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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 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

  6. 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.

  7. 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.

  8. 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…

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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).

  14. 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…

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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…

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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

  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. 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

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. Functional self-assembled DNA nanostructures for molecular recognition

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaojuan; Yadavalli, Vamsi K.

    2012-03-01

    Nucleic acids present a wonderful toolkit of structural motifs for nanoconstruction. Functional DNA nanostructures can enable protein recognition by the use of aptamers attached to a basic core shape formed by DNA self-assembly. Here, we present a facile, programmable strategy for the assembly of discrete aptamer-tagged DNA shapes and nanostructures that can function for molecular recognition and binding in an aqueous environment. These nanostructures, presented here to bind two different protein targets, are easily synthesized in large numbers, and are portable and stable over long periods of time. This construction modality can facilitate on-demand production of libraries of diverse shapes to recognize and bind proteins or catalyze reactions via functional nucleic acid tags.Nucleic acids present a wonderful toolkit of structural motifs for nanoconstruction. Functional DNA nanostructures can enable protein recognition by the use of aptamers attached to a basic core shape formed by DNA self-assembly. Here, we present a facile, programmable strategy for the assembly of discrete aptamer-tagged DNA shapes and nanostructures that can function for molecular recognition and binding in an aqueous environment. These nanostructures, presented here to bind two different protein targets, are easily synthesized in large numbers, and are portable and stable over long periods of time. This construction modality can facilitate on-demand production of libraries of diverse shapes to recognize and bind proteins or catalyze reactions via functional nucleic acid tags. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr11711h

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  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. 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.

  15. 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.

  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 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.

  20. 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

  1. 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

  2. Molecular recognition and optical detection of biological pathogens at biomimetic membrane interfaces

    NASA Astrophysics Data System (ADS)

    Pan, John J.; Charych, Deborah H.

    1997-02-01

    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 (polydiacetylene) can, on a simple level, mimic membrane processes of molecular recognition and signal transduction. The ganglioside, GMI was incorporated into polydiacetylene liposomes. Molecular recognition of cholera toxin at the interface of the liposome resulted in a change of the membrane color due to conformational changes 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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).

  9. 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.

  10. 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.

  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. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. "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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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…

  15. 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.

  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. 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

  18. 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.

  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. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. [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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

    2017-02-20

    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.

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone

    PubMed Central

    Street, Timothy O.; Zeng, Xiaohui; Pellarin, Riccardo; Bonomi, Massimiliano; Sali, Andrej; Kelly, Mark J.S.; Chu, Feixia; Agard, David A.

    2017-01-01

    Hsp90 is a conformationally dynamic molecular chaperone known to promote the folding and activation of a broad array of protein substrates (“clients”). Hsp90 is believed to preferentially interact with partially folded substrates, and it has been hypothesized that the chaperone can significantly alter substrate structure as a mechanism to alter the substrate functional state. However, critically testing the mechanism of substrate recognition and remodeling by Hsp90 has been challenging. Using a partially folded protein as a model system, we find that the bacterial Hsp90 adapts its conformation to the substrate, forming a binding site that spans the middle and C-terminal domains of the chaperone. Crosslinking and NMR measurements indicate that Hsp90 binds to a large partially-folded region of the substrate and significantly alters both its local and long-range structure. These findings implicate Hsp90’s conformational dynamics in its ability to bind and remodel partially folded proteins. Moreover, native-state hydrogen exchange indicates that Hsp90 can also interact with partially folded states only transiently populated from within a thermodynamically stable native state ensemble. These results suggest a general mechanism by which Hsp90 can recognize and remodel native proteins by binding and remodeling partially folded states that are transiently sampled from within the native ensemble. PMID:24726919

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  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. 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

  3. 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.

  4. 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

  5. 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

  6. Exploration micromechanism of VP35 IID interaction and recognition dsRNA: A molecular dynamics simulation.

    PubMed

    Zhang, Yan-Jun; Ding, Jing-Na; Zhong, Hui; Han, Ju-Guang

    2017-02-16

    Multifunctional viral protein (VP35) encoded by the highly pathogenic Ebola viruses (EBOVs) can antagonize host double-stranded RNA (dsRNA) sensors and immune response because of the simultaneous recognition of dsRNA backbone and blunt ends. Mutation of select hydrophobic conserved basic residues within the VP35 inhibitory domain (IID) abrogates its dsRNA-binding activity, and impairs VP35-mediated interferon (IFN) antagonism. Herein the detailed binding mechanism between dsRNA and WT, single mutant, and double mutant were investigated by all-atom molecular dynamics (MD) simulation and binding energy calculation. R312A/R322A double mutations results in a completely different binding site and orientation upon the structure analyses. The calculated binding free energy results reveal that R312A, R322A, and K339A single mutations decrease the binding free energies by 17.82, 13.18, and 13.68 kcal/mol, respectively. The binding energy decomposition indicates that the strong binding affinity of the key residues are mainly due to the contributions of electrostatic interactions in the gas phase, where come from the positively charged side chain and the negatively charged dsRNA backbone. R312A, R322A, and K339A single mutations have no significant effect on VP35 IID conformation, but the mutations influence the contributions of electrostatic interactions in the gas phase. The calculated results reveal that end-cap residues which mainly contribute VDW interactions can recognize and capture dsRNA blunt ends, and the central basic residues (R312, R322, and K339) which mainly contribute favorable electrostatic interactions with dsRNA backbone can fix dsRNA binding site and orientation. This article is protected by copyright. All rights reserved.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. “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

  15. 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.

  16. 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.

  17. 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.

  18. Novel hybrid structure silica/CdTe/molecularly imprinted polymer: synthesis, specific recognition, and quantitative fluorescence detection of bovine hemoglobin.

    PubMed

    Li, Dong-Yan; He, Xi-Wen; Chen, Yang; Li, Wen-You; Zhang, Yu-Kui

    2013-12-11

    This work presented a novel strategy for the synthesis of the hybrid structure silica/CdTe/molecularly imprinted polymer (Si-NP/CdTe/MIP) to recognize and detect the template bovine hemoglobin (BHb). First, amino-functionalized silica nanoparticles (Si-NP) and carboxyl-terminated CdTe quantum dots (QDs) were assembled into composite nanoparticles (Si-NP/CdTe) using the EDC (1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride) chemistry. Next, Si-NP/CdTe/MIP was synthesized by anchoring molecularly imprinted polymer (MIP) layer on the surface of Si-NP/CdTe through the sol-gel technique and surface imprinting technique. The hybrid structure possessed the selectivity of molecular imprinting technique and the sensitivity of CdTe QDs as well as well-defined morphology. The binding experiment and fluorescence method demonstrated its special recognition performance toward the template BHb. Under the optimized conditions, the fluorescence intensity of the Si-NP/CdTe/MIP decreased linearly with the increase of BHb in the concentration range 0.02-2.1 μM, and the detection limit was 9.4 nM. Moreover, the reusability and reproducibility and the successful applications in practical samples indicated the synthesis of Si-NP/CdTe/MIP provided an alternative solution for special recognition and determination of protein from real samples.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. The Selective Separation of Anions and Cations in Nuclear Waste Using Commercially Available Molecular Recognition Technology (MRT) Products

    SciTech Connect

    Izatt, S. R.; Bruening, R. L.; Krakowiak, K. E.; Izatt, R. M.

    2003-02-25

    This paper describes the use of some of IBC's SuperLig{reg_sign}, MacroLig{reg_sign}, and AnaLig{reg_sign} molecular recognition technology products to effectively and selectively separate and recover cesium, technetium, strontium, and radium from radioactive waste solutions. Distinct advantages are given over conventional separation techniques. Separations are described and results given for the target ions over chemically similar ions often present at much higher concentrations. The separations are performed in solutions of either high or low pH and usually containing high concentrations of salts. Other separations involving components of radioactive and mixed waste are noted.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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).

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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

  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. Unraveling the molecular recognition of amino acid derivatives by a pseudopeptidic macrocycle: ESI-MS, NMR, fluorescence, and modeling studies.

    PubMed

    Alfonso, Ignacio; Burguete, M Isabel; Galindo, Francisco; Luis, Santiago V; Vigara, Laura

    2009-08-21

    The binding between a pseudopeptidic macrocyclic naphthalenophane and different N-protected amino acid derivatives has been thoroughly studied by ESI-MS, NMR, fluorescence, and molecular modeling. Careful NMR titration experiments led to the characterization of the intermolecular noncovalent interactions, reflecting a slight side chain and l-stereoselectivity of the host-guest complexes. The data suggest the formation of an intimate ionic pair after the proton transfer from the carboxylic substrate to the amino macrocycle. Additional intermolecular interactions like H-bonding and pi-pi contacts are also important. This receptor shows a stronger interaction with substrates bearing aromatic rings, either in the side chain or in the N-protecting group. Besides, for N-Z-Phe-OH, a moderate enantioselectivity has been observed. Mass spectrometry suggests the formation of supramolecular complexes with stoichiometries higher than 1:1. The dual nature of the fluorescence emission of the macrocyclic receptor allowed determining binding constants and pertinent thermodynamic parameters. On the basis of the experimental data (NMR titrations, intermolecular ROESY, VT-NMR) and with the help of molecular modeling, a reasonable structure for the supramolecular complexes can be proposed, in which the interactions with the naphthyl ring of the receptor play a fundamental role in the strength and selectivity of the molecular recognition event.

  11. 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.

  12. 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.

  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. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  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. 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.

  4. 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.

  5. 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

  6. 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

  7. (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

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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.

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

    PubMed Central

    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. PMID:28084463

  5. A physical approach to reduce nonspecific adhesion in molecular recognition atomic force microscopy.

    PubMed

    Willemsen, O H; Snel, M M; Kuipers, L; Figdor, C G; Greve, J; De Grooth, B G

    1999-02-01

    Atomic force microscopy is one of the few techniques that allow analysis of biological recognition processes at the single-molecule level. A major limitation of this approach is the nonspecific interaction between the force sensor and substrate. We have modeled the nonspecific interaction by looking at the interaction potential between a conical Si3N4 tip with a spherical end face and a mica surface in solution, using DLVO (Derjaguin, Landau, Verwey, Overbeek) theory and numerical calculations. Insertion of the tip-sample potential in a simulation of an approach-retract cycle of the cantilever gives the well-known force-distance curve. Simulating a force-distance curve at low salt concentration predicts a discrete hopping of the tip, caused by thermal fluctuations. This hopping behavior was observed experimentally and gave rise to a novel approach to making measurements in adhesion mode that essentially works in the repulsive regime. The distance between tip and sample will still be small enough to allow spacer-involved specific interactions, and the percentage of nonspecific interactions of the bare tip with the mica is minimized. We have validated this physical model by imaging intercellular adhesion molecule 1 (ICAM-1) antigen with a tip functionalized with anti-ICAM-1 antibody. The measurement demonstrated that a significant decrease in the number of nonspecific interactions was realized, and the topographical image quality and the specific bonding capability of the tip were not affected.

  6. 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.

  7. 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 that produce tripeptides have been identified, and nothing is known about substrate specificity in these enzymes. We report biochemical properties and crystal structures of the LD-carboxypeptidases LdcB from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis. The enzymes are active against bacterial cell wall tetrapeptides and adopt a zinc-carboxypeptidase fold characteristic of the LAS superfamily. We have also solved the structure of S. pneumoniae LdcB with a product mimic, elucidating the residues essential for peptidoglycan recognition and the conformational changes that occur on ligand binding.

  8. Molecular recognition using ruthenium(II) porphyrin thiol complexes as probes.

    PubMed

    Rebouças, Júlio S; James, Brian R

    2013-01-18

    In situ (1)H NMR data are reported for 106 Ru(porp)(RSH)(2) species, where porp is the dianion of β-octaethylporphyrin (OEP), meso-tetraphenylporphyrin (TPP), and its para-substituted tetraphenyl analogues (T-p-XPP; X = OMe, Me, F, Cl, CO(2)Me, CF(3)), meso-tetrakis(3,5-dimethylphenyl)porphyrin (T-m,m'-Me(2)PP), and meso-tetramesitylporphyrin (TMP), and R = Me, Et, (n)Pr, (i)Pr, (n)Bu, (t)Bu, (n)Hex, Bn (benzyl), Ph, and p-MeOC(6)H(4). The upfield shifts in the SH resonances upon coordination of the thiol reflect changes in the porphyrin ring current and are analyzed using an empirical model that depicts quantitatively the nonbonding, electronic, and steric interactions between the thiol ligands, where steric factors dominate, and the porphyrin plane, where electronic factors dominate; such interactions are typically involved in small-molecule recognition within metalloporphyrin systems. Implications of the findings to hemethiolate proteins and surface coordination chemistry are also briefly presented.

  9. Characterization of the molecular basis of group II intron RNA recognition by CRS1-CRM domains.

    PubMed

    Keren, Ido; Klipcan, Liron; Bezawork-Geleta, Ayenachew; Kolton, Max; Shaya, Felix; Ostersetzer-Biran, Oren

    2008-08-22

    CRM (chloroplast RNA splicing and ribosome maturation) is a recently recognized RNA-binding domain of ancient origin that has been retained in eukaryotic genomes only within the plant lineage. Whereas in bacteria CRM domains exist as single domain proteins involved in ribosome maturation, in plants they are found in a family of proteins that contain between one and four repeats. Several members of this family with multiple CRM domains have been shown to be required for the splicing of specific plastidic group II introns. Detailed biochemical analysis of one of these factors in maize, CRS1, demonstrated its high affinity and specific binding to the single group II intron whose splicing it facilitates, the plastid-encoded atpF intron RNA. Through its association with two intronic regions, CRS1 guides the folding of atpF intron RNA into its predicted "catalytically active" form. To understand how multiple CRM domains cooperate to achieve high affinity sequence-specific binding to RNA, we analyzed the RNA binding affinity and specificity associated with each individual CRM domain in CRS1; whereas CRM3 bound tightly to the RNA, CRM1 associated specifically with a unique region found within atpF intron domain I. CRM2, which demonstrated only low binding affinity, also seems to form specific interactions with regions localized to domains I, III, and IV. We further show that CRM domains share structural similarities and RNA binding characteristics with the well known RNA recognition motif domain.

  10. 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.

  11. Well-defined hydrophilic molecularly imprinted polymer microspheres for efficient molecular recognition in real biological samples by facile RAFT coupling chemistry.

    PubMed

    Zhao, Man; Chen, Xiaojing; Zhang, Hongtao; Yan, Husheng; Zhang, Huiqi

    2014-05-12

    A facile and highly efficient new approach (namely RAFT coupling chemistry) to obtain well-defined hydrophilic molecularly imprinted polymer (MIP) microspheres with excellent specific recognition ability toward small organic analytes in the real, undiluted biological samples is described. It involves the first synthesis of "living" MIP microspheres with surface-bound vinyl and dithioester groups via RAFT precipitation polymerization (RAFTPP) and their subsequent grafting of hydrophilic polymer brushes by the simple coupling reaction of hydrophilic macro-RAFT agents (i.e., hydrophilic polymers with a dithioester end group) with vinyl groups on the "living" MIP particles in the presence of a free radical initiator. The successful grafting of hydrophilic polymer brushes onto the obtained MIP particles was confirmed by SEM, FT-IR, static contact angle and water dispersion studies, elemental analyses, and template binding experiments. Well-defined MIP particles with densely grafted hydrophilic polymer brushes (∼1.8 chains/nm(2)) of desired chemical structures and molecular weights were readily obtained, which showed significantly improved surface hydrophilicity and could thus function properly in real biological media. The origin of the high grafting densities of the polymer brushes was clarified and the general applicability of the strategy was demonstrated. In particular, the well-defined characteristics of the resulting hydrophilic MIP particles allowed the first systematic study on the effects of various structural parameters of the grafted hydrophilic polymer brushes on their water-compatibility, which is of great importance for rationally designing more advanced real biological sample-compatible MIPs.

  12. Influence of ligand presentation density on the molecular recognition of mannose-functionalised glyconanoparticles by bacterial lectin BC2L-A.

    PubMed

    Reynolds, Michael; Marradi, Marco; Imberty, Anne; Penadés, Soledad; Pérez, Serge

    2013-11-01

    Polyvalent carbohydrate-protein interactions play a key role in bio- and pathological processes, including cell-cell communication and pathogen invasion. In order to study, control and manipulate these interactions gold nanoparticles have been employed as a 3D scaffold, presenting carbohydrate ligands in a multivalent fashion for use as high affinity binding partners and a model system for oligosaccharide presentation at biomacromolecular surfaces. In this study, the binding of a series of mannose-functionalised gold nanoparticles to the dimeric BC2L-A lectin from Burkholderia cenocepacia has been evaluated. BC2L-A is known to exhibit a high specificity for (oligo)mannosides. Due to the unique structure and binding nature of this lectin, it provides a useful tool to study (oligo)saccharides presented on multivalent scaffolds. Surface plasmon resonance and isothermal titration calorimetric assays were used to investigate the effect of ligand presentation density towards binding to the bacterial lectin. We show how a combination of structural complementarities between ligand presentation and lectin architecture and statistical re-binding effects are important for increasing the avidity of multivalent ligands for recognition by their protein receptors; further demonstrating the application of glyconanotechnology towards fundamental glycobiology research as well as a potential towards biomedical diagnostics and therapeutic treatments.

  13. Understanding the molecular recognition between antibody fragments and protein A biomimetic ligand.

    PubMed

    Branco, Ricardo J F; Dias, Ana M G C; Roque, Ana C A

    2012-06-29

    Affinity chromatography with protein A from Staphylococcus aureus (SpA) is the most widespread and accepted methodology for antibody capture during the downstream process of antibody manufacturing. A triazine based ligand (ligand 22/8) was previously developed as an inexpensive and robust alternative to SpA chromatography (Li et al. and Teng et al.). Despite the experimental success, there is no structural information on the binding modes of ligand 22/8 to antibodies, namely to Immunoglobulin G (IgG) molecules and fragments. In this work, we addressed this issue by a molecular docking approach allied to molecular dynamics simulations. Theoretical results confirmed the preference of the synthetic ligand to bind IgG through the binding site found in the crystallographic structure of the natural complex between SpA and the Fc fragment of IgG. Our studies also suggested other unknown "hot-spots" for specific binding of the affinity ligand at the hinge between V(H) and C(H)1 domains of Fab fragment. The best docking poses were further analysed by molecular dynamics studies at three different protonation states (pH 3, 7 and 11). The main interactions between ligand 22/8 and the IgG fragments found at pH 7 were weaker at pH 3 and pH 11 and in these conditions the ligand start losing tight contact with the binding site, corroborating the experimental evidence for protein elution from the chromatographic adsorbents at these pH conditions.

  14. Chemokine production and pattern recognition receptor (PRR) expression in whole blood stimulated with pathogen-associated molecular patterns (PAMPs).

    PubMed

    Møller, Anne-Sophie W; Ovstebø, Reidun; Haug, Kari Bente F; Joø, Gun Britt; Westvik, Ase-Brit; Kierulf, Peter

    2005-12-21

    Recognition of conserved bacterial structures called pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs), may lead to induction of a variety of "early immediate genes" such as chemokines. In the current study, we have in an ex vivo whole blood model studied the induction of the chemokines MIP-1alpha, MCP-1 and IL-8 by various PAMPs. The rate of appearance of Escherichia coli-Lipopolysaccharide (LPS) induced chemokines differed. The production of MIP-1alpha and IL-8 was after 1 h of stimulation significantly higher when compared to unstimulated whole blood, whereas MCP-1 was not significantly elevated until after 3 h. At peak levels the MIP-1alpha concentration induced by E. coli-LPS was 3-5-fold higher than MCP-1 and IL-8. By specific cell depletion, we demonstrated that all three chemokines were mainly produced by monocytes. However, the mRNA results showed that IL-8 was induced in both monocytes and granulocytes. The production of all three chemokines, induced by the E. coli-LPS and Neisseria meningitidis-LPS, was significantly inhibited by antibodies against CD14 and TLR4, implying these receptors to be of importance for the effects of LPS in whole blood. The chemokine production induced by lipoteichoic acid (LTA) and non-mannose-capped lipoarabinomannan (AraLAM) was, however, less efficiently blocked by antibodies against CD14 and TLR2. E. coli-LPS and LTA induced a dose-dependent increase of CD14, TLR2 and TLR4 expression on monocytes in whole blood. These data show that PAMPs may induce chemokine production in whole blood and that antibodies against PRRs inhibit the production to different extent.

  15. Molecular Determinants of Antibiotic Recognition and Resistance by Aminoglycoside Phosphotransferase (3′)-IIIa: A Calorimetric and Mutational Analysis

    PubMed Central

    Kaul, Malvika; Barbieri, Christopher M.; Srinivasan, Annankoil R.; Pilch, Daniel S.

    2007-01-01

    Summary The growing threat from the emergence of multidrug resistant pathogens highlight a critical need to expand our currently available arsenal of broad-spectrum antibiotics. In this connection, new antibiotics must be developed that exhibit the abilities to circumvent known resistance pathways. An important step toward achieving this goal is to define the key molecular interactions that govern antibiotic resistance. Here, we use site-specific mutagenesis, coupled with calorimetric, NMR, and enzymological techniques, to define the key interactions that govern the binding of the aminoglycoside antibiotics neomycin and kanamycin B to APH(3′)-IIIa (an antibiotic phosphorylating enzyme that produces resistance). Our mutational analyses identify the D261, E262, and C-terminal F264 residues of the enzyme as being critical for recognition of the two drugs as well as the manifestation of the resistance phenotype. In addition, the E160 residue is more important for recognition of kanamycin B than neomycin, with mutation of this residue partially restoring sensitivity to kanamycin B but not to neomycin. By contrast, the D193 residue partially restores sensitivity to neomycin but not to kanamycin B, with the origins of this differential effect being due to the importance of D193 for catalyzing the phosphorylation of neomycin. These collective mutational results, coupled with 15N NMR-derived pKa and calorimetrically-derived binding-linked drug protonation data, identify the 1-, 3-, and 2′-amino groups of both neomycin and kanamycin B as being critical functionalities for binding to APH(3′)-IIIa. These drug amino functionalities represent potential sites of modification in the design of next-generation compounds that can overcome APH(3′)-IIIa-induced resistance. PMID:17418235

  16. Molecular Recognition of Fluorine Impacts Substrate Selectivity in the Fluoroacetyl-CoA Thioesterase FlK

    PubMed Central

    2015-01-01

    The fluoroacetate-producing bacterium Streptomyces cattleya has evolved a fluoroacetyl-CoA thioesterase (FlK) that exhibits a remarkably high level of discrimination for its cognate substrate compared to the cellularly abundant analogue acetyl-CoA, which differs only by the absence of the fluorine substitution. A major determinant of FlK specificity derives from its ability to take advantage of the unique properties of fluorine to enhance the reaction rate, allowing fluorine discrimination under physiological conditions where both substrates are likely to be present at saturating concentrations. Using a combination of pH–rate profiles, pre-steady-state kinetic experiments, and Taft analysis of wild-type and mutant FlKs with a set of substrate analogues, we explore the role of fluorine in controlling the enzyme acylation and deacylation steps. Further analysis of chiral (R)- and (S)-[2H1]fluoroacetyl-CoA substrates demonstrates that a kinetic isotope effect (1.7 ± 0.2) is observed for only the (R)-2H1 isomer, indicating that deacylation requires recognition of the prochiral fluoromethyl group to position the α-carbon for proton abstraction. Taken together, the selectivity for the fluoroacetyl-CoA substrate appears to rely not only on the enhanced polarization provided by the electronegative fluorine substitution but also on molecular recognition of fluorine in both formation and breakdown of the acyl-enzyme intermediate to control active site reactivity. These studies provide insights into the basis of fluorine selectivity in a naturally occurring enzyme–substrate pair, with implications for drug design and the development of fluorine-selective biocatalysts. PMID:24635371

  17. Molecular recognition of fluorine impacts substrate selectivity in the fluoroacetyl-CoA thioesterase FlK.

    PubMed

    Weeks, Amy M; Keddie, Neil S; Wadoux, Rudy D P; O'Hagan, David; Chang, Michelle C Y

    2014-04-01

    The fluoroacetate-producing bacterium Streptomyces cattleya has evolved a fluoroacetyl-CoA thioesterase (FlK) that exhibits a remarkably high level of discrimination for its cognate substrate compared to the cellularly abundant analogue acetyl-CoA, which differs only by the absence of the fluorine substitution. A major determinant of FlK specificity derives from its ability to take advantage of the unique properties of fluorine to enhance the reaction rate, allowing fluorine discrimination under physiological conditions where both substrates are likely to be present at saturating concentrations. Using a combination of pH-rate profiles, pre-steady-state kinetic experiments, and Taft analysis of wild-type and mutant FlKs with a set of substrate analogues, we explore the role of fluorine in controlling the enzyme acylation and deacylation steps. Further analysis of chiral (R)- and (S)-[(2)H1]fluoroacetyl-CoA substrates demonstrates that a kinetic isotope effect (1.7 ± 0.2) is observed for only the (R)-(2)H1 isomer, indicating that deacylation requires recognition of the prochiral fluoromethyl group to position the α-carbon for proton abstraction. Taken together, the selectivity for the fluoroacetyl-CoA substrate appears to rely not only on the enhanced polarization provided by the electronegative fluorine substitution but also on molecular recognition of fluorine in both formation and breakdown of the acyl-enzyme intermediate to control active site reactivity. These studies provide insights into the basis of fluorine selectivity in a naturally occurring enzyme-substrate pair, with implications for drug design and the development of fluorine-selective biocatalysts.

