing; Landry, Markita P; Barone, Paul W; Kim, Jong-Ho; Lin, Shangchao; Ulissi, Zachary W; Lin, Dahua; Mu, Bin; Boghossian, Ardemis A; Hilmer, Andrew J; Rwei, Alina; Hinckley, Allison C; Kruss, Sebastian; Shandell, Mia A; Nair, Nitish; Blake, Steven; Şen, Fatih; Şen, Selda; Croy, Robert G; Li, Deyu; Yum, Kyungsuk; Ahn, Jin-Ho; Jin, Hong; Heller, Daniel A; Essigmann, John M; Blankschtein, Daniel; Strano, Michael S

    2013-12-01

    Understanding molecular recognition is of fundamental importance in applications such as therapeutics, chemical catalysis and sensor design. The most common recognition motifs involve biological macromolecules such as antibodies and aptamers. The key to biorecognition consists of a unique three-dimensional structure formed by a folded and constrained bioheteropolymer that creates a binding pocket, or an interface, able to recognize a specific molecule. Here, we show that synthetic heteropolymers, once constrained onto a single-walled carbon nanotube by chemical adsorption, also form a new corona phase that exhibits highly selective recognition for specific molecules. To prove the generality of this phenomenon, we report three examples of heteropolymer-nanotube recognition complexes for riboflavin, L-thyroxine and oestradiol. In each case, the recognition was predicted using a two-dimensional thermodynamic model of surface interactions in which the dissociation constants can be tuned by perturbing the chemical structure of the heteropolymer. Moreover, these complexes can be used as new types of spatiotemporal sensors based on modulation of the carbon nanotube photoemission in the near-infrared, as we show by tracking riboflavin diffusion in murine macrophages.

  11. Molecular recognition using corona phase complexes made of synthetic polymers adsorbed on carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Zhang, Jingqing; Landry, Markita P.; Barone, Paul W.; Kim, Jong-Ho; Lin, Shangchao; Ulissi, Zachary W.; Lin, Dahua; Mu, Bin; Boghossian, Ardemis A.; Hilmer, Andrew J.; Rwei, Alina; Hinckley, Allison C.; Kruss, Sebastian; Shandell, Mia A.; Nair, Nitish; Blake, Steven; Şen, Fatih; Şen, Selda; Croy, Robert G.; Li, Deyu; Yum, Kyungsuk; Ahn, Jin-Ho; Jin, Hong; Heller, Daniel A.; Essigmann, John M.; Blankschtein, Daniel; Strano, Michael S.

    2013-12-01

    Understanding molecular recognition is of fundamental importance in applications such as therapeutics, chemical catalysis and sensor design. The most common recognition motifs involve biological macromolecules such as antibodies and aptamers. The key to biorecognition consists of a unique three-dimensional structure formed by a folded and constrained bioheteropolymer that creates a binding pocket, or an interface, able to recognize a specific molecule. Here, we show that synthetic heteropolymers, once constrained onto a single-walled carbon nanotube by chemical adsorption, also form a new corona phase that exhibits highly selective recognition for specific molecules. To prove the generality of this phenomenon, we report three examples of heteropolymer-nanotube recognition complexes for riboflavin, L-thyroxine and oestradiol. In each case, the recognition was predicted using a two-dimensional thermodynamic model of surface interactions in which the dissociation constants can be tuned by perturbing the chemical structure of the heteropolymer. Moreover, these complexes can be used as new types of spatiotemporal sensors based on modulation of the carbon nanotube photoemission in the near-infrared, as we show by tracking riboflavin diffusion in murine macrophages.

  12. Macrocyclic peptides self-assemble into robust vesicles with molecular recognition capabilities.

    PubMed

    Jeong, Woo-jin; Lim, Yong-beom

    2014-11-19

    In this study, we developed macrocyclic peptide building blocks that formed self-assembled peptide vesicles with molecular recognition capabilities. Macrocyclic peptides were significantly different from conventional amphiphiles, in that they could self-assemble into vesicles at very high hydrophilic-to-total mass ratios. The flexibility of the hydrophobic self-assembly segment was critical for vesicle formation. The unique features of this peptide vesicle system include a homogeneous size distribution, unusually small size, and robust structural and thermal stability. The peptide vesicles successfully entrapped a hydrophilic model drug, released the payload very slowly, and were internalized by cells in a highly efficient manner. Moreover, the peptide vesicles exhibited molecular recognition capabilities, in that they selectively bound to target RNA through surface-displayed peptides. This study demonstrates that self-assembled peptide vesicles can be used as strong intracellular delivery vehicles that recognize specific biomacromolecular targets.

  13. Aminoglycosides: Molecular Insights on the Recognition of RNA and Aminoglycoside Mimics

    PubMed Central

    Chittapragada, Maruthi; Roberts, Sarah; Ham, Young Wan

    2009-01-01

    RNA is increasingly recognized for its significant functions in biological systems and has recently become an important molecular target for therapeutics development. Aminoglycosides, a large class of clinically significant antibiotics, exert their biological functions by binding to prokaryotic ribosomal RNA (rRNA) and interfering with protein translation, resulting in bacterial cell death. They are also known to bind to viral mRNAs such as HIV-1 RRE and TAR. Consequently, aminoglycosides are accepted as the single most important model in understanding the principles that govern small molecule-RNA recognition, which is essential for the development of novel antibacterial, antiviral or even anti-oncogenic agents. This review outlines the chemical structures and mechanisms of molecular recognition and antibacterial activity of aminoglycosides and various aminoglycoside mimics that have recently been devised to improve biological efficacy, binding affinity and selectivity, or to circumvent bacterial resistance. PMID:19812740

  14. N-haloacetylimino neonicotinoids: potency and molecular recognition at the insect nicotinic receptor.

    PubMed

    Tomizawa, Motohiro; Durkin, Kathleen A; Ohno, Ikuya; Nagura, Kyoko; Manabe, Mio; Kumazawa, Satoru; Kagabu, Shinzo

    2011-06-15

    This structure-activity relationship study for neonicotinoids with an N-haloacetylimino pharmacophore identifies several candidate compounds showing outstanding insecticidal potency and consequently leads to establishing their molecular recognition at an insect nicotinic receptor structural model, wherein the neonicotinoid halogen atoms (fluorine, chlorine, bromine, and iodine) variously interact with the receptor loops C-D interfacial niche via H-bonding and/or hydrophobic interactions.

  15. The Physical-Organic Chemistry of Surfaces, and Its Relevance to Molecular Recognition

    DTIC Science & Technology

    1989-11-01

    THE PHYSICAL-ORGANiC CHEMISTRY OF SURFACES , 0AND ITS RELEVANCE TO MOLECULAR RECOGNITION L N George M. Whitesides and Hans Biebuyck Department of...DEFENSE ADVANCED RESEARCH PROJECTS AGENCY 1400 Wilson Boulevard Arlington VA 22209 DEPARTMENT OF THE NAVY Offic- of Naval Research , Code 1130P 800...Advanced Research Projects Agency or the U.S. Government. LDIST-R-UTI ,j STAApprovcd for pu8bU Y9 1e; 9 Dibu fonl Unlimited SECURITY CLASSIFICATION OF THIS

  16. Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

    PubMed Central

    Wereszczynski, Jeff; McCammon, J. Andrew

    2012-01-01

    Molecular recognition plays a central role in biochemical processes. Although well studied, understanding the mechanisms of recognition is inherently difficult due to the range of potential interactions, the molecular rearrangement associated with binding, and the time and length scales involved. Computational methods have the potential for not only complementing experiments that have been performed, but also in guiding future ones through their predictive abilities. In this review, we discuss how molecular dynamics (MD) simulations may be used in advancing our understanding of the thermodynamics that drive biomolecular recognition. We begin with a brief review of the statistical mechanics that form a basis for these methods. This is followed by a description of some of the most commonly used methods: thermodynamic pathways employing alchemical transformations and potential of mean force calculations, along with end-point calculations for free energy differences, and harmonic and quasi-harmonic analysis for entropic calculations. Finally, a few of the fundamental findings that have resulted from these methods are discussed, such as the role of configurational entropy and solvent in intermolecular interactions, along with selected results of the model system T4 lysozyme to illustrate potential and current limitations of these methods. PMID:22082669

  17. Surface plasmon resonance sensor based on magnetic molecularly imprinted polymers amplification for pesticide recognition.

    PubMed

    Yao, Gui-Hong; Liang, Ru-Ping; Huang, Chun-Fang; Wang, Ying; Qiu, Jian-Ding

    2013-12-17

    We reported here a method to enhance detection sensitivity in surface plasmon resonance (SPR) spectroscopy integrated with a surface molecular imprinting recognition system and employing magnetic molecular imprinting polymer nanoparticles for amplifying SPR response. The proposed magnetic molecular imprinting polymer was designed by self-polymerization of dopamine on the Fe3O4 NPs surface in weak base aqueous solution in the presence of template chlorpyrifos (CPF). The imprinted Fe3O4@polydopamine nanoparticles (Fe3O4@PDA NPs) were characterized by Fourier transform infrared spectroscopy, UV-vis absorption spectroscopy, and transmission electron microscopy. The biosensor showed a good linear relationship between the SPR angle shift and the chlorpyrifos concentration over a range from 0.001 to 10 μM with a detection limit of 0.76 nM. A significant increase in sensitivity was therefore afforded through the use of imprinted Fe3O4@PDA NPs as an amplifier, and meanwhile, the imprinted Fe3O4@PDA NPs had an excellent recognition capacity to chlorpyrifos over other pesticides. The excellent sensitivity and selectivity and high stability of the designed biosensor make this magnetic imprinted Fe3O4@PDA NP an attractive recognition element for various SPR sensors for detecting pesticide residuals and other environmentally deleterious chemicals.

  18. Magnetic deep eutectic solvents molecularly imprinted polymers for the selective recognition and separation of protein.

    PubMed

    Liu, Yanjin; Wang, Yuzhi; Dai, Qingzhou; Zhou, Yigang

    2016-09-14

    A novel and facile magnetic deep eutectic solvents (DES) molecularly imprinted polymers (MIPs) for the selective recognition and separation of Bovine hemoglobin (BHb) was prepared. The new-type DES was adopted as the functional monomer which would bring molecular imprinted technology to a new direction. The amounts of DES were optimized. The obtained magnetic DES-MIPs were characterized with fourier transform infrared spectrometry (FT-IR), thermogravimetric analysis (TGA), field emission scanning electron microscope (FESEM), dynamic light scattering (DLS), elemental analysis and vibrating sample magnetometer (VSM). The results suggested that the imprinted polymers were successfully formed and possessed a charming magnetism. The maximum adsorption capability (Qmax) and dissociation constant (KL) were analyzed by Langmuir isotherms (R(2) = 0.9983) and the value were estimated to be 175.44 mg/g and 0.035 mg/mL for the imprinted particles. And the imprinted particles showed a high imprinting factor of 4.77. In addition, the magnetic DES-MIPs presented outstanding recognition specificity and selectivity so that it can be utilized to separate template protein from the mixture of proteins and real samples. Last but not least, the combination of deep eutectic solvents and molecular imprinted technology in this paper provides a new perspective for the recognition and separation of proteins. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Organization of inorganic nanomaterials via programmable DNA self-assembly and peptide molecular recognition.

    PubMed

    Carter, Joshua D; LaBean, Thomas H

    2011-03-22

    An interesting alternative to top-down nanofabrication is to imitate biology, where nanoscale materials frequently integrate organic molecules for self-assembly and molecular recognition with ordered, inorganic minerals to achieve mechanical, sensory, or other advantageous functions. Using biological systems as inspiration, researchers have sought to mimic the nanoscale composite materials produced in nature. Here, we describe a combination of self-assembly, molecular recognition, and templating, relying on an oligonucleotide covalently conjugated to a high-affinity gold-binding peptide. After integration of the peptide-coupled DNA into a self-assembling superstructure, the templated peptides recognize and bind gold nanoparticles. In addition to providing new ways of building functional multinanoparticle systems, this work provides experimental proof that a single peptide molecule is sufficient for immobilization of a nanoparticle. This molecular construction strategy, combining DNA assembly and peptide recognition, can be thought of as programmable, granular, artificial biomineralization. We also describe the important observation that the addition of 1-2% Tween 20 surfactant to the solution during gold particle binding allows the gold nanoparticles to remain soluble within the magnesium-containing DNA assembly buffer under conditions that usually lead to the aggregation and precipitation of the nanoparticles.

  20. Exploring Protein-Peptide Recognition Pathways Using a Supervised Molecular Dynamics Approach.

    PubMed

    Salmaso, Veronica; Sturlese, Mattia; Cuzzolin, Alberto; Moro, Stefano

    2017-04-04

    Peptides have gained increased interest as therapeutic agents during recent years. The high specificity and relatively low toxicity of peptide drugs derive from their extremely tight binding to their targets. Indeed, understanding the molecular mechanism of protein-peptide recognition has important implications in the fields of biology, medicine, and pharmaceutical sciences. Even if crystallography and nuclear magnetic resonance are offering valuable atomic insights into the assembling of the protein-peptide complexes, the mechanism of their recognition and binding events remains largely unclear. In this work we report, for the first time, the use of a supervised molecular dynamics approach to explore the possible protein-peptide binding pathways within a timescale reduced up to three orders of magnitude compared with classical molecular dynamics. The better and faster understating of the protein-peptide recognition pathways could be very beneficial in enlarging the applicability of peptide-based drug design approaches in several biotechnological and pharmaceutical fields. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Molecular mechanism for differential recognition of membrane phosphatidylserine by the immune regulatory receptor Tim4.

    PubMed

    Tietjen, Gregory T; Gong, Zhiliang; Chen, Chiu-Hao; Vargas, Ernesto; Crooks, James E; Cao, Kathleen D; Heffern, Charles T R; Henderson, J Michael; Meron, Mati; Lin, Binhua; Roux, Benot; Schlossman, Mark L; Steck, Theodore L; Lee, Ka Yee C; Adams, Erin J

    2014-04-15

    Recognition of phosphatidylserine (PS) lipids exposed on the extracellular leaflet of plasma membranes is implicated in both apoptotic cell removal and immune regulation. The PS receptor T cell immunoglobulin and mucin-domain-containing molecule 4 (Tim4) regulates T-cell immunity via phagocytosis of both apoptotic (high PS exposure) and nonapoptotic (intermediate PS exposure) activated T cells. The latter population must be removed at lower efficiency to sensitively control immune tolerance and memory cell population size, but the molecular basis for how Tim4 achieves this sensitivity is unknown. Using a combination of interfacial X-ray scattering, molecular dynamics simulations, and membrane binding assays, we demonstrate how Tim4 recognizes PS in the context of a lipid bilayer. Our data reveal that in addition to the known Ca(2+)-coordinated, single-PS binding pocket, Tim4 has four weaker sites of potential ionic interactions with PS lipids. This organization makes Tim4 sensitive to PS surface concentration in a manner capable of supporting differential recognition on the basis of PS exposure level. The structurally homologous, but functionally distinct, Tim1 and Tim3 are significantly less sensitive to PS surface density, likely reflecting the differences in immunological function between the Tim proteins. These results establish the potential for lipid membrane parameters, such as PS surface density, to play a critical role in facilitating selective recognition of PS-exposing cells. Furthermore, our multidisciplinary approach overcomes the difficulties associated with characterizing dynamic protein/membrane systems to reveal the molecular mechanisms underlying Tim4's recognition properties, and thereby provides an approach capable of providing atomic-level detail to uncover the nuances of protein/membrane interactions.

  2. Mechanisms underlying molecularly imprinted polymer molecular memory and the role of crosslinker: resolving debate on the nature of template recognition in phenylalanine anilide imprinted polymers.

    PubMed

    Olsson, Gustaf D; Karlsson, Björn C G; Shoravi, Siamak; Wiklander, Jesper G; Nicholls, Ian A

    2012-02-01

    A series of molecular dynamics simulations of prepolymerization mixtures for phenylalanine anilide imprinted co-(ethylene glycol dimethacrylate-methacrylic acid) molecularly imprinted polymers have been employed to investigate the mechanistic basis for template selective recognition in these systems. This has provided new insights on the mechanisms underlying template recognition, in particular the significant role played by the crosslinking agent. Importantly, the study supports the occurrence of template self-association events that allows us to resolve debate between the two previously proposed models used to explain this system's underlying recognition mechanisms. Moreover, the complexity of the molecular level events underlying template complexation is highlighted by this study, a factor that should be considered in rational molecularly imprinted polymer design, especially with respect to recognition site heterogeneity.

  3. Particle-assisted semidirect breath figure method: a facile way to endow the honeycomb-structured petri dish with molecular recognition capability.

    PubMed

    Tu, Zhengkai; Tang, Haolin; Shen, Xiantao

    2014-08-13

    Recently, we have developed a semidirect breath figure (sDBF) method for direct fabrication of large-area and ordered honeycomb structures on commercial polystyrene (PS) Petri dishes without the use of an external polymer solution. In this work, we showed that both the pore size and the pore uniformity of the breath figure patterns were controllable by solvent amount. The cross-sectional image shows that only one layer of pores was formed on the BF figure patterns. By combing the sDBF method and Pickering emulsion and using the modular building blocks, we endowed the honeycomb-structured Petri dish with molecular recognition capability via the decoration of molecularly imprinted polymer (MIP) nanoparticles into the honeycomb pores. The radioligand binding experiments show that the MIP nanoparticles on the resultant honeycomb structures maintained high molecular binding selectivity. The reusability study indicates that MIP-BF patterns had excellent mechanical stability during the radioligand binding process. We believe that the modular approach demonstrated in this work will open up further opportunities for honeycomb structure-based chemical sensors for drug analysis, substrates for catalysts, and scaffold for cell growth.

  4. Site of Tagging Influences the Ochratoxin Recognition by Peptide NFO4: A Molecular Dynamics Study.

    PubMed

    Thyparambil, Aby A; Abramyan, Tigran M; Bazin, Ingrid; Guiseppi-Elie, Anthony

    2017-08-28

    Molecular recognition by synthetic peptides is growing in importance in the design of biosensing elements used in the detection and monitoring of a wide variety of hapten bioanlaytes. Conferring specificity via bioimmobilization and subsequent recovery and purification of such sensing elements are aided by the use of affinity tags. However, the tag and its site of placement can potentially compromise the hapten recognition capabilities of the peptide, necessitating a detailed experimental characterization and optimization of the tagged molecular recognition entity. The objective of this study was to assess the impact of site-specific tags on a native peptide's fold and hapten recognition capabilities using an advanced molecular dynamics (MD) simulation approach involving bias-exchange metadynamics and Markov State Models. The in-solution binding preferences of affinity tagged NFO4 (VYMNRKYYKCCK) to chlorinated (OTA) and non-chlorinated (OTB) analogues of ochratoxin were evaluated by appending hexa-histidine tags (6× His-tag) to the peptide's N-terminus (NterNFO4) or C-terminus (CterNFO4), respectively. The untagged NFO4 (NFO4), previously shown to bind with high affinity and selectivity to OTA, served as the control. Results indicate that the addition of site-specific 6× His-tags altered the peptide's native fold and the ochratoxin binding mechanism, with the influence of site-specific affinity tags being most evident on the peptide's interaction with OTA. The tags at the N-terminus of NFO4 preserved the native fold and actively contributed to the nonbonded interactions with OTA. In contrast, the tags at the C-terminus of NFO4 altered the native fold and were agnostic in its nonbonded interactions with OTA. The tags also increased the penalty associated with solvating the peptide-OTA complex. Interestingly, the tags did not significantly influence the nonbonded interactions or the penalty associated with solvating the peptide-OTB complex. Overall, the combined

  5. Molecular recognition of oxygen by protein mimics: dynamics on the femtosecond to microsecond time scale.

    PubMed

    Zou, Shouzhong; Baskin, J Spencer; Zewail, Ahmed H

    2002-07-23

    Molecular recognition by biological macromolecules involves many elementary steps, usually convoluted by diffusion processes. Here we report studies of the dynamics, from the femtosecond to the microsecond time scale, of the different elementary processes involved in the bimolecular recognition of a protein mimic, cobalt picket-fence porphyrin, with varying oxygen concentration at controlled temperatures. Electron transfer, bond breakage, and thermal "on" (recombination) and "off" (dissociation) reactions are the different processes involved. The reaction on-rate is 30 to 60 times smaller than that calculated from standard Smoluchowski theory. Introducing a two-step recognition model, with reversibility being part of both steps, removes the discrepancy and provides consistency for the reported thermodynamics, kinetics, and dynamics. The transient intermediates are configurations defined by the contact between oxygen (diatomic) and the picket-fence porphyrin (macromolecule). This intermediate is critical in the description of the potential energy landscape but, as shown here, both enthalpic and entropic contributions to the free energy are important. In the recognition process, the net entropy decrease is -33 cal mol(-1) K(-1); Delta H is -13.4 kcal mol(-1).

  6. Understanding Molecular Recognition by G protein βγ Subunits on the Path to Pharmacological Targeting

    PubMed Central

    Lin, Yuan

    2011-01-01

    Heterotrimeric G proteins, composed of Gα and Gβγ subunits, transduce extracellular signals via G-protein-coupled receptors to modulate many important intracellular responses. The Gβγ subunits hold a central position in this signaling system and have been implicated in multiple aspects of physiology and the pathophysiology of disease. The Gβ subunit belongs to a large family of WD40 repeat proteins with a circular β-bladed propeller structure. This structure allows Gβγ to interact with a broad range of proteins to play diverse roles. How Gβγ interacts with and regulates such a wide variety of partners yet maintains specificity is an interesting problem in protein-protein molecular recognition in signal transduction, where signal transfer by proteins is often driven by modular conserved recognition motifs. Evidence has accumulated that one mechanism for Gβγ multitarget recognition is through an intrinsically flexible protein surface or “hot spot” that accommodates multiple modes of binding. Because each target has a unique recognition mode for Gβγ subunits, it suggests that these interactions could be selectively manipulated with small molecules, which could have significant therapeutic potential. PMID:21737569

  7. Molecular recognition in myxobacterial outer membrane exchange: Functional, social and evolutionary implications

    PubMed Central

    Wall, Daniel

    2014-01-01

    Summary Through cooperative interactions, bacteria can build multicellular communities. To ensure that productive interactions occur, bacteria must recognize their neighbors and respond accordingly. Molecular recognition between cells is thus a fundamental behavior, and in bacteria important discoveries have been made. This MicroReview focuses on a recently described recognition system in myxobacteria that is governed by a polymorphic cell surface receptor called TraA. TraA regulates outer membrane exchange (OME), whereby myxobacterial cells transiently fuse their OMs to efficiently transfer proteins and lipids between cells. Unlike other transport systems, OME is rather indiscriminate in what OM goods are transferred. In contrast, the recognition of partnering cells is discriminatory and only occurs between cells that bear identical or closely related TraA proteins. Therefore TraA functions in kin recognition and, in turn, OME helps regulate social interactions between myxobacteria. Here, I discuss and speculate on the social and evolutionary implications of OME and suggest it helps to guide their transition from free-living cells into coherent and functional populations. PMID:24261719

  8. Molecular recognition in myxobacterial outer membrane exchange: functional, social and evolutionary implications.

    PubMed

    Wall, Daniel

    2014-01-01

    Through cooperative interactions, bacteria can build multicellular communities. To ensure that productive interactions occur, bacteria must recognize their neighbours and respond accordingly. Molecular recognition between cells is thus a fundamental behaviour, and in bacteria important discoveries have been made. This MicroReview focuses on a recently described recognition system in myxobacteria that is governed by a polymorphic cell surface receptor called TraA. TraA regulates outer membrane exchange (OME), whereby myxobacterial cells transiently fuse their OMs to efficiently transfer proteins and lipids between cells. Unlike other transport systems, OME is rather indiscriminate in what OM goods are transferred. In contrast, the recognition of partnering cells is discriminatory and only occurs between cells that bear identical or closely related TraA proteins. Therefore TraA functions in kin recognition and, in turn, OME helps regulate social interactions between myxobacteria. Here, I discuss and speculate on the social and evolutionary implications of OME and suggest it helps to guide their transition from free-living cells into coherent and functional populations. © 2013 John Wiley & Sons Ltd.

  9. Surface-imprinted nanostructured layer-by-layer film for molecular recognition of theophylline derivatives.

    PubMed

    Niu, Jia; Liu, Zhihua; Fu, Long; Shi, Feng; Ma, Hongwei; Ozaki, Yukihiro; Zhang, Xi

    2008-10-21

    In this article we report the introduction of the cooperativity of various specific interactions combined with photo-cross-linking of the interlayers to yield binding sites that can realize better selectivity and imprinting efficiency of a surface molecularly imprinted LbL film (SMILbL), thus providing a new approach toward fabrication of nanostructured molecularly imprinted thin films. It involves preassembly of poly(acrylic acid) (PAA) conjugated of the theophylline residue template via a disulfide bridge, denoted as PAAtheo 15, in solution, and layer-by-layer (LbL) assembly of PAAtheo 15 and a positively charged photoreactive diazo resin (DAR) to form multilayer thin film with designed architecture. After photo-cross-linking of the film and template removal, binding sites specific to 7-(beta-hydroxyethyl)theophylline (Theo-ol) molecules are introduced within the film. Binding assay demonstrates that the SMILbL has a high selectivity of SMILbL to Theo-ol over caffeine. A control experiment demonstrates that the selectivity of SMILbL derives from nanostructured recognition sites among the layers. The imprinting amount per unit mass of the film can be 1 order of magnitude larger than that of the conventional bulk molecular imprinting systems. As this concept of construction SMILbL can be easily extended to the other molecules by the following similar protocol: its applications in building many other different molecular recognition systems are greatly anticipated.

  10. Design Molecular Recognition Materials for Chiral Sensors, Separtations and Catalytic Materials

    SciTech Connect

    Jia, S.; Nenoff, T.M.; Provencio, P.; Qiu, Y.; Shelnutt, J.A.; Thoma, S.G.; Zhang, J.

    1998-11-01

    The goal is the development of materials that are highly sensitive and selective for chid chemicals and biochemical (such as insecticides, herbicides, proteins, and nerve agents) to be used as sensors, catalysts and separations membranes. Molecular modeling methods are being used to tailor chiral molecular recognition sites with high affinity and selectivity for specified agents. The work focuses on both silicate and non-silicate materials modified with chirally-pure fictional groups for the catalysis or separations of enantiomerically-pure molecules. Surfactant and quaternary amine templating is being used to synthesize porous frameworks, containing mesopores of 30 to 100 angstroms. Computer molecukw modeling methods are being used in the design of these materials, especially in the chid surface- modi~ing agents. Molecular modeling is also being used to predict the catalytic and separations selectivities of the modified mesoporous materials. The ability to design and synthesize tailored asymmetric molecular recognition sites for sensor coatings allows a broader range of chemicals to be sensed with the desired high sensitivity and selectivity. Initial experiments target the selective sensing of small molecule gases and non-toxic model neural compounds. Further efforts will address designing sensors that greatly extend the variety of resolvable chemical species and forming a predictive, model-based method for developing advanced sensors.

  11. A molecular code dictates sequence-specific DNA recognition by homeodomains.

    PubMed Central

    Damante, G; Pellizzari, L; Esposito, G; Fogolari, F; Viglino, P; Fabbro, D; Tell, G; Formisano, S; Di Lauro, R

    1996-01-01

    Most homeodomains bind to DNA sequences containing the motif 5'-TAAT-3'. The homeodomain of thyroid transcription factor 1 (TTF-1HD) binds to sequences containing a 5'-CAAG-3' core motif, delineating a new mechanism for differential DNA recognition by homeodomains. We investigated the molecular basis of the DNA binding specificity of TTF-1HD by both structural and functional approaches. As already suggested by the three-dimensional structure of TTF-1HD, the DNA binding specificities of the TTF-1, Antennapedia and Engrailed homeodomains, either wild-type or mutants, indicated that the amino acid residue in position 54 is involved in the recognition of the nucleotide at the 3' end of the core motif 5'-NAAN-3'. The nucleotide at the 5' position of this core sequence is recognized by the amino acids located in position 6, 7 and 8 of the TTF-1 and Antennapedia homeodomains. These data, together with previous suggestions on the role of amino acids in position 50, indicate that the DNA binding specificity of homeodomains can be determined by a combinatorial molecular code. We also show that some specific combinations of the key amino acid residues involved in DNA recognition do not follow a simple, additive rule. Images PMID:8890172

  12. Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches.

    PubMed

    Jiang, Hanlun; Zhu, Lizhe; Héliou, Amélie; Gao, Xin; Bernauer, Julie; Huang, Xuhui

    2017-01-01

    MicroRNA (miRNA) and Argonaute (AGO) protein together form the RNA-induced silencing complex (RISC) that plays an essential role in the regulation of gene expression. Elucidating the underlying mechanism of AGO-miRNA recognition is thus of great importance not only for the in-depth understanding of miRNA function but also for inspiring new drugs targeting miRNAs. In this chapter we introduce a combined computational approach of molecular dynamics (MD) simulations, Markov state models (MSMs), and protein-RNA docking to investigate AGO-miRNA recognition. Constructed from MD simulations, MSMs can elucidate the conformational dynamics of AGO at biologically relevant timescales. Protein-RNA docking can then efficiently identify the AGO conformations that are geometrically accessible to miRNA. Using our recent work on human AGO2 as an example, we explain the rationale and the workflow of our method in details. This combined approach holds great promise to complement experiments in unraveling the mechanisms of molecular recognition between large, flexible, and complex biomolecules.

  13. Molecularly imprinted titania nanoparticles for selective recognition and assay of uric acid

    NASA Astrophysics Data System (ADS)

    Mujahid, Adnan; Khan, Aimen Idrees; Afzal, Adeel; Hussain, Tajamal; Raza, Muhammad Hamid; Shah, Asma Tufail; uz Zaman, Waheed

    2015-06-01

    Molecularly imprinted titania nanoparticles are su ccessfully synthesized by sol-gel method for the selective recognition of uric acid. Atomic force microscopy is used to study the morphology of uric acid imprinted titania nanoparticles with diameter in the range of 100-150 nm. Scanning electron microscopy images of thick titania layer indicate the formation of fine network of titania nanoparticles with uniform distribution. Molecular imprinting of uric acid as well as its subsequent washing is confirmed by Fourier transformation infrared spectroscopy measurements. Uric acid rebinding studies reveal the recognition capability of imprinted particles in the range of 0.01-0.095 mmol, which is applicable in monitoring normal to elevated levels of uric acid in human blood. The optical shift (signal) of imprinted particles is six times higher in comparison with non-imprinted particles for the same concentration of uric acid. Imprinted titania particles have shown substantially reduced binding affinity toward interfering and structurally related substances, e.g. ascorbic acid and guanine. These results suggest the possible application of titania nanoparticles in uric acid recognition and quantification in blood serum.

  14. Macromolecular semi-rigid nanocavities for cooperative recognition of specific large molecular shapes.

    PubMed

    Imaoka, Takane; Kawana, Yuki; Kurokawa, Takuto; Yamamoto, Kimihisa

    2013-01-01

    Molecular shape recognition for larger guest molecules (typically over 1 nm) is a difficult task because it requires cooperativity within a wide three-dimensional nanospace coincidentally probing every molecular aspect (size, outline shape, flexibility and specific groups). Although the intelligent functions of proteins have fascinated many researchers, the reproduction by artificial molecules remains a significant challenge. Here we report the construction of large, well-defined cavities in macromolecular hosts. Through the use of semi-rigid dendritic phenylazomethine backbones, even subtle differences in the shapes of large guest molecules (up to ~2 nm) may be discriminated by the cooperative mechanism. A conformationally fixed complex with the best-fitting guest is supported by a three-dimensional model based on a molecular simulation. Interestingly, the simulated cavity structure also predicts catalytic selectivity by a ruthenium porphyrin centre, demonstrating the high shape persistence and wide applicability of the cavity.

  15. Conformational diversity of bacterial FabH: Implications for molecular recognition specificity

    PubMed Central

    Mittal, Anuradha; Johnson, Michael E.

    2015-01-01

    The molecular basis of variable substrate and inhibitor specificity of the highly conserved bacterial fatty acid synthase enzyme, FabH, across different bacterial species remains poorly understood. In the current work, we explored the conformational diversity of FabH enzymes to understand the determinants of diverse interaction specificity across Gram-positive and Gram-negative bacteria. Atomistic molecular dynamics simulations reveal that FabH from E. coli and E. faecalis exhibit distinct native state conformational ensembles and dynamic behaviors. Despite strikingly similar substrate binding pockets, hot spot assessment using computational solvent mapping identified quite different favorable binding interactions between the two homologs. Our data suggest that FabH utilizes protein dynamics and seemingly minor sequence and structural differences to modulate its molecular recognition and substrate specificity across bacterial species. These insights will potentially facilitate the rational design and development of antibacterial inhibitors against FabH enzymes. PMID:25437098

  16. ADAPT, a Novel Scaffold Protein-Based Probe for Radionuclide Imaging of Molecular Targets That Are Expressed in Disseminated Cancers.

    PubMed

    Garousi, Javad; Lindbo, Sarah; Nilvebrant, Johan; Åstrand, Mikael; Buijs, Jos; Sandström, Mattias; Honarvar, Hadis; Orlova, Anna; Tolmachev, Vladimir; Hober, Sophia

    2015-10-15

    Small engineered scaffold proteins have attracted attention as probes for radionuclide-based molecular imaging. One class of these imaging probes, termed ABD-Derived Affinity Proteins (ADAPT), has been created using the albumin-binding domain (ABD) of streptococcal protein G as a stable protein scaffold. In this study, we report the development of a clinical lead probe termed ADAPT6 that binds HER2, an oncoprotein overexpressed in many breast cancers that serves as a theranostic biomarker for several approved targeting therapies. Surface-exposed amino acids of ABD were randomized to create a combinatorial library enabling selection of high-affinity binders to various proteins. Furthermore, ABD was engineered to enable rapid purification, to eradicate its binding to albumin, and to enable rapid blood clearance. Incorporation of a unique cysteine allowed site-specific conjugation to a maleimido derivative of a DOTA chelator, enabling radionuclide labeling, ¹¹¹In for SPECT imaging and ⁶⁸Ga for PET imaging. Pharmacologic studies in mice demonstrated that the fully engineered molecule (111)In/⁶⁸Ga-DOTA-(HE)3-ADAPT6 was specifically bound and taken up by HER2-expressing tumors, with a high tumor-to-normal tissue ratio in xenograft models of human cancer. Unbound tracer underwent rapid renal clearance followed by high renal reabsorption. HER2-expressing xenografts were visualized by gamma-camera or PET at 1 hour after infusion. PET experiments demonstrated feasibility for discrimination of xenografts with high or low HER2 expression. Our results offer a preclinical proof of concept for the use of ADAPT probes for noninvasive in vivo imaging.

  17. High-resolution crystal structure reveals molecular details of target recognition by bacitracin

    PubMed Central

    Economou, Nicoleta J.; Cocklin, Simon; Loll, Patrick J.

    2013-01-01

    Bacitracin is a metalloantibiotic agent that is widely used as a medicine and feed additive. It interferes with bacterial cell-wall biosynthesis by binding undecaprenyl-pyrophosphate, a lipid carrier that serves as a critical intermediate in cell wall production. Despite bacitracin’s broad use, the molecular details of its target recognition have not been elucidated. Here we report a crystal structure for the ternary complex of bacitracin A, zinc, and a geranyl-pyrophosphate ligand at a resolution of 1.1 Å. The antibiotic forms a compact structure that completely envelopes the ligand’s pyrophosphate group, together with flanking zinc and sodium ions. The complex adopts a highly amphipathic conformation that offers clues to antibiotic function in the context of bacterial membranes. Bacitracin’s efficient sequestration of its target represents a previously unseen mode for the recognition of lipid pyrophosphates, and suggests new directions for the design of next-generation antimicrobial agents. PMID:23940351

  18. Anion recognition and cation-induced molecular motion in a heteroditopic [2]rotaxane.

    PubMed

    Leontiev, Alexandre V; Jemmett, Charlotte A; Beer, Paul D

    2011-01-17

    A heteroditopic [2]rotaxane consisting of a calix[4]diquinone-isophthalamide macrocycle and 3,5-bis-amide pyridinium axle components with the capability of switching between two positional isomers in response to barium cation recognition is synthesised. The anion binding properties of the rotaxane's interlocked cavity together with Na(+) , K(+) , NH(4) (+) and Ba(2+) cation recognition capabilities are elucidated by (1) H NMR and UV-visible spectroscopic titration experiments. Upon binding of Ba(2+) , molecular displacement of the axle's positively charged pyridinium group from the rotaxane's macrocyclic cavity occurs, whereas the monovalent cations Na(+) , K(+) and NH(4) (+) are bound without causing significant co-conformational change. The barium cation induced shuttling motion can be reversed on addition of tetrabutylammonium sulfate.

  19. Selective Nitrate Recognition by a Halogen-Bonding Four-Station [3]Rotaxane Molecular Shuttle.

    PubMed

    Barendt, Timothy A; Docker, Andrew; Marques, Igor; Félix, Vítor; Beer, Paul D

    2016-09-05

    The synthesis of the first halogen bonding [3]rotaxane host system containing a bis-iodo triazolium-bis-naphthalene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate, hydrogen carbonate and dihydrogen phosphate oxoanions and chloride, and exhibits enhanced recognition of anions relative to a hydrogen bonding analogue. This elaborate interlocked anion receptor functions via a novel dynamic pincer mechanism where upon nitrate anion binding, both macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodo-triazolium station anion recognition sites to form a unique 1:1 stoichiometric nitrate anion-rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corroborate the (1) H NMR anion binding results.

  20. Selective Nitrate Recognition by a Halogen‐Bonding Four‐Station [3]Rotaxane Molecular Shuttle

    PubMed Central

    Barendt, Timothy A.; Docker, Andrew; Marques, Igor; Félix, Vítor

    2016-01-01

    Abstract The synthesis of the first halogen bonding [3]rotaxane host system containing a bis‐iodo triazolium‐bis‐naphthalene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate, hydrogen carbonate and dihydrogen phosphate oxoanions and chloride, and exhibits enhanced recognition of anions relative to a hydrogen bonding analogue. This elaborate interlocked anion receptor functions via a novel dynamic pincer mechanism where upon nitrate anion binding, both macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodo‐triazolium station anion recognition sites to form a unique 1:1 stoichiometric nitrate anion–rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corroborate the 1H NMR anion binding results. PMID:27436297

  1. Preparation and characterization of novel molecularly imprinted polymers based on thiourea receptors for nitrocompounds recognition.

    PubMed

    Athikomrattanakul, Umporn; Katterle, Martin; Gajovic-Eichelmann, Nenad; Scheller, Frieder W

    2011-04-15

    Molecularly imprinted polymers (MIPs) for the recognition of nitro derivatives are prepared from three different (thio)urea-bearing functional monomers. The binding capability of the polymers is characterized by a batch binding experiment. The imprinting factors and affinity constants (K) of the imprinted polymers exhibit the same tendency as the binding constants (K(a)) of the functional monomers to the target substance in solution. Not only nitrofurantoin is efficiently bound by these MIPs but also a broad spectrum of other nitro compounds is bound with at the intermediate level, addressing that these (thio)urea-based monomers can be utilized to prepare a family of MIPs for various nitro compounds, which can be applied as recognition elements in separation and analytical application.

  2. Novel hybrid probe based on double recognition of aptamer-molecularly imprinted polymer grafted on upconversion nanoparticles for enrofloxacin sensing.

    PubMed

    Liu, Xiuying; Ren, Jing; Su, Lihong; Gao, Xue; Tang, Yiwei; Ma, Tao; Zhu, Lijie; Li, Jianrong

    2017-01-15

    A novel luminescent "double recognition" method for the detection of enrofloxacin (ENR) is developed to overcome some of the challenges faced by conventional molecularly imprinting. Biotinylated ENR aptamers immobilised on upconversion nanoparticles (UCNPs) surface are implemented to capture and concentrate ENR as the first imprinting recognition safeguard. After correct folding of the aptamer upon the existing targets, polymerization of methacrylic acid monomers around the ENR-aptamer complexes to interact with the residual functional groups of ENR by using molecularly imprinting techniques is the second imprinting recognition safeguard. The "double recognition" imprinting cavities are formed after removal of ENR, displaying recognition properties superior to that of aptamer or traditional molecularly imprinting alone. Another interest of this method is simultaneous molecular recognition and signal conversion by fabricating the "double recognition" receptor on to the surface of UCNPs to form a hybrid sensing system of apta-MIP/UCNPs. The proposed sensing method is applied to measure ENR in different fish samples. Good recoveries between 87.05% and 96.24%, and relative standard deviation (RSD) values in the range of 1.19-4.83% are obtained, with the limits of detection and quantification of 0.04 and 0.12ng/mL, respectively. It indicates that the sensing method is feasible for the quantification of target ENRs in real samples, and show great potential for wide-ranging application in bioassays. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Molecular recognition of parathyroid hormone by its G protein-coupled receptor

    SciTech Connect

    Pioszak, Augen A.; Xu, H. Eric

    2008-08-07

    Parathyroid hormone (PTH) is central to calcium homeostasis and bone maintenance in vertebrates, and as such it has been used for treating osteoporosis. It acts primarily by binding to its receptor, PTH1R, a member of the class B G protein-coupled receptor (GPCR) family that also includes receptors for glucagon, calcitonin, and other therapeutically important peptide hormones. Despite considerable interest and much research, determining the structure of the receptor-hormone complex has been hindered by difficulties in purifying the receptor and obtaining diffraction-quality crystals. Here, we present a method for expression and purification of the extracellular domain (ECD) of human PTH1R engineered as a maltose-binding protein (MBP) fusion that readily crystallizes. The 1.95-{angstrom} structure of PTH bound to the MBP-PTH1R-ECD fusion reveals that PTH docks as an amphipathic helix into a central hydrophobic groove formed by a three-layer {alpha}-{beta}-{beta}{alpha} fold of the PTH1R ECD, resembling a hot dog in a bun. Conservation in the ECD scaffold and the helical structure of peptide hormones emphasizes this hot dog model as a general mechanism of hormone recognition common to class B GPCRs. Our findings reveal critical insights into PTH actions and provide a rational template for drug design that targets this hormone signaling pathway.

  4. Integrated structural biology to unravel molecular mechanisms of protein-RNA recognition.

    PubMed

    Schlundt, Andreas; Tants, Jan-Niklas; Sattler, Michael

    2017-03-16

    Recent advances in RNA sequencing technologies have greatly expanded our knowledge of the RNA landscape in cells, often with spatiotemporal resolution. These techniques identified many new (often non-coding) RNA molecules. Large-scale studies have also discovered novel RNA binding proteins (RBPs), which exhibit single or multiple RNA binding domains (RBDs) for recognition of specific sequence or structured motifs in RNA. Starting from these large-scale approaches it is crucial to unravel the molecular principles of protein-RNA recognition in ribonucleoprotein complexes (RNPs) to understand the underlying mechanisms of gene regulation. Structural biology and biophysical studies at highest possible resolution are key to elucidate molecular mechanisms of RNA recognition by RBPs and how conformational dynamics, weak interactions and cooperative binding contribute to the formation of specific, context-dependent RNPs. While large compact RNPs can be well studied by X-ray crystallography and cryo-EM, analysis of dynamics and weak interaction necessitates the use of solution methods to capture these properties. Here, we illustrate methods to study the structure and conformational dynamics of protein-RNA complexes in solution starting from the identification of interaction partners in a given RNP. Biophysical and biochemical techniques support the characterization of a protein-RNA complex and identify regions relevant in structural analysis. Nuclear magnetic resonance (NMR) is a powerful tool to gain information on folding, stability and dynamics of RNAs and characterize RNPs in solution. It provides crucial information that is complementary to the static pictures derived from other techniques. NMR can be readily combined with other solution techniques, such as small angle X-ray and/or neutron scattering (SAXS/SANS), electron paramagnetic resonance (EPR), and Förster resonance energy transfer (FRET), which provide information about overall shapes, internal domain

  5. Molecular recognition with nanostructures fabricated by photopolymerization within metallic subwavelength apertures

    NASA Astrophysics Data System (ADS)

    Urraca, J. L.; Barrios, C. A.; Canalejas-Tejero, V.; Orellana, G.; Moreno-Bondi, M. C.

    2014-07-01

    The first demonstration of fabrication of submicron lateral resolution molecularly imprinted polymer (MIP) patterns by photoinduced local polymerization within metal subwavelength apertures is reported. The size of the photopolymerized MIP features is finely tuned by the dose of 532 nm radiation. Rhodamine 123 (R123) has been selected as a fluorescent model template to prove the recognition capability of the MIP nanostructures, which has been evaluated by fluorescence lifetime imaging microscopy (FLIM) with single photon timing measurements. The binding selectivity provided by the imprinting effect has been confirmed in the presence of compounds structurally related to R123. These results pave the way to the development of nanomaterial architectures with biomimetic artificial recognition properties for environmental, clinical and food testing.The first demonstration of fabrication of submicron lateral resolution molecularly imprinted polymer (MIP) patterns by photoinduced local polymerization within metal subwavelength apertures is reported. The size of the photopolymerized MIP features is finely tuned by the dose of 532 nm radiation. Rhodamine 123 (R123) has been selected as a fluorescent model template to prove the recognition capability of the MIP nanostructures, which has been evaluated by fluorescence lifetime imaging microscopy (FLIM) with single photon timing measurements. The binding selectivity provided by the imprinting effect has been confirmed in the presence of compounds structurally related to R123. These results pave the way to the development of nanomaterial architectures with biomimetic artificial recognition properties for environmental, clinical and food testing. Electronic supplementary information (ESI) available: Fig. SI.1: chemical structure and acronyms of the different fluorescent dyes; optimization of polymer composition; Table SI.1. Template recovery after polymerization; determination of the binding capacity by equilibrium rebinding

  6. Two dimensional molecular electronics spectroscopy for molecular fingerprinting, DNA sequencing, and cancerous DNA recognition.

    PubMed

    Rajan, Arunkumar Chitteth; Rezapour, Mohammad Reza; Yun, Jeonghun; Cho, Yeonchoo; Cho, Woo Jong; Min, Seung Kyu; Lee, Geunsik; Kim, Kwang S

    2014-02-25

    Laser-driven molecular spectroscopy of low spatial resolution is widely used, while electronic current-driven molecular spectroscopy of atomic scale resolution has been limited because currents provide only minimal information. However, electron transmission of a graphene nanoribbon on which a molecule is adsorbed shows molecular fingerprints of Fano resonances, i.e., characteristic features of frontier orbitals and conformations of physisorbed molecules. Utilizing these resonance profiles, here we demonstrate two-dimensional molecular electronics spectroscopy (2D MES). The differential conductance with respect to bias and gate voltages not only distinguishes different types of nucleobases for DNA sequencing but also recognizes methylated nucleobases which could be related to cancerous cell growth. This 2D MES could open an exciting field to recognize single molecule signatures at atomic resolution. The advantages of the 2D MES over the one-dimensional (1D) current analysis can be comparable to those of 2D NMR over 1D NMR analysis.

  7. Exploring the molecular basis of RNA recognition by the dimeric RNA-binding protein via molecular simulation methods.

    PubMed

    Chang, Shan; Zhang, Da-Wei; Xu, Lei; Wan, Hua; Hou, Ting-Jun; Kong, Ren

    2016-11-01

    RNA-binding protein with multiple splicing (RBPMS) is critical for axon guidance, smooth muscle plasticity, and regulation of cancer cell proliferation and migration. Recently, different states of the RNA-recognition motif (RRM) of RBPMS, one in its free form and another in complex with CAC-containing RNA, were determined by X-ray crystallography. In this article, the free RRM domain, its wild type complex and 2 mutant complex systems are studied by molecular dynamics (MD) simulations. Through comparison of free RRM domain and complex systems, it's found that the RNA binding facilitates stabilizing the RNA-binding interface of RRM domain, especially the C-terminal loop. Although both R38Q and T103A/K104A mutations reduce the binding affinity of RRM domain and RNA, the underlining mechanisms are different. Principal component analysis (PCA) and Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) methods were used to explore the dynamical and recognition mechanisms of RRM domain and RNA. R38Q mutation is positioned on the homodimerization interface and mainly induces the large fluctuations of RRM domains. This mutation does not directly act on the RNA-binding interface, but some interfacial hydrogen bonds are weakened. In contrast, T103A/K104A mutations are located on the RNA-binding interface of RRM domain. These mutations obviously break most of high occupancy hydrogen bonds in the RNA-binding interface. Meanwhile, the key interfacial residues lose their favorable energy contributions upon RNA binding. The ranking of calculated binding energies in 3 complex systems is well consistent with that of experimental binding affinities. These results will be helpful in understanding the RNA recognition mechanisms of RRM domain.

