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Sample records for supramolecular peptide structures

  1. Supramolecular structures of peptide assemblies in membranes by neutron off-plane scattering: method of analysis.

    Science.gov (United States)

    Yang, L; Weiss, T M; Harroun, T A; Heller, W T; Huang, H W

    1999-11-01

    In a previous paper (Yang et al., Biophys. J. 75:641-645, 1998), we showed a simple, efficient method of recording the diffraction patterns of supramolecular peptide assemblies in membranes where the samples were prepared in the form of oriented multilayers. Here we develop a method of analysis based on the diffraction theory of two-dimensional liquids. Gramicidin was used as a prototype model because its pore structure in membrane in known. At full hydration, the diffraction patterns of alamethicin and magainin are similar to gramicidin except in the scale of q (the momentum transfer of scattering), clearly indicating that both alamethicin and magainin form pores in membranes but of different sizes. When the hydration of the multilayer samples was decreased while the bilayers were still fluid, the in-plane positions of the membrane pores became correlated from one bilayer to the next. We believe that this is a new manifestation of the hydration force. The effect is most prominent in magainin patterns, which are used to demonstrate the method of analysis. When magainin samples were further dehydrated or cooled, the liquid-like diffraction turned into crystal-like patterns. This discovery points to the possibility of investigating the supramolecular structures with high-order diffraction.

  2. Control over Structure and Function of Peptide Amphiphile Supramolecular Assemblies through Molecular Design and Energy Landscapes

    Science.gov (United States)

    Tantakitti, Faifan

    Supramolecular chemistry is a powerful tool to create a material of a defined structure with tunable properties. This strategy has led to catalytically active, bioactive, and environment-responsive materials, among others, that are valuable in applications ranging from sensor technology to energy and medicine. Supramolecular polymers formed by peptide amphiphiles (PAs) have been especially relevant in tissue regeneration due to their ability to form biocompatible structures and mimic many important signaling molecules in biology. These supramolecular polymers can form nanofibers that create networks which mimic natural extracellular matrices. PA materials have been shown to induce growth of blood vessels, bone, cartilage, and nervous tissue, among others. The work described in this thesis not only studied the relationship between molecular structure and functions of PA assemblies, but also uncovered a powerful link between the energy landscape of their supramolecular self-assembly and the ability of PA materials to interact with cells. In chapter 2, it is argued that fabricating fibrous nanostructures with defined mechanical properties and decoration with bioactive molecules is not sufficient to create a material that can effectively communicate with cells. By systemically placing the fibronectin-derived RGDS epitope at increasing distances from the surface of PA nanofibers through a linker of one to five glycine residues, integrin-mediated RGDS signaling was enhanced. The results suggested that the spatial presentation of an epitope on PA nanofibers strongly influences the bioactivity of the PA substrates. In further improving functionality of a PA-based scaffold to effectively direct cell growth and differentiation, chapter 3 explored the use of a cell microcarrier to compartmentalize and simultaneously tune insoluble and soluble signals in a single matrix. PA nanofibers were incorporated at the surface of the microcarrier in order to promote cell adhesion, while

  3. Application of atomic force microscopy to protein anatomy:. Imaging of supramolecular structures of self-assemblies formed from synthetic peptides

    Science.gov (United States)

    Shibata-Seki, T.; Masai, J.; Ogawa, Y.; Sato, K.; Yanagawa, H.

    This paper reports morphological studies of structures of self-assemblies from synthetic peptide fragments with the use of atomic force microscope (AFM) and transmission electron microscope (TEM). Two systems of synthetic peptides have been examined: one is peptides from barnase (a ribonuclease) and the other is those from tau protein (Alzheimer's disease-related protein). The AFM observation was carried out by using a commercially available AFM operated in the tapping mode in air. The general appearance in shape and size of the peptide assemblies in AFM images was essentially similar to that in TEM images, except that the AFM images provide us with fruitful three-dimensional information about the assemblies. For assemblies from barnase peptides, possible formation processes of the supramolecular structures from the corresponding peptide fragment have been proposed on the basis of the AFM images.

  4. Physics and engineering of peptide supramolecular nanostructures.

    Science.gov (United States)

    Handelman, Amir; Beker, Peter; Amdursky, Nadav; Rosenman, Gil

    2012-05-14

    The emerging "bottom-up" nanotechnology reveals a new field of bioinspired nanomaterials composed of chemically synthesized biomolecules. They are formed from elementary constituents in supramolecular structures by the use of a developed nature self-assembly mechanism. The focus of this perspective paper is on intrinsic fundamental physical properties of bioinspired peptide nanostructures and their small building units linked by weak noncovalent bonds. The observed exceptional optical properties indicate a phenomenon of quantum confinement in these supramolecular structures, which originates from nanoscale size of their elementary building blocks. The dimensionality of the confinement gives insight into intrinsic packing of peptide supramolecular nanomaterials. QC regions, revealed in bioinspired nanostructures, were found by us in amyloid fibrils formed from insulin protein. We describe ferroelectric and related properties found at the nanoscale based on original crystalline asymmetry of the nanoscale building blocks, packing these structures. In this context, we reveal a classic solid state physics phenomenon such as reconstructive phase transition observed in bioorganic peptide nanotubes. This irreversible phase transformation leads to drastic reshaping of their quantum structure from quantum dots to quantum wells, which is followed by variation of their space group symmetry from asymmetric to symmetric. We show that the supramolecular origin of these bioinspired nanomaterials provides them a unique chance to be disassembled into elementary building block peptide nanodots of 1-2 nm size possessing unique electronic, optical and ferroelectric properties. These multifunctional nanounits could lead to a new future step in nanotechnology and nanoscale advanced devices in the fields of nanophotonics, nanobiomedicine, nanobiopiezotronics, etc. This journal is © the Owner Societies 2012

  5. Harnessing supramolecular peptide nanotechnology in biomedical applications.

    Science.gov (United States)

    Chan, Kiat Hwa; Lee, Wei Hao; Zhuo, Shuangmu; Ni, Ming

    2017-01-01

    The harnessing of peptides in biomedical applications is a recent hot topic. This arises mainly from the general biocompatibility of peptides, as well as from the ease of tunability of peptide structure to engineer desired properties. The ease of progression from laboratory testing to clinical trials is evident from the plethora of examples available. In this review, we compare and contrast how three distinct self-assembled peptide nanostructures possess different functions. We have 1) nanofibrils in biomaterials that can interact with cells, 2) nanoparticles that can traverse the bloodstream to deliver its payload and also be bioimaged, and 3) nanotubes that can serve as cross-membrane conduits and as a template for nanowire formation. Through this review, we aim to illustrate how various peptides, in their various self-assembled nanostructures, possess great promise in a wide range of biomedical applications and what more can be expected.

  6. Minimalistic peptide supramolecular co-assembly: expanding the conformational space for nanotechnology.

    Science.gov (United States)

    Makam, Pandeeswar; Gazit, Ehud

    2018-03-02

    Molecular self-assembly is a ubiquitous process in nature and central to bottom-up nanotechnology. In particular, the organization of peptide building blocks into ordered supramolecular structures has gained much interest due to the unique properties of the products, including biocompatibility, chemical and structural diversity, robustness and ease of large-scale synthesis. In addition, peptides, as short as dipeptides, contain all the molecular information needed to spontaneously form well-ordered structures at both the nano- and the micro-scale. Therefore, peptide supramolecular assembly has been effectively utilized to produce novel materials with tailored properties for various applications in the fields of material science, engineering, medicine, and biology. To further expand the conformational space of peptide assemblies in terms of structural and functional complexity, multicomponent (two or more) peptide supramolecular co-assembly has recently evolved as a promising extended approach, similar to the structural diversity of natural sequence-defined biopolymers (proteins) as well as of synthetic covalent co-polymers. The use of this methodology was recently demonstrated in various applications, such as nanostructure physical dimension control, the creation of non-canonical complex topologies, mechanical strength modulation, the design of light harvesting soft materials, fabrication of electrically conducting devices, induced fluorescence, enzymatic catalysis and tissue engineering. In light of these significant advancements in the field of peptide supramolecular co-assembly in the last few years, in this tutorial review, we provide an updated overview and future prospects of this emerging subject.

  7. Harnessing supramolecular peptide nanotechnology in biomedical applications

    Directory of Open Access Journals (Sweden)

    Chan KH

    2017-02-01

    Full Text Available Kiat Hwa Chan,1 Wei Hao Lee,2 Shuangmu Zhuo,3 Ming Ni3 1Division of Science, Yale-NUS College, Singapore; 2Department of Chemistry, Krieger School of Arts & Sciences, Johns Hopkins University, Baltimore, MD, USA; 3Fujian Provincial Key Laboratory for Photonics Technology, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou, People’s Republic of China Abstract: The harnessing of peptides in biomedical applications is a recent hot topic. This arises mainly from the general biocompatibility of peptides, as well as from the ease of tunability of peptide structure to engineer desired properties. The ease of progression from laboratory testing to clinical trials is evident from the plethora of examples available. In this review, we compare and contrast how three distinct self-assembled peptide nanostructures possess different functions. We have 1 nanofibrils in biomaterials that can interact with cells, 2 nanoparticles that can traverse the bloodstream to deliver its payload and also be bioimaged, and 3 nanotubes that can serve as cross-membrane conduits and as a template for nanowire formation. Through this review, we aim to illustrate how various peptides, in their various self-assembled nanostructures, possess great promise in a wide range of biomedical applications and what more can be expected. Keywords: peptides, self-assembly, nanotechnology

  8. Supramolecular Structure and Function 9

    CERN Document Server

    Pifat-Mrzljak, Greta

    2007-01-01

    The book is based on International Summer Schools on Biophysics held in Croatia which, contrary to other workshops centered mainly on one topic or technique, has very broad scope providing advanced training in areas related to biophysics. This volume is presenting papers in the field of biophysics for studying biological phenomena by using physical methods (NMR, EPR, FTIR, Mass Spectrometry, etc.) and/or concepts (predictions of protein-protein interactions, virtual ligand screening etc.). The interrelationship of supramolecular structures and there functions is enlightened by applications of principals of these physical methods in the biophysical and molecular biology context.

  9. Amyloid formation via supramolecular peptide assemblies.

    Science.gov (United States)

    Moore, Roger A; Hayes, Stanley F; Fischer, Elizabeth R; Priola, Suzette A

    2007-06-19

    Amyloid fibrils have been classically defined as linear, nonbranched polymeric proteins with a cross beta-sheet structure and the ability to alter the optical properties of the amyloid-specific dye Congo Red. Mounting evidence suggests that soluble oligomeric peptide assemblies approximately 2-20 nm in diameter are critical intermediates in amyloid formation. Using a pathogenic prion protein peptide comprised of residues 23-144, we demonstrate that, under quiescent but not agitated conditions, much larger globular assemblies up to 1 mum in diameter are made. These globules precede fibril formation and directly interact with growing fibril bundles. Fibrils made via these large spherical peptide assemblies displayed a remarkable diversity of ultrastructural features. Fibrillization of the Abeta1-40 peptide under similar conditions yielded similar results, suggesting a mechanism of general amyloid formation that can proceed through intermediates much larger than those previously described. Our data suggest that simply changing the physical microenvironment can profoundly influence the mechanism of amyloid formation and yield fibrils with novel ultrastructural properties.

  10. Structural, thermal and spectroscopic properties of supramolecular ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 118; Issue 6. Structural, thermal and spectroscopic properties of supramolecular coordination solids ... trans-[M(NC5H4--CO2)2(OH2)4], participate in exhaustive hydrogen-bond formation among themselves to lead to a robust 3D supramolecular network in the solid ...

  11. Harnessing supramolecular peptide nanotechnology in biomedical applications

    OpenAIRE

    Chan, Kiat Hwa; Lee, Wei Hao; Zhuo, Shuangmu; Ni, Ming

    2017-01-01

    Kiat Hwa Chan,1 Wei Hao Lee,2 Shuangmu Zhuo,3 Ming Ni3 1Division of Science, Yale-NUS College, Singapore; 2Department of Chemistry, Krieger School of Arts & Sciences, Johns Hopkins University, Baltimore, MD, USA; 3Fujian Provincial Key Laboratory for Photonics Technology, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou, People’s Republic of China Abstract: The harnessing of peptides in biomedic...

  12. Synthesis, spectroscopy and supramolecular structures of two ...

    Indian Academy of Sciences (India)

    TECS

    2007-05-16

    May 16, 2007 ... Indian Academy of Sciences. 243. #. Dedicated to Prof. Dr. Werner Weisweiler on the occasion of his 69th birthday. *For correspondence. Synthesis, spectroscopy and supramolecular structures of two magnesium 4-nitrobenzoate complexes. #. BIKSHANDARKOIL R SRINIVASAN,. 1,. * JYOTI V SAWANT,.

  13. Structural modifications leading to changes in supramolecular ...

    Indian Academy of Sciences (India)

    1347–1356. c Indian Academy of Sciences. Structural modifications leading to changes in supramolecular aggregation of thiazolo[3, 2-a]pyrimidines: Insights into their conformational features. H NAGARAJAIAH and NOOR SHAHINA BEGUM. ∗. Department of Studies in Chemistry, Bangalore University, Bangalore 560 001, ...