  18. Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein

    PubMed Central

    Wang, Yong; Chu, Xiakun; Longhi, Sonia; Roche, Philippe; Han, Wei; Wang, Erkang; Wang, Jin

    2013-01-01

    Numerous relatively short regions within intrinsically disordered proteins (IDPs) serve as molecular recognition elements (MoREs). They fold into ordered structures upon binding to their partner molecules. Currently, there is still a lack of in-depth understanding of how coupled binding and folding occurs in MoREs. Here, we quantified the unbound ensembles of the α-MoRE within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein. We developed a multiscaled approach by combining a physics-based and an atomic hybrid model to decipher the mechanism by which the α-MoRE interacts with the X domain of the measles virus phosphoprotein. Our multiscaled approach led to remarkable qualitative and quantitative agreements between the theoretical predictions and experimental results (e.g., chemical shifts). We found that the free α-MoRE rapidly interconverts between multiple discrete partially helical conformations and the unfolded state, in accordance with the experimental observations. We quantified the underlying global folding–binding landscape. This leads to a synergistic mechanism in which the recognition event proceeds via (minor) conformational selection, followed by (major) induced folding. We also provided evidence that the α-MoRE is a compact molten globule-like IDP and behaves as a downhill folder in the induced folding process. We further provided a theoretical explanation for the inherent connections between “downhill folding,” “molten globule,” and “intrinsic disorder” in IDP-related systems. Particularly, we proposed that binding and unbinding of IDPs proceed in a stepwise way through a “kinetic divide-and-conquer” strategy that confers them high specificity without high affinity. PMID:24043820

  19. Regulation of sporulation initiation by NprR and its signaling peptide NprRB: molecular recognition and conformational changes.

    PubMed

    Cabrera, Rosina; Rocha, Jorge; Flores, Víctor; Vázquez-Moreno, Luz; Guarneros, Gabriel; Olmedo, Gabriela; Rodríguez-Romero, Adela; de la Torre, Mayra

    2014-11-01

    NprR belongs to the RNPP family of quorum-sensing receptors, a group of intracellular regulators activated directly by signaling oligopeptides in Gram-positive bacteria. In Bacillus thuringiensis (Bt), nprR is located in a transcriptional cassette with nprRB that codes for the precursor of the signaling peptide NprRB. NprR is a transcriptional regulator activated by binding of reimported NprRB; however, several reports suggest that NprR also participates in sporulation but the mechanism is unknown. Our in silico results, based on the structural similarity between NprR from Bt and Spo0F-binding Rap proteins from Bacillus subtilis, suggested that NprR could bind Spo0F to modulate the sporulation phosphorelay in Bt. Deletion of nprR-nprRB cassette from Bt caused a delay in sporulation and defective trigger of the Spo0A∼P-activated genes spoIIA and spoIIIG. The DNA-binding domain of NprR was not necessary for this second function, since truncated NprRΔHTH together with nprRB gene was able to restore the sporulation wild type phenotype in the ΔnprR-nprRB mutant. Fluorescence assays showed direct binding between NprR and Spo0F, supporting that NprR is a bifunctional protein. To understand how the NprR activation by NprRB could result in two different functions, we studied the molecular recognition mechanism between the signaling peptide and the receptor. Using synthetic variants of NprRB, we found that SSKPDIVG displayed the highest affinity (Kd = 7.19 nM) toward the recombinant NprR and demonstrated that recognition involves conformational selection. We propose that the peptide concentration in the cell controls the oligomerization state of the NprR-NprRB complex for switching between its two functions.

  20. Nanosilica-based molecularly imprinted polymer nanoshell for specific recognition and determination of rhodamine B in red wine and beverages.

    PubMed

    Long, Zerong; Xu, Weiwei; Lu, Yi; Qiu, Hongdeng

    2016-09-01

    A new and facile rhodamine B (RhB)-imprinted polymer nanoshell coating for SiO2 nanoparticles was readily prepared by a combination of silica gel modification and molecular surface imprinting. The RhB-imprinted polymers (RhB-MIPs) were characterized by Fourier transform infrared spectroscopy, scanning electron microscopy, and UV-vis spectroscopy; the binding properties and selectivity of these MIPs were investigated in detail. The uniformly imprinted nanoparticles displayed a rather thin shell thickness (23nm) with highly effective recognition sites, showing homogenous distribution and monolayer adsorption. The maximum MIP adsorption capacity (Qm) was as high as 45.2mgg(-1), with an adsorption equilibrium time of about 15min at ambient temperature. Dynamic rebinding experiments showed that chemical adsorption is crucial for RhB binding to RhB-MIPs. The adsorption isotherm for RhB-MIPs binding could also be described by the Langmuir equation at different temperatures and pH values. Increasing temperature led to an enhanced Qm, a decreased dissociation constant (K'd), and a more negative free energy (ΔG), indicating that adsorption is favored at higher temperatures. Moreover, the adsorption capacity of RhB was remarkably affected by pH. At pH>7, the adsorption of RhB was driven by hydrogen bonding interactions, while at pH<7 electrostatic forces were dominant. Additionally, the MIPs also showed specific recognition of RhB from the standard mixture solution containing five structurally analogs. This method was also successfully employed to determine RhB content in red wine and beverages using three levels of spiking, with recoveries in the range of 91.6-93.1% and relative standard deviations lower than 4.1%.

  1. Molecular determinants of antibiotic recognition and resistance by aminoglycoside phosphotransferase (3')-IIIa: a calorimetric and mutational analysis.

    PubMed

    Kaul, Malvika; Barbieri, Christopher M; Srinivasan, Annankoil R; Pilch, Daniel S

    2007-05-25

    The growing threat from the emergence of multidrug resistant pathogens highlights a critical need to expand our currently available arsenal of broad-spectrum antibiotics. In this connection, new antibiotics must be developed that exhibit the abilities to circumvent known resistance pathways. An important step toward achieving this goal is to define the key molecular interactions that govern antibiotic resistance. Here, we use site-specific mutagenesis, coupled with calorimetric, NMR, and enzymological techniques, to define the key interactions that govern the binding of the aminoglycoside antibiotics neomycin and kanamycin B to APH(3')-IIIa (an antibiotic phosphorylating enzyme that confers resistance). Our mutational analyses identify the D261, E262, and C-terminal F264 residues of the enzyme as being critical for recognition of the two drugs as well as for the manifestation of the resistance phenotype. In addition, the E160 residue is more important for recognition of kanamycin B than neomycin, with mutation of this residue partially restoring sensitivity to kanamycin B but not to neomycin. By contrast, the D193 residue partially restores sensitivity to neomycin but not to kanamycin B, with the origins of this differential effect being due to the importance of D193 for catalyzing the phosphorylation of neomycin. These collective mutational results, coupled with (15)N NMR-derived pK(a) and calorimetrically derived binding-linked drug protonation data, identify the 1-, 3-, and 2'-amino groups of both neomycin and kanamycin B as being critical functionalities for binding to APH(3')-IIIa. These drug amino functionalities represent potential sites of modification in the design of next-generation compounds that can overcome APH(3')-IIIa-induced resistance.

  2. Molecular recognition of ketamine by a subset of olfactory G protein–coupled receptors

    PubMed Central

    Saven, Jeffery G.; Matsunami, Hiroaki; Eckenhoff, Roderic G.

    2015-01-01

    Ketamine elicits various neuropharmacological effects, including sedation, analgesia, general anesthesia, and antidepressant activity. Through an in vitro screen, we identified four mouse olfactory receptors (ORs) that responded to ketamine. In addition to their presence in the olfactory epithelium, these G protein (heterotrimeric guanine nucleotide–binding protein)–coupled receptors (GPCRs) are distributed throughout the central nervous system. To better understand the molecular basis of the interactions between ketamine and ORs, we used sequence comparison and molecular modeling to design mutations that (i) increased, reduced, or abolished ketamine responsiveness in responding receptors, and (ii) rendered non-responding receptors responsive to ketamine. We showed that olfactory sensory neurons (OSNs) that expressed distinct ORs responded to ketamine in vivo, suggesting that ORs may serve as functional targets for ketamine. The ability to both abolish and introduce responsiveness to ketamine in GPCRs enabled us to identify and confirm distinct interaction loci in the binding site, which suggested a signature ketamine-binding pocket that may guide exploration of additional receptors for this general anesthetic drug. PMID:25829447

  3. Molecular recognition and binding of beta-lactamase II from Bacillus cereus with penicillin V and sulbactam by spectroscopic analysis in combination with docking simulation.

    PubMed

    Zhang, Yeli; Qiao, Pan; Li, Shuaihua; Feng, Xuan; Bian, Liujiao

    2017-02-10

    The molecular recognition and binding interaction of beta-lactamase II from Bacillus cereus (Bc II) with penicillin V (PV) and sulbactam (Sul) at 277 K were studied by spectroscopic analysis and molecular docking. The results showed that a non-fluorescence static complex was separately formed between Bc II and two ligands, the molecular ratio of Bc II to PV or Sul was both 1:1 in the binding and the binding constants were 2.00 × 10(6) and 3.98 × 10(5) (L/mol), respectively. The negative free energy changes and apparent activation energies indicated that both the binding processes were spontaneous. Molecular docking showed that in the binding process, the whole Sul molecule entered into the binding pocket of Bc II while only part of the whole PV molecule entered into the pocket due to a long side chain, and electrostatic interactions were the major contribution to the binding processes. In addition, a weak conformational change of Bc II was also observed in the molecular recognition and binding process of Bc II with PV or Sul. This study may provide some valuable information for exploring the recognition and binding of proteins with ligands in the binding process and for the design of novel super-antibiotics.

  4. Light-driven linear helical supramolecular polymer formed by molecular-recognition-directed self-assembly of bis(p-sulfonatocalix[4]arene) and pseudorotaxane.

    PubMed

    Sun, Ruyi; Xue, Chenming; Ma, Xiang; Gao, Min; Tian, He; Li, Quan

    2013-04-24

    A light-driven, linear, chiral supramolecular polymer was constructed in water by host-guest molecular recognition between bis(p-sulfonatocalix[4]arene) and the α-cyclodextrin-based pseudo[3]rotaxane containing axially chiral 1,1'-binaphthyl and photoresponsive azobenzene moieties. The successful supramolecular polymerization by non-covalent host-guest molecular recognition was confirmed by (1)H NMR spectroscopy and dynamic light scattering (DLS) measurements, and its photoresponsive behavior was investigated by UV-vis absorption spectroscopy, scanning electron microscopy (SEM), atomic force microscopy (AFM), and transmission electron microscopy (TEM). The chirality of this supramolecular polymer was confirmed by circular dichroism spectroscopy. The dramatic morphology change of this chiral polymer driven by light was observed in SEM, AFM and TEM images. More interestingly, dynamically self-assembled, light-driven, single-helical linear supramolecular polymer molecules with lengths of hundreds of nanometers to micrometers in water were directly observed in their native state using cryo-TEM measurements. The observation of considerably lengthy individual supramolecular polymer molecules indicates that the molecular self-assembly in water by non-covalent host-guest molecular recognition is sufficiently strong to form the supramolecular polymer. Moreover, preliminary molecular modeling was performed to substantiate this interesting photoresponsive supramolecular structure.

  5. The multiple Tudor domain-containing protein TDRD1 is a molecular scaffold for mouse Piwi proteins and piRNA biogenesis factors.

    PubMed

    Mathioudakis, Nikolas; Palencia, Andres; Kadlec, Jan; Round, Adam; Tripsianes, Konstantinos; Sattler, Michael; Pillai, Ramesh S; Cusack, Stephen

    2012-11-01

    Piwi-interacting RNAs (piRNAs) are small noncoding RNAs expressed in the germline of animals. They associate with Argonaute proteins of the Piwi subfamily, forming ribonucleoprotein complexes that are involved in maintaining genome integrity. The N-terminal region of some Piwi proteins contains symmetrically dimethylated arginines. This modification is thought to enable recruitment of Tudor domain-containing proteins (TDRDs), which might serve as platforms mediating interactions between various proteins in the piRNA pathway. We measured the binding affinity of the four individual extended Tudor domains (TDs) of murine TDRD1 protein for three different methylarginine-containing peptides from murine Piwi protein MILI. The results show a preference of TD2 and TD3 for consecutive MILI peptides, whereas TD4 and TD1 have, respectively, lower and very weak affinity for any peptide. The affinity of TD1 for methylarginine peptides can be restored by a single-point mutation back to the consensus aromatic cage sequence. These observations were confirmed by pull-down experiments with endogenous Piwi and Piwi-associated proteins. The crystal structure of TD3 bound to a methylated MILI peptide shows an unexpected orientation of the bound peptide, with additional contacts of nonmethylated residues being made outside of the aromatic cage, consistent with solution NMR titration experiments. Finally, the molecular envelope of the four tandem Tudor domains of TDRD1, derived from small angle scattering data, reveals a flexible, elongated shape for the protein. Overall, the results show that TDRD1 can accommodate different peptides from different proteins, and can therefore act as a scaffold protein for complex assembly in the piRNA pathway.

  6. Three-dimensional fiber-deposited PEOT/PBT copolymer scaffolds for tissue engineering: influence of porosity, molecular network mesh size, and swelling in aqueous media on dynamic mechanical properties.

    PubMed

    Moroni, L; de Wijn, J R; van Blitterswijk, C A

    2005-12-15

    Among novel scaffold fabrication techniques, 3D fiber deposition (3DF) has recently emerged as a means to fabricate well-defined and custom-made scaffolds for tissue regeneration, with 100% interconnected pores. The mechanical behavior of these constructs is dependent not only on different three-dimensional architectural and geometric features, but also on the intrinsic chemical properties of the material used. These affect the mechanics of the solid material and eventually of 3D porous constructs derived from them. For instance, poly(ethylene oxide terephthalate)-poly(butylene terephthalate) (PEOT/PBT) block copolymers are known to have mechanical properties, depending on the PEOT/PBT weight ratio in block form and on the molecular weight of the initial poly(ethylene glycol) (PEG) blocks. These differences are enhanced even more by their different swelling properties in aqueous media. Therefore, this article examines the influence of copolymer compositions in terms of their swelling on dynamic mechanical properties of solid material and porous 3DF scaffolds. The molecular weight of the starting PEG blocks used in the copolymer synthesis varied from 300 to 1000 g/mol. The PEOT/PBT weight ratio in the blocks used varied from 55/45 to 80/20. This corresponded to an increase of the swelling ratio Q from 1.06 to 2.46, and of the mesh size xi from approximately 9 Angstrom to approximately 47 Angstrom. With increased swelling, dynamic mechanical analysis (DMA) revealed a decrease in elastic response and an increase of viscoelasticity. Thus, by coupling structural and chemical characteristics, the viscoelastic properties of PEOT/PBT 3DF scaffolds may be fine tuned to achieve mechanical requirements for a variety of engineered tissues. Ultimately, the combination of 3DF and DMA may be useful to validate the hypothesis that mimicking the biomechanical behavior of a specific tissue for its optimal replacement is an important issue for at least some tissue

  7. Supramolecular adhesives to hard surfaces: adhesion between host hydrogels and guest glass substrates through molecular recognition.

    PubMed

    Takashima, Yoshinori; Sahara, Taiga; Sekine, Tomoko; Kakuta, Takahiro; Nakahata, Masaki; Otsubo, Miyuki; Kobayashi, Yuichiro; Harada, Akira

    2014-10-01

    Supramolecular materials based on host-guest interactions should exhibit high selectivity and external stimuli-responsiveness. Among various stimuli, redox and photo stimuli are useful for its wide application. An external stimuli-responsive adhesive system between CD host-gels (CD gels) and guest molecules modified glass substrates (guest Sub) is focused. Here, the selective adhesion between host gels and guest substrates where adhesion depends on molecular complementarity is reported. Initially, it is thought that adhesion of a gel material onto a hard material might be difficult unless many guest molecules modified linear polymers immobilize on the surface of hard materials. However, reversible adhesion of the CD gels is observed by dissociating and re-forming inclusion complex in response to redox and photo stimuli.

  8. Molecular Recognition of Muramyl Dipeptide Occurs in the Leucine-rich Repeat Domain of Nod2.

    PubMed

    Lauro, Mackenzie L; D'Ambrosio, Elizabeth A; Bahnson, Brian J; Grimes, Catherine Leimkuhler

    2017-04-14

    Genetic mutations in the innate immune receptor nucleotide-binding oligomerization domain-containing 2 (Nod2) have demonstrated increased susceptibility to Crohn's disease, an inflammatory bowel disease that is hypothesized to be accompanied by changes in the gut microbiota. Nod2 responds to the presence of bacteria, specifically a fragment of the bacterial cell wall, muramyl dipeptide (MDP). The proposed site of this interaction is the leucine-rich repeat (LRR) domain. Surface plasmon resonance and molecular modeling were used to investigate the interaction of the LRR domain with MDP. A functional and pure LRR domain was obtained from Escherichia coli expression in high yield. The LRR domain binds to MDP with high affinity, with a KD of 212 ± 24 nM. Critical portions of the receptor were determined by mutagenesis of putative binding residues. Fragment analysis of MDP revealed that both the peptide and carbohydrate portion contribute to the binding interaction.

  9. Molecular and morphological evidence for recognition of two species within Harpagonella (Amsinckiinae, Boraginaceae).

    PubMed

    Guilliams, C Matt; Jang, Timothy; Baldwin, Bruce G

    2016-01-01

    Recent taxonomic treatments of the genus Harpagonella have included only one lower taxon, Harpagonella palmeri A. Gray. However, a larger-fruited variety of Harpagonella palmeri from Arizona and Sonora was described by I.M. Johnston in 1924. He continued to recognize this taxon - Harpagonella palmeri var. arizonica - in his treatment of the genus in Kearney and Peebles's Arizona Flora in 1960. Here, we provide two lines of molecular evidence and quantitative morphological evidence from calyx characters showing that plants of Harpagonella from Arizona, Sonora, and central Baja California, corresponding to Johnston's var. arizonica, are distinct from Harpagonella palmeri of southern California and Baja California. We make the new combination Harpagonella arizonica (I.M. Johnston) Guilliams & B.G. Baldwin, comb. nov. for the plants from Arizona, Sonora, and central Baja California.

  10. Molecular and morphological evidence for recognition of two species within Harpagonella (Amsinckiinae, Boraginaceae)

    PubMed Central

    Guilliams, C. Matt; Jang, Timothy; Baldwin, Bruce G.

    2016-01-01

    Abstract Recent taxonomic treatments of the genus Harpagonella have included only one lower taxon, Harpagonella palmeri A. Gray. However, a larger-fruited variety of Harpagonella palmeri from Arizona and Sonora was described by I.M. Johnston in 1924. He continued to recognize this taxon – Harpagonella palmeri var. arizonica – in his treatment of the genus in Kearney and Peebles’s Arizona Flora in 1960. Here, we provide two lines of molecular evidence and quantitative morphological evidence from calyx characters showing that plants of Harpagonella from Arizona, Sonora, and central Baja California, corresponding to Johnston’s var. arizonica, are distinct from Harpagonella palmeri of southern California and Baja California. We make the new combination Harpagonella arizonica (I.M. Johnston) Guilliams & B.G. Baldwin, comb. nov. for the plants from Arizona, Sonora, and central Baja California. PMID:27829796

  11. Engineering Molecular Recognition with Bio-mimetic Polymers on Single Walled Carbon Nanotubes.

    PubMed

    Del Bonis-O'Donnell, Jackson T; Beyene, Abraham; Chio, Linda; Demirer, Gözde; Yang, Darwin; Landry, Markita P

    2017-01-10

    Semiconducting single-wall carbon nanotubes (SWNTs) are a class of optically active nanomaterial that fluoresce in the near infrared, coinciding with the optical window where biological samples are most transparent. Here, we outline techniques to adsorb amphiphilic polymers and polynucleic acids onto the surface of SWNTs to engineer their corona phases and create novel molecular sensors for small molecules and proteins. These functionalized SWNT sensors are both biocompatible and stable. Polymers are adsorbed onto the nanotube surface either by direct sonication of SWNTs and polymer or by suspending SWNTs using a surfactant followed by dialysis with polymer. The fluorescence emission, stability, and response of these sensors to target analytes are confirmed using absorbance and near-infrared fluorescence spectroscopy. Furthermore, we demonstrate surface immobilization of the sensors onto glass slides to enable single-molecule fluorescence microscopy to characterize polymer adsorption and analyte binding kinetics.

  12. Self-assembly and molecular "recognition" phenomena in solutions of (bio)polyelectrolyte complexes

    NASA Astrophysics Data System (ADS)

    Izumrudov, V. A.

    2008-04-01

    Recently published data on polyelectrolyte complexes formed by both oppositely charged synthetic polyions and natural polyelectrolytes (proteins, enzymes, nucleic acids) are summarised. The properties of these complexes and the phase behaviour of their solutions is shown to obey the general trends found in the studies of cooperative interpolyelectrolyte interactions. The principles of functioning of polyelectrolyte complexes that underlie the self-assembly of complexes in solution and determine the ability of complexes to retain stability over a specified broad range of external conditions and then to quickly and reversibly respond with high sensitivity to a change in the environment by changing their molecular characteristics and phase state are considered. The successful use of the results of fundamental research of (bio)polyelectrolyte complexes for the solution of topical problems of biotechnology, materials science and medicine are demonstrated.

  13. Molecular basis of substrate recognition and specificity revealed in family 12 glycoside hydrolases.

    PubMed

    Calzado, Felipe; Prates, Erica T; Gonçalves, Thiago A; Rubio, Marcelo V; Zubieta, Mariane P; Squina, Fabio M; Skaf, Munir S; Damásio, André R L

    2016-12-01

    Fungal GH12 enzymes are classified as xyloglucanases when they specifically target xyloglucans, or promiscuous endoglucanases when they exhibit catalytic activity against xyloglucan and β-glucan chains. Several structural and functional studies involving GH12 enzymes tried to explain the main patterns of xyloglucan activity, but what really determines xyloglucanase specificity remains elusive. Here, three fungal GH12 enzymes from Aspergillus clavatus (AclaXegA), A. zonatus (AspzoGH12), and A. terreus (AtEglD) were studied to unveil the molecular basis for substrate specificity. Using functional assays, site-directed mutagenesis, and molecular dynamics simulations, we demonstrated that three main regions are responsible for substrate selectivity: (i) the YSG group in loop 1; (ii) the SST group in loop 2; and (iii) loop A3-B3 and neighboring residues. Functional assays and sequence alignment showed that while AclaXegA is specific to xyloglucan, AtEglD cleaves β-glucan, and xyloglucan. However, AspzoGH12 was also shown to be promiscuous contrarily to a sequence alignment-based prediction. We find that residues Y111 and R93 in AtEglD harbor the substrate in an adequate orientation for hydrolysis in the catalytic cleft entrance and that residues Y19 in AclaXegA and Y30 in AspzoGH12 partially compensate the absence of the YSG segment, typically found in promiscuous enzymes. The results point out the multiple structural factors underlying the substrate specificity of GH12 enzymes. Biotechnol. Bioeng. 2016;113: 2577-2586. © 2016 Wiley Periodicals, Inc.

  14. A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins

    PubMed Central

    Májek, Peter; Elber, Ron

    2009-01-01

    A coarse grained potential for protein simulations and fold ranking is presented. The potential is based on a two-point model of individual amino acids and a specific implementation of hydrogen bonding. Parameters are determined for distance dependent pair interactions, pseudo bonds, angles, and torsions. A scaling factor for a hydrogen bonding term is also determined. Iterative sampling for 4867 proteins reproduces distributions of internal coordinates and distances observed in the Protein Data Bank. The adjustment of the potential and re-sampling are in the spirit of the generalized ensemble approach. No native structure information (e.g. secondary structure) is used in the calculation of the potential, or in the simulation of a particular protein. The potential is subject to two tests: (i) simulations of 956 globular proteins in the neighborhood of their native folds (these proteins were not used in the training set), and (ii) discrimination between native and decoy structures for 2470 proteins with 305,000 decoys, and the “Decoys ‘R’ Us” dataset. In the first test, 58% of tested proteins stay within 5 Å from the native fold in Molecular Dynamics simulations of more than twenty nanoseconds using the new potential. The potential is also useful in differentiating between correct and approximate folds providing significant signal for structure prediction algorithms. Sampling with the potential consistently regenerates the distribution of distances and internal coordinates it learned. Nevertheless, during Molecular Dynamics simulations structures are found that reproduce the learned distributions but are far from the native fold. PMID:19291741

  15. A Targeted "Capture" and "Removal" Scavenger toward Multiple Pollutants for Water Remediation based on Molecular Recognition.

    PubMed

    Wang, Jie; Shen, Haijing; Hu, Xiaoxia; Li, Yan; Li, Zhihao; Xu, Jinfan; Song, Xiufeng; Zeng, Haibo; Yuan, Quan

    2016-03-01

    For the water remediation techniques based on adsorption, the long-standing contradictories between selectivity and multiple adsorbability, as well as between affinity and recyclability, have put it on weak defense amid more and more severe environment crisis. Here, a pollutant-targeting hydrogel scavenger is reported for water remediation with both high selectivity and multiple adsorbability for several pollutants, and with strong affinity and good recyclability through rationally integrating the advantages of multiple functional materials. In the scavenger, aptamers fold into binding pockets to accommodate the molecular structure of pollutants to afford perfect selectivity, and Janus nanoparticles with antibacterial function as well as anisotropic surfaces to immobilize multiple aptamers allow for simultaneously handling different kinds of pollutants. The scavenger exhibits high efficiencies in removing pollutants from water and it can be easily recycled for many times without significant loss of loading capacities. Moreover, the residual concentrations of each contaminant are well below the drinking water standards. Thermodynamic behavior of the adsorption process is investigated and the rate-controlling process is determined. Furthermore, a point of use device is constructed and it displays high efficiency in removing pollutants from environmental water. The scavenger exhibits great promise to be applied in the next generation of water purification systems.