  8. Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy

    PubMed Central

    Li, Mi; Dang, Dan; Liu, Lianqing; Xi, Ning; Wang, Yuechao

    2017-01-01

    The advent of atomic force microscopy (AFM) has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface) was summarized. The challenges and future directions were also discussed. PMID:28117741

  9. Molecular Basis for Unidirectional Scaffold Switching of Human Plk4 in Centriole Biogenesis

    PubMed Central

    Park, Suk-Youl; Park, Jung-Eun; Kim, Tae-Sung; Kim, Ju Hee; Kwak, Mi-Jeong; Ku, Bonsu; Tian, Lan; Murugan, Ravichandran N.; Ahn, Mija; Komiya, Shinobu; Hojo, Hironobu; Kim, Nam-Hyung; Kim, Bo Yeon; Bang, Jeong K.; Erikson, Raymond L.; Lee, Ki Won; Kim, Seung Jun; Oh, Byung-Ha; Yang, Wei; Lee, Kyung S.

    2014-01-01

    Polo-like kinase 4 (Plk4) is a key regulator of centriole duplication, an event critical for the maintenance of genomic integrity. Here we showed that Plk4 relocalizes from the inner Cep192 ring to the outer Cep152 ring as newly recruited Cep152 assembles around the Cep192-encircled daughter centriole. Crystal structure analyses revealed that Cep192 - and Cep152-derived peptides bind the cryptic polo box (CPB) of Plk4 in opposite orientations and in a mutually exclusive manner. The Cep152-peptide bound to the CPB markedly better than the Cep192-peptide and effectively snatched the CPB away from a preformed CPB–Cep192-peptide complex. A cancer-associated Cep152 mutation impairing the Plk4 interaction induced defects in procentriole assembly and chromosome segregation. Thus, Plk4 is intricately regulated in time and space through ordered interactions with two distinct scaffolds, Cep192 and Cep152, and a failure in this process may lead to human cancer. PMID:24997597

  10. Label-Free Sensing of Adenosine Based on Force Variations Induced by Molecular Recognition

    PubMed Central

    Li, Jingfeng; Li, Qing; Colombi Ciacchi, Lucio; Wei, Gang

    2015-01-01

    We demonstrate a simple force-based label-free strategy for the highly sensitive sensing of adenosine. An adenosine ssDNA aptamer was bound onto an atomic force microscopy (AFM) probe by covalent modification, and the molecular-interface adsorption force between the aptamer and a flat graphite surface was measured by single-molecule force spectroscopy (SMFS). In the presence of adenosine, the molecular recognition between adenosine and the aptamer resulted in the formation of a folded, hairpin-like DNA structure and hence caused a variation of the adsorption force at the graphite/water interface. The sensitive force response to molecular recognition provided an adenosine detection limit in the range of 0.1 to 1 nM. The addition of guanosine, cytidine, and uridine had no significant interference with the sensing of adenosine, indicating a strong selectivity of this sensor architecture. In addition, operational parameters that may affect the sensor, such as loading rate and solution ionic strength, were investigated. PMID:25808841

  11. Metal Oxide Nanosensors Using Polymeric Membranes, Enzymes and Antibody Receptors as Ion and Molecular Recognition Elements

    PubMed Central

    Willander, Magnus; Khun, Kimleang; Ibupoto, Zafar Hussain

    2014-01-01

    The concept of recognition and biofunctionality has attracted increasing interest in the fields of chemistry and material sciences. Advances in the field of nanotechnology for the synthesis of desired metal oxide nanostructures have provided a solid platform for the integration of nanoelectronic devices. These nanoelectronics-based devices have the ability to recognize molecular species of living organisms, and they have created the possibility for advanced chemical sensing functionalities with low limits of detection in the nanomolar range. In this review, various metal oxides, such as ZnO-, CuO-, and NiO-based nanosensors, are described using different methods (receptors) of functionalization for molecular and ion recognition. These functionalized metal oxide surfaces with a specific receptor involve either a complex formation between the receptor and the analyte or an electrostatic interaction during the chemical sensing of analytes. Metal oxide nanostructures are considered revolutionary nanomaterials that have a specific surface for the immobilization of biomolecules with much needed orientation, good conformation and enhanced biological activity which further improve the sensing properties of nanosensors. Metal oxide nanostructures are associated with certain unique optical, electrical and molecular characteristics in addition to unique functionalities and surface charge features which shows attractive platforms for interfacing biorecognition elements with effective transducing properties for signal amplification. There is a great opportunity in the near future for metal oxide nanostructure-based miniaturization and the development of engineering sensor devices. PMID:24841244

  12. Exploiting β-cyclodextrin in molecular imprinting for achieving recognition of benzylparaben in aqueous media.

    PubMed

    Asman, Saliza; Mohamad, Sharifah; Sarih, Norazilawati Muhamad

    2015-02-06

    The molecularly imprinted polymer (MIP) based on methacrylic acid functionalized β-cyclodextrin (MAA-β-CD) monomer was synthesized for the purpose of selective recognition of benzylparaben (BzP). The MAA-β-CD monomer was produced by bridging a methacrylic acid (MAA) and β-cyclodextrin (β-CD) using toluene-2,4-diisocyanate (TDI) by reacting the -OH group of MAA and one of the primary -OH groups of β-CD. This monomer comprised of triple interactions that included an inclusion complex, π-π interaction, and hydrogen bonding. To demonstrate β-CD performance in MIPs, two MIPs were prepared; molecularly imprinted polymer-methacrylic acid functionalized β-cyclodextrin, MIP(MAA-β-CD), and molecularly imprinted polymer-methacrylic acid, MIP(MAA); both prepared by a reversible addition fragmentation chain transfer polymerization (RAFT) in the bulk polymerization process. Both MIPs were characterized using the Fourier Transform Infrared Spectroscopy (FTIR), Field Emission Scanning Electron Microscopy (FESEM), and Brunauer-Emmett-Teller (BET). The presence of β-CD not only influenced the morphological structure, it also affected the specific surface area, average pore diameter, and total pore volume of the MIP. The rebinding of the imprinting effect was evaluated in binding experiments, which proved that the β-CD contributed significantly to the enhancement of the recognition affinity and selective adsorption of the MIP.

  13. Exploiting β-Cyclodextrin in Molecular Imprinting for Achieving Recognition of Benzylparaben in Aqueous Media

    PubMed Central

    Asman, Saliza; Mohamad, Sharifah; Muhamad Sarih, Norazilawati

    2015-01-01

    The molecularly imprinted polymer (MIP) based on methacrylic acid functionalized β-cyclodextrin (MAA-β-CD) monomer was synthesized for the purpose of selective recognition of benzylparaben (BzP). The MAA-β-CD monomer was produced by bridging a methacrylic acid (MAA) and β-cyclodextrin (β-CD) using toluene-2,4-diisocyanate (TDI) by reacting the –OH group of MAA and one of the primary –OH groups of β-CD. This monomer comprised of triple interactions that included an inclusion complex, π–π interaction, and hydrogen bonding. To demonstrate β-CD performance in MIPs, two MIPs were prepared; molecularly imprinted polymer-methacrylic acid functionalized β-cyclodextrin, MIP(MAA-β-CD), and molecularly imprinted polymer-methacrylic acid, MIP(MAA); both prepared by a reversible addition fragmentation chain transfer polymerization (RAFT) in the bulk polymerization process. Both MIPs were characterized using the Fourier Transform Infrared Spectroscopy (FTIR), Field Emission Scanning Electron Microscopy (FESEM), and Brunauer-Emmett-Teller (BET). The presence of β-CD not only influenced the morphological structure, it also affected the specific surface area, average pore diameter, and total pore volume of the MIP. The rebinding of the imprinting effect was evaluated in binding experiments, which proved that the β-CD contributed significantly to the enhancement of the recognition affinity and selective adsorption of the MIP. PMID:25667978

  14. Role for the propofol hydroxyl in anesthetic protein target molecular recognition.

    PubMed

    Woll, Kellie A; Weiser, Brian P; Liang, Qiansheng; Meng, Tao; McKinstry-Wu, Andrew; Pinch, Benika; Dailey, William P; Gao, Wei Dong; Covarrubias, Manuel; Eckenhoff, Roderic G

    2015-06-17

    Propofol is a widely used intravenous general anesthetic. We synthesized 2-fluoro-1,3-diisopropylbenzene, a compound that we call "fropofol", to directly assess the significance of the propofol 1-hydroxyl for pharmacologically relevant molecular recognition in vitro and for anesthetic efficacy in vivo. Compared to propofol, fropofol had a similar molecular volume and only a small increase in hydrophobicity. Isothermal titration calorimetry and competition assays revealed that fropofol had higher affinity for a protein site governed largely by van der Waals interactions. Within another protein model containing hydrogen bond interactions, propofol demonstrated higher affinity. In vivo, fropofol demonstrated no anesthetic efficacy, but at high concentrations produced excitatory activity in tadpoles and mice; fropofol also antagonized propofol-induced hypnosis. In a propofol protein target that contributes to hypnosis, α1β2γ2L GABAA receptors, fropofol demonstrated no significant effect alone or on propofol positive allosteric modulation of the ion channel, suggesting an additional requirement for the 1-hydroxyl within synaptic GABAA receptor site(s). However, fropofol caused similar adverse cardiovascular effects as propofol by a dose-dependent depression of myocardial contractility. Our results directly implicate the propofol 1-hydroxyl as contributing to molecular recognition within protein targets leading to hypnosis, but not necessarily within protein targets leading to side effects of the drug.

  15. Biologically-validated HIV integrase inhibitors with nucleobase scaffolds: structure, synthesis, chemical biology, molecular modeling, and antiviral activity.

    PubMed

    Nair, Vasu; Uchil, Vinod; Chi, Guochen; Dams, Iwona; Cox, Arthur; Seo, Byung

    2007-01-01

    Integrase, an enzyme of the pol gene of HIV, is a significant viral target for the discovery of anti-HIV agents. In this presentation, we report on the continuation of our work on the discovery of diketo acids, constructed on nucleobase scaffolds, that are inhibitors of HIV integrase. An example of our synthetic approach to inhibitors with purine nucleobase scaffolds is given. Comparison is made between integrase inhibition data arising from compounds with pyrimidine versus purine nucleobase scaffold. Antiviral results are cited.

  16. Towards understanding the molecular recognition process in prokaryotic zinc-finger domain.

    PubMed

    Russo, Luigi; Palmieri, Maddalena; Caso, Jolanda Valentina; D'Abrosca, Gianluca; Diana, Donatella; Malgieri, Gaetano; Baglivo, Ilaria; Isernia, Carla; Pedone, Paolo V; Fattorusso, Roberto

    2015-02-16

    Eukaryotic Cys2His2 zinc finger domain is one of the most common and important structural motifs involved in protein-DNA interaction. The recognition motif is characterized by the tetrahedral coordination of a zinc ion by conserved cysteine and histidine residues. We have characterized the prokaryotic Cys2His2 zinc finger motif, included in the DNA binding region (Ros87) of Ros protein from Agrobacterium tumefaciens, demonstrating that, although possessing a similar zinc coordination sphere, this domain presents significant differences from its eukaryotic counterpart. Furthermore, basic residues flanking the zinc binding region on either side have been demonstrated, by Electrophoretic Mobility Shift Assay (EMSA) experiments, to be essential for Ros DNA binding. In spite of this wealth of knowledge, the structural details of the mechanism through which the prokaryotic zinc fingers recognize their target genes are still unclear. Here, to gain insights into the molecular DNA recognition process of prokaryotic zinc finger domains we applied a strategy in which we performed molecular docking studies using a combination of Nuclear Magnetic Resonance (NMR) and Molecular Dynamics (MD) simulations data. The results demonstrate that the MD ensemble provides a reasonable picture of Ros87 backbone dynamics in solution. The Ros87-DNA model indicates that the interaction involves the first two residue of the first α-helix, and several residues located in the basic regions flanking the zinc finger domain. Interestingly, the prokaryotic zinc finger domain, mainly with the C-terminal tail that is wrapped around the DNA, binds a more extended recognition site than the eukaryotic counterpart. Our analysis demonstrates that the introduction of the protein flexibility in docking studies can improve, in terms of accuracy, the quality of the obtained models and could be particularly useful for protein showing high conformational heterogeneity as well as for computational drug design

  17. Molecular Recognition of DNA. Synthesis of Novel Bases for Triple Helix Formation

    DTIC Science & Technology

    1991-01-01

    to the purine strand in the major groove of the Watson - Crick double helical DNA (TAT, C+GC triplets). Purine oligonucleotides bind antiparallel to...R&T Code 4135018 S MAy 05 199411 "Molecular Recognition of DNA . Synthesis of Novel Bases for Triple Helix Formation" Peter B. Dervan cv _California...035 T"IQA""D PART I A) Completed work (1988-91) Triple Helix Formation by Oligonucleotides on DNA Extended to the Physiological pH Range. T. J. Povsic

  18. In Vitro Selection of Cancer Cell-Specific Molecular Recognition Elements from Amino Acid Libraries

    PubMed Central

    Williams, Ryan M.; Sooter, Letha J.

    2015-01-01

    Differential cell systematic evolution of ligands by exponential enrichment (SELEX) is an in vitro selection method for obtaining molecular recognition elements (MREs) that specifically bind to individual cell types with high affinity. MREs are selected from initial large libraries of different nucleic or amino acids. This review outlines the construction of peptide and antibody fragment libraries as well as their different host types. Common methods of selection are also reviewed. Additionally, examples of cancer cell MREs are discussed, as well as their potential applications. PMID:26436100

  19. Unprecedented selectivity in molecular recognition of carbohydrates by a metal-organic framework.

    PubMed

    Yabushita, Mizuho; Li, Peng; Bernales, Varinia; Kobayashi, Hirokazu; Fukuoka, Atsushi; Gagliardi, Laura; Farha, Omar K; Katz, Alexander

    2016-06-04

    Metal-organic framework (MOF) material NU-1000 adsorbs dimers cellobiose and lactose from aqueous solution, in amounts exceeding 1250 mg gNU-1000(-1) while completely excluding the adsorption of the monomer glucose, even in a competitive mode with cellobiose. The MOF also discriminates between dimers consisting of α and β linkages, showing no adsorption of maltose. Electronic structure calculations demonstrate that key to this selective molecular recognition is the number of favorable CH-π interactions made by the sugar with pyrene units of the MOF.

  20. In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element Specific for Bromacil

    PubMed Central

    Williams, Ryan M.; Kulick, Amanda R.; Yedlapalli, Srilakshmi; Battistella, Louisa; Hajiran, Cyrus J.; Sooter, Letha J.

    2014-01-01

    Bromacil is a widely used herbicide that is known to contaminate environmental systems. Due to the hazards it presents and inefficient detection methods, it is necessary to create a rapid and efficient sensing device. Towards this end, we have utilized a stringent in vitro selection method to identify single-stranded DNA molecular recognition elements (MRE) specific for bromacil. We have identified one MRE with high affinity (Kd = 9.6 nM) and specificity for bromacil compared to negative targets of selection and other pesticides. The selected ssDNA MRE will be useful as the sensing element in a field-deployable bromacil detection device. PMID:25400940

  1. Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics

    SciTech Connect

    De Hatten, Xavier; Cournia, Zoe; Smith, Jeremy C; Huc, I; Metzler-Nolte, Nils

    2007-08-01

    The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1'-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C{sub 2}-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1 {micro}s MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline-1'-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 {micro}s MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.

  2. Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics.

    SciTech Connect

    De Hatten, Xavier; Cournia, Zoe; Smith, Jeremy C; Metzler-Nolte, Nils

    2007-08-01

    The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1{prime}-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C2-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1{micro}s MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline{prime}-1-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 s MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.

  3. Nanoporous poly(3-hexylthiophene) thin film structures from self-organization of a tunable molecular bottlebrush scaffold

    DOE PAGES

    Ahn, Suk-kyun; Carrillo, Jan-Michael Y.; Keum, Jong K.; ...

    2017-04-07

    The ability to widely tune the design of macromolecular bottlebrushes provides access to self-assembled nanostructures formed by microphase segregation in melt, thin film and solution that depart from structures adopted by simple linear copolymers. A series of random bottlebrush copolymers containing poly(3-hexylthiophene) (P3HT) and poly(D,L-lactide) (PLA) side chains grafted on a poly(norbornene) backbone were synthesized via ring-opening metathesis polymerization (ROMP) using the grafting through approach. P3HT side chains induce a physical aggregation of the bottlebrush copolymers upon solvent removal by vacuum drying, primarily driven by attractive π–π interactions; however, the amount of aggregation can be controlled by adjusting side chainmore » composition or by adding linear P3HT chains to the bottlebrush copolymers. Coarse-grained molecular dynamics simulations reveal that linear P3HT chains preferentially associate with P3HT side chains of bottlebrush copolymers, which tends to reduce the aggregation. The nanoscale morphology of microphase segregated thin films created by casting P3HT–PLA random bottlebrush copolymers is highly dependent on the composition of P3HT and PLA side chains, while domain spacing of nanostructures is mainly determined by the length of the side chains. The selective removal of PLA side chains under alkaline conditions generates nanoporous P3HT structures that can be tuned by manipulating molecular design of the bottlebrush scaffold, which is affected by molecular weight and grafting density of the side chains, and their sequence. Furthermore, the ability to exploit the unusual architecture of bottlebrushes to fabricate tunable nanoporous P3HT thin film structures may be a useful way to design templates for optoelectronic applications or membranes for separations.« less

  4. Molecular Recognition of Azelaic Acid and Related Molecules with DNA Polymerase I Investigated by Molecular Modeling Calculations.

    PubMed

    Shawon, Jakaria; Khan, Akib Mahmud; Rahman, Adhip; Hoque, Mohammad Mazharol; Khan, Mohammad Abdul Kader; Sarwar, Mohammed G; Halim, Mohammad A

    2016-10-01

    Molecular recognition has central role on the development of rational drug design. Binding affinity and interactions are two key components which aid to understand the molecular recognition in drug-receptor complex and crucial for structure-based drug design in medicinal chemistry. Herein, we report the binding affinity and the nonbonding interactions of azelaic acid and related compounds with the receptor DNA polymerase I (2KFN). Quantum mechanical calculation was employed to optimize the modified drugs using B3LYP/6-31G(d,p) level of theory. Charge distribution, dipole moment and thermodynamic properties such as electronic energy, enthalpy and free energy of these optimized drugs are also explored to evaluate how modifications impact the drug properties. Molecular docking calculation was performed to evaluate the binding affinity and nonbonding interactions between designed molecules and the receptor protein. We notice that all modified drugs are thermodynamically more stable and some of them are more chemically reactive than the unmodified drug. Promise in enhancing hydrogen bonds is found in case of fluorine-directed modifications as well as in the addition of trifluoroacetyl group. Fluorine participates in forming fluorine bonds and also stimulates alkyl, pi-alkyl interactions in some drugs. Designed drugs revealed increased binding affinity toward 2KFN. A1, A2 and A3 showed binding affinities of -8.7, -8.6 and -7.9 kcal/mol, respectively against 2KFN compared to the binding affinity -6.7 kcal/mol of the parent drug. Significant interactions observed between the drugs and Thr358 and Asp355 residues of 2KFN. Moreover, designed drugs demonstrated improved pharmacokinetic properties. This study disclosed that 9-octadecenoic acid and drugs containing trifluoroacetyl and trifluoromethyl groups are the best 2KFN inhibitors. Overall, these results can be useful for the design of new potential candidates against DNA polymerase I.

  5. Molecular recognition of malachite green by hemoglobin and their specific interactions: insights from in silico docking and molecular spectroscopy.

    PubMed

    Peng, Wei; Ding, Fei; Peng, Yu-Kui; Sun, Ying

    2014-01-01

    Malachite green is an organic compound that can be widely used as a dyestuff for various materials; it has also emerged as a controversial agent in aquaculture. Since malachite green is proven to be carcinogenic and mutagenic, it may become a hazard to public health. For this reason, it is urgently required to analyze this controversial dye in more detail. In our current research, the interaction between malachite green and hemoglobin under physiological conditions was investigated by the methods of molecular modeling, fluorescence spectroscopy, circular dichroism (CD) as well as hydrophobic ANS displacement experiments. From the molecular docking, the central cavity of hemoglobin was assigned to possess high-affinity for malachite green, this result was corroborated by time-resolved fluorescence and hydrophobic ANS probe results. The recognition mechanism was found to be of static type, or rather the hemoglobin-malachite green complex formation occurred via noncovalent interactions such as π-π interactions, hydrogen bonds and hydrophobic interactions with an association constant of 10(4) M(-1). Moreover, the results also show that the spatial structure of the biopolymer was changed in the presence of malachite green with a decrease of the α-helix and increase of the β-sheet, turn and random coil suggesting protein damage, as derived from far-UV CD and three-dimensional fluorescence. Results of this work will help to further comprehend the molecular recognition of malachite green by the receptor protein and the possible toxicological profiles of other compounds, which are the metabolites and ramifications of malachite green.

  6. Molecular crowding drives active Pin1 into nonspecific complexes with endogenous proteins prior to substrate recognition.

    PubMed

    Luh, Laura M; Hänsel, Robert; Löhr, Frank; Kirchner, Donata K; Krauskopf, Katharina; Pitzius, Susanne; Schäfer, Birgit; Tufar, Peter; Corbeski, Ivan; Güntert, Peter; Dötsch, Volker

    2013-09-18

    Proteins and nucleic acids maintain the crowded interior of a living cell and can reach concentrations in the order of 200-400 g/L which affects the physicochemical parameters of the environment, such as viscosity and hydrodynamic as well as nonspecific strong repulsive and weak attractive interactions. Dynamics, structure, and activity of macromolecules were demonstrated to be affected by these parameters. However, it remains controversially debated, which of these factors are the dominant cause for the observed alterations in vivo. In this study we investigated the globular folded peptidyl-prolyl isomerase Pin1 in Xenopus laevis oocytes and in native-like crowded oocyte extract by in-cell NMR spectroscopy. We show that active Pin1 is driven into nonspecific weak attractive interactions with intracellular proteins prior to substrate recognition. The substrate recognition site of Pin1 performs specific and nonspecific attractive interactions. Phosphorylation of the WW domain at Ser16 by PKA abrogates both substrate recognition and the nonspecific interactions with the endogenous proteins. Our results validate the hypothesis formulated by McConkey that the majority of globular folded proteins with surface charge properties close to neutral under physiological conditions reside in macromolecular complexes with other sticky proteins due to molecular crowding. In addition, we demonstrate that commonly used synthetic crowding agents like Ficoll 70 are not suitable to mimic the intracellular environment due to their incapability to simulate biologically important weak attractive interactions.

  7. Molecular Recognition by a Polymorphic Cell Surface Receptor Governs Cooperative Behaviors in Bacteria

    PubMed Central

    Dey, Arup; Wall, Daniel

    2013-01-01

    Cell-cell recognition is a fundamental process that allows cells to coordinate multicellular behaviors. Some microbes, such as myxobacteria, build multicellular fruiting bodies from free-living cells. However, how bacterial cells recognize each other by contact is poorly understood. Here we show that myxobacteria engage in recognition through interactions between TraA cell surface receptors, which leads to the fusion and exchange of outer membrane (OM) components. OM exchange is shown to be selective among 17 environmental isolates, as exchange partners parsed into five major recognition groups. TraA is the determinant of molecular specificity because: (i) exchange partners correlated with sequence conservation within its polymorphic PA14-like domain and (ii) traA allele replacements predictably changed partner specificity. Swapping traA alleles also reprogrammed social interactions among strains, including the regulation of motility and conferred immunity from inter-strain killing. We suggest that TraA helps guide the transition of single cells into a coherent bacterial community, by a proposed mechanism that is analogous to mitochondrial fusion and fission cycling that mixes contents to establish a homogenous population. In evolutionary terms, traA functions as a rare greenbeard gene that recognizes others that bear the same allele to confer beneficial treatment. PMID:24244178

  8. Molecular-basis of single-walled carbon nanotube recognition by single-stranded DNA.

    PubMed

    Roxbury, Daniel; Mittal, Jeetain; Jagota, Anand

    2012-03-14

    Hybrids of biological molecules and single-walled carbon nanotubes (SWCNT) have proven useful for SWCNT sorting and are enabling several biomedical applications in sensing, imaging, and drug delivery. In the DNA-SWCNT system, certain short (10-20mer) sequences of single-stranded DNA recognize specific SWCNT, allowing the latter to be sorted from a chirality diverse mixture. (1) However, little is known about the DNA secondary structures that underlie their recognition of SWCNTs. Using replica exchange molecular dynamics (REMD) of multiple strands on a single SWCNT, we report that DNA forms ordered structures on SWCNTs that are strongly DNA sequence and SWCNT dependent. DNA sequence (TAT)(4) on its recognition partner, the (6,5) SWCNT, (1) forms an ordered right-handed helically wrapped barrel, stabilized by intrastrand, self-stitching hydrogen bonds and interstrand hydrogen bonding. The same sequence on the larger diameter (8,7)-SWCNT forms a different and less-stable structure, demonstrating SWCNT selectivity. In contrast, homopolymer (T)(12), with weaker tendency for intrastrand hydrogen bonding, forms a distinctly left-handed wrap on the (6,5)-SWCNT, demonstrating DNA sequence specificity. Experimental measurements show that (TAT)(4) selectively disperses smaller diameter SWCNTs more efficiently than (T)(12), establishing a relationship between recognition motifs and binding strength. The developing understanding of DNA secondary structure on nanomaterials can shed light on a number of issues involving hybrids of nanomaterials and biological molecules, including nanomedicine, health-effects of nanomaterials, and nanomaterial processing.

  9. Molecular recognition by a polymorphic cell surface receptor governs cooperative behaviors in bacteria.

    PubMed

    Pathak, Darshankumar T; Wei, Xueming; Dey, Arup; Wall, Daniel

    2013-11-01

    Cell-cell recognition is a fundamental process that allows cells to coordinate multicellular behaviors. Some microbes, such as myxobacteria, build multicellular fruiting bodies from free-living cells. However, how bacterial cells recognize each other by contact is poorly understood. Here we show that myxobacteria engage in recognition through interactions between TraA cell surface receptors, which leads to the fusion and exchange of outer membrane (OM) components. OM exchange is shown to be selective among 17 environmental isolates, as exchange partners parsed into five major recognition groups. TraA is the determinant of molecular specificity because: (i) exchange partners correlated with sequence conservation within its polymorphic PA14-like domain and (ii) traA allele replacements predictably changed partner specificity. Swapping traA alleles also reprogrammed social interactions among strains, including the regulation of motility and conferred immunity from inter-strain killing. We suggest that TraA helps guide the transition of single cells into a coherent bacterial community, by a proposed mechanism that is analogous to mitochondrial fusion and fission cycling that mixes contents to establish a homogenous population. In evolutionary terms, traA functions as a rare greenbeard gene that recognizes others that bear the same allele to confer beneficial treatment.

  10. Using polymeric materials to generate an amplified response to molecular recognition events

    NASA Astrophysics Data System (ADS)

    Sikes, Hadley D.; Hansen, Ryan R.; Johnson, Leah M.; Jenison, Robert; Birks, John W.; Rowlen, Kathy L.; Bowman, Christopher N.

    2008-01-01

    Clinical and field-portable diagnostic devices require the detection of atto- to zeptomoles of biological molecules rapidly, easily and at low cost, with stringent requirements in terms of robustness and reliability. Though a number of creative approaches to this difficult problem have been reported, numerous unmet needs remain in the marketplace, particularly in resource-poor settings. Using rational materials design, we investigated harnessing the amplification inherent in a radical chain polymerization reaction to detect molecular recognition. Polymerization-based amplification is shown to yield a macroscopically observable polymer, easily visible to the unaided eye, as a result of as few as ~1,000 recognition events (10 zeptomoles). Design and synthesis of a dual-functional macromolecule that is capable both of selective recognition and of initiating a polymerization reaction was central to obtaining high sensitivity and eliminating the need for any detection equipment. Herein, we detail the design criteria that were used and compare our findings with those obtained using enzymatic amplification. Most excitingly, this new approach is general in that it is readily adaptable to facile detection at very low levels of specific biological interactions of any kind.

  11. Investigation of imprinting parameters and their recognition nature for quinine-molecularly imprinted polymers

    NASA Astrophysics Data System (ADS)

    He, Jian-feng; Zhu, Quan-hong; Deng, Qin-ying

    2007-08-01

    A series of molecularly imprinted polymers (MIPs) was prepared using quinine as the template molecules by bulk polymerization. The presence of monomer-template solution complexes in non-covalent MIPs systems has been verified by both fluorescence and UV-vis spectrometric detection. The influence of different synthetic conditions (porogen, functional monomer, cross-linkers, initiation methods, monomer-template ratio, etc.) on recognition properties of the polymers was investigated. Scatchard analysis revealed that two classes of binding sites were formed in the imprinted polymer. The corresponding dissociation constants were estimated to be 45.00 μmol l -1 and 1.42 mmol l -1, respectively, by utilizing a multi-site recognition model. The binding characteristics of the imprinted polymers were explored in various solvents using equilibrium binding experiments. In the organic media, results suggested that polar interactions (hydrogen bonding, ionic interactions, etc.) between acidic monomer/polymer and template molecules were mainly responsible for the recognition, whereas in aqueous media, hydrophobic interactions had a remarkable non-specific contribution to the overall binding. The specificity of MIP was evaluated by rebinding the other structurally similar compounds. The results indicated that the imprinted polymers exhibited an excellent stereo-selectivity toward quinine.

  12. Efficient synthesis of narrowly dispersed hydrophilic and magnetic molecularly imprinted polymer microspheres with excellent molecular recognition ability in a real biological sample.

    PubMed

    Zhao, Man; Zhang, Cong; Zhang, Ying; Guo, Xianzhi; Yan, Husheng; Zhang, Huiqi

    2014-02-28

    A facile and highly efficient approach to obtain narrowly dispersed hydrophilic and magnetic molecularly imprinted polymer microspheres with molecular recognition ability in a real biological sample as good as what they show in the organic solvent-based media is described for the first time.

  13. Structure and behavior of human α-thrombin upon ligand recognition: thermodynamic and molecular dynamics studies.

    PubMed

    Silva, Vivian de Almeira; Cargnelutti, Maria Thereza; Giesel, Guilherme M; Palmieri, Leonardo C; Monteiro, Robson Q; Verli, Hugo; Lima, Luis Mauricio T R

    2011-01-01

    Thrombin is a serine proteinase that plays a fundamental role in coagulation. In this study, we address the effects of ligand site recognition by alpha-thrombin on conformation and energetics in solution. Active site occupation induces large changes in secondary structure content in thrombin as shown by circular dichroism. Thrombin-D-Phe-Pro-Arg-chloromethyl ketone (PPACK) exhibits enhanced equilibrium and kinetic stability compared to free thrombin, whose difference is rooted in the unfolding step. Small-angle X-ray scattering (SAXS) measurements in solution reveal an overall similarity in the molecular envelope of thrombin and thrombin-PPACK, which differs from the crystal structure of thrombin. Molecular dynamics simulations performed with thrombin lead to different conformations than the one observed in the crystal structure. These data shed light on the diversity of thrombin conformers not previously observed in crystal structures with distinguished catalytic and conformational behaviors, which might have direct implications on novel strategies to design direct thrombin inhibitors.

  14. Molecularly imprinted protein recognition thin films constructed by controlled/living radical polymerization.

    PubMed

    Sasaki, Shogo; Ooya, Tooru; Kitayama, Yukiya; Takeuchi, Toshifumi

    2015-02-01

    We demonstrated the synthesis of molecularly imprinted polymers (MIPs) with binding affinity toward a target protein, ribonuclease A (RNase) by atom transfer radical polymerization (ATRP) of acrylic acid, acrylamide, and N,N'-methylenebisacrylamide in the presence of RNase. The binding activity of the MIPs was evaluated by surface plasmon resonance (SPR) of the MIP thin layers prepared on the gold-coated sensor chips. The MIPs prepared by ATRP (MIP-ATRP) had a binding affinity toward RNase with larger binding amount compared to MIPs prepared by conventional free radical polymerization methods (MIP-RP). Moreover, protein selectivity was evaluated using reference proteins (cytochrome c, myoglobin, and α-lactalbumin) and was confirmed in MIP-ATRP of optimum film thickness determined experimentally to be 15-30 nm; however, protein selectivity was not achieved in all MIP-RP. We have shown that ATRP is powerful technique for preparing protein recognition materials by molecular imprinting.

  15. The ribosome as an optimal decoder: a lesson in molecular recognition

    NASA Astrophysics Data System (ADS)

    Tlusty, Tsvi; Savir, Yonatan

    2013-03-01

    The ribosome is a complex molecular machine that, in order to synthesize proteins, has to decode mRNAs by pairing their codons with matching tRNAs. Decoding is a major determinant of fitness and requires accurate and fast selection of correct tRNAs among many similar competitors. However, it is unclear whether the present ribosome, and in particular its large deformations during decoding, are the outcome of adaptation to its task as a decoder or the result of other constraints. Here, we derive the energy landscape that provides optimal discrimination between competing substrates, and thereby optimal tRNA decoding. We show that the measured landscape of the prokaryotic ribosome is indeed sculpted in this way. This suggests that conformational changes of the ribosome and tRNA during decoding are means to obtain an optimal decoder. Our analysis puts forward a generic mechanism that may be utilized by other ribosomes and other molecular recognition systems.

  16. Lighten the Load: Scaffolding Visual Literacy in Biochemistry and Molecular Biology

    ERIC Educational Resources Information Center

    Offerdahl, Erika G.; Arneson, Jessie B.; Byrne, Nicholas

    2017-01-01

    The development of scientific visual literacy has been identified as critical to the training of tomorrow's scientists and citizens alike. Within the context of the molecular life sciences in particular, visual representations frequently incorporate various components, such as discipline-specific graphical and diagrammatic features, varied levels…

  17. Lighten the Load: Scaffolding Visual Literacy in Biochemistry and Molecular Biology

    ERIC Educational Resources Information Center

    Offerdahl, Erika G.; Arneson, Jessie B.; Byrne, Nicholas

    2017-01-01

    The development of scientific visual literacy has been identified as critical to the training of tomorrow's scientists and citizens alike. Within the context of the molecular life sciences in particular, visual representations frequently incorporate various components, such as discipline-specific graphical and diagrammatic features, varied levels…

  18. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.

    PubMed Central

    Katchalski-Katzir, E; Shariv, I; Eisenstein, M; Friesem, A A; Aflalo, C; Vakser, I A

    1992-01-01

    A geometric recognition algorithm was developed to identify molecular surface complementarity. It is based on a purely geometric approach and takes advantage of techniques applied in the field of pattern recognition. The algorithm involves an automated procedure including (i) a digital representation of the molecules (derived from atomic coordinates) by three-dimensional discrete functions that distinguishes between the surface and the interior; (ii) the calculation, using Fourier transformation, of a correlation function that assesses the degree of molecular surface overlap and penetration upon relative shifts of the molecules in three dimensions; and (iii) a scan of the relative orientations of the molecules in three dimensions. The algorithm provides a list of correlation values indicating the extent of geometric match between the surfaces of the molecules; each of these values is associated with six numbers describing the relative position (translation and rotation) of the molecules. The procedure is thus equivalent to a six-dimensional search but much faster by design, and the computation time is only moderately dependent on molecular size. The procedure was tested and validated by using five known complexes for which the correct relative position of the molecules in the respective adducts was successfully predicted. The molecular pairs were deoxyhemoglobin and methemoglobin, tRNA synthetase-tyrosinyl adenylate, aspartic proteinase-peptide inhibitor, and trypsin-trypsin inhibitor. A more realistic test was performed with the last two pairs by using the structures of uncomplexed aspartic proteinase and trypsin inhibitor, respectively. The results are indicative of the extent of conformational changes in the molecules tolerated by the algorithm. Images PMID:1549581

  19. Investigating the binding behaviour of two avidin-based testosterone binders using molecular recognition force spectroscopy.

    PubMed

    Rangl, Martina; Leitner, Michael; Riihimäki, Tiina; Lehtonen, Soili; Hytönen, Vesa P; Gruber, Hermann J; Kulomaa, Markku; Hinterdorfer, Peter; Ebner, Andreas

    2014-02-01

    Molecular recognition force spectroscopy, a biosensing atomic force microscopy technique allows to characterise the dissociation of ligand-receptor complexes at the molecular level. Here, we used molecular recognition force spectroscopy to study the binding capability of recently developed testosterone binders. The two avidin-based proteins called sbAvd-1 and sbAvd-2 are expected to bind both testosterone and biotin but differ in their binding behaviour towards these ligands. To explore the ligand binding and dissociation energy landscape of these proteins, we tethered biotin or testosterone to the atomic force microscopy probe while the testosterone-binding protein was immobilized on the surface. Repeated formation and rupture of the ligand-receptor complex at different pulling velocities allowed determination of the loading rate dependence of the complex-rupturing force. In this way, we obtained the molecular dissociation rate (k(off)) and energy landscape distances (x(β)) of the four possible complexes: sbAvd-1-biotin, sbAvd-1-testosterone, sbAvd-2-biotin and sbAvd-2-testosterone. It was found that the kinetic off-rates for both proteins and both ligands are similar. In contrast, the x(β) values, as well as the probability of complex formations, varied considerably. In addition, competitive binding experiments with biotin and testosterone in solution differ significantly for the two testosterone-binding proteins, implying a decreased cross-reactivity of sbAvd-2. Unravelling the binding behaviour of the investigated testosterone-binding proteins is expected to improve their usability for possible sensing applications.

  20. Forces in molecular recognition: Comparison of experimental data and molecular mechanics calculations

    NASA Astrophysics Data System (ADS)

    Waltho, J. P.; Vinter, J. G.; Davis, A.; Williams, D. H.

    1988-04-01

    NMR studies of the rotation barrier of the disaccharide of the glycopeptide antibiotic vancomycin have been used to test the performance of computer simulation techniques using molecular mechanics. In the absence of any solvated water, no correlation could be found between experiment and calculation. By introducing solvent water molecules into the binding region of the antibiotic, the NMR results could be simulated both qualitatively and quantitatively within experimental error without using massive computational resources.

  1. Molecular basis for bacterial peptidoglycan recognition by LysM domains.

    PubMed

    Mesnage, Stéphane; Dellarole, Mariano; Baxter, Nicola J; Rouget, Jean-Baptiste; Dimitrov, Jordan D; Wang, Ning; Fujimoto, Yukari; Hounslow, Andrea M; Lacroix-Desmazes, Sébastien; Fukase, Koichi; Foster, Simon J; Williamson, Michael P

    2014-06-30

    Carbohydrate recognition is essential for growth, cell adhesion and signalling in all living organisms. A highly conserved carbohydrate binding module, LysM, is found in proteins from viruses, bacteria, fungi, plants and mammals. LysM modules recognize polysaccharides containing N-acetylglucosamine (GlcNAc) residues including peptidoglycan, an essential component of the bacterial cell wall. However, the molecular mechanism underpinning LysM-peptidoglycan interactions remains unclear. Here we describe the molecular basis for peptidoglycan recognition by a multimodular LysM domain from AtlA, an autolysin involved in cell division in the opportunistic bacterial pathogen Enterococcus faecalis. We explore the contribution of individual modules to the binding, identify the peptidoglycan motif recognized, determine the structures of free and bound modules and reveal the residues involved in binding. Our results suggest that peptide stems modulate LysM binding to peptidoglycan. Using these results, we reveal how the LysM module recognizes the GlcNAc-X-GlcNAc motif present in polysaccharides across kingdoms.

  2. A case for molecular recognition in nuclear separations: sulfate separation from nuclear wastes.

    PubMed

    Moyer, Bruce A; Custelcean, Radu; Hay, Benjamin P; Sessler, Jonathan L; Bowman-James, Kristin; Day, Victor W; Kang, Sung-Ok

    2013-04-01

    In this paper, we present the case for molecular-recognition approaches for sulfate removal from radioactive wastes via the use of anion-sequestering systems selective for sulfate, using either liquid-liquid extraction or crystallization. Potential benefits of removing sulfate from the waste include improved vitrification of the waste, reduced waste-form volume, and higher waste-form performance, all of which lead to potential cleanup schedule acceleration and cost savings. The need for sulfate removal from radioactive waste, especially legacy tank wastes stored at the Hanford site, is reviewed in detail and primarily relates to the low solubility of sulfate in borosilicate glass. Traditional methods applicable to the separation of sulfate from radioactive wastes are also reviewed, with the finding that currently no technology has been identified and successfully demonstrated to meet this need. Fundamental research in the authors' laboratories targeting sulfate as an important representative of the class of oxoanions is based on the hypothesis that designed receptors may provide the needed ability to recognize sulfate under highly competitive conditions, in particular where the nitrate anion concentration is high. Receptors that have been shown to have promising affinity for sulfate, either in extraction or in crystallization experiments, include hexaurea tripods, tetraamide macrocycles, cyclo[8]pyrroles, calixpyrroles, and self-assembled urea-lined cages. Good sulfate selectivity observed in the laboratory provides experimental support for the proposed molecular-recognition approach.

  3. Nanomaterials for diagnosis: challenges and applications in smart devices based on molecular recognition.

    PubMed

    Oliveira, Osvaldo N; Iost, Rodrigo M; Siqueira, José R; Crespilho, Frank N; Caseli, Luciano

    2014-09-10

    Clinical diagnosis has always been dependent on the efficient immobilization of biomolecules in solid matrices with preserved activity, but significant developments have taken place in recent years with the increasing control of molecular architecture in organized films. Of particular importance is the synergy achieved with distinct materials such as nanoparticles, antibodies, enzymes, and other nanostructures, forming structures organized on the nanoscale. In this review, emphasis will be placed on nanomaterials for biosensing based on molecular recognition, where the recognition element may be an enzyme, DNA, RNA, catalytic antibody, aptamer, and labeled biomolecule. All of these elements may be assembled in nanostructured films, whose layer-by-layer nature is essential for combining different properties in the same device. Sensing can be done with a number of optical, electrical, and electrochemical methods, which may also rely on nanostructures for enhanced performance, as is the case of reporting nanoparticles in bioelectronics devices. The successful design of such devices requires investigation of interface properties of functionalized surfaces, for which a variety of experimental and theoretical methods have been used. Because diagnosis involves the acquisition of large amounts of data, statistical and computational methods are now in widespread use, and one may envisage an integrated expert system where information from different sources may be mined to generate the diagnostics.

  4. A Case for Molecular Recognition in Nuclear Separations: Sulfate Separation from Nuclear Wastes

    SciTech Connect

    Moyer, Bruce A; Custelcean, Radu; Hay, Benjamin; Sessler, Jonathan L.; Bowman-James, Kristin; Day, Victor W.; Kang, S.O.

    2013-01-01

    In this paper, we present the case for molecular-recognition approaches for sulfate removal from radioactive wastes via the use of anion-sequestering systems selective for sulfate, using either liquid liquid extraction or crystallization. Potential benefits of removing sulfate from the waste include improved vitrification of the waste, reduced waste-form volume, and higher waste-form performance, all of which lead to potential cleanup schedule acceleration and cost savings. The need for sulfate removal from radioactive waste, especially legacy tank wastes stored at the Hanford site, is reviewed in detail and primarily relates to the low solubility of sulfate in borosilicate glass. Traditional methods applicable to the separation of sulfate from radioactive wastes are also reviewed, with the finding that currently no technology has been identified and successfully demonstrated to meet this need. Fundamental research in the authors laboratories targeting sulfate as an important representative of the class of oxoanions is based on the hypothesis that designed receptors may provide the needed ability to recognize sulfate under highly competitive conditions, in particular where the nitrate anion concentration is high. Receptors that have been shown to have promising affinity for sulfate, either in extraction or in crystallization experiments, include hexaurea tripods, tetraamide macrocycles, cyclo[8]pyrroles, calixpyrroles, and self-assembled urea-lined cages. Good sulfate selectivity observed in the laboratory provides experimental support for the proposed molecular-recognition approach.

  5. "Off-On"switching electrochemiluminescence biosensor for mercury(II) detection based on molecular recognition technology.

    PubMed

    Cheng, Lin; Wei, BingGuo; He, Ling Ling; Mao, Ling; Zhang, Jie; Ceng, JinXiang; Kong, DeRong; Chen, ChaDan; Cui, HanFeng; Hong, Nian; Fan, Hao

    2017-02-01

    A novel "off-On" electrogenerated chemiluminescence (ECL) biosensor has been developed for the detection of mercury(II) based on molecular recognition technology. The ECL mercury(II) biosensor comprises two main parts: an ECL substrate and an ECL intensity switch. The ECL substrate was made by modifying the complex of Ruthenium(II) tris-(bipyridine)(Ru(bpy)3(2+))/Cyclodextrins-Au nanoparticles(CD-AuNps)/Nafion on the surface of glass carbon electrode (GCE), and the ECL intensity switch is the single hairpin DNA probe designed according to the "molecular recognition" strategy which was functionalized with ferrocene tag at one end and attached to Cyclodextrins (CD) on modified GCE through supramolecular noncovalent interaction. We demonstrated that, in the absence of Hg(II) ion, the probe keeps single hairpin structure and resulted in a quenching of ECL of Ru(bpy)3(2+). Whereas, in the presence of Hg(II) ion, the probe prefers to form the T-Hg(II)-T complex and lead to an obvious recovery of ECL of Ru(bpy)3(2+), which provided a sensing platform for the detection of Hg(II) ion. Using this sensing platform, a simple, rapid and selective "off-On" ECL biosensor for the detection of mercury(II) with a detection limit of 0.1 nM has been developed.

  6. Molecular basis for bacterial peptidoglycan recognition by LysM domains

    PubMed Central

    Mesnage, Stéphane; Dellarole, Mariano; Baxter, Nicola J.; Rouget, Jean-Baptiste; Dimitrov, Jordan D.; Wang, Ning; Fujimoto, Yukari; Hounslow, Andrea M.; Lacroix-Desmazes, Sébastien; Fukase, Koichi; Foster, Simon J.; Williamson, Michael P.

    2014-01-01

    Carbohydrate recognition is essential for growth, cell adhesion and signalling in all living organisms. A highly conserved carbohydrate binding module, LysM, is found in proteins from viruses, bacteria, fungi, plants and mammals. LysM modules recognize polysaccharides containing N-acetylglucosamine (GlcNAc) residues including peptidoglycan, an essential component of the bacterial cell wall. However, the molecular mechanism underpinning LysM–peptidoglycan interactions remains unclear. Here we describe the molecular basis for peptidoglycan recognition by a multimodular LysM domain from AtlA, an autolysin involved in cell division in the opportunistic bacterial pathogen Enterococcus faecalis. We explore the contribution of individual modules to the binding, identify the peptidoglycan motif recognized, determine the structures of free and bound modules and reveal the residues involved in binding. Our results suggest that peptide stems modulate LysM binding to peptidoglycan. Using these results, we reveal how the LysM module recognizes the GlcNAc-X-GlcNAc motif present in polysaccharides across kingdoms. PMID:24978025

  7. Protein-templated fragment ligations - from molecular recognition to drug discovery.

    PubMed

    Jaegle, Mike; Wong, Ee Lin; Tauber, Carolin; Nawrotzky, Eric; Arkona, Christoph; Rademann, Jörg

    2017-01-24

    The understanding and manipulation of molecular recognition events is the key to modern approaches in drug discovery. Protein-templated fragment ligation is a novel concept to support drug discovery and can help to improve the efficacy of already existing protein ligands. Protein-templated fragment ligations are chemical reactions between small molecules ("fragments") that utilize a protein´s surface as a template to combine and to form a protein ligand with increased binding affinity. The approach exploits the molecular recognition of reactive small molecule fragments by proteins both for ligand assembly and for the identification of bioactive fragment combinations. Chemical synthesis and bioassay are thus integrated in one single step. In this article we portrait the biophysical basis of reversible and irreversible fragment ligations and the available methods to detect protein-templated ligation products. The scope of known chemical reactions providing templated ligation products is reviewed and the possibilities to extend the reaction portfolio are discussed. Selected recent applications of the method in protein ligand discovery are reported. Finally, the strengths and limitations of the concept are discussed and an outlook on the future impact of templated fragment ligations on the drug discovery process is given.