  14. Synthesis, properties and supramolecular structure of ...

    Indian Academy of Sciences (India)

    Synthesis, properties and supramolecular structure of piperazinediium thiosulfate monohydrate. +. BIKSHANDARKOIL R SRINIVASANa*, ASHISH R NAIKa. , SUNDER N DHURIa. ,. CHRISTIAN NÄTHERb and WOLFGANG BENSCHb. aDepartment of Chemistry, Goa University, Goa 403 206, India. bInstitut für ...

  15. Co-assembly of Peptide Amphiphiles and Lipids into Supramolecular Nanostructures Driven by Anion-π Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Zhilin; Erbas, Aykut; Tantakitti, Faifan; Palmer, Liam C.; Jackman, Joshua A.; Olvera de la Cruz, Monica; Cho, Nam-Joon; Stupp, Samuel I. (Nanyang); (NWU)

    2017-06-01

    Co-assembly of binary systems driven by specific non-covalent interactions can greatly expand the structural and functional space of supramolecular nanostructures. We report here on the self-assembly of peptide amphiphiles and fatty acids driven primarily by anion-π interactions. The peptide sequences investigated were functionalized with a perfluorinated phenylalanine residue to promote anion-π interactions with carboxylate headgroups in fatty acids. These interactions were verified here by NMR and circular dichroism experiments as well as investigated using atomistic simulations. Positioning the aromatic units close to the N-terminus of the peptide backbone near the hydrophobic core of cylindrical nanofibers leads to strong anion-π interactions between both components. With a low content of dodecanoic acid in this position, the cylindrical morphology is preserved. However, as the aromatic units are moved along the peptide backbone away from the hydrophobic core, the interactions with dodecanoic acid transform the cylindrical supramolecular morphology into ribbon-like structures. Increasing the ratio of dodecanoic acid to PA leads to either the formation of large vesicles in the binary systems where the anion-π interactions are strong, or a heterogeneous mixture of assemblies when the peptide amphiphiles associate weakly with dodecanoic acid. Our findings reveal how co-assembly involving designed specific interactions can drastically change supramolecular morphology and even cross from nano to micro scales.

  16. Magnetic structure of two- and three-dimensional supramolecular compounds

    Energy Technology Data Exchange (ETDEWEB)

    Decurtins, S.; Schmalle, H.W.; Pellaux, R. [Zurich Univ. (Switzerland); Fischer, P.; Fauth, F. [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Ouladdiaf, B. [Institut Max von Laue - Paul Langevin, 75 - Paris (France)

    1997-09-01

    Supramolecular chiral networks of oxalato-bridged transition metals show either two- or three-dimensional structural features. The magnetic structures of such compounds have been investigated by means of elastic neutron powder diffraction. (author) 2 figs., 2 refs.

  17. Synthesis and crystal structure of a wheel-shaped supramolecular ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 126; Issue 5. Synthesis and crystal structure of a wheel-shaped supramolecular coordination complex. Deepak Gupta Palanisamy Rajakannu Bhaskaran Shankar Firasat Hussain Malaichamy Sathiyendiran. Special issue on Chemical Crystallography Volume 126 ...

  18. Supramolecular Peptide Nanofiber Morphology Affects Mechanotransduction of Stem Cells.

    Science.gov (United States)

    Arslan, Elif; Hatip Koc, Meryem; Uysal, Ozge; Dikecoglu, Begum; Topal, Ahmet E; Garifullin, Ruslan; Ozkan, Alper D; Dana, Aykutlu; Hermida-Merino, Daniel; Castelletto, Valeria; Edwards-Gayle, Charlotte; Baday, Sefer; Hamley, Ian; Tekinay, Ayse B; Guler, Mustafa O

    2017-10-09

    Chirality and morphology are essential factors for protein function and interactions with other biomacromolecules. Extracellular matrix (ECM) proteins are also similar to other proteins in this sense; however, the complexity of the natural ECM makes it difficult to study these factors at the cellular level. The synthetic peptide nanomaterials harbor great promise in mimicking specific ECM molecules as model systems. In this work, we demonstrate that mechanosensory responses of stem cells are directly regulated by the chirality and morphology of ECM-mimetic peptide nanofibers with strictly controlled characteristics. Structural signals presented on l-amino acid containing cylindrical nanofibers (l-VV) favored the formation of integrin β1-based focal adhesion complexes, which increased the osteogenic potential of stem cells through the activation of nuclear YAP. On the other hand, twisted ribbon-like nanofibers (l-FF and d-FF) guided the cells into round shapes and decreased the formation of focal adhesion complexes, which resulted in the confinement of YAP proteins in the cytosol and a corresponding decrease in osteogenic potential. Interestingly, the d-form of twisted-ribbon like nanofibers (d-FF) increased the chondrogenic potential of stem cells more than their l-form (l-FF). Our results provide new insights into the importance and relevance of morphology and chirality of nanomaterials in their interactions with cells and reveal that precise control over the chemical and physical properties of nanostructures can affect stem cell fate even without the incorporation of specific epitopes.

  19. Supramolecular structures constructed from three novel rare earth ...

    Indian Academy of Sciences (India)

    Three complexes assembled into 3D frameworks based on C-H··· O, O-H··· O hydrogen bond linkages. Keywords. Rare earth metal complex; crystal structure; hydrogen bonds; 3D supramolecular structure. 1. Introduction. The self-assembly of supramolecules via non-covalent bonds is currently an interesting topic of ...

  20. Comparison of Cellulose Supramolecular Structures Between Nanocrystals of Different Origins

    Science.gov (United States)

    Umesh P. Agarwal; Richard S. Reiner; Christopher G. Hunt; Jeffery Catchmark; E. Johan Foster; Akira Isogai

    2015-01-01

    In this study, morphologies and supramolecular structures of CNCs from wood-pulp, cotton, bacteria, tunicate, and cladophora were investigated. TEM was used to study the morphological aspects of the nanocrystals whereas Raman spectroscopy provided information on the cellulose molecular structure and its organization within a CNC. Dimensional differences between the...

  1. Supramolecular structure of S-(+)-marmesin—a linear ...

    Indian Academy of Sciences (India)

    Unknown

    The crystal structure was determined from X-ray diffraction data using direct methods. The compound crys- tallizes into monoclinic space group P21 with unit cell ... Supramolecular structure; direct methods; hydrogen bond; π–π interaction; envelope; furano- coumarin. 1. Introduction. Furanocoumarins are found to possess ...

  2. Rational design of fiber forming supramolecular structures

    Science.gov (United States)

    Wang, Benjamin K; Kanahara, Satoko M

    2016-01-01

    Recent strides in the development of multifunctional synthetic biomimetic materials through the self-assembly of multi-domain peptides and proteins over the past decade have been realized. Such engineered systems have wide-ranging application in bioengineering and medicine. This review focuses on fundamental fiber forming α-helical coiled-coil peptides, peptide amphiphiles, and amyloid-based self-assembling peptides; followed by higher order collagen- and elastin-mimetic peptides with an emphasis on chemical / biological characterization and biomimicry. PMID:27022140

  3. Dielectric electroactive polymers comprising an ionic supramolecular structure

    DEFF Research Database (Denmark)

    2014-01-01

    The present invention relates to an ionic interpenetrating polymer network comprising at least one elastomer and an ionic supramolecular structure comprising the reaction product of at least two chemical compounds wherein each of said compounds has at least two functional groups and wherein said...

  4. Synthesis and crystal structure of a wheel-shaped supramolecular ...

    Indian Academy of Sciences (India)

    Synthesis and crystal structure of a wheel-shaped supramolecular coordination complex. DEEPAK GUPTA, PALANISAMY RAJAKANNU, BHASKARAN SHANKAR,. FIRASAT HUSSAIN and MALAICHAMY SATHIYENDIRAN. ∗. Department of Chemistry, University of Delhi, Delhi 110 007, India e-mail: mvdiran@yahoo.com; ...

  5. Self-assembly of boron-based supramolecular structures

    OpenAIRE

    Christinat, Nicolas

    2008-01-01

    This work describes the synthesis and characterization of boronic acid-based supramolecular structures. Macrocycles, dendritic structures, polymers, rotaxanes, and cages were assembled using four types of reversible reactions. The key point of the strategy is the parallel utilization of two –or more– of these reactions. Initially, aryl and alkylboronic acids were condensed with dihydroxypyridine ligands to give tetrameric or pentameric macrocycles, in which four or five boronate esters are co...

  6. Dielectric properties of supramolecular ionic structures obtained from multifunctional carboxylic acids and amines

    DEFF Research Database (Denmark)

    Gonzalez, Lidia; Yu, Liyun; Hvilsted, Søren

    2014-01-01

    networks, formed by mixing multifunctional carboxylic acids such as citric acid (CA), tricarballylic acid (TCAA), trimesic acid (TMA), ethylenediaminetetraacetic acid (EDTA) and diethylenetriaminepentaacetic acid (DETPA) with two di ff erent Je ff amine polyetheramines (designated as D400 and D2000......), are investigated. Here the relative dielectric permittivities of the supramolecular ionic structures formed with the multifunctional carboxylic acids were lower than those from the supramolecular ionic structures formed with the two carboxymethyl ether-terminated poly(ethylene glycol)s....

  7. Controlling molecular deposition and layer structure with supramolecular surface assemblies

    Science.gov (United States)

    Theobald, James A.; Oxtoby, Neil S.; Phillips, Michael A.; Champness, Neil R.; Beton, Peter H.

    2003-08-01

    Selective non-covalent interactions have been widely exploited in solution-based chemistry to direct the assembly of molecules into nanometre-sized functional structures such as capsules, switches and prototype machines. More recently, the concepts of supramolecular organization have also been applied to two-dimensional assemblies on surfaces stabilized by hydrogen bonding, dipolar coupling or metal co-ordination. Structures realized to date include isolated rows, clusters and extended networks, as well as more complex multi-component arrangements. Another approach to controlling surface structures uses adsorbed molecular monolayers to create preferential binding sites that accommodate individual target molecules. Here we combine these approaches, by using hydrogen bonding to guide the assembly of two types of molecules into a two-dimensional open honeycomb network that then controls and templates new surface phases formed by subsequently deposited fullerene molecules. We find that the open network acts as a two-dimensional array of large pores of sufficient capacity to accommodate several large guest molecules, with the network itself also serving as a template for the formation of a fullerene layer.

  8. Supramolecular Structure of the Mitochondrial Oxidative Phosphorylation System

    NARCIS (Netherlands)

    Boekema, Egbert J.; Braun, Hans-Peter

    2007-01-01

    The protein complexes of the mitochondrial oxidative phosphorylation system were recently reported to form supramolecular assemblies termed respiratory supercomplexes or respirasomes. These supercomplexes are considered to be of great functional importance. Here we review new insights into

  9. Influence of supramolecular structures in crystals on parallel stacking interactions between pyridine molecules.

    Science.gov (United States)

    Janjić, Goran V; Ninković, Dragan B; Zarić, Snezana D

    2013-08-01

    Parallel stacking interactions between pyridines in crystal structures and the influence of hydrogen bonding and supramolecular structures in crystals on the geometries of interactions were studied by analyzing data from the Cambridge Structural Database (CSD). In the CSD 66 contacts of pyridines have a parallel orientation of molecules and most of these pyridines simultaneously form hydrogen bonds (44 contacts). The geometries of stacked pyridines observed in crystal structures were compared with the geometries obtained by calculations and explained by supramolecular structures in crystals. The results show that the mean perpendicular distance (R) between pyridine rings with (3.48 Å) and without hydrogen bonds (3.62 Å) is larger than that calculated, because of the influence of supramolecular structures in crystals. The pyridines with hydrogen bonds show a pronounced preference for offsets of 1.25-1.75 Å, close to the position of the calculated minimum (1.80 Å). However, stacking interactions of pyridines without hydrogen bonds do not adopt values at or close to that of the calculated offset. This is because stacking interactions of pyridines without hydrogen bonds are less strong, and they are more susceptible to the influence of supramolecular structures in crystals. These results show that hydrogen bonding and supramolecular structures have an important influence on the geometries of stacked pyridines in crystals.

  10. PEG-bis phosphonic acid based ionic supramolecular structures

    DEFF Research Database (Denmark)

    Gonzalez, Lidia; Skov, Anne Ladegaard; Hvilsted, Søren

    2014-01-01

    . The resulting ionic assemblies are very comprehensively characterized by ATR-FTIR, proton, and carbon-13 NMR spectroscopy that unequivocally demonstrate the ionic network formation through ammonium phophonates. The resulting salt and ionic networks are additionally analyzed by differential scanning calorimetry...... and thermogravimetric analysis. The conclusion is that mixing the virgin components at room temperature spontaneously form either a salt or ionic supramolecular networks. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim....

  11. Structural Determinants of the Supramolecular Organization of G Protein-Coupled Receptors in Bilayers

    NARCIS (Netherlands)

    Periole, Xavier; Knepp, Adam M.; Sakmar, Thomas P.; Marrink, Siewert J.; Huber, Thomas

    2012-01-01

    The G protein-coupled receptor (GPCR) rhodopsin self-assembles into supramolecular structures in native bilayers, but the structural determinants of receptor oligomerization are not known. We carried out multiple self-assembly coarse-grained molecular dynamics (CGMD) simulations of model membranes

  12. Exploiting Biocatalysis in the Synthesis of Supramolecular Polymers

    Science.gov (United States)

    Roy, Sangita; Ulijn, Rein V.