  16. QAARM: Quasi-anharmonic auto-regressive model reveals molecular recognition pathways in ubiquitin

    SciTech Connect

    Ramanathan, Arvind; Agarwal, Pratul K

    2011-01-01

    Molecular dynamics (MD) simulations have dramatically improved the atomistic understanding of protein motions, energetics and function. These growing datasets have necessitated a corresponding emphasis on trajectory analysis methods for characterizing simulation data, particularly since functional protein motions and transitions are often rare and/or intricate events. Observing that such events give rise to long-tailed spatial distributions, we recently developed a higher-order statistics based dimensionality reduction method, called quasi-anharmonic analysis (QAA), for identifying biophysically-relevant reaction coordinates and substates within MD simulations. Further characterization of conformation space should consider the temporal dynamics specific to each identified substate. Our model uses hierarchical clustering to learn energetically coherent substates and dynamic modes of motion from a 0.5 {mu}s ubiqutin simulation. Autoregressive (AR) modeling within and between states enables a compact and generative description of the conformational landscape as it relates to functional transitions between binding poses. Lacking a predictive component, QAA is extended here within a general AR model appreciative of the trajectory's temporal dependencies and the specific, local dynamics accessible to a protein within identified energy wells. These metastable states and their transition rates are extracted within a QAA-derived subspace using hierarchical Markov clustering to provide parameter sets for the second-order AR model. We show the learned model can be extrapolated to synthesize trajectories of arbitrary length.

  17. Understanding Molecular Recognition of Promiscuity of Thermophilic Methionine Adenosyltransferase, sMAT from Sulfolobus solfataricus

    PubMed Central

    Wang, Fengbin; Singh, Shanteri; Zhang, Jianjun; Huber, Tyler D.; Helmich, Kate E.; Sunkara, Manjula; Hurley, Katherine A.; Goff, Randal D.; Bingman, Craig A.; Morris, Andrew J.; Thorson, Jon S.; Phillips, George N.

    2014-01-01

    Methionine adenosyltransferase (MAT) is a family of enzymes that utilizes ATP and methionine to produce S-adenosylmethionine (AdoMet), the most crucial methyl donor in the biological methylation of biomolecules and bioactive natural products. Here, we report that the MAT from Sulfolobus solfataricus (sMAT), an enzyme from a poorly explored class of the MAT family, has the ability to produce a range of differentially alkylated AdoMet analogs in the presence of non-native methionine analogs and ATP. To investigate the molecular basis for AdoMet analog production, we have crystallized the sMAT in the AdoMet bound, S-adenosylethionine (AdoMet) bound, and unbound forms. Notably, among these structures, the AdoEth-bound form offers the first MAT structure containing a non-native product and cumulatively, these structures add new structural insight into the MAT family and allow for detailed active site comparison with its homologs in E. coli and human. As a thermostable MAT structure from archaea, the structures herein also provide as a basis for future engineering to potentially broaden AdoMet analog production as reagents for methyltransferase-catalyzed ‘alkylrandomization’ and/or the study of methylation in the context of biological processes. PMID:24649856

  18. Hypovirus molecular biology: from Koch's postulates to host self-recognition genes that restrict virus transmission.

    PubMed

    Dawe, Angus L; Nuss, Donald L

    2013-01-01

    The idea that viruses can be used to control fungal diseases has been a driving force in mycovirus research since the earliest days. Viruses in the family Hypoviridae associated with reduced virulence (hypovirulence) of the chestnut blight fungus, Cryphonectria parasitica, have held a prominent place in this research. This has been due in part to the severity of the chestnut blight epidemics in North America and Europe and early reports of hypovirulence-mediated mitigation of disease in European forests and successful application for control of chestnut blight in chestnut orchards. A more recent contributing factor has been the development of a hypovirus/C. parasitica experimental system that has overcome many of the challenges associated with mycovirus research, stemming primarily from the exclusive intracellular lifestyle shared by all mycoviruses. This chapter will focus on hypovirus molecular biology with an emphasis on the development of the hypovirus/C. parasitica experimental system and its contributions to fundamental and practical advances in mycovirology and the broader understanding of virus-host interactions and fungal pathogenesis.

  19. Molecularly imprinted polymer doped with Hectorite for selective recognition of sinomenine hydrochloride.

    PubMed

    Zhang, W; Fu, H L; Li, X Y; Zhang, H; Wang, N; Li, W; Zhang, X X

    2016-01-01

    In this work, a new and facile method was introduced to prepare molecularly imprinted polymers (MIPs) based on nano clay hectorite (Hec) for sinomenine hydrochloride (SM) analysis. Hec was firstly dissolved in distilled water in order to swell adequately, followed by a common precipitation polymerization with SM as the template, methacrylic acid as monomer, ethylene glycol dimethacrylate as a crosslinker and 2,2-azobisisobutyronitrile as an initiator. Hec@SM-MIPs were characterized by Fourier transform infrared spectrometer, transmission electron microscopy, scanning electron microscopy, energy dispersive X-ray spectroscopy and X-ray diffraction. The maximum binding capacity of Hec@SM-MIPs, SM-MIPs and non-imprinted polymers (NIPs) (Hec@NIPs) was 57.4, 16.8 and 11.6 mg/g, respectively. The reason for this result may be that Hec@SM-MIPs have more binding sites and imprinted cavities for template molecule. Equilibrium data were described by the Langmuir and Freundlich isotherm models. The results showed that the Hec@SM-MIPs adsorption data correlated better with the Langmuir equation than the Freundlich equation under the studied concentration range. In vitro drug release experiment, Hec@SM-MIPs have a better ability to control SM release than SM-MIPs. Therefore, Hec@SM-MIPs were successfully applied to extraction of SM and used as the materials for drug delivery system.

  20. Molecular basis of phosphatidylinositol 4-phosphate and ARF1 GTPase recognition by the FAPP1 pleckstrin homology (PH) domain.

    PubMed

    He, Ju; Scott, Jordan L; Heroux, Annie; Roy, Siddhartha; Lenoir, Marc; Overduin, Michael; Stahelin, Robert V; Kutateladze, Tatiana G

    2011-05-27

    Four-phosphate-adaptor protein 1 (FAPP1) regulates secretory transport from the trans-Golgi network (TGN) to the plasma membrane. FAPP1 is recruited to the Golgi through binding of its pleckstrin homology (PH) domain to phosphatidylinositol 4-phosphate (PtdIns(4)P) and a small GTPase ADP-ribosylation factor 1 (ARF1). Despite the critical role of FAPP1 in membrane trafficking, the molecular basis of its dual function remains unclear. Here, we report a 1.9 Å resolution crystal structure of the FAPP1 PH domain and detail the molecular mechanisms of the PtdIns(4)P and ARF1 recognition. The FAPP1 PH domain folds into a seven-stranded β-barrel capped by an α-helix at one edge, whereas the opposite edge is flanked by three loops and the β4 and β7 strands that form a lipid-binding pocket within the β-barrel. The ARF1-binding site is located on the outer side of the β-barrel as determined by NMR resonance perturbation analysis, mutagenesis, and measurements of binding affinities. The two binding sites have little overlap, allowing FAPP1 PH to associate with both ligands simultaneously and independently. Binding to PtdIns(4)P is enhanced in an acidic environment and is required for membrane penetration and tubulation activity of FAPP1, whereas the GTP-bound conformation of the GTPase is necessary for the interaction with ARF1. Together, these findings provide structural and biochemical insight into the multivalent membrane anchoring by the PH domain that may augment affinity and selectivity of FAPP1 toward the TGN membranes enriched in both PtdIns(4)P and GTP-bound ARF1.

  1. Flow injection chemiluminescence sensor using core-shell molecularly imprinted polymers as recognition element for determination of dapsone.

    PubMed

    Lu, Fuguang; Yang, Jinlong; Sun, Min; Fan, Lulu; Qiu, Huamin; Li, Xiangjun; Luo, Chuannan

    2012-07-01

    This paper reports the preparation of dapsone (DDS) imprinted polymer layer-coated silica submicron particles (SiO(2)) combined with chemiluminescence (CL) toward analysis of tracing DDS in practical samples. To induce the selective occurrence of surface polymerization, the amino groups were first grafted at the surface of SiO(2) by the (3-aminopropyl)triethoxysilane (APTES). The molecularly imprinted polymers (MIP) were coated at the surface of modified SiO(2) by the graft copolymerization. After the removal of templates, recognition sites of DDS were exposed in the polymer layers. The DDS-imprinted products were characterized by FT-IR, SEM, TEM, dynamic adsorption, and static adsorption tests. The proximity between the thickness of MIP layer and the spatial size of DDS indicated that the imprinted sites almost situated at the surface of MIP, leading to rapid adsorption saturation within 90 min. The apparent maximum binding amount of MIP toward DDS was evaluated as 14.98 mg·g(-1), which was much higher than that of non-molecularly imprinted polymers. The CL sensor provided a wide linear range for DDS within 1.0 × 10(-6) to 1.0 × 10(-4) mol·L(-1) with a detection limit of 5.27 × 10(-7) mol·L(-1) and the relative standard deviation of 1.8 % (n = 11) by determinations of 5.0 × 10(-6) mol·L(-1) DDS. This method was applied to determine DDS in urine samples and satisfactory results were obtained.

  2. Interfacial molecular interactions based on the conformation recognition between the insoluble antitumor drug AD-1 and DSPC.

    PubMed

    Yin, Tian; Cao, Xiuxiu; Liu, Xiaolin; Wang, Jian; Shi, Caihong; Su, Jia; Zhang, Yu; Gou, Jingxin; He, Haibing; Guo, Haiyan; Tang, Xing; Zhao, Yuqing

    2016-10-01

    In this study, molecular interactions between the anti-cancer agent 20(R)-25-methoxyl-dammarane-3β, 12β, 20-triol (AD-1) and phospholipid 1,2-Distearoyl-sn-glycero-3-phosphocholine (DSPC) were investigated using the Langmuir film balance technique. The characteristics of binary Langmuir monolayers consisting of DSPC and AD-1 were conducted on the basis of the surface pressure-area per molecule (π-A) isotherms. It was found that the drug was able to become efficiently inserted into preformed DSPC monolayers, indicating a preferential interaction between AD-1 and DSPC. For the examined lateral pressure at 20mN/m, the largest negative values of ΔGex were found for the AD-1/DSPC monolayer, which should be the most stable. Based on the calculated values of ΔGex, we found that the AD-1/DSPC systems exhibited the best mixed characteristics when the molar fraction of the AD-1 was 0.8; at that relative concentration, the AD-1 molecules can mix better and interact with the phospholipid molecules. In addition, the drug-DSPC binary supramolecular structure was also deposited on the mica plates as shown by atomic force microscopy (AFM). Finally, molecular docking calculations explained satisfactorily that, based on the conformations interactions (conformation recognition), even at an AD-1/DSPC molar ratio as high as 8:2, the interfacial stabilization of the AD-1/DSPC system was fairly strong due to hydrophobic interactions. A higher loading capacity of DSPC might be possible, as it is associated with a more flexible geometrical environment, which allows these supramolecular structures to accept larger increases in drug loading upon steric binding.

  3. Specific recognition of the collagen triple helix by chaperone HSP47: minimal structural requirement and spatial molecular orientation.

    PubMed

    Koide, Takaki; Asada, Shinichi; Takahara, Yoshifumi; Nishikawa, Yoshimi; Nagata, Kazuhiro; Kitagawa, Kouki

    2006-02-10

    The unique folding of procollagens in the endoplasmic reticulum is achieved with the assistance of procollagen-specific molecular chaperones. Heat-shock protein 47 (HSP47) is an endoplasmic reticulum-resident chaperone that plays an essential role in normal procollagen folding, although its molecular function has not yet been clarified. Recent advances in studies on the binding specificity of HSP47 have revealed that Arg residues at Yaa positions in collagenous Gly-Xaa-Yaa repeats are critical for its interactions (Koide, T., Takahara, Y., Asada, S., and Nagata, K. (2002) J. Biol. Chem. 277, 6178-6182; Tasab, M., Jenkinson, L., and Bulleid, N. J. (2002) J. Biol. Chem. 277, 35007-35012). In the present study, we further examined the client recognition mechanism of HSP47 by taking advantage of systems employing engineered collagen model peptides. First, in vitro binding studies using conformationally constrained collagen-like peptides revealed that HSP47 only recognized correctly folded triple helices and that the interaction with the corresponding single-chain polypeptides was negligible. Second, a binding study using heterotrimeric model clients for HSP47 demonstrated a minimal requirement for the number of Arg residues in the triple helix. Finally, a cross-linking study using photoreactive collagenous peptides provided information about the spatial orientation of an HSP47 molecule in the chaperone-collagen complex. The obtained results led to the development of a new model of HSP47-collagen complexes that differs completely from the previously proposed "flying capstan model" (Dafforn, T. R., Della, M., and Miller, A. D. (2001) J. Biol. Chem. 276, 49310-49319).

  4. Electrochemical sensor for catechol and dopamine based on a catalytic molecularly imprinted polymer-conducting polymer hybrid recognition element.

    PubMed

    Lakshmi, Dhana; Bossi, Alessandra; Whitcombe, Michael J; Chianella, Iva; Fowler, Steven A; Subrahmanyam, Sreenath; Piletska, Elena V; Piletsky, Sergey A

    2009-05-01

    One of the difficulties with using molecularly imprinted polymers (MIPs) and other electrically insulating materials as the recognition element in electrochemical sensors is the lack of a direct path for the conduction of electrons from the active sites to the electrode. We have sought to address this problem through the preparation and characterization of novel hybrid materials combining a catalytic MIP, capable of oxidizing the template, catechol, with an electrically conducting polymer. In this way a network of "molecular wires" assists in the conduction of electrons from the active sites within the MIP to the electrode surface. This was made possible by the design of a new monomer that combines orthogonal polymerizable functionality; comprising an aniline group and a methacrylamide. Conducting films were prepared on the surface of electrodes (Au on glass) by electropolymerization of the aniline moiety. A layer of MIP was photochemically grafted over the polyaniline, via N,N'-diethyldithiocarbamic acid benzyl ester (iniferter) activation of the methacrylamide groups. Detection of catechol by the hybrid-MIP sensor was found to be specific, and catechol oxidation was detected by cyclic voltammetry at the optimized operating conditions: potential range -0.6 V to +0.8 V (vs Ag/AgCl), scan rate 50 mV/s, PBS pH 7.4. The calibration curve for catechol was found to be linear to 144 microM, with a limit of detection of 228 nM. Catechol and dopamine were detected by the sensor, whereas analogues and potentially interfering compounds, including phenol, resorcinol, hydroquinone, serotonin, and ascorbic acid, had minimal effect (< or = 3%) on the detection of either analyte. Non-imprinted hybrid electrodes and bare gold electrodes failed to give any response to catechol at concentrations below 0.5 mM. Finally, the catalytic properties of the sensor were characterized by chronoamperometry and were found to be consistent with Michaelis-Menten kinetics.

  5. 2D equation-of-state model for corona phase molecular recognition on single-walled carbon nanotube and graphene surfaces.

    PubMed

    Ulissi, Zachary W; Zhang, Jingqing; Sresht, Vishnu; Blankschtein, Daniel; Strano, Michael S

    2015-01-13

    Corona phase molecular recognition (CoPhMoRe) has been recently introduced as a means of generating synthetic molecular recognition sites on nanoparticle surfaces. A synthetic heteropolymer is adsorbed and confined to the surface of a nanoparticle, forming a corona phase capable of highly selective molecular recognition due to the conformational imposition of the particle surface on the polymer. In this work, we develop a computationally predictive model for analytes adsorbing onto one type of polymer corona phase composed of hydrophobic anchors on hydrophilic loops around a single-walled carbon nanotube (SWCNT) surface using a 2D equation of state that takes into consideration the analyte-polymer, analyte-nanoparticle, and polymer-nanoparticle interactions using parameters determined independently from molecular simulation. The SWCNT curvature is found to contribute weakly to the overall interaction energy, exhibiting no correlation for three of the corona phases considered, and differences of less than 5% and 20% over a larger curvature range for two other corona phases, respectively. Overall, the resulting model for this anchor-loop CoPhMoRe is able to correctly predict 83% of an experimental 374 analyte-polymer library, generating experimental fluorescence responses within 20% error of the experimental values. The modeling framework presented here represents an important step forward in the design of suitable polymers to target specific analytes.

  6. dsRNA-protein interactions studied by molecular dynamics techniques. Unravelling dsRNA recognition by DCL1.

    PubMed

    Drusin, Salvador I; Suarez, Irina P; Gauto, Diego F; Rasia, Rodolfo M; Moreno, Diego M

    2016-04-15

    Double stranded RNA (dsRNA) participates in several biological processes, where RNA molecules acquire secondary structure inside the cell through base complementarity. The double stranded RNA binding domain (dsRBD) is one of the main protein folds that is able to recognize and bind to dsRNA regions. The N-terminal dsRBD of DCL1 in Arabidopsis thaliana (DCL1-1), in contrast to other studied dsRBDs, lacks a stable structure, behaving as an intrinsically disordered protein. DCL1-1 does however recognize dsRNA by acquiring a canonical fold in the presence of its substrate. Here we present a detailed modeling and molecular dynamics study of dsRNA recognition by DCL1-1. We found that DCL1-1 forms stable complexes with different RNAs and we characterized the residues involved in binding. Although the domain shows a binding loop substantially shorter than other homologs, it can still interact with the dsRNA and results in bending of the dsRNA A-type helix. Furthermore, we found that R8, a non-conserved residue located in the first dsRNA binding region, recognizes preferentially mismatched base pairs. We discuss our findings in the context of the function of DCL1-1 within the microRNA processing complex.

  7. Hydrophilic gallic acid-imprinted polymers over magnetic mesoporous silica microspheres with excellent molecular recognition ability in aqueous fruit juices.

    PubMed

    Hu, Xin; Xie, Lianwu; Guo, Junfang; Li, Hui; Jiang, Xinyu; Zhang, Yuping; Shi, Shuyun

    2015-07-15

    Hydrophilic molecularly imprinted polymers (MIPs) for gallic acid (GA) were prepared with excellent recognition ability in an aqueous solution. The proposed MIPs were designed by self-polymerization of dopamine (DA) on magnetic mesoporous silica (Fe3O4@SiO2@mSiO2, MMS) using GA as template. Resulting Fe3O4@SiO2@mSiO2@MIPs (MMS-MIPs) were characterized by transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), thermo-gravimetric analysis (TGA), Brunauer-Emmett-Teller (BET), vibrating sample magnetometer (VSM), and evaluated by adsorption isotherms/kinetics and competitive adsorption. The adsorption behavior between GA and MMS-MIPs followed Langmuir and Sips adsorption isotherms with a maximum adsorption capacity at 88.7 mg/g and pseudo-second-order reaction kinetics with fast binding (equilibrium time at 100 min). In addition, MMS-MIPs showed rapid magnetic separation (10 s) and stability (retained 95.2% after six cycles). Subsequently, MMS-MIPs were applied for the selective extraction and determination of GA from grape, apple, peach and orange juices (4.02, 3.91, 5.97, and 0.67 μg/g, respectively). Generally, the described method may pave the way towards rationally designing more advanced hydrophilic MIPs.

  8. Molecular modeling studies demonstrate key mutations that could affect the ligand recognition by influenza AH1N1 neuraminidase.

    PubMed

    Ramírez-Salinas, Gema L; García-Machorro, J; Quiliano, Miguel; Zimic, Mirko; Briz, Verónica; Rojas-Hernández, Saul; Correa-Basurto, J

    2015-11-01

    The goal of this study was to identify neuraminidase (NA) residue mutants from human influenza AH1N1 using sequences from 1918 to 2012. Multiple alignment studies of complete NA sequences (5732) were performed. Subsequently, the crystallographic structure of the 1918 influenza (PDB ID: 3BEQ-A) was used as a wild-type structure and three-dimensional (3-D) template for homology modeling of the mutated selected NA sequences. The 3-D mutated NAs were refined using molecular dynamics (MD) simulations (50 ns). The refined 3-D models were used to perform docking studies using oseltamivir. Multiple sequence alignment studies showed seven representative mutations (A232V, K262R, V263I, T264V, S367L, S369N, and S369K). MD simulations applied to 3-D NAs showed that each NA had different active-site shapes according to structural surface visualization and docking results. Moreover, Cartesian principal component analyses (cPCA) show structural differences among these NA structures caused by mutations. These theoretical results suggest that the selected mutations that are located outside of the active site of NA could affect oseltamivir recognition and could be associated with resistance to oseltamivir.

  9. Lung epithelium as a sentinel and effector system in pneumonia--molecular mechanisms of pathogen recognition and signal transduction.

    PubMed

    Hippenstiel, Stefan; Opitz, Bastian; Schmeck, Bernd; Suttorp, Norbert

    2006-07-08

    Pneumonia, a common disease caused by a great diversity of infectious agents is responsible for enormous morbidity and mortality worldwide. The bronchial and lung epithelium comprises a large surface between host and environment and is attacked as a primary target during lung infection. Besides acting as a mechanical barrier, recent evidence suggests that the lung epithelium functions as an important sentinel system against pathogens. Equipped with transmembranous and cytosolic pathogen-sensing pattern recognition receptors the epithelium detects invading pathogens. A complex signalling results in epithelial cell activation, which essentially participates in initiation and orchestration of the subsequent innate and adaptive immune response. In this review we summarize recent progress in research focussing on molecular mechanisms of pathogen detection, host cell signal transduction, and subsequent activation of lung epithelial cells by pathogens and their virulence factors and point to open questions. The analysis of lung epithelial function in the host response in pneumonia may pave the way to the development of innovative highly needed therapeutics in pneumonia in addition to antibiotics.

  10. High-resolution single-molecule recognition imaging of the molecular details of ricin-aptamer interaction.

    PubMed

    Wang, Bin; Guo, Cunlan; Zhang, Mengmeng; Park, Bosoon; Xu, Bingqian

    2012-05-03

    We studied the molecular details of DNA aptamer-ricin interactions. The toxic protein ricin molecules were immobilized on a Au(111) surface using a N-hydroxysuccinimide (NHS) ester to specifically react with lysine residues located on the ricin B chains. A single ricin molecule was visualized in situ using the AFM tip modified with an antiricin aptamer. Computer simulation was used to illustrate the protein and aptamer structures, the single-molecule ricin images on a Au(111) surface, and the binding conformations of ricin-aptamer and ricin-antibody complexes. The various ricin conformations on a Au(111) surface were caused by the different lysine residues reacting with the NHS ester. It was also observed that most of the binding sites for aptamer and antibody on the A chains of ricin molecules were not interfered by the immobilization reaction. The different locations of the ricin binding sites to aptamer and antibody were also distinguished by AFM recognition images and interpreted by simulations.

  11. The molecular mechanism of species-specific recognition of lipopolysaccharides by the MD-2/TLR4 receptor complex.

    PubMed

    Oblak, Alja; Jerala, Roman

    2015-02-01

    Lipid A, a component of bacterial lipopolysaccharide, is a conserved microbe-associated molecular pattern that activates the MD-2/TLR4 receptor complex. Nevertheless, bacteria produce lipid A molecules of considerable structural diversity. The human MD-2/TLR4 receptor most efficiently recognizes hexaacylated bisphosphorylated lipid A produced by enterobacteria, but in some animal species the immune response can be elicited also by alternative lipid A varieties, such as tetraacylated lipid IVa or pentaacylated lipid A of Rhodobacter spheroides. Several crystal structures revealed that hexaacylated lipid A and tetraacylated lipid IVa activate the murine MD-2/TLR4 in a similar manner, but failed to explain the antagonistic vs. agonistic activity of lipid IVa in the human vs. equine receptor, respectively. Targeted mutagenesis studies of the receptor complex revealed intricate combination of electrostatic and hydrophobic interactions primarily within the MD-2 co-receptor, but with a contribution of TLR4 as well, that contribute to species-specific recognition of lipid A. We will review current knowledge regarding lipid A diversity and species-specific activation of the MD-2/TLR4 receptor complex in different species (e.g. human, mouse or equine) by lipid A varieties.

  12. Enzymatic synthesis of complex glycosaminotrioses and study of their molecular recognition by hevein domains.

    PubMed

    Aboitiz, Nuria; Cañada, F Javier; Husakova, Lucie; Kuzma, Marek; Kren, Vladimír; Jiménez-Barbero, Jesús

    2004-07-21

    Hevein, a protein found in Hevea brasiliensis, has a CRD domain, which is known to bind chitin and GlcNAc-containing oligosaccharides. By using NMR and molecular modeling as major tools we have demonstrated that trisaccharides containing GalNAc and ManNAc residues are also recognized by hevein domains. Thus far unknown trisaccharides GlcNAcbeta(1-->4)GlcNAcbeta(1-->4)ManNAc (1) and GalNAcbeta(1-->4)GlcNAcbeta(1-->4)ManNAc (2) were synthesized with the use of beta-N-acetylhexosaminidase from Aspergillus oryzae. This method is based on the rather unique phenomenon that some fungal beta-N-acetylhexosaminidases cannot hydrolyze disaccharide GlcNAcbeta(1-->4)ManNAc (5) contrary to chitobiose GlcNAcbeta(1-->4)GlcNAc (4) that is cleaved and, therefore, cannot be used as an acceptor for further transglycosylation. Both trisaccharides 1 and 2 were prepared by transglycosylation from disaccharidic acceptor in good yields ranging from 35% to 40%. Our observations strongly indicate that the present nature of the modifications of chitotriose (GlcNAcbeta(1-->lcNAcbeta(1-->4)GlcNAc, 3) at either the non-reducing end (GalNAc instead of GlcNAc) or at the reducing end (ManNAc instead of GlcNAc) do not modify the mode of binding of the trisaccharide to hevein. The association constant values indicate that chitotriose (3) binding is better than that of 1 and 2, and that the binding of (with ManNAc at the reducing end) is favored with respect to that of 2 (with ManNAc at the reducing end with a non-reducing GalNAc moiety).