  8. Magnetic-graphene based molecularly imprinted polymer nanocomposite for the recognition of bovine hemoglobin.

    PubMed

    Guo, Junxia; Wang, Yuzhi; Liu, Yanjin; Zhang, Cenjin; Zhou, Yigang

    2015-11-01

    The protein imprinted technique combining surface imprinting and nanomaterials has been an attractive strategy for recognition and rapid separation of proteins. In this work, magnetic-graphene (MG) was chosen as the supporting substrate for the magnetic nanomaterials, which served to absorb the targeting imprinting molecules, bovine hemoglobin (BHb). Acryl amide (AAm) with a high affinity to BHb and N,N'- methylenebisacrylamide (MBA) were selected as the functional monomer and cross-linking agent, respectively. After in-situ polymerization, the proposed magnetic-graphene based molecularly imprinted polymer (MG-MIP) was obtained with a further extraction step of imprinted BHb. Fourier transform infrared (FT-IR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), raman spectroscopy(RS), X-ray diffraction (XRD) and vibrating sample magnetometer (VSM) were employed to characterize the resulted MG-MIP. The maximum adsorption capability (Qmax) was determined by Langmuir Isotherm Plots and was 186.73 mg/g for imprinted nanomaterials (MIP) with an imprinting factor of 1.96. The selectivity of MG-MIP was investigated by using several proteins that are different in molecular mass and isoelectric points as the reference. The results showed that the shape memory effect of imprinted cavities, the size of proteins and the charge effect of proteins were the major factors for the selective recognition. The proposed method was also employed to specifically capture BHb from a binary protein mixture.

  9. Enzymatic elucidation of haemocyanin from Kuruma shrimp Marsupenaeus japonicus and its molecular recognition mechanism towards pathogens.

    PubMed

    Sivakamavalli, Jeyachandran; Vaseeharan, Baskaralingam

    2015-01-01

    Haemocyanin is an important non-specific immune protein present in the hemolymph of invertebrates, which have the ability to recognize the microbial pathogens and trigger the innate immune system. In this study, we isolated and purified the haemocyanin using gel filtration chromatography and investigated its microbial recognition mechanism against the invading pathogens. Kuruma shrimp Marsupenaeus japonicus haemocyanin showed the single band with a molecular weight of 76 kDa on SDS-PAGE and its molecular mass was analysed through the MALDI. Pathogen recognition mechanism of M. japonicus haemocyanin was detected through bacterial agglutination, agglutination inhibition and prophenoloxidase activity. M. japonicus haemocyanin agglutinate all human blood RBC types and showed the bacterial agglutination against all tested Gram positive Staphylococcus aureus, Enterococcus faecalis and Bacillus subtilis and Gram negative Pseudomonas aeruginosa, Proteus vulgaris and Vibrio parahaemolyticus at the concentrations ranging from 30 to 50 μg/ml. Agglutination was inhibited by 50-200 mM of N-acetylneuraminic acid, a-D-glucose, D-galactose and D-xylose. Our results suggest that, 76 kDa subunit of M. japonicus haemocyanin recognize the pathogenic surface proteins which are present on the outer membrane of the bacteria and mediates the bacterial agglutination through haemocytes. This bacterial agglutination was visualized through Confocal Laser Scanning Microscopy (CLSM). This present study would be helpful to explore the importance of haemocyanin in innate immune response of M. japonicus and its eliciting pathogen recognition mechanism leads to the development of innate immunity in crustaceans.

  10. Novel High-Viscosity Polyacrylamidated Chitosan for Neural Tissue Engineering: Fabrication of Anisotropic Neurodurable Scaffold via Molecular Disposition of Persulfate-Mediated Polymer Slicing and Complexation

    PubMed Central

    Kumar, Pradeep; Choonara, Yahya E.; du Toit, Lisa C.; Modi, Girish; Naidoo, Dinesh; Pillay, Viness

    2012-01-01

    Macroporous polyacrylamide-grafted-chitosan scaffolds for neural tissue engineering were fabricated with varied synthetic and viscosity profiles. A novel approach and mechanism was utilized for polyacrylamide grafting onto chitosan using potassium persulfate (KPS) mediated degradation of both polymers under a thermally controlled environment. Commercially available high molecular mass polyacrylamide was used instead of the acrylamide monomer for graft copolymerization. This grafting strategy yielded an enhanced grafting efficiency (GE = 92%), grafting ratio (GR = 263%), intrinsic viscosity (IV = 5.231 dL/g) and viscometric average molecular mass (MW = 1.63 × 106 Da) compared with known acrylamide that has a GE = 83%, GR = 178%, IV = 3.901 dL/g and MW = 1.22 × 106 Da. Image processing analysis of SEM images of the newly grafted neurodurable scaffold was undertaken based on the polymer-pore threshold. Attenuated Total Reflectance-FTIR spectral analyses in conjugation with DSC were used for the characterization and comparison of the newly grafted copolymers. Static Lattice Atomistic Simulations were employed to investigate and elucidate the copolymeric assembly and reaction mechanism by exploring the spatial disposition of chitosan and polyacrylamide with respect to the reactional profile of potassium persulfate. Interestingly, potassium persulfate, a peroxide, was found to play a dual role initially degrading the polymers—“polymer slicing”—thereby initiating the formation of free radicals and subsequently leading to synthesis of the high molecular mass polyacrylamide-grafted-chitosan (PAAm-g-CHT)—“polymer complexation”. Furthermore, the applicability of the uniquely grafted scaffold for neural tissue engineering was evaluated via PC12 neuronal cell seeding. The novel PAAm-g-CHT exhibited superior neurocompatibility in terms of cell infiltration owing to the anisotropic porous architecture, high molecular mass mediated robustness, superior

  11. Physical, Spatial, and Molecular Aspects of Extracellular Matrix of In Vivo Niches and Artificial Scaffolds Relevant to Stem Cells Research

    PubMed Central

    Akhmanova, Maria; Osidak, Egor; Domogatsky, Sergey; Rodin, Sergey; Domogatskaya, Anna

    2015-01-01

    Extracellular matrix can influence stem cell choices, such as self-renewal, quiescence, migration, proliferation, phenotype maintenance, differentiation, or apoptosis. Three aspects of extracellular matrix were extensively studied during the last decade: physical properties, spatial presentation of adhesive epitopes, and molecular complexity. Over 15 different parameters have been shown to influence stem cell choices. Physical aspects include stiffness (or elasticity), viscoelasticity, pore size, porosity, amplitude and frequency of static and dynamic deformations applied to the matrix. Spatial aspects include scaffold dimensionality (2D or 3D) and thickness; cell polarity; area, shape, and microscale topography of cell adhesion surface; epitope concentration, epitope clustering characteristics (number of epitopes per cluster, spacing between epitopes within cluster, spacing between separate clusters, cluster patterns, and level of disorder in epitope arrangement), and nanotopography. Biochemical characteristics of natural extracellular matrix molecules regard diversity and structural complexity of matrix molecules, affinity and specificity of epitope interaction with cell receptors, role of non-affinity domains, complexity of supramolecular organization, and co-signaling by growth factors or matrix epitopes. Synergy between several matrix aspects enables stem cells to retain their function in vivo and may be a key to generation of long-term, robust, and effective in vitro stem cell culture systems. PMID:26351461

  12. Syntheses of molecularly imprinted polymers: Molecular recognition of cyproheptadine using original print molecules and azatadine as dummy templates.

    PubMed

    Feás, X; Seijas, J A; Vázquez-Tato, M P; Regal, P; Cepeda, A; Fente, C

    2009-01-12

    The use of custom-made polymeric materials with high selectivities as target molecules in solid-phase extraction (SPE), known as molecularly imprinted solid-phase extraction (MISPE), is becoming an increasingly important sample preparation technique. However, the potential risk of leakage of the imprinting molecules during the desorption phase has limited application. The use of a mimicking template, called a dummy molecular imprinting polymer (DMIP), that bears the structure of a related molecule and acts as a putative imprinting molecule may provide a useful solution to this problem. In the current study, cyproheptadine (CPH) and azatadine (AZA) were used as templates in the development of an MIP and DMIP for acrylic acid and methacrylic acid monomers. Our results indicate that DMIPs have equal recognition of CPH, avoiding the problem of leakage of original template during the desorption phase relative to MIPs synthesized in presence of the print molecule CPH. Examination of the surface structure of the two polymer products by SEM shows appreciable differences in structural morphology and function of the monomers employed. These results are well supplemented by data obtained for swelling ratios and solvent uptake. Molecular modelling of CPH and AZA suggests that both substrates are similar in shape and volume.

  13. Indirect rapid prototyping of sol-gel hybrid glass scaffolds for bone regeneration - Effects of organic crosslinker valence, content and molecular weight on mechanical properties.

    PubMed

    Hendrikx, Stephan; Kascholke, Christian; Flath, Tobias; Schumann, Dirk; Gressenbuch, Mathias; Schulze, F Peter; Hacker, Michael C; Schulz-Siegmund, Michaela

    2016-04-15

    We present a series of organic/inorganic hybrid sol-gel derived glasses, made from a tetraethoxysilane-derived silica sol (100% SiO2) and oligovalent organic crosslinkers functionalized with 3-isocyanatopropyltriethoxysilane. The material was susceptible to heat sterilization. The hybrids were processed into pore-interconnected scaffolds by an indirect rapid prototyping method, described here for the first time for sol-gel glass materials. A large panel of polyethylene oxide-derived 2- to 4-armed crosslinkers of molecular weights ranging between 170 and 8000Da were incorporated and their effect on scaffold mechanical properties was investigated. By multiple linear regression, 'organic content' and the 'content of ethylene oxide units in the hybrid' were identified as the main factors that determined compressive strength and modulus, respectively. In general, 3- and 4-armed crosslinkers performed better than linear molecules. Compression tests and cell culture experiments with osteoblast-like SaOS-2 cells showed that macroporous scaffolds can be produced with compressive strengths of up to 33±2MPa and with a pore structure that allows cells to grow deep into the scaffolds and form mineral deposits. Compressive moduli between 27±7MPa and 568±98MPa were obtained depending on the hybrid composition and problems associated with the inherent brittleness of sol-gel glass materials could be overcome. SaOS-2 cells showed cytocompatibility on hybrid glass scaffolds and mineral accumulation started as early as day 7. On day 14, we also found mineral accumulation on control hybrid glass scaffolds without cells, indicating a positive effect of the hybrid glass on mineral accumulation. We produced a hybrid sol-gel glass material with significantly improved mechanical properties towards an application in bone regeneration and processed the material into macroporous scaffolds of controlled architecture by indirect rapid prototyping. We were able to produce macroporous materials

  14. Hydration shells of molecules in molecular association: A mechanism for biomolecular recognition

    PubMed Central

    Lim, Valery I.; Curran, James F.; Garber, Maria B.

    2013-01-01

    It has become clear that water should not be treated as an inert environment, but rather as an integral and active component of molecules. Here, we consider molecules and their hydration shells together as single entities. We show that: (1) the rate of association of molecules should be determined by the energetic barriers arising from interactions between their hydration shells; (2) replacing non-polar atoms of molecular surfaces with polar atoms increases these barriers; (3) reduction of the hydration shells during molecular association is the driving force for association not only of non-polar, but of polar molecules as well; (4) in most cases the dehydration of polar atoms during molecular association thermodynamically counteracts association; (5) on balance the thermodynamic stability of associated complexes is basically determined by the action of these two opposing factors: reduction of the hydration shells and dehydration of polar atoms; (6) molecular crowding reduces the energetic barriers counteracting association and changes the thermodynamic stability of associated complexes. These results lead to a mechanism for biomolecular recognition in the context of which the formation of unique structures is provided by rapidly forming kinetic traps with a biologically necessary lifetime but with a marginal thermodynamic stability. The mechanism gives definitive answers to questions concerning the heart of specific interactions between biomolecules, their folding and intracellular organization. Predictions are given that can be subjected to direct experimental tests. PMID:22365908

  15. Computer simulation of reactions in beta-cyclodextrin molecular reactors: transition state recognition.

    PubMed

    Yeguas, Violeta; López, Ramón; Lambert, Alexandrine; Monard, Gérald; Ruiz-López, Manuel F

    2010-10-07

    Cyclodextrins have attracted much interest in recent years because of their potential use as molecular reactors allowing organic reactions in aqueous solution. To better understand their effect on reaction mechanisms, we have carried out a computational study of a prototypical process (neutral ester hydrolysis) in a beta-cyclodextrin (beta-CD). Two models have been used for the reactor. The first and simpler one assumes that the medium can be described by a polarizable dielectric continuum. The second one takes into account the discrete nature of the beta-CD and water molecules thanks to a computational approach that combines the use of Quantum Mechanics, Molecular Mechanics and Molecular Dynamics techniques. We focus on neutral pH processes for which either acceleration or inhibition has experimentally been observed depending on ester derivatives. Our calculations rationalize such observations by showing that the two reaction mechanisms usually invoked for hydrolysis, stepwise (involving two transitions states with formation of a -C(OH)(2)OR tetrahedral intermediate) and concerted, undergo opposite effects in the beta-CD environment. The results highlight the role played by molecular shape recognition. Thus, in spite of a higher polarity exhibited by the three transition states with respect to the reactants, the interactions with the beta-CD cavity may either increase or decrease the activation barrier due to different 3D-arrangements of the chemical structures.

  16. Hydration shells of molecules in molecular association: A mechanism for biomolecular recognition.

    PubMed

    Lim, Valery I; Curran, James F; Garber, Maria B

    2012-05-21

    It has become clear that water should not be treated as an inert environment, but rather as an integral and active component of molecules. Here, we consider molecules and their hydration shells together as single entities. We show that: (1) the rate of association of molecules should be determined by the energetic barriers arising from interactions between their hydration shells; (2) replacing non-polar atoms of molecular surfaces with polar atoms increases these barriers; (3) reduction of the hydration shells during molecular association is the driving force for association not only of non-polar, but of polar molecules as well; (4) in most cases the dehydration of polar atoms during molecular association thermodynamically counteracts association; (5) on balance the thermodynamic stability of associated complexes is basically determined by the action of these two opposing factors: reduction of the hydration shells and dehydration of polar atoms; (6) molecular crowding reduces the energetic barriers counteracting association and changes the thermodynamic stability of associated complexes. These results lead to a mechanism for biomolecular recognition in the context of which the formation of unique structures is provided by rapidly forming kinetic traps with a biologically necessary lifetime but with a marginal thermodynamic stability. The mechanism gives definitive answers to questions concerning the heart of specific interactions between biomolecules, their folding and intracellular organization. Predictions are given that can be subjected to direct experimental tests.

  17. Molecular recognition and colorimetric detection of cholera toxin by poly(diacetylene) liposomes incorporating G{sub m1} ganglioside

    SciTech Connect

    Pan, J.J.; Charych, D.

    1997-03-19

    Molecular recognition sites on cell membranes serve as the main communication channels between the inside of a cell and its surroundings. Upon receptor binding, cellular messages such as ion channel opening or activation of enzymes are triggered. In this report, we demonstrate that artificial cell membranes made from conjugated lipid polymers (poly(diacetylene)) can, on a simple level, mimic membrane processes of molecular recognition and signal transduction. The ganglioside GM1 was incorporated into poly(diacetylene) liposomes. Molecular recognition of cholera toxin at the interface of the liposome resulted in a change of the membrane color due to conformational charges in the conjugated (ene-yne) polymer backbone. The `colored liposomes` might be used as simple colorimetric sensors for drug screening or as new tools to study membrane-membrane or membrane-receptor interactions. 21 refs., 3 figs.

  18. AKAP-Lbc: a molecular scaffold for the integration of cyclic AMP and Rho transduction pathways.

    PubMed

    Diviani, Dario; Baisamy, Laurent; Appert-Collin, Aline

    2006-07-01

    A Kinase-anchoring proteins (AKAPs) are a family of functionally related proteins involved in the targeting of the PKA holoenzyme towards specific physiological substrates. We have recently identified a novel anchoring protein expressed in cardiomyocytes, called AKAP-Lbc, that functions as a PKA-targeting protein as well as a guanine nucleotide exchange factor (GEF) that activates the GTPase RhoA. Here, we discuss the most recent findings elucidating the molecular mechanisms and the transduction pathways involved in the regulation of the AKAP-Lbc signaling complex inside cells. We could show that AKAP-Lbc is regulated in a bi-directional manner by signals that activate or deactivate its Rho-GEF activity. Activation of AKAP-Lbc occurs in response to agonists that stimulate G proteins coupled receptors linked to the heterotrimeric G protein G12, whereas inactivation occurs through mechanisms that require phosphorylation of AKAP-Lbc by anchored PKA and subsequent recruitment of the regulatory protein 14-3-3. Interestingly, we could demonstrate that AKAP-Lbc can form homo-oligomers inside cells and that 14-3-3 can inhibit the Rho-GEF activity of AKAP-Lbc only when the anchoring protein adopts an oligomeric conformation. These findings reveal the molecular architecture of the AKAP-Lbc transduction complex and provide a mechanistic explanation of how upstream signaling pathways can be integrated within the AKAP-Lbc transduction complex to precisely modulate the activation of Rho.

  19. Combining Molecular Scaffolds from FDA Approved Drugs: Application to Drug Discovery.

    PubMed

    Taylor, Richard D; MacCoss, Malcolm; Lawson, Alastair D G

    2017-03-09

    We have enumerated all linear combinations of ring systems from FDA approved drugs, up to three rings in length and up to four bonds linkers to give an in silico database of approximately 14 million molecules. This virtual library was compared with molecular databases of published and commercially available compounds to assess the prevalence of drug ring combinations in modern medicinal chemistry and to identify areas of under-represented, but clinically validated, chemical space. From the 10 trillion molecular comparisons, we found that less than 1% of the possible combinations of drug ring systems appear in commercially available libraries. This key observation highlights significant opportunities to design new fragment-like and lead-like libraries aimed at improving success rates and reducing risk in small molecule drug discovery, as, based on our previous analysis ( Taylor J. Med. Chem. 2014 , 57 , 5845 - 5849 ), approximately 70% of all new drugs are made up of only ring systems that have been used in existing drugs.

  20. γ-Cyclodextrin capped silver nanoparticles for molecular recognition and enhancement of antibacterial activity of chloramphenicol.

    PubMed

    Gannimani, Ramesh; Ramesh, Muthusamy; Mtambo, Sphamandla; Pillay, Karen; Soliman, Mahmoud E; Govender, Patrick

    2016-04-01

    Computational studies were conducted to identify the favourable formation of the inclusion complex of chloramphenicol with cyclodextrins. The results of molecular docking and molecular dynamics predicted the strongest interaction of chloramphenicol with γ-cyclodextrin. Further, the inclusion complex of chloramphenicol with γ-cyclodextrin was experimentally prepared and a phenomenon of inclusion was verified by using different characterization techniques such as thermogravimetric analysis, differential scanning calorimetry, (1)H nuclear magnetic resonance (NMR) and two dimensional nuclear overhauser effect spectroscopy (NOESY) experiments. From these results it was concluded that γ-cyclodextrins could be an appropriate cyclodextrin polymer which can be used to functionalize chloramphenicol on the surface of silver nanoparticles. In addition, γ-cyclodextrin capped silver nanoparticles were synthesized and characterized using UV-visible spectroscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive X-ray analysis (EDX), Fourier transform infrared spectroscopy (FTIR) and zeta potential analysis. Molecular recognition of chloramphenicol by these cyclodextrin capped silver nanoparticles was confirmed by surface enhanced raman spectroscopy (SERS) experiments. Synergistic antibacterial effect of chloramphenicol with γ-cyclodextrin capped silver nanoparticles was evaluated against Pseudomonas aeruginosa (ATCC 27853), Enterococcus faecalis (ATCC 5129), Klebsiella pneumoniae (ATCC 700603) and Staphylococcus aureus (ATCC 43300). The results from the antibacterial experiment were favourable thus allowing us to conclude that the approach of modifying organic drug molecules with cyclodextrin capped inorganic silver nanoparticles could help to enhance the antibacterial activity of them.

  1. Ultrasound Molecular Imaging of the Breast Cancer Neovasculature using Engineered Fibronectin Scaffold Ligands: A Novel Class of Targeted Contrast Ultrasound Agent

    PubMed Central

    Abou-Elkacem, Lotfi; Wilson, Katheryne E.; Johnson, Sadie M.; Chowdhury, Sayan M.; Bachawal, Sunitha; Hackel, Benjamin J.; Tian, Lu; Willmann, Jürgen K.

    2016-01-01

    Molecularly-targeted microbubbles (MBs) are increasingly being recognized as promising contrast agents for oncological molecular imaging with ultrasound. With the detection and validation of new molecular imaging targets, novel binding ligands are needed that bind to molecular imaging targets with high affinity and specificity. In this study we assessed a novel class of potentially clinically translatable MBs using an engineered 10th type III domain of human-fibronectin (MB-FN3VEGFR2) scaffold-ligand to image VEGFR2 on the neovasculature of cancer. The in vitro binding of MB-FN3VEGFR2 to a soluble VEGFR2 was assessed by flow-cytometry (FACS) and binding to VEGFR2-expressing cells was assessed by flow-chamber cell attachment studies under flow shear stress conditions. In vivo binding of MB-FN3VEGFR2 was tested in a transgenic mouse model (FVB/N Tg(MMTV/PyMT634Mul) of breast cancer and control litter mates with normal mammary glands. In vitro FACS and flow-chamber cell attachment studies showed significantly (P<0.01) higher binding to VEGFR2 using MB-FN3VEGFR2 than control agents. In vivo ultrasound molecular imaging (USMI) studies using MB-FN3VEGFR2 demonstrated specific binding to VEGFR2 and was significantly higher (P<0.01) in breast cancer compared to normal breast tissue. Ex vivo immunofluorescence-analysis showed significantly (P<0.01) increased VEGFR2-expression in breast cancer compared to normal mammary tissue. Our results suggest that MBs coupled to FN3-scaffolds can be designed and used for USMI of breast cancer neoangiogenesis. Due to their small size, stability, solubility, the lack of glycosylation and disulfide bonds, FN3-scaffolds can be recombinantly produced with the advantage of generating small, high affinity ligands in a cost efficient way for USMI. PMID:27570547

  2. Molecular recognition by multiple metal coordination inside wavy-stacked macrocycles.

    PubMed

    Nakamura, Takashi; Kaneko, Yuya; Nishibori, Eiji; Nabeshima, Tatsuya

    2017-07-25

    Most biological and synthetic receptors for small organic molecules employ a combination of relatively weak intermolecular interactions such as hydrogen bonds. A host compound that utilizes stronger yet reversible bonding in a synergistic manner could realize precise recognition, but the regulation and spatial arrangement of such reactive interaction moieties have been a challenge. Here, we show a multinuclear zinc complex synthesized from a macrocyclic ligand hexapap, which inwardly arranges labile metal coordination sites for external molecules. The metallomacrocycle forms a unique wavy-stacked structure upon binding a suitable length of dicarboxylic acids via multipoint coordination bonding. The saddle-shaped deformation and dimerization realize the differentiation of the interaction moieties, and change of guest-binding modes at specific metal coordination sites among the many present have been achieved utilizing acid/base as external stimuli.Synergistic use of coordination bonds that are strong and reversible realizes unique molecular recognition in artificial systems. Here, the authors show that a zinc-based metallomacrocyle can bind dicarboxylic acids of suitable length at specific metal sites by shape deformation and dimerization.

  3. Molecular Understanding of USP7 Substrate Recognition and C-Terminal Activation.

    PubMed

    Rougé, Lionel; Bainbridge, Travis W; Kwok, Michael; Tong, Raymond; Di Lello, Paola; Wertz, Ingrid E; Maurer, Till; Ernst, James A; Murray, Jeremy

    2016-08-02

    The deubiquitinating enzyme USP7 has a pivotal role in regulating the stability of proteins involved in fundamental cellular processes of normal biology and disease. Despite the importance of USP7, the mechanisms underlying substrate recognition and catalytic activation are poorly understood. Here we present structural, biochemical, and biophysical analyses elucidating the molecular mechanism by which the C-terminal 19 amino acids of USP7 (residues 1084-1102) enhance the ubiquitin cleavage activity of the deubiquitinase (DUB) domain. Our data demonstrate that the C-terminal peptide binds the activation cleft in the catalytic domain and stabilizes the catalytically competent conformation of USP7. Additional structures of longer fragments of USP7, as well as solution studies, provide insight into full-length USP7, the role of the UBL domains, and demonstrate that both substrate recognition and deubiquitinase activity are highly regulated by the catalytic and noncatalytic domains of USP7, a feature that could be essential for the proper function of multi-domain DUBs. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Electrospun Nanofibers from a Tricyanofuran-Based Molecular Switch for Colorimetric Recognition of Ammonia Gas.

    PubMed

    Khattab, Tawfik A; Abdelmoez, Sherif; Klapötke, Thomas M

    2016-03-14

    A chromophore based on tricyanofuran (TCF) with a hydrazone (H) recognition moiety was developed. Its molecular-switching performance is reversible and has differential sensitivity towards aqueous ammonia at comparable concentrations. Nanofibers were fabricated from the TCF-H chromophore by electrospinning. The film fabricated from these nanofibers functions as a solid-state optical chemosensor for probing ammonia vapor. Recognition of ammonia vapor occurs by proton transfer from the hydrazone fragment of the chromophore to the ammonia nitrogen atom and is facilitated by the strongly electron withdrawing TCF fragment. The TCF-H chromophore was added to a solution of poly(acrylic acid), which was electrospun to obtain a nanofibrous sensor device. The morphology of the nanofibrous sensor was determined by SEM, which showed that nanofibers with a diameter range of 200-450 nm formed a nonwoven mat. The resultant nanofibrous sensor showed very good sensitivity in ammonia-vapor detection. Furthermore, very good reversibility and short response time were also observed.

  5. Polydopamine-based superparamagnetic molecularly imprinted polymer nanospheres for efficient protein recognition.

    PubMed

    Lan, Fang; Ma, Shaohua; Yang, Qi; Xie, Liqin; Wu, Yao; Gu, Zhongwei

    2014-11-01

    A new strategy for synthesis of superparamagnetic molecularly imprinted polymer nanospheres (MIPNSs) for efficient protein recognition is described here. Homogeneous hydroxyl group functionalized Fe3O4/polymethyl methacrylate (PMMA) composite nanospheres were prepared using improved miniemulsion polymerization. Uniform superparamagnetic MIPNSs were obtained via self-polymerization of dopamine (DA) on the surface of Fe3O4/PMMA composite nanospheres in the presence of lysozyme (lyz) template. The as-synthesized Fe3O4/PMMA/PDA MIPNSs had average diameters of 180 nm, high saturation magnetization and a good magnetic response. The lyz-imprinted Fe3O4/PMMA/PDA MIPNSs exhibited specific recognition and efficient adsorption capacity toward lyz template. The amount of lyz adsorbed onto the lyz-imprinted Fe3O4/PMMA/PDA MIPNSs was about 4 times greater than that of the Fe3O4/PMMA/PDA non-imprinted polymer nanospheres (NIPNSs) and about 14, 5, and 5 times greater than that of BSA, BHb, and cyt C, respectively. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Molecular Basis of Substrate Recognition and Degradation by Human Presequence Protease

    PubMed Central

    King, John V.; Liang, Wenguang G.; Scherpelz, Kathryn P.; Schilling, Alexander B.; Meredith, Stephen C.; Tang, Wei-Jen

    2014-01-01

    Summary Human Presequence Protease (hPreP) is an M16 metalloprotease localized in mitochondria. There, hPreP facilitates proteostasis by utilizing a ∼13,300Å3 catalytic chamber to degrade a diverse array of potentially toxic peptides, including mitochondrial presequences and amyloid-β (Aβ), the latter of which contributes to Alzheimer's disease pathogenesis. Here we report crystal structures for hPreP alone and in complex with Aβ, which show that hPreP uses size-exclusion and charge complementation for substrate recognition. These structures also reveal hPreP-specific features that permit a diverse array of peptides, with distinct distributions of charged and hydrophobic residues, to be specifically captured, cleaved, and their amyloidogenic features destroyed. SAXS analysis demonstrates that hPreP in solution exists in dynamic equilibrium between closed and open states, with the former being preferred. Furthermore, Aβ binding induces the closed state and hPreP dimerization. Together, these data reveal the molecular basis for flexible yet specific substrate recognition and degradation by hPreP. PMID:24931469

  7. Quartz crystal microbalance for the detection of carbaryl using molecularly imprinted polymers as recognition element.

    PubMed

    Yao, Wei; Gao, Zhixian; Cheng, Yiyong

    2009-10-01

    A new piezoelectric quartz crystal sensor using molecularly imprinted polymers (MIPs) as recognition element has been prepared for the fast detection of carbaryl. The MIPs were prepared by precipitation polymerization in ACN, and then the polymer particles were fixed on the surface of the electrode. Computer simulation technology was employed to investigate the interaction between carbaryl and methacrylic acid (MAA) for elucidating the recognition mechanism. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) were employed to evaluate the obtained imprinted polymer particles and the MIP sensitive film coated on the electrode. The sensor developed exhibits a liner relationship between the frequency shift and carbaryl concentration in the range of 10-1000 ng/mL (y = 0.139 x + 2.99, r = 0.9981), and the detection limit was 12.5 ng/mL (S/N = 3). Furthermore, the influencing factors were investigated, and the experiments indicated that the obtained sensor has high sensitivity, excellent selectivity, good reproducibility, and reusable property.

  8. Preparation of a magnetic molecularly imprinted polymer for selective recognition of rhodamine B

    NASA Astrophysics Data System (ADS)

    Liu, Xiuying; Yu, Dan; Yu, Yingchao; Ji, Shujuan

    2014-11-01

    A novel magnetic molecularly imprinted polymer (MMIP) was developed as an adsorbent to selectively remove rhodamine B from real samples. The polymer was characterized by scanning electron microscopy, Fourier-transform infrared spectroscopy, and thermo-gravimetric analysis. Static adsorption, kinetic adsorption, and selective recognition experiments were also performed to investigate the specific adsorption equilibrium, kinetics, and selective recognition ability of the MMIP. The MMIPs had outstanding thermal stability, large adsorption capacity, and high competitive selectivity. When they were used as dispersed solid-phase extraction adsorbents in real samples, rhodamine B recovery was 79.97-81.88% and 75.56-79.74% in intra-day and inter-day reproducibility experiments with relative standard deviations lower than 2.62% and 4.28%, respectively. Extraction was optimized for yield and efficiency. Precision, accuracy, and linear working range were determined under optimal experimental conditions. The limits of detection and quantification were 1.05 and 3.49 μg L-1, respectively. These results suggest MMIPs may be used for determination of rhodamine B in real samples.

  9. Green synthesis and molecular recognition ability of patuletin coated gold nanoparticles.

    PubMed

    Ateeq, Muhammad; Shah, Muhammad Raza; ul Ain, Noor; Bano, Samina; Anis, Itrat; Lubna; Faizi, Shaheen; Bertino, Massimo F; Sohaila Naz, Syeda

    2015-01-15

    Patuletin isolated from Tagetespatula was used as a capping and reducing agent to synthesize in one pot gold nanoparticles capped with patuletin. Conjugation of gold with patuletin was confirmed by FT-IR and UV-visible spectroscopy and amount of patuletin conjugated to gold nanoparticles was found to be 63.2% by weight. Particle sizes were measured by atomic force microscopy (AFM) and were found to have a mean diameter of about 45 nm. Patuletin-coated gold nanoparticles were found to be highly fluorescent. To examine their potential as chemical sensors, they were contacted with fourteen different drugs. Of these drugs, only one, piroxicam, was found to quench luminescence. Quenching obeyed Beer's law in a concentration range of 20-260 µM. Important for molecular recognition applications, fluorescence quenching by piroxicam was not affected by pH variation, elevated temperatures, addition of other drugs and addition of blood plasma to the colloidal suspensions.

  10. Molecular basis for oncohistone H3 recognition by SETD2 methyltransferase

    PubMed Central

    Yang, Shuang; Zheng, Xiangdong; Lu, Chao; Li, Guo-Min; Allis, C. David; Li, Haitao

    2016-01-01

    High-frequency point mutations of genes encoding histones have been identified recently as novel drivers in a number of tumors. Specifically, the H3K36M/I mutations were shown to be oncogenic in chondroblastomas and undifferentiated sarcomas by inhibiting H3K36 methyltransferases, including SETD2. Here we report the crystal structures of the SETD2 catalytic domain bound to H3K36M or H3K36I peptides with SAH (S-adenosylhomocysteine). In the complex structure, the catalytic domain adopts an open conformation, with the K36M/I peptide snuggly positioned in a newly formed substrate channel. Our structural and biochemical data reveal the molecular basis underying oncohistone recognition by and inhibition of SETD2. PMID:27474439

  11. Similarity recognition of molecular structures by optimal atomic matching and rotational superposition.

    PubMed

    Helmich, Benjamin; Sierka, Marek

    2012-01-15

    An algorithm for similarity recognition of molecules and molecular clusters is presented which also establishes the optimum matching among atoms of different structures. In the first step of the algorithm, a set of molecules are coarsely superimposed by transforming them into a common reference coordinate system. The optimum atomic matching among structures is then found with the help of the Hungarian algorithm. For this, pairs of structures are represented as complete bipartite graphs with a weight function that uses intermolecular atomic distances. In the final step, a rotational superposition method is applied using the optimum atomic matching found. This yields the minimum root mean square deviation of intermolecular atomic distances with respect to arbitrary rotation and translation of the molecules. Combined with an effective similarity prescreening method, our algorithm shows robustness and an effective quadratic scaling of computational time with the number of atoms.

  12. Tert-butylhydroquinone recognition of molecular imprinting electrochemical sensor based on core-shell nanoparticles.

    PubMed

    Zhao, Peini; Hao, Jingcheng

    2013-08-15

    One novel electrochemistry-molecular imprinting sensor for determining tert-butylhydroquinone (TBHQ) in foodstuff was developed. TBHQ-imprinted core-shell nanoparticles (TICSNs) were fabricated using silica nanoparticles as core material. The silica nanoparticles were modified with (3-chloropropyl) trimethoxysilan and polyethylenimine, respectively, and polymerised to form the TICSNs with ethylene glycol dimethacrylate as cross-linker. The specific core-shell structure demonstrates extremely high specific surface area which greatly increases the effective binding sites and improves the recognition capability for model molecules. Under the optimal conditions, the linear range of the calibration curve was 0.1-50.0 mg kg(-1) with the detection limit of 0.27 mg kg(-1). The sensor has been successfully applied to the determination of TBHQ in food samples and achieved high sensitivity and selectivity. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Precise Macroscopic Supramolecular Assembly by Combining Spontaneous Locomotion Driven by the Marangoni Effect and Molecular Recognition.

    PubMed

    Xiao, Meng; Xian, Yiming; Shi, Feng

    2015-07-27

    Macroscopic supramolecular assembly bridges fundamental research on molecular recognition and the potential applications as bulk supramolecular materials. However, challenges remain to realize stable precise assembly, which is significant for further functions. To handle this issue, the Marangoni effect is applied to achieve spontaneous locomotion of macroscopic building blocks to reach interactive distance, thus contributing to formation of ordered structures. By increasing the density of the building blocks, the driving force for assembly transforms from a hydrophobic-hydrophobic interaction to hydrophilic-hydrophilic interaction, which is favorable for introducing hydrophilic coatings with supramolecular interactive groups on matched surfaces, consequently realizing the fabrication of stable precise macroscopic supramolecular assemblies. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Miniature Chemical Sensor combining Molecular Recognition with Evanescent Wave Cavity Ring-Down Spectroscopy

    SciTech Connect

    Pipino, Andrew C. R.; Meuse, Curtis W.

    2003-06-15

    To address the chemical sensing needs of DOE, a new class of chemical sensors is being developed that enables qualitative and quantitative, remote, real-time, optical diagnostics of chemical species in hazardous gas, liquid, and semi-solid phases by employing evanescent wave cavity ring-down spectroscopy (EW-CRDS). The feasibility and sensitivity of EW-CRDS was demonstrated previously under Project No.60231. The objective of this project is to enhance the selectivity and domain of application of EW-CRDS. Selectivity is enhanced by using molecular recognition (MR) chemistry and polarized ''fingerprint'' near-IR spectroscopy, while the domain of application is expanded by combining EW-CRDS with the unique optical properties of nanoparticles and by extending the technique to liquids.

  15. Nitrogen and oxygen bridged calixaromatics: synthesis, structure, functionalization, and molecular recognition.

    PubMed

    Wang, Mei-Xiang

    2012-02-21

    heteracalixaromatics had been reported, owing to the formidable synthetic challenges involved. Apart from thiacalixarene, the synthesis of nitrogen- and oxygen-bridged calixarenes appeared very difficult. But since our first publications in 2004, we have been delighted to see the rapid and tremendous development of the supramolecular chemistry of this new generation of macrocycles. In this Account, I summarize the synthesis of N- and O-bridged calixaromatics and their regiospecific functionalization on the rims and bridging positions, focusing on the fragment coupling approach and contributions from our laboratory. I describe the construction of molecular cages based on heteracalixaromatics and discuss the effect of both bridging heteroatoms and substituents on macrocyclic conformations and cavity sizes. Molecular recognition of neutral organic molecules and charged guest species is also demonstrated. The easy accessibility, rich molecular diversity, unique conformation, and cavity tunability of heteracalixaromatics make them invaluable macrocycles for research in supramolecular chemistry. New heteracalixaromatics, with well-defined conformations and cavity properties, will provide powerful tools for probing noncovalent interactions, leading to the development of new molecular sensing and imaging systems. Multicomponent molecular self-assembly of heteracalixaromatics as functional modules with metals, metal clusters, or charge-neutral species should result in multidimensional solid and soft materials with diverse applications. The profitable incorporation of heteracalixaromatics into molecular devices can also be anticipated in the future. Moreover, the construction of enantiopure, inherently chiral heteracalixaromatics should provide important applications in chiral recognition and asymmetric catalysis.

  16. Characterization and Synthesis of Eudistidine C, a Bioactive Marine Alkaloid with an Intriguing Molecular Scaffold.

    PubMed

    Chan, Susanna T S; Nani, Roger R; Schauer, Evan A; Martin, Gary E; Williamson, R Thomas; Saurí, Josep; Buevich, Alexei V; Schafer, Wes A; Joyce, Leo A; Goey, Andrew K L; Figg, William D; Ransom, Tanya T; Henrich, Curtis J; McKee, Tawnya C; Moser, Arvin; MacDonald, Scott A; Khan, Shabana; McMahon, James B; Schnermann, Martin J; Gustafson, Kirk R

    2016-11-18

    An extract of Eudistoma sp. provided eudistidine C (1), a heterocyclic alkaloid with a novel molecular framework. Eudistidine C (1) is a racemic natural product composed of a tetracyclic core structure further elaborated with a p-methoxyphenyl group and a phenol-substituted aminoimidazole moiety. This compound presented significant structure elucidation challenges due to the large number of heteroatoms and fully substituted carbons. These issues were mitigated by application of a new NMR pulse sequence (LR-HSQMBC) optimized to detect four- and five-bond heteronuclear correlations and the use of computer-assisted structure elucidation software. Synthesis of eudistidine C (1) was accomplished in high yield by treating eudistidine A (2) with 4(2-amino-1H-imidazol-5-yl)phenol (4) in DMSO. Synthesis of eudistidine C (1) confirmed the proposed structure and provided material for further biological characterization. Treatment of 2 with various nitrogen heterocycles and electron-rich arenes provided a series of analogues (5-10) of eudistidine C. Chiral-phase HPLC resolution of epimeric eudistidine C provided (+)-(R)-eudistidine C (1a) and (-)-(S)-eudistidine C (1b). The absolute configuration of these enantiomers was assigned by ECD analysis. (-)-(S)-Eudistidine C (1b) modestly inhibited interaction between the protein binding domains of HIF-1α and p300. Compounds 1, 2, and 6-10 exhibited significant antimalarial activity against Plasmodium falciparum.

  17. Lighten the Load: Scaffolding Visual Literacy in Biochemistry and Molecular Biology

    PubMed Central

    Offerdahl, Erika G.; Arneson, Jessie B.; Byrne, Nicholas

    2017-01-01

    The development of scientific visual literacy has been identified as critical to the training of tomorrow’s scientists and citizens alike. Within the context of the molecular life sciences in particular, visual representations frequently incorporate various components, such as discipline-specific graphical and diagrammatic features, varied levels of abstraction, and spatial arrangements of visual elements to convey information. Visual literacy is achieved when an individual understands the various ways in which a discipline uses these components to represent a particular way of knowing. Owing to the complex nature of visual representations, the activities through which visual literacy is developed have high cognitive load. Cognitive load can be reduced by first helping students to become fluent with the discrete components of visual representations before asking them to simultaneously integrate these components to extract the intended meaning of a representation. We present a taxonomy for characterizing one component of visual representations—the level of abstraction—as a first step in understanding the opportunities afforded students to develop fluency. Further, we demonstrate how our taxonomy can be used to analyze course assessments and spur discussions regarding the extent to which the development of visual literacy skills is supported by instruction within an undergraduate biochemistry curriculum. PMID:28130273

  18. Chalcone scaffolds as anti-infective agents: structural and molecular target perspectives.

    PubMed

    Mahapatra, Debarshi Kar; Bharti, Sanjay Kumar; Asati, Vivek

    2015-08-28

    In recent years, widespread outbreak of numerous infectious diseases across the globe has created havoc among the population. Particularly, the inhabitants of tropical and sub-tropical regions are mainly affected by these pathogens. Several natural and (semi) synthetic chalcones deserve the credit of being potential anti-infective candidates that inhibit various parasitic, malarial, bacterial, viral, and fungal targets like cruzain-1/2, trypanopain-Tb, trans-sialidase, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), fumarate reductase, falcipain-1/2, β-hematin, topoisomerase-II, plasmepsin-II, lactate dehydrogenase, protein kinases (Pfmrk and PfPK5), and sorbitol-induced hemolysis, DEN-1 NS3, H1N1, HIV (Integrase/Protease), protein tyrosine phosphatase A/B (Ptp-A/B), FtsZ, FAS-II, lactate/isocitrate dehydrogenase, NorA efflux pump, DNA gyrase, fatty acid synthase, chitin synthase, and β-(1,3)-glucan synthase. In this review, a comprehensive study (from Jan. 1982 to May 2015) of the structural features of anti-infective chalcones, their mechanism of actions (MOAs) and structure activity relationships (SARs) have been highlighted. With the knowledge of molecular targets, structural insights and SARs, this review may be helpful for (medicinal) chemists to design more potent, safe, selective and cost effective anti-infective agents.

  19. Computational modeling on the recognition of the HRE motif by HIF-1: molecular docking and molecular dynamics studies.

    PubMed

    Sokkar, Pandian; Sathis, Vani; Ramachandran, Murugesan

    2012-05-01

    Hypoxia inducible factor-1 (HIF-1) is a bHLH-family transcription factor that controls genes involved in glycolysis, angiogenesis, migration, as well as invasion factors that are important for tumor progression and metastasis. HIF-1, a heterodimer of HIF-1α and HIF-1β, binds to the hypoxia responsive element (HRE) present in the promoter regions of hypoxia responsive genes, such as vascular endothelial growth factor (VEGF). Neither the structure of free HIF-1 nor that of its complex with HRE is available. Computational modeling of the transcription factor-DNA complex has always been challenging due to their inherent flexibility and large conformational space. The present study aims to model the interaction between the DNA-binding domain of HIF-1 and HRE. Experiments showed that rigid macromolecular docking programs (HEX and GRAMM-X) failed to predict the optimal dimerization of individually modeled HIF-1 subunits. Hence, the HIF-1 heterodimer was modeled based on the phosphate system positive regulatory protein (PHO4) homodimer. The duplex VEGF-DNA segment containing HRE with flanking nucleotides was modeled in the B form and equilibrated via molecular dynamics (MD) simulation. A rigid docking approach was used to predict the crude binding mode of HIF-1 dimer with HRE, in which the putative contacts were found to be present. An MD simulation (5 ns) of the HIF-1-HRE complex in explicit water was performed to account for its flexibility and to optimize its interactions. All of the conserved amino acid residues were found to play roles in the recognition of HRE. The present work, which sheds light on the recognition of HRE by HIF-1, could be beneficial in the design of peptide or small molecule therapeutics that can mimic HIF-1 and bind with the HRE sequence.

  20. Engineering responsive polymer building blocks with host-guest molecular recognition for functional applications.

    PubMed

    Hu, Jinming; Liu, Shiyong

    2014-07-15

    CONSPECTUS: All living organisms and soft matter are intrinsically responsive and adaptive to external stimuli. Inspired by this fact, tremendous effort aiming to emulate subtle responsive features exhibited by nature has spurred the invention of a diverse range of responsive polymeric materials. Conventional stimuli-responsive polymers are constructed via covalent bonds and can undergo reversible or irreversible changes in chemical structures, physicochemical properties, or both in response to a variety of external stimuli. They have been imparted with a variety of emerging applications including drug and gene delivery, optical sensing and imaging, diagnostics and therapies, smart coatings and textiles, and tissue engineering. On the other hand, in comparison with molecular chemistry held by covalent bonds, supramolecular chemistry built on weak and reversible noncovalent interactions has emerged as a powerful and versatile strategy for materials fabrication due to its facile accessibility, extraordinary reversibility and adaptivity, and potent applications in diverse fields. Typically involving more than one type of noncovalent interactions (e.g., hydrogen bonding, metal coordination, hydrophobic association, electrostatic interactions, van der Waals forces, and π-π stacking), host-guest recognition refers to the formation of supramolecular inclusion complexes between two or more entities connected together in a highly controlled and cooperative manner. The inherently reversible and adaptive nature of host-guest molecular recognition chemistry, stemming from multiple noncovalent interactions, has opened up a new platform to construct novel types of stimuli-responsive materials. The introduction of host-guest chemistry not only enriches the realm of responsive materials but also confers them with promising new applications. Most intriguingly, the integration of responsive polymer building blocks with host-guest recognition motifs will endow the former with

  1. Serine versus threonine glycosylation with α-O-GalNAc: unexpected selectivity in their molecular recognition with lectins.

    PubMed

    Madariaga, David; Martínez-Sáez, Nuria; Somovilla, Víctor J; García-García, Laura; Berbis, M Álvaro; Valero-Gónzalez, Jessika; Martín-Santamaría, Sonsoles; Hurtado-Guerrero, Ramon; Asensio, Juan L; Jiménez-Barbero, Jesús; Avenoza, Alberto; Busto, Jesús H; Corzana, Francisco; Peregrina, Jesús M

    2014-09-22

    The molecular recognition of several glycopeptides bearing Tn antigen (α-O-GalNAc-Ser or α-O-GalNAc-Thr) in their structure by three lectins with affinity for this determinant has been analysed. The work yields remarkable results in terms of epitope recognition, showing that the underlying amino acid of Tn (serine or threonine) plays a key role in the molecular recognition. In fact, while Soybean agglutinin and Vicia villosa agglutinin lectins prefer Tn-threonine, Helix pomatia agglutinin shows a higher affinity for the glycopeptides carrying Tn-serine. The different conformational behaviour of the two Tn biological entities, the residues of the studied glycopeptides in the close proximity to the Tn antigen and the topology of the binding site of the lectins are at the origin of these differences. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Phthalocyanines as Molecular Scaffolds to Block Disease-Associated Protein Aggregation.