    This chapter details the exploitation of biocatalysis in generating supramolecular polymers. This approach provides highly dynamic supramolecular structures, inspired by biological polymeric systems found in the intra- and extracellular space. The molecular design of the self-assembling precursors is discussed in terms of enzyme recognition, molecular switching mechanisms and non-covalent interactions that drive the supramolecular polymerisation process, with an emphasis on aromatic peptide amphiphiles. We discuss a number of unique features of these systems, including spatiotemporal control of nucleation and growth of supramolecular polymers and the possibility of kinetically controlling mechanical properties. Fully reversible systems that operate under thermodynamic control allow for defect correction and selection of the most stable structures from mixtures of monomers. Finally, a number of potential applications of enzymatic supramolecular polymerisations are discussed in the context of biomedicine and nanotechnology.

  13. The crystal structures of three pyrazine-2,5-dicarboxamides: three-dimensional supramolecular structures

    Directory of Open Access Journals (Sweden)

    Dilovan S. Cati

    2017-05-01

    Full Text Available The complete molecules of the title compounds, N2,N5-bis(pyridin-2-ylmethylpyrazine-2,5-dicarboxamide, C18H16N6O2 (I, 3,6-dimethyl-N2,N5-bis(pyridin-2-ylmethylpyrazine-2,5-dicarboxamide, C20H20N6O2 (II, and N2,N5-bis(pyridin-4-ylmethylpyrazine-2,5-dicarboxamide, C18H16N6O2 (III, are generated by inversion symmetry, with the pyrazine rings being located about centres of inversion. Each molecule has an extended conformation with the pyridine rings inclined to the pyrazine ring by 89.17 (7° in (I, 75.83 (8° in (II and by 82.71 (6° in (III. In the crystal of (I, molecules are linked by N—H...N hydrogen bonds, forming layers lying parallel to the bc plane. The layers are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. In the crystal of (II, molecules are also linked by N—H...N hydrogen bonds, forming layers lying parallel to the (10-1 plane. As in (I, the layers are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. In the crystal of (III, molecules are again linked by N—H...N hydrogen bonds, but here form corrugated sheets lying parallel to the bc plane. Within the sheets, neighbouring pyridine rings are linked by offset π–π interactions [intercentroid distance = 3.739 (1 Å]. The sheets are linked by C—H...O hydrogen bonds, forming a three-dimensional supramolecular structure. Compound (I crystallizes in the monoclinic space group P21/c. Another monoclinic polymorph, space group C2/c, has been reported on by Cockriel et al. [Inorg. Chem. Commun. (2008, 11, 1–4]. The molecular structures of the two polymorphs are compared.

  14. Neutronographic investigations of supramolecular structures on upgraded small-angle spectrometer YuMO

    International Nuclear Information System (INIS)

    Kuklin, A I; Rogachev, A V; Soloviov, D V; Ivankov, O I; Kovalev, Yu S; Kutuzov, S A; Soloviev, A G; Rulev, M I; Gordeliy, V I; Utrobin, P K

    2017-01-01

    Abstract.The work is a review of neutronographic investigations of supramolecular structures on upgraded small-angle spectrometer YuMO. Here, key parameters of small-angle spectrometers are considered. It is shown that two-detector system is the basis of YuMO upgrade. It allows to widen the dynamic q-range twice. In result, the available q-range is widened and dynamic q-range and data collection rate are doubled. The detailed description of YuMO spectrometer is given.The short review of experimental researches made on the spectrometer in the polymers field, biology, material science and physical chemistry is given. The current investigations also have a methodological aspect. It is shown that upgraded spectrometer provides advanced world level of research of supramolecular structures. (paper)

  15. Supramolecular structure of jackfruit seed starch and its relationship with digestibility and physicochemical properties.

    Science.gov (United States)

    Chen, Jin; Liang, Yi; Li, Xiaoxi; Chen, Ling; Xie, Fengwei

    2016-10-05

    The influence of supramolecular structure on the physicochemical properties and digestibility of jackfruit seed starch (JSS) were investigated. Compared with maize and cassava starches (MS and CS), JSS had smaller granules and higher amylose content (JSS: 24.90%; CS: 16.68%; and MS: 22.42%), which contributed to higher gelatinization temperature (To: 81.11°C) and setback viscosity (548.9mPas). From scanning electron microscopy, the digestion of JSS was observed mainly at the granule surface. Due to its higher crystallinity (JSS: 30.6%; CS: 30.3%; and MS: 27.4%) and more ordered semi-crystalline lamellae, JSS had a high RS content (74.26%) and melting enthalpy (19.61J/g). In other words, the supramolecular structure of JSS extensively determined its digestibility and resistance to heat and mechanical shear treatment. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Supramolecular structure of a perylene derivative in thin films deposited by physical vapor deposition

    International Nuclear Information System (INIS)

    Fernandes, Jose D.; Aoki, Pedro H.B.; Constantino, Carlos J.J.; Junior, Wagner D.M.; Teixeira, Silvio R.

    2014-01-01

    Full text: Thin films of a perylene derivative, the bis butylimido perylene (BuPTCD), were produced using thermal evaporation (PVD, physical vapor deposition). The main objective is to investigate the supramolecular structure of the BuPTCD in these PVD films, which implies to control the thickness and to determine the molecular organization, morphology at micro and nanometer scales and crystallinity. This supramolecular structure is a key factor in the optical and electrical properties of the film. The ultraviolet-visible absorption revealed an uniform growth of the PVD films. The optical and atomic force microscopy images showed a homogeneous surface of the film at micro and nanometer scales. A preferential orientation of the molecules in the PVD films was determined via infrared absorption. The X-ray diffraction showed that both powder and PVD film are in the crystalline form. (author)

  17. Rapid fabrication of hierarchically structured supramolecular nanocomposite thin films in one minute

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Ting; Kao, Joseph

    2016-11-08

    Functional nanocomposites containing nanoparticles of different chemical compositions may exhibit new properties to meet demands for advanced technology. It is imperative to simultaneously achieve hierarchical structural control and to develop rapid, scalable fabrication to minimize degradation of nanoparticle properties and for compatibility with nanomanufacturing. The assembly kinetics of supramolecular nanocomposite in thin films is governed by the energetic cost arising from defects, the chain mobility, and the activation energy for inter-domain diffusion. By optimizing only one parameter, the solvent fraction in the film, the assembly kinetics can be precisely tailored to produce hierarchically structured thin films of supramolecular nanocomposites in approximately one minute. Moreover, the strong wavelength dependent optical anisotropy in the nanocomposite highlights their potential applications for light manipulation and information transmission. The present invention opens a new avenue in designing manufacture-friendly continuous processing for the fabrication of functional nanocomposite thin films.

  18. Formation and thermodynamic stability of (polymer + porphyrin) supramolecular structures in aqueous solutions

    International Nuclear Information System (INIS)

    Costa, Viviana C.P. da; Hwang, Barrington J.; Eggen, Spencer E.; Wallace, Megan J.; Annunziata, Onofrio

    2014-01-01

    Highlights: • Thermodynamic stability of a (polymer + porphyrin) supramolecular structure was characterized. • Isothermal titration calorimetry provided two ways to determine reaction enthalpies. • Exothermic (polymer + porphyrin) binding competes with porphyrin self-association. • (Polymer + porphyrin) binding is entropically favored with respect to porphyrin self-association. • Spectral shifts show importance of porphyrin central hydrogens in polymer binding. - Abstract: Optical properties of porphyrins can be tuned through (polymer + porphyrin) (host + guest) binding in solution. This gives rise to the formation of supramolecular structures. In this paper, the formation, thermodynamic stability and spectroscopic properties of (polymer + porphyrin) supramolecular structures and their competition with porphyrin self-association were investigated by both isothermal titration calorimetry (ITC) and absorption spectroscopy. Specifically, reaction enthalpies and equilibrium constants were measured for meso-tetrakis(4-sulfonatophenyl) porphyrin (TPPS) self-association and TPPS binding to the polymer poly(vinylpyrrolidone) (PVP, 40 kg/mol) in aqueous solutions at pH 7 and three different temperatures (12, 25 and 37 °C). ITC, compared to spectroscopic techniques, provides two independent means to determine reaction enthalpies: direct measurements and Van’t Hoff plot. This was used as a criterion to assess that (1) self-association of TPPS is limited to the formation of dimers and (2) TPPS binds to PVP in its monomeric state only. The formation of TPPS dimers and (PVP + TPPS) supramolecular structures are both enthalpically driven. However, (polymer + porphyrin) binding was found to be entropically favored compared to dimerization. Furthermore, the reaction enthalpies of these two processes significantly depend on temperature. This behavior was attributed to hydrophobic interactions. Finally, the limiting absorption spectra of monomeric, dimeric and polymer

  19. Synthesis and crystal structure of a wheel-shaped supramolecular ...

    Indian Academy of Sciences (India)

    elucidation of the structure of the final product. The details of the structural parameters and the non-covalent ... tra for 1 and the bulk product were recorded on a. Bruker AMX-400 FT-NMR spectrometer. ICPMS was .... certed fashion to complete the ring structure (figure 2).6. Examples of metal-based trigonal-prisms were ...

  20. Hydrogen-Bonded Polymer-Porphyrin Assemblies in Water: Supramolecular Structures for Light Energy Conversion.

    Science.gov (United States)

    Kutz, Anne; Alex, Wiebke; Krieger, Anja; Gröhn, Franziska

    2017-09-01

    In this study, a new type of functional, self-assembled nanostructure formed from porphyrins and polyamidoamine dendrimers based on hydrogen bonding in an aqueous solution is presented. As the aggregates formed are promising candidates for solar-energy conversion, their photocatalytic activity is tested using the model reaction of methyl viologen reduction. The self-assembled structures show significantly increased activity as compared to unassociated porphyrins. Details of interaction forces driving the supramolecular structure formation and regulating catalytic efficiency are fundamentally discussed. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Irreversible transformation of the porphyrin supramolecular structures under a water vapor environment

    International Nuclear Information System (INIS)

    Ye Ming; Zhang Yi

    2011-01-01

    Supramolecular structures formed by H 4 TPPS 4 2- have been widely used for different applications. In this paper, the stability of H 4 TPPS 4 2- nanorods on mica substrate is investigated by atom force microscopy (AFM) observation.An irreversible transformation of H 4 TPPS 4 2- from nanorods (3.8±0.4 nm in height) to a lower film structure (1.9±0.4 nm in height) was found with the samples incubated at various relative humidities (RH). The transformation rate depends strongly on the RH and environment temperature. (authors)

  2. Differences in Cellulosic Supramolecular Structure of Compositionally Similar Rice Straw Affect Biomass Metabolism by Paddy Soil Microbiota.

    Directory of Open Access Journals (Sweden)

    Tatsuki Ogura

    Full Text Available Because they are strong and stable, lignocellulosic supramolecular structures in plant cell walls are resistant to decomposition. However, they can be degraded and recycled by soil microbiota. Little is known about the biomass degradation profiles of complex microbiota based on differences in cellulosic supramolecular structures without compositional variations. Here, we characterized and evaluated the cellulosic supramolecular structures and composition of rice straw biomass processed under different milling conditions. We used a range of techniques including solid- and solution-state nuclear magnetic resonance (NMR and Fourier transform infrared spectroscopy followed by thermodynamic and microbial degradability characterization using thermogravimetric analysis, solution-state NMR, and denaturing gradient gel electrophoresis. These measured data were further analyzed using an "ECOMICS" web-based toolkit. From the results, we found that physical pretreatment of rice straw alters the lignocellulosic supramolecular structure by cleaving significant molecular lignocellulose bonds. The transformation from crystalline to amorphous cellulose shifted the thermal degradation profiles to lower temperatures. In addition, pretreated rice straw samples developed different microbiota profiles with different metabolic dynamics during the biomass degradation process. This is the first report to comprehensively characterize the structure, composition, and thermal degradation and microbiota profiles using the ECOMICS toolkit. By revealing differences between lignocellulosic supramolecular structures of biomass processed under different milling conditions, our analysis revealed how the characteristic compositions of microbiota profiles develop in addition to their metabolic profiles and dynamics during biomass degradation.

  3. Supramolecular Nanostructures Based on Cyclodextrin and Poly(ethylene oxide: Syntheses, Structural Characterizations and Applications for Drug Delivery

    Directory of Open Access Journals (Sweden)

    Yue Zheng

    2016-05-01

    Full Text Available Cyclodextrins (CDs have been extensively studied as drug delivery carriers through host–guest interactions. CD-based poly(pseudorotaxanes, which are composed of one or more CD rings threading on the polymer chain with or without bulky groups (or stoppers, have attracted great interest in the development of supramolecular biomaterials. Poly(ethylene oxide (PEO is a water-soluble, biocompatible polymer. Depending on the molecular weight, PEO can be used as a plasticizer or as a toughening agent. Moreover, the hydrogels of PEO are also extensively studied because of their outstanding characteristics in biological drug delivery systems. These biomaterials based on CD and PEO for controlled drug delivery have received increasing attention in recent years. In this review, we summarize the recent progress in supramolecular architectures, focusing on poly(pseudorotaxanes, vesicles and supramolecular hydrogels based on CDs and PEO for drug delivery. Particular focus will be devoted to the structures and properties of supramolecular copolymers based on these materials as well as their use for the design and synthesis of supramolecular hydrogels. Moreover, the various applications of drug delivery techniques such as drug absorption, controlled release and drug targeting based CD/PEO supramolecular complexes, are also discussed.