  13. Molecular determinants of the recognition of ulipristal acetate by oxo-steroid receptors.

    PubMed

    Petit-Topin, I; Fay, M; Resche-Rigon, M; Ulmann, A; Gainer, E; Rafestin-Oblin, M-E; Fagart, J

    2014-10-01

    The human progesterone receptor (PR) plays a key role in reproductive function in women. PR antagonists have numerous applications in female health care including regular and emergency contraception, and treatment of hormone-related pathological conditions such as breast cancer, endometriosis, and leiomyoma. The main factor limiting their long-term administration is the fact that they cross-bind to other oxo-steroid receptors. Ulipristal acetate (UPA), a highly potent PR antagonist, has recently come onto the market and is much more selective for PR than the other oxo-steroid receptors (androgen, AR, glucocorticoid, GR, and mineralocorticoid, MR receptors) and, remarkably, it displays lower GR-inactivating potency than RU486. We adopted a structural approach to characterizing the binding of UPA to the oxo-steroid receptors at the molecular level. We solved the X-ray crystal structure of the ligand-binding domain (LBD) of the human PR complexed with UPA and a peptide from the transcriptional corepressor SMRT. We used the X-ray crystal structure of the GR in its antagonist conformation to dock UPA within its ligand-binding cavity. Finally, we generated three-dimensional models of the LBD of androgen and mineralocorticoid receptors (AR and MR) in an antagonist conformation and docked UPA within them. Comparing the structures revealed that the network of stabilizing contacts between the UPA C11 aryl group and the LBD is responsible for its high PR antagonist potency. It also showed that it is the inability of UPA to contact Gln642 in GR that explains why it has lower potency in inactivating GR than RU486. Finally, we found that the binding pockets of AR and MR are too small to accommodate UPA, and allowed us to propose that the extremely low sensitivity of MR to UPA is due to inappropriate interactions with the C11 substituent. All these findings open new avenues for designing new PR antagonist compounds displaying greater selectivity.

  14. Molecular Mechanism of Flocculation Self-Recognition in Yeast and Its Role in Mating and Survival

    PubMed Central

    Goossens, Katty V. Y.; Ielasi, Francesco S.; Nookaew, Intawat; Stals, Ingeborg; Alonso-Sarduy, Livan; Daenen, Luk; Van Mulders, Sebastiaan E.; Stassen, Catherine; van Eijsden, Rudy G. E.; Siewers, Verena; Delvaux, Freddy R.; Kasas, Sandor; Nielsen, Jens; Devreese, Bart

    2015-01-01

    ABSTRACT We studied the flocculation mechanism at the molecular level by determining the atomic structures of N-Flo1p and N-Lg-Flo1p in complex with their ligands. We show that they have similar ligand binding mechanisms but distinct carbohydrate specificities and affinities, which are determined by the compactness of the binding site. We characterized the glycans of Flo1p and their role in this binding process and demonstrate that glycan-glycan interactions significantly contribute to the cell-cell adhesion mechanism. Therefore, the extended flocculation mechanism is based on the self-interaction of Flo proteins and this interaction is established in two stages, involving both glycan-glycan and protein-glycan interactions. The crucial role of calcium in both types of interaction was demonstrated: Ca2+ takes part in the binding of the carbohydrate to the protein, and the glycans aggregate only in the presence of Ca2+. These results unify the generally accepted lectin hypothesis with the historically first-proposed “Ca2+-bridge” hypothesis. Additionally, a new role of cell flocculation is demonstrated; i.e., flocculation is linked to cell conjugation and mating, and survival chances consequently increase significantly by spore formation and by introduction of genetic variability. The role of Flo1p in mating was demonstrated by showing that mating efficiency is increased when cells flocculate and by differential transcriptome analysis of flocculating versus nonflocculating cells in a low-shear environment (microgravity). The results show that a multicellular clump (floc) provides a uniquely organized multicellular ultrastructure that provides a suitable microenvironment to induce and perform cell conjugation and mating. PMID:25873380

  15. Moleculary imprinted polymers with metalloporphyrin-based molecular recognition sites coassembled with methacrylic acid.

    PubMed

    Takeuchi, T; Mukawa, T; Matsui, J; Higashi, M; Shimizu, K D

    2001-08-15

    A diastereoselective molecularly imprinted polymer (MIP) for (-)-cinchonidine, PPM(CD), was prepared by the combined use of methacrylic acid and vinyl-substituted zinc(II) porphyrin as functional monomers. Compared to MIPs using only methacrylic acid or zinc porphyrin as a functional monomer, PM(CD) and PP(CD), respectively, PPM(CD) showed higher binding ability for (-)-cinchonidine in chromatographic tests using the MIP-packed columns. Scatchard analysis gave a higher association constant of PPM(CD) for (-)-cinchonidine (1.14 x 10(7) M(-1)) than those of PP(CD) (1.45 x 10(6) M(-1)) and PM(CD) (6.78 x 10(6) M(-1)). The affinity distribution of binding sites estimated by affinity spectrum analysis showed a higher percentage of high-affinity sites and a lower percentage of low-affinity sites in PPM(CD). The MIPs containing a zinc(II) porphyrin in the binding sites, PPM(CD) and PP(CD), showed fluorescence quenching according to the binding of (-)-cinchonidine, and the quenching was significant in the low-concentration range, suggesting that the high-affinity binding sites contain the porphyrin residue. The correlation of the relative fluorescence intensity against log of (-)-cinchonidine concentrations showed a linear relationship. These results revealed that the MIP having highly specific binding sites was assembled by the two functional monomers, vinyl-substituted zinc(II) porphyrin and methacrylic acid, and they cooperatively worked to yield the specific binding. In addition, the zinc(II) porphyrin-based MIPs appeared to act as fluorescence sensor selectively responded by binding events of the template molecule.

  16. Molecular Dynamics Analysis of Antibody Recognition and Escape by Human H1N1 Influenza Hemagglutinin

    PubMed Central

    Ieong, Pek; Amaro, Rommie E.; Li, Wilfred W.

    2015-01-01

    The antibody immunoglobulin (Ig) 2D1 is effective against the 1918 hemagglutinin (HA) and also known to cross-neutralize the 2009 pandemic H1N1 influenza HA through a similar epitope. However, the detailed mechanism of neutralization remains unclear. We conducted molecular dynamics (MD) simulations to study the interactions between Ig-2D1 and the HAs from the 1918 pandemic flu (A/South Carolina/1/1918, 18HA), the 2009 pandemic flu (A/California/04/2009, 09HA), a 2009 pandemic flu mutant (A/California/04/2009, 09HA_mut), and the 2006 seasonal flu (A/Solomon Islands/3/2006, 06HA). MM-PBSA analyses suggest the approximate free energy of binding (ΔG) between Ig-2D1 and 18HA is −74.4 kcal/mol. In comparison with 18HA, 09HA and 06HA bind Ig-2D1 ∼6 kcal/mol (ΔΔG) weaker, and the 09HA_mut bind Ig-2D1 only half as strong. We also analyzed the contributions of individual epitope residues using the free-energy decomposition method. Two important salt bridges are found between the HAs and Ig-2D1. In 09HA, a serine-to-asparagine mutation coincided with a salt bridge destabilization, hydrogen bond losses, and a water pocket formation between 09HA and Ig-2D1. In 09HA_mut, a lysine-to-glutamic-acid mutation leads to the loss of both salt bridges and destabilizes interactions with Ig-2D1. Even though 06HA has a similar ΔG to 09HA, it is not recognized by Ig-2D1 in vivo. Because 06HA contains two potential glycosylation sites that could mask the epitope, our results suggest that Ig-2D1 may be active against 06HA only in the absence of glycosylation. Overall, our simulation results are in good agreement with observations from biological experiments and offer novel mechanistic insights, to our knowledge, into the immune escape of the influenza virus. PMID:26039171

  17. Contig-Layout-Authenticator (CLA): A Combinatorial Approach to Ordering and Scaffolding of Bacterial Contigs for Comparative Genomics and Molecular Epidemiology

    PubMed Central

    Shaik, Sabiha; Kumar, Narender; Lankapalli, Aditya K.; Tiwari, Sumeet K.; Baddam, Ramani; Ahmed, Niyaz

    2016-01-01

    A wide variety of genome sequencing platforms have emerged in the recent past. High-throughput platforms like Illumina and 454 are essentially adaptations of the shotgun approach generating millions of fragmented single or paired sequencing reads. To reconstruct whole genomes, the reads have to be assembled into contigs, which often require further downstream processing. The contigs can be directly ordered according to a reference, scaffolded based on paired read information, or assembled using a combination of the two approaches. While the reference-based approach appears to mask strain-specific information, scaffolding based on paired-end information suffers when repetitive elements longer than the size of the sequencing reads are present in the genome. Sequencing technologies that produce long reads can solve the problems associated with repetitive elements but are not necessarily easily available to researchers. The most common high-throughput technology currently used is the Illumina short read platform. To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CLA also hints at probable misassemblies and contaminations, for the users to cross-check before constructing the consensus draft. The CLA pipeline was designed and trained extensively on various bacterial genome datasets for the ordering and scaffolding of large repetitive contigs. The tool has been validated and compared favorably with other widely-used scaffolding and ordering tools using both simulated and real sequence datasets. CLA is a user friendly tool that requires a single command line input to generate ordered scaffolds. PMID:27248146

  18. Contig-Layout-Authenticator (CLA): A Combinatorial Approach to Ordering and Scaffolding of Bacterial Contigs for Comparative Genomics and Molecular Epidemiology.

    PubMed

    Shaik, Sabiha; Kumar, Narender; Lankapalli, Aditya K; Tiwari, Sumeet K; Baddam, Ramani; Ahmed, Niyaz

    2016-01-01

    A wide variety of genome sequencing platforms have emerged in the recent past. High-throughput platforms like Illumina and 454 are essentially adaptations of the shotgun approach generating millions of fragmented single or paired sequencing reads. To reconstruct whole genomes, the reads have to be assembled into contigs, which often require further downstream processing. The contigs can be directly ordered according to a reference, scaffolded based on paired read information, or assembled using a combination of the two approaches. While the reference-based approach appears to mask strain-specific information, scaffolding based on paired-end information suffers when repetitive elements longer than the size of the sequencing reads are present in the genome. Sequencing technologies that produce long reads can solve the problems associated with repetitive elements but are not necessarily easily available to researchers. The most common high-throughput technology currently used is the Illumina short read platform. To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CLA also hints at probable misassemblies and contaminations, for the users to cross-check before constructing the consensus draft. The CLA pipeline was designed and trained extensively on various bacterial genome datasets for the ordering and scaffolding of large repetitive contigs. The tool has been validated and compared favorably with other widely-used scaffolding and ordering tools using both simulated and real sequence datasets. CLA is a user friendly tool that requires a single command line input to generate ordered scaffolds.

  19. Structural basis for xyloglucan specificity within GH5 family and the molecular determinants for a-D-Xylp(1¿6)-D-Glcp recognition at the -1 subsite

    Technology Transfer Automated Retrieval System (TEKTRAN)

    GH5 is one of the most versatile and largest glycoside hydrolase families, comprising at least 20 distinct activities within a common structural scaffold. However, the molecular basis for the functional differentiation among GH5 members is still not fully understood, principally for xyloglucan speci...

  20. Molecular recognition by thrombin. Role of the slow-->fast transition, site-specific ion binding energetics and thermodynamic mapping of structural components.

    PubMed

    Ayala, Y; Di Cera, E

    1994-01-14

    The interaction of thrombin with the potent natural inhibitor hirudin is controlled in a complex fashion by the binding of Na+ and Cl- to the enzyme and allosteric transitions. Binding of hirudin is positively linked to Na+ binding, but is opposed in a competitive fashion by the binding of Cl-. Since Na+ binding induces the slow-->fast transition of thrombin, it follows from linkage principles that hirudin binds to the fast form with higher affinity. Hence, the slow-->fast transition is a key component of molecular recognition of hirudin by thrombin. We propose a three-step mechanism for molecular recognition of hirudin by thrombin, which is also relevant for recognition of fibrinogen and possibly the platelet receptor and thrombomodulin. First, the C-terminal acidic tail of hirudin binds to the fibrinogen recognition site of thrombin displacing one Cl ion from the thrombin surface. Then, the enzyme undergoes a conformational transition that gives rise to increased accessibility of the catalytic pocket to small synthetic substrates through movement of the Trp148 loop. The changes in the catalytic moiety triggered allosterically by binding to the fibrinogen recognition site are linked to the uptake of Na+ and are similar to, if not identical with, those observed in the Na(+)-induced slow-->fast transition. Finally, the compact N-terminal domain is accommodated in the region surrounding the catalytic pocket. Hirudin binding is also used as a probe of site-specific ion-binding interactions of Na+ and Cl- with the enzyme, characterized by cooperativity between the Na+ and Cl- binding domains. The structural components directly involved or linked to Na+ and Cl- binding have been explored in terms of free energy perturbations of the binding of hirudin and a number of ligands. The fibrinogen recognition site stores most of the free energy of coupling with Cl- binding, while regions surrounding the access to the catalytic pocket provide most of the free energy of coupling

  1. Molecular recognition of T:G mismatched base pairs in DNA as studied by electrospray ionization mass spectrometry.

    PubMed

    Riccardi Sirtori, Federico; Aldini, Giancarlo; Colombo, Maristella; Colombo, Nicoletta; Malyszko, Jan; Vistoli, Giulio; D'Alessio, Roberto

    2012-06-01

    Postreplicative mismatch repair (MMR) is a cellular system involved in the recognition and correction of DNA polymerase errors that escape detection in proofreading. Of the various mismatched bases, T:G pairing in DNA is one of the more common mutations leading to the formation of tumors in humans. In addition, the absence of the MMR system can generate resistance to several chemotherapeutic agents, particularly DNA-damaging substances. The main purpose of this study was the setup and validation of an electrospray ionization (ESI) mass spectrometry method for the identification of small molecules that are able to recognize T:G mismatches in DNA targets. These findings could be useful for the discovery of new antitumor drugs. The analytical method is based on the ability of electrospray to preserve the noncovalent adducts present in solution and transfer them to the gas phase. Lexitropsin derivatives (polyimidazole compounds) have been previously described as selective for T:G mismatch binding by NMR and ITC studies. We synthesized and tested various polyimidazole derivatives, one of which in particular (NMS-057) showed a higher affinity for an oligonucleotide DNA sequence containing a T:G mismatched base pair. To rationalize these findings, molecular docking studies were performed using available NMR structures. Moreover, ESI-MS experiments, performed on an orbitrap mass spectrometer, highlighted the formation of heterodimeric complexes between DNA sequences, distamycin A, and polyimidazole compounds. Our results confirm that this ESI method could be a valuable tool for the identification of new molecules able to specifically recognize T:G mismatched base pairs.

  2. Molecular Modeling Study of Chiral Separation and Recognition Mechanism of β-Adrenergic Antagonists by Capillary Electrophoresis

    PubMed Central

    Li, Wuhong; Liu, Changhai; Tan, Guangguo; Zhang, Xinrong; Zhu, Zhenyu; Chai, Yifeng

    2012-01-01

    Chiral separations of five β-adrenergic antagonists (propranolol, esmolol, atenolol, metoprolol, and bisoprolol) were studied by capillary electrophoresis using six cyclodextrins (CDs) as the chiral selectors. Carboxymethylated-β-cyclodextrin (CM-β-CD) exhibited a higher enantioselectivity power compared to the other tested CDs. The influences of the concentration of CM-β-CD, buffer pH, buffer concentration, temperature, and applied voltage were investigated. The good chiral separation of five β-adrenergic antagonists was achieved using 50 mM Tris buffer at pH 4.0 containing 8 mM CM-β-CD with an applied voltage of 24 kV at 20 °C. In order to understand possible chiral recognition mechanisms of these racemates with CM-β-CD, host-guest binding procedures of CM-β-CD and these racemates were studied using the molecular docking software Autodock. The binding free energy was calculated using the Autodock semi-empirical binding free energy function. The results showed that the phenyl or naphthyl ring inserted in the hydrophobic cavity of CM-β-CD and the side chain was found to point out of the cyclodextrin rim. Hydrogen bonding between CM-β-CD and these racemates played an important role in the process of enantionseparation and a model of the hydrogen bonding interaction positions was constructed. The difference in hydrogen bonding formed with the –OH next to the chiral center of the analytes may help to increase chiral discrimination and gave rise to a bigger separation factor. In addition, the longer side chain in the hydrophobic phenyl ring of the enantiomer was not beneficial for enantioseparation and the chiral selectivity factor was found to correspond to the difference in binding free energy. PMID:22312281

  3. Electrospinning and crosslinking of low-molecular-weight poly(trimethylene carbonate-co-(L)-lactide) as an elastomeric scaffold for vascular engineering.

    PubMed

    Dargaville, Bronwin L; Vaquette, Cédryck; Rasoul, Firas; Cooper-White, Justin J; Campbell, Julie H; Whittaker, Andrew K

    2013-06-01

    The growth of suitable tissue to replace natural blood vessels requires a degradable scaffold material that is processable into porous structures with appropriate mechanical and cell growth properties. This study investigates the fabrication of degradable, crosslinkable prepolymers of l-lactide-co-trimethylene carbonate into porous scaffolds by electrospinning. After crosslinking by γ-radiation, dimensionally stable scaffolds were obtained with up to 56% trimethylene carbonate incorporation. The fibrous mats showed Young's moduli closely matching human arteries (0.4-0.8MPa). Repeated cyclic extension yielded negligible change in mechanical properties, demonstrating the potential for use under dynamic physiological conditions. The scaffolds remained elastic and resilient at 30% strain after 84days of degradation in phosphate buffer, while the modulus and ultimate stress and strain progressively decreased. The electrospun mats are mechanically superior to solid films of the same materials. In vitro, human mesenchymal stem cells adhered to and readily proliferated on the three-dimensional fiber network, demonstrating that these polymers may find use in growing artificial blood vessels in vivo.

  4. Biomimetic magnetic silk scaffolds.

    PubMed

    Samal, Sangram K; Dash, Mamoni; Shelyakova, Tatiana; Declercq, Heidi A; Uhlarz, Marc; Bañobre-López, Manuel; Dubruel, Peter; Cornelissen, Maria; Herrmannsdörfer, Thomas; Rivas, Jose; Padeletti, Giuseppina; De Smedt, Stefaan; Braeckmans, Kevin; Kaplan, David L; Dediu, V Alek

    2015-03-25

    Magnetic silk fibroin protein (SFP) scaffolds integrating magnetic materials and featuring magnetic gradients were prepared for potential utility in magnetic-field assisted tissue engineering. Magnetic nanoparticles (MNPs) were introduced into SFP scaffolds via dip-coating methods, resulting in magnetic SFP scaffolds with different strengths of magnetization. Magnetic SFP scaffolds showed excellent hyperthermia properties achieving temperature increases up to 8 °C in about 100 s. The scaffolds were not toxic to osteogenic cells and improved cell adhesion and proliferation. These findings suggest that tailored magnetized silk-based biomaterials can be engineered with interesting features for biomaterials and tissue-engineering applications.

  5. Molecular recognition of N-protected dipeptides by pseudopeptidic macrocycles: a comparative study of the supramolecular complexes by ESI-MS and NMR.

    PubMed

    Alfonso, Ignacio; Bolte, Michael; Bru, Miriam; Burguete, M Isabel; Luis, Santiago V; Vicent, Cristian

    2010-03-21

    The molecular recognition properties of pseudopeptidic macrocycles have been studied by ESI-MS and NMR spectroscopy, as highly complementary experimental techniques in solution and in the gas phase. We used ESI-MS competition experiments for the high throughput screening of the supramolecular interaction between four macrocyclic receptors and different peptide-like substrates in solution, rendering the best-fitted host-guest pairs. Further insights on the non-covalent recognition process in the gas-phase were obtained through collision induced dissociation (CID) experiments. Solution studies using NMR spectroscopy ((1)H NMR titrations, NOESY and DOSY) were carried out to prove the validity of ESI-MS as a high-throughput screening method for studying the molecular recognition of the investigated pseudopeptidic macrocycles. A clear selectivity for N-protected dipeptides over N-protected amino acids, and a slight preference for dipeptides bearing aromatic side chains were observed. On the basis of the results obtained from this approach, a mode of binding has been proposed.

  6. Bio-inspired artificial functional photocatalyst: biomimetic enzyme-like TiO2/reduced graphene oxide nanocomposite with excellent molecular recognition ability.

    PubMed

    Li, Wentao; Pei, Xule; Deng, Fang; Luo, Xubiao; Li, Fengcong; Xiao, Yong

    2015-05-01

    An enzyme-like TiO(2)/reduced graphene oxide (enzyme-TiO(2)/rGO) nanocomposite with molecular recognition ability was fabricated by biomimicking the geometrical and chemical complementation of the enzyme and substrate. The anatase TiO(2) nanocrystals were densely dispersed on rGO nanosheets with close interfacial contacts. With geometrical and chemical matching of target molecules and memorized cavities, the adsorption capacity of enzyme-TiO(2)/rGO nanocomposites for 4-nitrophenol (4.71 mg g(-1)) is about six times that of control TiO(2)/rGO without the enzyme-like feature (0.79 mg g(-1)), and the enzyme-TiO(2)/rGO shows a relative selectivity coefficient of 7.24. Moreover, enzyme-TiO(2)/rGO exhibits molecular recognitive photocatalytic degradation for a particular contaminant. The results demonstrate that enzyme-substrate recognition provides a convenient and powerful basis on which to biomimic and construct efficient photocatalysts with high selectivity.

  7. Diversity in recognition of glycans by F-type lectins and galectins: molecular, structural, and biophysical aspects

    PubMed Central

    Vasta, Gerardo R.; Ahmed, Hafiz; Bianchet, Mario A.; Fernández-Robledo, José A.; Amzel, L. Mario

    2013-01-01

    Although lectins are “hard-wired” in the germline, the presence of tandemly arrayed carbohydrate recognition domains (CRDs), of chimeric structures displaying distinct CRDs, of polymorphic genes resulting in multiple isoforms, and in some cases, of a considerable recognition plasticity of their carbohydrate binding sites, significantly expand the lectin ligand-recognition spectrum and lectin functional diversification. Analysis of structural/functional aspects of galectins and F-lectins—the most recently identified lectin family characterized by a unique CRD sequence motif (a distinctive structural fold) and nominal specificity for l-Fuc—has led to a greater understanding of self/nonself recognition by proteins with tandemly arrayed CRDs. For lectins with a single CRD, however, recognition of self and nonself glycans can only be rationalized in terms of protein oligomerization and ligand clustering and presentation. Spatial and temporal changes in lectin expression, secretion, and local concentrations in extracellular microenvironments, as well as structural diversity and spatial display of their carbohydrate ligands on the host or microbial cell surface, are suggestive of a dynamic interplay of their recognition and effector functions in development and immunity. PMID:22973821

  8. Biomimetic nanoclay scaffolds for bone tissue engineering

    NASA Astrophysics Data System (ADS)

    Ambre, Avinash Harishchandra

    Tissue engineering offers a significant potential alternative to conventional methods for rectifying tissue defects by evoking natural regeneration process via interactions between cells and 3D porous scaffolds. Imparting adequate mechanical properties to biodegradable scaffolds for bone tissue engineering is an important challenge and extends from molecular to macroscale. This work focuses on the use of sodium montmorillonite (Na-MMT) to design polymer composite scaffolds having enhanced mechanical properties along with multiple interdependent properties. Materials design beginning at the molecular level was used in which Na-MMT clay was modified with three different unnatural amino acids and further characterized using Fourier Transform Infrared (FTIR) spectroscopy, X-ray diffraction (XRD). Based on improved bicompatibility with human osteoblasts (bone cells) and intermediate increase in d-spacing of MMT clay (shown by XRD), 5-aminovaleric acid modified clay was further used to prepare biopolymer (chitosan-polygalacturonic acid complex) scaffolds. Osteoblast proliferation in biopolymer scaffolds containing 5-aminovaleric acid modified clay was similar to biopolymer scaffolds containing hydroxyapatite (HAP). A novel process based on biomineralization in bone was designed to prepare 5-aminovaleric acid modified clay capable of imparting multiple properties to the scaffolds. Bone-like apatite was mineralized in modified clay and a novel nanoclay-HAP hybrid (in situ HAPclay) was obtained. FTIR spectroscopy indicated a molecular level organic-inorganic association between the intercalated 5-aminovaleric acid and mineralized HAP. Osteoblasts formed clusters on biopolymer composite films prepared with different weight percent compositions of in situ HAPclay. Human MSCs formed mineralized nodules on composite films and mineralized extracellular matrix (ECM) in composite scaffolds without the use of osteogenic supplements. Polycaprolactone (PCL), a synthetic polymer, was

  9. Co-assembly of CdTe and Fe3O4 with molecularly imprinted polymer for recognition and separation of endocrine disrupting chemicals

    NASA Astrophysics Data System (ADS)

    Chang, Limin; Chen, Shaona; Chu, Jia; Li, Xin

    2013-11-01

    In this study, we present a general protocol to fabricate imprinting matrix co-loaded with CdTe quantum dots and Fe3O4 nanoparticles for the recognition of endocrine disrupting chemicals (EDCs). The resultant composites were characterized by transmission electron microscopy, fluorescence spectroscopy, and energy dispersive spectroscopy. The materials have been demonstrated to be characterized with spherical shape with a saturation magnetization value of 1.7 emu g-1. Furthermore, the rebinding experiments show that the resultant materials have greater affinity and selectivity towards p-nitrophenol (model EDCs) over structurally related compounds. We believe that the effective method proposed in this work might provide a platform to prepare magnetic and fluorescent molecularly imprinted polymers for the recognition and separation of EDCs.