    PubMed

    Valiente-Gabioud, Ariel A; Miotto, Marco C; Chesta, María E; Lombardo, Verónica; Binolfi, Andres; Fernández, Claudio O

    2016-05-17

    amyloidogenic proteins. Analysis of the structure-activity relationship in phthalocyanines revealed that their anti-amyloid activity is highly dependent on the type of metal ion coordinated to the tetrapyrrolic system but is not sensitive to the number of peripheral charged substituents. The tendency of phthalocyanines to oligomerize (self-association) via aromatic-aromatic stacking interactions correlates precisely with their binding capabilities to target proteins and, more importantly, determines their efficiency as anti-amyloid agents. The ability to block different types of disease-associated protein aggregation raises the possibility that these cyclic tetrapyrrole compounds have a common mechanism of action to impair the formation of a variety of pathological aggregates. Because the structural and molecular basis for the anti-amyloid effects of these molecules is starting to emerge, combined efforts from the fields of structural, cellular, and animal biology will result critical for the rational design and discovery of new drugs for the treatment of amyloid related neurological disorders.

  3. Boronic acid chemistry in MALDI MS: a step forward in designing a reactive matrix with molecular recognition capabilities.

    PubMed

    Monopoli, A; Calvano, C D; Nacci, A; Palmisano, F

    2014-04-28

    A boronic analogue of the archetype matrix α-cyano-4-hydroxycinnamic acid (CHCA) has been synthesised providing a new "reactive matrix" that possesses molecular recognition properties. This matrix selectively recognizes vic-diols, α-hydroxyacids, aminols and first allowed the detection of anions as fluoride (unaffordable by usual matrices).

  4. [Experiment and analyse on the effect of magnetic nanoparticles upon relaxation time of proton in molecular recognition by MRI].

    PubMed

    Hu, Lili; Song, Tao; Yang, Wenhui; Wang, Ming; Zhang, Fang; Tao, Chunjing

    2007-06-01

    To research on the effect of three different magnetic nanoparticles upon relaxation time of proton. The detection by magnetic resonance imaging (MRI) indicates that there is the effect of marked difference to right control experiment and to analyze the difference from theory. The result discloses that will be able to perform the experiment of molecular recognition using magnetic nanoparticles later.

  5. Molecular basis for epitope recognition by non-neutralizing anti-gp41 antibody F240

    PubMed Central

    Gohain, Neelakshi; Tolbert, William D.; Orlandi, Chiara; Richard, Jonathan; Ding, Shilei; Chen, Xishan; Bonsor, Daniel A.; Sundberg, Eric J.; Lu, Wuyuan; Ray, Krishanu; Finzi, Andrés; Lewis, George K.; Pazgier, Marzena

    2016-01-01

    Antibody-dependent cell-mediated cytotoxicity (ADCC) by non-neutralizing antibodies (nnAbs) specific to the HIV envelope (Env) glycoproteins present at the surface of virus sensitized or infected cells plays a role in the effective adaptive immune response to HIV. Here, we explore the molecular basis for the epitope at the disulfide loop region (DLR) of the principal immunodominant domain of gp41, recognized by the well-known nnAb F240. Our structural studies reveal details of the F240-gp41 interface and describe a structure of DLR that is distinct from known conformations of this region studied in the context of either CD4-unliganded Env trimer or the gp41 peptide in the unbound state. These data coupled with binding and functional analyses indicate that F240 recognizes non-trimeric Env forms which are significantly overexpressed on intact virions but poorly represented at surfaces of cells infected with infectious molecular clones and endogenously-infected CD4 T cells from HIV-1-infected individuals. Furthermore, although we detect ADCC activities of F240 against cells spinoculated with intact virions, our data suggest that these activities result from F240 recognition of gp41 stumps or misfolded Env variants present on virions rather than its ability to recognize functional gp41 transition structures emerging on trimeric Env post CD4 receptor engagement. PMID:27827447

  6. Aptamers as promising molecular recognition elements for diagnostics and therapeutics in the central nervous system.

    PubMed

    McConnell, Erin M; Holahan, Matthew R; DeRosa, Maria C

    2014-12-01

    Oligonucleotide aptamers are short, synthetic, single-stranded DNA or RNA able to recognize and bind to a multitude of targets ranging from small molecules to cells. Aptamers have emerged as valuable tools for fundamental research, clinical diagnosis, and therapy. Due to their small size, strong target affinity, lack of immunogenicity, and ease of chemical modification, aptamers are an attractive alternative to other molecular recognition elements, such as antibodies. Although it is a challenging environment, the central nervous system and related molecular targets present an exciting potential area for aptamer research. Aptamers hold promise for targeted drug delivery, diagnostics, and therapeutics. Here we review recent advances in aptamer research for neurotransmitter and neurotoxin targets, demyelinating disease and spinal cord injury, cerebrovascular disorders, pathologies related to protein aggregation (Alzheimer's, Parkinson's, and prions), brain cancer (glioblastomas and gliomas), and regulation of receptor function. Challenges and limitations posed by the blood brain barrier are described. Future perspectives for the application of aptamers to the central nervous system are also discussed.

  7. Molecular basis of non-self recognition by the horseshoe crab tachylectins.

    PubMed

    Kawabata, Shun-ichiro; Tsuda, Ryoko

    2002-09-19

    The self/non-self discrimination by innate immunity through simple ligands universally expressed both on pathogens and hosts, such as monosaccharides and acetyl group, depends on the density or clustering patterns of the ligands. The specific recognition by the horseshoe crab tachylectins with a propeller-like fold or a propeller-like oligomeric arrangement is reinforced by the short distance between the individual binding sites that interact with pathogen-associated molecular patterns (PAMPs). There is virtually no conformational change in the main or side chains of tachylectins upon binding with the ligands. This low structural flexibility of the propeller structures must be very important for specific interaction with PAMPs. Mammalian lectins, such as mannose-binding lectin and ficolins, trigger complement activation through the lectin pathway in the form of opsonins. However, tachylectins have no effector collagenous domains and no lectin-associated serine proteases found in the mammalian lectins. Furthermore, no complement-like proteins have been found in horseshoe crabs, except for alpha(2)-macroglobulin. The mystery of the molecular mechanism of the scavenging pathway of pathogens in horseshoe crabs remains to be solved.

  8. Multibody cofactor and substrate molecular recognition in the myo-inositol monophosphatase enzyme

    PubMed Central

    Ferruz, Noelia; Tresadern, Gary; Pineda-Lucena, Antonio; De Fabritiis, Gianni

    2016-01-01

    Molecular recognition is rarely a two-body protein-ligand problem, as it often involves the dynamic interplay of multiple molecules that together control the binding process. Myo-inositol monophosphatase (IMPase), a drug target for bipolar disorder, depends on 3 Mg2+ ions as cofactor for its catalytic activity. Although the crystallographic pose of the pre-catalytic complex is well characterized, the binding process by which substrate, cofactor and protein cooperate is essentially unknown. Here, we have characterized cofactor and substrate cooperative binding by means of large-scale molecular dynamics. Our study showed the first and second Mg2+ ions identify the binding pocket with fast kinetics whereas the third ion presents a much higher energy barrier. Substrate binding can occur in cooperation with cofactor, or alone to a binary or ternary cofactor-IMPase complex, although the last scenario occurs several orders of magnitude faster. Our atomic description of the three-body mechanism offers a particularly challenging example of pathway reconstruction, and may prove particularly useful in realistic contexts where water, ions, cofactors or other entities cooperate and modulate the binding process. PMID:27440438

  9. Molecular basis for epitope recognition by non-neutralizing anti-gp41 antibody F240.

    PubMed

    Gohain, Neelakshi; Tolbert, William D; Orlandi, Chiara; Richard, Jonathan; Ding, Shilei; Chen, Xishan; Bonsor, Daniel A; Sundberg, Eric J; Lu, Wuyuan; Ray, Krishanu; Finzi, Andrés; Lewis, George K; Pazgier, Marzena

    2016-11-09

    Antibody-dependent cell-mediated cytotoxicity (ADCC) by non-neutralizing antibodies (nnAbs) specific to the HIV envelope (Env) glycoproteins present at the surface of virus sensitized or infected cells plays a role in the effective adaptive immune response to HIV. Here, we explore the molecular basis for the epitope at the disulfide loop region (DLR) of the principal immunodominant domain of gp41, recognized by the well-known nnAb F240. Our structural studies reveal details of the F240-gp41 interface and describe a structure of DLR that is distinct from known conformations of this region studied in the context of either CD4-unliganded Env trimer or the gp41 peptide in the unbound state. These data coupled with binding and functional analyses indicate that F240 recognizes non-trimeric Env forms which are significantly overexpressed on intact virions but poorly represented at surfaces of cells infected with infectious molecular clones and endogenously-infected CD4 T cells from HIV-1-infected individuals. Furthermore, although we detect ADCC activities of F240 against cells spinoculated with intact virions, our data suggest that these activities result from F240 recognition of gp41 stumps or misfolded Env variants present on virions rather than its ability to recognize functional gp41 transition structures emerging on trimeric Env post CD4 receptor engagement.

  10. Peptides as new smart bionanomaterials: molecular-recognition and self-assembly capabilities.

    PubMed

    Sawada, Toshiki; Mihara, Hisakazu; Serizawa, Takeshi

    2013-04-01

    Biomolecules express exquisite properties that are required for molecular recognition and self-assembly on the nanoscale. These smart capabilities have developed through evolution and such biomolecules operate based on smart functions in natural systems. Recently, these remarkable smart capabilities have been utilized in not only biologically related fields, but also in materials science and engineering. A peptide-screening technology that uses phage-display systems has been developed based on this natural smart evolution for the generation of new functional peptide bionanomaterials. We focused on peptides that specifically bound to synthetic polymers. These polymer-binding peptides were screened by using a phage-display peptide library to recognize nanostructures that were derived from polymeric structural features and were utilized for possible applications as new bionanomaterials. We also focused on self-assembling peptides with β-sheet structures that formed nanoscale, fibrous structures for applications in new bottom-up nanomaterials. Moreover, nanofiber-binding peptides were also screened to introduce the desired functionalities into nanofibers without the need for additional molecular design. Our approach to construct new bionanomaterials that employ peptides will open up excellent opportunities for the next generation of materials science and technology. Copyright © 2013 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. The molecular basis of ceramide-1-phosphate recognition by C2 domains[S

    PubMed Central

    Ward, Katherine E.; Bhardwaj, Nitin; Vora, Mohsin; Chalfant, Charles E.; Lu, Hui; Stahelin, Robert V.

    2013-01-01

    Group IVA cytosolic phospholipase A2 (cPLA2α), which harbors an N-terminal lipid binding C2 domain and a C-terminal lipase domain, produces arachidonic acid from the sn-2 position of zwitterionic lipids such as phosphatidylcholine. The C2 domain has been shown to bind zwitterionic lipids, but more recently, the anionic phosphomonoester sphingolipid metabolite ceramide-1-phosphate (C1P) has emerged as a potent bioactive lipid with high affinity for a cationic patch in the C2 domain β-groove. To systematically analyze the role that C1P plays in promoting the binding of cPLA2α-C2 to biological membranes, we employed biophysical measurements and cellular translocation studies along with mutagenesis. Biophysical and cellular translocation studies demonstrate that C1P specificity is mediated by Arg59, Arg61, and His62 (an RxRH sequence) in the C2 domain. Computational studies using molecular dynamics simulations confirm the origin of C1P specificity, which results in a spatial shift of the C2 domain upon membrane docking to coordinate the small C1P headgroup. Additionally, the hydroxyl group on the sphingosine backbone plays an important role in the interaction with the C2 domain, further demonstrating the selectivity of the C2 domain for C1P over phosphatidic acid. Taken together, this is the first study demonstrating the molecular origin of C1P recognition. PMID:23277511

  12. Chemiluminescence sensor for sulfonylurea herbicide using molecular imprinted microspheres as recognition element.

    PubMed

    Xie, Cheng-gen; Gao, Shan; Zhou, Han-kun; Li, Huai-fen

    2011-01-01

    Uniform molecular imprinting microspheres were prepared using precipitation polymerization with thifensulfuron-methyl (TFM) as template, acrylamide as functional monomer and ethylene glycol dimethacrylate as cross-linker. TFM could be selectively adsorbed on the molecularly imprinted polymers (MIPs) matrix through the hydrogen bonding interaction and the adsorbed TFM could be sensed by its strikingly enhancing effect on the weak chemiluminescence (CL) reaction between luminol and hydrogen peroxide. On this basis, a novel CL sensor for the determination of TFM using MIPs as recognition elements was established. The logarithm of net CL intensity (ΔI) is linearly proportional to the logarithm of TFM concentration (C) in the range from 1.0 × 10(-9) to 5.0 × 10(-5)  mol L(-1) with a detection limit of 8.3 × 10(-10)  mol L(-1) (3σ). The results demonstrated that the MIP-CL sensor was reversible and reusable and that it could strikingly improve the selectivity and sensitivity of CL analysis. Furthermore, it is suggested that the CL enhancement of luminol-H(2)O(2) by TFM might be ascribed to the enhancement effect of CO(2), which came from TFM hydrolysis in basic medium.

  13. Electrochemical sensor for dopamine based on a novel graphene-molecular imprinted polymers composite recognition element.

    PubMed

    Mao, Yan; Bao, Yu; Gan, Shiyu; Li, Fenghua; Niu, Li

    2011-10-15

    A novel composite of graphene sheets/Congo red-molecular imprinted polymers (GSCR-MIPs) was synthesized through free radical polymerization (FRP) and applied as a molecular recognition element to construct dopamine (DA) electrochemical sensor. The template molecules (DA) were firstly absorbed at the GSCR surface due to their excellent affinity, and subsequently, selective copolymerization of methacrylic acid (MAA) and ethylene glycol dimethacrylate (EGDMA) was further achieved at the GSCR surface. Potential scanning was presented to extract DA molecules from the imprinted polymers film, and as a result, DA could be rapidly and completely removed by this way. With regard to the traditional MIPs, the GSCR-MIPs not only possessed a faster desorption and adsorption dynamics, but also exhibited a higher selectivity and binding capacity toward DA molecule. As a consequence, an electrochemical sensor for highly sensitive and selective detection of DA was successfully constructed as demonstration based on the synthesized GSCR-MIPs nanocomposites. Under experimental conditions, selective detection of DA in a linear concentration range of 1.0 × 10(-7)-8.3 × 10(-4)M was obtained, which revealed a lower limit of detection and wider linear response compared to some previously reported DA electrochemical MIPs sensors. The new DA electrochemical sensor based on GSCR-MIPs composites also exhibited excellent repeatability, which expressed as relative standard deviation (RSD) was about 2.50% for 30 repeated analyses of 20 μM DA.

  14. Nanostructured organic and inorganic thin films with novel molecular recognition properties

    NASA Astrophysics Data System (ADS)

    Twardowski, Mariusz Z.

    An important theme in surface/interface science is the development of molecular level understandings of interactions at solid-liquid interfaces. The study of molecular recognition at such interfaces is well suited for modeling with self-assembled monolayers of alkanethiols (SAMs). For optimal studies, the SAM must be defect-free. Towards this end, a chemical treatment of the gold substrate was developed, consisting of a sequential treatment in "piranha" followed by dilute aqua regia. We found that the SAMs assembled on these treated substrates had exceptional barrier properties as measured by cyclic voltammetry(CV). X-ray diffraction(XRD) indicated that oxidative treatment induces significant bulk recrystallization of the metal. The dynamics suggest that recrystallization results from preferential dissolution of Au and/or impurities present at grain boundaries, leading to unpinning and merger into larger grains. Supported lipid layers were formed via fusion of unilamellar vesicles of 1,2-dimyristoyl-sn-glycero-3-phosphocholine(DMPC) to mixed SAMs containing ferrocene-functionalized hexadecanethiol chains(FcCO 2C16SH). The structures were characterized by several methods, including CV, ellipsometry and surface plasmon resonance(SPR). Studies revealed that the adsorbed DMPC strongly influences the interactions of the tethered ferrocene groups with secondary aqueous molecular redox probes. Permselective properties are seen. We believe that molecular scale defect structures in the adsorbed DMPC layer confer these molecular discrimination properties. Unilamellar vesicles of DMPC and varying quantities of 1,2-dimyristoyl-sn-glycero-3-[phospho-rac-(1-glycerol)(sodium salt)(DMPG) were used to deposit lipid bilayer assemblies on SAMs. The coverages of the layers were measured with SPR and decreased with increasing DMPG. The assembly is reversible and the lipid adlayer removable with ethanol. Effects of the adsorbed lipid layer on the electrochemical interactions of the

  15. Molecular recognition of genomic DNA in a condensate with a model surfactant for potential gene-delivery applications.

    PubMed

    Singh, Priya; Choudhury, Susobhan; Chandra, Goutam Kumar; Lemmens, Peter; Pal, Samir Kumar

    2016-04-01

    The functionality of a gene carrying nucleic acid in an artificial gene-delivery system is important for the overall efficiency of the vehicle in vivo. Here, we have studied a well-known artificial gene-delivery system, which is a condensate of calf thymus DNA (CT-DNA) with a model cationic surfactant cetyltrimethylammonium bromide (CTAB) to investigate the molecular recognition of the genomic DNA in the condensate. While dynamic light scattering (DLS) and circular dichroism (CD) reveal structural aspects of the condensate and the constituting DNA respectively, picosecond resolved polarization gated spectroscopy and Förster resonance energy transfer (FRET) reveal molecular recognition of the genomic DNA in the condensate. We have considered ethidium bromide (EB) and crystal violet (CV), which are well known DNA-binding agents through intercalative (specific) and electrostatic (non-specific) interactions, respectively, as model ligands for the molecular recognition studies. A fluorescent cationic surfactant, Nonyl Acridine Orange (NAO) is considered to be a mimic of CTAB in the condensate. The polarization gated fluorescence of NAO at various temperatures has been used to investigate the local microviscosity of the condensate. The excellent spectral overlap of NAO emission and the absorption spectra of both EB and CV allow us to investigate FRET-distances of the ligands with respect to NAO in the condensate at various temperatures and thermal stability of ligand-binding of the genomic DNA. The thermodynamic properties of the molecular recognition have also been explored using Van't Hoff equation. We have also extended our studies to molecular recognition of the genomic DNA in the condensate as dried thin films. This has important implications for its application in bioelectronics.

  16. Preparation, Characterization and Application of a Molecularly Imprinted Polymer for Selective Recognition of Sulpiride.

    PubMed

    Zhang, Wei; She, Xuhui; Wang, Liping; Fan, Huajun; Zhou, Qing; Huang, Xiaowen; Tang, James Z

    2017-04-28

    A novel molecular imprinting polymer (MIP) was prepared by bulk polymerization using sulpiride as the template molecule, itaconic acid (ITA) as the functional monomer and ethylene glycol dimethacrylate (EGDMA) as the crosslinker. The formation of the MIP was determined as the molar ratio of sulpiride-ITA-EGDMA of 1:4:15 by single-factor experiments. The MIP showed good adsorption property with imprinting factor α of 5.36 and maximum adsorption capacity of 61.13 μmol/g, and was characterized by scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FT-IR) and surface area analysis. With the structural analogs (amisulpride, tiapride, lidocaine and cisapride) and small molecules containing a mono-functional group (p-toluenesulfonamide, formamide and 1-methylpyrrolidine) as substrates, static adsorption, kinetic adsorption, and rebinding experiments were also performed to investigate the selective adsorption ability, kinetic characteristic, and recognition mechanism of the MIP. A serial study suggested that the highly selective recognition ability of the MIP mainly depended on binding sites provided by N-functional groups of amide and amine. Moreover, the MIP as solid-phase extractant was successfully applied to extraction of sulpiride from the mixed solution (consisted of p-toluenesulfonamide, sulfamethoxazole, sulfanilamide, p-nitroaniline, acetanilide and trimethoprim) and serum sample, and extraction recoveries ranged from 81.57% to 86.63%. The tentative tests of drug release in stimulated intestinal fluid (pH 6.8) demonstrated that the tablet with the MIP-sulpiride could obviously inhibit sulpiride release rate. Thus, ITA-based MIP is an efficient and promising alternative to solid-phase adsorbent for extraction of sulpiride and removal of interferences in biosample analysis, and could be used as a potential carrier for controlled drug release.

  17. Molecularly imprinted nanopatterns for the recognition of biological warfare agent ricin.

    PubMed

    Pradhan, Santwana; Boopathi, M; Kumar, Om; Baghel, Anuradha; Pandey, Pratibha; Mahato, T H; Singh, Beer; Vijayaraghavan, R

    2009-11-15

    Molecularly imprinted polymer (MIP) for biological warfare agent (BWA) ricin was synthesized using silanes in order to avoid harsh environments during the synthesis of MIP. The synthesized MIP was utilized for the recognition of ricin. The complete removal of ricin from polymer was confirmed by fluorescence spectrometer and SEM-EDAX. SEM and EDAX studies confirmed the attachment of silane polymer on the surface of silica gel matrix. SEM image of Ricin-MIP exhibited nanopatterns and it was found to be entirely different from the SEM image of non-imprinted polymer (NIP). BET surface area analysis revealed more surface area (227 m(2)/g) for Ricin-MIP than that of NIP (143 m(2)/g). In addition, surface area study also showed more pore volume (0.5010 cm(3)/g) for Ricin-MIP than that of NIP (0.2828 cm(3)/g) at 12 nm pore diameter confirming the presence of imprinted sites for ricin as the reported diameter of ricin is 12 nm. The recognition and rebinding ability of the Ricin-MIP was tested in aqueous solution. Ricin-MIP rebound more ricin when compared to the NIP. Chromatogram obtained with Ricin-MIP exhibited two peaks due to imprinting, however, chromatogram of NIP exhibited only one peak for free ricin. SDS-PAGE result confirmed the second peak observed in chromatogram of Ricin-MIP as ricin peak. Ricin-MIP exhibited an imprinting efficiency of 1.76 and it also showed 10% interference from the structurally similar protein abrin.

  18. Molecular Dissection of Xyloglucan Recognition in a Prominent Human Gut Symbiont

    DOE PAGES

    Tauzin, Alexandra S.; Kwiatkowski, Kurt J.; Orlovsky, Nicole I.; ...

    2016-04-26

    Polysaccharide utilization loci (PUL) within the genomes of resident human gutBacteroidetesare central to the metabolism of the otherwise indigestible complex carbohydrates known as “dietary fiber.” However, functional characterization of PUL lags significantly behind sequencing efforts, which limits physiological understanding of the human-bacterial symbiosis. In particular, the molecular basis of complex polysaccharide recognition, an essential prerequisite to hydrolysis by cell surface glycosidases and subsequent metabolism, is generally poorly understood. Here, we present the biochemical, structural, and reverse genetic characterization of two unique cell surface glycan-binding proteins (SGBPs) encoded by a xyloglucan utilization locus (XyGUL) fromBacteroides ovatus, which are integral to growthmore » on this key dietary vegetable polysaccharide. Biochemical analysis reveals that these outer membrane-anchored proteins are in fact exquisitely specific for the highly branched xyloglucan (XyG) polysaccharide. The crystal structure of SGBP-A, a SusD homolog, with a bound XyG tetradecasaccharide reveals an extended carbohydrate-binding platform that primarily relies on recognition of the β-glucan backbone. The unique, tetra-modular structure of SGBP-B is comprised of tandem Ig-like folds, with XyG binding mediated at the distal C-terminal domain. Despite displaying similar affinities for XyG, reverse-genetic analysis reveals that SGBP-B is only required for the efficient capture of smaller oligosaccharides, whereas the presence of SGBP-A is more critical than its carbohydrate-binding ability for growth on XyG. Finally, together, these data demonstrate that SGBP-A and SGBP-B play complementary, specialized roles in carbohydrate capture byB. ovatusand elaborate a model of how vegetable xyloglucans are accessed by theBacteroidetes.« less

  19. Molecular Dissection of Xyloglucan Recognition in a Prominent Human Gut Symbiont

    SciTech Connect

    Tauzin, Alexandra S.; Kwiatkowski, Kurt J.; Orlovsky, Nicole I.; Smith, Christopher J.; Creagh, A. Louise; Haynes, Charles A.; Wawrzak, Zdzislaw; Brumer, Harry; Koropatkin, Nicole M.

    2016-04-26

    Polysaccharide utilization loci (PUL) within the genomes of resident human gutBacteroidetesare central to the metabolism of the otherwise indigestible complex carbohydrates known as “dietary fiber.” However, functional characterization of PUL lags significantly behind sequencing efforts, which limits physiological understanding of the human-bacterial symbiosis. In particular, the molecular basis of complex polysaccharide recognition, an essential prerequisite to hydrolysis by cell surface glycosidases and subsequent metabolism, is generally poorly understood. Here, we present the biochemical, structural, and reverse genetic characterization of two unique cell surface glycan-binding proteins (SGBPs) encoded by a xyloglucan utilization locus (XyGUL) fromBacteroides ovatus, which are integral to growth on this key dietary vegetable polysaccharide. Biochemical analysis reveals that these outer membrane-anchored proteins are in fact exquisitely specific for the highly branched xyloglucan (XyG) polysaccharide. The crystal structure of SGBP-A, a SusD homolog, with a bound XyG tetradecasaccharide reveals an extended carbohydrate-binding platform that primarily relies on recognition of the β-glucan backbone. The unique, tetra-modular structure of SGBP-B is comprised of tandem Ig-like folds, with XyG binding mediated at the distal C-terminal domain. Despite displaying similar affinities for XyG, reverse-genetic analysis reveals that SGBP-B is only required for the efficient capture of smaller oligosaccharides, whereas the presence of SGBP-A is more critical than its carbohydrate-binding ability for growth on XyG. Finally, together, these data demonstrate that SGBP-A and SGBP-B play complementary, specialized roles in carbohydrate capture byB. ovatusand elaborate a model of how vegetable xyloglucans are accessed by theBacteroidetes.

  20. Designing and preparation of cytisine alkaloid surface-imprinted material and its molecular recognition characteristics

    NASA Astrophysics Data System (ADS)

    Gao, Baojiao; Bi, Concon; Fan, Li

    2015-03-01

    Based on molecular design, a cytisine surface-imprinted material was prepared using the new surface-imprinting technique of "pre-graft polymerizing and post-imprinting". The graft-polymerization of glycidyl methacrylate (GMA) on the surfaces of micron-sized silica gel particles was first performed with a surface-initiating system, preparing the grafted particles PGMA/SiO2. Subsequently, a polymer reaction, the ring-opening reaction of the epoxy groups of the grafted PGMA, was conducted with sodium 2,4-diaminobenzene sulfonate (SAS) as reagent, resulting in the functional grafted particles SAS-PGMA/SiO2. The adsorption of cytisine on SAS-PGMA/SiO2 particles reached saturation via strong electrostatic interaction between the sulfonate groups of SAS-PGMA/SiO2 particles and the protonated N atoms in cytisine molecule. Finally, cytisine surface-imprinting was successfully carried out with glutaraldehyde as crosslinker, obtaining cytisine surface-imprinted material MIP-SASP/SiO2. The binding and recognition characteristics of MIP-SASP/SiO2 towards cytisine were investigated in depth. The experimental results show that there is strong electrostatic interaction between particles and cytisine molecules, and on this basis, cytisine surface-imprinting can be smoothly performed. The surface-imprinted MIP-SASP/SiO2 has special recognition selectivity and excellent binding affinity for cytisine, and the selectivity coefficients of MIP-SASP/SiO2 particles for cytisine relative to matrine and oxymatrine, which were used as two contrast alkaloids, are 9.5 and 6.5, respectively.

  1. Molecular Dissection of Xyloglucan Recognition in a Prominent Human Gut Symbiont

    PubMed Central

    Tauzin, Alexandra S.; Kwiatkowski, Kurt J.; Orlovsky, Nicole I.; Smith, Christopher J.; Creagh, A. Louise; Haynes, Charles A.; Wawrzak, Zdzislaw

    2016-01-01

    ABSTRACT Polysaccharide utilization loci (PUL) within the genomes of resident human gut Bacteroidetes are central to the metabolism of the otherwise indigestible complex carbohydrates known as “dietary fiber.” However, functional characterization of PUL lags significantly behind sequencing efforts, which limits physiological understanding of the human-bacterial symbiosis. In particular, the molecular basis of complex polysaccharide recognition, an essential prerequisite to hydrolysis by cell surface glycosidases and subsequent metabolism, is generally poorly understood. Here, we present the biochemical, structural, and reverse genetic characterization of two unique cell surface glycan-binding proteins (SGBPs) encoded by a xyloglucan utilization locus (XyGUL) from Bacteroides ovatus, which are integral to growth on this key dietary vegetable polysaccharide. Biochemical analysis reveals that these outer membrane-anchored proteins are in fact exquisitely specific for the highly branched xyloglucan (XyG) polysaccharide. The crystal structure of SGBP-A, a SusD homolog, with a bound XyG tetradecasaccharide reveals an extended carbohydrate-binding platform that primarily relies on recognition of the β-glucan backbone. The unique, tetra-modular structure of SGBP-B is comprised of tandem Ig-like folds, with XyG binding mediated at the distal C-terminal domain. Despite displaying similar affinities for XyG, reverse-genetic analysis reveals that SGBP-B is only required for the efficient capture of smaller oligosaccharides, whereas the presence of SGBP-A is more critical than its carbohydrate-binding ability for growth on XyG. Together, these data demonstrate that SGBP-A and SGBP-B play complementary, specialized roles in carbohydrate capture by B. ovatus and elaborate a model of how vegetable xyloglucans are accessed by the Bacteroidetes. PMID:27118585

  2. Preparation, Characterization and Application of a Molecularly Imprinted Polymer for Selective Recognition of Sulpiride

    PubMed Central

    Zhang, Wei; She, Xuhui; Wang, Liping; Fan, Huajun; Zhou, Qing; Huang, Xiaowen; Tang, James Z.

    2017-01-01

    A novel molecular imprinting polymer (MIP) was prepared by bulk polymerization using sulpiride as the template molecule, itaconic acid (ITA) as the functional monomer and ethylene glycol dimethacrylate (EGDMA) as the crosslinker. The formation of the MIP was determined as the molar ratio of sulpiride-ITA-EGDMA of 1:4:15 by single-factor experiments. The MIP showed good adsorption property with imprinting factor α of 5.36 and maximum adsorption capacity of 61.13 μmol/g, and was characterized by scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FT-IR) and surface area analysis. With the structural analogs (amisulpride, tiapride, lidocaine and cisapride) and small molecules containing a mono-functional group (p-toluenesulfonamide, formamide and 1-methylpyrrolidine) as substrates, static adsorption, kinetic adsorption, and rebinding experiments were also performed to investigate the selective adsorption ability, kinetic characteristic, and recognition mechanism of the MIP. A serial study suggested that the highly selective recognition ability of the MIP mainly depended on binding sites provided by N-functional groups of amide and amine. Moreover, the MIP as solid-phase extractant was successfully applied to extraction of sulpiride from the mixed solution (consisted of p-toluenesulfonamide, sulfamethoxazole, sulfanilamide, p-nitroaniline, acetanilide and trimethoprim) and serum sample, and extraction recoveries ranged from 81.57% to 86.63%. The tentative tests of drug release in stimulated intestinal fluid (pH 6.8) demonstrated that the tablet with the MIP–sulpiride could obviously inhibit sulpiride release rate. Thus, ITA-based MIP is an efficient and promising alternative to solid-phase adsorbent for extraction of sulpiride and removal of interferences in biosample analysis, and could be used as a potential carrier for controlled drug release. PMID:28772831

  3. Production of anti-amoxicillin ScFv antibody and simulation studying its molecular recognition mechanism for penicillins.

    PubMed

    Liu, Jing; Zhang, Hui C; Duan, Chang F; Dong, Jun; Zhao, Guo X; Wang, Jian P; Li, Nan; Liu, Jin Z; Li, Yu W

    2016-11-01

    The molecular recognition mechanism of an antibody for its hapten is very interesting. The objective of this research was to study the intermolecular interactions of an anti-amoxicillin antibody with penicillin drugs. The single chain variable fragment (ScFv) antibody was generated from a hybridoma cell strain excreting the monoclonal antibody for amoxicillin. The recombinant ScFv antibody showed similar recognition ability for penicillins to its parental monoclonal antibody: simultaneous recognizing 11 penicillins with cross-reactivities of 18-107%. The three-dimensional structure of the ScFv antibody was simulated by using homology modeling, and its intermolecular interactions with 11 penicillins were studied by using molecular docking. Results showed that three CDRs are involved in antibody recognition; CDR L3 Arg 100, CDR H3 Tyr226, and CDR H3 Arg 228 were the key contact amino acid residues; hydrogen bonding was the main antibody-drug intermolecular force; and the core structure of penicillin drugs was the main antibody binding position. These results could explain the recognition mechanism of anti-amoxicillin antibody for amoxicillin and its analogs. This is the first study reporting the production of ScFv antibody for penicillins and stimulation studying its recognition mechanism.

  4. Double Recognition and Selective Extraction of Glycoprotein Based on the Molecular Imprinted Graphene Oxide and Boronate Affinity.

    PubMed

    Luo, Jing; Huang, Jing; Cong, Jiaojiao; Wei, Wei; Liu, Xiaoya

    2017-03-01

    Specific recognition and separation of glycoproteins from complex biological solutions is very important in clinical diagnostics considering the close relationship between glycoproteins with the occurrence of diverse diseases, but the lack of materials with high selectivity and superior capture capacity still makes it a challenge. In this work, graphene oxide (GO) based molecularly imprinted polymers (MIPs) possessing double recognition abilities have been synthesized and applied as highly efficient adsorbents for glycoprotein recognition and separation. Boronic acid functionalized graphene oxide (GO-APBA) was first prepared and a template glycoprotein (ovalbumin, OVA) was then immobilized onto the surface of GO-APBA through boronate affinity. An imprinting layer was subsequently deposited onto GO-APBA surface by a sol-gel polymerization of organic silanes in aqueous solution. After the removal of the template glycoprotein, 3D cavities with double recognition abilities toward OVA were obtained in the as-prepared imprinted materials (GO-APBA/MIPs) because of the combination of boronate affinity and molecularly imprinted spatial matched cavities. The obtained GO-APBA/MIPs exhibited superior specific recognition toward OVA with imprinted factor (α) as high as 9.5, significantly higher than the corresponding value (4.0) of GO/MIPs without the introduction of boronic acid groups. Meanwhile, because of the synergetic effect of large surface area of graphene and surface imprinting, high binding capacity and fast adsorption/elution rate of GO-APBA/MIPs toward OVA were demonstrated and the saturation binding capacity of GO-APBA/MIPs could reach 278 mg/g within 40 min. The outstanding recognizing behavior (high adsorption capacity, highly specific recognition, and rapid binding rate) coupled to the facile and environmentally friendly preparation procedure makes GO-APBA/MIPs promising in the recognition, separation, and analysis of glycoproteins in clinics in the future.

  5. Structure of the ectodomain of Drosophila peptidoglycan-recognition protein LCa suggests a molecular mechanism for pattern recognition.

    PubMed

    Chang, Chung-I; Ihara, Kentaro; Chelliah, Yogarany; Mengin-Lecreulx, Dominique; Wakatsuki, Soichi; Deisenhofer, Johann

    2005-07-19

    The peptidoglycan-recognition protein LCa (PGRP-LCa) is a transmembrane receptor required for activation of the Drosophila immune deficiency pathway by monomeric Gram-negative peptidoglycan. We have determined the crystal structure of the ectodomain of PGRP-LCa at 2.5-A resolution and found two unique helical insertions in the LCa ectodomain that disrupt an otherwise L-shaped peptidoglycan-docking groove present in all other known PGRP structures. The deficient binding of PGRP-LCa to monomeric peptidoglycan was confirmed by biochemical pull-down assays. Recognition of monomeric peptidoglycan involves both PGRP-LCa and -LCx. We showed that association of the LCa and LCx ectodomains in vitro depends on monomeric peptidoglycan. The presence of a defective peptidoglycan-docking groove, while preserving a unique role in mediating monomeric peptidoglycan induction of immune response, suggests that PGRP-LCa recognizes the exposed structural features of a monomeric muropeptide when the latter is bound to and presented by the ectodomain of PGRP-LCx. Such features include N-acetyl glucosamine and the anhydro bond in the glycan of the muropeptide, which have been demonstrated to be critical for immune stimulatory activity.

  6. Structure of the ectodomain of Drosophila peptidoglycan-recognition protein LCa suggests a molecular mechanism for pattern recognition

    PubMed Central

    Chang, Chung-I; Ihara, Kentaro; Chelliah, Yogarany; Mengin-Lecreulx, Dominique; Wakatsuki, Soichi; Deisenhofer, Johann

    2005-01-01

    The peptidoglycan-recognition protein LCa (PGRP-LCa) is a transmembrane receptor required for activation of the Drosophila immune deficiency pathway by monomeric Gram-negative peptidoglycan. We have determined the crystal structure of the ectodomain of PGRP-LCa at 2.5-Å resolution and found two unique helical insertions in the LCa ectodomain that disrupt an otherwise L-shaped peptidoglycan-docking groove present in all other known PGRP structures. The deficient binding of PGRP-LCa to monomeric peptidoglycan was confirmed by biochemical pull-down assays. Recognition of monomeric peptidoglycan involves both PGRP-LCa and -LCx. We showed that association of the LCa and LCx ectodomains in vitro depends on monomeric peptidoglycan. The presence of a defective peptidoglycan-docking groove, while preserving a unique role in mediating monomeric peptidoglycan induction of immune response, suggests that PGRP-LCa recognizes the exposed structural features of a monomeric muropeptide when the latter is bound to and presented by the ectodomain of PGRP-LCx. Such features include N-acetyl glucosamine and the anhydro bond in the glycan of the muropeptide, which have been demonstrated to be critical for immune stimulatory activity. PMID:16006509

  7. Molecular dynamics of β-hairpin models of epigenetic recognition motifs.

    PubMed

    Zheng, Xiange; Wu, Chuanjie; Ponder, Jay W; Marshall, Garland R

    2012-09-26

    The conformations and stabilities of the β-hairpin model peptides of Waters (Riemen, A. J.; Waters, M. L. Biochemistry 2009, 48, 1525; Hughes, R. M.; Benshoff, M. L.; Waters, M. L. Chemistry 2007, 13, 5753) have been experimentally characterized as a function of lysine ε-methylation. These models were developed to explore molecular recognition of known epigenetic recognition motifs. This system offered an opportunity to computationally examine the role of cation-π interactions, desolvation of the ε-methylated ammonium groups, and aromatic/aromatic interactions on the observed differences in NMR spectra. AMOEBA, a second-generation force field (Ponder, J. W.; Wu, C.; Ren, P.; Pande, V. S.; Chodera, J. D.; Schnieders, M. J.; Haque, I.; Mobley, D. L.; Lambrecht, D. S.; DiStasio, R. A., Jr.; Head-Gordon, M.; Clark, G. N.; Johnson, M. E.; Head-Gordon, T. J. Phys. Chem. B 2010, 114, 2549), was chosen as it includes both multipole electrostatics and polarizability thought to be essential to accurately characterize such interactions. Independent parametrization of ε-methylated amines was required from which aqueous solvation free energies were estimated and shown to agree with literature values. Molecular dynamics simulations (100 ns) using the derived parameters with model peptides, such as Ac-R-W-V-W-V-N-G-Orn-K(Me)(n)-I-L-Q-NH(2), where n = 0, 1, 2, or 3, were conducted in explicit solvent. Distances between the centers of the indole rings of the two-tryptophan residues, 2 and 4, and the ε-methylated ammonium group on Lys-9 as well as the distance between the N- and C-termini were monitored to estimate the strength and orientation of the cation-π and aromatic/aromatic interactions. In agreement with the experimental data, the stability of the β-hairpin increased significantly with lysine ε-methylation. The ability of MD simulations to reproduce the observed NOEs for the four peptides was further estimated for the monopole-based force fields, AMBER, CHARMM, and

  8. Molecular Recognition of Methyl α-d-Mannopyranoside by Antifreeze (Glyco)Proteins

    PubMed Central

    2015-01-01

    Antifreeze proteins and glycoproteins [AF(G)Ps] have been well-known for more than three decades for their ability to inhibit the growth and recrystallization of ice through binding to specific ice crystal faces, and they show remarkable structural compatibility with specific ice crystal faces. Here, we show that the crystal growth faces of methyl α-d-mannopyranoside (MDM), a representative pyranose sugar, also show noteworthy structural compatibility with the known periodicities of AF(G)Ps. We selected fish AFGPs (AFGP8, AFGP1–5), and a beetle AFP (DAFP1) with increasing antifreeze activity as potential additives for controlling MDM crystal growth. Similar to their effects on ice growth, the AF(G)Ps can inhibit MDM crystal growth and recrystallization, and more significantly, the effectiveness for the AF(G)Ps are well correlated with their antifreeze activity. MDM crystals grown in the presence of AF(G)Ps are smaller and have better defined shapes and are of higher quality as indicated by single crystal X-ray diffraction and polarized microscopy than control crystals, but no new polymorphs of MDM were identified by single crystal X-ray diffraction, solid-state NMR, and attenuated total reflectance infrared spectroscopy. The observed changes in the average sizes of the MDM crystals can be related to the changes in the number of the MDM nuclei in the presence of the AF(G)Ps. The critical free energy change differences of the MDM nucleation in the absence and presence of the additives were calculated. These values are close to those of the ice nucleation in the presence of AF(G)Ps suggesting similar interactions are involved in the molecular recognition of MDM by the AF(G)Ps. To our knowledge this is the first report where AF(G)Ps have been used to control crystal growth of carbohydrates and on AFGPs controlling non-ice-like crystals. Our finding suggests MDM might be a possible alternative to ice for studying the detailed mechanism of AF

  9. Deciphering the molecular basis of multidrug recognition: crystal structures of the Staphylococcus aureus multidrug binding transcription regulator QacR.

    PubMed

    Schumacher, Maria A; Brennan, Richard G

    2003-03-01

    Multidrug transporters and their transcriptional regulators are key components of bacterial multidrug resistance (MDR). How these multidrug binding proteins can recognize such chemically disparate compounds represents a fascinating question from a structural standpoint and an important question in future drug development efforts. The Staphylococcus aureus multidrug binding regulator, QacR, is soluble and recognizes an especially wide range of structurally dissimilar compounds, properties making it an ideal model system for deciphering the molecular basis of multidrug recognition. Recent structures of QacR have afforded the first view of any MDR protein bound to multiple drugs, revealing key structural features of multidrug recognition, including a multisite binding pocket.

  10. Genetic and molecular requirements for function of the Pto/Prf effector recognition complex in tomato and Nicotiana benthamiana.

    PubMed

    Balmuth, Alexi; Rathjen, John P

    2007-09-01

    The Pto gene of tomato (Solanum lycopersicum) confers specific recognition of the unrelated bacterial effector proteins AvrPto and AvrPtoB. Pto resides in a constitutive molecular complex with the nucleotide binding site-leucine rich repeats protein Prf. Prf is absolutely required for specific recognition of both effectors. Here, using stable transgenic lines, we show that expression of Pto from its genomic promoter in susceptible tomatoes was sufficient to complement recognition of Pseudomonas syringae pv. tomato (Pst) bacteria expressing either avrPto or avrPtoB. Pto kinase activity was absolutely required for specific immunity. Expression of the Pto N-myristoylation mutant, pto(G2A), conferred recognition of Pst (avrPtoB), but not Pst (avrPto), although bacterial growth in these lines was intermediate between resistant and susceptible lines. Overexpression of pto(G2A) complemented recognition of avrPto. Transgenic tomato plants overexpressing wild-type Pto exhibited constitutive growth phenotypes, but these were absent in lines overexpressing pto(G2A). Therefore, Pto myristoylation is a quantitative factor for effector recognition in tomato, but is absolutely required for overexpression phenotypes. Native expression of Pto in the heterologous species Nicotiana benthamiana did not confer resistance to P. syringae pv. tabaci (Pta) expressing avrPto or avrPtoB, but recognition of both effectors was complemented by Prf co-expression. Thus, specific resistance conferred solely by Pto in N. benthamiana is an artefact of overexpression. Finally, pto(G2A) did not confer recognition of either avrPto or avrPtoB in N. benthamiana, regardless of the presence of Prf. Thus, co-expression of Prf in N. benthamiana complements many but not all aspects of normal Pto function.

  11. Uniformly sized molecularly imprinted polymer for d-chlorpheniramine. Evaluation of retention and molecular recognition properties in an aqueous mobile phase.

    PubMed

    Haginaka, Jun; Kagawa, Chino

    2002-03-01

    A uniformly sized molecularly imprinted polymer (MIP) for d-chlorpheniramine has been prepared by a multi-step swelling and polymerization method using methacrylic acid and ethylene glycol dimethacrylate as a functional monomer and cross-linker, respectively. The retentive and enantioselective properties of chlorpheniramine and its structurally related compounds on the MIP were evaluated using an aqueous mobile phase. Electrostatic and hydrophobic interactions could mainly work for the retention and enantioseparation of chlorpheniramine in aqueous mobile phase. Further, the MIP showed the highest recognition for chlorpheniramine and slight recognition for its structurally related compounds, and enantioseparation of pheniramine was attained.

  12. Tailoring molecularly imprinted polymer beads for alternariol recognition and analysis by a screening with mycotoxin surrogates.

    PubMed

    Abou-Hany, Rahma A G; Urraca, Javier L; Descalzo, Ana B; Gómez-Arribas, Lidia N; Moreno-Bondi, María C; Orellana, Guillermo

    2015-12-18

    Molecularly imprinted porous polymer microspheres have been prepared for selective binding of alternariol (AOH), a phenolic mycotoxin produced by Alternaria fungi. In order to lead the synthesis of recognition materials, four original AOH surrogates have been designed, prepared and characterized. They bear different number of phenol groups in various positions and different degree of O-methylation on the dibenzo[b,d]pyran-6-one skeleton. A comprehensive library of mixtures of basic, acidic or neutral monomers, with divinylbenzene or ethyleneglycol dimethacrylate as cross-linkers, were polymerized at a small scale in the presence of the four molecular mimics of the toxin molecule. This polymer screening has allowed selection of the optimal composition of the microbeads (N-(2-aminoethyl)methacrylamide, EAMA, and ethylene glycol dimethacrylate). The latter are able to bind AOH in water-acetonitrile (80:20, v/v) with an affinity constant of 109±10mM(-1) and a total number of binding sites of 35±2μmolg(-1), being alternariol monomethylether the only competitor species. Moreover, (1)H NMR titrations have unveiled a 1:2 surrogate-to-EAMA stoichiometry, the exact interaction sites and a binding constant of 1.5×10(4)M(-2). A molecularly imprinted solid phase extraction (MISPE) method has been optimized for selective isolation of the mycotoxin from aqueous samples upon a discriminating wash with 3mL of acetonitrile/water (20:80, v/v) followed by determination by HPLC with fluorescence detection. The method has been applied, in combination to ultrasound-assisted extraction, to the analysis of AOH in tomato samples fortified with the mycotoxin at five concentration levels (33-110μgkg(-1)), with recoveries in the range of 81-103% (RSD n=6). To the best of our knowledge, this is the first imprinted material capable of molecularly recognizing this widespread food contaminant. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Molecular recognition of DNA by ligands: Roughness and complexity of the free energy profile

    NASA Astrophysics Data System (ADS)

    Zheng, Wenwei; Vargiu, Attilio Vittorio; Rohrdanz, Mary A.; Carloni, Paolo; Clementi, Cecilia

    2013-10-01

    Understanding the molecular mechanism by which probes and chemotherapeutic agents bind to nucleic acids is a fundamental issue in modern drug design. From a computational perspective, valuable insights are gained by the estimation of free energy landscapes as a function of some collective variables (CVs), which are associated with the molecular recognition event. Unfortunately the choice of CVs is highly non-trivial because of DNA's high flexibility and the presence of multiple association-dissociation events at different locations and/or sliding within the grooves. Here we have applied a modified version of Locally-Scaled Diffusion Map (LSDMap), a nonlinear dimensionality reduction technique for decoupling multiple-timescale dynamics in macromolecular systems, to a metadynamics-based free energy landscape calculated using a set of intuitive CVs. We investigated the binding of the organic drug anthramycin to a DNA 14-mer duplex. By performing an extensive set of metadynamics simulations, we observed sliding of anthramycin along the full-length DNA minor groove, as well as several detachments from multiple sites, including the one identified by X-ray crystallography. As in the case of equilibrium processes, the LSDMap analysis is able to extract the most relevant collective motions, which are associated with the slow processes within the system, i.e., ligand diffusion along the minor groove and dissociation from it. Thus, LSDMap in combination with metadynamics (and possibly every equivalent method) emerges as a powerful method to describe the energetics of ligand binding to DNA without resorting to intuitive ad hoc reaction coordinates.