  4. Self assembly of amphiphilic C60 fullerene derivatives into nanoscale supramolecular structures

    Directory of Open Access Journals (Sweden)

    Casscells S Ward

    2007-08-01

    Full Text Available Abstract Background The amphiphilic fullerene monomer (AF-1 consists of a "buckyball" cage to which a Newkome-like dendrimer unit and five lipophilic C12 chains positioned octahedrally to the dendrimer unit are attached. In this study, we report a novel fullerene-based liposome termed 'buckysome' that is water soluble and forms stable spherical nanometer sized vesicles. Cryogenic electron microscopy (Cryo-EM, transmission electron microscopy (TEM, and dynamic light scattering (DLS studies were used to characterize the different supra-molecular structures readily formed from the fullerene monomers under varying pH, aqueous solvents, and preparative conditions. Results Electron microscopy results indicate the formation of bilayer membranes with a width of ~6.5 nm, consistent with previously reported molecular dynamics simulations. Cryo-EM indicates the formation of large (400 nm diameter multilamellar, liposome-like vesicles and unilamellar vesicles in the size range of 50–150 nm diameter. In addition, complex networks of cylindrical, tube-like aggregates with varying lengths and packing densities were observed. Under controlled experimental conditions, high concentrations of spherical vesicles could be formed. In vitro results suggest that these supra-molecular structures impose little to no toxicity. Cytotoxicity of 10–200 μM buckysomes were assessed in various cell lines. Ongoing studies are aimed at understanding cellular internalization of these nanoparticle aggregates. Conclusion In this current study, we have designed a core platform based on a novel amphiphilic fullerene nanostructure, which readily assembles into supra-molecular structures. This delivery vector might provide promising features such as ease of preparation, long-term stability and controlled release.

  5. Supramolecular structure of S-(+)-marmesin-a linear ...

    Indian Academy of Sciences (India)

    The title compound, C14H14O4, a linear dihydrofuranocoumarin, was isolated from the bark of Aegle marmelos, a plant widely used in Ayurvedic system of medicine for the treatment of various ailments. The crystal structure was determined from X-ray diffraction data using direct methods. The compound crystallizes into ...

  6. Supramolecular Assembly of Calcium Metal - Organic Frameworks with Structural Transformation

    Czech Academy of Sciences Publication Activity Database

    Liang, P.-Ch.; Liu, H.-K.; Yeh, Ch.-T.; Lin, Ch.-H.; Zima, Vítězslav

    2011-01-01

    Roč. 11, č. 3 (2011), 699-708 ISSN 1528-7483 R&D Projects: GA ČR GA203/08/0208 Institutional research plan: CEZ:AV0Z40500505 Keywords : metal - organic frameworks * calcium * structure Subject RIV: CA - Inorganic Chemistry Impact factor: 4.720, year: 2011

  7. Role of supramolecular cellulose structures in enzymatic hydrolysis of plant cell walls

    DEFF Research Database (Denmark)

    Thygesen, Lisbeth Garbrecht; Hidayat, Budi Juliman; Johansen, Katja Salomon

    2011-01-01

    The study of biomass deconstruction by enzymatic hydrolysis has hitherto not focussed on the importance of supramolecular structures of cellulose. In lignocellulose fibres, regions with a different organisation of the microfibrils are present. These regions are called dislocations or slip planes...... mixture on hydrothermally treated wheat straw, it was found that the fibres were cut into segments corresponding to the sections between the dislocations initially present, as has previously been observed for acid hydrolysis of softwood pulps. The results indicate that dislocations are important during...

  8. Ordered supramolecular oligothiophene structures on passivated silicon surfaces

    Science.gov (United States)

    Liu, Renjie

    Carbon nanotubes (CNTs) with extraordinary properties and thus many potential applications have been predicted to be the best reinforcements for the next-generation multifunctional composite materials. Difficulties exist in transferring the most use of the unprecedented properties of individual CNTs to macroscopic forms of CNT assemblies. Therefore, this thesis focuses on two main goals: 1) discussing the issues that influence the performance of bulk CNT products, and 2) fabricating high-performance dry CNT films and composite films with an understanding of the fundamental structure-property relationship in these materials. Dry CNT films were fabricated by a winding process using CNT arrays with heights of 230 mum, 300 im and 360 mum. The structures of the as-produced films, as well as their mechanical and electrical properties were examined in order to find out the effects of different CNT lengths. It was found that the shorter CNTs synthesized by shorter time in the CVD furnace exhibited less structural defects and amorphous carbon, resulting in more compact packing and better nanotube alignment when made into dry films, thus, having better mechanical and electrical performance. A novel microcombing approach was developed to mitigate the CNT waviness and alignment in the dry films, and ultrahigh mechanical properties and exceptional electrical performance were obtained. This method utilized a pair of sharp surgical blades with microsized features at the blade edges as micro-combs to, for the first time, disentangle and straighten the wavy CNTs in the dry-drawn CNT sheet at single-layer level. The as-combed CNT sheet exhibited high level of nanotube alignment and straightness, reduced structural defects, and enhanced nanotube packing density. The dry CNT films produced by microcombing had a very high Young's modulus of 172 GPa, excellent tensile strength of 3.2 GPa, and unprecedented electrical conductivity of 1.8x10 5 S/m, which were records for CNT films or

  9. Early in-situ cellularization of a supramolecular vascular graft is modified by synthetic stromal cell-derived factor-1α derived peptides.

    Science.gov (United States)

    Muylaert, Dimitri E P; van Almen, Geert C; Talacua, Hanna; Fledderus, Joost O; Kluin, Jolanda; Hendrikse, Simone I S; van Dongen, Joost L J; Sijbesma, Eline; Bosman, Anton W; Mes, Tristan; Thakkar, Shraddha H; Smits, Anthal I P M; Bouten, Carlijn V C; Dankers, Patricia Y W; Verhaar, Marianne C

    2016-01-01

    In an in-situ approach towards tissue engineered cardiovascular replacement grafts, cell-free scaffolds are implanted that engage in endogenous tissue formation. Bioactive molecules can be incorporated into such grafts to facilitate cellular recruitment. Stromal cell derived factor 1α (SDF1α) is a powerful chemoattractant of lymphocytes, monocytes and progenitor cells and plays an important role in cellular signaling and tissue repair. Short SDF1α-peptides derived from its receptor-activating domain are capable of activating the SDF1α-specific receptor CXCR4. Here, we show that SDF1α-derived peptides can be chemically modified with a supramolecular four-fold hydrogen bonding ureido-pyrimidinone (UPy) moiety, that allows for the convenient incorporation of the UPy-SDF1α-derived peptides into a UPy-modified polymer scaffold. We hypothesized that a UPy-modified material bioactivated with these UPy-SDF1α-derived peptides can retain and stimulate circulating cells in an anti-inflammatory, pro-tissue formation signaling environment. First, the early recruitment of human peripheral blood mononuclear cells to the scaffolds was analyzed in vitro in a custom-made mesofluidic device applying physiological pulsatile fluid flow. Preferential adhesion of lymphocytes with reduced expression of inflammatory factors TNFα, MCP1 and lymphocyte activation marker CD25 was found in the bioactivated scaffolds, indicating a reduction in inflammatory signaling. As a proof of concept, in-vivo implantation of the bioactivated scaffolds as rat abdominal aorta interposition grafts showed increased cellularity by CD68+ cells after 7 days. These results indicate that a completely synthetic, cell-free biomaterial can attract and stimulate specific leukocyte populations through supramolecular incorporation of short bioactive SDF1α derived peptides. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Influence of the electric field on supramolecular structure and properties of amyloid-specific reagent Congo red.

    Science.gov (United States)

    Spólnik, Paweł; Król, Marcin; Stopa, Barbara; Konieczny, Leszek; Piekarska, Barbara; Rybarska, Janina; Zemanek, Grzegorz; Jagusiak, Anna; Piwowar, Piotr; Szoniec, Grzegorz; Roterman, Irena

    2011-10-01

    Among specific amyloid ligands, Congo red and its analogues are often considered potential therapeutic compounds. However, the results of the studies so far have not been univocal because the properties of this dye, derived mostly from its supramolecular nature, are still poorly understood. The supramolecular structure of Congo red, formed by π-π stacking of dye molecules, is susceptible to the influence of the electric field, which may significantly facilitate electron delocalization. Consequently, the electric field may generate altered physico-chemical properties of the dye. Enhanced electron delocalization, induced by the electric field, alters the total charge of Congo red, making the dye more acidic (negatively charged). This is a consequence of withdrawing electrons from polar substituents of aromatic rings-sulfonic and amino groups-thus increasing their tendency to dissociate protons. The electric field-induced charge alteration observed in electrophoresis depends on dye concentration. This concentration-dependent charge alteration effect disappears when the supramolecular structure disintegrates in DMSO. Dipoles formed from supramolecular fibrillar species in the electric field become ordered in the solution, introducing the modified arrangement to liquid crystalline phase. Experimental results and theoretical studies provide evidence confirming predictions that the supramolecular character of Congo red is the main reason for its specific properties and reactivity.

  11. Structural Characterization of Peptide Antibodies

    DEFF Research Database (Denmark)

    Chailyan, Anna; Marcatili, Paolo

    2015-01-01

    The role of proteins as very effective immunogens for the generation of antibodies is indisputable. Nevertheless, cases in which protein usage for antibody production is not feasible or convenient compelled the creation of a powerful alternative consisting of synthetic peptides. Synthetic peptides...... can be modified to obtain desired properties or conformation, tagged for purification, isotopically labeled for protein quantitation or conjugated to immunogens for antibody production. The antibodies that bind to these peptides represent an invaluable tool for biological research and discovery...

  12. Gain of local structure in an amphipathic peptide does not require a specific tertiary framework.

    Science.gov (United States)

    Roman, Ernesto A; Rosi, Pablo; González Lebrero, Mariano C; Wuilloud, Rodolfo; González Flecha, F Luis; Delfino, José M; Santos, Javier

    2010-10-01

    In this work, we studied how an amphipathic peptide of the surface of the globular protein thioredoxin, TRX94-108, acquires a native-like structure when it becomes involved in an apolar interaction network. We designed peptide variants where the tendency to form alpha-helical conformation is modulated by replacing each of the leucine amino acid residues by an alanine. The induction of structure caused by sodium dodecyl sulfate (SDS) binding was studied by capillary zone electrophoresis, circular dichroism, DOSY-NMR, and molecular dynamics simulations (MDS). In addition, we analyzed the strength of the interaction between a C18 RP-HPLC matrix and the peptides. The results presented here reveal that (a) critical elements in the sequence of the wild-type peptide stabilize a SDS/peptide supramolecular cluster; (b) the hydrophobic nature of the interaction between SDS molecules and the peptide constrains the ensemble of conformations; (c) nonspecific apolar surfaces are sufficient to stabilize peptide secondary structure. Remarkably, MDS shed light on a contact network formed by a limited number of SDS molecules that serves as a structural scaffold preserving the helical conformation of this module. This mechanism might prevail when a peptide with low helical propensity is involved in structure consolidation. We suggest that folding of peptides sharing this feature does not require a preformed tightly-packed protein core. Thus, the formation of specific tertiary interactions would be the consequence of peptide folding and not its cause. In this scenario, folding might be thought of as a process that includes unspecific rounds of structure stabilization guiding the protein to the native state. 2010 Wiley-Liss, Inc.

  13. From helical supramolecular arrays to gel-forming networks: lattice restructuring and aggregation control in peptide-based sulfamides to integrate new functional attributes.

    Science.gov (United States)

    Raghava, Saripalli V; Srivastava, Bhartendu K; Ramshad, Kalluruttimmal; Antharjanam, Sudhadevi; Varghese, Babu; Muraleedharan, Kannoth M

    2018-03-02

    While supramolecular organisation is central to both crystallization and gelation, the latter is more complex considering its dynamic nature and multifactorial dependence. This makes the rational design of gelators an extremely difficult task. In this report, the assembly preference of a group of peptide-based sulfamides was modulated by making them part of an acid-amine two-component system to drive the tendency from crystallization to gelation. Here, the peptide core directed the assembly while the long-chain amines, introduced through salt-bridges, promoted layering and anisotropic development of primary aggregates. This proved to be very successful, leading to gelation of a number of solvents. Apart from this, it was possible to fine-tune their aggregation using an amphiphilic polymer like F-127 as an additive to get honey-comb-like 3D molecular architectures. These gels also proved to be excellent matrices for entrapping silver nanoparticles with superior emissive properties.