  10. Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.

    PubMed

    Wang, Bo; Li, Liwei; Hurley, Thomas D; Meroueh, Samy O

    2013-10-28

    End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal·mol(-1) highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10), but larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the nonpolar and entropy components, rather than a better representation of the electrostatics. The SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal-mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo, and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by prescoring

  11. The Molecular Chaperone HSPA2 Plays a Key Role in Regulating the Expression of Sperm Surface Receptors That Mediate Sperm-Egg Recognition

    PubMed Central

    Redgrove, Kate A.; Nixon, Brett; Baker, Mark A.; Hetherington, Louise; Baker, Gordon; Liu, De-Yi; Aitken, R. John

    2012-01-01

    A common defect encountered in the spermatozoa of male infertility patients is an idiopathic failure of sperm–egg recognition. In order to resolve the molecular basis of this condition we have compared the proteomic profiles of spermatozoa exhibiting an impaired capacity for sperm-egg recognition with normal cells using label free mass spectrometry (MS)-based quantification. This analysis indicated that impaired sperm–zona binding was associated with reduced expression of the molecular chaperone, heat shock 70 kDa protein 2 (HSPA2), from the sperm proteome. Western blot analysis confirmed this observation in independent patients and demonstrated that the defect did not extend to other members of the HSP70 family. HSPA2 was present in the acrosomal domain of human spermatozoa as a major component of 5 large molecular mass complexes, the most dominant of which was found to contain HSPA2 in close association with just two other proteins, sperm adhesion molecule 1 (SPAM1) and arylsulfatase A (ARSA), both of which that have previously been implicated in sperm-egg interaction. The interaction between SPAM1, ARSA and HSPA2 in a multimeric complex mediating sperm-egg interaction, coupled with the complete failure of this process when HSPA2 is depleted in infertile patients, provides new insights into the mechanisms by which sperm function is impaired in cases of male infertility. PMID:23209833

  12. Glyconectin glycans as the self-assembling nano-molecular-velcrosystem mediating self-nonself recognition and adhesion implicated in evolution of multicellularity.

    PubMed

    Misevic, Gradimir N; Misevic, Nikola; Popescu, Octavian

    2012-01-01

    The goal of this chapter is to make a specific contribution about glyconectin glycan as the self-assembling nano-molecular-velcro system mediating initial steps of self-nonself recognition and cell adhesion in Porifera, the first descendants of the most simple primordial multicellular organisms. Two original findings will be described: (i) Velcro like concept based on highly polyvalent and specific intermolecular glycan to glycan associations with extremely low affinity of the single binding site and (ii) novel structures of the large and newly emerging family of glyconectin like glycan molecules. The emphasis will be put on the interdisciplinary approach for studying structure to function relationship at the different size scale levels by combining the knowledge and technologies (instrumentation and methods) of physics, chemistry, biology and mathematics. Applying such strategy which is crossing the boundaries of different science disciplines enabled us to develop a new Atomic Force Microscopy (AFM) based nano-bio-technology and perform the first quantitative measurements of intermolecular binding forces at the single molecular level under physiological conditions. We propose that nano-velcro systems of the glyconectin glycans, which are the constituents on the cell surface that are the most exposed to the environment, were responsible for the molecular self-nonself recognition and adhesion processes that underpinned the emergence of multicellular life forms.

  13. The molecular chaperone HSPA2 plays a key role in regulating the expression of sperm surface receptors that mediate sperm-egg recognition.

    PubMed

    Redgrove, Kate A; Nixon, Brett; Baker, Mark A; Hetherington, Louise; Baker, Gordon; Liu, De-Yi; Aitken, R John

    2012-01-01

    A common defect encountered in the spermatozoa of male infertility patients is an idiopathic failure of sperm-egg recognition. In order to resolve the molecular basis of this condition we have compared the proteomic profiles of spermatozoa exhibiting an impaired capacity for sperm-egg recognition with normal cells using label free mass spectrometry (MS)-based quantification. This analysis indicated that impaired sperm-zona binding was associated with reduced expression of the molecular chaperone, heat shock 70 kDa protein 2 (HSPA2), from the sperm proteome. Western blot analysis confirmed this observation in independent patients and demonstrated that the defect did not extend to other members of the HSP70 family. HSPA2 was present in the acrosomal domain of human spermatozoa as a major component of 5 large molecular mass complexes, the most dominant of which was found to contain HSPA2 in close association with just two other proteins, sperm adhesion molecule 1 (SPAM1) and arylsulfatase A (ARSA), both of which that have previously been implicated in sperm-egg interaction. The interaction between SPAM1, ARSA and HSPA2 in a multimeric complex mediating sperm-egg interaction, coupled with the complete failure of this process when HSPA2 is depleted in infertile patients, provides new insights into the mechanisms by which sperm function is impaired in cases of male infertility.

  14. A systematic approach to diverse, lead-like scaffolds from α,α-disubstituted amino acids.

    PubMed

    Foley, Daniel J; Doveston, Richard G; Churcher, Ian; Nelson, Adam; Marsden, Stephen P

    2015-06-30

    A powerful strategy for the efficient lead-oriented synthesis of novel molecular scaffolds is demonstrated. Twenty two scaffolds were prepared from just four α-amino acid-derived building blocks and a toolkit of six connective reactions. Importantly, each individual scaffold has the ability to specifically target lead-like chemical space.

  15. Active scaffolds for on-demand drug and cell delivery

    PubMed Central

    Zhao, Xuanhe; Kim, Jaeyun; Cezar, Christine A.; Huebsch, Nathaniel; Lee, Kangwon; Bouhadir, Kamal; Mooney, David J.

    2011-01-01

    Porous biomaterials have been widely used as scaffolds in tissue engineering and cell-based therapies. The release of biological agents from conventional porous scaffolds is typically governed by molecular diffusion, material degradation, and cell migration, which do not allow for dynamic external regulation. We present a new active porous scaffold that can be remotely controlled by a magnetic field to deliver various biological agents on demand. The active porous scaffold, in the form of a macroporous ferrogel, gives a large deformation and volume change of over 70% under a moderate magnetic field. The deformation and volume variation allows a new mechanism to trigger and enhance the release of various drugs including mitoxantrone, plasmid DNA, and a chemokine from the scaffold. The porous scaffold can also act as a depot of various cells, whose release can be controlled by external magnetic fields. PMID:21149682

  16. Homology modeling, molecular dynamics, and docking studies of pattern-recognition transmembrane protein-lipopolysaccharide and β-1,3 glucan-binding protein from Fenneropenaeus indicus.

    PubMed

    Sivakamavalli, Jeyachandran; Tripathi, Sunil Kumar; Singh, Sanjeev Kumar; Vaseeharan, Baskaralingam

    2015-01-01

    Lipopolysaccharide and β-1,3 glucan-binding protein (LGBP) is a family of pattern-recognition transmembrane proteins (PRPs) which plays a vital role in the immune mechanism of crustaceans in adverse conditions. Fenneropenaeus indicus LGBP-deduced amino acid has conserved potential recognition motif for β-1,3 linkages of polysaccharides and putative RGD (Arg-Gly-Asp) cell adhesion sites for the activation of innate defense mechanism. In order to understand the stimulating activity of β-1,3 glucan (β-glucan) and its interaction with LGBP, a 3D model of LGBP is generated. Molecular docking is performed with this model, and the results indicate Arg71 with strong hydrogen bond from RGD domain of LGBP. Moreover, from the docking studies, we also suggest that Arg34, Lys68, Val135, and Ala146 in LGBP are important amino acid residues in binding as they have strong bonding interaction in the active site of LGBP. In our in vitro studies, yeast agglutination results suggest that shrimp F. indicus LGBP possesses sugar binding and recognition sites in its structure, which is responsible for agglutination reaction. Our results were synchronized with the already reported evidence both in vivo and in vitro experiments. This investigation may be valuable for further experimental investigation in the synthesis of novel immunomodulator.

  17. Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism.

    PubMed

    Ren, Aiming; Rajashankar, Kanagalaghatta R; Patel, Dinshaw J

    2015-08-04

    ZTP, the pyrophosphorylated analog of ZMP (5-amino-4-imidazole carboxamide ribose-5'-monophosphate), was identified as an alarmone that senses 10-formyl-tetrahydroflate deficiency in bacteria. Recently, a pfl riboswitch was identified that selectively binds ZMP and regulates genes associated with purine biosynthesis and one-carbon metabolism. We report on the structure of the ZMP-bound Thermosinus carboxydivorans pfl riboswitch sensing domain, thereby defining the pseudoknot-based tertiary RNA fold, the binding-pocket architecture, and principles underlying ligand recognition specificity. Molecular recognition involves shape complementarity, with the ZMP 5-amino and carboxamide groups paired with the Watson-Crick edge of an invariant uracil, and the imidazole ring sandwiched between guanines, while the sugar hydroxyls form intermolecular hydrogen bond contacts. The burial of the ZMP base and ribose moieties, together with unanticipated coordination of the carboxamide by Mg(2+), contrasts with exposure of the 5'-phosphate to solvent. Our studies highlight the principles underlying RNA-based recognition of ZMP, a master regulator of one-carbon metabolism.

  18. Kin Recognition in Bacteria.

    PubMed

    Wall, Daniel

    2016-09-08

    The ability of bacteria to recognize kin provides a means to form social groups. In turn these groups can lead to cooperative behaviors that surpass the ability of the individual. Kin recognition involves specific biochemical interactions between a receptor(s) and an identification molecule(s). Recognition specificity, ensuring that nonkin are excluded and kin are included, is critical and depends on the number of loci and polymorphisms involved. After recognition and biochemical perception, the common ensuing cooperative behaviors include biofilm formation, quorum responses, development, and swarming motility. Although kin recognition is a fundamental mechanism through which cells might interact, microbiologists are only beginning to explore the topic. This review considers both molecular and theoretical aspects of bacterial kin recognition. Consideration is also given to bacterial diversity, genetic relatedness, kin selection theory, and mechanisms of recognition.

  19. New Trends in Inspecting GPCR-ligand Recognition Process: the Contribution of the Molecular Modeling Section (MMS) at the University of Padova.

    PubMed

    Ciancetta, Antonella; Cuzzolin, Alberto; Deganutti, Giuseppe; Sturlese, Mattia; Salmaso, Veronica; Cristiani, Andrea; Sabbadin, Davide; Moro, Stefano

    2016-09-01

    In this review, we present a survey of the recent advances carried out by our research groups in the field of ligand-GPCRs recognition process simulations recently implemented at the Molecular Modeling Section (MMS) of the University of Padova. We briefly describe a platform of tools we have tuned to aid the identification of novel GPCRs binders and the better understanding of their binding mechanisms, based on two extensively used computational techniques such as molecular docking and MD simulations. The developed methodologies encompass: (i) the selection of suitable protocols for docking studies, (ii) the exploration of the dynamical evolution of ligand-protein interaction networks, (iii) the detailed investigation of the role of water molecules upon ligand binding, and (iv) a glance at the way the ligand might go through prior reaching the binding site.

  20. Development of a molecular recognition based approach for multi-residue extraction of estrogenic endocrine disruptors from biological fluids coupled to liquid chromatography-tandem mass spectrometry measurement.

    PubMed

    Bousoumah, Radia; Antignac, Jean Philippe; Camel, Valérie; Grimaldi, Marina; Balaguer, Patrick; Courant, Frederique; Bichon, Emmanuelle; Morvan, Marie-Line; Le Bizec, Bruno

    2015-11-01

    Multi-residue methods permitting the high-throughput and affordable simultaneous determination of an extended range of endocrine disrupting chemicals (EDCs) with reduced time and cost of analysis is of prime interest in order to characterize a whole set of bioactive compounds. Such a method based on UHPLC-MS/MS measurement and dedicated to 13 estrogenic EDCs was developed and applied to biological matrices. Two molecular recognition-based strategies, either molecular imprinted polymer (MIP) with phenolic template or estrogen receptors (ERα) immobilized on a sorbent, were assessed in terms of recovery and purification efficiency. Both approaches demonstrated their suitability to measure ultra-trace levels of estrogenic EDCs in aqueous samples. Applicability of the MIP procedure to urine and serum samples has also been demonstrated.

  1. Fabrication of functional PLGA-based electrospun scaffolds and their applications in biomedical engineering.

    PubMed

    Zhao, Wen; Li, Jiaojiao; Jin, Kaixiang; Liu, Wenlong; Qiu, Xuefeng; Li, Chenrui

    2016-02-01

    Electrospun PLGA-based scaffolds have been applied extensively in biomedical engineering, such as tissue engineering and drug delivery system. Due to lack of the recognition sites on cells, hydropholicity and single-function, the applications of PLGA fibrous scaffolds are limited. In order to tackle these issues, many works have been done to obtain functional PLGA-based scaffolds, including surface modifications, the fabrication of PLGA-based composite scaffolds and drug-loaded scaffolds. The functional PLGA-based scaffolds have significantly improved cell adhesion, attachment and proliferation. Moreover, the current study has summarized the applications of functional PLGA-based scaffolds in wound dressing, vascular and bone tissue engineering area as well as drug delivery system.

  2. Hydrogels and scaffolds for immunomodulation.

    PubMed

    Singh, Ankur; Peppas, Nicholas A

    2014-10-01

    For over two decades, immunologists and biomaterials scientists have co-existed in parallel world with the rationale of understanding the molecular profile of immune responses to vaccination, implantation, and treating incurable diseases. Much of the field of biomaterial-based immunotherapy has relied on evaluating model antigens such as chicken egg ovalbumin in mouse models but their relevance to humans has been point of much discussion. Nevertheless, such model antigens have provided important insights into the mechanisms of immune regulation and served as a proof-of-concept for plethora of biomaterial-based vaccines. After years of extensive development of numerous biomaterials for immunomodulation, it is only recently that an experimental scaffold vaccine implanted beneath the skin has begun to use the human model to study the immune responses to cancer vaccination by co-delivering patient-derived tumor lysates and immunomodulatory proteins. If successful, this scaffold vaccine will change the way we approached untreatable cancers, but more importantly, will allow a faster and more rational translation of therapeutic regimes to other cancers, chronic infections, and autoimmune diseases. Most materials reviews have focused on immunomodulatory adjuvants and micro-nano-particles. Here we provide an insight into emerging hydrogel and scaffold based immunomodulatory approaches that continue to demonstrate efficacy against immune associated diseases.

  3. Rational design of a cytotoxic dinuclear Cu2 complex that binds by molecular recognition at two neighboring phosphates of the DNA backbone.

    PubMed

    Jany, Thomas; Moreth, Alexander; Gruschka, Claudia; Sischka, Andy; Spiering, Andre; Dieding, Mareike; Wang, Ying; Samo, Susan Haji; Stammler, Anja; Bögge, Hartmut; Fischer von Mollard, Gabriele; Anselmetti, Dario; Glaser, Thorsten

    2015-03-16

    The mechanism of the cytotoxic function of cisplatin and related anticancer drugs is based on their binding to the nucleobases of DNA. The development of new classes of anticancer drugs requires establishing other binding modes. Therefore, we performed a rational design for complexes that target two neighboring phosphates of the DNA backbone by molecular recognition resulting in a family of dinuclear complexes based on 2,7-disubstituted 1,8-naphthalenediol. This rigid backbone preorganizes the two metal ions for molecular recognition at the distance of two neighboring phosphates in DNA of 6-7 Å. Additionally, bulky chelating pendant arms in the 2,7-position impede nucleobase complexation by steric hindrance. We successfully synthesized the Cu(II)2 complex of the designed family of dinuclear complexes and studied its binding to dsDNA by independent ensemble and single-molecule methods like gel electrophoresis, precipitation, and titration experiments followed by UV-vis spectroscopy, atomic force microscopy (AFM), as well as optical tweezers (OT) and magnetic tweezers (MT) DNA stretching. The observed irreversible binding of our dinuclear Cu(II)2 complex to dsDNA leads to a blocking of DNA synthesis as studied by polymerase chain reactions and cytotoxicity for human cancer cells.

  4. Recognition and binding of β-lactam antibiotics to bovine serum albumin by frontal affinity chromatography in combination with spectroscopy and molecular docking.

    PubMed

    Li, Qian; Zhang, Tianlong; Bian, Liujiao

    2016-03-01

    Serum albumins are the most abundant carrier proteins in blood plasma and participate in the binding and transportation of various exogenous and endogenous compounds in the body. This work was designed to investigate the recognition and binding of three typical β-lactam antibiotics including penicillin G (Pen G), penicillin V (Pen V) and cefalexin (Cef) with bovine serum albumin (BSA) by frontal affinity chromatography in combination with UV-vis absorption spectra, fluorescence emission spectra, binding site marker competitive experiment and molecular docking under simulated physiological conditions. The results showed that a BSA only bound with one antibiotic molecule in the binding process, and the binding constants for Pen G-BSA, Pen V-BSA and Cef-BSA complexes were 4.22×10(1), 4.86×10(2) and 3.32×10(3) (L/mol), respectively. All the three β-lactam antibiotics were mainly inserted into the subdomain IIA (binding site 1) of BSA by hydrogen bonds and Van der Waals forces. The binding capacity between the antibiotics and BSA was closely related to the functional groups and flexibility of side chains in antibiotics. This study provided an important insight into the molecular recognition and binding interaction of BSA with β-lactam antibiotics, which may be a useful guideline for the innovative clinical medications and new antibiotic designs with effective pharmacological properties.

  5. Molecular basis for the recognition of cyclic-di-AMP by PstA, a PII-like signal transduction protein

    PubMed Central

    Choi, Philip H; Sureka, Kamakshi; Woodward, Joshua J; Tong, Liang

    2015-01-01

    Cyclic-di-AMP (c-di-AMP) is a broadly conserved bacterial second messenger that is of importance in bacterial physiology. The molecular receptors mediating the cellular responses to the c-di-AMP signal are just beginning to be discovered. PstA is a previously uncharacterized PII-like protein which has been identified as a c-di-AMP receptor. PstA is widely distributed and conserved among Gram-positive bacteria in the phylum Firmicutes. Here, we report the biochemical, structural, and functional characterization of PstA from Listeria monocytogenes. We have determined the crystal structures of PstA in the c-di-AMP-bound and apo forms at 1.6 and 2.9 Å resolution, respectively, which provide the molecular basis for its specific recognition of c-di-AMP. PstA forms a homotrimer structure that has overall similarity to the PII protein family which binds ATP. However, PstA is markedly different from PII proteins in the loop regions, and these structural differences mediate the specific recognition of their respective nucleotide ligand. The residues composing the c-di-AMP binding pocket are conserved, suggesting that c-di-AMP recognition by PstA is of functional importance. Disruption of pstA in L. monocytogenes affected c-di-AMP-mediated alterations in bacterial growth and lysis. Overall, we have defined the PstA family as a conserved and specific c-di-AMP receptor in bacteria. PMID:25693966

  6. Protein–DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors

    PubMed Central

    Etheve, Loïc; Martin, Juliette; Lavery, Richard

    2016-01-01

    We have studied the dynamics of three transcription factor–DNA complexes using all-atom, microsecond-scale MD simulations. In each case, the salt bridges and hydrogen bond interactions formed at the protein–DNA interface are found to be dynamic, with lifetimes typically in the range of tens to hundreds of picoseconds, although some interactions, notably those involving specific binding to DNA bases, can be a hundred times longer lived. Depending on the complex studied, this dynamics may or may not lead to the existence of distinct conformational substates. Using a sequence threading technique, it has been possible to determine whether DNA sequence recognition is sensitive or not to such conformational changes, and, in one case, to show that recognition appears to be locally dependent on protein-mediated cation distributions. PMID:27658967

  7. Molecularly imprinted polymer grafted on polysaccharide microsphere surface by the sol-gel process for protein recognition.

    PubMed

    Li, Feng; Li, Jing; Zhang, Shusheng

    2008-02-15

    An interfacial organic-inorganic hybridization concept was applied to the preparation of a new spherical imprinted material for protein recognition. The functional biopolymer chitosan (CS), shaped as microsphere and high-density cross-linked, constituted of the polysaccharide core for surface imprinting. After the model template protein, bovine serum albumin, was covalently immobilized by forming imine bonds with the functional amine groups of CS, two kinds of organic siloxane (3-aminopropyltrimethoxysiloxane: APTMS, and tetraethoxysiloxane: TEOS) assembled and polymerized on the polysaccharide-protein surface via sol-gel process in aqueous solution at room temperature. After template removal, the protein-imprinted sol-gel surface exhibited a prevalent preference for the template protein in adsorption experiments, as compared with four contrastive proteins. Bioinformatics methods were also employed to investigate the imprinting process and the recognition effect. The influence of siloxane type, pH, siloxane/water ratio on template removal and recognition selectivity was assessed. Under optimized imprinting conditions, a large quantity of well-distributed pores was observed on the immobilized-template imprinted surface. The surface-imprinted adsorbent offered a fast kinetics for template re-adsorption and could be reused. Compared with the imprinted material prepared with free-template, material prepared with immobilized-template possessed higher adsorption capacity towards template protein. Easy preparation of the described imprinted material, high affinity and good reusability make this approach attractive and broadly applicable in biotechnology for down-stream processing and biosensor.

  8. Danger- and pathogen-associated molecular patterns recognition by pattern-recognition receptors and ion channels of the transient receptor potential family triggers the inflammasome activation in immune cells and sensory neurons.

    PubMed

    Santoni, Giorgio; Cardinali, Claudio; Morelli, Maria Beatrice; Santoni, Matteo; Nabissi, Massimo; Amantini, Consuelo

    2015-02-03

    An increasing number of studies show that the activation of the innate immune system and inflammatory mechanisms play an important role in the pathogenesis of numerous diseases. The innate immune system is present in almost all multicellular organisms and its activation occurs in response to pathogens or tissue injury via pattern-recognition receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs) or danger-associated molecular patterns (DAMPs). Intracellular pathways, linking immune and inflammatory response to ion channel expression and function, have been recently identified. Among ion channels, the transient receptor potential (TRP) channels are a major family of non-selective cation-permeable channels that function as polymodal cellular sensors involved in many physiological and pathological processes. In this review, we summarize current knowledge of interactions between immune cells and PRRs and ion channels of TRP families with PAMPs and DAMPs to provide new insights into the pathogenesis of inflammatory diseases. TRP channels have been found to interfere with innate immunity via both nuclear factor-kB and procaspase-1 activation to generate the mature caspase-1 that cleaves pro-interleukin-1β cytokine into the mature interleukin-1β.Sensory neurons are also adapted to recognize dangers by virtue of their sensitivity to intense mechanical, thermal and irritant chemical stimuli. As immune cells, they possess many of the same molecular recognition pathways for danger. Thus, they express PRRs including Toll-like receptors 3, 4, 7, and 9, and stimulation by Toll-like receptor ligands leads to induction of inward currents and sensitization in TRPs. In addition, the expression of inflammasomes in neurons and the involvement of TRPs in central nervous system diseases strongly support a role of TRPs in inflammasome-mediated neurodegenerative pathologies. This field is still at its beginning and further studies may be required.Overall, these

  9. Molecular recognition modes between adenine or adeniniun(1+) ion and binary M(II)(pdc) chelates (MCoZn; pdc=pyridine-2,6-dicarboxylate(2-) ion).

    PubMed

    Del Pilar Brandi-Blanco, María; Choquesillo-Lazarte, Duane; Domínguez-Martín, Alicia; Matilla-Hernández, Antonio; González-Pérez, Josefa María; Castiñeiras, Alfonso; Niclós-Gutiérrez, Juan

    2013-10-01

    Mixed ligand M(II)-complexes (MCoZn) with pyridine-2,6-dicarboxylate(2-) chelator (pdc) and adenine (Hade) have been synthesized and studied by X-ray diffraction and other spectral and thermal methods: [Cu(pdc)(H(N9)ade)(H2O)] (1), [Cu2(pdc)2(H2O)2(μ2-N3,N7-H(N9)ade)]·3H2O (2), trans-[M(pdc)(H(N9)ade)(H2O)2]·nH2O for MCo (3-L, 3-M, 3-H) or Zn (4-L, 4-H), where n is 0, 1 or 3 for the 'lowest' (L), 'medium' (M) and 'highest' (H) hydrated forms, and the salt trans-[Ni(pdc)(H2(N1,N9)ade)(H2O)2]Cl·2H2O (5). In all the nine compounds, both neutral and cationic adenine exist as their most stable tautomer and the molecular recognition pattern between the metal-pdc chelates and the adenine or adeninium(1+) ligands involves the MN7 bond in cooperation with an intra-molecular N6H⋯O(coordinated carboxylate) interligand interaction. In addition the dinuclear copper(II) compound (2) has the CuN3 bond and the N9H⋯O(coord. carboxylate) interaction. The structures of mononuclear ternary complexes proved that the molecular recognition pattern is the same irrespective of (a) the coordination geometry of the complex molecule, (b) the different hydrated forms of crystals with Co or Zn, and (c) the neutral of cationic form of the adenine ligand. These features are related to the mer-NO2 chelating ligand conformation (imposed by the planar rigidity of pdc) as a driving force for the observed metal binding mode.