  14. Conformational Melding Permits a Conserved Binding Geometry in TCR Recognition of Foreign and Self Molecular Mimics

    SciTech Connect

    Borbulevych, Oleg Y.; Piepenbrink, Kurt H.; Baker, Brian M.

    2012-03-16

    Molecular mimicry between foreign and self Ags is a mechanism of TCR cross-reactivity and is thought to contribute to the development of autoimmunity. The {alpha}{beta} TCR A6 recognizes the foreign Ag Tax from the human T cell leukemia virus-1 when presented by the class I MHC HLA-A2. In a possible link with the autoimmune disease human T cell leukemia virus-1-associated myelopathy/tropical spastic paraparesis, A6 also recognizes a self peptide from the neuronal protein HuD in the context of HLA-A2. We found in our study that the complexes of the HuD and Tax epitopes with HLA-A2 are close but imperfect structural mimics and that in contrast with other recent structures of TCRs with self Ags, A6 engages the HuD Ag with the same traditional binding mode used to engage Tax. Although peptide and MHC conformational changes are needed for recognition of HuD but not Tax and the difference of a single hydroxyl triggers an altered TCR loop conformation, TCR affinity toward HuD is still within the range believed to result in negative selection. Probing further, we found that the HuD-HLA-A2 complex is only weakly stable. Overall, these findings help clarify how molecular mimicry can drive self/nonself cross-reactivity and illustrate how low peptide-MHC stability can permit the survival of T cells expressing self-reactive TCRs that nonetheless bind with a traditional binding mode.

  15. Molecular insights into the recognition of N-terminal histone modifications by the BRPF1 bromodomain

    PubMed Central

    Poplawski, Amanda; Hu, Kaifeng; Lee, Woonghee; Natesan, Senthil; Peng, Danni; Carlson, Samuel; Shi, Xiaobing; Balaz, Stefan; Markley, John L.; Glass, Karen C.

    2014-01-01

    The monocytic leukemic zinc-finger (MOZ) histone acetyltransferase (HAT) acetylates free histones H3, H4, H2A, and H2B in vitro and is associated with up-regulation of gene transcription. The MOZ HAT functions as a quaternary complex with the bromodomain-PHD finger protein 1 (BRPF1), inhibitor of growth 5 (ING5), and hEaf6 subunits. BRPF1 links the MOZ catalytic subunit to the ING5 and hEaf6 subunits, thereby promoting MOZ HAT activity. Human BRPF1 contains multiple effector domains with known roles in gene transcription, and chromatin binding and remodeling. However, the biological function of the BRPF1 bromodomain remains unknown. Our findings reveal novel interactions of the BRPF1 bromodomain with multiple acetyllysine residues on the N-terminus of histones, and show it preferentially selects for H2AK5ac, H4K12ac and H3K14ac. We used chemical shift perturbation data from NMR titration experiments to map the BRPF1 bromodomain ligand binding pocket and identified key residues responsible for coordination of the post-translationally modified histones. Extensive molecular dynamics simulations were used to generate structural models of bromodomain-histone ligand complexes, to analyze H-bonding and other interactions, and to calculate the binding free energies. Our results outline the molecular mechanism driving binding specificity of the BRPF1 bromodomain for discrete acetyllysine residues on the N-terminal histone tails. Together these data provide insights on how histone recognition by the bromodomain directs the biological function of BRPF1, ultimately targeting the MOZ HAT complex to chromatin substrates. PMID:24333487

  16. Synthesis and computational investigation of molecularly imprinted nanospheres for selective recognition of alpha-tocopherol succinate

    PubMed Central

    Piacham, Theeraphon; Nantasenamat, Chanin; Isarankura-Na-Ayudhya, Chartchalerm; Prachayasittikul, Virapong

    2013-01-01

    Molecularly imprinted polymers (MIPs) are macromolecular matrices that can mimic the functional properties of antibodies, receptors and enzymes while possessing higher durability. As such, these polymers are interesting materials for applications in biomimetic sensor, drug synthesis, drug delivery and separation. In this study, we prepared MIPs and molecularly imprinted nanospheres (MINs) as receptors with specific recognition properties toward tocopherol succinate (TPS) in comparison to tocopherol (TP) and tocopherol nicotinate (TPN). MIPs were synthesized using methacrylic acid (MAA) as functional monomer, ethylene glycol dimethacrylate (EGDMA) as crosslinking agent and dichloromethane or acetronitrile as porogenic solvent under thermal-induced polymerization condition. Results indicated that imprinted polymers of TPS-MIP, TP-MIP and TPN-MIP all bound specifically to their template molecules at 2 folds greater than the non-imprinted polymers. The calculated binding capacity of all MIP was approximately 2 mg per gram of polymer when using the optimal rebinding solvent EtOH:H2O (3:2, v/v). Furthermore, the MINs toward TPS and TP were prepared by precipitation polymerization that yielded particles that are 200-400 nm in size. The binding capacities of MINs to their templates were greater than that of the non-imprinted nanospheres when using the optimal rebinding solvent EtOH:H2O (4:1, v/v). Computer simulation was performed to provide mechanistic insights on the binding modalities of template-monomer complexes. In conclusion, we had successful prepared MIPs and MINs for binding specifically to TP and TPS. Such MIPs and MINs have great potential for industrial and medical applications, particularly for the selective separation of TP and TPS. PMID:26622214

  17. Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile.

    PubMed

    Zheng, Wenwei; Vargiu, Attilio Vittorio; Vargiu, Attlio Vittorio; Rohrdanz, Mary A; Carloni, Paolo; Clementi, Cecilia

    2013-10-14

    Understanding the molecular mechanism by which probes and chemotherapeutic agents bind to nucleic acids is a fundamental issue in modern drug design. From a computational perspective, valuable insights are gained by the estimation of free energy landscapes as a function of some collective variables (CVs), which are associated with the molecular recognition event. Unfortunately the choice of CVs is highly non-trivial because of DNA's high flexibility and the presence of multiple association-dissociation events at different locations and/or sliding within the grooves. Here we have applied a modified version of Locally-Scaled Diffusion Map (LSDMap), a nonlinear dimensionality reduction technique for decoupling multiple-timescale dynamics in macromolecular systems, to a metadynamics-based free energy landscape calculated using a set of intuitive CVs. We investigated the binding of the organic drug anthramycin to a DNA 14-mer duplex. By performing an extensive set of metadynamics simulations, we observed sliding of anthramycin along the full-length DNA minor groove, as well as several detachments from multiple sites, including the one identified by X-ray crystallography. As in the case of equilibrium processes, the LSDMap analysis is able to extract the most relevant collective motions, which are associated with the slow processes within the system, i.e., ligand diffusion along the minor groove and dissociation from it. Thus, LSDMap in combination with metadynamics (and possibly every equivalent method) emerges as a powerful method to describe the energetics of ligand binding to DNA without resorting to intuitive ad hoc reaction coordinates.

  18. Synthesis and computational investigation of molecularly imprinted nanospheres for selective recognition of alpha-tocopherol succinate.

    PubMed

    Piacham, Theeraphon; Nantasenamat, Chanin; Isarankura-Na-Ayudhya, Chartchalerm; Prachayasittikul, Virapong

    2013-01-01

    Molecularly imprinted polymers (MIPs) are macromolecular matrices that can mimic the functional properties of antibodies, receptors and enzymes while possessing higher durability. As such, these polymers are interesting materials for applications in biomimetic sensor, drug synthesis, drug delivery and separation. In this study, we prepared MIPs and molecularly imprinted nanospheres (MINs) as receptors with specific recognition properties toward tocopherol succinate (TPS) in comparison to tocopherol (TP) and tocopherol nicotinate (TPN). MIPs were synthesized using methacrylic acid (MAA) as functional monomer, ethylene glycol dimethacrylate (EGDMA) as crosslinking agent and dichloromethane or acetronitrile as porogenic solvent under thermal-induced polymerization condition. Results indicated that imprinted polymers of TPS-MIP, TP-MIP and TPN-MIP all bound specifically to their template molecules at 2 folds greater than the non-imprinted polymers. The calculated binding capacity of all MIP was approximately 2 mg per gram of polymer when using the optimal rebinding solvent EtOH:H2O (3:2, v/v). Furthermore, the MINs toward TPS and TP were prepared by precipitation polymerization that yielded particles that are 200-400 nm in size. The binding capacities of MINs to their templates were greater than that of the non-imprinted nanospheres when using the optimal rebinding solvent EtOH:H2O (4:1, v/v). Computer simulation was performed to provide mechanistic insights on the binding modalities of template-monomer complexes. In conclusion, we had successful prepared MIPs and MINs for binding specifically to TP and TPS. Such MIPs and MINs have great potential for industrial and medical applications, particularly for the selective separation of TP and TPS.

  19. On the energy components governing molecular recognition in the framework of continuum approaches.

    PubMed

    Li, Lin; Wang, Lin; Alexov, Emil

    2015-01-01

    Molecular recognition is a process that brings together several biological macromolecules to form a complex and one of the most important characteristics of the process is the binding free energy. Various approaches exist to model the binding free energy, provided the knowledge of the 3D structures of bound and unbound molecules. Among them, continuum approaches are quite appealing due to their computational efficiency while at the same time providing predictions with reasonable accuracy. Here we review recent developments in the field emphasizing on the importance of adopting adequate description of physical processes taking place upon the binding. In particular, we focus on the efforts aiming at capturing some of the atomistic details of the binding phenomena into the continuum framework. When possible, the energy components are reviewed independently of each other. However, it is pointed out that rigorous approaches should consider all energy contributions on the same footage. The two major schemes for utilizing the individual energy components to predict binding affinity are outlined as well.

  20. An improved microfluidics approach for monitoring real-time interaction profiles of ultrafast molecular recognition

    NASA Astrophysics Data System (ADS)

    Batabyal, Subrata; Rakshit, Surajit; Kar, Shantimoy; Pal, Samir Kumar

    2012-04-01

    Our study illustrates the development of a microfluidics (MF) platform combining fluorescence microscopy and femtosecond/picosecond-resolved spectroscopy to investigate ultrafast chemical processes in liquid-phase diffusion-controlled reactions. By controlling the flow rates of two reactants in a specially designed MF chip, sub-100 ns time resolution for the exploration of chemical intermediates of the reaction in the MF channel has been achieved. Our system clearly rules out the possibility of formation of any intermediate reaction product in a so-called fast ionic reaction between sodium hydroxide and phenolphthalein, and reveals a microsecond time scale associated with the formation of the reaction product. We have also used the developed system for the investigation of intermediate states in the molecular recognition of various macromolecular self-assemblies (micelles) and genomic DNA by small organic ligands (Hoechst 33258 and ethidium bromide). We propose our MF-based system to be an alternative to the existing millisecond-resolved "stopped-flow" technique for a broad range of time-resolved (sub-100 ns to minutes) experiments on complex chemical/biological systems.

  1. In Vitro Selection of a Single-Stranded DNA Molecular Recognition Element against Atrazine

    PubMed Central

    Williams, Ryan M.; Crihfield, Cassandra L.; Gattu, Srikanth; Holland, Lisa A.; Sooter, Letha J.

    2014-01-01

    Widespread use of the chlorotriazine herbicide, atrazine, has led to serious environmental and human health consequences. Current methods of detecting atrazine contamination are neither rapid nor cost-effective. In this work, atrazine-specific single-stranded DNA (ssDNA) molecular recognition elements (MRE) were isolated. We utilized a stringent Systematic Evolution of Ligands by Exponential Enrichment (SELEX) methodology that placed the greatest emphasis on what the MRE should not bind to. After twelve rounds of SELEX, an atrazine-specific MRE with high affinity was obtained. The equilibrium dissociation constant (Kd) of the ssDNA sequence is 0.62 ± 0.21 nM. It also has significant selectivity for atrazine over atrazine metabolites and other pesticides found in environmentally similar locations and concentrations. Furthermore, we have detected environmentally relevant atrazine concentrations in river water using this MRE. The strong affinity and selectivity of the selected atrazine-specific ssDNA validated the stringent SELEX methodology and identified a MRE that will be useful for rapid atrazine detection in environmental samples. PMID:25196435

  2. Molecular Recognition of Corticotropin releasing Factor by Its G protein-coupled Receptor CRFR1

    SciTech Connect

    Pioszak, Augen A.; Parker, Naomi R.; Suino-Powell, Kelly; Xu, H. Eric

    2009-01-15

    The bimolecular interaction between corticotropin-releasing factor (CRF), a neuropeptide, and its type 1 receptor (CRFR1), a class B G-protein-coupled receptor (GPCR), is crucial for activation of the hypothalamic-pituitary-adrenal axis in response to stress, and has been a target of intense drug design for the treatment of anxiety, depression, and related disorders. As a class B GPCR, CRFR1 contains an N-terminal extracellular domain (ECD) that provides the primary ligand binding determinants. Here we present three crystal structures of the human CRFR1 ECD, one in a ligand-free form and two in distinct CRF-bound states. The CRFR1 ECD adopts the alpha-beta-betaalpha fold observed for other class B GPCR ECDs, but the N-terminal alpha-helix is significantly shorter and does not contact CRF. CRF adopts a continuous alpha-helix that docks in a hydrophobic surface of the ECD that is distinct from the peptide-binding site of other class B GPCRs, thereby providing a basis for the specificity of ligand recognition between CRFR1 and other class B GPCRs. The binding of CRF is accompanied by clamp-like conformational changes of two loops of the receptor that anchor the CRF C terminus, including the C-terminal amide group. These structural studies provide a molecular framework for understanding peptide binding and specificity by the CRF receptors as well as a template for designing potent and selective CRFR1 antagonists for therapeutic applications.

  3. Molecular recognition by van der Waals interaction between polymers with sequence-specific polarizabilities

    NASA Astrophysics Data System (ADS)

    Lu, Bing-Sui; Naji, Ali; Podgornik, Rudolf

    2015-06-01

    We analyze van der Waals interactions between two rigid polymers with sequence-specific, anisotropic polarizabilities along the polymer backbones, so that the dipole moments fluctuate parallel to the polymer backbones. Assuming that each polymer has a quenched-in polarizability sequence which reflects, for example, the polynucleotide sequence of a double-stranded DNA molecule, we study the van der Waals interaction energy between a pair of such polymers with rod-like structure for the cases where their respective polarizability sequences are (i) distinct and (ii) identical, with both zero and non-zero correlation length of the polarizability correlator along the polymer backbones in the latter case. For identical polymers, we find a novel r-5 scaling behavior of the van der Waals interaction energy for small inter-polymer separation r, in contradistinction to the r-4 scaling behavior of distinct polymers, with furthermore a pronounced angular dependence favoring attraction between sufficiently aligned identical polymers. Such behavior can assist the molecular recognition between polymers.

  4. New biosourced chiral molecularly imprinted polymer: Synthesis, characterization, and evaluation of the recognition capacity of methyltestosterone.

    PubMed

    Saadaoui, Asma; Sanglar, Corinne; Medimagh, Raouf; Bonhomme, Anne; Baudot, Robert; Chatti, Saber; Marque, Sylvain; Prim, Damien; Zina, Mongia Saïd; Casabianca, Herve

    2017-04-01

    New biosourced chiral cross-linkers were reported for the first time in the synthesis of methyltestosterone (MT) chiral molecularly imprinted polymers (cMIPs). Isosorbide and isomannide, known as 1,4:3,6-dianhydrohexitols, were selected as starting diols. The cMIPs were synthesized following a noncovalent approach via thermal radical polymerization and monitored by Raman spectroscopy. These cross-linkers were fully characterized by (1) H and (13) C nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry. The cross-polarization magic angle spinning (13) C NMR, Fourier transform infrared spectroscopy, scanning electron microscopy, and specific surface areas following the Brunauer-Emmett-Teller (BET) method were used to characterize the cMIPs. The effect of stereochemistry of cross-linkers on the reactivity of polymerization, morphology, and adsorption-recognition properties of the MIP was evaluated. The results showed that the cMIP exhibited an obvious improvement in terms of rebinding capacity for MT as compared with the nonimprinted polymer (NIP). The highest binding capacity was observed for cMIP-Is (27.298 mg g(-1) ) for high concentrations (500 mg L(-1) ). However, the isomannide homologue cMIP-Im showed higher recovery-up to 65% and capacity for low concentrations (15 mg L(-1) ). The experimental data were properly fitted by the Freundlich adsorption isothermal model.

  5. Molecular Mechanisms of Taste Recognition: Considerations about the Role of Saliva

    PubMed Central

    Fábián, Tibor Károly; Beck, Anita; Fejérdy, Pál; Hermann, Péter; Fábián, Gábor

    2015-01-01

    The gustatory system plays a critical role in determining food preferences and food intake, in addition to nutritive, energy and electrolyte balance. Fine tuning of the gustatory system is also crucial in this respect. The exact mechanisms that fine tune taste sensitivity are as of yet poorly defined, but it is clear that various effects of saliva on taste recognition are also involved. Specifically those metabolic polypeptides present in the saliva that were classically considered to be gut and appetite hormones (i.e., leptin, ghrelin, insulin, neuropeptide Y, peptide YY) were considered to play a pivotal role. Besides these, data clearly indicate the major role of several other salivary proteins, such as salivary carbonic anhydrase (gustin), proline-rich proteins, cystatins, alpha-amylases, histatins, salivary albumin and mucins. Other proteins like glucagon-like peptide-1, salivary immunoglobulin-A, zinc-α-2-glycoprotein, salivary lactoperoxidase, salivary prolactin-inducible protein and salivary molecular chaperone HSP70/HSPAs were also expected to play an important role. Furthermore, factors including salivary flow rate, buffer capacity and ionic composition of saliva should also be considered. In this paper, the current state of research related to the above and the overall emerging field of taste-related salivary research alongside basic principles of taste perception is reviewed. PMID:25782158

  6. Boronate affinity materials for separation and molecular recognition: structure, properties and applications.

    PubMed

    Li, Daojin; Chen, Yang; Liu, Zhen

    2015-11-21

    Boronate affinity materials, as unique sorbents, have emerged as important media for the selective separation and molecular recognition of cis-diol-containing compounds. With the introduction of boronic acid functionality, boronate affinity materials exhibit several significant advantages, including broad-spectrum selectivity, reversible covalent binding, pH-controlled capture/release, fast association/desorption kinetics, and good compatibility with mass spectrometry. Because cis-diol-containing biomolecules, including nucleosides, saccharides, glycans, glycoproteins and so on, are the important targets in current research frontiers such as metabolomics, glycomics and proteomics, boronate affinity materials have gained rapid development and found increasing applications in the last decade. In this review, we critically survey recent advances in boronate affinity materials. We focus on fundamental considerations as well as important progress and new boronate affinity materials reported in the last decade. We particularly discuss on the effects of the structure of boronate ligands and supporting materials on the properties of boronate affinity materials, such as binding pH, affinity, selectivity, binding capacity, tolerance for interference and so on. A variety of promising applications, including affinity separation, proteomics, metabolomics, disease diagnostics and aptamer selection, are introduced with main emphasis on how boronate affinity materials can solve the issues in the applications and what merits boronate affinity materials can provide.

  7. Thiol-functionalized polymeric micelles: from molecular recognition to improved mucoadhesion.

    PubMed

    Dufresne, Marie-Hélène; Gauthier, Marc A; Leroux, Jean-Christophe

    2005-01-01

    Surface-modified colloids which can selectively interact with biological species or surfaces show promise as drug delivery systems. However, the preparation of such targeted devices remains challenging, especially when considering polyion complex micelles for which side reactions with the ionic core components (typically carboxylic acid or amino groups) can occur. To solve this issue, an innovative synthetic strategy is proposed and used to prepare an asymmetric poly(ethylene glycol)-block-poly(2-(N,N-dimethylamino)ethyl methacrylate) copolymer presenting a thiol group at the end of the poly(ethylene glycol) chain. Thiol groups are highly appealing given that they react almost exclusively and quantitatively with maleimides under physiological conditions, thereby facilitating the chemical functionalization of the copolymer. The simplicity of the derivatization procedure is illustrated by preparing model biotin-capped copolymers. The biotinylated copolymers are shown to self-assemble with an oligonucleotide in aqueous media to form polyion complex micelles with biotin groups at their outer surface. These micelles are capable of molecular recognition toward streptavidin. Alternatively, thiol-decorated (nonderivatized) micelles are prepared and show improved mucoadhesion through the formation of disulfide bonds with mucin. Finally, intermicellar disulfide bonds are generated under oxidative conditions to promote the formation of stimuli-responsive micellar networks.

  8. Mechanistic basis for the recognition of a misfolded protein by the molecular chaperone Hsp90.

    PubMed

    Oroz, Javier; Kim, Jin Hae; Chang, Bliss J; Zweckstetter, Markus

    2017-04-01

    The critical toxic species in over 40 human diseases are misfolded proteins. Their interaction with molecular chaperones such as Hsp90, which preferentially interacts with metastable proteins, is essential for the blocking of disease progression. Here we used nuclear magnetic resonance (NMR) spectroscopy to determine the three-dimensional structure of the misfolded cytotoxic monomer of the amyloidogenic human protein transthyretin, which is characterized by the release of the C-terminal β-strand and perturbations of the A-B loop. The misfolded transthyretin monomer, but not the wild-type protein, binds to human Hsp90. In the bound state, the Hsp90 dimer predominantly populates an open conformation, and transthyretin retains its globular structure. The interaction surface for the transthyretin monomer comprises the N-terminal and middle domains of Hsp90 and overlaps with that of the Alzheimer's-disease-related protein tau. Taken together, the data suggest that Hsp90 uses a mechanism for the recognition of aggregation-prone proteins that is largely distinct from those of other Hsp90 clients.

  9. Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases.

    PubMed

    Redondo, Pilar; Prieto, Jesús; Muñoz, Inés G; Alibés, Andreu; Stricher, Francois; Serrano, Luis; Cabaniols, Jean-Pierre; Daboussi, Fayza; Arnould, Sylvain; Perez, Christophe; Duchateau, Philippe; Pâques, Frédéric; Blanco, Francisco J; Montoya, Guillermo

    2008-11-06

    Xeroderma pigmentosum is a monogenic disease characterized by hypersensitivity to ultraviolet light. The cells of xeroderma pigmentosum patients are defective in nucleotide excision repair, limiting their capacity to eliminate ultraviolet-induced DNA damage, and resulting in a strong predisposition to develop skin cancers. The use of rare cutting DNA endonucleases-such as homing endonucleases, also known as meganucleases-constitutes one possible strategy for repairing DNA lesions. Homing endonucleases have emerged as highly specific molecular scalpels that recognize and cleave DNA sites, promoting efficient homologous gene targeting through double-strand-break-induced homologous recombination. Here we describe two engineered heterodimeric derivatives of the homing endonuclease I-CreI, produced by a semi-rational approach. These two molecules-Amel3-Amel4 and Ini3-Ini4-cleave DNA from the human XPC gene (xeroderma pigmentosum group C), in vitro and in vivo. Crystal structures of the I-CreI variants complexed with intact and cleaved XPC target DNA suggest that the mechanism of DNA recognition and cleavage by the engineered homing endonucleases is similar to that of the wild-type I-CreI. Furthermore, these derivatives induced high levels of specific gene targeting in mammalian cells while displaying no obvious genotoxicity. Thus, homing endonucleases can be designed to recognize and cleave the DNA sequences of specific genes, opening up new possibilities for genome engineering and gene therapy in xeroderma pigmentosum patients whose illness can be treated ex vivo.

  10. Recombinase-based isothermal amplification of nucleic acids with self-avoiding molecular recognition systems (SAMRS).

    PubMed

    Sharma, Nidhi; Hoshika, Shuichi; Hutter, Daniel; Bradley, Kevin M; Benner, Steven A

    2014-10-13

    Recombinase polymerase amplification (RPA) is an isothermal method to amplify nucleic acid sequences without the temperature cycling that classical PCR uses. Instead of using heat to denature the DNA duplex, RPA uses recombination enzymes to swap single-stranded primers into the duplex DNA product; these are then extended using a strand-displacing polymerase to complete the cycle. Because RPA runs at low temperatures, it never forces the system to recreate base-pairs following Watson-Crick rules, and therefore it produces undesired products that impede the amplification of the desired product, complicating downstream analysis. Herein, we show that most of these undesired side products can be avoided if the primers contain components of a self-avoiding molecular recognition system (SAMRS). Given the precision that is necessary in the recombination systems for them to function biologically, it is surprising that they accept SAMRS. SAMRS-RPA is expected to be a powerful tool within the range of amplification techniques available to scientists.

  11. Leukemia-Associated Mutations in Nucleophosmin Alter Recognition by CRM1: Molecular Basis of Aberrant Transport

    PubMed Central

    Arregi, Igor; Falces, Jorge; Olazabal-Herrero, Anne; Alonso-Mariño, Marián; Taneva, Stefka G.; Rodríguez, José A.; Urbaneja, María A.; Bañuelos, Sonia

    2015-01-01

    Nucleophosmin (NPM) is a nucleocytoplasmic shuttling protein, normally enriched in nucleoli, that performs several activities related to cell growth. NPM mutations are characteristic of a subtype of acute myeloid leukemia (AML), where mutant NPM seems to play an oncogenic role. AML-associated NPM mutants exhibit altered subcellular traffic, being aberrantly located in the cytoplasm of leukoblasts. Exacerbated export of AML variants of NPM is mediated by the nuclear export receptor CRM1, and due, in part, to a mutationally acquired novel nuclear export signal (NES). To gain insight on the molecular basis of NPM transport in physiological and pathological conditions, we have evaluated the export efficiency of NPM in cells, and present new data indicating that, in normal conditions, wild type NPM is weakly exported by CRM1. On the other hand, we have found that AML-associated NPM mutants efficiently form complexes with CRM1HA (a mutant CRM1 with higher affinity for NESs), and we have quantitatively analyzed CRM1HA interaction with the NES motifs of these mutants, using fluorescence anisotropy and isothermal titration calorimetry. We have observed that the affinity of CRM1HA for these NESs is similar, which may help to explain the transport properties of the mutants. We also describe NPM recognition by the import machinery. Our combined cellular and biophysical studies shed further light on the determinants of NPM traffic, and how it is dramatically altered by AML-related mutations. PMID:26091065

  12. Molecular recognition by van der Waals interaction between polymers with sequence-specific polarizabilities.

    PubMed

    Lu, Bing-Sui; Naji, Ali; Podgornik, Rudolf

    2015-06-07

    We analyze van der Waals interactions between two rigid polymers with sequence-specific, anisotropic polarizabilities along the polymer backbones, so that the dipole moments fluctuate parallel to the polymer backbones. Assuming that each polymer has a quenched-in polarizability sequence which reflects, for example, the polynucleotide sequence of a double-stranded DNA molecule, we study the van der Waals interaction energy between a pair of such polymers with rod-like structure for the cases where their respective polarizability sequences are (i) distinct and (ii) identical, with both zero and non-zero correlation length of the polarizability correlator along the polymer backbones in the latter case. For identical polymers, we find a novel r(-5) scaling behavior of the van der Waals interaction energy for small inter-polymer separation r, in contradistinction to the r(-4) scaling behavior of distinct polymers, with furthermore a pronounced angular dependence favoring attraction between sufficiently aligned identical polymers. Such behavior can assist the molecular recognition between polymers.

  13. Facile synthesis of polydopamine-coated molecularly imprinted silica nanoparticles for protein recognition and separation.

    PubMed

    Xia, Zhiwei; Lin, Zian; Xiao, Yun; Wang, Ling; Zheng, Jiangnan; Yang, Huanghao; Chen, Guonan

    2013-09-15

    Surface imprinting over nanostructured matrices is an effective solution to overcome template removal and achieve high binding capacity. In this work, a facile method was developed for synthesis of polydopamine-coated molecularly imprinted silica nanoparticles (PDA-coated MIP silica NPs) based on self-polymerization of dopamine (DA) on the surface of silica NPs in the presence of template protein. Transmission electronic microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR) and thermogravimetric analysis (TGA) showed that PDA layers were successfully attached on the surface of silica NPs and the corresponding thickness was about 5nm, which enabled the MIP silica NPs to have fast binding kinetics and high binding capacity. Under the aqueous media, the imprinted silica NPs showed much higher binding affinity toward template than non-imprinted (NIP) silica NPs. The protein recognition properties were examined by single-protein or competitive batch rebinding experiments and rebinding kinetics study, validating that the imprinted silica NPs have high selectivity for the template. The resultant BHb-MIP silica NPs could not only selectively separate BHb from the protein mixture, but also specifically deplete high-abundance BHb from cattle whole blood. In addition, the stability and regeneration were also investigated, which indicated that the imprinted silica NPs had excellent reusability. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. 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

  15. A metal–ion-responsive adhesive material via switching of molecular recognition properties

    PubMed Central

    Nakamura, Takashi; Takashima, Yoshinori; Hashidzume, Akihito; Yamaguchi, Hiroyasu; Harada, Akira

    2014-01-01

    Common adhesives stick to a wide range of materials immediately after they are applied to the surfaces. To prevent indiscriminate sticking, smart adhesive materials that adhere to a specific target surface only under particular conditions are desired. Here we report a polymer hydrogel modified with both β-cyclodextrin (βCD) and 2,2′-bipyridyl (bpy) moieties (βCD–bpy gel) as a functional adhesive material responding to metal ions as chemical stimuli. The adhesive property of βCD–bpy gel based on interfacial molecular recognition is expressed by complexation of metal ions to bpy that controlled dissociation of supramolecular cross-linking of βCD–bpy. Moreover, adhesion of βCD–bpy gel exhibits selectivity on the kinds of metal ions, depending on the efficiency of metal–bpy complexes in cross-linking. Transduction of two independent chemical signals (metal ions and host–guest interactions) is achieved in this adhesion system, which leads to the development of highly orthogonal macroscopic joining of multiple objects. PMID:25099995

  16. Molecular basis for the recognition of methylated adenines in RNA by the eukaryotic YTH domain

    PubMed Central

    Luo, Shukun; Tong, Liang

    2014-01-01

    Methylation of the N6 position of selected internal adenines (m6A) in mRNAs and noncoding RNAs is widespread in eukaryotes, and the YTH domain in a collection of proteins recognizes this modification. We report the crystal structure of the splicing factor YT521-B homology (YTH) domain of Zygosaccharomyces rouxii MRB1 in complex with a heptaribonucleotide with an m6A residue in the center. The m6A modification is recognized by an aromatic cage, being sandwiched between a Trp and Tyr residue and with the methyl group pointed toward another Trp residue. Mutations of YTH domain residues in the RNA binding site can abolish the formation of the complex, confirming the structural observations. These residues are conserved in the human YTH proteins that also bind m6A RNA, suggesting a conserved mode of recognition. Overall, our structural and biochemical studies have defined the molecular basis for how the YTH domain functions as a reader of methylated adenines. PMID:25201973

  17. Atomic interactions of neonicotinoid agonists with AChBP: Molecular recognition of the distinctive electronegative pharmacophore

    SciTech Connect

    Talley, Todd T.; Harel, Michal; Hibbs, Ryan E.; Radi, Zoran; Tomizawa, Motohiro; Casida, John E.; Taylor, Palmer

    2008-07-28

    Acetylcholine-binding proteins (AChBPs) from mollusks are suitable structural and functional surrogates of the nicotinic acetylcholine receptors when combined with transmembrane spans of the nicotinic receptor. These proteins assemble as a pentamer with identical ACh binding sites at the subunit interfaces and show ligand specificities resembling those of the nicotinic receptor for agonists and antagonists. A subset of ligands, termed the neonicotinoids, exhibit specificity for insect nicotinic receptors and selective toxicity as insecticides. AChBPs are of neither mammalian nor insect origin and exhibit a distinctive pattern of selectivity for the neonicotinoid ligands. We define here the binding orientation and determinants of differential molecular recognition for the neonicotinoids and classical nicotinoids by estimates of kinetic and equilibrium binding parameters and crystallographic analysis. Neonicotinoid complex formation is rapid and accompanied by quenching of the AChBP tryptophan fluorescence. Comparisons of the neonicotinoids imidacloprid and thiacloprid in the binding site from Aplysia californica AChBP at 2.48 and 1.94 {angstrom} in resolution reveal a single conformation of the bound ligands with four of the five sites occupied in the pentameric crystal structure. The neonicotinoid electronegative pharmacophore is nestled in an inverted direction compared with the nicotinoid cationic functionality at the subunit interfacial binding pocket. Characteristic of several agonists, loop C largely envelops the ligand, positioning aromatic side chains to interact optimally with conjugated and hydrophobic regions of the neonicotinoid. This template defines the association of interacting amino acids and their energetic contributions to the distinctive interactions of neonicotinoids.

  18. Molecular recognition of aromatic rings by flavin: electrostatics and dispersion determine ring positioning above isoalloxazine.

    PubMed

    Koziol, Lucas; Kumar, Neeraj; Wong, Sergio E; Lightstone, Felice C

    2013-12-05

    Aromatic stacking interactions between isoalloxazine (ISA) of flavin and three prototypical aromatics (benzene, pyridine, chlorobenzene) were investigated using electronic structure calculations with Monte Carlo simulated annealing. The Effective Fragment Potential (EFP) method was used to locate the low-energy equilibrium configurations for the three dimer systems. These structures were further characterized through DFT (M06-2X) and MP2 calculations. One equilibrium configuration exists for ISA-benzene; characterizing the stacked dimer surface revealed a steep, single-welled potential that funnels benzene directly between rings II and III, positioning a substituent hydrogen adjacent to the redox-active N5. ISA-pyridine and ISA-chlorobenzene minimum-energy structures contain the aromatic ring in very similar position to that in ISA-benzene. However, the added rotational degree of freedom leads to two distinct binding motifs, having approximately antiparallel or parallel dipole moment alignment with ISA. The existence of the latter binding configuration was unexpected but is explained by the shape of the ISA electrostatic potential. Dispersion is the primary noncovalent interaction driving the positioning of aromatic rings above ISA, while electrostatics determine the orientation in dipole-containing substituted benzenes. The interplay of these interactions can be used to tune molecular recognition properties of synthetic redox cofactors, including positioning desired functional groups adjacent to the redox-active N5.

  19. Designs for the self-assembly of open and closed macromolecular structures and a molecular switch using DNA methyltransferases to order proteins on nucleic acid scaffolds

    NASA Astrophysics Data System (ADS)

    Smith, Steven S.

    2002-06-01

    The methyltransferase-directed addressing of fusion proteins to DNA scaffolds offers an approach to the construction of protein/nucleic acid biostructures with potential in a variety of applications. The technology is currently only limited by the yield of high occupancy structures. However, current evidence shows that DNA scaffolds that contain three or four targeted proteins can be reliably constructed. This permits a variety of macromolecular designs, several of which are given in this paper. Designs for open and closed two-dimensional and three-dimensional assemblies and a design for a molecular switch are discussed. The closed two-dimensional assembly takes the form of a square, and could find application as a component of other systems including a macromolecular rotaxane. The closed three-dimensional system takes the form of a trigonal bipyramid and could find application as a macromolecular carcerand. The molecular switch could find application as a peptide biosensor. Guidelines for the construction and structural verification of these designs are reported.

  20. Extended Calix[4]arene-Based Receptors for Molecular Recognition and Sensing

    PubMed Central

    Lo, Pik Kwan; Wong, Man Shing

    2008-01-01

    Recent advances in the area of recognition and sensing have shown that artificial receptors derived from extended calix[4]arenes bearing multiple π-conjugated fluorophoric or chromophoric systems have found useful to enhance binding affinity, selectivity and sensitivity for recognition and sensing of a targeted ion or molecule. A comprehensive review of various π-conjugation-extended calix[4]arene-based receptors with the highlight on the design and binding characterization for recognition and sensing is presented. PMID:27873816

  1. Molecular recognition, fluorescence sensing, and biological assay of phosphate anion derivatives using artificial Zn(II)-Dpa complexes.

    PubMed

    Sakamoto, Takashi; Ojida, Akio; Hamachi, Itaru

    2009-01-08

    In this Feature Article, we focus on recent advances in our research on molecular recognition and fluorescence sensing of phosphate anion derivatives of biological importance. Because of their significant roles in biological systems, considerable efforts have been devoted to developing detection or determination systems. However, the recognition and sensing of these anion species under aqueous biological conditions using small-molecular chemosensors still remain as a challenging research topic. We have been developing a variety of artificial receptors and fluorescent chemosensors for phosphoproteins and nucleoside polyphosphates in recent years. They consist of a binuclear Zn(II)-dipicolylamine (Dpa) complex as a common binding motif for phosphate anion derivatives. Taking advantage of their strong binding affinities or high sensing abilities, a variety of biological assay systems have also been successfully developed, which includes the enzyme assays such as the kinase, phosphatase and glycosyltransferase reaction, as well as an inhibitor assay for the phosphoprotein-protein surface interaction.

  2. High-Throughput Screen in Cryptococcus neoformans Identifies a Novel Molecular Scaffold That Inhibits Cell Wall Integrity Pathway Signaling

    PubMed Central

    2015-01-01

    Cryptococcus neoformans is one of the most important human fungal pathogens; however, no new therapies have been developed in over 50 years. Fungicidal activity is crucially important for an effective anticryptococal agent and, therefore, we screened 361,675 molecules against C. neoformans using an adenylate kinase release assay that specifically detects fungicidal activity. A set of secondary assays narrowed the set of hits to molecules that interfere with fungal cell wall integrity and identified three benzothioureas with low in vitro mammalian toxicity and good in vitro anticryptococcal (minimum inhibitory concentration = 4 μg/mL). This scaffold inhibits signaling through the cell wall integrity MAP kinase cascade. Structure–activity studies indicate that the thiocarbonyl moiety is crucial for activity. Genetic and biochemical data suggest that benzothioureas inhibit signaling upstream of the kinase cascade. Thus, the benzothioureas appear to be a promising new scaffold for further exploration in the search for new anticryptococcal agents. PMID:26807437

  3. Demonstration of Removal, Separation, and Recovery of Heavy Metals from Industrial Wastestreams Using Molecular Recognition Technology (MRT)

    DTIC Science & Technology

    2002-11-01

    Treatment Plant”, TM-2123-ENV, April 1995. 3. Ford, K.H., 1996, “ Heavy Metal Adsorption/ Biosorption Studies for Zero Discharge Industrial Wastewater...SEPARATION, AND RECOVERY OF HEAVY METALS FROM INDUSTRIAL WASTESTREAMS USING MOLECULAR RECOGNITION TECHNOLOGY (MRT) Final Report by Dr. Katherine...GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER DEMONSTRATION OF REMOVAL, SEPARATION, AND RECOVERY OF HEAVY METALS FROM INDUSTRIAL WASTEWATERS USING

  4. A core-shell surface magnetic molecularly imprinted polymers with fluorescence for λ-cyhalothrin selective recognition.

    PubMed

    Gao, Lin; Wang, Jixiang; Li, Xiuying; Yan, Yongsheng; Li, Chunxiang; Pan, Jianming

    2014-11-01

    In this study, we report here a general protocol for making core-shell magnetic Fe3O4/SiO2-MPS/MIPs (MPS = 3-(methacryloxyl) propyl trimethoxysilane, MIPs = molecularly imprinted polymers, Fe3O4/SiO2-MPS as core, MIPs as shell) via a surface molecular imprinting technique for optical detection of trace λ-cyhalothrin. The fluorescent molecularly imprinted polymer shell was first prepared by copolymerization of acrylamide with a small quantity of allyl fluorescein in the presence of λ-cyhalothrin to form recognition sites without doping. The magnetic Fe3O4/SiO2-MPS/MIPs exhibited paramagnetism, high fluorescence intensity, and highly selective recognition. Using fluorescence quenching as a detecting tool, Fe3O4/SiO2-MPS/MIPs were successfully applied to selectively and sensitively detect λ-cyhalothrin, and a linear relationship could be obtained covering a wide concentration range of 0-50 nM with a correlation coefficient of 0.9962 described by the Stern-Volmer equation. The experimental results of practical detection revealed that magnetic Fe3O4/SiO2-MPS/MIPs as an attractive recognition element was satisfactory for determination of trace λ-cyhalothrin in honey samples. This study, therefore, demonstrated the potential of MIPs for detection of λ-cyhalothrin in food.

  5. Atomic interactions of neonicotinoid agonists with AChBP: Molecular recognition of the distinctive electronegative pharmacophore

    PubMed Central

    Talley, Todd T.; Harel, Michal; Hibbs, Ryan E.; Radić, Zoran; Tomizawa, Motohiro; Casida, John E.; Taylor, Palmer

    2008-01-01

    Acetylcholine-binding proteins (AChBPs) from mollusks are suitable structural and functional surrogates of the nicotinic acetylcholine receptors when combined with transmembrane spans of the nicotinic receptor. These proteins assemble as a pentamer with identical ACh binding sites at the subunit interfaces and show ligand specificities resembling those of the nicotinic receptor for agonists and antagonists. A subset of ligands, termed the neonicotinoids, exhibit specificity for insect nicotinic receptors and selective toxicity as insecticides. AChBPs are of neither mammalian nor insect origin and exhibit a distinctive pattern of selectivity for the neonicotinoid ligands. We define here the binding orientation and determinants of differential molecular recognition for the neonicotinoids and classical nicotinoids by estimates of kinetic and equilibrium binding parameters and crystallographic analysis. Neonicotinoid complex formation is rapid and accompanied by quenching of the AChBP tryptophan fluorescence. Comparisons of the neonicotinoids imidacloprid and thiacloprid in the binding site from Aplysia californica AChBP at 2.48 and 1.94 Å in resolution reveal a single conformation of the bound ligands with four of the five sites occupied in the pentameric crystal structure. The neonicotinoid electronegative pharmacophore is nestled in an inverted direction compared with the nicotinoid cationic functionality at the subunit interfacial binding pocket. Characteristic of several agonists, loop C largely envelops the ligand, positioning aromatic side chains to interact optimally with conjugated and hydrophobic regions of the neonicotinoid. This template defines the association of interacting amino acids and their energetic contributions to the distinctive interactions of neonicotinoids. PMID:18477694

  6. Molecular Basis of mRNA Cap Recognition by Influenza B Polymerase PB2 Subunit.

    PubMed

    Xie, Lili; Wartchow, Charles; Shia, Steven; Uehara, Kyoko; Steffek, Micah; Warne, Robert; Sutton, James; Muiru, Gladys T; Leonard, Vincent H J; Bussiere, Dirksen E; Ma, Xiaolei

    2016-01-01

    Influenza virus polymerase catalyzes the transcription of viral mRNAs by a process known as "cap-snatching," where the 5'-cap of cellular pre-mRNA is recognized by the PB2 subunit and cleaved 10-13 nucleotides downstream of the cap by the endonuclease PA subunit. Although this mechanism is common to both influenza A (FluA) and influenza B (FluB) viruses, FluB PB2 recognizes a wider range of cap structures including m(7)GpppGm-, m(7)GpppG-, and GpppG-RNA, whereas FluA PB2 utilizes methylated G-capped RNA specifically. Biophysical studies with isolated PB2 cap-binding domain (PB2(cap)) confirm that FluB PB2 has expanded mRNA cap recognition capability, although the affinities toward m(7)GTP are significantly reduced when compared with FluA PB2. The x-ray co-structures of the FluB PB2(cap) with bound cap analogs m(7)GTP and GTP reveal an inverted GTP binding mode that is distinct from the cognate m(7)GTP binding mode shared between FluA and FluB PB2. These results delineate the commonalities and differences in the cap-binding site between FluA and FluB PB2 and will aid structure-guided drug design efforts to identify dual inhibitors of both FluA and FluB PB2. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Molecular Recognition Enables Nanosubstrate-Mediated Delivery of Gene-Encapsulated Nanoparticles with High Efficiency

    PubMed Central

    2015-01-01

    Substrate-mediated gene delivery is a promising method due to its unique ability to preconcentrate exogenous genes onto designated substrates. However, many challenges remain to enable continuous and multiround delivery of the gene using the same substrates without depositing payloads and immobilizing cells in each round of delivery. Herein we introduce a gene delivery system, nanosubstrate-mediated delivery (NSMD) platform, based on two functional components with nanoscale features, including (1) DNA⊂SNPs, supramolecular nanoparticle (SNP) vectors for gene encapsulation, and (2) Ad-SiNWS, adamantane (Ad)-grafted silicon nanowire substrates. The multivalent molecular recognition between the Ad motifs on Ad-SiNWS and the β-cyclodextrin (CD) motifs on DNA⊂SNPs leads to dynamic assembly and local enrichment of DNA⊂SNPs from the surrounding medium onto Ad-SiNWS. Subsequently, once cells settled on the substrate, DNA⊂SNPs enriched on Ad-SiNWS were introduced through the cell membranes by intimate contact with individual nanowires on Ad-SiNWS, resulting in a highly efficient delivery of exogenous genes. Most importantly, sequential delivery of multiple batches of exogenous genes on the same batch cells settled on Ad-SiNWS was realized by sequential additions of the corresponding DNA⊂SNPs with equivalent efficiency. Moreover, using the NSMD platform in vivo, cells recruited on subcutaneously transplanted Ad-SiNWS were also efficiently transfected with exogenous genes loaded into SNPs, validating the in vivo feasibility of this system. We believe that this nanosubstrate-mediated delivery platform will provide a superior system for in vitro and in vivo gene delivery and can be further used for the encapsulation and delivery of other biomolecules. PMID:24708312

  8. Differential scanning calorimetry in life science: thermodynamics, stability, molecular recognition and application in drug design.

    PubMed

    Bruylants, G; Wouters, J; Michaux, C

    2005-01-01

    All biological phenomena depend on molecular recognition, which is either intermolecular like in ligand binding to a macromolecule or intramolecular like in protein folding. As a result, understanding the relationship between the structure of proteins and the energetics of their stability and binding with others (bio)molecules is a very interesting point in biochemistry and biotechnology. It is essential to the engineering of stable proteins and to the structure-based design of pharmaceutical ligands. The parameter generally used to characterize the stability of a system (the folded and unfolded state of the protein for example) is the equilibrium constant (K) or the free energy (deltaG(o)), which is the sum of enthalpic (deltaH(o)) and entropic (deltaS(o)) terms. These parameters are temperature dependent through the heat capacity change (deltaCp). The thermodynamic parameters deltaH(o) and deltaCp can be derived from spectroscopic experiments, using the van't Hoff method, or measured directly using calorimetry. Along with isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC) is a powerful method, less described than ITC, for measuring directly the thermodynamic parameters which characterize biomolecules. In this article, we summarize the principal thermodynamics parameters, describe the DSC approach and review some systems to which it has been applied. DSC is much used for the study of the stability and the folding of biomolecules, but it can also be applied in order to understand biomolecular interactions and can thus be an interesting technique in the process of drug design.