  14. A systematic structural study of halogen bonding versus hydrogen bonding within competitive supramolecular systems

    Directory of Open Access Journals (Sweden)

    Christer B. Aakeröy

    2015-09-01

    Full Text Available As halogen bonds gain prevalence in supramolecular synthesis and materials chemistry, it has become necessary to examine more closely how such interactions compete with or complement hydrogen bonds whenever both are present within the same system. As hydrogen and halogen bonds have several fundamental features in common, it is often difficult to predict which will be the primary interaction in a supramolecular system, especially as they have comparable strength and geometric requirements. To address this challenge, a series of molecules containing both hydrogen- and halogen-bond donors were co-crystallized with various monotopic, ditopic symmetric and ditopic asymmetric acceptor molecules. The outcome of each reaction was examined using IR spectroscopy and, whenever possible, single-crystal X-ray diffraction. 24 crystal structures were obtained and subsequently analyzed, and the synthon preferences of the competing hydrogen- and halogen-bond donors were rationalized against a background of calculated molecular electrostatic potential values. It has been shown that readily accessible electrostatic potentials can offer useful practical guidelines for predicting the most likely primary synthons in these co-crystals as long as the potential differences are weighted appropriately.

  15. Luminescent lanthanide complexes with 4-acetamidobenzoate: Synthesis, supramolecular assembly via hydrogen bonds, crystal structures and photoluminescence

    International Nuclear Information System (INIS)

    Yin Xia; Fan Jun; Wang Zhihong; Zheng Shengrun; Tan Jingbo; Zhang Weiguang

    2011-01-01

    Four new luminescent complexes, namely, [Eu(aba) 2 (NO 3 )(C 2 H 5 OH) 2 ] (1), [Eu(aba) 3 (H 2 O) 2 ].0.5 (4, 4'-bpy).2H 2 O (2), [Eu 2 (aba) 4 (2, 2'-bpy) 2 (NO 3 ) 2 ].4H 2 O (3) and [Tb 2 (aba) 4 (phen) 2 (NO 3 ) 2 ].2C 2 H 5 OH (4) were obtained by treating Ln(NO 3 ) 3 .6H 2 O and 4-acetamidobenzoic acid (Haba) with different coligands (4, 4'-bpy=4, 4'-bipyridine, 2, 2'-bpy=2, 2'-bipyridine, and phen=1, 10-phenanthroline). They exhibit 1D chains (1-2) and dimeric structures (3-4), respectively. This structural variation is mainly attributed to the change of coligands and various coordination modes of aba molecules. Moreover, the coordination units are further connected via hydrogen bonds to form 2D even 3D supramolecular networks. These complexes show characteristic emissions in the visible region at room temperature. In addition, thermal behaviors of four complexes have been investigated under air atmosphere. The relationship between the structures and physical properties has been discussed. - Graphical abstract: Structure variation of four complexes is attributed to the change of coligands and various coordination modes of aba molecules. Moreover, they show characteristic emissions in the visible region. Highlights: → Auxiliary ligands have played the crucial roles on the structures of the resulting complexes. → Isolated structure units are further assembled via H-bonds to form supramolecular networks. → These solid-state complexes exhibit strong, characteristic emissions in the visible region.

  16. Combining supramolecular chemistry with biology.

    Science.gov (United States)

    Uhlenheuer, Dana A; Petkau, Katja; Brunsveld, Luc

    2010-08-01

    Supramolecular chemistry has primarily found its inspiration in biological molecules, such as proteins and lipids, and their interactions. Currently the supramolecular assembly of designed compounds can be controlled to great extent. This provides the opportunity to combine these synthetic supramolecular elements with biomolecules for the study of biological phenomena. This tutorial review focuses on the possibilities of the marriage of synthetic supramolecular architectures and biological systems. It highlights that synthetic supramolecular elements are for example ideal platforms for the recognition and modulation of proteins and cells. The unique features of synthetic supramolecular systems with control over size, shape, valency, and interaction strength allow the generation of structures fitting the demands to approach the biological problems at hand. Supramolecular chemistry has come full circle, studying the biology and its molecules which initially inspired its conception.

  17. Supramolecular Structure and Mechanical Characteristics of Ultrahigh-Molecular-Weight Polyethylene-Inorganic Nanoparticle Nanocomposites

    Energy Technology Data Exchange (ETDEWEB)

    Okhlopkova, T. A.; Borisova, R. V.; Nikiforov, L. A.; Spiridonov, A. M.; Okhlopkova, A. A.; Cho, Jin-Ho [North-Eastern Federal University, Yakutsk (Russian Federation); Jeong, Dae-Yong [Inha University, Incheon (Korea, Republic of)

    2016-04-15

    We investigated the mechanical properties and structure of polymeric nanocomposites (PNCs) with anultrahigh-molecular-weight polyethylene (UHMWPE) matrix and aluminum and silicon oxide and nitride nanoparticle (NP) fillers. Mixing with a paddle mixer or by joint mechanical activation in a planetary mill was used for the PNC preparation. Joint mechanical activation afforded PNCs with better mechanical properties than paddle mixing. Scanning electron microscopy suggested that the poorer mechanical properties can be attributed to the disordered regions and imperfect spherulites in the PNC supramolecular structure arising from paddle mixing. The better mechanical properties observed with joint mechanical activation may derive from the uniform NP distribution in the polymer matrix and absence of disordered regions.

  18. Synthesis, crystal and supramolecular structure of rac-N-acetyl-2- thiohydantoin-asparagine

    Directory of Open Access Journals (Sweden)

    Gerzon E. Delgado

    2014-05-01

    Full Text Available The title compound, C7H9N3O3S, also known as rac-N-acetyl-5-propionamide-2-thioxo-imidazolidin-4-one, crystallize in the monoclinic system with space group P21/n (Nº14, Z=4, and unit cell parameters a= 9.338 (7 Å, b= 7.545 (5 Å, c= 13.212 (10 Å, E= 97.10 (2°, V= 932.8 (12 Å3. The acetyl group and the mean plane of the ureido group form an angle of 81.0 (2°. In the supramolecular structure, the molecules are joined by N--H···O hydrogen bonds into cyclic structures with graph-set R2 2(14 and R2 2(16, forming a three-dimensional network.

  19. Supramolecular structure of a perylene derivative in thin films made by vacuum thermal evaporation

    International Nuclear Information System (INIS)

    Fernandes, Jose Diego

    2015-01-01

    The supramolecular arrangement of organic thin films is a factor that influences both optical and electrical properties of these films and, consequently, the technological applications involving organic electronics. In this dissertation, thin films of a perylene derivative (bis butylimido perylene, acronym BuPTCD) were produced by physical vapor deposition (PVD) using vacuum thermal evaporation. The aim of this work was to investigate the supramolecular arrangement of BuPTCD films, which implies to control the thickness at nanometer scale and to determine the molecular organization, the morphology (at nano and micrometer scales) and the crystallinity, besides the stability of this arrangement as a function of the temperature. Optical properties (such as absorption and emission) and electrical properties (such as conductivity and photoconductivity) were also determined. The UV-Vis absorption spectra revealed a controlled growth (uniform) of the BuPTCD films. Atomic force and optical microscopy images showed a homogeneous surface of the film at nano and micrometer scales, respectively. The X-ray diffraction showed that the BuPTCD powder and PVD film have different crystalline structures, with the BuPTCD molecules head-on oriented in the PVD films, supported on the substrate surface by the side group (FTIR). This structure favors the light emission (photoluminescence) by the formation of excimers. The thermal treatment (200°C for 10 min) does not affect the molecular organization of the PVD films, showing a thermal stability of the BuPTCD supramolecular arrangement under these circumstances. The electrical measurements (DC) showed a linear increase of the current as a function of the tension, which is characteristic of ohmic behavior. Also, the films exhibited an increase of current by 2 orders of magnitude when exposed to light (photoconductive properties). Finally, BuPTCD films were exposed to vapor of trifluoroacetic acid (TFA) to verify the sensitivity of the Bu

  20. Mirror image supramolecular helical tapes formed by the enantiomeric-depsipeptide derivatives of the amyloidogenic peptide amylin(20-29)

    NARCIS (Netherlands)

    Elgersma, Ronald C.; Mulder, Gwenn E.; Posthuma, George; Rijkers, Dirk T. S.; Liskamp, Rob M. J.

    2008-01-01

    Factors that determine the chirality of supramolecular helical tapes formed by a backbone-modified amylin(20-29) depsipeptide and inverso-depsipeptide, were studied by Fourier transform infrared spectroscopy, circular dichroism and transmission electron microscopy. Although P-sheet propensity was

  1. The supramolecular structure of liquid water and quantum coherent processes in biology

    International Nuclear Information System (INIS)

    Ninno, A De; Castellano, A Congiu; Giudice, E Del

    2013-01-01

    Vibrational spectroscopy provides a powerful tool to understand the molecular structures. When applied to the liquid water, this technique reveals so many details which can also shed a light on the supramolecular arrangement of the most ubiquitous of the substances. In particular, the two fluid model of water, proposed several decades ago, founds experimental evidence. Moreover, some fundamental parameters calculated in the realm of the theory of Quantum ElectroDynamics applied to liquid water can be actually measured showing an excellent agreement with the theory. This allows to add a dynamical origin to the mixed cluster model of water well known by the biologists for fifty years and opens the way to the dawn of a real quantum biology.

  2. Dragging Human Mesenchymal Stem Cells with the Aid of Supramolecular Assemblies of Single-Walled Carbon Nanotubes, Molecular Magnets, and Peptides in a Magnetic Field

    Directory of Open Access Journals (Sweden)

    Ana Cláudia C. de Paula

    2015-01-01

    Full Text Available Human adipose-derived stem cells (hASCs are an attractive cell source for therapeutic applicability in diverse fields for the repair and regeneration of damaged or malfunctioning tissues and organs. There is a growing number of cell therapies using stem cells due to their characteristics of modulation of immune system and reduction of acute rejection. So a challenge in stem cells therapy is the delivery of cells to the organ of interest, a specific site. The aim of this paper was to investigate the effects of a supramolecular assembly composed of single-walled carbon nanotubes (SWCNT, molecular magnets (lawsone-Co-phenanthroline, and a synthetic peptide (FWYANHYWFHNAFWYANHYWFHNA in the hASCs cultures. The hASCs were isolated, characterized, expanded, and cultured with the SWCNT supramolecular assembly (SWCNT-MA. The assembly developed did not impair the cell characteristics, viability, or proliferation. During growth, the cells were strongly attached to the assembly and they could be dragged by an applied magnetic field of less than 0.3 T. These assemblies were narrower than their related allotropic forms, that is, multiwalled carbon nanotubes, and they could therefore be used to guide cells through thin blood capillaries within the human body. This strategy seems to be useful as noninvasive and nontoxic stem cells delivery/guidance and tracking during cell therapy.

  3. Dragging Human Mesenchymal Stem Cells with the Aid of Supramolecular Assemblies of Single-Walled Carbon Nanotubes, Molecular Magnets, and Peptides in a Magnetic Field

    Science.gov (United States)

    de Paula, Ana Cláudia C.; Sáfar, Gustavo A. M.; Góes, Alfredo M.; Bemquerer, Marcelo P.; Ribeiro, Marcos A.; Stumpf, Humberto O.

    2015-01-01

    Human adipose-derived stem cells (hASCs) are an attractive cell source for therapeutic applicability in diverse fields for the repair and regeneration of damaged or malfunctioning tissues and organs. There is a growing number of cell therapies using stem cells due to their characteristics of modulation of immune system and reduction of acute rejection. So a challenge in stem cells therapy is the delivery of cells to the organ of interest, a specific site. The aim of this paper was to investigate the effects of a supramolecular assembly composed of single-walled carbon nanotubes (SWCNT), molecular magnets (lawsone-Co-phenanthroline), and a synthetic peptide (FWYANHYWFHNAFWYANHYWFHNA) in the hASCs cultures. The hASCs were isolated, characterized, expanded, and cultured with the SWCNT supramolecular assembly (SWCNT-MA). The assembly developed did not impair the cell characteristics, viability, or proliferation. During growth, the cells were strongly attached to the assembly and they could be dragged by an applied magnetic field of less than 0.3 T. These assemblies were narrower than their related allotropic forms, that is, multiwalled carbon nanotubes, and they could therefore be used to guide cells through thin blood capillaries within the human body. This strategy seems to be useful as noninvasive and nontoxic stem cells delivery/guidance and tracking during cell therapy. PMID:25688350

  4. Rigidity of poly-L-glutamic acid scaffolds: Influence of secondary and supramolecular structure

    Energy Technology Data Exchange (ETDEWEB)

    Perticaroli, Stefania [ORNL; Ehlers, Georg [ORNL; Feygenson, Mikhail [ORNL; Sokolov, Alexei P [ORNL

    2015-01-01

    Poly-L-glutamic acid (PGA) is a widely used biomaterial, with applications ranging from drug delivery and biological glues to food products and as a tissue engineering scaffold. A biodegradable material with flexible conjugation functional groups, tunable secondary structure, and mechanical properties, PGA has potential as a tunable matrix material in mechanobiology. Some recent studies in proteins connecting dynamics, nanometer length scale rigidity, and secondary structure suggest a new point of view from which to analyze and develop this promising material. Our paper characterizes the structure, topology, and rigidity properties of PGA prepared with different molecular weights and secondary structures through various techniques including scanning electron microscopy, FTIR, light, and neutron scattering spectroscopy. On the length scale of a few nanometers, rigidity is determined by hydrogen bonding interactions in the presence of neutral species and by electrostatic interactions when the polypeptide is negatively charged. Finally, when probed over hundreds of nanometers, the rigidity of these materials is modified by long range intermolecular interactions that are introduced by the supramolecular structure.