  10. On the influence of crosslinker on template complexation in molecularly imprinted polymers: a computational study of prepolymerization mixture events with correlations to template-polymer recognition behavior and NMR spectroscopic studies.

    PubMed

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

    2014-06-12

    Aspects of the molecular-level basis for the function of ethylene glycol dimethacrylate and trimethylolproprane trimethacrylate crosslinked methacrylic acid copolymers molecularly imprinted with (S)-propranolol have been studied using a series of all-component and all-atom molecular dynamics studies of the corresponding prepolymerization systems. The crosslinking agents were observed to contribute to template complexation, and the results were contrasted with previously reported template-recognition behavior of the corresponding polymers. Differences in the extent to which the two crosslinkers interacted with the functional monomer were identified, and correlations were made to polymer-ligand recognition behavior and the results of nuclear magnetic resonance spectroscopic studies studies. This study demonstrates the importance of considering the functional monomer-crosslinker interaction when designing molecularly imprinted polymers, and highlights the often neglected general contribution of crosslinker to determining the nature of molecularly imprinted polymer-template selectivity.

  11. On the Influence of Crosslinker on Template Complexation in Molecularly Imprinted Polymers: A Computational Study of Prepolymerization Mixture Events with Correlations to Template-Polymer Recognition Behavior and NMR Spectroscopic Studies

    PubMed Central

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

    2014-01-01

    Aspects of the molecular-level basis for the function of ethylene glycol dimethacrylate and trimethylolproprane trimethacrylate crosslinked methacrylic acid copolymers molecularly imprinted with (S)-propranolol have been studied using a series of all-component and all-atom molecular dynamics studies of the corresponding prepolymerization systems. The crosslinking agents were observed to contribute to template complexation, and the results were contrasted with previously reported template-recognition behavior of the corresponding polymers. Differences in the extent to which the two crosslinkers interacted with the functional monomer were identified, and correlations were made to polymer-ligand recognition behavior and the results of nuclear magnetic resonance spectroscopic studies studies. This study demonstrates the importance of considering the functional monomer–crosslinker interaction when designing molecularly imprinted polymers, and highlights the often neglected general contribution of crosslinker to determining the nature of molecularly imprinted polymer-template selectivity. PMID:24927149

  12. Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides

    PubMed Central

    Buchmueller, Karen L.; Staples, Andrew M.; Uthe, Peter B.; Howard, Cameron M.; Pacheco, Kimberly A. O.; Cox, Kari K.; Henry, James A.; Bailey, Suzanna L.; Horick, Sarah M.; Nguyen, Binh; Wilson, W. David; Lee, Moses

    2005-01-01

    Polyamides containing an N-terminal formamido (f) group bind to the minor groove of DNA as staggered, antiparallel dimers in a sequence-specific manner. The formamido group increases the affinity and binding site size, and it promotes the molecules to stack in a staggered fashion thereby pairing itself with either a pyrrole (Py) or an imidazole (Im). There has not been a systematic study on the DNA recognition properties of the f/Py and f/Im terminal pairings. These pairings were analyzed here in the context of f-ImPyPy, f-ImPyIm, f-PyPyPy and f-PyPyIm, which contain the central pairing modes, –ImPy– and –PyPy–. The specificity of these triamides towards symmetrical recognition sites allowed for the f/Py and f/Im terminal pairings to be directly compared by SPR, CD and ΔTM experiments. The f/Py pairing, when placed next to the –ImPy– or –PyPy– central pairings, prefers A/T and T/A base pairs to G/C base pairs, suggesting that f/Py has similar DNA recognition specificity to Py/Py. With –ImPy– central pairings, f/Im prefers C/G base pairs (>10 times) to the other Watson–Crick base pairs; therefore, f/Im behaves like the Py/Im pair. However, the f/Im pairing is not selective for the C/G base pair when placed next to the –PyPy– central pairings. PMID:15703305

  13. The Interaction between an Acidic Transcriptional Activator and Its Inhibitor: The Molecular Basis of Ga14p Recognition by Ga180p

    SciTech Connect

    Thoden, James B.; Ryan, Louise A.; Reece, Richard J.; Holden, Hazel M.

    2009-02-16

    The GAL genes, which encode the enzymes required for normal galactose metabolism in yeast, are transcriptionally regulated by three proteins: Gal4p, an activator; Gal80p, an inhibitor; and Gal3p, a galactose sensor. These proteins control the switch between inert and active gene expression. The transcriptional activation function of Gal4p is rendered inactive in the presence of Gal80p. Here we present the three-dimensional structure of a complex between the acidic activation domain of Gal4p and Gal80p. The transactivation domain initiates with an extended region of polypeptide chain followed by two turns of an amphipathic alpha-helix. It fits into and across a deep cleft within the Gal80p dimer with the protein-protein interface defined primarily by hydrophobic interactions. A disordered loop in the apo-Gal80p structure (Asp-309 to Ser-316) becomes well-defined upon binding of the transactivation domain. This investigation provides a new molecular scaffold for understanding previous biochemical and genetic studies.

  14. Molecular Basis for the Recognition of Structurally Distinct Autoinducer Mimics by the Pseudomonas aeruginosa LasR Quorum-Sensing Signaling Receptor

    SciTech Connect

    Zou, Yaozhong; Nair, Satish K.

    2010-01-12

    The human pathogen Pseudomonas aeruginosa coordinates the expression of virulence factors using quorum sensing, a signaling cascade triggered by the activation of signal receptors by small-molecule autoinducers. These homoserine lactone autoinducers stabilize their cognate receptors and activate their functions as transcription factors. Because quorum sensing regulates the progression of infection and host immune resistance, significant efforts have been devoted toward the identification of small molecules that disrupt this process. Screening efforts have identified a class of triphenyl compounds that are structurally distinct from the homoserine lactone autoinducer, yet interact specifically and potently with LasR receptor to modulate quorum sensing (Muh et al., 2006a). Here we present the high-resolution crystal structures of the ligand binding domain of LasR in complex with the autoinducer N-3-oxo-dodecanoyl homoserine lactone (1.4 {angstrom} resolution), and with the triphenyl mimics TP-1, TP-3, and TP-4 (to between 1.8 {angstrom} and 2.3 {angstrom} resolution). These crystal structures provide a molecular rationale for understanding how chemically distinct compounds can be accommodated by a highly selective receptor, and provide the framework for the development of novel quorum-sensing regulators, utilizing the triphenyl scaffold.

  15. Exploring new molecular architectures for anion recognition: synthesis and ATP binding properties of new cyclam-based ditopic polyammonium receptors.

    PubMed

    Pouessel, Jacky; Bazzicalupi, Carla; Bencini, Andrea; Bernard, Hélène; Giorgi, Claudia; Handel, Henri; Matera, Irene; Le Bris, Nathalie; Tripier, Raphaël; Valtancoli, Barbara

    2011-06-06

    Synthesis and characterization of three new polyamine receptors, composed of a cyclam unit (cyclam=1,4,8,11-tetraazacyclotetradecane) linked by a 2,6-dimethylpyridinyl spacer to the linear polyamines 1,4,8,11-tetraazaundecane (L1py), 1,4,7-triazaheptane (L2py), and to a quaternary ammonium group (L3py(+)), are reported. All receptors form highly charged polyammonium cations at neutral pH, suitable for anion recognition studies. ATP recognition was analyzed by using potentiometric, calorimetric, (1)H and (31)P NMR measurements in aqueous solution. All receptors form 1:1 adducts with ATP in aqueous solution, stabilized by charge-charge and hydrogen-bonding interactions between their ammonium groups and the anionic triphosphate chain of ATP. The binding ability of the three receptors for ATP increases in the order of L3py(+)

  16. Dual-source dual-power electrospinning and characteristics of multifunctional scaffolds for bone tissue engineering.

    PubMed

    Wang, Chong; Wang, Min

    2012-10-01

    Electrospun tissue engineering scaffolds are attractive due to their distinctive advantages over other types of scaffolds. As both osteoinductivity and osteoconductivity play crucial roles in bone tissue engineering, scaffolds possessing both properties are desirable. In this investigation, novel bicomponent scaffolds were constructed via dual-source dual-power electrospinning (DSDPES). One scaffold component was emulsion electrospun poly(D,L-lactic acid) (PDLLA) nanofibers containing recombinant human bone morphogenetic protein (rhBMP-2), and the other scaffold component was electrospun calcium phosphate (Ca-P) particle/poly(lactic-co-glycolic acid) (PLGA) nanocomposite fibers. The mass ratio of rhBMP-2/PDLLA fibers to Ca-P/PLGA fibers in bicomponent scaffolds could be controlled in the DSDPES process by adjusting the number of syringes used to supply solutions for electrospinning. Through process optimization, both types of fibers could be evenly distributed in bicomponent scaffolds. The structure and properties of each type of fibers in the scaffolds were studied. The morphological and structural properties and wettability of scaffolds were assessed. The effects of emulsion composition for rhBMP-2/PDLLA fibers and mass ratio of fibrous components in bicomponent scaffolds on in vitro release of rhBMP-2 from scaffolds were investigated. In vitro degradation of scaffolds was also studied by monitoring their morphological changes, weight losses and decreases in average molecular weight of fiber matrix polymers.

  17. Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition

    PubMed Central

    Hayashi, Tomohiko; Oshima, Hiraku; Mashima, Tsukasa; Nagata, Takashi; Katahira, Masato; Kinoshita, Masahiro

    2014-01-01

    It is a central issue to elucidate the new type of molecular recognition accompanied by a global structural change of a molecule upon binding to its targets. Here we investigate the driving force for the binding of R12 (a ribonucleic acid aptamer) and P16 (a partial peptide of a prion protein) during which P16 exhibits the global structural change. We calculate changes in thermodynamic quantities upon the R12–P16 binding using a statistical-mechanical approach combined with molecular models for water which is currently best suited to studies on hydration of biomolecules. The binding is driven by a water-entropy gain originating primarily from an increase in the total volume available to the translational displacement of water molecules in the system. The energy decrease due to the gain of R12–P16 attractive (van der Waals and electrostatic) interactions is almost canceled out by the energy increase related to the loss of R12–water and P16–water attractive interactions. We can explain the general experimental result that stacking of flat moieties, hydrogen bonding and molecular-shape and electrostatic complementarities are frequently observed in the complexes. It is argued that the water-entropy gain is largely influenced by the geometric characteristics (overall shapes, sizes and detailed polyatomic structures) of the biomolecules. PMID:24803670

  18. A molecularly imprinted polymer-coated CdTe quantum dot nanocomposite for tryptophan recognition based on the Förster resonance energy transfer process

    NASA Astrophysics Data System (ADS)

    Tirado-Guizar, Antonio; Paraguay-Delgado, Francisco; Pina-Luis, Georgina E.

    2016-12-01

    A new ‘turn-on’ Förster resonance energy transfer (FRET) nanosensor for l-tryptophan based on molecularly imprinted quantum dots (QDs) is proposed. The approach combines the advantages of the molecular imprinting technique, the fluorescent characteristics of the QDs and the energy transfer process. Silica-coated CdTe QDs were first synthesized and then molecularly imprinted using a sol-gel process without surfactants. The final composite presents stable fluorescence which increases with the addition of l-tryptophan. This ‘turn-on’ response is due to a FRET mechanism from the l-tryptophan as donor to the imprinted QD as acceptor. QDs are rarely applied as acceptors in FRET systems. The nanosensor shows selectivity towards l-tryptophan in the presence of other amino acids and interfering ions. The l-tryptophan nanosensor exhibits a linear range between 0 and 8 µM concentration, a detection limit of 350 nM and high selectivity. The proposed sensor was successfully applied for the detection of l-tryptophan in saliva. This novel sensor may offer an alternative approach to the design of a new generation of imprinted nanomaterials for the recognition of different analytes.

  19. Discovery of non-competitive thrombin inhibitor derived from competitive tryptase inhibitor skeleton: Shift in molecular recognition resulted from skeletal conversion of carboxylate into phosphonate.

    PubMed

    Aoyama, Hiroshi; Ijuin, Ryosuke; Kato, Jun-ya; Urushiyama, Sarasa; Tetsuhashi, Masashi; Hashimoto, Yuichi; Yokomatsu, Tsutomu

    2015-09-01

    A novel series of terminal and internal phosphonate esters based on our previously developed aryl carboxylate-type tryptase selective inhibitor 1 was synthesized. The potency of these synthesized compounds was assessed in vitro with an enzyme inhibition assay using three available serine proteases, that is, tryptase, trypsin, and thrombin. The internal phosphonate derivative 6 showed potent thrombin inhibitory activity with an IC50 value of 1.0 μM, whereas it exhibited no or only weak tryptase and trypsin inhibition at 10 μM. The Lineweaver-Burk plot analysis indicates that the inhibition pattern of thrombin with 6 is non-competitive in spite of the fact that the lead carboxylate compound 1 is competitive inhibitor. Therefore, the skeletal conversion of the carboxylate into a phosphonate alters the mode of molecular recognition of these inhibitors by thrombin.

  20. Synthesis of molecularly imprinted organic-inorganic hybrid azobenzene materials by sol-gel for radiation induced selective recognition of 2,4-dichlorophenoxyacetic acid

    NASA Astrophysics Data System (ADS)

    Shuai Jiang, Guang; An Zhong, Shi; Chen, Lan; Blakey, Idriss; Whitaker, Andrew

    2011-02-01

    A novel photoresponsive functional monomer bearing a siloxane polymerisable group and azobenzene moieties was synthesized. This monomer was then used to prepare photoresponsive molecularly imprinted polymers (MIP), which have specific binding sites for 2,4-dichlorophenoxyacetic acid (2,4-D) through hydrogen bonding moieties. The binding affinity of the imprinted recognition sites was switchable by alternate irradiations with ultraviolet and visible light, suggesting that azobenzene groups located inside the binding sites could be used as chemical sensors and the trans-cis isomerization could regulate the affinity for the 2,4-D. In addition, the concentration of the 2,4-D was able to be quantified by monitoring the trans-to-cis photoisomerization rate constant.

  1. [Strategies to choose scaffold materials for tissue engineering].

    PubMed

    Gao, Qingdong; Zhu, Xulong; Xiang, Junxi; Lü, Yi; Li, Jianhui

    2016-02-01

    Current therapies of organ failure or a wide range of tissue defect are often not ideal. Transplantation is the only effective way for long time survival. But it is hard to meet huge patients demands because of donor shortage, immune rejection and other problems. Tissue engineering could be a potential option. Choosing a suitable scaffold material is an essential part of it. According to different sources, tissue engineering scaffold materials could be divided into three types which are natural and its modified materials, artificial and composite ones. The purpose of tissue engineering scaffold is to repair the tissues or organs damage, so could reach the ideal recovery in its function and structure aspect. Therefore, tissue engineering scaffold should even be as close as much to the original tissue or organs in function and structure. We call it "organic scaffold" and this strategy might be the drastic perfect substitute for the tissues or organs in concern. Optimized organization with each kind scaffold materials could make up for biomimetic structure and function of the tissue or organs. Scaffold material surface modification, optimized preparation procedure and cytosine sustained-release microsphere addition should be considered together. This strategy is expected to open new perspectives for tissue engineering. Multidisciplinary approach including material science, molecular biology, and engineering might find the most ideal tissue engineering scaffold. Using the strategy of drawing on each other strength and optimized organization with each kind scaffold material to prepare a multifunctional biomimetic tissue engineering scaffold might be a good method for choosing tissue engineering scaffold materials. Our research group had differentiated bone marrow mesenchymal stem cells into bile canaliculi like cells. We prepared poly(L-lactic acid)/poly(ε-caprolactone) biliary stent. The scaffold's internal played a part in the long-term release of cytokines which

  2. Molecular recognition at methyl methacrylate/n-butyl acrylate (MMA/nBA) monomer unit boundaries of phospholipids at p-MMA/nBA copolymer surfaces.

    PubMed

    Yu, Min; Urban, Marek W; Sheng, Yinghong; Leszczynski, Jerzy

    2008-09-16

    Lipid structural features and their interactions with proteins provide a useful vehicle for further advances in membrane proteins research. To mimic one of potential lipid-protein interactions we synthesized poly(methyl methacrylate/ n-butyl acrylate) (p-MMA/nBA) colloidal particles that were stabilized by phospholipid (PLs). Upon the particle coalescence, PL stratification resulted in the formation of surface localized ionic clusters (SLICs). These entities are capable of recognizing MMA/nBA monomer interfaces along the p-MMA/nBA copolymer backbone and form crystalline SLICs at the monomer interface. By utilizing attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy and selected area electron diffraction (SAD) combined with ab initio calculations, studies were conducted that identified the origin of SLICs as well as their structural features formed on the surface of p-MMA/nBA copolymer films stabilized by 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) PL. Specific entities responsible for SLIC formation are selective noncovalent bonds of anionic phosphate and cationic quaternary ammonium segments of DLPC that interact with two neighboring carbonyl groups of nBA and MMA monomers of the p-MMA/nBA polymer backbone. To the best of our knowledge this is the first example of molecular recognition facilitated by coalescence of copolymer colloidal particles and the ability of PLs to form SLICs at the boundaries of the neighboring MMA and nBA monomer units of the p-MMA/nBA chain. The dominating noncovalent bonds responsible for the molecular recognition is a combination of H-bonding and electrostatic interactions.

  3. Use of UV-vis-NIR spectroscopy to monitor label-free interaction between molecular recognition elements and erythropoietin on a gold-coated polycarbonate platform.

    PubMed

    Citartan, Marimuthu; Gopinath, Subash C B; Tominaga, Junji; Chen, Yeng; Tang, Thean-Hock

    2014-08-01

    Label-free-based detection is pivotal for real-time monitoring of biomolecular interactions and to eliminate the need for labeling with tags that can occupy important binding sites of biomolecules. One simplest form of label-free-based detection is ultraviolet-visible-near-infrared (UV-vis-NIR) spectroscopy, which measure changes in reflectivity as a means to monitor immobilization and interaction of biomolecules with their corresponding partners. In biosensor development, the platform used for the biomolecular interaction should be suitable for different molecular recognition elements. In this study, gold (Au)-coated polycarbonate was used as a platform and as a proof-of-concept, erythropoietin (EPO), a doping substance widely abused by the athletes was used as the target. The interaction of EPO with its corresponding molecular recognition elements (anti-EPO monoclonal antibody and anti-EPO DNA aptamer) is monitored by UV-vis-NIR spectroscopy. Prior to this, to show that UV-vis-NIR spectroscopy is a suitable method for measuring biomolecular interaction, the interaction between biotin and streptavidin was demonstrated via this strategy and reflectivity of this interaction decreased by 25%. Subsequent to this, interaction of the EPO with anti-EPO monoclonal antibody and anti-EPO DNA aptamer resulted in the decrease of reflectivity by 5% and 10%, respectively. The results indicated that Au-coated polycarbonate could be an ideal biosensor platform for monitoring biomolecular interactions using UV-vis-NIR spectroscopy. A smaller version of the Au-coated polycarbonate substrates can be derived from the recent set-up, to be applied towards detecting EPO abuse among atheletes.

  4. Exact approaches for scaffolding

    PubMed Central

    2015-01-01

    This paper presents new structural and algorithmic results around the scaffolding problem, which occurs prominently in next generation sequencing. The problem can be formalized as an optimization problem on a special graph, the "scaffold graph". We prove that the problem is polynomial if this graph is a tree by providing a dynamic programming algorithm for this case. This algorithm serves as a basis to deduce an exact algorithm for general graphs using a tree decomposition of the input. We explore other structural parameters, proving a linear-size problem kernel with respect to the size of a feedback-edge set on a restricted version of Scaffolding. Finally, we examine some parameters of scaffold graphs, which are based on real-world genomes, revealing that the feedback edge set is significantly smaller than the input size. PMID:26451725

  5. A malonitrile-functionalized metal-organic framework for hydrogen sulfide detection and selective amino acid molecular recognition

    PubMed Central

    Li, Haiwei; Feng, Xiao; Guo, Yuexin; Chen, Didi; Li, Rui; Ren, Xiaoqian; Jiang, Xin; Dong, Yuping; Wang, Bo

    2014-01-01

    A novel porous polymeric fluorescence probe, MN-ZIF-90, has been designed and synthesized for quantitative hydrogen sulfide (H2S) fluorescent detection and highly selective amino acid recognition. This distinct crystalline structure, derived from rational design and malonitrile functionalization, can trigger significant enhancement of its fluorescent intensity when exposed to H2S or cysteine molecules. Indeed this new metal-organic framework (MOF) structure shows high selectivity of biothiols over other amino acids and exhibits favorable stability. Moreover, in vitro viability assays on HeLa cells show low cytotoxicity of MN-ZIF-90 and its imaging contrast efficiency is further demonstrated by fluorescence microscopy studies. This facile yet powerful strategy also offers great potential of using open-framework materials (i.e. MOFs) as the novel platform for sensing and other biological applications. PMID:24621614

  6. Scaffold: Quantum Programming Language

    DTIC Science & Technology

    2012-07-24

    it in pointer and addressing errors. • C2QG: A key feature of Scaffold is a Classical code to Quantum Gates sequence (C2QG) mod- ule. C2QG modules...Scaffold: Quantum Programming Language Ali Javadi Abhari, Arvin Faruque, Mohammad Javad Dousti, Lukas Svec, Oana Catu, Amlan Chakrabati, Chen-Fu...endorsements, either expressed or implied, of IARPA, DoI/NBC, or the U.S. Government. 1 Introduction Quantum computing is of significant research

  7. Syntheses, structures, molecular and cationic recognitions and catalytic properties of two lanthanide coordination polymers based on a flexible tricarboxylate

    SciTech Connect

    Zhu, Yu; Wang, Yan-Mei; Xu, Ji; Liu, Pan; Weththasinha, H.A.B.M.D.; Wu, Yun-Long; Lu, Xiao-Qing; Xie, Ji-Min

    2014-11-15

    Two lanthanide coordination polymers, namely, ([La(TTTA)(H{sub 2}O){sub 2}]·2H{sub 2}O){sub n} (La-TTTA) and [Nd(TTTA)(H{sub 2}O){sub 2}]·2H{sub 2}O){sub n} (Nd-TTTA) have been hydrothermally synthesized through the reaction of lanthanide ions (La{sup 3+} and Nd{sup 3+}) with the flexible tripodal ligand 2,2′,2″-[1,3,5-triazine-2,4,6-triyltris(thio)]tris-acetic acid (H{sub 3}TTTA). La-TTTA and Nd-TTTA are isostructural and both show three dimensional structures. La-TTTA and Nd-TTTA show good recognition of amine molecules via quenching the luminescent intensities in amines emulsions. They can also recognize Fe{sup 3+}, Cu{sup 2+}, Mg{sup 2+}, Cr{sup 3+} and Co{sup 2+} ions with the quenching the peak around 361 nm when the compounds immersed in ionic solutions. The two compounds act as efficient Lewis acid catalysts for the cyanosilylation of benzaldehyde and derivatives in high yields shortly due to the strong Lewis acidity and the possible open sites of the lanthanide ions. - Graphical abstract: We have synthesized two isostructural 3D compounds based on H{sub 3}TTTA. They are chemical sensor of amine solvents and cations. They have higher yields and TOFs to catalyze cyanosilylation reactions. - Highlights: • The compounds show recognition of amine molecules via quenching luminescent intensities. • The compounds recognize Fe{sup 3+}, Cu{sup 2+}, Mg{sup 2+}, Cr{sup 3+} and Co{sup 2+} ions via quenching the peak around 361 nm. • They act as efficient Lewis acid catalysts for the cyanosilylation reactions in high yields.

  8. Pathogen-Associated Molecular Pattern Recognition of Hepatitis C Virus Transmitted/Founder Variants by RIG-I Is Dependent on U-Core Length

    PubMed Central

    Kell, Alison; Stoddard, Mark; Li, Hui; Marcotrigiano, Joe; Shaw, George M.

    2015-01-01

    ABSTRACT Despite the introduction of direct-acting antiviral (DAA) drugs against hepatitis C virus (HCV), infection remains a major public health concern because DAA therapeutics do not prevent reinfection and patients can still progress to chronic liver disease. Chronic HCV infection is supported by a variety of viral immune evasion strategies, but, remarkably, 20% to 30% of acute infections spontaneously clear prior to development of adaptive immune responses, thus implicating innate immunity in resolving acute HCV infection. However, the virus-host interactions regulating acute infection are unknown. Transmission of HCV involves one or a few transmitted/founder (T/F) variants. In infected hepatocytes, the retinoic acid-inducible gene I (RIG-I) protein recognizes 5′ triphosphate (5′ppp) of the HCV RNA and a pathogen-associated molecular pattern (PAMP) motif located within the 3′ untranslated region consisting of poly-U/UC. PAMP binding activates RIG-I to induce innate immune signaling and type 1 interferon antiviral defenses. HCV poly-U/UC sequences can differ in length and complexity, suggesting that PAMP diversity in T/F genomes could regulate innate immune control of acute HCV infection. Using 14 unique poly-U/UC sequences from HCV T/F genomes recovered from acute-infection patients, we tested whether RIG-I recognition and innate immune activation correlate with PAMP sequence characteristics. We show that T/F variants are recognized by RIG-I in a manner dependent on length of the U-core motif of the poly-U/UC PAMP and are recognized by RIG-I to induce innate immune responses that restrict acute infection. PAMP recognition of T/F HCV variants by RIG-I may therefore impart innate immune signaling and HCV restriction to impact acute-phase-to-chronic-phase transition. IMPORTANCE Recognition of nonself molecular patterns such as those seen with viral nucleic acids is an essential step in triggering the immune response to virus infection. Innate immunity is

  9. RECOGNITION OF PYRENE USING MOLECULARLY-IMPRINTED ELECTROCHEMICALLY-DEPOSITED POLY (2-MERCAPTOBENZIMIDAZOLE) OR POLY(RESORCINOL) ON GOLD ELECTRODES

    EPA Science Inventory

    The feasibility of using thiol chemistry to form molecularly imprinted polymer-coated gold electrodes to measure pyrene is reported. For the first approach, poly(2-mercaptoimidazole) (2-MBI) was electrochemically deposited on gold electrodes in the presence or absence of the tem...