  9. Direct monitoring of molecular recognition processes using fluorescence enhancement at colloid-coated microplates.

    PubMed

    Lobmaier, C; Hawa, G; Götzinger, M; Wirth, M; Pittner, F; Gabor, F

    2001-01-01

    Direct monitoring of recognition processes at the molecular level is a valuable tool for studying reaction kinetics to assess affinity constants (e.g. drugs to receptors) and for designing rapid single step immunoassays. Methods currently used to gain information about binding processes predominantly depend on surface plasmon resonance. These systems use excitation with coherent light in attenuated total reflection geometry to obtain discrimination between surface-bound and free molecules in solution. Therefore labeling of the compounds is not necessary, but due to the complexity of the measuring setup the method is rather costly. In this contribution we present a simple method for performing kinetic single step biorecognition assays with fluorophore labeled compounds using the fluorescence enhancement properties of surface bound silver colloids. Silver colloids are bound to standard microplates via silanization of the plastic surface. Fluorophores close to this colloid coated surface show a significant gain in fluorescence compared to fluorophores farther away in the bulk solution. Therefore discrimination between surface bound and free fluorophores is possible and the binding of, for example, fluorophore labeled antibodies to antigens immobilized on the colloid surface results in increasing fluorescence intensity. Utilization of standard microplates makes this method fully compatible with conventional microplate processing and reading devices. Neither excitation with coherent laser light nor ATR geometry is required, the measurement is performed in a standard fluorescence microplate reader in front face geometry with a xenon flash lamp as excitation source. Methods for the preparation of colloid-coated microplates and fluorescence-enhanced biorecognition assays are presented. Additionally the dependence of the system performance on the structure and properties of the metal colloid coated surface is described. A two-component biorecognition model system shows a

  10. Replica exchange molecular dynamics simulations provide insight into substrate recognition by small heat shock proteins.

    PubMed

    Patel, Sunita; Vierling, Elizabeth; Tama, Florence

    2014-06-17

    The small heat shock proteins (sHSPs) are a virtually ubiquitous and diverse group of molecular chaperones that can bind and protect unfolding proteins from irreversible aggregation. It has been suggested that intrinsic disorder of the N-terminal arm (NTA) of sHSPs is important for substrate recognition. To investigate conformations of the NTA that could recognize substrates we performed replica exchange molecular dynamics simulations. Behavior at normal and stress temperatures of the dimeric building blocks of dodecameric HSPs from wheat (Ta16.9) and pea (Ps18.1) were compared because they display high sequence similarity, but Ps18.1 is more efficient in binding specific substrates. In our simulations, the NTAs of the dimer are flexible and dynamic; however, rather than exhibiting highly extended conformations they retain considerable α-helical character and contacts with the conserved α-crystallin domain (ACD). Network analysis and clustering methods reveal that there are two major conformational forms designated either "open" or "closed" based on the relative position of the two NTAs and their hydrophobic solvent accessible surface area. The equilibrium constant for the closed to open transition is significantly different for Ta16.9 and Ps18.1, with the latter showing more open conformations at elevated temperature correlated with its more effective chaperone activity. In addition, the Ps18.1 NTAs have more hydrophobic solvent accessible surface than those of Ta16.9. NTA hydrophobic patches are comparable in size to the area buried in many protein-protein interactions, which would enable sHSPs to bind early unfolding intermediates. Reduced interactions of the Ps18.1 NTAs with each other and with the ACD contribute to the differences in dynamics and hydrophobic surface area of the two sHSPs. These data support a major role for the conformational equilibrium of the NTA in substrate binding and indicate features of the NTA that contribute to sHSP chaperone

  11. Recognition Properties and Competitive Assays of a Dual Dopamine/Serotonin Selective Molecularly Imprinted Polymer

    PubMed Central

    Suedee, Roongnapa; Seechamnanturakit, Vatcharee; Suksuwan, Acharee; Canyuk, Bhutorn

    2008-01-01

    A molecularly imprinted polymer (MIP) with dual dopamine/serotonin-like binding sites (DS-MIP) was synthesized for use as a receptor model of study the drug-interaction of biological mixed receptors at a molecular level. The polymer material was produced using methacrylic acid (MAA) and acrylamide (ACM) as functional monomers, N,N′-methylene bisacrylamide (MBAA) as cross-linker, methanol/water mixture (4:1, v/v) as porogen and a mixture of dopamine (D) and serotonin (S) as templates. The prepared DS-MIP exhibited the greatest rebinding of the template(s) in aqueous methanol solution with decreased recognition in acetonitrile, water and methanol solvent. The binding affinity and binding capacity of DS-MIP with S were found to be higher than those of DS-MIP with D. The selectivity profiles of DS-MIP suggest that the D binding site of DS-MIP has sufficient integrity to discriminate between species of non-optimal functional group orientation, whilst the S binding site of DS-MIP is less selective toward species having structural features and functional group orientations different from S. The ligand binding activities of a series of ergot derivatives (ergocryptine, ergocornine, ergocristine, ergonovine, agroclavine, pergolide and terguride) have been studied with the DS-MIP using a competitive ligand binding assay protocol. The binding affinities of DS-MIP were demonstrated in the micro- or submicro-molar range for a series of ergot derivatives, whereas the binding affinities were considerably greater to natural receptors derived from the rat hypothalamus. The DS-MIP afforded the same pattern of differentiation as the natural receptors, i.e. affinity for the clavines > lysergic acid derivatives > ergopeptines. The results suggest that the discrimination for the ergot derivatives by the dopamine and serotonin sites of DS-MIP is due to the structural features and functional orientation of the phenylethylamine and indolylethylamine entities at the binding sites, and the

  12. Polycation-π interactions are a driving force for molecular recognition by an intrinsically disordered oncoprotein family.

    PubMed

    Song, Jianhui; Ng, Sheung Chun; Tompa, Peter; Lee, Kevin A W; Chan, Hue Sun

    2013-01-01

    Molecular recognition by intrinsically disordered proteins (IDPs) commonly involves specific localized contacts and target-induced disorder to order transitions. However, some IDPs remain disordered in the bound state, a phenomenon coined "fuzziness", often characterized by IDP polyvalency, sequence-insensitivity and a dynamic ensemble of disordered bound-state conformations. Besides the above general features, specific biophysical models for fuzzy interactions are mostly lacking. The transcriptional activation domain of the Ewing's Sarcoma oncoprotein family (EAD) is an IDP that exhibits many features of fuzziness, with multiple EAD aromatic side chains driving molecular recognition. Considering the prevalent role of cation-π interactions at various protein-protein interfaces, we hypothesized that EAD-target binding involves polycation- π contacts between a disordered EAD and basic residues on the target. Herein we evaluated the polycation-π hypothesis via functional and theoretical interrogation of EAD variants. The experimental effects of a range of EAD sequence variations, including aromatic number, aromatic density and charge perturbations, all support the cation-π model. Moreover, the activity trends observed are well captured by a coarse-grained EAD chain model and a corresponding analytical model based on interaction between EAD aromatics and surface cations of a generic globular target. EAD-target binding, in the context of pathological Ewing's Sarcoma oncoproteins, is thus seen to be driven by a balance between EAD conformational entropy and favorable EAD-target cation-π contacts. Such a highly versatile mode of molecular recognition offers a general conceptual framework for promiscuous target recognition by polyvalent IDPs.

  13. Mining for bioactive scaffolds with scaffold networks: improved compound set enrichment from primary screening data.

    PubMed

    Varin, Thibault; Schuffenhauer, Ansgar; Ertl, Peter; Renner, Steffen

    2011-07-25

    Identification of meaningful chemical patterns in the increasing amounts of high-throughput-generated bioactivity data available today is an increasingly important challenge for successful drug discovery. Herein, we present the scaffold network as a novel approach for mapping and navigation of chemical and biological space. A scaffold network represents the chemical space of a library of molecules consisting of all molecular scaffolds and smaller "parent" scaffolds generated therefrom by the pruning of rings, effectively leading to a network of common scaffold substructure relationships. This algorithm provides an extension of the scaffold tree algorithm that, instead of a network, generates a tree relationship between a heuristically rule-based selected subset of parent scaffolds. The approach was evaluated for the identification of statistically significantly active scaffolds from primary screening data for which the scaffold tree approach has already been shown to be successful. Because of the exhaustive enumeration of smaller scaffolds and the full enumeration of relationships between them, about twice as many statistically significantly active scaffolds were identified compared to the scaffold-tree-based approach. We suggest visualizing scaffold networks as islands of active scaffolds.

  14. Preparation of boronate-functionalized molecularly imprinted monolithic column with polydopamine coating for glycoprotein recognition and enrichment.

    PubMed

    Lin, Zian; Wang, Juan; Tan, Xiaoqing; Sun, Lixiang; Yu, Ruifang; Yang, Huanghao; Chen, Guonan

    2013-12-06

    A novel imprinting strategy using reversible covalent complexation of glycoprotein was described for creating glycoprotein-specific recognition cavities on boronate-functionalized monolithic column. Based on it, a molecularly imprinted monolithic column was prepared by self-polymerization of dopamine (DA) on the surface of 4-vinylphenylboronic acid (VPBA)-based polymeric skeletons after reversible immobilization of horseradish peroxidase (HRP). Due to the combination of boronate affinity and surface imprinting of DA, the stable and accessible recognition sites in the as-prepared imprinted monolith could be obtained after the removal of the template, which facilitated the rebinding of the template and provided good reproducibility and lifetime of use. The recognition behaviors of proteins on the bare VPBA-based, HRP-imprinted and nonimprinted monolithic columns were evaluated in detail and the results showed that the HRP-imprinted monolith exhibited higher recognition ability toward the template than another two monolithic columns. Not only nonglycoproteins but also glycoproteins can be well separated with the HRP-imprinted monolith. In addition, the feasibility of the HRP-imprinted monolith, adopted as an in-tube solid phase microextraction (in-tube SPME), was further assessed by selective extraction and enrichment of HRP from human serum. The good results demonstrated its potential in glycoproteome analysis. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Polydopamine-based molecular imprinting on silica-modified magnetic nanoparticles for recognition and separation of bovine hemoglobin.

    PubMed

    Jia, Xiaoping; Xu, Minli; Wang, Yuzhi; Ran, Dan; Yang, Shan; Zhang, Min

    2013-01-21

    Surface molecular imprinting, especially on the surface of silica-modified magnetic nanoparticles, has been proposed as a promising strategy for protein recognition and separation. Inspired by the self-polymerization of dopamine, we synthesized a polydopamine-based molecular imprinted film coating on silica-Fe(3)O(4) nanoparticles for recognition and separation of bovine hemoglobin (BHb). Magnetic molecularly imprinted nanoparticles (about 860 nm) possess a core-shell structure. Magnetic molecularly imprinted nanoparticles (MMIP) show a relatively high adsorption capacity (4.65 ± 0.38 mg g(-1)) and excellent selectivity towards BHb with a separation factor of 2.19. MMIP with high saturation magnetization (10.33 emu g(-1)) makes it easy to separate the target protein from solution by an external magnetic field. After three continuous adsorption and elution processes, the adsorption capacity of MMIP remained at 4.30 mg g(-1). Our results suggest that MMIPs are suitable for the removal of high abundance of protein and the enrichment of low abundance of protein in proteomics.

  16. Molecular weight recognition in the multiple-stranded helix of a synthetic polymer without specific monomer-monomer interaction.

    PubMed

    Kumaki, Jiro; Kawauchi, Takehiro; Ute, Koichi; Kitayama, Tatsuki; Yashima, Eiji

    2008-05-21

    Stereoregular isotactic and syndiotactic poly(methyl methacrylate)s (it- and st-PMMAs) are known to form a multiple-stranded complementary helix, so-called stereocomplex (SC) through van der Waals interactions, which is a rare example of helical supramolecular structures formed by a commodity polymer. In this study, we prepared SCs by using uniform it- and st-PMMAs and those with a narrow molecular weight distribution having different molecular weights and investigated their structures in detail using high-resolution atomic force microscopy as a function of the molecular weight and molecular weight distribution of the component PMMAs. We found that complementary it- and st-PMMAs with the longer molecular length determine the total length of the SC, and molecules of the shorter component associate until they fill up or cover the longer component. These observations support a supramolecular triple-stranded helical structure of the SCs composed of a double-stranded helix of two intertwined it-PMMA chains included in a single helix of st-PMMA, and this triple-stranded helix model of the SCs appears to be applicable to the it- and st-PMMAs having a wide range of molecular weights we employed in this study. In homogeneous double-stranded helices of it-PMMA, it has been found that, in mixtures of two it-PMMAs with different molecular weights, chains of the same molecular weight selectively form a double-stranded it-PMMA helix, or recognize the molecular weights of each other ("molecular sorting"). We thus demonstrate that molecular weight recognition is possible, without any specific interaction between monomer units, through the formation of a topological multiple-stranded helical structure based upon van der Waals interaction.

  17. Recent Progress in the Molecular Recognition and Therapeutic Importance of Interleukin-1 Receptor-Associated Kinase 4.

    PubMed

    Patra, Mahesh Chandra; Choi, Sangdun

    2016-11-13

    Toll-like receptors (TLRs) are the most upstream pattern recognition receptors in the cell, which detect pathogen associated molecular patterns and initiate signal transduction, culminating in the transcription of pro-inflammatory cytokines and antiviral interferon. Interleukin-1 receptor-associated kinase 4 (IRAK4) is a key mediator in TLR (except for TLR3) and interleukin-1 receptor signaling pathways. The loss of kinase function of IRAK4 is associated with increased susceptibility to various pathogens, while its over-activation causes autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematosus, and cancer. The therapeutic importance of this master kinase has been advocated by a number of recent preclinical studies, where potent inhibitors have been administered to improve various TLR-mediated pathologies. Increasing studies of X-ray crystallographic structures with bound inhibitors have improved our knowledge on the molecular recognition of ligands by IRAK4, which will be crucial for the development of new inhibitors with improved potencies. In this review, we briefly discuss the structural aspect of ligand recognition by IRAK4 and highlight its therapeutic importance in the context of TLR-associated unmet medical needs.

  18. A three-arm scaffold carrying affinity molecules for multiplex recognition imaging by atomic force microscopy: the synthesis, attachment to silicon tips, and detection of proteins.

    PubMed

    Manna, Saikat; Senapati, Subhadip; Lindsay, Stuart; Zhang, Peiming

    2015-06-17

    We have developed a multiplex imaging method for detection of proteins using atomic force microscopy (AFM), which we call multiplex recognition imaging (mRI). AFM has been harnessed to identify protein using a tip functionalized with an affinity molecule at a single molecule level. However, many events in biochemistry require identification of colocated factors simultaneously, and this is not possible with only one type of affinity molecule on an AFM tip. To enable AFM detection of multiple analytes, we designed a recognition head made from conjugating two different affinity molecules to a three-arm linker. When it is attached to an AFM tip, the recognition head would allow the affinity molecules to function in concert. In the present study, we synthesized two recognition heads: one was composed of two nucleic acid aptamers, and the other one composed of an aptamer and a cyclic peptide. They were attached to AFM tips through a catalyst-free click reaction. Our imaging results show that each affinity unit in the recognition head can recognize its respective cognate in an AFM scanning process independently and specifically. The AFM method was sensitive, only requiring 2 to 3 μL of protein solution with a concentration of ∼2 ng/mL for the detection with our current setup. When a mixed sample was deposited on a surface, the ratio of proteins could be determined by counting numbers of the analytes. Thus, this mRI approach has the potential to be used as a label-free system for detection of low-abundance protein biomarkers.

  19. Water-compatible temperature and magnetic dual-responsive molecularly imprinted polymers for recognition and extraction of bisphenol A.

    PubMed

    Wu, Xiaqing; Wang, Xiaoyan; Lu, Wenhui; Wang, Xinran; Li, Jinhua; You, Huiyan; Xiong, Hua; Chen, Lingxin

    2016-02-26

    Versatile molecularly imprinted polymers (MIPs) have been widely applied to various sample matrices, however, molecular recognition in aqueous media is still difficult. Stimuli-responsive MIPs have received increasing attentions due to their unique feature that the molecular recognition is regulated by specific external stimuli. Herein, water-compatible temperature and magnetic dual-responsive MIPs (WC-TMMIPs) with hydrophilic brushes were prepared via reversible addition-fragmentation chain transfer precipitation polymerization for reversible and selective recognition and extraction of bisphenol A (BPA). Transmission electron microscopy (TEM), Fourier transform infrared spectrometer (FT-IR) and vibrating sample magnetometry (VSM) as characterization methods were used to examine the successful synthesis of polymers, and the resultant WC-TMMIPs showed excellent thermosensitivity and simple rapid magnetic separation. Controlled adsorption and release of BPA by temperature regulation were investigated systematically, and the maximum adsorption and removal efficiency toward BPA in aqueous solutions were attained at 35 °C and 45 °C, respectively, as well as a good recoverability was exhibited with the precision less than 5% through five adsorption-desorption cycles. Phenolic structural analogs were tested and good recognition specificity for BPA was displayed. Accordingly, the WC-TMMIPs were employed as adsorbents for magnetic solid-phase extraction (MSPE) and packed SPE of BPA from seawater samples. Using the two modes followed by HPLC-UV determination, excellent linearity was attained in the range of 0.1-14.5 μM and 1.3-125 nM, with low detection limits of 0.02 μM and 0.18 nM, respectively. Satisfactory recoveries for spiked seawater samples were achieved ranging from 86.3-103.5% and 96.2-104.3% with RSD within 2.12-4.33%. The intelligent WC-TMMIPs combining water-compatibility, molecular recognition, magnetic separation, and temperature regulation proved

  20. Molecular construction of HIV-gp120 discontinuous epitope mimics by assembly of cyclic peptides on an orthogonal alkyne functionalized TAC-scaffold.

    PubMed

    Werkhoven, P R; Elwakiel, M; Meuleman, T J; Quarles van Ufford, H C; Kruijtzer, J A W; Liskamp, R M J

    2016-01-14

    Mimics of discontinuous epitopes of for example bacterial or viral proteins may have considerable potential for the development of synthetic vaccines, especially if conserved epitopes can be mimicked. However, due to the structural complexity and size of discontinuous epitopes molecular construction of these mimics remains challeging. We present here a convergent route for the assembly of discontinuous epitope mimics by successive azide alkyne cycloaddition on an orthogonal alkyne functionalized scaffold. Here the synthesis of mimics of the HIV gp120 discontinuous epitope that interacts with the CD4 receptor is described. The resulting protein mimics are capable of inhibition of the gp120-CD4 interaction. The route is convergent, robust and should be applicable to other discontinuous epitopes.

  1. Optimized solid phase-assisted synthesis of dendrons applicable as scaffolds for radiolabeled bioactive multivalent compounds intended for molecular imaging.

    PubMed

    Fischer, Gabriel; Wängler, Björn; Wängler, Carmen

    2014-05-27

    Dendritic structures, being highly homogeneous and symmetric, represent ideal scaffolds for the multimerization of bioactive molecules and thus enable the synthesis of compounds of high valency which are e.g., applicable in radiolabeled form as multivalent radiotracers for in vivo imaging. As the commonly applied solution phase synthesis of dendritic scaffolds is cumbersome and time-consuming, a synthesis strategy was developed that allows for the efficient assembly of acid amide bond-based highly modular dendrons on solid support via standard Fmoc solid phase peptide synthesis protocols. The obtained dendritic structures comprised up to 16 maleimide functionalities and were derivatized on solid support with the chelating agent DOTA. The functionalized dendrons furthermore could be efficiently reacted with structurally variable model thiol-bearing bioactive molecules via click chemistry and finally radiolabeled with 68Ga. Thus, this solid phase-assisted dendron synthesis approach enables the fast and straightforward assembly of bioactive multivalent constructs for example applicable as radiotracers for in vivo imaging with Positron Emission Tomography (PET).

  2. Molecular Recognition in Mitochondrial Cytochromes P450 That Catalyze the Terminal Steps of Corticosteroid Biosynthesis.

    PubMed

    Peng, Hwei-Ming; Auchus, Richard J

    2017-05-02

    The mitochondrial cytochromes P450 11B1 and P450 11B2 are responsible for the final stages of cortisol and aldosterone synthesis, respectively. Dysregulation of both enzymes has been implicated in secondary forms of hypertension. Molecular recognition of the cytochromes P450 with their corresponding redox partner is a key step in the catalytic cycle, yet the precise nature of the interaction of P450 11B1 or P450 11B2 with their proximal partner, adrenodoxin (Adx), is still unknown. Here, we obtained P450 11B1·Adx2 and P450 11B2·Adx2 complexes using the zero-length cross-linker ethyl-3-[3-(dimethylamino)propyl]carbodiimide, which formed best under low-ionic strength conditions. R-to-K mutations were introduced into the P450s at residues predicted to form salt bridges with Adx and allow cross-linking with the carbodiimide reagent. Mass spectrometric analysis of the chymotrypsin-digested ternary complexes identified seven cross-linked peptide pairs. Consistent with the electrostatic interaction of K370 in P450 11B1-WT and K366 in P450 11B2-R366K with D79 of Adx, Adx mutation L80K abolished complex formation. Using these sites of interaction as constraints, protein docking calculations based on the crystal structures of the two proteins yielded a structural model of the P450 11B1·Adx2 complex. The appositional surfaces include R/K366, K370, and K357 of P450 11B1, which interact with D79, D76, and D113 (second molecule) of Adx, respectively. Similar to P450 11B1, P450 11B2 also forms a complex with the Adx dimer via three lysine residues. We describe similarities and differences in our models of the P450 11B1·Adx2 and P450 11B2·Adx2 complexes with the structure of the P450 11A1-Adx fusion protein.

  3. “One Ring to Bind Them All”—Part I: The Efficiency of the Macrocyclic Scaffold for G-Quadruplex DNA Recognition

    PubMed Central

    Monchaud, David; Granzhan, Anton; Saettel, Nicolas; Guédin, Aurore; Mergny, Jean-Louis; Teulade-Fichou, Marie-Paule

    2010-01-01

    Macrocyclic scaffolds are particularly attractive for designing selective G-quadruplex ligands essentially because, on one hand, they show a poor affinity for the “standard” B-DNA conformation and, on the other hand, they fit nicely with the external G-quartets of quadruplexes. Stimulated by the pioneering studies on the cationic porphyrin TMPyP4 and the natural product telomestatin, follow-up studies have developed, rapidly leading to a large diversity of macrocyclic structures with remarkable-quadruplex binding properties and biological activities. In this review we summarize the current state of the art in detailing the three main categories of quadruplex-binding macrocycles described so far (telomestatin-like polyheteroarenes, porphyrins and derivatives, polyammonium cyclophanes), and in addressing both synthetic issues and biological aspects. PMID:20725629

  4. Molecular basis for TANK recognition by TRAF1 revealed by the crystal structure of TRAF1/TANK complex.

    PubMed

    Kim, Chang Min; Jeong, Jae-Hee; Son, Young-Jin; Choi, Jun-Hyuk; Kim, Sunghwan; Park, Hyun Ho

    2017-02-02

    Tumor necrosis factor receptor-associated factor 1 (TRAF1) is a multifunctional adaptor protein involved in important processes of cellular signaling, including innate immunity and apoptosis. TRAF family member-associated NF-kappaB activator (TANK) has been identified as a competitive intracellular inhibitor of TRAF2 function. Although TRAF recognition by various receptors has been studied extensively in the field of TRAF-mediated biology, molecular and functional details of TANK recognition and interaction with TRAF1 have not been studied. In this study, we report the crystal structure of the TRAF1/TANK peptide complex. Quantitative interaction experiments showed that TANK peptide interacts with both TRAF1 and TRAF2 with similar affinity in a micromolar range. Our structural study also reveals that TANK binds TRAF1 using a minor minimal consensus motif for TRAF binding, Px(Q/E)xT.

  5. Assembling of G-strands into novel tetra-molecular parallel G4-DNA nanostructures using avidin–biotin recognition

    PubMed Central

    Borovok, Natalia; Iram, Natalie; Zikich, Dragoslav; Ghabboun, Jamal; Livshits, Gideon I.; Kotlyar, Alexander B.

    2008-01-01

    We describe a method for the preparation of novel long (hundreds of nanometers), uniform, inter-molecular G4-DNA molecules composed of four parallel G-strands. The only long continuous G4-DNA reported so far are intra-molecular structures made of a single G-strand. To enable a tetra-molecular assembly of the G-strands we developed a novel approach based on avidin–biotin biological recognition. The steps of the G4-DNA production include: (i) Enzymatic synthesis of long poly(dG)-poly(dC) molecules with biotinylated poly(dG)-strand; (ii) Formation of a complex between avidin-tetramer and four biotinylated poly(dG)-poly(dC) molecules; (iii) Separation of the poly(dC) strands from the poly(dG)-strands, which are connected to the avidin; (iv) Assembly of the four G-strands attached to the avidin into tetra-molecular G4-DNA. The average contour length of the formed structures, as measured by AFM, is equal to that of the initial poly(dG)-poly(dC) molecules, suggesting a tetra-molecular mechanism of the G-strands assembly. The height of tetra-molecular G4-nanostructures is larger than that of mono-molecular G4-DNA molecules having similar contour length. The CD spectra of the tetra- and mono-molecular G4-DNA are markedly different, suggesting different structural organization of these two types of molecules. The tetra-molecular G4-DNA nanostructures showed clear electrical polarizability. This suggests that they may be useful for molecular electronics. PMID:18663013

  6. Scaffolded biology.

    PubMed

    Minelli, Alessandro

    2016-09-01

    Descriptions and interpretations of the natural world are dominated by dichotomies such as organism vs. environment, nature vs. nurture, genetic vs. epigenetic, but in the last couple of decades strong dissatisfaction with those partitions has been repeatedly voiced and a number of alternative perspectives have been suggested, from perspectives such as Dawkins' extended phenotype, Turner's extended organism, Oyama's Developmental Systems Theory and Odling-Smee's niche construction theory. Last in time is the description of biological phenomena in terms of hybrids between an organism (scaffolded system) and a living or non-living scaffold, forming unit systems to study processes such as reproduction and development. As scaffold, eventually, we can define any resource used by the biological system, especially in development and reproduction, without incorporating it as happens in the case of resources fueling metabolism. Addressing biological systems as functionally scaffolded systems may help pointing to functional relationships that can impart temporal marking to the developmental process and thus explain its irreversibility; revisiting the boundary between development and metabolism and also regeneration phenomena, by suggesting a conceptual framework within which to investigate phenomena of regular hypermorphic regeneration such as characteristic of deer antlers; fixing a periodization of development in terms of the times at which a scaffolding relationship begins or is terminated; and promoting plant galls to legitimate study objects of developmental biology.

  7. Supramolecular polymers constructed from macrocycle-based host-guest molecular recognition motifs.

    PubMed

    Dong, Shengyi; Zheng, Bo; Wang, Feng; Huang, Feihe

    2014-07-15

    /physical properties, including stimuli responsiveness, self-healing, and environmental adaptation. It has been reported that macrocycle-based supramolecular polymers can respond to pH change, photoirradition, anions, cations, temperature, and solvent. Macrocycle-based supramolecular polymers have been prepared in solution, in gel, and in the solid state. Furthermore, the solvent has a very important influence on the formation of these supramolecular polymers. Crown ether- and pillararene-based supramolecular polymers have mainly formed in organic solvents, such as chloroform, acetone, and acetonitrile, while cyclodextrin- and cucurbituril-based supramolecular polymerizations have been usually observed in aqueous solutions. For calixarenes, both organic solvents and water have been used as suitable media for supramolecular polymerization. With the development of supramolecular chemistry and polymer science, various methods, such as nuclear magnetic resonance spectroscopy, X-ray techniques, electron microscopies, and theoretical calculation and computer simulation, have been applied for characterizing supramolecular polymers. The fabrication of macrocycle-based supramolecular polymers has become a currently hot research topic. In this Account, we summarize recent results in the investigation of supramolecular polymers constructed from macrocycle-based host-guest molecular recognition motifs. These supramolecular polymers are classified based on the different macrocycles used in them. Their monomer design, structure control, stimuli-responsiveness, and applications in various areas are discussed, and future research directions are proposed. It is expected that the development of supramolecular polymers will not only change the way we live and work but also exert significant influence on scientific research.

  8. Allosteric Inhibitory Molecular Recognition of a Photochromic Dye by a Digestive Enzyme: Dihydroindolizine makes α-chymotrypsin Photo-responsive

    PubMed Central

    Bagchi, Damayanti; Ghosh, Abhijit; Singh, Priya; Dutta, Shreyasi; Polley, Nabarun; Althagafi, Ismail.I.; Jassas, Rabab S.; Ahmed, Saleh A.; Pal, Samir Kumar

    2016-01-01

    The structural-functional regulation of enzymes by the administration of an external stimulus such as light could create photo-switches that exhibit unique biotechnological applications. However, molecular recognition of small ligands is a central phenomenon involved in all biological processes. We demonstrate herein that the molecular recognition of a photochromic ligand, dihydroindolizine (DHI), by serine protease α-chymotrypsin (CHT) leads to the photo-control of enzymatic activity. We synthesized and optically characterized the photochromic DHI. Light-induced reversible pyrroline ring opening and a consequent thermal back reaction via 1,5-electrocyclization are responsible for the photochromic behavior. Furthermore, DHI inhibits the enzymatic activity of CHT in a photo-controlled manner. Simultaneous binding of the well-known inhibitors 4-nitrophenyl anthranilate (NPA) or proflavin (PF) in the presence of DHI displays spectral overlap between the emission of CHT-NPA or CHT-PF with the respective absorption of cis or trans DHI. The results suggest an opportunity to explore the binding site of DHI using Förster resonance energy transfer (FRET). Moreover, to more specifically evaluate the DHI binding interactions, we employed molecular docking calculations, which suggested binding near the hydrophobic site of Cys-1-Cys-122 residues. Variations in the electrostatic interactions of the two conformers of DHI adopt unfavorable conformations, leading to the allosteric inhibition of enzymatic activity. PMID:27677331

  9. Molecular Recognition of PTS-1 Cargo Proteins by Pex5p: Implications for Protein Mistargeting in Primary Hyperoxaluria

    PubMed Central

    Mesa-Torres, Noel; Tomic, Nenad; Albert, Armando; Salido, Eduardo; Pey, Angel L.

    2015-01-01

    Peroxisomal biogenesis and function critically depends on the import of cytosolic proteins carrying a PTS1 sequence into this organelle upon interaction with the peroxin Pex5p. Recent structural studies have provided important insights into the molecular recognition of cargo proteins by Pex5p. Peroxisomal import is a key feature in the pathogenesis of primary hyperoxaluria type 1 (PH1), where alanine:glyoxylate aminotransferase (AGT) undergoes mitochondrial mistargeting in about a third of patients. Here, we study the molecular recognition of PTS1 cargo proteins by Pex5p using oligopeptides and AGT variants bearing different natural PTS1 sequences, and employing an array of biophysical, computational and cell biology techniques. Changes in affinity for Pex5p (spanning over 3–4 orders of magnitude) reflect different thermodynamic signatures, but overall bury similar amounts of molecular surface. Structure/energetic analyses provide information on the contribution of ancillary regions and the conformational changes induced in Pex5p and the PTS1 cargo upon complex formation. Pex5p stability in vitro is enhanced upon cargo binding according to their binding affinities. Moreover, we provide evidence that the rational modulation of the AGT: Pex5p binding affinity might be useful tools to investigate mistargeting and misfolding in PH1 by pulling the folding equilibria towards the native and peroxisomal import competent state. PMID:25689234

  10. Allosteric Inhibitory Molecular Recognition of a Photochromic Dye by a Digestive Enzyme: Dihydroindolizine makes α-chymotrypsin Photo-responsive

    NASA Astrophysics Data System (ADS)

    Bagchi, Damayanti; Ghosh, Abhijit; Singh, Priya; Dutta, Shreyasi; Polley, Nabarun; Althagafi, Ismail. I.; Jassas, Rabab S.; Ahmed, Saleh A.; Pal, Samir Kumar

    2016-09-01

    The structural-functional regulation of enzymes by the administration of an external stimulus such as light could create photo-switches that exhibit unique biotechnological applications. However, molecular recognition of small ligands is a central phenomenon involved in all biological processes. We demonstrate herein that the molecular recognition of a photochromic ligand, dihydroindolizine (DHI), by serine protease α-chymotrypsin (CHT) leads to the photo-control of enzymatic activity. We synthesized and optically characterized the photochromic DHI. Light-induced reversible pyrroline ring opening and a consequent thermal back reaction via 1,5-electrocyclization are responsible for the photochromic behavior. Furthermore, DHI inhibits the enzymatic activity of CHT in a photo-controlled manner. Simultaneous binding of the well-known inhibitors 4-nitrophenyl anthranilate (NPA) or proflavin (PF) in the presence of DHI displays spectral overlap between the emission of CHT-NPA or CHT-PF with the respective absorption of cis or trans DHI. The results suggest an opportunity to explore the binding site of DHI using Förster resonance energy transfer (FRET). Moreover, to more specifically evaluate the DHI binding interactions, we employed molecular docking calculations, which suggested binding near the hydrophobic site of Cys-1-Cys-122 residues. Variations in the electrostatic interactions of the two conformers of DHI adopt unfavorable conformations, leading to the allosteric inhibition of enzymatic activity.

  11. Allosteric Inhibitory Molecular Recognition of a Photochromic Dye by a Digestive Enzyme: Dihydroindolizine makes α-chymotrypsin Photo-responsive.

    PubMed

    Bagchi, Damayanti; Ghosh, Abhijit; Singh, Priya; Dutta, Shreyasi; Polley, Nabarun; Althagafi, Ismail I; Jassas, Rabab S; Ahmed, Saleh A; Pal, Samir Kumar

    2016-09-28

    The structural-functional regulation of enzymes by the administration of an external stimulus such as light could create photo-switches that exhibit unique biotechnological applications. However, molecular recognition of small ligands is a central phenomenon involved in all biological processes. We demonstrate herein that the molecular recognition of a photochromic ligand, dihydroindolizine (DHI), by serine protease α-chymotrypsin (CHT) leads to the photo-control of enzymatic activity. We synthesized and optically characterized the photochromic DHI. Light-induced reversible pyrroline ring opening and a consequent thermal back reaction via 1,5-electrocyclization are responsible for the photochromic behavior. Furthermore, DHI inhibits the enzymatic activity of CHT in a photo-controlled manner. Simultaneous binding of the well-known inhibitors 4-nitrophenyl anthranilate (NPA) or proflavin (PF) in the presence of DHI displays spectral overlap between the emission of CHT-NPA or CHT-PF with the respective absorption of cis or trans DHI. The results suggest an opportunity to explore the binding site of DHI using Förster resonance energy transfer (FRET). Moreover, to more specifically evaluate the DHI binding interactions, we employed molecular docking calculations, which suggested binding near the hydrophobic site of Cys-1-Cys-122 residues. Variations in the electrostatic interactions of the two conformers of DHI adopt unfavorable conformations, leading to the allosteric inhibition of enzymatic activity.

  12. Molecular recognition of PTS-1 cargo proteins by Pex5p: implications for protein mistargeting in primary hyperoxaluria.

    PubMed

    Mesa-Torres, Noel; Tomic, Nenad; Albert, Armando; Salido, Eduardo; Pey, Angel L

    2015-02-13

    Peroxisomal biogenesis and function critically depends on the import of cytosolic proteins carrying a PTS1 sequence into this organelle upon interaction with the peroxin Pex5p. Recent structural studies have provided important insights into the molecular recognition of cargo proteins by Pex5p. Peroxisomal import is a key feature in the pathogenesis of primary hyperoxaluria type 1 (PH1), where alanine:glyoxylate aminotransferase (AGT) undergoes mitochondrial mistargeting in about a third of patients. Here, we study the molecular recognition of PTS1 cargo proteins by Pex5p using oligopeptides and AGT variants bearing different natural PTS1 sequences, and employing an array of biophysical, computational and cell biology techniques. Changes in affinity for Pex5p (spanning over 3-4 orders of magnitude) reflect different thermodynamic signatures, but overall bury similar amounts of molecular surface. Structure/energetic analyses provide information on the contribution of ancillary regions and the conformational changes induced in Pex5p and the PTS1 cargo upon complex formation. Pex5p stability in vitro is enhanced upon cargo binding according to their binding affinities. Moreover, we provide evidence that the rational modulation of the AGT: Pex5p binding affinity might be useful tools to investigate mistargeting and misfolding in PH1 by pulling the folding equilibria towards the native and peroxisomal import competent state.

  13. Selective photoelectrocatalytic degradation of recalcitrant contaminant driven by an n-P heterojunction nanoelectrode with molecular recognition ability.

    PubMed

    Chai, Shouning; Zhao, Guohua; Zhang, Ya-nan; Wang, Yujing; Nong, Fuqiao; Li, Mingfang; Li, Dongming

    2012-09-18

    With in situ molecular imprinting technique, a novel nanoelectrode (MI, n-P)-TiO(2) with n-P heterojunction and molecular recognition ability was fabricated by liquid phase deposition at low temperature. Using bisphenol A (BPA) as template, the spindle-like TiO(2) particles 40-80 nm in size compactly grew on the boron-doped diamond (BDD) substrate. Several spectroscopy measurements demonstrate that the BPA molecules were successfully imprinted on the TiO(2) matrix and numerous specific recognition sites to template were formed after calcination. The transient photocurrent response experiments have confirmed that the (MI, n-P)-TiO(2) nanoelectrode displays outstanding photoelectrocatalytic (PEC) activity and selectivity. The (MI, n-P)-TiO(2) is further employed in degrading the mixture containing BPA and interference 2-naphthol (2-NP). After 2 h, BPA removal reaches 97%, and corresponding kinetic constant is 1.76 h(-1), which is 4.6 times that of 2-NP removal even if 2-NP is much more concentrated. On the electrode without molecular imprint, the removal rate constants of BPA and 2-NP approximately equal, only about 0.5 h(-1). The results indicate that selective PEC oxidation can be realized readily on the (MI, n-P)-TiO(2) nanoelectrode due to the synergetic effects including strong recognition adsorption, formation of n-P heteojunction, and external electrostatic field. The effect of formation of n-P heterojunction on the enhanced PEC performances is also discussed.

  14. Dynamics and recognition within a protein–DNA complex: a molecular dynamics study of the SKN-1/DNA interaction

    PubMed Central

    Etheve, Loïc; Martin, Juliette; Lavery, Richard

    2016-01-01

    Molecular dynamics simulations of the Caenorhabditis elegans transcription factor SKN-1 bound to its cognate DNA site show that the protein–DNA interface undergoes significant dynamics on the microsecond timescale. A detailed analysis of the simulation shows that movements of two key arginine side chains between the major groove and the backbone of DNA generate distinct conformational sub-states that each recognize only part of the consensus binding sequence of SKN-1, while the experimentally observed binding specificity results from a time-averaged view of the dynamic recognition occurring within this complex. PMID:26721385

  15. Diverse molecular recognition properties of blood group A binding monoclonal antibodies.

    PubMed

    Gildersleeve, Jeffrey C; Wright, Whitney Shea

    2016-05-01

    Information about specificity and affinity is critical for use of carbohydrate-binding antibodies. Herein, we evaluated eight monoclonal antibodies to the blood group A (BG-A) antigen. Antibodies 87-G, 9A, HE-10, HE-24, HE-193, HE-195, T36 and Z2A were profiled on a glycan microarray to assess specificity, relative affinity and the influence of glycan density on recognition. Our studies highlight several noteworthy recognition properties. First, most antibodies bound GalNAcα1-3Gal and the BG-A trisaccharide nearly as well as larger BG-A oligosaccharides. Second, several antibodies only bound the BG-A trisaccharide when displayed on certain glycan chains. These first two points indicate that the carrier glycan chains primarily influence selectivity, rather than binding strength. Third, binding of some antibodies was highly dependent on glycan density, illustrating the importance of glycan presentation for recognition. Fourth, some antibodies recognized the tumor-associated Tn antigen, and one antibody only bound the variant composed of a GalNAc-alpha-linked to a serine residue. Collectively, these results provide new insights into the recognition properties of anti-BG-A antibodies.

  16. Molecular Recognition in the Oxidation of Catechols by Dicobalt-BISDIEN Dioxygen Complexes

    DTIC Science & Technology

    1992-01-30

    Recognition in the Oxidation of Catechols by Dicobalt-RISDIEN Dioxygen Complexes Lizete F S Cezar and Bruno Szpoganicz Departamento de Quimica ...bridged bi- nuclear Co(II)-BISDIEN dioxygen complexes; Co20 2 LCat2 + is the bivalent form, and Co20 2 (OH)LCat + and Co 20 2 (OH)2 Cat° are hydroxo

  17. One-pot preparation of a molecularly imprinted hybrid monolithic capillary column for selective recognition and capture of lysozyme.

    PubMed

    Lin, Zian; Lin, Yao; Sun, Xiaobo; Yang, Huanghao; Zhang, Lan; Chen, Guonan

    2013-04-05

    A molecularly imprinted inorganic-organic hybrid monolithic capillary column (MIP hybrid monolith) was synthesized by one-pot process and its application in selective recognition and capture of lysozyme (Lyz) from complex biological samples was described for the first time. Due to a combination of rigid silica matrices and flexible organic hydrogels in one-pot process, stable and accessible recognition sites in the as-prepared MIP hybrid monolith could be obtained after the removal of template protein, which facilitated the rebinding of template and provided good reproducibility and lifetime of use. The morphology, permeability, and pore properties of the as-prepared MIP hybrid monolith were characterized and a uniform monolithic matrix with high surface area and large through-pores was observed. The recognition behavior of MIP and non-imprinted (NIP) hybrid monolith was evaluated by separating template protein from unfractionated protein mixture and the result indicated that the MIP hybrid monolith has much higher affinity toward the template protein than NIP hybrid monolith. High imprinted factor (IF) and separation efficiency could be obtained. In addition, the practicality of the Lyz-MIP hybrid monolith was further evaluated by selective separation of Lyz from egg white and capture of Lyz from human serum by adopting it as an in-tube solid phase microextraction (in-tube SPME), and the good results demonstrated its potential in proteome analysis.

  18. Boronate affinity-based surface molecularly imprinted polymers using glucose as fragment template for excellent recognition of glucosides.

    PubMed

    Peng, Mijun; Xiang, Haiyan; Hu, Xin; Shi, Shuyun; Chen, Xiaoqing

    2016-11-25

    Rapid and efficient extraction of bioactive glycosides from complex natural origins poses a difficult challenge, and then is often inherent bottleneck for their highly utilization. Herein, we propose a strategy to fabricate boronate affinity based surface molecularly imprinted polymers (MIPs) for excellent recognition of glucosides. d-glucose was used as fragment template. Boronic acid, dynamic covalent binding with d-glucose under different pH conditions, was selected as functional monomer to improve specificity. Fe3O4 solid core for surface imprinting using tetraethyl orthosilicate (TEOS) as crosslinker could control imprinted shell thickness for favorable adsorption capacity and satisfactory mass transfer rate, improve hydrophilicity, separate easily by a magnet. Model adsorption studies showed that the resulting MIPs show specific recognition of glucosides. The equilibrium data fitted well to Langmuir equation and the adsorption process could be described by pseudo-second order model. Furthermore, the MIPs were successfully applied for selective extraction of three flavonoid glucosides (daidzin, glycitin, and genistin) from soybean. Results indicated that selective extraction of glucosides from complex aqueous media based on the prepared MIPs is simple, rapid, efficient and specific. Moreover, this method opens up a universal route for imprinting saccharide with cis-diol group for glycosides recognition. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Potentiometric chemosensor for neopterin, a cancer biomarker, using an electrochemically synthesized molecularly imprinted polymer as the recognition unit.

    PubMed

    Sharma, Piyush Sindhu; Wojnarowicz, Agnieszka; Sosnowska, Marta; Benincori, Tiziana; Noworyta, Krzysztof; D'Souza, Francis; Kutner, Wlodzimierz

    2016-03-15

    With an established procedure of molecular imprinting, a synthetic polymer receptor for the neopterin cancer biomarker was devised and used as a recognition unit of a potentiometric chemosensor. For that, bis-bithiophene derivatized with cytosine and bithiophene derivatized with boronic acid were used as functional monomers. The open-circuit potential (OCP) based transduction under flow-injection analysis conditions (FIA) determined neopterin in the concentration range of 0.15-2.5mM with the 22 µM limit of detection (LOD) and 7.01(±0.15) mVmM(-1) sensitivity indicating its potential suitability in clinical analysis applications. The molecularly imprinted polymer (MIP) film showed an appreciable apparent imprinting factor of ~6. The chemosensor successfully discriminated the interferences including the 6-biopterin and pterin structural analogs of neopterin as well as glucose and creatinine. Moreover, it determined neopterin in synthetic serum samples. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Determination of association constant of host-guest supramolecular complex (molecular recognition of carbamazepine, antiseizure drug, with calix(4)arene).

    PubMed

    Meenakshi, C; Jayabal, P; Ramakrishnan, V

    2015-12-05

    The thermodynamic property of the host-guest, inclusion complex formed between p-t-butyl calix(4)arene which is a supramolecule, and the antiseizure drug, carbamazepine was studied. p-t-Butyl calix(4)arene has been used as a host molecule and carbamazepine as a guest molecule. Optical absorption spectral studies were carried out to investigate the molecular recognition properties of p-t-butyl calix(4)arene with carbamazepine. The stochiometry of the host-guest complexes formed and the association constant were determined. An interesting 1:2 stochiometric host-guest complex was formed. Job's continuous method of variation and Benesi-Hildebrand expression were used for the determination of binding constant and the stochiometry of the host-guest complex formed. Molecular dimension of the host molecule plays a vital role in the formation of the host-guest stochiometric complexes.

  1. Single cell molecular recognition of migrating and invading tumor cells using a targeted fluorescent probe to receptor PTPmu.

    PubMed

    Burden-Gulley, Susan M; Qutaish, Mohammed Q; Sullivant, Kristin E; Tan, Mingqian; Craig, Sonya E L; Basilion, James P; Lu, Zheng-Rong; Wilson, David L; Brady-Kalnay, Susann M

    2013-04-01

    Detection of an extracellular cleaved fragment of a cell-cell adhesion molecule represents a new paradigm in molecular recognition and imaging of tumors. We previously demonstrated that probes that recognize the cleaved extracellular domain of receptor protein tyrosine phosphatase mu (PTPmu) label human glioblastoma brain tumor sections and the main tumor mass of intracranial xenograft gliomas. In this article, we examine whether one of these probes, SBK2, can label dispersed glioma cells that are no longer connected to the main tumor mass. Live mice with highly dispersive glioma tumors were injected intravenously with the fluorescent PTPmu probe to test the ability of the probe to label the dispersive glioma cells in vivo. Analysis was performed using a unique three-dimensional (3D) cryo-imaging technique to reveal highly migratory and invasive glioma cell dispersal within the brain and the extent of colabeling by the PTPmu probe. The PTPmu probe labeled the main tumor site and dispersed cells up to 3.5 mm away. The cryo-images of tumors labeled with the PTPmu probe provide a novel, high-resolution view of molecular tumor recognition, with excellent 3D detail regarding the pathways of tumor cell migration. Our data demonstrate that the PTPmu probe recognizes distant tumor cells even in parts of the brain where the blood-brain barrier is likely intact. The PTPmu probe has potential translational significance for recognizing tumor cells to facilitate molecular imaging, a more complete tumor resection and to serve as a molecular targeting agent to deliver chemotherapeutics to the main tumor mass and distant dispersive tumor cells.

  2. Silylated melamine and cyanuric acid as precursors for imprinted and hybrid silica materials with molecular recognition properties.

    PubMed

    Arrachart, Guilhem; Carcel, Carole; Trens, Philippe; Moreau, Jöel J E; Wong Chi Man, Michel

    2009-06-15

    Two monotrialkoxysilylated compounds that consist of complementary fragments of melamine (M) and cyanuric acid (CA) have been synthesised. The molecular recognition properties of the M and CA fragments through complementary hydrogen bonds (DAD and ADA; D=donor, A=acceptor) are the key factor used to direct the formation of hybrid silica materials by using a sol-gel process. These materials were synthesised following two methods: First, an organo-bridged silsesquioxane was obtained by the hydrolysis of the two complementary monotrialkoxysilylated melamine and cyanuric acid derivatives, with fluoride ions as a catalyst. The hydrogen-bonding interactions between the two organic fragments are responsible for the formation of the bridging unit. The transcription of the assembly into the hybrid material was characterised and evidenced by solid-state NMR (29Si, 13C) and FTIR spectroscopic experiments. Second, the molecular recognition was exploited to synthesise an imprinted hybrid silica. This material was prepared by co-condensation of tetraethyl orthosilicate (TEOS) with the monosilylated cyanuric acid derivative (CA) templated by nonsilylated melamine. The melamine template was completely removed by treating the solid material with hydrochloric acid. The reintroduction of the template was performed by treating the resulting material with an aqueous suspension of melamine. These steps were monitored and analysed by several techniques, such as solid-state NMR (29Si, 13C) and FTIR spectroscopic analysis and nitrogen adsorption-desorption isotherms.