  5. Controllable supramolecular structures and luminescent properties of unique trimeric Zn(II) 8-hydroxyquinolinates tuned by functional substituents.

    Science.gov (United States)

    Yuan, Guozan; Huo, Yanping; Nie, Xiaoli; Jiang, Hong; Liu, Bin; Fang, Xiaoming; Zhao, Fenghua

    2013-02-28

    We reported here the self-assembly of two supramolecular structures based on similar trimeric Zn(II) units that are built from novel 2-substituted 8-hydroxyquinoline ligands and coordination Zn(II) ions. The aggregation behavior of zinc salt and ligand in solution was investigated by a variety of techniques, including (1)H NMR, UV-vis and photoluminescence (PL). In the solid state, the supramolecular structures can be controlled by the substituted groups (-NO(2) and -F) via intermolecular interaction, such as π···π stacking, C-H···O, and C-F···F-C interactions. As a result, the two trimeric Zn(II) complexes exhibit disparate photophysical properties. The present research holds great promise in the development of novel multinuclear Zn(II) materials, and may contribute to the understanding of structure-property relationships.

  6. Luminescent lanthanide complexes with 4-acetamidobenzoate: Synthesis, supramolecular assembly via hydrogen bonds, crystal structures and photoluminescence

    Science.gov (United States)

    Yin, Xia; Fan, Jun; Wang, Zhi Hong; Zheng, Sheng Run; Tan, Jing Bo; Zhang, Wei Guang

    2011-07-01

    Four new luminescent complexes, namely, [Eu(aba) 2(NO 3)(C 2H 5OH) 2] ( 1), [Eu(aba) 3(H 2O) 2]·0.5 (4, 4'-bpy)·2H 2O ( 2), [Eu 2(aba) 4(2, 2'-bpy) 2(NO 3) 2]·4H 2O ( 3) and [Tb 2(aba) 4(phen) 2(NO 3) 2]·2C 2H 5OH ( 4) were obtained by treating Ln(NO 3) 3·6H 2O and 4-acetamidobenzoic acid (Haba) with different coligands (4, 4'-bpy=4, 4'-bipyridine, 2, 2'-bpy=2, 2'-bipyridine, and phen=1, 10-phenanthroline). They exhibit 1D chains ( 1- 2) and dimeric structures ( 3- 4), respectively. This structural variation is mainly attributed to the change of coligands and various coordination modes of aba molecules. Moreover, the coordination units are further connected via hydrogen bonds to form 2D even 3D supramolecular networks. These complexes show characteristic emissions in the visible region at room temperature. In addition, thermal behaviors of four complexes have been investigated under air atmosphere. The relationship between the structures and physical properties has been discussed.

  7. Structural Consequences of Anionic Host-Cationic Guest Interactions in a Supramolecular Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Pluth, Michael D.; Johnson, Darren W.; Szigethy, Geza; Davis, Anna V.; Teat, Simon J.; Oliver, Allen G.; Bergman, Robert G.; Raymond, Kenneth N.

    2008-07-09

    The molecular structure of the self-assembled supramolecular assembly [M{sub 4}L{sub 6}]{sup 12-} has been explored with different metals (M = Ga{sup III}, Fe{sup III}, Ti{sup IV}) and different encapsulated guests (NEt{sub 4}{sup +}, BnNMe{sub 3}{sup +}, Cp{sub 2}Co{sup +}, Cp*{sub 2}Co{sup +}) by X-ray crystallography. While the identity of the metal ions at the vertices of the M{sub 4}L{sub 6} structure is found to have little effect on the assembly structure, encapsulated guests significantly distort the size and shape of the interior cavity of the assembly. Cations on the exterior of the assembly are found to interact with the assembly through either {pi}-{pi}, cation-{pi}, or CH-{pi} interactions. In some cases, the exterior guests interact with only one assembly, but cations with the ability to form multiple {pi}-{pi} interactions are able to interact with adjacent assemblies in the crystal lattice. The solvent accessible cavity of the assembly is modeled using the rolling probe method and found to range from 253-434 {angstrom}{sup 3}, depending on the encapsulated guest. Based on the volume of the guest and the volume of the cavity, the packing coefficient for each host-guest complex is found to range from 0.47-0.67.

  8. Hydrogen bonded 1D-3D supramolecular structures from Benzylamine and organic acidic components

    Science.gov (United States)

    Gao, Xingjun; Li, XiaoLiang; Jin, Shouwen; Hu, Kaikai; Guo, Jianzhong; Guo, Ming; Xu, Weiqiang; Wang, Daqi

    2018-03-01

    Cocrystallization of the commonly available organic amine, benzylamine, with a series of organic acids afforded a total of seven organic salts with the compositions: (benzylamine)2: (p-nitrophenol)2: (H2O) (1) [(HL)2+⋯(npl-)2⋯(H2O), npl- = p-nitrophenolate], (benzylamine): (4-tert-butylbenzoic acid) (2) [(HL+)⋯(tba-), tba- = 4-tert-butylbenzoate], (benzylamine): (3,4-dichlorobenzoic acid) (3) [(HL+)⋯dcba-), dcba- = 3,4-dichlorobenzoate], (benzylamine): (2,5-dihydroxybenzoic acid) (4) [(HL+)⋯(dhba-), dhba- = 2,5-dihydroxybenzoate], (benzylamine): (2-bromo-but-2-enedioic acid) (5) [(HL+)⋯(Hbba-), Hbba- = 2-bromo-hydrogenbut-2-enedioate], (benzylamine): (2,6-pyridinedicarboxylic acid) (6) [(HL+)⋯(Hpdc-), Hpdc- = 2,6-pyridine hydrogendicarboxylate], and (benzylamine)2: (3-nitrophthalic acid): 2(H2O) (7) [(HL+)2⋯(npa2-)⋯(H2O)2, npa2- = 3-nitrophthalate]. The seven salts have been characterised by X-ray diffraction analysis, IR, and elemental analysis, and the melting points of all the salts were also reported. And their structural and supramolecular aspects are fully analyzed. The results reveal that among the seven investigated crystals the NH2 in the benzylamine are protonated when the organic acids are deprotonated, and the crystal packing is interpreted in terms of the strong charge-assisted Nsbnd H⋯O hydrogen bond between the NH3+ and deprotonated acidic groups. Except the Nsbnd H⋯O hydrogen bond, the Osbnd H⋯O hydrogen bonds (charge assisted or neutral) were also found at the salts 1, 4, 5, 6, and 7. Further analysis of the crystal packing of the salts indicated that a different family of additional CHsbnd O/CH2sbnd O, CH-π/CH2-π, Cπ-Cπ, Osbnd O, O-Cπ, O-π, and Cl-π associations also contribute to the stabilization and expansion of the total high-dimensional framework structures. For the coexistence of the various weak nonbonding interactions, these structures adopted a variety of

  9. Solid structures of the stepwise self-assembled copillar[5]arene-based supramolecular polymers

    Energy Technology Data Exchange (ETDEWEB)

    Park, Yeon Sil; Hwang, Seong Min; Shin, Jae Yeon; Paek, Kyung Soo [Dept. of Chemistry, Soongsil University, Seoul (Korea, Republic of)

    2016-10-15

    Development of supramolecular polymer has attracted much interest because of their interesting properties such as stimuli-responsiveness, recycling, self-healing and degradability, and their consequential applications. The essential feature of this class of polymers is the self-assembly of discrete monomeric subunits via non-covalent interactions or dynamic covalent bonds. Among the many monomeric subunits, pillar[n]arenes have been ideal building blocks for the fabrication of polymeric supramolecules because of their intrinsic characteristics. The ring-shaped morphologies in supramolecular polymer P are probably due to the tendency of the end-to-end connection in the solid state of long flexible supramolecular chains. The size increase of nano-rings as the stepwise addition increases might be due to the fact that the linear supramolecular polymer P in solution seems to be maintained until the nano-ring formation by solidification.

  10. The crystal structures of three pyrazine-2,5-dicarb-oxamides: three-dimensional supra-molecular structures.

    Science.gov (United States)

    Cati, Dilovan S; Stoeckli-Evans, Helen

    2017-05-01

    The complete mol-ecules of the title compounds, N 2 , N 5 -bis-(pyridin-2-ylmeth-yl)pyrazine-2,5-dicarboxamide, C 18 H 16 N 6 O 2 (I), 3,6-dimethyl- N 2 , N 5 -bis-(pyridin-2-yl-meth-yl)pyrazine-2,5-dicarboxamide, C 20 H 20 N 6 O 2 (II), and N 2 , N 5 -bis-(pyridin-4-ylmeth-yl)pyrazine-2,5-dicarboxamide, C 18 H 16 N 6 O 2 (III), are generated by inversion symmetry, with the pyrazine rings being located about centres of inversion. Each mol-ecule has an extended conformation with the pyridine rings inclined to the pyrazine ring by 89.17 (7)° in (I), 75.83 (8)° in (II) and by 82.71 (6)° in (III). In the crystal of (I), mol-ecules are linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the bc plane. The layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (II), mol-ecules are also linked by N-H⋯N hydrogen bonds, forming layers lying parallel to the (10-1) plane. As in (I), the layers are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. In the crystal of (III), mol-ecules are again linked by N-H⋯N hydrogen bonds, but here form corrugated sheets lying parallel to the bc plane. Within the sheets, neighbouring pyridine rings are linked by offset π-π inter-actions [inter-centroid distance = 3.739 (1) Å]. The sheets are linked by C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular structure. Compound (I) crystallizes in the monoclinic space group P 2 1 / c . Another monoclinic polymorph, space group C 2/ c , has been reported on by Cockriel et al. [ Inorg. Chem. Commun. (2008), 11 , 1-4]. The mol-ecular structures of the two polymorphs are compared.

  11. Structural and morphological changes in supramolecular-structured polymer electrolyte membrane fuel cell on addition of phosphoric acid

    Science.gov (United States)

    Hendrana, S.; Pryliana, R. F.; Natanael, C. L.; Rahayu, I.

    2018-03-01

    Phosphoric acid is one agents used in membrane fuel cell to modify ionic conductivity. Therefore, its distribution in membrane is a key parameter to gain expected conductivity. Efforts have been made to distribute phosphoric acid in a supramolecular-structured membrane prepared with a matrix. To achieve even distribution across bulk of the membrane, the inclusion of the polyacid is carried out under pressurized chamber. Image of scanning electron microscopy (SEM) shows better phosphoric acid distribution for one prepared in pressurized state. It also leads in better performing in ionic conductivity. Moreover, data from differential scanning calorimetry (DSC) indicate that the addition of phosphoric acid is prominent in the change of membrane structure, while morphological changes are captured in SEM images.

  12. A new supramolecular chromium(III) complex: Synthesis, structural determination, optical study, magnetic and antibacterial activity

    Science.gov (United States)

    Dridi, Rihab; Dhieb, Cyrine; Cherni, Saoussen Namouchi; Boudjada, Nassira Chniba; Sadfi Zouaoui, Najla; Zid, Mohamed Faouzi

    2018-01-01

    A new chromium (III) complex 1,5-Naphthyridine Trans-diaquadioxalatochromate (III) dihydrate, had been synthesized by self-assembly of chromium (III) nitrate with oxalic acid and 1,5-Naphthyridine. The complex was characterized by X-ray diffraction, Fourier Transform Infrared spectroscopy, thermogravimetric analysis and UV-Visible spectroscopy. The crystal morphology was carried out using Bravais-Friedel-Donnay-Harker (BFDH) model. Single crystal X-Ray structure determination revealed that the complex posses two crystallographically independent Cr(III) centers. Each Cr(III) has a distorted octahedron geometry involving two axial O atoms from two water molecules and four equatorial O atoms from two oxalate dianions forming trans-[Cr(C2O4)2(H2O)2]- complex anions. The charge compensation is accomplished by the incorporation of 1,5-Naphthyridine cations. Connection between these entities is ensured by means of strong hydrogen bonds giving rise to 3D supramolecular architecture. Hirshfeld surface analysis and the related 2D fingerprint plots were used for decoding plausible intermolecular interactions in the crystal packing. The magnetic properties of the complex had been investigated and discussed in the context of its structure. The antimicrobial activity was evaluated by disc diffusion method highlighting an antagonistic effect of the synthesized complex against Gram-positive and Gram-negative species.