  10. High-resolution single-molecule recognition imaging of the molecular details of ricin-aptamer interaction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The molecular details of DNA aptamer-ricin interactions were investigated. The toxic protein ricin molecules were immobilized on Au(111) surface using N-hydroxysuccinimide (NHS) ester to specifically react with lysine residues located on the ricin B chains. A single ricin molecule was visualized in ...

  11. Water participation in molecular recognition and protein-ligand association: Probing the drug binding site "Sudlow I" in human serum albumin

    NASA Astrophysics Data System (ADS)

    Al-Lawatia, Najla; Steinbrecher, Thomas; Abou-Zied, Osama K.

    2012-03-01

    Human serum albumin (HSA) plays an important role in the transport and disposition of endogenous and exogenous ligands present in blood. Its capacity to reversibly bind a large variety of drugs results in its prevailing role in drug pharmacokinetics and pharmacodynamics. In this work, we used 7-hydroxyquinoline (7HQ) as a probe to study the binding nature of one of the major drug binding sites of HSA (Sudlow I) and to reveal the local environment around the probe in the binding site. The interaction between 7HQ and HSA at a physiological pH of 7.2 was investigated using steady-state and lifetime spectroscopic measurements, molecular docking and molecular dynamics (MD) simulations methods. The fluorescence results indicate a selective interaction between 7HQ and the Trp214 residue. The reduction in both the intensity and lifetime of the Trp214 fluorescence upon probe binding indicates the dominant role of static quenching. Molecular docking and MD simulations show that 7HQ binds in Sudlow site I close to Trp214, confirming the experimental results, and pinpoint the dominant role of hydrophobic interaction in the binding site. Electrostatic interactions were also found to be important in which two water molecules form strong hydrogen bonds with the polar groups of 7HQ. Detection of water in the binding site agrees with the absorption and fluorescence results that show the formation of a zwitterion tautomer of 7HQ. The unique spectral signatures of 7HQ in water make this molecule a potential probe for detecting the presence of water in nanocavities of proteins. Interaction of 7HQ with water in the binding site shows that water molecules can be crucial for molecular recognition and association in protein binding sites.

  12. Scaffolds in Tendon Tissue Engineering

    PubMed Central

    Longo, Umile Giuseppe; Lamberti, Alfredo; Petrillo, Stefano; Maffulli, Nicola; Denaro, Vincenzo

    2012-01-01

    Tissue engineering techniques using novel scaffold materials offer potential alternatives for managing tendon disorders. Tissue engineering strategies to improve tendon repair healing include the use of scaffolds, growth factors, cell seeding, or a combination of these approaches. Scaffolds have been the most common strategy investigated to date. Available scaffolds for tendon repair include both biological scaffolds, obtained from mammalian tissues, and synthetic scaffolds, manufactured from chemical compounds. Preliminary studies support the idea that scaffolds can provide an alternative for tendon augmentation with an enormous therapeutic potential. However, available data are lacking to allow definitive conclusion on the use of scaffolds for tendon augmentation. We review the current basic science and clinical understanding in the field of scaffolds and tissue engineering for tendon repair. PMID:22190961

  13. Scaffold mining of kinase hinge binders in crystal structure database

    NASA Astrophysics Data System (ADS)

    Xing, Li; Rai, Brajesh; Lunney, Elizabeth A.

    2014-01-01

    Protein kinases are the second most prominent group of drug targets, after G-protein-coupled receptors. Despite their distinct inhibition mechanisms, the majority of kinase inhibitors engage the conserved hydrogen bond interactions with the backbone of hinge residues. We mined Pfizer internal crystal structure database (CSDb) comprising of several thousand of public as well as internal X-ray binary complexes to compile an inclusive list of hinge binding scaffolds. The minimum ring scaffolds with directly attached hetero-atoms and functional groups were extracted from the full compounds by applying a rule-based filtering procedure employing a comprehensive annotation of ATP-binding site of the human kinase complements. The results indicated large number of kinase inhibitors of diverse chemical structures are derived from a relatively small number of common scaffolds, which serve as the critical recognition elements for protein kinase interaction. Out of the nearly 4,000 kinase-inhibitor complexes in the CSDb we identified approximately 600 unique scaffolds. Hinge scaffolds are overwhelmingly flat with very little sp3 characteristics, and are less lipophilic than their corresponding parent compounds. Examples of the most common as well as the uncommon hinge scaffolds are presented. Although the most common scaffolds are found in complex with multiple kinase targets, a large number of them are uniquely bound to a specific kinase, suggesting certain scaffolds could be more promiscuous than the others. The compiled collection of hinge scaffolds along with their three-dimensional binding coordinates could serve as basis set for hinge hopping, a practice frequently employed to generate novel invention as well as to optimize existing leads in medicinal chemistry.

  14. Vascularizing Bone Scaffolds for Craniofacial Reconstruction

    DTIC Science & Technology

    2011-07-01

    7-17kDa (75: 25 ); Medium, 38-54kDa (50:50); High, 66-117kDa (75: 25 )) were fabricated in three different concentrations (10, 15 and 20%). For these...beta- TCP ( Therics ) to a dimension of 6x6x6 mm with 70% porosity. All scaffolds were sterilized using ethelyene oxide gas for 20 hours at 37C. Bone...molecular weight (LMW, 75: 25 ), medium molecular weight (MMW, 50:50) and high molecular weight (HMW, 75: 25 ) polymers at the concentrations of 10, 15 and

  15. CARMA2sh and ULK2 control pathogen-associated molecular patterns recognition in human keratinocytes: psoriasis-linked CARMA2sh mutants escape ULK2 censorship.

    PubMed

    Scudiero, Ivan; Mazzone, Pellegrino; D'Andrea, Luca E; Ferravante, Angela; Zotti, Tiziana; Telesio, Gianluca; De Rubis, Gabriele; Reale, Carla; Pizzulo, Maddalena; Muralitharan, Shanmugakonar; Vito, Pasquale; Stilo, Romania

    2017-02-23

    The molecular complexes formed by specific members of the family of CARMA proteins, the CARD domain-containing adapter molecule BCL10 and MALT1 (CBM complex) represent a central hub in regulating activation of the pleiotropic transcription factor NF-κB. Recently, missense mutations in CARMA2sh have been shown to cause psoriasis in a dominant manner and with high penetrancy. Here, we demonstrate that in human keratinocytes CARMA2sh plays an essential role in the signal transduction pathway that connects pathogen-associated molecular patterns recognition to NF-κB activation. We also find that the serine/threonine kinase ULK2 binds to and phosphorylates CARMA2sh, thereby inhibiting its capacity to activate NF-κB by promoting lysosomal degradation of BCL10, which is essential for CARMA2sh-mediated NF-κB signaling. Remarkably, CARMA2sh mutants associated with psoriasis escape ULK2 inhibition. Finally, we show that a peptide blocking CARD-mediated BCL10 interactions reduces the capacity of psoriasis-linked CARMA2sh mutants to activate NF-κB. Our work elucidates a fundamental signaling mechanism operating in human keratinocytes and opens to novel potential tools for the therapeutical treatment of human skin disorders.

  16. Recognition, signaling, and repair of DNA double-strand breaks produced by ionizing radiation in mammalian cells: the molecular choreography.

    PubMed

    Thompson, Larry H

    2012-01-01

    The faithful maintenance of chromosome continuity in human cells during DNA replication and repair is critical for preventing the conversion of normal diploid cells to an oncogenic state. The evolution of higher eukaryotic cells endowed them with a large genetic investment in the molecular machinery that ensures chromosome stability. In mammalian and other vertebrate cells, the elimination of double-strand breaks with minimal nucleotide sequence change involves the spatiotemporal orchestration of a seemingly endless number of proteins ranging in their action from the nucleotide level to nucleosome organization and chromosome architecture. DNA DSBs trigger a myriad of post-translational modifications that alter catalytic activities and the specificity of protein interactions: phosphorylation, acetylation, methylation, ubiquitylation, and SUMOylation, followed by the reversal of these changes as repair is completed. "Superfluous" protein recruitment to damage sites, functional redundancy, and alternative pathways ensure that DSB repair is extremely efficient, both quantitatively and qualitatively. This review strives to integrate the information about the molecular mechanisms of DSB repair that has emerged over the last two decades with a focus on DSBs produced by the prototype agent ionizing radiation (IR). The exponential growth of molecular studies, heavily driven by RNA knockdown technology, now reveals an outline of how many key protein players in genome stability and cancer biology perform their interwoven tasks, e.g. ATM, ATR, DNA-PK, Chk1, Chk2, PARP1/2/3, 53BP1, BRCA1, BRCA2, BLM, RAD51, and the MRE11-RAD50-NBS1 complex. Thus, the nature of the intricate coordination of repair processes with cell cycle progression is becoming apparent. This review also links molecular abnormalities to cellular pathology as much a possible and provides a framework of temporal relationships.

  17. Interconnectivity analysis of supercritical CO₂-foamed scaffolds.

    PubMed

    Lemon, Greg; Reinwald, Yvonne; White, Lisa J; Howdle, Steven M; Shakesheff, Kevin M; King, John R

    2012-06-01

    This paper describes a computer algorithm for the determination of the interconnectivity of the pore space inside scaffolds used for tissue engineering. To validate the algorithm and its computer implementation, the algorithm was applied to a computer-generated scaffold consisting of a set of overlapping spherical pores, for which the interconnectivity was calculated exactly. The algorithm was then applied to micro-computed X-ray tomography images of supercritical CO(2)-foamed scaffolds made from poly(lactic-co-glycolic acid) (PLGA), whereby the effect of using different weight average molecular weight polymer on the interconnectivity was investigated.

  18. C3 -Symmetric Boron Lewis Acid with a Cage-Shape for Chiral Molecular Recognition and Asymmetric Catalysis.

    PubMed

    Konishi, Akihito; Nakaoka, Koichi; Maruyama, Hikaru; Nakajima, Hideto; Eguchi, Tomohiro; Baba, Akio; Yasuda, Makoto

    2017-01-26

    Chiral Lewis acids play an important role in the precise construction of various types of chiral molecules. Here, a cage-shaped borate 2 was designed and synthesized as a chiral Lewis acid that possesses a unique C3 -symmetric structure composed of three homochiral binaphthyl moieties. The highly symmetrical structure of 2 with homochirality was clearly elucidated by X-ray crystallographic analysis. The peculiar chiral environment of 2⋅THF exhibited chiral recognition of some simple amines and a sulfoxide. Moreover, the application of 2⋅THF to hetero-Diels-Alder reactions as a chiral Lewis-acid catalyst afforded the enantioselective products, which were obtained through an entropy-controlled pathway according to the analysis of the relationship between optical yield and reaction temperature. In particular, the robust chiral reaction field of 2⋅THF allowed the first example of an asymmetric hetero-Diels-Alder reaction with a simple diene despite the requirement of high temperature.

  19. Molecular Mechanisms of Viral and Host Cell Substrate Recognition by Hepatitis C Virus NS3/4A Protease

    SciTech Connect

    Romano, Keith P.; Laine, Jennifer M.; Deveau, Laura M.; Cao, Hong; Massi, Francesca; Schiffer, Celia A.

    2011-08-16

    Hepatitis C NS3/4A protease is a prime therapeutic target that is responsible for cleaving the viral polyprotein at junctions 3-4A, 4A4B, 4B5A, and 5A5B and two host cell adaptor proteins of the innate immune response, TRIF and MAVS. In this study, NS3/4A crystal structures of both host cell cleavage sites were determined and compared to the crystal structures of viral substrates. Two distinct protease conformations were observed and correlated with substrate specificity: (i) 3-4A, 4A4B, 5A5B, and MAVS, which are processed more efficiently by the protease, form extensive electrostatic networks when in complex with the protease, and (ii) TRIF and 4B5A, which contain polyproline motifs in their full-length sequences, do not form electrostatic networks in their crystal complexes. These findings provide mechanistic insights into NS3/4A substrate recognition, which may assist in a more rational approach to inhibitor design in the face of the rapid acquisition of resistance.

  20. Syntheses, structures, molecular and cationic recognitions and catalytic properties of two lanthanide coordination polymers based on a flexible tricarboxylate

    NASA Astrophysics Data System (ADS)

    Zhu, Yu; Wang, Yan-Mei; Xu, Ji; Liu, Pan; Weththasinha, H. A. B. M. D.; Wu, Yun-Long; Lu, Xiao-Qing; Xie, Ji-Min

    2014-11-01

    Two lanthanide coordination polymers, namely, {[La(TTTA)(H2O)2]·2H2O}n (La-TTTA) and [Nd(TTTA)(H2O)2]·2H2O}n (Nd-TTTA) have been hydrothermally synthesized through the reaction of lanthanide ions (La3+ and Nd3+) with the flexible tripodal ligand 2,2‧,2″-[1,3,5-triazine-2,4,6-triyltris(thio)]tris-acetic acid (H3TTTA). La-TTTA and Nd-TTTA are isostructural and both show three dimensional structures. La-TTTA and Nd-TTTA show good recognition of amine molecules via quenching the luminescent intensities in amines emulsions. They can also recognize Fe3+, Cu2+, Mg2+, Cr3+ and Co2+ ions with the quenching the peak around 361 nm when the compounds immersed in ionic solutions. The two compounds act as efficient Lewis acid catalysts for the cyanosilylation of benzaldehyde and derivatives in high yields shortly due to the strong Lewis acidity and the possible open sites of the lanthanide ions.

  1. Molecular recognition and interaction between uracil and urea in solid-state studied by terahertz time-domain spectroscopy.

    PubMed

    Yang, Jingqi; Li, Shaoxian; Zhao, Hongwei; Song, Bo; Zhang, Guoxin; Zhang, Jianbing; Zhu, Yiming; Han, Jiaguang

    2014-11-20

    Using terahertz time-domain spectroscopy characterization, we observe that urea is able to recognize and interact with uracil efficiently even in the solid phase without involving water or solvents. A cocrystal configuration linked by a pair of hydrogen bonds between uracil and urea was formed. The terahertz absorption spectrum of the cocrystal shows a distinct new absorption at 0.8 THz (26.7 cm(-1)), which originates from the intermolecular hydrogen bonding. Both mechanical milling and heating can accelerate the reaction efficiently. Density functional theory was adopted to simulate the vibrational modes of the cocrystal, and the results agree well with the experimental observation. Multiple techniques, including powder X-ray diffraction, scanning electron microscopy, and Fourier transform infrared spectroscopy, were performed to investigate the reaction process, and they presented supportive evidence. This work enables in-depth understanding of recognition and interaction of urea with nucleobases and comprehension of the denaturation related to RNA. We also demonstrate that terahertz spectroscopy is an effective and alternative tool for online measurement and quality control in pharmaceutical and chemical industries.

  2. Molecular Mechanisms of Viral and Host Cell Substrate Recognition by Hepatitis C Virus NS3/4A Protease▿

    PubMed Central

    Romano, Keith P.; Laine, Jennifer M.; Deveau, Laura M.; Cao, Hong; Massi, Francesca; Schiffer, Celia A.

    2011-01-01

    Hepatitis C NS3/4A protease is a prime therapeutic target that is responsible for cleaving the viral polyprotein at junctions 3-4A, 4A4B, 4B5A, and 5A5B and two host cell adaptor proteins of the innate immune response, TRIF and MAVS. In this study, NS3/4A crystal structures of both host cell cleavage sites were determined and compared to the crystal structures of viral substrates. Two distinct protease conformations were observed and correlated with substrate specificity: (i) 3-4A, 4A4B, 5A5B, and MAVS, which are processed more efficiently by the protease, form extensive electrostatic networks when in complex with the protease, and (ii) TRIF and 4B5A, which contain polyproline motifs in their full-length sequences, do not form electrostatic networks in their crystal complexes. These findings provide mechanistic insights into NS3/4A substrate recognition, which may assist in a more rational approach to inhibitor design in the face of the rapid acquisition of resistance. PMID:21507982

  3. Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex.

    PubMed

    Edelmann, Franziska Theresia; Schlundt, Andreas; Heym, Roland Gerhard; Jenner, Andreas; Niedner-Boblenz, Annika; Syed, Muhammad Ibrahim; Paillart, Jean-Christophe; Stehle, Ralf; Janowski, Robert; Sattler, Michael; Jansen, Ralf-Peter; Niessing, Dierk

    2017-02-01

    mRNA localization is an essential mechanism of gene regulation and is required for processes such as stem-cell division, embryogenesis and neuronal plasticity. It is not known which features in the cis-acting mRNA localization elements (LEs) are specifically recognized by motor-containing transport complexes. To the best of our knowledge, no high-resolution structure is available for any LE in complex with its cognate protein complex. Using X-ray crystallography and complementary techniques, we carried out a detailed assessment of an LE of the ASH1 mRNA from yeast, its complex with its shuttling RNA-binding protein She2p, and its highly specific, cytoplasmic complex with She3p. Although the RNA alone formed a flexible stem loop, She2p binding induced marked conformational changes. However, only joining by the unstructured She3p resulted in specific RNA recognition. The notable RNA rearrangements and joint action of a globular and an unfolded RNA-binding protein offer unprecedented insights into the step-wise maturation of an mRNA-transport complex.

  4. Protein-ligand recognition using spherical harmonic molecular surfaces: towards a fast and efficient filter for large virtual throughput screening.

    PubMed

    Cai, Wensheng; Shao, Xueguang; Maigret, Bernard

    2002-01-01

    Molecular surfaces are important because surface-shape complementarity is often a necessary condition in protein-ligand interactions and docking studies. We have previously described a fast and efficient method to obtain triangulated surface-meshes by topologically mapping ellipsoids on molecular surfaces. In this paper, we present an extension of our work to spherical harmonic surfaces in order to approximate molecular surfaces of both ligands and receptor-cavities and to easily check the surface-shape complementarity. The method consists of (1) finding lobes and holes on both ligand and cavity surfaces using contour maps of radius functions with spherical harmonic expansions, (2) superposing the surfaces around a given binding site by minimizing the distance between their respective expansion coefficients. This docking procedure capabilities was demonstrated by application to 35 protein-ligand complexes of known crystal structures. The method can also be easily and efficiently used as a filter to detect in a large conformational sampling the possible conformations presenting good complementarity with the receptor site, and being, therefore, good candidates for further more elaborate docking studies. This "virtual screening" was demonstrated on the platelet thrombin receptor.

  5. Binding of fluorescent acridine dyes acridine orange and 9-aminoacridine to hemoglobin: Elucidation of their molecular recognition by spectroscopy, calorimetry and molecular modeling techniques.

    PubMed

    Chatterjee, Sabyasachi; Kumar, Gopinatha Suresh

    2016-06-01

    The molecular interaction between hemoglobin (HHb), the major human heme protein, and the acridine dyes acridine orange (AO) and 9-aminoacridine (9AA) was studied by various spectroscopic, calorimetric and molecular modeling techniques. The dyes formed stable ground state complex with HHb as revealed from spectroscopic data. Temperature dependent fluorescence data showed the strength of the dye-protein complexation to be inversely proportional to temperature and the fluorescence quenching was static in nature. The binding-induced conformational change in the protein was investigated using circular dichroism, synchronous fluorescence, 3D fluorescence and FTIR spectroscopy results. Circular dichroism data also quantified the α-helicity change in hemoglobin due to the binding of acridine dyes. Calorimetric studies revealed the binding to be endothermic in nature for both AO and 9AA, though the latter had higher affinity, and this was also observed from spectroscopic data. The binding of both dyes was entropy driven. pH dependent fluorescence studies revealed the existence of electrostatic interaction between the protein and dye molecules. Molecular modeling studies specified the binding site and the non-covalent interactions involved in the association. Overall, the results revealed that a small change in the acridine chromophore leads to remarkable alteration in the structural and thermodynamic aspects of binding to HHb.

  6. Subchronic metformin pretreatment enhances novel object recognition memory task in forebrain ischemia: behavioural, molecular, and electrophysiological studies.

    PubMed

    Ashabi, Ghorbangol; Sarkaki, Alireza; Khodagholi, Fariba; Zareh Shahamati, Shima; Goudarzvand, Mahdi; Farbood, Yaghoob; Badavi, Mohammad; Khalaj, Leila

    2016-11-04

    Metformin exerts its effect via AMP-activated protein kinase (AMPK), which is a key sensor for energy homeostasis that regulates different intracellular pathways. Metformin attenuates oxidative stress and cognitive impairment. In our experiment, rats were divided into 8 groups; some were pretreated with metformin (Met, 200 mg/kg) and (or) the AMPK inhibitor Compound C (CC) for 14 days. On day 14, rats underwent transient forebrain global ischemia. Data indicated that pretreatment of ischemic rats with metformin reduced working memory deficits in a novel object recognition test compared to group with ischemia-reperfusion (I-R) (P < 0.01). Pretreatment of the I-R animals with metformin increased phosphorylated cyclic-AMP response element-binding protein (pCREB) and c-fos levels compared to the I-R group (P < 0.001 for both). The level of CREB and c-fos was significantly lower in ischemic rats pretreated with Met + CC compared to the Met + I-R group. Field excitatory postsynaptic potential (fEPSP) amplitude and slope was significantly lower in the I-R group compared to the sham operation group (P < 0.001). Data showed that fEPSP amplitude and slope was significantly higher in the Met + I-R group compared to the I-R group (P < 0.001). Treatment of ischemic animals with Met + CC increased fEPSP amplitude and slope compared to the Met + I-R group (P < 0.01). We unravelled new aspects of the protective role of AMPK activation by metformin, further emphasizing the potency of metformin pretreatment against cerebral ischemia.

  7. Recognition of RNA by amide modified backbone nucleic acids: molecular dynamics simulations of DNA-RNA hybrids in aqueous solution.

    PubMed

    Nina, Mafalda; Fonné-Pfister, Raymonde; Beaudegnies, Renaud; Chekatt, Habiba; Jung, Pierre M J; Murphy-Kessabi, Fiona; De Mesmaeker, Alain; Wendeborn, Sebastian

    2005-04-27

    Thermodynamic and structural properties of a chemically modified DNA-RNA hybrid in which a phosphodiester linkage is replaced by a neutral amide-3 linkage (3'-CH(2)-CONH-5') were investigated using UV melting experiments, molecular dynamics simulations in explicit water, and continuum solvent models. van't Hoff analysis of the experimental UV melting curves suggests that the significant increase of the thermodynamic stability of a 15-mer DNA-RNA with seven alternated amide-3 modifications (+11 degrees C) is mainly due to an increased binding enthalpy. To further evaluate the origin in the observed affinities differences, the electrostatic contribution to the binding free energy was calculated by solving the Poisson-Boltzmann equation numerically. The nonelectrostatic contribution was estimated as the product of a hydrophobic surface tension coefficient and the surface area that is buried upon double strand formation. Structures were taken from 10 ns molecular dynamics simulations computed in a consistent fashion using explicit solvent, counterions, and the particle-mesh Ewald procedure. The present preliminary thermodynamic study suggests that the favorable binding free energy of the amide-3 DNA single strand to the complementary RNA is equally driven by electrostatic and nonpolar contributions to the binding compared to their natural analogues. In addition, molecular dynamics simulations in explicit water were performed on an amide-3 DNA single strand and the corresponding natural DNA. Results from the conformations cluster analysis of the simulated amide-3 DNA single strand ensembles suggest that the 25% of the population sampled within 10 ns has a pre-organized conformation where the sugar C3' endo pucker is favored at the 3'-flanking nucleotides. These structural and thermodynamic features contribute to the understanding of the observed increased affinities of the amide-3 DNA-RNA hybrids at the microscopic level.

  8. Synthesis of carbohydrate-scaffolded thymine glycoconjugates to organize multivalency

    PubMed Central

    Ciuk, Anna K

    2015-01-01

    Summary Multivalency effects are essential in carbohydrate recognition processes as occurring on the cell surface. Thus many synthetic multivalent glycoconjugates have been developed as important tools for glycobiological research. We are expanding this collection of molecules by the introduction of carbohydrate-scaffolded divalent glycothymine derivatives that can be intramolecularily dimerized by [2 + 2] photocycloaddition. Thus, thymine functions as a control element that allows to restrict the conformational flexibility of the scaffolded sugar ligands and thus to “organize” multivalency. With this work we add a parameter to multivalency studies additional to valency. PMID:26124869

  9. Insight into the intermolecular recognition mechanism between Keap1 and IKKβ combining homology modelling, protein-protein docking, molecular dynamics simulations and virtual alanine mutation.