  3. The case for intrinsically disordered proteins playing contributory roles in molecular recognition without a stable 3D structure

    PubMed Central

    Uversky, Vladimir N.

    2013-01-01

    The classical ‘lock-and-key’ and ‘induced-fit’ mechanisms for binding both originated in attempts to explain features of enzyme catalysis. For both of these mechanisms and for their recent refinements, enzyme catalysis requires exquisite spatial and electronic complementarity between the substrate and the catalyst. Thus, binding models derived from models originally based on catalysis will be highly biased towards mechanisms that utilize structural complementarity. If mere binding without catalysis is the endpoint, then the structural requirements for the interaction become much more relaxed. Recent observations on specific examples suggest that this relaxation can reach an extreme lack of specific 3D structure, leading to molecular recognition with biological consequences that depend not only upon structural and electrostatic complementarity between the binding partners but also upon kinetic, entropic, and generalized electrostatic effects. In addition to this discussion of binding without fixed structure, examples in which unstructured regions carry out important biological functions not involving molecular recognition will also be discussed. Finally, we discuss whether ‘intrinsically disordered protein’ (IDP) represents a useful new concept. PMID:23361308

  4. Structural analysis and unique molecular recognition properties of a Bauhinia forficata lectin that inhibits cancer cell growth.

    PubMed

    Lubkowski, Jacek; Durbin, Sarah V; Silva, Mariana C C; Farnsworth, David; Gildersleeve, Jeffrey C; Oliva, Maria Luiza V; Wlodawer, Alexander

    2017-02-01

    Lectins have been used at length for basic research and clinical applications. New insights into the molecular recognition properties enhance our basic understanding of carbohydrate-protein interactions and aid in the design/development of new lectins. In this study, we used a combination of cell-based assays, glycan microarrays, and X-ray crystallography to evaluate the structure and function of the recombinant Bauhinia forficata lectin (BfL). The lectin was shown to be cytostatic for several cancer cell lines included in the NCI-60 panel; in particular, it inhibited growth of melanoma cancer cells (LOX IMVI) by over 95%. BfL is dimeric in solution and highly specific for binding of oligosaccharides and glycopeptides with terminal N-acetylgalactosamine (GalNAc). BfL was found to have especially strong binding (apparent Kd  = 0.5-1.0 nm) to the tumor-associated Tn antigen. High-resolution crystal structures were determined for the ligand-free lectin, as well as for its complexes with three Tn glycopeptides, globotetraose, and the blood group A antigen. Extensive analysis of the eight crystal structures and comparison to structures of related lectins revealed several unique features of GalNAc recognition. Of special note, the carboxylate group of Glu126, lining the glycan-binding pocket, forms H-bonds with both the N-acetyl of GalNAc and the peptide amido group of Tn antigens. Stabilization provided by Glu126 is described here for the first time for any GalNAc-specific lectin. Taken together, the results provide new insights into the molecular recognition of carbohydrates and provide a structural understanding that will enable rational engineering of BfL for a variety of applications.

  5. Molecularly Imprinted Sol-Gel-Based QCM Sensor Arrays for the Detection and Recognition of Volatile Aldehydes

    PubMed Central

    Liu, Chuanjun; Wyszynski, Bartosz; Yatabe, Rui; Hayashi, Kenshi; Toko, Kiyoshi

    2017-01-01

    The detection and recognition of metabolically derived aldehydes, which have been identified as important products of oxidative stress and biomarkers of cancers; are considered as an effective approach for early cancer detection as well as health status monitoring. Quartz crystal microbalance (QCM) sensor arrays based on molecularly imprinted sol-gel (MISG) materials were developed in this work for highly sensitive detection and highly selective recognition of typical aldehyde vapors including hexanal (HAL); nonanal (NAL) and bezaldehyde (BAL). The MISGs were prepared by a sol-gel procedure using two matrix precursors: tetraethyl orthosilicate (TEOS) and tetrabutoxytitanium (TBOT). Aminopropyltriethoxysilane (APT); diethylaminopropyltrimethoxysilane (EAP) and trimethoxy-phenylsilane (TMP) were added as functional monomers to adjust the imprinting effect of the matrix. Hexanoic acid (HA); nonanoic acid (NA) and benzoic acid (BA) were used as psuedotemplates in view of their analogous structure to the target molecules as well as the strong hydrogen-bonding interaction with the matrix. Totally 13 types of MISGs with different components were prepared and coated on QCM electrodes by spin coating. Their sensing characters towards the three aldehyde vapors with different concentrations were investigated qualitatively. The results demonstrated that the response of individual sensors to each target strongly depended on the matrix precursors; functional monomers and template molecules. An optimization of the 13 MISG materials was carried out based on statistical analysis such as principle component analysis (PCA); multivariate analysis of covariance (MANCOVA) and hierarchical cluster analysis (HCA). The optimized sensor array consisting of five channels showed a high discrimination ability on the aldehyde vapors; which was confirmed by quantitative comparison with a randomly selected array. It was suggested that both the molecularly imprinting (MIP) effect and the matrix

  6. Molecular Recognition in Mn-Catalyzed C-H Oxidation. Reaction Mechanism and Origin of Selectivity from a DFT Perspective

    PubMed Central

    Balcells, David; Moles, Pamela; Blakemore, James; Raynaud, Christophe; Brudvig, Gary W.; Crabtree, Robert H.

    2010-01-01

    Experimental studies have shown that the C-H oxidation of ibuprofen and methylcyclohexane acetic acid can be carried out with high selectivies using [(terpy’)Mn(OH2)(μ-O)2Mn(OH2)(terpy’)]3+ as catalyst, where terpy’ is a terpyridine ligand functionalized with a phenylene linker and a Kemp’s triacid serving to recognize the reactant via H-bonding. Experiments, described here, suggest that the sulfate counter anion, present in stochiometric amounts, coordinates to manganese in place of water. DFT calculations have been carried out using [(terpy’)Mn(O)(μ-O)2Mn(SO4)(terpy’)]+ as model catalyst, to analyze the origin of selectivity and its relation to molecular recognition, as well as the mechanism of catalyst inhibition by tert-butyl benzoic acid. The calculations show that a number of spin states, all having radical oxygen character, are energetically accessible. All these spin states promote C-H oxidation via a rebound mechanism. The catalyst recognizes the substrate by a double H bond. This interaction orients the substrate inducing highly selective C-H oxidation. The double hydrogen bond stabilizes the reactant, the transition state and the product to the same extent. Consequently, the reaction occurs at lower energy than without molecular recognition. The association of the catalyst with tert-butyl benzoic acid is shown to shield the access of unbound substrate to the reactive oxo site, hence preventing non-selective hydroxylation. It is shown that the two recognition sites of the catalyst can be used in a cooperative manner to control the access to the reactive centre. PMID:19623399

  7. Molecularly Imprinted Sol-Gel-Based QCM Sensor Arrays for the Detection and Recognition of Volatile Aldehydes.

    PubMed

    Liu, Chuanjun; Wyszynski, Bartosz; Yatabe, Rui; Hayashi, Kenshi; Toko, Kiyoshi

    2017-02-16

    The detection and recognition of metabolically derived aldehydes, which have been identified as important products of oxidative stress and biomarkers of cancers; are considered as an effective approach for early cancer detection as well as health status monitoring. Quartz crystal microbalance (QCM) sensor arrays based on molecularly imprinted sol-gel (MISG) materials were developed in this work for highly sensitive detection and highly selective recognition of typical aldehyde vapors including hexanal (HAL); nonanal (NAL) and bezaldehyde (BAL). The MISGs were prepared by a sol-gel procedure using two matrix precursors: tetraethyl orthosilicate (TEOS) and tetrabutoxytitanium (TBOT). Aminopropyltriethoxysilane (APT); diethylaminopropyltrimethoxysilane (EAP) and trimethoxy-phenylsilane (TMP) were added as functional monomers to adjust the imprinting effect of the matrix. Hexanoic acid (HA); nonanoic acid (NA) and benzoic acid (BA) were used as psuedotemplates in view of their analogous structure to the target molecules as well as the strong hydrogen-bonding interaction with the matrix. Totally 13 types of MISGs with different components were prepared and coated on QCM electrodes by spin coating. Their sensing characters towards the three aldehyde vapors with different concentrations were investigated qualitatively. The results demonstrated that the response of individual sensors to each target strongly depended on the matrix precursors; functional monomers and template molecules. An optimization of the 13 MISG materials was carried out based on statistical analysis such as principle component analysis (PCA); multivariate analysis of covariance (MANCOVA) and hierarchical cluster analysis (HCA). The optimized sensor array consisting of five channels showed a high discrimination ability on the aldehyde vapors; which was confirmed by quantitative comparison with a randomly selected array. It was suggested that both the molecularly imprinting (MIP) effect and the matrix

  8. Application of pattern recognition in molecular spectroscopy: Automatic line search in high-resolution spectra

    NASA Astrophysics Data System (ADS)

    Bykov, A. D.; Pshenichnikov, A. M.; Sinitsa, L. N.; Shcherbakov, A. P.

    2004-07-01

    An expert system has been developed for the initial analysis of a recorded spectrum, namely, for the line search and the determination of line positions and intensities. The expert system is based on pattern recognition algorithms. Object recognition learning allows the system to achieve the needed flexibility and automatically detect groups of overlapping lines, whose profiles should be fit together. Gauss, Lorentz, and Voigt profiles are used as model profiles to which spectral lines are fit. The expert system was applied to processing of the Fourier transform spectrum of the D2O molecule in the region 3200-4200 cm-1, and it detected 4670 lines in the spectrum, which consisted of 439000 dots. No one experimentally observed line exceeding the noise level was missed.

  9. Polymer-based separations: Synthesis and application of polymers for ionic and molecular recognition

    SciTech Connect

    Alexandratos, S.D.

    1992-01-01

    Polymer-based separations have utilized resins such as sulfonic, acrylic, and iminodiacetic acid resins and the XAD series. Selective polymeric reagents for reaction with a targeted metal ion were synthesized as polymers with two different types of functional groups, each operating on the ions through a different mechanism. There are 3 classes of DMBPs (dual mechanism bifunctional polymers). Research during this period dealing with metal ion recognition focused on two of these classes (reduction of metal ions to metal; selective complexation).

  10. Dynamic chemistry of anion recognition

    SciTech Connect

    Custelcean, Radu

    2012-01-01

    In the past 40 years, anion recognition by synthetic receptors has grown into a rich and vibrant research topic, developing into a distinct branch of Supramolecular Chemistry. Traditional anion receptors comprise organic scaffolds functionalized with complementary binding groups that are assembled by multistep organic synthesis. Recently, a new approach to anion receptors has emerged, in which the host is dynamically self-assembled in the presence of the anionic guest, via reversible bond formation between functional building units. While coordination bonds were initially employed for the self-assembly of the anion hosts, more recent studies demonstrated that reversible covalent bonds can serve the same purpose. In both cases, due to their labile connections, the molecular constituents have the ability to assemble, dissociate, and recombine continuously, thereby creating a dynamic combinatorial library (DCL) of receptors. The anionic guests, through specific molecular recognition, may then amplify (express) the formation of a particular structure among all possible combinations (real or virtual) by shifting the equilibria involved towards the most optimal receptor. This approach is not limited to solution self-assembly, but is equally applicable to crystallization, where the fittest anion-binding crystal may be selected. Finally, the pros and cons of employing dynamic combinatorial chemistry (DCC) vs molecular design for developing anion receptors, and the implications of both approaches to selective anion separations, will be discussed.

  11. Molecular determinants of prokaryotic voltage-gated sodium channels for recognition of local anesthetics.

    PubMed

    Shimomura, Takushi; Irie, Katsumasa; Fujiyoshi, Yoshinori

    2016-08-01

    Local anesthetics (LAs) inhibit mammalian voltage-gated Na(+) channels (Navs) and are thus clinically important. LAs also inhibit prokaryotic Navs (BacNavs), which have a simpler structure than mammalian Navs. To elucidate the detailed mechanisms of LA inhibition to BacNavs, we used NavBh, a BacNav from Bacillus halodurans, to analyze the interactions of several LAs and quaternary ammoniums (QAs). Based on the chemical similarity of QA with the tertiary-alkylamine (TAA) group of LAs, QAs were used to determine the residues required for the recognition of TAA by NavBh. We confirmed that two residues, Thr220 and Phe227, are important for LA binding; a methyl group of Thr220 is important for recognizing both QAs and LAs, whereas Phe227 is involved in holding blockers at the binding site. In addition, we found that NavBh holds blockers in a closed state, consistent with the large inner cavity observed in the crystal structures of BacNavs. These findings reveal the inhibition mechanism of LAs in NavBh, where the methyl group of Thr220 provides the main receptor site for the TAA group and the bulky phenyl group of Phe227 holds the blockers inside the large inner cavity. These two residues correspond to the two LA recognition residues in mammalian Navs, which suggests the relevance of the LA recognition between BacNavs and mammalian Navs. © 2016 Federation of European Biochemical Societies.

  12. Selective recognition of Triamterene in biological samples by molecularly imprinted monolithic column with a pseudo template employed.

    PubMed

    Zhao, Xiao-Yun; Zhang, Hong-Wu; Liang, Zhen-Jie; Shu, Ya-Ping; Liang, Yong

    2013-05-01

    Melamine (MAM) was employed as a pseudo template to prepare a molecularly imprinted polymer monolithic column which presents the ability of selective recognition to Triamterene (TAT), whose structure was similar to that of MAM. Methacrylic acid and ethylene glycol dimethacrylate were applied as functional monomer and cross-linker, respectively, during the in situ polymerization process. Chromatographic behaviors were evaluated, the results indicated that the molecularly imprinted polymer monolithic column possessed excellent affinity and selectivity for TAT, and the imprinting factor was high up to 3.99 when 7:3 of ACN/water v/v was used as mobile phase. In addition, the dissociation constant and the binding sites were also determined by frontal chromatography as 134.31 μmol/L and 132.28 μmol/g, respectively, which demonstrated that the obtained molecularly imprinted polymer monolith had a high binding capacity and strong affinity ability to TAT. Furthermore, biological samples could be directly injected into the column and TAT was enriched with the optimized mobile phase. These assays gave recovery values higher than 91.60% with RSD values that were always less than 3.5%. The molecularly imprinted monolithic column greatly simplified experiment procedure and can be applied to preconcentration, purification, and analysis of TAT in biological samples.

  13. Fabrication of dopamine modified polylactide-poly(ethylene glycol) scaffolds with adjustable properties.

    PubMed

    Shen, Jiali; Shi, Dongjian; Shi, Chang; Li, Xiaojie; Chen, Mingqing

    2017-12-01

    Bio-based polymers have been widely used to be as scaffolds for repairing the bone defects. However, the polymer scaffolds are generally lack of bioactivity and cell recognition site. Seeking effective ways to improve the bioactivity and interaction between materials and tissue or cells is clinically important for long-term performance of bone repair materials. In this work, polylactide-b-poly(ethylene glycol)-b-polylactide (PLA-PEG-PLA, PLEL) tri-block copolymers were firstly synthesized by ring-opening polymerization of lactide using PEG with various molecular weights. Inspired by excellent adhesion of dopamine (DA), a facile and effective method was developed to fabricate polydopamine (PDA) and polydopamine/nano-hydroxyapatite (PDA/n-HA) modified PLEL scaffolds by deposition of PDA and PDA/n-HA coating. The surface structure, degradation rates and mineralization of the modified PLEL scaffolds were investigated, and obviously improved after immobilization of PDA and PDA/n-HA coatings. Moreover, the biocompatible results showed a significant increase in cells viability and adhesion. Therefore, the surface modification with PDA and PDA/n-HA could not only adjust the properties of scaffolds, but also reinforce the interfacial adhesion between the PLEL and cells.

  14. Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula

    PubMed Central

    2011-01-01

    Background We studied patterns of molecular adaptation in the wild Mediterranean legume Medicago truncatula. We focused on two phenotypic traits that are not functionally linked: flowering time and perception of symbiotic microbes. Phenology is an important fitness component, especially for annual plants, and many instances of molecular adaptation have been reported for genes involved in flowering pathways. While perception of symbiotic microbes is also integral to adaptation in many plant species, very few reports of molecular adaptation exist for symbiotic genes. Here we used data from 57 individuals and 53 gene fragments to quantify the overall strength of both positive and purifying selection in M. truncatula and asked if footprints of positive selection can be detected at key genes of rhizobia recognition pathways. Results We examined nucleotide variation among 57 accessions from natural populations in 53 gene fragments: 5 genes involved in nitrogen-fixing bacteria recognition, 11 genes involved in flowering, and 37 genes used as control loci. We detected 1757 polymorphic sites yielding an average nucleotide diversity (pi) of 0.003 per site. Non-synonymous variation is under sizable purifying selection with 90% of amino-acid changing mutations being strongly selected against. Accessions were structured in two groups consistent with geographical origins. Each of these two groups harboured an excess of rare alleles, relative to expectations of a constant-sized population, suggesting recent population expansion. Using coalescent simulations and an approximate Bayesian computation framework we detected several instances of genes departing from selective neutrality within each group and showed that the polymorphism of two nodulation and four flowering genes has probably been shaped by recent positive selection. Conclusion We quantify the intensity of purifying selection in the M. truncatula genome and show that putative footprints of natural selection can be

  15. Molecular recognition of H3/H4 histone tails by the tudor domains of JMJD2A: a comparative molecular dynamics simulations study.

    PubMed

    Ozboyaci, Musa; Gursoy, Attila; Erman, Burak; Keskin, Ozlem

    2011-03-25

    Histone demethylase, JMJD2A, specifically recognizes and binds to methylated lysine residues at histone H3 and H4 tails (especially trimethylated H3K4 (H3K4me3), trimethylated H3K9 (H3K9me3) and di,trimethylated H4K20 (H4K20me2, H4K20me3)) via its tandem tudor domains. Crystal structures of JMJD2A-tudor binding to H3K4me3 and H4K20me3 peptides are available whereas the others are not. Complete picture of the recognition of the four histone peptides by the tandem tudor domains yet remains to be clarified. We report a detailed molecular dynamics simulation and binding energy analysis of the recognition of JMJD2A-tudor with four different histone tails. 25 ns fully unrestrained molecular dynamics simulations are carried out for each of the bound and free structures. We investigate the important hydrogen bonds and electrostatic interactions between the tudor domains and the peptide molecules and identify the critical residues that stabilize the complexes. Our binding free energy calculations show that H4K20me2 and H3K9me3 peptides have the highest and lowest affinity to JMJD2A-tudor, respectively. We also show that H4K20me2 peptide adopts the same binding mode with H4K20me3 peptide, and H3K9me3 peptide adopts the same binding mode with H3K4me3 peptide. Decomposition of the enthalpic and the entropic contributions to the binding free energies indicate that the recognition of the histone peptides is mainly driven by favourable van der Waals interactions. Residue decomposition of the binding free energies with backbone and side chain contributions as well as their energetic constituents identify the hotspots in the binding interface of the structures. Energetic investigations of the four complexes suggest that many of the residues involved in the interactions are common. However, we found two receptor residues that were related to selective binding of the H3 and H4 ligands. Modifications or mutations on one of these residues can selectively alter the recognition of the H3

  16. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition

    SciTech Connect

    Melero, Cristina; Ollikainen, Noah; Harwood, Ian; Karpiak, Joel; Kortemme, Tanja

    2014-10-13

    Re-engineering protein–protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of “second-site suppressors,” where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein–protein interfaces. To extend this approach, it would be advantageous to be able to “transplant” existing engineered and experimentally validated specificity changes to other homologous protein–protein complexes. Here, we test this strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain–peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein–protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. The context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein–protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context.

  17. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition

    DOE PAGES

    Melero, Cristina; Ollikainen, Noah; Harwood, Ian; ...

    2014-10-13

    Re-engineering protein–protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of “second-site suppressors,” where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein–protein interfaces. To extend this approach, it would be advantageous to be able to “transplant” existing engineered and experimentally validated specificity changes to other homologous protein–protein complexes. Here, we test thismore » strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain–peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein–protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. The context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein–protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context.« less

  18. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition

    PubMed Central

    Melero, Cristina; Ollikainen, Noah; Harwood, Ian; Karpiak, Joel; Kortemme, Tanja

    2014-01-01

    Reengineering protein–protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of “second-site suppressors,” where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein–protein interfaces. To extend this approach, it would be advantageous to be able to “transplant” existing engineered and experimentally validated specificity changes to other homologous protein–protein complexes. Here, we test this strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain–peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein–protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. Although the context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein–protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context. PMID:25313039

  19. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition.

    PubMed

    Melero, Cristina; Ollikainen, Noah; Harwood, Ian; Karpiak, Joel; Kortemme, Tanja

    2014-10-28

    Reengineering protein-protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of "second-site suppressors," where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein-protein interfaces. To extend this approach, it would be advantageous to be able to "transplant" existing engineered and experimentally validated specificity changes to other homologous protein-protein complexes. Here, we test this strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain-peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein-protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. Although the context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein-protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context.

  20. Discrimination of herbal medicines by molecular spectroscopy and chemical pattern recognition

    NASA Astrophysics Data System (ADS)

    Mao, Jianjiang; Xu, Jingwei

    2006-10-01

    The molecular spectroscopy (including near infrared diffuse reflection spectroscopy, Raman spectroscopy and infrared spectroscopy) with OPUS/Ident software was applied to clustering ginsengs according to species and processing methods. The results demonstrate that molecular spectroscopic analysis could provide a rapid, nondestructive and reliable method for identification of Chinese traditional medicine. It's found that the result of Raman spectroscopic analysis was the best one among these three methods. Comparing with traditional methods, which are laborious and time consuming, the molecular spectroscopic analysis is more effective.

  1. Small-molecule recognition for controlling molecular motion in hydrogen-bond-assembled rotaxanes.

    PubMed

    Martinez-Cuezva, Alberto; Berna, Jose; Orenes, Raul-Angel; Pastor, Aurelia; Alajarin, Mateo

    2014-06-23

    Di(acylamino)pyridines successfully template the formation of hydrogen-bonded rotaxanes through five-component clipping reactions. A solid-state study showed the participation of the pyridine nitrogen atom in the stabilization of the mechanical bond between the thread and the benzylic amide macrocycle. The addition of external complementary binders to a series of interlocked bis(2,6-di(acylamino)pyridines) promoted restraint of the back and forward ring motion. The original translation can be restored through a competitive recognition event by the addition of a preorganized bis(di(acylamino)pyridine) that forms stronger ADA-DAD complexes with the external binders.

  2. Interactive exploration of chemical space with Scaffold Hunter.

    PubMed

    Wetzel, Stefan; Klein, Karsten; Renner, Steffen; Rauh, Daniel; Oprea, Tudor I; Mutzel, Petra; Waldmann, Herbert

    2009-08-01

    We describe Scaffold Hunter, a highly interactive computer-based tool for navigation in chemical space that fosters intuitive recognition of complex structural relationships associated with bioactivity. The program reads compound structures and bioactivity data, generates compound scaffolds, correlates them in a hierarchical tree-like arrangement, and annotates them with bioactivity. Brachiation along tree branches from structurally complex to simple scaffolds allows identification of new ligand types. We provide proof of concept for pyruvate kinase.

  3. A molecular mechanism realizing sequence-specific recognition of nucleic acids by TDP-43

    PubMed Central

    Furukawa, Yoshiaki; Suzuki, Yoh; Fukuoka, Mami; Nagasawa, Kenichi; Nakagome, Kenta; Shimizu, Hideaki; Mukaiyama, Atsushi; Akiyama, Shuji

    2016-01-01

    TAR DNA-binding protein 43 (TDP-43) is a DNA/RNA-binding protein containing two consecutive RNA recognition motifs (RRM1 and RRM2) in tandem. Functional abnormality of TDP-43 has been proposed to cause neurodegeneration, but it remains obscure how the physiological functions of this protein are regulated. Here, we show distinct roles of RRM1 and RRM2 in the sequence-specific substrate recognition of TDP-43. RRM1 was found to bind a wide spectrum of ssDNA sequences, while no binding was observed between RRM2 and ssDNA. When two RRMs are fused in tandem as in native TDP-43, the fused construct almost exclusively binds ssDNA with a TG-repeat sequence. In contrast, such sequence-specificity was not observed in a simple mixture of RRM1 and RRM2. We thus propose that the spatial arrangement of multiple RRMs in DNA/RNA binding proteins provides steric effects on the substrate-binding site and thereby controls the specificity of its substrate nucleotide sequences. PMID:26838063

  4. Molecular cloning, tissue expression, and subcellular localization of porcine peptidoglycan recognition proteins 3 and 4.

    PubMed

    Ueda, Wataru; Tohno, Masanori; Shimazu, Tomoyuki; Fujie, Hitomi; Aso, Hisashi; Kawai, Yasushi; Numasaki, Muneo; Saito, Tadao; Kitazawa, Haruki

    2011-09-15

    Peptidoglycan recognition proteins (PGRPs) are innate immune molecules that are present in most invertebrates and vertebrates. Mammals have four PGRPs, PGLYRP1-4. In the present study, we cloned the cDNAs encoding porcine PGLYRP3 and 4 from the esophagus of adult swine. The length of the complete open reading frames of porcine PGLYRP3 and 4 are identical and contain 1125bp encoding 374 amino acid residues. The amino acid sequences of these two proteins were more similar to their human orthologs (78.9% [PGLYRP3] and 73.9% [PGLYRP4]) than to their mouse orthologs (71.3% [PGLYRP3] and 67.9% [PGLYRP4]). Expression analysis revealed that both PGLYRP3 and 4 were more strongly expressed in digestive tract, especially the esophagus, than in immune organs such as spleen or mesenteric lymph nodes in both newborn and adult swine. To analyze the subcellular distribution of porcine PGLYRP1-4, we constructed transfectant cell lines. Western blot and flow cytometric analyses revealed that porcine PGLYRP3 and 4 are not only secreted, but also expressed on the cell surface, unlike PGLYRP1 and 2. These results should help contribute to the understanding of PGLYRP3- and 4-mediated immune responses via their recognition of intestinal microorganisms in newborn and adult swine.

  5. Aptamer-Based Molecular Recognition of Lysergamine, Metergoline and Small Ergot Alkaloids

    PubMed Central

    Rouah-Martin, Elsa; Mehta, Jaytry; van Dorst, Bieke; de Saeger, Sarah; Dubruel, Peter; Maes, Bert U. W.; Lemiere, Filip; Goormaghtigh, Erik; Daems, Devin; Herrebout, Wouter; van Hove, François; Blust, Ronny; Robbens, Johan

    2012-01-01

    Ergot alkaloids are mycotoxins produced by fungi of the genus Claviceps, which infect cereal crops and grasses. The uptake of ergot alkaloid contaminated cereal products can be lethal to humans and animals. For food safety assessment, analytical techniques are currently used to determine the presence of ergot alkaloids in food and feed samples. However, the number of samples which can be analyzed is limited, due to the cost of the equipment and the need for skilled personnel. In order to compensate for the lack of rapid tests for the detection of ergot alkaloids, the aim of this study was to develop a specific recognition element for ergot alkaloids, which could be further applied to produce a colorimetric reaction in the presence of these toxins. As recognition elements, single-stranded DNA ligands were selected by using an iterative selection procedure named SELEX, i.e., Systematic Evolution of Ligands by EXponential enrichment. After several selection cycles, the resulting aptamers were cloned and sequenced. A surface plasmon resonance analysis enabled determination of the dissociation constants of the complexes of aptamers and lysergamine. Dissociation constants in the nanomolar range were obtained with three selected aptamers. One of the selected aptamers, having a dissociation constant of 44 nM, was linked to gold nanoparticles and it was possible to produce a colorimetric reaction in the presence of lysergamine. This system could also be applied to small ergot alkaloids in an ergot contaminated flour sample. PMID:23242153

  6. Atomic force microscopy-based molecular studies on the recognition of immunogenic chlorinated ovalbumin by macrophage receptors.

    PubMed

    Zapotoczny, Szczepan; Biedroń, Rafał; Marcinkiewicz, Janusz; Nowakowska, Maria

    2012-02-01

    This report presents simple and reliable approach developed to study the specific recognition events between chlorinated ovalbumin (OVA) and macrophages using atomic force microscopy (AFM). Thanks to the elimination of nonspecific adhesion, the interactions of the native and chlorinated OVA with a membrane of macrophages could be quantified using exclusively the so-called adhesion frequency (AF). The proposed system not only enabled the application of AFM-based force measurements for such poorly defined ligand-receptor pairs but also significantly improved both the acquisition and the processing of the data. The proteins were immobilized on the gold-coated AFM tips from the aqueous solutions containing charged thiol adsorbates. Such surface dilution of the proteins ensured the presence of single or just a few macromolecules at the tip-surface contact. The formation of negatively charged monolayer on the tip dramatically limited its nonspecific interactions with the macrophage surface. In such systems, AF was used as a measure of the recognition events even if the interaction forces varied significantly for sets of measurements. The system with the native OVA, a weak immunogen, showed only negligible AF compared with 85% measured for the immunogenic chlorinated OVA. The AF values varied with the tip-macrophage contact time and loading velocity. Blocking of the receptors by the chlorinated OVA was also confirmed. The developed approach can be also used to study other ligand-receptor interactions in poorly defined biological systems with intrinsically broad distribution of the rupture forces, thus opening new fields for AFM-based recognition on molecular level.

  7. Binding of ibuprofen to human hemoglobin: Elucidation of their molecular recognition by spectroscopy, calorimetry and molecular modeling techniques.

    PubMed

    Seal, Paromita; Sikdar, Jyotirmoy; Roy, Amartya; Haldar, Rajen

    2017-09-22

    Ibuprofen, used for the treatment of acute and chronic pain, osteoarthritis, rheumatoid arthritis, and related conditions has ample affinity to globular proteins. Here we have explored this fundamental study pertaining to the interaction of ibuprofen with human hemoglobin (HHb), using multispectroscopic, calorimetric, and molecular modeling techniques to gain insights into molecular aspects of binding mechanism. Ibuprofen-induced graded decrease in absorption spectra indicates protein disruption along with sedimentation of HHb particle. Red shifting of absorption peak at 195 nm indicates alteration in the secondary structure of HHb upon interaction with ibuprofen. Flouremetric and isothermal titration calorimetric (ITC) studies suggested one binding site in HHb for ibuprofen at 298.15 K. However, with increase in temperature, ITC revealed increasing number of binding sites. The negative values of Gibbs energy change (ΔG(0)) and enthalpy change (ΔH(0)) along with positive value of entropy change (ΔS(0)) strongly suggest that it is entropy-driven spontaneous exothermic reaction. Moreover, hydrophobic interaction, hydrogen bonding and π-π interaction play major role in this binding process as evidenced from ANS (8-anilino-1-napthalenesulphonic acid), sucrose binding, and molecular modeling studies. The interaction impacts on structural integrity and functional aspects of HHb as confirmed by CD spectroscopy, increased free iron release, increased rate of co-oxidation and decreased rate of esterase activity. These findings suggest us to conclude that ibuprofen upon interaction perturbs both structural and functional aspects of HHb.

  8. Superhydrophilic molecularly imprinted polymers based on a water-soluble functional monomer for the recognition of gastrodin in water media.

    PubMed

    Ji, Wenhua; Zhang, Mingming; Wang, Daijie; Wang, Xiao; Liu, Jianhua; Huang, Luqi

    2015-12-18

    In this study, the first successfully developed superhydrophilic molecularly imprinted polymers (MIPs) for gastrodin recognition have been described. MIPs were prepared via the bulk polymerization process in an aqueous solution using alkenyl glycosides glucose (AGG) as the water-soluble functional monomer. The non-imprinted polymers (NIPs) were also synthesized using the same method without the use of the template. The dynamic water contact angles and photographs of the dispersion properties confirmed that the molecularly imprinted polymers displayed excellent superhydrophilicity. The results demonstrated that the MIPs exhibited high selectivity and an excellent imprinting effect. A molecularly imprinted solid phase extraction (MISPE) method was established. Optimization of various parameters affecting MISPE was investigated. Under the optimized conditions, a wide linear range (0.001-100.0μgmL(-1)) and low limits of detection (LOD) and quantification (LOQ) (0.03 and 0.09ngmL(-1), respectively) were achieved. When compared with the NIPs, higher recoveries (90.5% to 97.6%) of gastrodin with lower relative standard deviations values (below 6.4%) using high performance liquid chromatography were obtained at three spiked levels in three blank samples. These results demonstrated one efficient, highly selective and environmentally-friendly MISPE technique with excellent reproducibility for the purification and pre-concentration of gastrodin from an aqueous extract of Gastrodia elata roots.

  9. Molecular characteristics of a fluorescent chemosensor for the recognition of ferric ion based on photoresponsive azobenzene derivative

    NASA Astrophysics Data System (ADS)

    Chi, Zhen; Ran, Xia; Shi, Lili; Lou, Jie; Kuang, Yanmin; Guo, Lijun

    2017-01-01

    Metal ion recognition is of great significance in biological and environmental detection. So far, there is very few research related to the ferric ion sensing based on photoresponsive azobenzene derivatives. In this work, we report a highly selective fluorescent ;turn-off; sensor for Fe3 + ions and the molecular sensing characteristics based on an azobenzene derivative, N-(3,4,5-octanoxyphenyl)-N‧-4-[(4-hydroxyphenyl)azophenyl]1,3,4-oxadiazole (AOB-t8). The binding association constant was determined to be 6.07 × 103 M- 1 in ethanol and the stoichiometry ratio of 2:2 was obtained from Job's plot and MS spectra. The AOB-t8 might be likely to form the dimer structure through the chelation of ferric ion with the azobenzene moiety. Meanwhile, it was found that the photoisomerization property of AOB-t8 was regulated by the binding with Fe3 +. With the chelation of Fe3 +, the regulated molecular rigidity and the perturbed of electronic state and molecular geometry was suggested to be responsible for the accelerated isomerization of AOB-t8 to UV irradiation and the increased fluorescence lifetime of both trans- and cis-AOB-t8-Fe(III). Moreover, the reversible sensing of AOB-t8 was successfully observed by releasing the iron ion from AOB-t8-Fe(III) with the addition of citric acid.

  10. Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition.

    PubMed

    Duss, Olivier; Michel, Erich; Diarra dit Konté, Nana; Schubert, Mario; Allain, Frédéric H-T

    2014-04-01

    The carbon storage regulator/regulator of secondary metabolism (Csr/Rsm) type of small non-coding RNAs (sRNAs) is widespread throughout bacteria and acts by sequestering the global translation repressor protein CsrA/RsmE from the ribosome binding site of a subset of mRNAs. Although we have previously described the molecular basis of a high affinity RNA target bound to RsmE, it remains unknown how other lower affinity targets are recognized by the same protein. Here, we have determined the nuclear magnetic resonance solution structures of five separate GGA binding motifs of the sRNA RsmZ of Pseudomonas fluorescens in complex with RsmE. The structures explain how the variation of sequence and structural context of the GGA binding motifs modulate the binding affinity for RsmE by five orders of magnitude (∼10 nM to ∼3 mM, Kd). Furthermore, we see that conformational adaptation of protein side-chains and RNA enable recognition of different RNA sequences by the same protein contributing to binding affinity without conferring specificity. Overall, our findings illustrate how the variability in the Csr/Rsm protein-RNA recognition allows a fine-tuning of the competition between mRNAs and sRNAs for the CsrA/RsmE protein.

  11. Molecular basis for the wide range of affinity found in Csr/Rsm protein–RNA recognition

    PubMed Central

    Duss, Olivier; Michel, Erich; Diarra dit Konté, Nana; Schubert, Mario; Allain, Frédéric H.-T.

    2014-01-01

    The carbon storage regulator/regulator of secondary metabolism (Csr/Rsm) type of small non-coding RNAs (sRNAs) is widespread throughout bacteria and acts by sequestering the global translation repressor protein CsrA/RsmE from the ribosome binding site of a subset of mRNAs. Although we have previously described the molecular basis of a high affinity RNA target bound to RsmE, it remains unknown how other lower affinity targets are recognized by the same protein. Here, we have determined the nuclear magnetic resonance solution structures of five separate GGA binding motifs of the sRNA RsmZ of Pseudomonas fluorescens in complex with RsmE. The structures explain how the variation of sequence and structural context of the GGA binding motifs modulate the binding affinity for RsmE by five orders of magnitude (∼10 nM to ∼3 mM, Kd). Furthermore, we see that conformational adaptation of protein side-chains and RNA enable recognition of different RNA sequences by the same protein contributing to binding affinity without conferring specificity. Overall, our findings illustrate how the variability in the Csr/Rsm protein–RNA recognition allows a fine-tuning of the competition between mRNAs and sRNAs for the CsrA/RsmE protein. PMID:24561806

  12. Sorting of C4 olefins with interpenetrated hybrid ultramicroporous materials by combining molecular recognition and size-sieving.

    PubMed

    Zhang, Zhaoqiang; Yang, Qiwei; Cui, Xili; Yang, Lifeng; Bao, Zongbi; Ren, Qilong; Xing, Huabin

    2017-10-05

    C4 olefin separations present one of the grand challenges in hydrocarbon purifications due to their similar structures, in which case single separation mechanism often met with limited success. Here we report a series of anion-pillared interpenetrated copper coordination networks with fine-tuning cavity and functional site disposition in 0.2 Å scale increments through rational altering the anion pillars and organic linkers (GeFSIX-2-Cu-i (ZU-32), NbFSIX-2-Cu-i (ZU-52), GeFSIX-14-Cu-i (ZU-33)), which enable selective recognition of different C4 olefins. These materials achieve simultaneously an exquisite control on the rotation of organic linkers to create a contracted flexible pore window that excludes specific C4 olefins, while still adsorbs significant 1, 3-butadiene (C4H6) or 1-butene (n-C4H8). Combining the molecular recognition and size-sieving effect, these materials unexpectedly realized the sieving of C4H6/n-C4H8, C4H6/iso-C4H8 and n-C4H8/iso-C4H8 along with high capacity. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics

    PubMed Central

    2011-01-01

    Background Phosphopeptide-binding domains mediate many vital cellular processes such as signal transduction and protein recognition. We studied three well-known domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated (FHA) domain. The first two recognize both phosphothreonine (pThr) and phosphoserine (pSer) residues, but FHA has high specificity for pThr residues. Here we used molecular dynamics (MD) simulations to reveal how FHA exclusively chooses pThr and how BRCT and WW recognize both pThr/pSer. The work also investigated the energies and thermodynamic information of intermolecular interactions. Results Simulations carried out included wide-type and mutated systems. Through analysis of MD simulations, we found that the conserved His residue defines dual loops feature of the FHA domain, which creates a small cavity reserved for only the methyl group of pThr. These well-organized loop interactions directly response to the pThr binding selectivity, while single loop (the 2nd phosphobinding site of FHA) or in combination with α-helix (BRCT repeats) or β-sheet (WW domain) fail to differentiate pThr/pSer. Conclusions Understanding the domain pre-organizations constructed by conserved residues and the driving force of domain-phosphopeptide recognition provides structural insight into pThr specific binding, which also helps in engineering proteins and designing peptide inhibitors. PMID:21612598

  14. Carbohydrate-protein recognition: molecular dynamics simulations and free energy analysis of oligosaccharide binding to concanavalin A.

    PubMed Central

    Bryce, R A; Hillier, I H; Naismith, J H

    2001-01-01

    Carbohydrate ligands are important mediators of biomolecular recognition. Microcalorimetry has found the complex-type N-linked glycan core pentasaccharide beta-GlcNAc-(1-->2)-alpha-Man-(1-->3)-[beta-GlcNAc-(1-->2)-alpha-Man-(1-->6)]-Man to bind to the lectin, Concanavalin A, with almost the same affinity as the trimannoside, Man-alpha-(1-->6)-[Man-alpha-(1-->3)]-Man. Recent determination of the structure of the pentasaccharide complex found a glycosidic linkage psi torsion angle to be distorted by 50 degrees from the NMR solution value and perturbation of some key mannose-protein interactions observed in the structures of the mono- and trimannoside complexes. To unravel the free energy contributions to binding and to determine the structural basis for this degeneracy, we present the results of a series of nanosecond molecular dynamics simulations, coupled to analysis via the recently developed MM-GB/SA approach (Srinivasan et al., J. Am. Chem. Soc. 1998, 120:9401-9409). These calculations indicate that the strength of key mannose-protein interactions at the monosaccharide site is preserved in both the oligosaccharides. Although distortion of the pentasaccharide is significant, the principal factor in reduced binding is incomplete offset of ligand and protein desolvation due to poorly matched polar interactions. This analysis implies that, although Concanavalin A tolerates the additional 6 arm GlcNAc present in the pentasaccharide, it does not serve as a key recognition determinant. PMID:11509352

  15. Effective Use of Molecular Recognition in Gas Sensing: Results from Acoustic Wave and In-Situ FTIR Measurements

    SciTech Connect

    Bodenhofer, K,; Gopel, W.; Hierlemann, A.; Ricco, A.J.

    1998-12-09

    To probe directly the analyte/film interactions that characterize molecular recognition in gas sensors, we recorded changes to the in-situ surface vibrational spectra of specifically fictionalized surface acoustic wave (SAW) devices concurrently with analyte exposure and SAW measurement of the extent of sorption. Fourier-lmnsform infrared external- reflectance spectra (FTIR-ERS) were collected from operating 97-MH2 SAW delay lines during exposure to a range of analytes as they interacted with thin-film coatings previously shown to be selective: cyclodextrins for chiral recognition, Ni-camphorates for Lewis bases such as pyridine and organophosphonates, and phthalocyanines for aromatic compounds. In most cases where specific chemical interactions-metal coordination, "cage" compound inclusion, or z stacking-were expected, analyte dosing caused distinctive changes in the IR spectr~ together with anomalously large SAW sensor responses. In contrast, control experiments involving the physisorption of the same analytes by conventional organic polymers did not cause similar changes in the IR spectra, and the SAW responses were smaller. For a given conventional polymer, the partition coefficients (or SAW sensor signals) roughly followed the analyte fraction of saturation vapor pressure. These SAW/FTIR results support earlier conclusions derived from thickness-shear mode resonator data.

  16. Molecular recognition of 6'-N-5-hexynoate kanamycin A and RNA 1x1 internal loops containing CA mismatches.

    PubMed

    Tran, Tuan; Disney, Matthew D

    2011-02-15

    In our previous study to identify the RNA internal loops that bind an aminoglycoside derivative, we determined that 6'-N-5-hexynoate kanamycin A prefers to bind 1x1 nucleotide internal loops containing C·A mismatches. In this present study, the molecular recognition between a variety of RNAs that are mutated around the C·A loop and the ligand was investigated. Studies show that both loop nucleotides and loop closing pairs affect binding affinity. Most interestingly, it was shown that there is a correlation between the thermodynamic stability of the C·A internal loops and ligand affinity. Specifically, C·A loops that had relatively high or low stability bound the ligand most weakly whereas loops with intermediate stability bound the ligand most tightly. In contrast, there is no correlation between the likelihood that a loop forms a C-A(+) pair at lower pH and ligand affinity. It was also found that a 1x1 nucleotide C·A loop that bound to the ligand with the highest affinity is identical to the consensus site in RNAs that are edited by adenosine deaminases acting on RNA type 2 (ADAR2). These studies provide a detailed investigation of factors affecting small molecule recognition of internal loops containing C·A mismatches, which are present in a variety of RNAs that cause disease.

  17. The challenges involved in elucidating the molecular basis of sperm-egg recognition in mammals and approaches to overcome them.

    PubMed

    Wright, Gavin J; Bianchi, Enrica

    2016-01-01

    Sexual reproduction is used by many different organisms to create a new generation of genetically distinct progeny. Cells originating from separate sexes or mating types segregate their genetic material into haploid gametes which must then recognize and fuse with each other in a process known as fertilization to form a diploid zygote. Despite the central importance of fertilization, we know remarkably little about the molecular mechanisms that are involved in how gametes recognize each other, particularly in mammals, although the proteins that are displayed on their surfaces are almost certainly involved. This paucity of knowledge is largely due to both the unique biological properties of mammalian gametes (sperm and egg) which make them experimentally difficult to manipulate, and the technical challenges of identifying interactions between membrane-embedded cell surface receptor proteins. In this review, we will discuss our current knowledge of animal gamete recognition, highlighting where important contributions to our understanding were made, why particular model systems were helpful, and why progress in mammals has been particularly challenging. We discuss how the development of mammalian in vitro fertilization and targeted gene disruption in mice were important technological advances that triggered progress. We argue that approaches employed to discover novel interactions between cell surface gamete recognition proteins should account for the unusual biochemical properties of membrane proteins and the typically highly transient nature of their interactions. Finally, we describe how these principles were applied to identify Juno as the egg receptor for sperm Izumo1, an interaction that is essential for mammalian fertilization.

  18. Evaluation of molecularly imprinted polymers using 2',3',5'-tri-O-acyluridines as templates for pyrimidine nucleoside recognition.

    PubMed

    Krstulja, Aleksandra; Lettieri, Stefania; Hall, Andrew J; Delépée, Raphael; Favetta, Patrick; Agrofoglio, Luigi A

    2014-10-01

    In this paper, we describe the synthesis and evaluation of molecularly imprinted polymers (MIPs), prepared using 2',3',5'-tri-O-acyluridines as 'dummy' templates, for the selective recognition of uridine nucleosides. The MIPs were synthesised using a non-covalent approach with 2,6-bis-acrylamidopyridine (BAAPy) acting as the binding monomer and ethylene glycol dimethacrylate (EGDMA) as the cross-linking agent. The MIPs were evaluated in terms of capacity, selectivity and specificity by analytical and frontal liquid chromatography measurements. The results obtained in organic mobile phases suggest that the nucleosides are specifically bound to the polymer by the complementary hydrogen bonding motifs of the binding monomer and the nucleoside bases. The MIPs exhibited relatively high imprinting factors for 2',3',5'-tri-O-acyluridines, while they did not show any binding capacity for other nucleosides lacking the imide moiety on their base. Moreover, the presence of ester-COO groups in the EGDMA cross-linker may lead to the formation of additional hydrogen bonds with the 2',3' and/or 5'-OH of sugar part, allowing enhancement of the recognition of the uridine nucleosides. In aqueous media, results show that the binding is driven by hydrophobic interactions.

  19. Molecular recognition of avirulence protein (avrxa5) by eukaryotic transcription factor xa5 of rice (Oryza sativa L.): insights from molecular dynamics simulations.

    PubMed

    Dehury, Budheswar; Maharana, Jitendra; Sahoo, Bikash Ranjan; Sahu, Jagajjit; Sen, Priyabrata; Modi, Mahendra Kumar; Barooah, Madhumita

    2015-04-01

    The avirulence gene avrxa5 of bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) recognized by the resistant rice lines having corresponding resistance (xa5) gene in a gene-for-gene manner. We used a combinatorial approach involving protein-protein docking, molecular dynamics (MD) simulations and binding free energy calculations to gain novel insights into the gene-for-gene mechanism that governs the direct interaction of R-Avr protein. From the best three binding poses predicted by molecular docking, MD simulations were performed to explore the dynamic binding mechanism of xa5 and avrxa5. Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) techniques were employed to calculate the binding free energy and to uncover the thriving force behind the molecular recognition of avrxa5 by eukaryotic transcription factor xa5. Binding free energy analysis revealed van der Waals term as the most constructive component that favors the xa5 and avrxa5 interaction. In addition, hydrogen bonds (H-bonds) and essential electrostatic interactions analysis highlighted amino acid residues Lys54/Asp870, Lys56/Ala868, Lys56/Ala866, Lys56/Glu871, Ile59/His862, Gly61/Phe858, His62/Arg841, His62/Leu856, Ser101/Ala872 and Ser105/Asp870 plays pivotal role for the energetically stability of the R-Avr complex. Insights gained from the present study are expected to unveil the molecular mechanisms that define the transcriptional activator mediated transcriptome modification in host plants. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Competitive fluorescence assay for specific recognition of atrazine by magnetic molecularly imprinted polymer based on Fe3O4-chitosan.