  13. Structural pattern matching of nonribosomal peptides

    Directory of Open Access Journals (Sweden)

    Leclère Valérie

    2009-03-01

    Full Text Available Abstract Background Nonribosomal peptides (NRPs, bioactive secondary metabolites produced by many microorganisms, show a broad range of important biological activities (e.g. antibiotics, immunosuppressants, antitumor agents. NRPs are mainly composed of amino acids but their primary structure is not always linear and can contain cycles or branchings. Furthermore, there are several hundred different monomers that can be incorporated into NRPs. The NORINE database, the first resource entirely dedicated to NRPs, currently stores more than 700 NRPs annotated with their monomeric peptide structure encoded by undirected labeled graphs. This opens a way to a systematic analysis of structural patterns occurring in NRPs. Such studies can investigate the functional role of some monomeric chains, or analyse NRPs that have been computationally predicted from the synthetase protein sequence. A basic operation in such analyses is the search for a given structural pattern in the database. Results We developed an efficient method that allows for a quick search for a structural pattern in the NORINE database. The method identifies all peptides containing a pattern substructure of a given size. This amounts to solving a variant of the maximum common subgraph problem on pattern and peptide graphs, which is done by computing cliques in an appropriate compatibility graph. Conclusion The method has been incorporated into the NORINE database, available at http://bioinfo.lifl.fr/norine. Less than one second is needed to search for a pattern in the entire database.

  14. Structure-directing star-shaped block copolymers: supramolecular vesicles for the delivery of anticancer drugs.

    Science.gov (United States)

    Yang, Chuan; Liu, Shao Qiong; Venkataraman, Shrinivas; Gao, Shu Jun; Ke, Xiyu; Chia, Xin Tian; Hedrick, James L; Yang, Yi Yan

    2015-06-28

    Amphiphilic polycarbonate/PEG copolymer with a star-like architecture was designed to facilitate a unique supramolecular transformation of micelles to vesicles in aqueous solution for the efficient delivery of anticancer drugs. The star-shaped amphipilic block copolymer was synthesized by initiating the ring-opening polymerization of trimethylene carbonate (TMC) from methyl cholate through a combination of metal-free organo-catalytic living ring-opening polymerization and post-polymerization chain-end derivatization strategies. Subsequently, the self-assembly of the star-like polymer in aqueous solution into nanosized vesicles for anti-cancer drug delivery was studied. DOX was physically encapsulated into vesicles by dialysis and drug loading level was significant (22.5% in weight) for DOX. Importantly, DOX-loaded nanoparticles self-assembled from the star-like copolymer exhibited greater kinetic stability and higher DOX loading capacity than micelles prepared from cholesterol-initiated diblock analogue. The advantageous disparity is believed to be due to the transformation of micelles (diblock copolymer) to vesicles (star-like block copolymer) that possess greater core space for drug loading as well as the ability of such supramolecular structures to encapsulate DOX. DOX-loaded vesicles effectively inhibited the proliferation of 4T1, MDA-MB-231 and BT-474 cells, with IC50 values of 10, 1.5 and 1.0mg/L, respectively. DOX-loaded vesicles injected into 4T1 tumor-bearing mice exhibited enhanced accumulation in tumor tissue due to the enhanced permeation and retention (EPR) effect. Importantly, DOX-loaded vesicles demonstrated greater tumor growth inhibition than free DOX without causing significant body weight loss or cardiotoxicity. The unique ability of the star-like copolymer emanating from the methyl cholate core provided the requisite modification in the block copolymer interfacial curvature to generate vesicles of high loading capacity for DOX with significant

  15. A new zinc(II supramolecular square: Synthesis, crystal structure, thermal behavior and luminescence

    Directory of Open Access Journals (Sweden)

    Wang Xiu-Yan

    2015-01-01

    Full Text Available A new square-shaped Zn(II complex, namely, [Zn4(L4(phen4]•6H2O (1 (L = 2-hydroxynicotinate and phen = 1,10- phenanthroline, has been synthesized under hydrothermal condition. The crystal of 1 belongs to triclinic, space group P -1 with a = 10.773(2 Å, b = 12.641(3 Å, c = 13.573(3 Å, α = 107.44(3º, β = 102.66(3º, γ = 93.89(3°, C72H56N12O18Zn4, Mr = 1638.77, V = 1702.8(6 Å3 , Z = 1, Dc = 1.598 g/cm3 , S = 1.045, μ(MoKα = 1.475 mm-1 , F(000 = 836, R = 0.0472 and wR = 0.0919. In 1, four L ligands bridge four Zn(II atoms to form a square-shaped structure, where four phen ligands are respectively located on four corners of the square. The π-π stacking interactions extend the adjacent squares into a 1D supramolecular chain. The thermal behavior of 1 has been characterized. Moreover, its solid state luminescence property has been studied at room temperature.

  16. Supramolecular chemistry and crystal engineering

    Indian Academy of Sciences (India)

    Advances in supramolecular chemistry and crystal engineering reported from India within the last decade are highlighted in the categories of new intermolecular interactions, designed supramolecular architectures, network structures, multi-component host–guest systems, cocrys- tals, and polymorphs. Understanding ...

  17. Supramolecular Chemistry

    Indian Academy of Sciences (India)

    antigen interactions. working in different areas such as chemical science, biological science, physical science, material science and so on. On the whole, supramolecular chemistry focuses on two over- lapping areas, 'supramolecules' and ...

  18. Correspondence between molecular functionality and crystal structures. Supramolecular chemistry of a family of homologated aminophenols.

    Science.gov (United States)

    Vangala, Venu R; Bhogala, Balakrishna R; Dey, Archan; Desiraju, Gautam R; Broder, Charlotte K; Smith, Philip S; Mondal, Raju; Howard, Judith A K; Wilson, Chick C

    2003-11-26

    The crystal structures and packing features of a family of 13 aminophenols, or supraminols, are analyzed and correlated. These compounds are divided into three groups: (a) compounds 1-5 with methylene spacers of the general type HO-C6H4-(CH2)n-C6H4-NH2 (n = 1 to 5) and both OH and NH2 in a para position; (b) compounds 1a, 2a, 2b, 2c, and 3a in which one or more of the methylene linkers in 1 to 3 are exchanged with an S-atom; and (c) compounds 2d, 1b, and 6a prepared with considerations of crystal engineering and where the crystal structures may be anticipated on the basis of structures 1-5,1a, 2a, 2b, 2c, and 3a. These 13 aminols can be described in terms of three major supramolecular synthons based on hydrogen bonding between OH and NH2 groups: the tetrameric loop or square motif, the infinite N(H)O chain, and the beta-As sheet. These three synthons are not completely independent of each other but interrelate, with the structures tending toward the more stable beta-As sheet in some cases. Compounds 1-5 show an alternation in melting points, and compounds with n = even exhibit systematically higher melting points compared to those with n = odd. The alternating melting points are reflected in, and explained by, the alternation in the crystal structures. The n = odd structures tend toward the beta-As sheet as n increases and can be considered as a variable series whereas for n = even, the beta-As sheet is invariably formed constituting a fixed series. Substitution of a methylene group by an isosteric S-atom may causes a change in the crystal structure. These observations are rationalized in terms of geometrical and chemical effects of the functional groups. This study shows that even for compounds with complex crystal structures the packing may be reasonably anticipated provided a sufficient number of examples are available.

  19. Self-assembly of a highly organized, hexameric supramolecular architecture: formation, structure and properties.

    Science.gov (United States)

    Schaeffer, Gaël; Fuhr, Olaf; Fenske, Dieter; Lehn, Jean-Marie

    2014-01-03

    Two derivatives, (3)L and (9)L, of a ditopic, multiply hydrogen-bonding molecule, known for more than a decade, have been found, in the solid state as well as in solvents of low polarity at room temperature, to exist not as monomers, but to undergo a remarkable self-assembly into a complex supramolecular species. The solid-state molecular structure of (3)L, determined by single-crystal X-ray crystallography, revealed that it forms a highly organized hexameric entity (3)L6 with a capsular shape, resulting from the interlocking of two sets of three monomolecular components, linked through hydrogen-bonding interactions. The complicated (1)H NMR spectra observed in o-dichlorobenzene (o-DCB) for (3)L and (9)L are consistent with the presence of a hexamer of D3 symmetry in both cases. DOSY measurements confirm the hexameric constitution in solution. In contrast, in a hydrogen-bond-disrupting solvent, such as DMSO, the (1)H NMR spectra are very simple and consistent with the presence of isolated monomers only. Extensive temperature-dependent (1)H NMR studies in o-DCB showed that the L6 species dissociated progressively into the monomeric unit on increasing th temperature, up to complete dissociation at about 90 °C. The coexistence of the hexamer and the monomer indicated that exchange was slow on the NMR timescale. Remarkably, no species other than hexamer and monomer were detected in the equilibrating mixtures. The relative amounts of each entity showed a reversible sigmoidal variation with temperature, indicating that the assembly proceeded with positive cooperativity. A full thermodynamic analysis has been applied to the data. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Synthesis, Structure and Properties of Melamine-Based pTHF-Urethane Supramolecular Compounds

    NARCIS (Netherlands)

    Öjelund, Karin; Loontjens, Ton; Steeman, Paul; Palmans, Anja; Maurer, Frans

    2003-01-01

    The properties of melamine based supramolecular compounds have been studied with rheological, thermal, mechanical, dielectric and scattering techniques and compared with similar covalently bonded materials. The complexes are based on a linear pTHF-diol (M¯n=1 000) connected via a diisocyanate with

  1. Magnetism: a supramolecular function

    International Nuclear Information System (INIS)

    Decurtins, S.; Pellaux, R.; Schmalle, H.W.

    1996-01-01

    The field of molecule-based magnetism has developed tremendously in the last few years. Two different extended molecular - hence supramolecular -systems are presented. The Prussian-blue analogues show some of the highest magnetic ordering temperature of any class of molecular magnets, T c = 315 K, whereas the class of transition-metal oxalate-bridged compounds exhibits a diversity of magnetic phenomena. Especially for the latter compounds, the elastic neutron scattering technique has successfully been proven to trace the magnetic structure of these supramolecular and chiral compounds. (author) 18 figs., 25 refs

  2. Magnetism: a supramolecular function

    Energy Technology Data Exchange (ETDEWEB)

    Decurtins, S.; Pellaux, R.; Schmalle, H.W. [Zurich Univ., Inst. fuer Anorganische Chemie, Zurich (Switzerland)

    1996-11-01

    The field of molecule-based magnetism has developed tremendously in the last few years. Two different extended molecular - hence supramolecular -systems are presented. The Prussian-blue analogues show some of the highest magnetic ordering temperature of any class of molecular magnets, T{sub c} = 315 K, whereas the class of transition-metal oxalate-bridged compounds exhibits a diversity of magnetic phenomena. Especially for the latter compounds, the elastic neutron scattering technique has successfully been proven to trace the magnetic structure of these supramolecular and chiral compounds. (author) 18 figs., 25 refs.

  3. Supra-molecular structure and chemical reactivity of cellulose I studied using CP/MAS (sup)13 C-NMR

    CSIR Research Space (South Africa)

    Chunilall, Viren

    2013-08-01

    Full Text Available medium, provided the original work is properly cited. Supra-Molecular Structure and Chemical Reactivity of Cellulose I Studied Using CP/MAS 13C-NMR Viren Chunilall, Tamara Bush and Per Tomas Larsson Additional information is available at the end... can be used in the production of many different types and qualities of pulp samples for a broad range of applications. The sulphite process can be categorised according to the pH into four different types of pulping namely Acid bi-sulphite, Bi...

  4. Promoting self-assembly of collagen-related peptides into various higher-order structures by metal-histidine coordination.

    Science.gov (United States)

    Hsu, Wei; Chen, Yi-Lun; Horng, Jia-Cherng

    2012-02-14

    Collagen is an important and widely used biomaterial and therapeutic. The construction of large-scale collagen structures via the self-assembly of small collagen-related peptides has been extensively studied in the past decade. Here, we report a highly effective and simple means to assemble small synthetic collagen-related peptides into various higher-order structures by utilizing metal-histidine coordination. In this work, two short collagen-related peptides in which histidine residues were incorporated as metal binding sites were designed and chemically synthesized: HG(PPG)(9)GH (X9) and HG(PPG)(4)(PHG)(PPG)(4)GH (PHG). Circular dichroism measurements indicated that these two peptides form only marginally stable collagen triple helices but that their stability can be increased upon the addition of metal ions. Dynamic light scattering analyses, turbidity measurements, TEM, and SEM results demonstrated the metal ion-dependent self-assembly of X9 and PHG into supramolecular structures ranging from various nanofibrils to microscale spherical, laminated, and granulated assemblies. The topology and size of these higher-order structures depends both on the metal ion identity and the location of the binding sites. Most intriguingly, the assembled fibrils show similar D-periodicity to that of natural collagen. Our results demonstrate that metal-histidine coordination can serve as an effective force to induce the self-assembly of unstable collagen-related peptides into higher-order structures.

  5. Constraining cyclic peptides to mimic protein structure motifs

    DEFF Research Database (Denmark)

    Hill, Timothy A.; Shepherd, Nicholas E.; Diness, Frederik

    2014-01-01

    Many proteins exert their biological activities through small exposed surface regions called epitopes that are folded peptides of well-defined three-dimensional structures. Short synthetic peptide sequences corresponding to these bioactive protein surfaces do not form thermodynamically stable...... and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic pepti-domimetics that refine peptide structure and confer biological properties....

  6. Unraveling the Solution-State Supramolecular Structures of Donor-Acceptor Polymers and their Influence on Solid-State Morphology and Charge-Transport Properties.