    PubMed

    Jiang, Zheng-Yu; Chu, Hong-Xi; Xi, Mei-Yang; Yang, Ting-Ting; Jia, Jian-Min; Huang, Jing-Jie; Guo, Xiao-Ke; Zhang, Xiao-Jin; You, Qi-Dong; Sun, Hao-Peng

    2013-01-01

    Degradation of certain proteins through the ubiquitin-proteasome pathway is a common strategy taken by the key modulators responsible for stress responses. Kelch-like ECH-associated protein-1(Keap1), a substrate adaptor component of the Cullin3 (Cul3)-based ubiquitin E3 ligase complex, mediates the ubiquitination of two key modulators, NF-E2-related factor 2 (Nrf2) and IκB kinase β (IKKβ), which are involved in the redox control of gene transcription. However, compared to the Keap1-Nrf2 protein-protein interaction (PPI), the intermolecular recognition mechanism of Keap1 and IKKβ has been poorly investigated. In order to explore the binding pattern between Keap1 and IKKβ, the PPI model of Keap1 and IKKβ was investigated. The structure of human IKKβ was constructed by means of the homology modeling method and using reported crystal structure of Xenopus laevis IKKβ as the template. A protein-protein docking method was applied to develop the Keap1-IKKβ complex model. After the refinement and visual analysis of docked proteins, the chosen pose was further optimized through molecular dynamics simulations. The resulting structure was utilized to conduct the virtual alanine mutation for the exploration of hot-spots significant for the intermolecular interaction. Overall, our results provided structural insights into the PPI model of Keap1-IKKβ and suggest that the substrate specificity of Keap1 depend on the interaction with the key tyrosines, namely Tyr525, Tyr574 and Tyr334. The study presented in the current project may be useful to design molecules that selectively modulate Keap1. The selective recognition mechanism of Keap1 with IKKβ or Nrf2 will be helpful to further know the crosstalk between NF-κB and Nrf2 signaling.

  10. How curvature-generating proteins build scaffolds on membrane nanotubes

    PubMed Central

    Evergren, Emma; Golushko, Ivan; Prévost, Coline; Renard, Henri-François; Johannes, Ludger; McMahon, Harvey T.; Lorman, Vladimir; Voth, Gregory A.; Bassereau, Patricia

    2016-01-01

    Bin/Amphiphysin/Rvs (BAR) domain proteins control the curvature of lipid membranes in endocytosis, trafficking, cell motility, the formation of complex subcellular structures, and many other cellular phenomena. They form 3D assemblies that act as molecular scaffolds to reshape the membrane and alter its mechanical properties. It is unknown, however, how a protein scaffold forms and how BAR domains interact in these assemblies at protein densities relevant for a cell. In this work, we use various experimental, theoretical, and simulation approaches to explore how BAR proteins organize to form a scaffold on a membrane nanotube. By combining quantitative microscopy with analytical modeling, we demonstrate that a highly curving BAR protein endophilin nucleates its scaffolds at the ends of a membrane tube, contrary to a weaker curving protein centaurin, which binds evenly along the tube’s length. Our work implies that the nature of local protein–membrane interactions can affect the specific localization of proteins on membrane-remodeling sites. Furthermore, we show that amphipathic helices are dispensable in forming protein scaffolds. Finally, we explore a possible molecular structure of a BAR-domain scaffold using coarse-grained molecular dynamics simulations. Together with fluorescence microscopy, the simulations show that proteins need only to cover 30–40% of a tube’s surface to form a rigid assembly. Our work provides mechanical and structural insights into the way BAR proteins may sculpt the membrane as a high-order cooperative assembly in important biological processes. PMID:27655892

  11. Selective recognition of 4-nitrophenol from aqueous solution by molecularly imprinted polymers with functionalized tetratitanate whisker composites as support.

    PubMed

    Guan, Wei; Pan, Jianming; Wang, Xue; Hu, Wei; Xu, Longcheng; Zou, Xiaohua; Li, Chunxiang

    2011-06-01

    Three kinds of molecularly imprinted polymers (MIPs) were obtained with surface molecular imprinting technique on functionalized potassium tetratitanate whisker (F-PTW). The results of adsorption experiments indicated that MIP prepared using PTW modified with N-(2-aminoethyl)-3-(trimethoxysilyl)propylamine (AAPTS) (F-PTW A) as support [MIP(1)] was superior to the other two polymers, then MIP(1) was selected to analyze the 4-nitrophenol (4-NP) adsorption process from aqueous solution in this study. AAPTS offered hydrophilic exterior that allowed to self-assemble with the template 4-NP through intermolecular interaction rather than based on the interactions between the functional monomers and template. Equilibrium adsorption data were analyzed by the Langmuir and Freundlich isotherm models at various temperatures. Kinetic properties were successfully investigated by pseudo-first-order model, pseudo-second-order model, intraparticle diffusion equation, initial adsorption rate, half-adsorption time. A diffusion-controlled process as the essential adsorption rate-controlling step was also proposed. The performance of such imprinted polymer was further demonstrated by high-performance liquid chromatography, and the results showed that the selectivity of MIP(1) exhibited higher affinity for template 4-NP over competitive phenolic compounds than that of non-imprinted polymer NIP(1). MIP(1) could be reused four times without significant loss in the adsorption capacity.

  12. Molecular based phylogenetic species recognition in the genus Pampus (Perciformes: Stromateidae) reveals hidden diversity in the Indian Ocean.

    PubMed

    Divya, P R; Mohitha, C; Rahul, G Kumar; Rajool Shanis, C P; Basheer, V S; Gopalakrishnan, A

    2017-04-01

    Pomfrets (Genus Pampus) are commercially important fishes in the Indo Pacific region. The systematics of this genus is complicated due to morphological similarities between species. The silver pomfret from Indian waters has long been considered to be Pampus argenteus. The objective of the study was to utilize the mitochondrial COI gene to establish the molecular identity of the silver pomfret distributed in Indian waters and to resolve the phylogenetic relationships among Pampus species in the world based on sequence data in the NCBI database. Seven valid Pampus species are identified in this study. The mean genetic divergence value calculated between clades representing these species was 7.9%. The mean genetic distance between the so-called Pampus argenteus from Indian waters and sequences attributed to P. argenteus from the South China Sea, where the neotype of this species was collected, was found to be greater than 12%, strongly supporting the likelihood of the Indian species being distinct. The Indian Pampus species show very close affinity to P. cinereus, with inter species differences less than 2%. The taxonomic identity of the silver pomfret in India is also discussed here, in light of molecular and morphological evidence.

  13. Molecular recognition of an ADP-ribosylating Clostridium botulinum C3 exoenzyme by RalA GTPase

    PubMed Central

    Holbourn, Kenneth P.; Sutton, J. Mark; Evans, Hazel R.; Shone, Clifford C.; Acharya, K. Ravi

    2005-01-01

    C3 exoenzymes (members of the ADP-ribosyltranferase family) are produced by Clostridium botulinum (C3bot1 and -2), Clostridium limosum (C3lim), Bacillus cereus (C3cer), and Staphylococcus aureus (C3stau1–3). These exoenzymes lack a translocation domain but are known to specifically inactivate Rho GTPases in host target cells. Here, we report the crystal structure of C3bot1 in complex with RalA (a GTPase of the Ras subfamily) and GDP at a resolution of 2.66 Å. RalA is not ADP-ribosylated by C3 exoenzymes but inhibits ADP-ribosylation of RhoA by C3bot1, C3lim, and C3cer to different extents. The structure provides an insight into the molecular interactions between C3bot1 and RalA involving the catalytic ADP-ribosylating turn–turn (ARTT) loop from C3bot1 and helix α4 and strand β6 (which are not part of the GDP-binding pocket) from RalA. The structure also suggests a molecular explanation for the different levels of C3-exoenzyme inhibition by RalA and why RhoA does not bind C3bot1 in this manner. PMID:15809419

  14. Molecular recognition of an ADP-ribosylating Clostridium botulinum C3 exoenzyme by RalA GTPase.

    PubMed

    Holbourn, Kenneth P; Sutton, J Mark; Evans, Hazel R; Shone, Clifford C; Acharya, K Ravi

    2005-04-12

    C3 exoenzymes (members of the ADP-ribosyltranferase family) are produced by Clostridium botulinum (C3bot1 and -2), Clostridium limosum (C3lim), Bacillus cereus (C3cer), and Staphylococcus aureus (C3stau1-3). These exoenzymes lack a translocation domain but are known to specifically inactivate Rho GTPases in host target cells. Here, we report the crystal structure of C3bot1 in complex with RalA (a GTPase of the Ras subfamily) and GDP at a resolution of 2.66 A. RalA is not ADP-ribosylated by C3 exoenzymes but inhibits ADP-ribosylation of RhoA by C3bot1, C3lim, and C3cer to different extents. The structure provides an insight into the molecular interactions between C3bot1 and RalA involving the catalytic ADP-ribosylating turn-turn (ARTT) loop from C3bot1 and helix alpha4 and strand beta6 (which are not part of the GDP-binding pocket) from RalA. The structure also suggests a molecular explanation for the different levels of C3-exoenzyme inhibition by RalA and why RhoA does not bind C3bot1 in this manner.

  15. Adaptive radiation in Lesser Antillean lizards: molecular phylogenetics and species recognition in the Lesser Antillean dwarf gecko complex, Sphaerodactylus fantasticus.

    PubMed

    Thorpe, R S; Jones, A G; Malhotra, A; Surget-Groba, Y

    2008-03-01

    The time associated with speciation varies dramatically among lower vertebrates. The nature and timing of divergence is investigated in the fantastic dwarf gecko Sphaerodactylus fantasticus complex, a nominal species that occurs on the central Lesser Antillean island of Guadeloupe and adjacent islands and islets. This is compared to the divergence in the sympatric anole clade from the Anolis bimaculatus group. A molecular phylogenetic analysis of numerous gecko populations from across these islands, based on three mitochondrial DNA genes, reveals several monophyletic groups occupying distinct geographical areas, these being Les Saintes, western Basse Terre plus Dominica, eastern Basse Terre, Grand Terre, and the northern and eastern islands (Montserrat, Marie Galante, Petite Terre, Desirade). Although part of the same nominal species, the molecular divergence within this species complex is extraordinarily high (27% patristic distance between the most divergent lineages) and is compatible with this group occupying the region long before the origin of the younger island arc. Tests show that several quantitative morphological traits are correlated with the phylogeny, but in general the lineages are not uniquely defined by these traits. The dwarf geckos show notably less nominal species-level adaptive radiation than that found in the sympatric southern clade of Anolis bimculatus, although both appear to have occupied the region for a broadly similar period of time. Nevertheless, the dwarf gecko populations on Les Saintes islets are the most morphologically distinct and are recognized as a full species (Sphaerodactylus phyzacinus), as are anoles on Les Saintes (Anolis terraealtae).

  16. Selective recognition and discrimination of water-soluble azo dyes by a seven-channel molecularly imprinted polymer sensor array.

    PubMed

    Long, Zerong; Lu, Yi; Zhang, Mingliang; Qiu, Hongdeng

    2014-10-01

    A seven-channel molecularly imprinted polymer sensor array was prepared and characterized by scanning electron microscopy, Fourier transform infrared spectroscopy, UV-Vis spectroscopy, and nitrogen physisorption studies. The results revealed that the imprinted polymers have distinct-binding affinities from those of structurally similar azo dyes. Analysis of the UV-Vis spectral response patterns of the seven dye analytes against the imprinted polymer array suggested that the different selectivity patterns of the array were closely connected to the imprinting process. To evaluate the effectiveness of the array format, the binding of a series of analytes was individually measured for each of the seven polymers, made with different templates (including one control polymer synthesized without the use of a template). The response patterns of the array to the selected azo dyes were processed by canonical discriminant analysis. The results showed that the molecularly imprinted array was able to discriminate each analyte with 100% accuracy. Moreover, the azo dyes in two real samples, spiked chrysoidin in smoked bean curd extract and Fanta lime soda (containing tartrazine), were successfully classified by the array.

  17. Molecular recognition and self-assembly special feature: Self-assembled biomimetic [2Fe2S]-hydrogenase-based photocatalyst for molecular hydrogen evolution.

    PubMed

    Kluwer, A M; Kapre, R; Hartl, F; Lutz, M; Spek, A L; Brouwer, A M; van Leeuwen, P W N M; Reek, J N H

    2009-06-30

    The large-scale production of clean energy is one of the major challenges society is currently facing. Molecular hydrogen is envisaged as a key green fuel for the future, but it becomes a sustainable alternative for classical fuels only if it is also produced in a clean fashion. Here, we report a supramolecular biomimetic approach to form a catalyst that produces molecular hydrogen using light as the energy source. It is composed of an assembly of chromophores to a bis(thiolate)-bridged diiron ([2Fe2S]) based hydrogenase catalyst. The supramolecular building block approach introduced in this article enabled the easy formation of a series of complexes, which are all thoroughly characterized, revealing that the photoactivity of the catalyst assembly strongly depends on its nature. The active species, formed from different complexes, appears to be the [Fe(2)(micro-pdt)(CO)(4){PPh(2)(4-py)}(2)] (3) with 2 different types of porphyrins (5a and 5b) coordinated to it. The modular supramolecular approach was important in this study as with a limited number of building blocks several different complexes were generated.

  18. Integrin priming dynamics: mechanisms of integrin antagonist-promoted alphaIIbbeta3:PAC-1 molecular recognition.

    PubMed

    Hantgan, Roy R; Stahle, Mary C

    2009-09-08

    This investigation addressed the paradox that disintegrins and small RGD-ligands readily bind to the resting alphaIIbbeta3 integrin, while macromolecules with similar integrin recognition motifs require an activated, or primed, receptor. Three structurally similar pharmaceutical integrin antagonists (eptifibatide, tirofiban, and roxifiban) were each incubated with resting alphaIIbbeta3; after drug wash-out, the receptor's ability to recognize PAC-1, an activation-dependent IgM with an RYD integrin-targeting site was measured. Their promotion of PAC-1:alphaIIbbeta3 binding (solid phase assay), eptifibatide > tirofiban > roxifiban, correlated with their ability to shift the receptor to an open conformer, as measured by analytical ultracentrifugation. Surface plasmon resonance (SPR) demonstrated that PAC-1 bound rapidly (k(on) approximately 5 x 10(5) l/mol-s, 25 degrees C) and tightly (Kd approximately 1 nM) to eptifibatide-primed integrins, captured on a biosensor using an IgG specific for alphaIIb's cytoplasmic domain. Varying the interval between integrin capture and antagonist dissociation indicated that transiently primed alphaIIbbeta3 retains the ability to rapidly bind PAC-1 from 2-90 min, although the dissociation rate increased at later times, indicative of a weakening of the complex. Fluorescence anisotropy (fluorophore-tagged analogue exchange assay) demonstrated that eptifibatide dissociates rapidly from alphaIIbbeta3 (half-time <2 min), consistent with the priming window determined by SPR. van't Hoff analysis of alphaIIbbeta3:PAC-1's temperature-dependent Kd indicated entropy/enthalpy compensation, similar to (resting) integrin binding to the disintegrin echistatin. Eyring analysis of k(on) yielded DeltaG degrees approximately 10 kcal/mol for PAC-1 binding to primed alphaIIbbeta3, 3 kcal/mol lower than that of echistatin. These observations suggest that priming lowers the transition-state energy barrier, enabling rapid macromolecular ligand binding to

  19. Molecularly imprinted poly(N-vinyl imidazole) based polymers grafted onto nonwoven fabrics for recognition/removal of phloretic acid

    NASA Astrophysics Data System (ADS)

    Llorina Rañada, Ma.; Akbulut, Meshude; Abad, Lucille; Güven, Olgun

    2014-01-01

    A solution of N-vinyl imidazole (VIm), ethylene glycol dimethylacrylate (EGDMA), and phloretic acid (p-hydroxyphenylpropionic acid, HPPA) as functional monomer, crosslinker and template, respectively, were used to graft molecularly imprinted polymer (MIP) onto polyethylene/polypropylene (PE/PP) nonwoven fabric via gamma radiation at room temperature. Control grafted films were also synthesized using the same procedure in the absence of HPPA. Binding performance of the MIP grafts was investigated for different template molecule concentrations and contact time. An imprinting factor for the sample prepared at 5 kGy dose was determined as 2.41 for 50 ppm HPPA solution for 3-h incubation. MIP graft layers were investigated by positron annihilation lifetime spectroscopy (PALS) as well as SEM.

  20. Macromolecular recognition: Recognition of polymer side chains by cyclodextrin

    NASA Astrophysics Data System (ADS)

    Hashidzume, Akihito; Harada, Akira

    2015-12-01

    The interaction of cyclodextrins (CD) with water soluble polymers possessing guest residues has been investigated as model systems in biological molecular recognition. The selectivity of interaction of CD with polymer-carrying guest residues is controlled by polymer chains, i.e., the steric effect of polymer main chain, the conformational effect of polymer main chain, and multi-site interaction. Macroscopic assemblies have been also realized based on molecular recognition using polyacrylamide-based gels possessing CD and guest residues.

  1. Engineered Biopolymeric Scaffolds for Chronic Wound Healing.

    PubMed

    Dickinson, Laura E; Gerecht, Sharon

    2016-01-01

    Skin regeneration requires the coordinated integration of concomitant biological and molecular events in the extracellular wound environment during overlapping phases of inflammation, proliferation, and matrix remodeling. This process is highly efficient during normal wound healing. However, chronic wounds fail to progress through the ordered and reparative wound healing process and are unable to heal, requiring long-term treatment at high costs. There are many advanced skin substitutes, which mostly comprise bioactive dressings containing mammalian derived matrix components, and/or human cells, in clinical use. However, it is presently hypothesized that no treatment significantly outperforms the others. To address this unmet challenge, recent research has focused on developing innovative acellular biopolymeric scaffolds as more efficacious wound healing therapies. These biomaterial-based skin substitutes are precisely engineered and fine-tuned to recapitulate aspects of the wound healing milieu and target specific events in the wound healing cascade to facilitate complete skin repair with restored function and tissue integrity. This mini-review will provide a brief overview of chronic wound healing and current skin substitute treatment strategies while focusing on recent engineering approaches that regenerate skin using synthetic, biopolymeric scaffolds. We discuss key polymeric scaffold design criteria, including degradation, biocompatibility, and microstructure, and how they translate to inductive microenvironments that stimulate cell infiltration and vascularization to enhance chronic wound healing. As healthcare moves toward precision medicine-based strategies, the potential and therapeutic implications of synthetic, biopolymeric scaffolds as tunable treatment modalities for chronic wounds will be considered.

  2. Engineered Biopolymeric Scaffolds for Chronic Wound Healing

    PubMed Central

    Dickinson, Laura E.; Gerecht, Sharon

    2016-01-01

    Skin regeneration requires the coordinated integration of concomitant biological and molecular events in the extracellular wound environment during overlapping phases of inflammation, proliferation, and matrix remodeling. This process is highly efficient during normal wound healing. However, chronic wounds fail to progress through the ordered and reparative wound healing process and are unable to heal, requiring long-term treatment at high costs. There are many advanced skin substitutes, which mostly comprise bioactive dressings containing mammalian derived matrix components, and/or human cells, in clinical use. However, it is presently hypothesized that no treatment significantly outperforms the others. To address this unmet challenge, recent research has focused on developing innovative acellular biopolymeric scaffolds as more efficacious wound healing therapies. These biomaterial-based skin substitutes are precisely engineered and fine-tuned to recapitulate aspects of the wound healing milieu and target specific events in the wound healing cascade to facilitate complete skin repair with restored function and tissue integrity. This mini-review will provide a brief overview of chronic wound healing and current skin substitute treatment strategies while focusing on recent engineering approaches that regenerate skin using synthetic, biopolymeric scaffolds. We discuss key polymeric scaffold design criteria, including degradation, biocompatibility, and microstructure, and how they translate to inductive microenvironments that stimulate cell infiltration and vascularization to enhance chronic wound healing. As healthcare moves toward precision medicine-based strategies, the potential and therapeutic implications of synthetic, biopolymeric scaffolds as tunable treatment modalities for chronic wounds will be considered. PMID:27547189

  3. L_RNA_scaffolder: scaffolding genomes with transcripts

    PubMed Central

    2013-01-01

    Background Generation of large mate-pair libraries is necessary for de novo genome assembly but the procedure is complex and time-consuming. Furthermore, in some complex genomes, it is hard to increase the N50 length even with large mate-pair libraries, which leads to low transcript coverage. Thus, it is necessary to develop other simple scaffolding approaches, to at least solve the elongation of transcribed fragments. Results We describe L_RNA_scaffolder, a novel genome scaffolding method that uses long transcriptome reads to order, orient and combine genomic fragments into larger sequences. To demonstrate the accuracy of the method, the zebrafish genome was scaffolded. With expanded human transcriptome data, the N50 of human genome was doubled and L_RNA_scaffolder out-performed most scaffolding results by existing scaffolders which employ mate-pair libraries. In these two examples, the transcript coverage was almost complete, especially for long transcripts. We applied L_RNA_scaffolder to the highly polymorphic pearl oyster draft genome and the gene model length significantly increased. Conclusions The simplicity and high-throughput of RNA-seq data makes this approach suitable for genome scaffolding. L_RNA_scaffolder is available at http://www.fishbrowser.org/software/L_RNA_scaffolder. PMID:24010822

  4. Bone tissue engineering scaffolding: computer-aided scaffolding techniques.

    PubMed

    Thavornyutikarn, Boonlom; Chantarapanich, Nattapon; Sitthiseripratip, Kriskrai; Thouas, George A; Chen, Qizhi

    Tissue engineering is essentially a technique for imitating nature. Natural tissues consist of three components: cells, signalling systems (e.g. growth factors) and extracellular matrix (ECM). The ECM forms a scaffold for its cells. Hence, the engineered tissue construct is an artificial scaffold populated with living cells and signalling molecules. A huge effort has been invested in bone tissue engineering, in which a highly porous scaffold plays a critical role in guiding bone and vascular tissue growth and regeneration in three dimensions. In the last two decades, numerous scaffolding techniques have been developed to fabricate highly interconnective, porous scaffolds for bone tissue engineering applications. This review provides an update on the progress of foaming technology of biomaterials, with a special attention being focused on computer-aided manufacturing (Andrade et al. 2002) techniques. This article starts with a brief introduction of tissue engineering (Bone tissue engineering and scaffolds) and scaffolding materials (Biomaterials used in bone tissue engineering). After a brief reviews on conventional scaffolding techniques (Conventional scaffolding techniques), a number of CAM techniques are reviewed in great detail. For each technique, the structure and mechanical integrity of fabricated scaffolds are discussed in detail. Finally, the advantaged and disadvantage of these techniques are compared (Comparison of scaffolding techniques) and summarised (Summary).

  5. Multivalent IDP assemblies: Unique properties of LC8-associated, IDP duplex scaffolds.

    PubMed

    Clark, Sarah A; Jespersen, Nathan; Woodward, Clare; Barbar, Elisar

    2015-09-14

    A wide variety of subcellular complexes are composed of one or more intrinsically disordered proteins (IDPs) that are multivalent, flexible, and characterized by dynamic binding of diverse partner proteins. These multivalent IDP assemblies, of broad functional diversity, are classified here into five categories distinguished by the number of IDP chains and the arrangement of partner proteins in the functional complex. Examples of each category are summarized in the context of the exceptional molecular and biological properties of IDPs. One type - IDP duplex scaffolds - is considered in detail. Its unique features include parallel alignment of two IDP chains, formation of new self-associated domains, enhanced affinity for additional bivalent ligands, and ubiquitous binding of the hub protein LC8. For two IDP duplex scaffolds, dynein intermediate chain IC and nucleoporin Nup159, these duplex features, together with the inherent flexibility of IDPs, are central to their assembly and function. A new type of IDP-LC8 interaction, distributed binding of LC8 among multiple IDP recognition sites, is described for Nup159 assembly.

  6. Molecular recognition and processing of periodic signals in cells: study of activation of membrane ATPases by alternating electric fields.

    PubMed

    Tsong, T Y

    1992-03-26

    other cells by these signals. The experimental data and mechanistic information presented in this communication give us a glimpse of the molecular electronic designs in living cells. This information is also relevant with respect to environmental issues. Environmental electromagnetic fields and sonic pollutants may interfere with normal communications of cells and organisms. Their benefit, if any, and detrimental effects can be assessed and dealt with only if we fully understand mechanisms of cellular interactions with these fields and pollutants, at the molecular level.

  7. Molecular recognition in a propazine-imprinted polymer and its application to the determination of triazines in environmental samples.

    PubMed

    Turiel, E; Martin-Esteban, A; Fernández, P; Pérez-Conde, C; Cámara, C

    2001-11-01

    An analytical methodology for the determination of triazines in environmental samples incorporating a molecularly imprinted solid-phase extraction (MISPE) process using a propazine-imprinted polymer was developed. Two different polymers were prepared using acetonitrile or toluene as porogen, and their optimum loading, washing, and elution conditions were established. Although both polymers were able to recognize several chlorotriazines (propazine, atrazine, simazine, desethylatrazine, and desisopropylatrazine), the polymer prepared in toluene showed the best performance and was also capable of recognizing a methylthiotriazine (prometryn). A binding study carried out in this polymer demonstrated that it possesses heterogeneous binding sites with different binding abilities. From this study, it was also concluded that desethylatrazine and desisopropylatrazine displace the other triazines at high concentrations, including the template molecule. The accuracy and selectivity of the MISPE process developed was verified using a certified reference material for drinking water containing atrazine and simazine among other commonly used pesticides. Finally, the MISPE procedure was successfully applied to the cleanup of drinking and groundwater, soil, and corn sample extra