    PubMed

    Liu, Guangyang; Li, Tengfei; Yang, Xin; She, Yongxin; Wang, Miao; Wang, Jing; Zhang, Min; Wang, Shanshan; Jin, Fen; Jin, Maojun; Shao, Hua; Jiang, Zejun; Yu, Hailong

    2016-02-10

    A novel fluorescence sensing strategy for determination of atrazine in tap water involving direct competition between atrazine and 5-(4,6-dichlorotriazinyl) aminofluorescein (5-DTAF), and which exploits magnetic molecularly imprinted polymer (MMIP), has been developed. The MMIP, based on Fe3O4-chitosan nanoparticles, was synthesized to recognize specific binding sites of atrazine. The recognition capability and selectivity of the MMIP for atrazine and other triazine herbicides was investigated. Under optimal conditions, the competitive reaction between 5-DTAF and atrazine was performed to permit quantitation. Fluorescence intensity changes at 515 nm was linearly related to the logarithm of the atrazine concentration for the range 2.32-185.4 μM. The detection limit for atrazine was 0.86μM (S/N=3) and recoveries were 77.6-115% in spiked tap water samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition.

    PubMed

    Kamada, Katsuhiko; Hanaoka, Fumio; Burley, Stephen K

    2003-04-01

    A structure of the Escherichia coli chromosomal MazE/MazF addiction module has been determined at 1.7 A resolution. Addiction modules consist of stable toxin and unstable antidote proteins that govern bacterial cell death. MazE (antidote) and MazF (toxin) form a linear heterohexamer composed of alternating toxin and antidote homodimers (MazF(2)-MazE(2)-MazF(2)). The MazE homodimer contains a beta barrel from which two extended C termini project, making interactions with flanking MazF homodimers that resemble the plasmid-encoded toxins CcdB and Kid. The MazE/MazF heterohexamer structure documents that the mechanism of antidote-toxin recognition is common to both chromosomal and plasmid-borne addiction modules, and provides general molecular insights into toxin function, antidote degradation in the absence of toxin, and promoter DNA binding by antidote/toxin complexes.

  2. Multiple hydrogen bonds tuning guest/host excited-state proton transfer reaction: its application in molecular recognition.

    PubMed

    Chou, He-Chun; Hsu, Chin-Hao; Cheng, Yi-Ming; Cheng, Chung-Chih; Liu, Hsiao-Wei; Pu, Shih-Chieh; Chou, Pi-Tai

    2004-02-18

    A molecular recognition concept exploiting multiple-hydrogen-bond fine-tuned excited-state proton-transfer (ESPT) was conveyed using 3,4,5,6-tetrahydrobis(pyrido[3,2-g]indolo)[2,3-a:3',2'-j]acridine (1a). The catalytic type 1a/carboxylic acids hydrogen-bonding (HB) complexes undergo ultrafast ESPT, resulting in an anomalously large Stokes shifted tautomer emission (lambdamax approximately 600 nm). Albeit forming a quadruple HB complex, ESPT is prohibited in the noncatalytic-type 1a/urea complexes (lambdamax approximately 430 nm). The HB configuration tuning ESPT properties lead to a feasible design for sensing multiple-HB-site analytes of biological interest.

  3. Ion and molecule sensors using molecular recognition in luminescent, conductive polymers. FY 1997 year-end progress report

    SciTech Connect

    Wasielewski, M.R.

    1997-01-01

    'The purpose of this project is to use molecular recognition strategies to develop sensor technology based on luminescent, conductive polymers that contain sites for binding specific molecules or ions in the presence of related molecules or ions. Selective binding of a particular molecule or ion of interest to these polymers will result in a large change in their luminescence and/or conductivity, which can be used to both qualitatively and quantitatively sense the presence of the bound molecules or ions. The main thrusts and accomplishments in the first year of this project involve developing polymer syntheses that yield conjugated polymers to which a wide variety of ligands for metal ion binding can be readily incorporated.'

  4. Molecular recognition of curcumin (Indian Ayurvedic medicine) by the supramolecular probe, p-t-butyl calix(8)arene.

    PubMed

    Meenakshi, C; Jayabal, P; Ramakrishnan, V

    2014-06-05

    The thermodynamic property of the host-guest complexes formed between the curcumin, component of Indian Ayurvedic medicine turmeric, a drug molecule, with the supra molecule, p-t-butyl calix(8)arene was studied. p-t-Butyl calix(8)arene has been used as a host molecule and curcumin as a guest molecule. Optical absorption spectral studies were carried out to investigate the molecular recognition properties of p-t-butyl calix(8)arene with curcumin. The stochiometry of the host-guest complexes formed and the binding constant were determined. An interesting 1:1 and 4:1 stochiometric host-guest complexes were formed. Job's continuous method of variation and Benesi-Hildebrand expression were used for the determination of binding constant and the stochiometry of the host-guest complex formed. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Molecular recognition of curcumin (Indian Ayurvedic medicine) by the supramolecular probe, p-t-butyl calix(8)arene

    NASA Astrophysics Data System (ADS)

    Meenakshi, C.; Jayabal, P.; Ramakrishnan, V.

    2014-06-01

    The thermodynamic property of the host-guest complexes formed between the curcumin, component of Indian Ayurvedic medicine turmeric, a drug molecule, with the supra molecule, p-t-butyl calix(8)arene was studied. p-t-Butyl calix(8)arene has been used as a host molecule and curcumin as a guest molecule. Optical absorption spectral studies were carried out to investigate the molecular recognition properties of p-t-butyl calix(8)arene with curcumin. The stochiometry of the host-guest complexes formed and the binding constant were determined. An interesting 1:1 and 4:1 stochiometric host-guest complexes were formed. Job's continuous method of variation and Benesi-Hildebrand expression were used for the determination of binding constant and the stochiometry of the host-guest complex formed.

  6. Electrochemical impedimetric sensor based on molecularly imprinted polymers/sol-gel chemistry for methidathion organophosphorous insecticide recognition.

    PubMed

    Bakas, Idriss; Hayat, Akhtar; Piletsky, Sergey; Piletska, Elena; Chehimi, Mohamed M; Noguer, Thierry; Rouillon, Régis

    2014-12-01

    We report here a novel method to detect methidathion organophosphorous insecticides. The sensing platform was architected by the combination of molecularly imprinted polymers and sol-gel technique on inexpensive, portable and disposable screen printed carbon electrodes. Electrochemical impedimetric detection technique was employed to perform the label free detection of the target analyte on the designed MIP/sol-gel integrated platform. The selection of the target specific monomer by electrochemical impedimetric methods was consistent with the results obtained by the computational modelling method. The prepared electrochemical MIP/sol-gel based sensor exhibited a high recognition capability toward methidathion, as well as a broad linear range and a low detection limit under the optimized conditions. Satisfactory results were also obtained for the methidathion determination in waste water samples.

  7. Bio-molecular architects: a scaffold provided by the C-terminal domain of eukaryotic RNA polymerase II.

    PubMed

    Zhang, Mengmeng; Gill, Gordon N; Zhang, Yan

    2010-01-01

    In eukaryotic cells, the transcription of genes is accurately orchestrated both spatially and temporally by the C-terminal domain of RNA polymerase II (CTD). The CTD provides a dynamic platform to recruit different regulators of the transcription apparatus. Different posttranslational modifications are precisely applied to specific sites of the CTD to coordinate transcription process. Regulators of the RNA polymerase II must identify specific sites in the CTD for cellular survival, metabolism, and development. Even though the CTD is disordered in the eukaryotic RNA polymerase II crystal structures due to its intrinsic flexibility, recent advances in the complex structural analysis of the CTD with its binding partners provide essential clues for understanding how selectivity is achieved for individual site recognition. The recent discoveries of the interactions between the CTD and histone modification enzymes disclose an important role of the CTD in epigenetic control of the eukaryotic gene expression. The intersection of the CTD code with the histone code discloses an intriguing yet complicated network for eukaryotic transcriptional regulation.

  8. Density functional theory based study of molecular interactions, recognition, engineering, and quantum transport in π molecular systems.

    PubMed

    Cho, Yeonchoo; Cho, Woo Jong; Youn, Il Seung; Lee, Geunsik; Singh, N Jiten; Kim, Kwang S

    2014-11-18

    CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium

  9. Solid state vibrational circular dichroism towards molecular recognition: chiral metal complexes intercalated in a clay mineral.

    PubMed

    Sato, Hisako; Tamura, Kenji; Takimoto, Kazuyoshi; Yamagishi, Akihiko

    2017-09-13

    Vibrational circular dichroism (VCD) spectroscopy was applied to study chirality recognition in the interlayer space of a clay mineral. Clay intercalation compounds including two kinds of chiral molecules were prepared. Firstly a cationic metal complex, Δ- or Λ-[Ru(phen)3](2+) (phen = 1,10-phenanthroline), was ion-exchanged into sodium montmorillonite. Thereafter a neutral organic molecule, R- or S-1,1'-bi-2-naphthol (denoted as R- or S-BINOL), was co-adsorbed. The solid state VCD spectra were recorded on the hybrid compounds thus prepared. The intensity of VCD peaks in the region of 1300-1400 cm(-1), which were assigned to the bending vibrations of OH groups in BINOL, was remarkably dependent on the chirality relation between the two intercalated species. This implied that BINOL took a different conformation in response to the chirality of co-existing [Ru(phen)3](2+).

  10. (Pseudo)amide-linked oligosaccharide mimetics: molecular recognition and supramolecular properties

    PubMed Central

    Ortega-Caballero, Fernando; Ortiz Mellet, Carmen; García Fernández, José M

    2010-01-01

    Summary Oligosaccharides are currently recognised as having functions that influence the entire spectrum of cell activities. However, a distinct disadvantage of naturally occurring oligosaccharides is their metabolic instability in biological systems. Therefore, much effort has been spent in the past two decades on the development of feasible routes to carbohydrate mimetics which can compete with their O-glycosidic counterparts in cell surface adhesion, inhibit carbohydrate processing enzymes, and interfere in the biosynthesis of specific cell surface carbohydrates. Such oligosaccharide mimetics are potential therapeutic agents against HIV and other infections, against cancer, diabetes and other metabolic diseases. An efficient strategy to access this type of compounds is the replacement of the glycosidic linkage by amide or pseudoamide functions such as thiourea, urea and guanidine. In this review we summarise the advances over the last decade in the synthesis of oligosaccharide mimetics that possess amide and pseudoamide linkages, as well as studies focussing on their supramolecular and recognition properties. PMID:20485602

  11. 3-(1H-Indol-3-yl)-2-[3-(4-nitrophenyl)ureido]propanamide Enantiomers With Human Formyl-Peptide Receptor Agonist Activity: Molecular Modeling of Chiral Recognition by FPR2

    PubMed Central

    Schepetkin, Igor A.; Kirpotina, Liliya N.; Khlebnikov, Andrei I.; Leopoldo, Marcello; Lucente, Ermelinda; Lacivita, Enza; De Giorgio, Paola; Quinn, Mark T.

    2012-01-01

    N-formyl peptide receptors (FPRs) are G protein-coupled receptors (GPCRs) that play critical roles in inflammatory reactions, and FPR-specific interactions can possibly be used to facilitate the resolution of pathological inflammatory reactions. Recent studies indicated that FPRs have stereo-selective preference for chiral ligands. Here, we investigated the structure-activity relationship of 24 chiral ureidopropanamides, including previously reported compounds PD168368/PD176252 and their close analogs, and used molecular modeling to define chiral recognition by FPR2. Unlike previously reported 6-methyl-2,4-disubstituted pyridazin-3(2H)-ones, whose R-forms preferentially activated FPR1/FPR2, we found that four S-enantiomers in the seven ureidopropanamide pairs tested preferentially activated intracellular Ca2+ flux in FPR2-transfected cells, while the R-counterpart was more active in two enantiomer pairs. Thus, active enantiomers of FPR2 agonists can be in either R- or S- configurations, depending on the molecular scaffold and specific substituents at the chiral center. Using molecular modeling approaches, including field point methodology, homology modeling, and docking studies, we propose a model that can explain stereoselective activity of chiral FPR2 agonists. Importantly, our docking studies of FPR2 chiral agonists correlated well with the FPR2 pharmacophore model derived previously. We conclude that the ability of FPR2 to discriminate between the enantiomers is the consequence of the arrangement of the three asymmetric hydrophobic subpockets at the main orthosteric FPR2 binding site with specific orientation of charged regions in the subpockets. PMID:23219934

  12. 3-(1H-indol-3-yl)-2-[3-(4-nitrophenyl)ureido]propanamide enantiomers with human formyl-peptide receptor agonist activity: molecular modeling of chiral recognition by FPR2.

    PubMed

    Schepetkin, Igor A; Kirpotina, Liliya N; Khlebnikov, Andrei I; Leopoldo, Marcello; Lucente, Ermelinda; Lacivita, Enza; De Giorgio, Paola; Quinn, Mark T

    2013-02-01

    N-formyl peptide receptors (FPRs) are G protein-coupled receptors (GPCRs) that play critical roles in inflammatory reactions, and FPR-specific interactions can possibly be used to facilitate the resolution of pathological inflammatory reactions. Recent studies indicated that FPRs have stereo-selective preference for chiral ligands. Here, we investigated the structure-activity relationship of 24 chiral ureidopropanamides, including previously reported compounds PD168368/PD176252 and their close analogs, and used molecular modeling to define chiral recognition by FPR2. Unlike previously reported 6-methyl-2,4-disubstituted pyridazin-3(2H)-ones, whose R-forms preferentially activated FPR1/FPR2, we found that four S-enantiomers in the seven ureidopropanamide pairs tested preferentially activated intracellular Ca(2+) flux in FPR2-transfected cells, while the R-counterpart was more active in two enantiomer pairs. Thus, active enantiomers of FPR2 agonists can be in either R- or S-configurations, depending on the molecular scaffold and specific substituents at the chiral center. Using molecular modeling approaches, including field point methodology, homology modeling, and docking studies, we propose a model that can explain stereoselective activity of chiral FPR2 agonists. Importantly, our docking studies of FPR2 chiral agonists correlated well with the FPR2 pharmacophore model derived previously. We conclude that the ability of FPR2 to discriminate between the enantiomers is the consequence of the arrangement of the three asymmetric hydrophobic subpockets at the main orthosteric FPR2 binding site with specific orientation of charged regions in the subpockets.

  13. Molecular cloning and functional characterization of peptidoglycan recognition protein 6 in grass carp Ctenopharyngodon idella.

    PubMed

    Li, Jun Hua; Yu, Zhang Long; Xue, Na Na; Zou, Peng Fei; Hu, Jing Yu; Nie, P; Chang, Ming Xian

    2014-02-01

    Peptidoglycan recognition proteins (PGRPs) are pattern recognition molecules of innate immunity. In this study, a long-form PGRP, designated as gcPGRP6, was identified from grass carp Ctenopharyngodon idella. The deduced amino acid sequence of gcPGRP6 is composed of 464 residues with a conserved PGRP domain at the C-terminus. The gcPGRP6 gene consists of four exons and three introns, spacing approximately 2.7 kb of genomic sequence. Phylogenetic analysis demonstrated that gcPGRP6 is clustered closely with zebrafish PGLYRP6, and formed a long-type PGRP subfamily together with PGLYRP2 members identified in teleosts and mammals. Real-time PCR and Western blotting analyses revealed that gcPGRP6 is constitutively expressed in organs/tissues examined, and its expression was significantly induced in liver and intestine of grass carp in response to PGN stimulation and in CIK cells treated with lipoteichoic acid (LTA), polyinosinic polycytidylic acid (Poly I:C) and peptidoglycan (PGN). Immunofluorescence microscopy and Western blotting analyses revealed that gcPGRP6 is effectively secreted to the exterior of CIK cells. The over-expression of gcPGRP6 in CIK cells leads to the activation of NF-κB and the inhibition of intracellular bacterial growth. Moreover, cell lysates from CIK cells transfected with pTurbo-gcPGRP6-GFP plasmid display the binding activity towards Lys-type PGN from Staphylococcus aureus and DAP-type PGN from Bacillus subtilis. Furthermore, proinflammatory cytokine IL-2 and intracellular PGN receptor NOD2 had a significantly increased expression in CIK cells overexpressed with gcPGRP6. It is demonstrated that the PGRP6 in grass carp has a role in binding PGN, in inhibiting the growth of intracellular bacteria, and in activating NF-κB, as well as in regulating innate immune genes.

  14. Molecular mechanisms of substrate recognition and specificity of New Delhi metallo-β-lactamase.

    PubMed

    Chiou, Jiachi; Leung, Thomas Yun-Chung; Chen, Sheng

    2014-09-01

    Carbapenems are one of the last lines of defense for Gram-negative pathogens, such as members of the Enterobacteriaceae. Despite the fact that most carbapenems are resistant to extended-spectrum β-lactamase (ESBL), emerging metallo-β-lactamases (MBLs), including New Delhi metallo-β-lactamase 1 (NDM-1), that can hydrolyze carbapenems have become prevalent and are frequently associated with the so-called "superbugs," for which treatments are extremely limited. Crystallographic study sheds light on the modes of antibiotic binding to NDM-1, yet the mechanisms governing substrate recognition and specificity are largely unclear. This study provides a connection between crystallographic study and the functional significance of NDM-1, with an emphasis on the substrate specificity and catalysis of various β-lactams. L1 loop residues L59, V67, and W87 were important for the activity of NDM-1, most likely through maintaining the partial folding of the L1 loop or active site conformation through hydrophobic interaction with the R groups of β-lactams or the β-lactam ring. Substitution of alanine for L59 showed greater reduction of MICs to ampicillin and selected cephalosporins, whereas substitutions of alanine for V67 had more impact on the MICs of carbapenems. K224 and N233 on the L3 loop played important roles in the recognition of substrate and contributed to substrate hydrolysis. These data together with the structure comparison of the B1 and B2 subclasses of MBLs revealed that the broad substrate specificity of NDM-1 could be due to the ability of its wide active site cavity to accommodate a wide range of β-lactams. This study provides insights into the development of efficient inhibitors for NDM-1 and offers an efficient tactic with which to study the substrate specificities of other β-lactamases.

  15. Uniformly sized molecularly imprinted polymers for bisphenol A and beta-estradiol: retention and molecular recognition properties in hydro-organic mobile phases.

    PubMed

    Sanbe, Haruyo; Haginaka, Jun

    2003-01-15

    Uniformly sized molecularly imprinted polymers (MIPs) for bisphenol A (BPA) have been prepared using ethylene glycol dimethacrylate (EDMA) as a cross-linker and methacrylic acid, 2-diethylaminoethyl methacrylate or 4-vinylpyridine (4-VPY) as a functional monomer or without use of a functional monomer. The MIPs obtained for BPA were evaluated using a mixture of phosphate buffer (or water) and acetonitrile or only acetonitrile as the mobile phase. Among the MIPs prepared, that using 4-VPY showed the highest retentivity and selectivity for BPA. The highest selectivity factor, which is defined as the ratio of the retention factors (k) on the molecularly imprinted and non-imprinted polymers, k(imprinted)/k(non-imprinted), was 9.4 for BPA on the BPA-imprinted 4-VPY-co-EDMA polymers, while that for beta-estradiol on the beta-estradiol-imprinted 4-VPY-co-EDMA polymers was 2.4. The differences in the selectivity factors between BPA and beta-estradiol on the respective MIPs could be ascribable to differences in the number of interaction sites. It is plausible that the phenol groups of BPA could interact with two pyridyl groups of the MIP by hydrogen bonding interactions, while there is only one such site for beta-estradiol. Furthermore, the results suggest that hydrophobic and hydrogen bonding interactions can play an important role in the retention and recognition of BPA and beta-estradiol in the hydro-organic mobile phase, while hydrogen bonding interactions seem to be useful for the retention and recognition when acetonitrile is used as the mobile phase.

  16. Cardiac-Oxidized Antigens Are Targets of Immune Recognition by Antibodies and Potential Molecular Determinants in Chagas Disease Pathogenesis

    PubMed Central

    Dhiman, Monisha; Zago, Maria Paola; Nunez, Sonia; Amoroso, Alejandro; Rementeria, Hugo; Dousset, Pierre; Burgos, Federico Nunez; Garg, Nisha Jain

    2012-01-01

    conclude that ROS-induced, cardiac-oxidized antigens are targets of immune recognition by antibodies and molecular determinants for pathogenesis during Chagas disease. PMID:22238578

  17. Dielectric and ferroelectric sensing based on molecular recognition in Cu(1,10-phenlothroline)2SeO4.(diol) systems

    NASA Astrophysics Data System (ADS)

    Ye, Heng-Yun; Liao, Wei-Qiang; Zhou, Qionghua; Zhang, Yi; Wang, Jinlan; You, Yu-Meng; Wang, Jin-Yun; Chen, Zhong-Ning; Li, Peng-Fei; Fu, Da-Wei; Huang, Songping D.; Xiong, Ren-Gen

    2017-02-01

    The process of molecular recognition is the assembly of two or more molecules through weak interactions. Information in the process of molecular recognition can be transmitted to us via physical signals, which may find applications in sensing and switching. The conventional signals are mainly limited to light signal. Here, we describe the recognition of diols with Cu(1,10-phenlothroline)2SeO4 and the transduction of discrete recognition events into dielectric and/or ferroelectric signals. We observe that systems of Cu(1,10-phenlothroline)2SeO4.(diol) exhibit significant dielectric and/or ferroelectric dependence on different diol molecules. The compounds including ethane-1,2-diol or propane-1,2-diol just show small temperature-dependent dielectric anomalies and no reversible polarization, while the compound including ethane-1,3-diol shows giant temperature-dependent dielectric anomalies as well as ferroelectric reversible spontaneous polarization. This finding shows that dielectricity and/or ferroelectricity has the potential to be used for signalling molecular recognition.

  18. Dielectric and ferroelectric sensing based on molecular recognition in Cu(1,10-phenlothroline)2SeO4·(diol) systems

    PubMed Central

    Ye, Heng-Yun; Liao, Wei-Qiang; Zhou, Qionghua; Zhang, Yi; Wang, Jinlan; You, Yu-Meng; Wang, Jin-Yun; Chen, Zhong-Ning; Li, Peng-Fei; Fu, Da-Wei; Huang, Songping D.; Xiong, Ren-Gen

    2017-01-01

    The process of molecular recognition is the assembly of two or more molecules through weak interactions. Information in the process of molecular recognition can be transmitted to us via physical signals, which may find applications in sensing and switching. The conventional signals are mainly limited to light signal. Here, we describe the recognition of diols with Cu(1,10-phenlothroline)2SeO4 and the transduction of discrete recognition events into dielectric and/or ferroelectric signals. We observe that systems of Cu(1,10-phenlothroline)2SeO4·(diol) exhibit significant dielectric and/or ferroelectric dependence on different diol molecules. The compounds including ethane-1,2-diol or propane-1,2-diol just show small temperature-dependent dielectric anomalies and no reversible polarization, while the compound including ethane-1,3-diol shows giant temperature-dependent dielectric anomalies as well as ferroelectric reversible spontaneous polarization. This finding shows that dielectricity and/or ferroelectricity has the potential to be used for signalling molecular recognition. PMID:28216653

  19. Molecular recognition in gas sensing: Results from acoustic wave and in-situ FTIR measurements

    SciTech Connect

    Hierlemann, A.; Ricco, A.J.; Bodenhoefer, K.; Goepel, W.

    1998-06-01

    Surface acoustic wave (SAW) measurements were combined with direct, in-situ molecular spectroscopy to understand the interactions of surface-confined sensing films with gas-phase analytes. This was accomplished by collecting Fourier-transform infrared external-reflectance spectra (FTIR-ERS) on operating SAW devices during dosing of their specifically coated surfaces with key analytes.

  20. Application of Machine Learning tools to recognition of molecular patterns in STM images

    NASA Astrophysics Data System (ADS)

    Maksov, Artem; Ziatdinov, Maxim; Fujii, Shintaro; Kiguchi, Manabu; Higashibayashi, Shuhei; Sakurai, Hidehiro; Kalinin, Sergei; Sumpter, Bobby

    The ability to utilize individual molecules and molecular assemblies as data storage elements has motivated scientist for years, concurrent with the continuous effort to shrink a size of data storage devices in microelectronics industry. One of the critical issues in this effort lies in being able to identify individual molecular assembly units (patterns), on a large scale in an automated fashion of complete information extraction. Here we present a novel method of applying machine learning techniques for extraction of positional and rotational information from scanning tunneling microscopy (STM) images of π-bowl sumanene molecules on gold. We use Markov Random Field (MRF) model to decode the polar rotational states for each molecule in a large scale STM image of molecular film. We further develop an algorithm that uses a convolutional Neural Network combined with MRF and input from density functional theory to classify molecules into different azimuthal rotational classes. Our results demonstrate that a molecular film is partitioned into distinctive azimuthal rotational domains consisting typically of 20-30 molecules. In each domain, the ``bowl-down'' molecules are generally surrounded by six nearest neighbor molecules in ``bowl-up'' configuration, and the resultant overall structure form a periodic lattice of rotational and polar states within each domain. Research was supported by the US Department of Energy.

  1. QSAR, DFT and molecular modeling studies of peptides from HIV-1 to describe their recognition properties by MHC-I.

    PubMed

    Andrade-Ochoa, S; García-Machorro, J; Bello, Martiniano; Rodríguez-Valdez, L M; Flores-Sandoval, C A; Correa-Basurto, J

    2017-08-03

    Human immunodeficiency virus type-1 (HIV-1) has infected more than 40 million people around the world. HIV-1 treatment still has several side effects, and the development of a vaccine, which is another potential option for decreasing human infections, has faced challenges. This work presents a computational study that includes a quantitative structure activity relationship(QSAR) using density functional theory(DFT) for reported peptides to identify the principal quantum mechanics descriptors related to peptide activity. In addition, the molecular recognition properties of these peptides are explored on major histocompatibility complex I (MHC-I) through docking and molecular dynamics (MD) simulations accompanied by the Molecular Mechanics Generalized Born Surface Area (MMGBSA) approach for correlating peptide activity reported elsewhere vs. theoretical peptide affinity. The results show that the carboxylic acid and hydroxyl groups are chemical moieties that have an inverse relationship with biological activity. The number of sulfides, pyrroles and imidazoles from the peptide structure are directly related to biological activity. In addition, the HOMO orbital energy values of the total absolute charge and the Ghose-Crippen molar refractivity of peptides are descriptors directly related to the activity and affinity on MHC-I. Docking and MD simulation studies accompanied by an MMGBSA analysis show that the binding free energy without considering the entropic contribution is energetically favorable for all the complexes. Furthermore, good peptide interaction with the most affinity is evaluated experimentally for three proteins. Overall, this study shows that the combination of quantum mechanics descriptors and molecular modeling studies could help describe the immunogenic properties of peptides from HIV-1.

  2. Fullerene recognition with molecular tweezers made up of efficient buckybowls: a dispersion-corrected DFT study.

    PubMed

    Josa, Daniela; Rodríguez-Otero, Jesús; Cabaleiro-Lago, Enrique M

    2015-05-28

    In 2007, Sygula and co-workers introduced a novel type of molecular tweezers with buckybowl pincers that have attracted the substantial interest of researchers due to their ideal architecture for recognizing fullerenes by concave-convex π∙∙∙π interactions (A. Sygula et al., J. Am. Chem. Soc., 2007, 129, 3842). Although in recent years some modifications have been performed on these original molecular tweezers to improve their ability for catching fullerenes, very few improvements were achieved to date. For that reason, in the present work a series of molecular tweezers have been devised and their supramolecular complexes with C60 studied at the B97-D2/TZVP//SCC-DFTB-D and B97-D2/TZVP levels. Three different strategies have been tested: (1) changing the corannulene pincers to other buckybowls, (2) replacing the tetrabenzocyclooctatetraene tether by a buckybowl, and (3) adding methyl groups on the molecular tweezers. According to the results, all the three approaches are effective, in such a way that a combination of the three strategies results in buckycatchers with complexation energies (with C60) up to 2.6 times larger than that of the original buckycatcher, reaching almost -100 kcal mol(-1). The B97-D2/TZVP//SCC-DFTB-D approach can be a rapid screening tool for testing new molecular tweezers. However, since this approach does not reproduce correctly the deformation energy and this energy represents an important contribution to the total complexation energy of complexes, subsequent higher-level re-optimization is compulsory to achieve reliable results (the full B97-D2/TZVP level is used herein). This re-optimization could be superfluous when quite rigid buckycatchers are studied.

  3. Molecular pathways involved in neuronal cell adhesion and membrane scaffolding contribute to schizophrenia and bipolar disorder susceptibility.

    PubMed

    O'Dushlaine, C; Kenny, E; Heron, E; Donohoe, G; Gill, M; Morris, D; Corvin, A

    2011-03-01

    Susceptibility to schizophrenia and bipolar disorder may involve a substantial, shared contribution from thousands of common genetic variants, each of small effect. Identifying whether risk variants map to specific molecular pathways is potentially biologically informative. We report a molecular pathway analysis using the single-nucleotide polymorphism (SNP) ratio test, which compares the ratio of nominally significant (P<0.05) to nonsignificant SNPs in a given pathway to identify the 'enrichment' for association signals. We applied this approach to the discovery (the International Schizophrenia Consortium (n=6909)) and validation (Genetic Association Information Network (n=2729)) of schizophrenia genome-wide association study (GWAS) data sets. We investigated each of the 212 experimentally validated pathways described in the Kyoto Encyclopaedia of Genes and Genomes in the discovery sample. Nominally significant pathways were tested in the validation sample, and five pathways were found to be significant (P=0.03-0.001); only the cell adhesion molecule (CAM) pathway withstood conservative correction for multiple testing. Interestingly, this pathway was also significantly associated with bipolar disorder (Wellcome Trust Case Control Consortium (n=4847)) (P=0.01). At a gene level, CAM genes associated in all three samples (NRXN1 and CNTNAP2), which were previously implicated in specific language disorder, autism and schizophrenia. The CAM pathway functions in neuronal cell adhesion, which is critical for synaptic formation and normal cell signaling. Similar pathways have also emerged from a pathway analysis of autism, suggesting that mechanisms involved in neuronal cell adhesion may contribute broadly to neurodevelopmental psychiatric phenotypes.

  4. LASSBio-1422: a new molecular scaffold with efficacy in animal models of schizophrenia and disorders of attention and cognition.

    PubMed

    Betti, Andresa H; Antonio, Camila B; Pompeu, Thais E T; Martins, Thaise S; Herzfeldt, Vivian; Stolz, Eveline D; Fraga, Carlos A M; Barreiro, Eliezer; Noël, François; Rates, Stela M K

    2017-02-01

    Aiming to identify new antipsychotic lead-compounds, our group has been working on the design and synthesis of new N-phenylpiperazine derivatives. Here, we characterized LASSBio-1422 as a pharmacological prototype of this chemical series. Adult male Wistar rats and CF1 mice were used for in-vitro and in-vivo assays, respectively. LASSBio-1422 [1 and 5 mg/kg, postoperatively (p.o.)] inhibited apomorphine-induced climbing as well as ketamine-induced hyperlocomotion (1 and 5 mg/kg, p.o.), animal models predictive of efficacy on positive symptoms. Furthermore, LASSBio-1422 (5 mg/kg, p.o.) prevented the prepulse impairment induced by apomorphine, (±)-2,5-dimethoxy-4-iodoamphetamine, and ketamine, as well as the memory impairment induced by ketamine in the novel object-recognition task at the acquisition, consolidation, and retrieval phases of memory formation. Potential extrapyramidal side-effects and sedation were assessed by catatonia, rota-rod, locomotion, and barbiturate sleeping time, and LASSBio-1422 (15 mg/kg, p.o.) did not affect any of the parameters observed. Binding assays showed that LASSBio-1422 has a binding profile different from the known atypical antipsychotic drugs: it does not bind to AMPA, kainate, N-methyl-D-aspartate, glicine, and mGluR2 receptors and has low or negligible affinity for D1, D2, and 5-HT2A/C receptors, but high affinity for D4 receptors (Ki=0.076 µmol/l) and, to a lesser extent, for 5-HT1A receptors (Ki=0.493 µmol/l). The antagonist action of LASSBio-1422 at D4 receptors was assessed through the classical GTP-shift assay. In conclusion, LASSBio-1422 is effective in rodent models of positive and cognitive symptoms of schizophrenia and its ability to bind to D4 and 5-HT1A receptors may at least in part explain its effects in these animal models.

  5. Rapid detection of IHNV by molecular padlock recognition and surface-associated isothermal amplification

    NASA Astrophysics Data System (ADS)

    McCarthy, Erik L.; Egeler, Teressa J.; Bickerstaff, Lee E.; Pereira da Cunha, Mauricio; Millard, Paul J.

    2005-11-01

    RNA sequences derived from infectious hematopoeitic necrosis virus (IHNV) could be detected using a combination of surface-associated molecular padlock DNA probes (MPP) and rolling circle amplification (RCA) in microcapillary tubes. DNA oligonucleotides with base sequences identical to RNA obtained from IHNV were recognized by MPP. Circularized MPP were then captured on the inner surface of glass microcapillary tubes by immobilized DNA oligonucleotide primers. Extension of the immobilized primers by isothermal RCA gave rise to DNA concatamers, which were in turn bound by the fluorescent reporter SYBR Green II nucleic acid stain, and measured by microfluorimetry. Surface-associated molecular padlock technology, combined with isothermal RCA, exhibited high selectivity and sensitivity without thermal cycling. This technology is applicable to direct RNA and DNA detection, permitting detection of a variety of viral or bacterial pathogens.

  6. Electron sharing and anion-π recognition in molecular triangular prisms.

    PubMed

    Schneebeli, Severin T; Frasconi, Marco; Liu, Zhichang; Wu, Yilei; Gardner, Daniel M; Strutt, Nathan L; Cheng, Chuyang; Carmieli, Raanan; Wasielewski, Michael R; Stoddart, J Fraser

    2013-12-02

    Stacking on a full belly: Triangular molecular prisms display electron sharing among their triangularly arranged naphthalenediimide (NDI) redox centers. Their electron-deficient cavities encapsulate linear triiodide anions, leading to the formation of supramolecular helices in the solid state. Chirality transfer is observed from the six chiral centers of the filled prisms to the single-handed helices. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Chiral recognition of metalaxyl enantiomers by human serum albumin: evidence from molecular modeling and photophysical approach.

    PubMed

    Ding, Fei; Li, Xiu-Nan; Diao, Jian-Xiong; Sun, Ye; Zhang, Li; Sun, Ying

    2012-06-01

    Metalaxyl is an acylamine fungicide, belonging to the most widely known member of the amide group. This task is aimed to scrutinize binding region and spatial structural change of principal vector human serum albumin (HSA) complex with (R)-/(S)-metalaxyl by exploiting molecular modeling, steady-state and time-resolved fluorescence, and circular dichroism (CD) approaches. According to molecular modeling, (R)-metalaxyl is situated within subdomains IIA and IIIA and the affinity of site I with (R)-metalaxyl is greater than site II, whereas (S)-metalaxyl is only located at subdomain IIA and the affinity of (S)-metalaxyl with site I is superior compared with that with (R)-metalaxyl. This coincides with the competitive ligand binding, guanidine hydrochloride-induced unfolding of protein, and hydrophobic 8-anilino-1-naphthalenesulfonic acid experiments; the acting forces between (R)-/(S)-metalaxyl and HSA are hydrophobic, π-π interactions, and hydrogen bonds, as derived from molecular modeling. Fluorescence emission manifested that the complex of (R)-/(S)-metalaxyl to HSA is the formation of adduct with an affinity of 10(4) M(-1), which corroborates the time-resolved fluorescence that the static type was operated. Furthermore, the changes of far-UV CD spectra evidence the polypeptide chain of HSA partially unfolded after conjugation with (R)-/(S)-metalaxyl. Through this work, we envisage that it can offer central clues on the biodistribution, absorption, and bioaccumulation of (R)-/(S)-metalaxyl. Copyright © 2012 Wiley Periodicals, Inc.

  8. Chiral recognition of Propranolol enantiomers by β-Cyclodextrin: Quantum chemical calculation and molecular dynamics simulation studies

    NASA Astrophysics Data System (ADS)

    Ghatee, Mohammad Hadi; Sedghamiz, Tahereh

    2014-12-01

    Enantiomeric recognition of Propranolol by complexation with β-Cyclodextrin was studied by PM3 method and molecular dynamics (MD) simulation. Gas phase results show that the R-enantiomer complex is more stable than the S-enantiomer complex by 8.54 kJ/mol (Hartree-Fock energy). Using polarized continuum model, solution phase of R-enantiomer complex was found to be more stable than S-enantiomer complex by 25.95 kJ/mol. Both complexes hardly occur at room temperature free-energy-wise, though, complexation with R-enantiomer is more favorable than with S-enantiomer enthalpy-wise. Also, complexes were studied by molecular dynamics simulation in gas and solution phases. More stability of R-enantiomer complex in gas phase is confirmed by MD van der Waals energy (5.04 kJ/mol) and closely by the counterpart PM3 binding energy (8.54 kJ/mol). Simulation in solution phase indicates more stability of R-enantiomer complex. Finally, simulated transport property provides insight into the high anisotropic atoms motion according to which S-Propranolol found possessing significantly higher dynamics.

  9. Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process

    PubMed Central

    Wickstrom, Lauren; He, Peng; Gallicchio, Emilio; Levy, Ronald M.

    2013-01-01

    Host-guest inclusion complexes are useful models for understanding the structural and energetic aspects of molecular recognition. Due to their small size relative to much larger protein-ligand complexes, converged results can be obtained rapidly for these systems thus offering the opportunity to more reliably study fundamental aspects of the thermodynamics of binding. In this work, we have performed a large scale binding affinity survey of 57 β-cyclodextrin (CD) host guest systems using the binding energy distribution analysis method (BEDAM) with implicit solvation (OPLS-AA/AGBNP2). Converged estimates of the standard binding free energies are obtained for these systems by employing techniques such as parallel Hamitionian replica exchange molecular dynamics, conformational reservoirs and multistate free energy estimators. Good agreement with experimental measurements is obtained in terms of both numerical accuracy and affinity rankings. Overall, average effective binding energies reproduce affinity rank ordering better than the calculated binding affinities, even though calculated binding free energies, which account for effects such as conformational strain and entropy loss upon binding, provide lower root mean square errors when compared to measurements. Interestingly, we find that binding free energies are superior rank order predictors for a large subset containing the most flexible guests. The results indicate that, while challenging, accurate modeling of reorganization effects can lead to ligand design models of superior predictive power for rank ordering relative to models based only on ligand-receptor interaction energies. PMID:25147485

  10. Molecular recognition of the environment and mechanisms of the origin of species in quantum-like modeling of evolution.

    PubMed

    Melkikh, Alexey V; Khrennikov, Andrei

    2017-05-05

    A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown that these mechanisms, at the molecular level, cannot work steadily in terms of classical mechanics. Quantum mechanisms of changes in the genome, based on the long-range interaction potential between biologically important molecules, are proposed as one of possible explanation. Different variants of interactions of the organism and environment based on molecular recognition and leading to new species origins are considered. Experiments to verify the model are proposed. This bio-physical study is completed by the general operational model of based on quantum information theory. The latter is applied to model of epigenetic evolution. We briefly present the basics of the quantum-like approach to modeling of bio-informational processes. This approach is illustrated by the quantum-like model of epigenetic evolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Gelation or molecular recognition; is the bis-(α,β-dihydroxy ester)s motif an omnigelator?

    PubMed Central

    Knight, David W; Morgan, Ian R; Ford, Amy; Brown, James; Davies, Ben; Heenan, Richard K; King, Stephen M; Dalgliesh, Robert M; Tomkinson, John; Prescott, Stuart; Schweins, Ralf; Paul, Alison

    2010-01-01

    Summary Understanding the gelation of liquids by low molecular weight solutes at low concentrations gives an insight into many molecular recognition phenomena and also offers a simple route to modifying the physical properties of the liquid. Bis-(α,β-dihydroxy ester)s are shown here to gel thermoreversibly a wide range of solvents, raising interesting questions as to the mechanism of gelation. At gelator concentrations of 5–50 mg ml−1, gels were successfully formed in acetone, ethanol/water mixtures, toluene, cyclohexane and chloroform (the latter, albeit at a higher gelator concentration). A range of neutron techniques – in particular small-angle neutron scattering (SANS) – have been employed to probe the structure of a selection of these gels. The universality of gelation in a range of solvent types suggests the gelation mechanism is a feature of the bis-(α,β-dihydroxy ester) motif, with SANS demonstrating the presence of regular structures in the 30–40 Å range. A correlation between the apparent rodlike character of the structures formed and the polarity of the solvent is evident. Preliminary spin-echo neutron scattering studies (SESANS) indicated the absence of any larger scale structures. Inelastic neutron spectroscopy (INS) studies demonstrated that the solvent is largely unaffected by gelation, but does reveal insights into the thermal history of the samples. Further neutron studies of this kind (particularly SESANS and INS) are warranted, and it is hoped that this work will stimulate others to pursue this line of research. PMID:21160568

  12. Synthesis of multi-core-shell magnetic molecularly imprinted microspheres for rapid recognition of dicofol in tea.

    PubMed

    Yan, Hongyuan; Cheng, Xiaoling; Sun, Ning

    2013-03-20

    Magnetic multi-core-shell molecularly imprinted microspheres (Fe3O4@MIMs) based on multi-Fe3O4 nanoparticles as core structures and dummy imprinted materials as shell structures have been synthesized by a surface-imprinted technique using dichlorodiphenyltrichloroethane as the dummy template and were successfully used as a specific adsorbent for rapid isolation of trace levels of dicofol from teas. The resulting Fe3O4@MIMs were characterized by scanning electron microscopy, Fourier transform infrared spectroscopy, X-ray diffraction, vibrating sample magnetometer, and thermogravimetric analysis. In comparison to the imprinted polymers prepared by the traditional polymerizations, the obtained Fe3O4@MIMs showed regularly spherical shape, porous morphologies, high saturation magnetization [56.8 electromagnetic units (emu)/g], and rapid response time (15 s). The as-synthesized Fe3O4@MIMs, which incorporated the excellent molecular recognition and magnetic separation properties, were successfully used as special adsorbents for rapid isolation and extraction of trace levels of dicofol and its analogues from a complicated tea matrix.

  13. Gelation or molecular recognition; is the bis-(α,β-dihydroxy ester)s motif an omnigelator?

    PubMed

    Griffiths, Peter C; Knight, David W; Morgan, Ian R; Ford, Amy; Brown, James; Davies, Ben; Heenan, Richard K; King, Stephen M; Dalgliesh, Robert M; Tomkinson, John; Prescott, Stuart; Schweins, Ralf; Paul, Alison

    2010-11-18

    Understanding the gelation of liquids by low molecular weight solutes at low concentrations gives an insight into many molecular recognition phenomena and also offers a simple route to modifying the physical properties of the liquid. Bis-(α,β-dihydroxy ester)s are shown here to gel thermoreversibly a wide range of solvents, raising interesting questions as to the mechanism of gelation. At gelator concentrations of 5-50 mg ml⁻¹, gels were successfully formed in acetone, ethanol/water mixtures, toluene, cyclohexane and chloroform (the latter, albeit at a higher gelator concentration). A range of neutron techniques - in particular small-angle neutron scattering (SANS) - have been employed to probe the structure of a selection of these gels. The universality of gelation in a range of solvent types suggests the gelation mechanism is a feature of the bis-(α,β-dihydroxy ester) motif, with SANS demonstrating the presence of regular structures in the 30-40 Å range. A correlation between the apparent rodlike character of the structures formed and the polarity of the solvent is evident. Preliminary spin-echo neutron scattering studies (SESANS) indicated the absence of any larger scale structures. Inelastic neutron spectroscopy (INS) studies demonstrated that the solvent is largely unaffected by gelation, but does reveal insights into the thermal history of the samples. Further neutron studies of this kind (particularly SESANS and INS) are warranted, and it is hoped that this work will stimulate others to pursue this line of research.

  14. Innate recognition of apoptotic cells: novel apoptotic cell-associated molecular patterns revealed by crossreactivity of anti-LPS antibodies.

    PubMed

    Tennant, I; Pound, J D; Marr, L A; Willems, J J L P; Petrova, S; Ford, C A; Paterson, M; Devitt, A; Gregory, C D

    2013-05-01

    Cells dying by apoptosis are normally cleared by phagocytes through mechanisms that can suppress inflammation and immunity. Molecules of the innate immune system, the pattern recognition receptors (PRRs), are able to interact not only with conserved structures on microbes (pathogen-associated molecular patterns, PAMPs) but also with ligands displayed by apoptotic cells. We reasoned that PRRs might therefore interact with structures on apoptotic cells - apoptotic cell-associated molecular patterns (ACAMPs) - that are analogous to PAMPs. Here we show that certain monoclonal antibodies raised against the prototypic PAMP, lipopolysaccharide (LPS), can crossreact with apoptotic cells. We demonstrate that one such antibody interacts with a constitutively expressed intracellular protein, laminin-binding protein, which translocates to the cell surface during apoptosis and can interact with cells expressing the prototypic PRR, mCD14 as well as with CD14-negative cells. Anti-LPS cross reactive epitopes on apoptotic cells colocalised with annexin V- and C1q-binding sites on vesicular regions of apoptotic cell surfaces and were released associated with apoptotic cell-derived microvesicles (MVs). These results confirm that apoptotic cells and microbes can interact with the immune system through common elements and suggest that anti-PAMP antibodies could be used strategically to characterise novel ACAMPs associated not only with apoptotic cells but also with derived MVs.

  15. 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.

  16. The molecular recognition of kink-turn structure by the L7Ae class of proteins

    PubMed Central

    Huang, Lin; Lilley, David M.J.

    2013-01-01

    L7Ae is a member of a protein family that binds kink-turns (k-turns) in many functional RNA species. We have solved the X-ray crystal structure of the near-consensus sequence Kt-7 of Haloarcula marismortui bound by Archaeoglobus fulgidus L7Ae at 2.3-Å resolution. We also present a structure of Kt-7 in the absence of bound protein at 2.2-Å resolution. As a result, we can describe a general mode of recognition of k-turn structure by the L7Ae family proteins. The protein makes interactions in the widened major groove on the outer face of the k-turn. Two regions of the protein are involved. One is an α-helix that enters the major groove of the NC helix, making both nonspecific backbone interactions and specific interactions with the guanine nucleobases of the conserved G•A pairs. A hydrophobic loop makes close contact with the L1 and L2 bases, and a glutamate side chain hydrogen bonds with L1. Taken together, these interactions are highly selective for the structure of the k-turn and suggest how conformational selection of the folded k-turn occurs. PMID:24149842

  17. Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition.

    PubMed

    Hoyland, Christopher N; Aldridge, Christine; Cleverley, Robert M; Duchêne, Marie-Clémence; Minasov, George; Onopriyenko, Olena; Sidiq, Karzan; Stogios, Peter J; Anderson, Wayne F; Daniel, Richard A; Savchenko, Alexei; Vollmer, Waldemar; Lewis, Richard J

    2014-07-08

    Peptidoglycan surrounds the bacterial cytoplasmic membrane to protect the cell against osmolysis. The biosynthesis of peptidoglycan, made of glycan strands crosslinked by short peptides, is the target of antibiotics like β-lactams and glycopeptides. Nascent peptidoglycan contains pentapeptides that are trimmed by carboxypeptidases to tetra- and tripeptides. The well-characterized DD-carboxypeptidases hydrolyze the terminal D-alanine from the stem pentapeptide to produce a tetrapeptide. However, few LD-carboxypeptidases