    Science.gov (United States)

    Zheng, Yu-Qing; Yao, Ze-Fan; Lei, Ting; Dou, Jin-Hu; Yang, Chi-Yuan; Zou, Lin; Meng, Xiangyi; Ma, Wei; Wang, Jie-Yu; Pei, Jian

    2017-11-01

    Polymer self-assembly in solution prior to film fabrication makes solution-state structures critical for their solid-state packing and optoelectronic properties. However, unraveling the solution-state supramolecular structures is challenging, not to mention establishing a clear relationship between the solution-state structure and the charge-transport properties in field-effect transistors. Here, for the first time, it is revealed that the thin-film morphology of a conjugated polymer inherits the features of its solution-state supramolecular structures. A "solution-state supramolecular structure control" strategy is proposed to increase the electron mobility of a benzodifurandione-based oligo(p-phenylene vinylene) (BDOPV)-based polymer. It is shown that the solution-state structures of the BDOPV-based conjugated polymer can be tuned such that it forms a 1D rod-like structure in good solvent and a 2D lamellar structure in poor solvent. By tuning the solution-state structure, films with high crystallinity and good interdomain connectivity are obtained. The electron mobility significantly increases from the original value of 1.8 to 3.2 cm 2 V -1 s -1 . This work demonstrates that "solution-state supramolecular structure" control is critical for understanding and optimization of the thin-film morphology and charge-transport properties of conjugated polymers. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Self-assembled materials and supramolecular chemistry within microfluidic environments: from common thermodynamic states to non-equilibrium structures.

    Science.gov (United States)

    Sevim, S; Sorrenti, A; Franco, C; Furukawa, S; Pané, S; deMello, A J; Puigmartí-Luis, J

    2018-05-01

    Self-assembly is a crucial component in the bottom-up fabrication of hierarchical supramolecular structures and advanced functional materials. Control has traditionally relied on the use of encoded building blocks bearing suitable moieties for recognition and interaction, with targeting of the thermodynamic equilibrium state. On the other hand, nature leverages the control of reaction-diffusion processes to create hierarchically organized materials with surprisingly complex biological functions. Indeed, under non-equilibrium conditions (kinetic control), the spatio-temporal command of chemical gradients and reactant mixing during self-assembly (the creation of non-uniform chemical environments for example) can strongly affect the outcome of the self-assembly process. This directly enables a precise control over material properties and functions. In this tutorial review, we show how the unique physical conditions offered by microfluidic technologies can be advantageously used to control the self-assembly of materials and of supramolecular aggregates in solution, making possible the isolation of intermediate states and unprecedented non-equilibrium structures, as well as the emergence of novel functions. Selected examples from the literature will be used to confirm that microfluidic devices are an invaluable toolbox technology for unveiling, understanding and steering self-assembly pathways to desired structures, properties and functions, as well as advanced processing tools for device fabrication and integration.

  8. Cryo-transmission electron microscopy structure of a gigadalton peptide fiber of de novo design.

    Science.gov (United States)

    Sharp, Thomas H; Bruning, Marc; Mantell, Judith; Sessions, Richard B; Thomson, Andrew R; Zaccai, Nathan R; Brady, R Leo; Verkade, Paul; Woolfson, Derek N

    2012-08-14

    Nature presents various protein fibers that bridge the nanometer to micrometer regimes. These structures provide inspiration for the de novo design of biomimetic assemblies, both to address difficulties in studying and understanding natural systems, and to provide routes to new biomaterials with potential applications in nanotechnology and medicine. We have designed a self-assembling fiber system, the SAFs, in which two small α-helical peptides are programmed to form a dimeric coiled coil and assemble in a controlled manner. The resulting fibers are tens of nm wide and tens of μm long, and, therefore, comprise millions of peptides to give gigadalton supramolecular structures. Here, we describe the structure of the SAFs determined to approximately 8 Å resolution using cryotransmission electron microscopy. Individual micrographs show clear ultrastructure that allowed direct interpretation of the packing of individual α-helices within the fibers, and the construction of a 3D electron density map. Furthermore, a model was derived using the cryotransmission electron microscopy data and side chains taken from a 2.3 Å X-ray crystal structure of a peptide building block incapable of forming fibers. This was validated using single-particle analysis techniques, and was stable in prolonged molecular-dynamics simulation, confirming its structural viability. The level of self-assembly and self-organization in the SAFs is unprecedented for a designed peptide-based material, particularly for a system of considerably reduced complexity compared with natural proteins. This structural insight is a unique high-resolution description of how α-helical fibrils pack into larger protein fibers, and provides a basis for the design and engineering of future biomaterials.

  9. A rapid pathway toward a superb gene delivery system: programming structural and functional diversity into a supramolecular nanoparticle library.

    Science.gov (United States)

    Wang, Hao; Liu, Kan; Chen, Kuan-Ju; Lu, Yujie; Wang, Shutao; Lin, Wei-Yu; Guo, Feng; Kamei, Ken-ichiro; Chen, Yi-Chun; Ohashi, Minori; Wang, Mingwei; Garcia, Mitch André; Zhao, Xing-Zhong; Shen, Clifton K-F; Tseng, Hsian-Rong

    2010-10-26

    Nanoparticles are regarded as promising transfection reagents for effective and safe delivery of nucleic acids into a specific type of cells or tissues providing an alternative manipulation/therapy strategy to viral gene delivery. However, the current process of searching novel delivery materials is limited due to conventional low-throughput and time-consuming multistep synthetic approaches. Additionally, conventional approaches are frequently accompanied with unpredictability and continual optimization refinements, impeding flexible generation of material diversity creating a major obstacle to achieving high transfection performance. Here we have demonstrated a rapid developmental pathway toward highly efficient gene delivery systems by leveraging the powers of a supramolecular synthetic approach and a custom-designed digital microreactor. Using the digital microreactor, broad structural/functional diversity can be programmed into a library of DNA-encapsulated supramolecular nanoparticles (DNA⊂SNPs) by systematically altering the mixing ratios of molecular building blocks and a DNA plasmid. In vitro transfection studies with DNA⊂SNPs library identified the DNA⊂SNPs with the highest gene transfection efficiency, which can be attributed to cooperative effects of structures and surface chemistry of DNA⊂SNPs. We envision such a rapid developmental pathway can be adopted for generating nanoparticle-based vectors for delivery of a variety of loads.

  10. Structures of self-assembled amphiphilic peptide-heterodimers: effects of concentration, pH, temperature and ionic strength

    KAUST Repository

    Luo, Zhongli

    2010-01-01

    The amphiphilic double-tail peptides AXG were studied regarding secondary structure and self-assembly in aqueous solution. The two tails A = Ala 6 and G = Gly6 are connected by a central pair X of hydrophilic residues, X being two aspartic acids in ADG, two lysines in AKG and two arginines in ARG. The peptide AD (Ala6Asp) served as a single-tail reference. The secondary structure of the four peptides was characterized by circular dichroism spectroscopy under a wide range of peptide concentrations (0.01-0.8 mM), temperatures (20-98 °C), pHs (4-9.5) and ionic strengths. In salt-free water both ADG and AD form a β-sheet type of structure at high concentration, low pH and low temperature, in a peptide-peptide driven assembly of individual peptides. The transition has a two-state character for ADG but not for AD, which indicates that the added tail in ADG makes the assembly more cooperative. By comparison the secondary structures of AKG and ARG are comparatively stable over the large range of conditions covered. According to dynamic light scattering the two-tail peptides form supra-molecular aggregates in water, but high-resolution AFM-imaging indicate that ordered (self-assembled) structures are only formed when salt (0.1 M NaCl) is added. Since the CD-studies indicate that the NaCl has only a minor effect on the peptide secondary structure we propose that the main role of the added salt is to screen the electrostatic repulsion between the peptide building blocks. According to the AFM images ADG and AKG support a correlation between nanofibers and a β-sheet or unordered secondary structure, whereas ARG forms fibers in spite of lacking β-sheet structure. Since the AKG and ARG double-tail peptides self-assemble into distinct nanostructures while their secondary structures are resistant to environment factors, these new peptides show potential as robust building blocks for nano-materials in various medical and nanobiotechnical applications. © 2010 The Royal Society

  11. Synthesis, spectral, crystal structure, thermal behavior, antimicrobial and DNA cleavage potential of two octahedral cadmium complexes: A supramolecular structure

    Science.gov (United States)

    Montazerozohori, M.; Musavi, S. A.; Masoudiasl, A.; Naghiha, A.; Dusek, M.; Kucerakova, M.

    2015-02-01

    Two new cadmium(II) complexes with the formula of CdL2(NCS)2 and CdL2(N3)2 (in which L is 2,2-dimethyl-N,N‧-bis-(3-phenyl-allylidene)-propane-1,3-diamine) have been synthesized and characterized by elemental analysis, molar conductivity measurements, FT/IR, UV-Visible, 1H and 13C NMR spectra and X-ray studies. The crystal structure analysis of CdL2(NCS)2 indicated that it crystallizes in orthorhombic system with space group of Pbca. Two Schiff base ligands are bonded to cadmium(II) ion as N2-donor chelate. Coordination geometry around the cadmium ion was found to be partially distorted octahedron. The Cd-Nimine bond distances are found in the range of 2.363(2)-2.427(2) Å while the Cd-Nisothiocyanate bond distances are 2.287(2) Å and 2.310(2) Å. The existence of C-H⋯π and C-H⋯S interactions in the CdL2(NCS)2 crystal leads to a supramolecular structure in its network. Then cadmium complexes were screened in vitro for their antibacterial and antifungal activities against two Gram-negative and two Gram-positive bacteria and also against Candida albicans as a fungus. Moreover, the compounds were subjected for DNA-cleavage potential by gel electrophoresis method. Finally thermo-gravimetric analysis of the complexes was applied for thermal behavior studies and then some thermo-kinetics activation parameters were evaluated.

  12. Syntheses, Crystal Structures and Thermal Behaviors of Two Supramolecular Salamo-Type Cobalt(II and Zinc(II Complexes

    Directory of Open Access Journals (Sweden)

    Gang Li

    2017-07-01

    Full Text Available This paper reports the syntheses of two new complexes, [Co(L1(H2O2] (1 and [{Zn(L2(μ-OAcZn(n-PrOH}2] (2, from asymmetric halogen-substituted Salamo-type ligands H2L1 and H3L2, respectively. Investigation of the crystal structure of complex 1 reveals that the complex includes one Co(II ion, one (L12− unit and two coordinated water molecules. Complex 1 shows slightly distorted octahedral coordination geometry, forming an infinite 2D supramolecular structure by intermolecular hydrogen bond and π–π stacking interactions. Complex 2 contains four Zn(IIions, two completely deprotonated (L23− moieties, two coordinated μ-OAc− ions and n-propanol molecules. The Zn(II ions in complex 2 display slightly distorted trigonal bipyramidal or square pyramidal geometries.

  13. Solid-state supramolecular structure of tetrakis(1-(diaminomethylene)thiouron-1-ium) pyromellate

    Science.gov (United States)

    Janczak, Jan

    2018-03-01

    The single crystals of tetrakis(1-(diaminomethylene)thiouron-1-ium) pyromellate suitable for the X-ray analysis were grown using a solution growth technique at room temperature. The compound crystallises in the centrosymmetric space group P21/c of the monoclinic system. Asymmetric unit consists of half of the tetrakis(1-(diaminomethylene)thiouron-1-ium) pyromellate molecule. Both independent parts of the 1-(diaminomethylene)-thiouron-1-ium cations are not strictly planar, but twisted. Both planar arms of the cation are oppositely rotated around the Csbnd N bonds involving the central N atom of the cation. The arrangement of the oppositely charged components, i.e. 1-(diaminomethylene)-thiouron-1-ium cations and pyromellate(4-) anion is determined by the Nsbnd H⋯O hydrogen bonds with R22(8) and R21(6) graphs forming supramolecular tetrakis(1-(diaminomethylene)-thiouron-1-ium) pyromellate units that further interact each other forming three dimensional hydrogen bonded network. Hirshfeld surface and the analysis of the 2D-fingerprint plots are illustrating both qualitatively and quantitatively interactions governing the formation of the supramolecular tetrakis(1-(diaminomethylene)-thiouron-1-ium) pyromellate complex as well as the mutual arrangement of the supramolecules in the crystal. The compound was also characterized by the FT-IR and Raman spectroscopy. Assignment of the bands have been supported by the isotropic frequency shift.

  14. Syntheses and structures of three supramolecular complexes based on 2-(pyridine-2-yl)-1H-imidazole-4,5-dicarboxylic acid

    Science.gov (United States)

    Yu, Xiao-Yang; Zhang, Xiao; Liu, Zhi-Gang; Cui, Xiao-Bing; Xu, Jia-Ning; Luo, Yu-Hui

    2017-11-01

    Three new supramolecular compounds, [Cu(o-HPIDC)(bpy)(H2O)]·2H2O 1, [Cu(o-H2PIDC)(phen)Cl]·[Cu(phen)2Cl]·10H2O·Cl 2 and {[Cd(o-H2PIDC)(H2O)2Cl]·H2O}23 (o-H3PIDC = 2-(pyridine-2-yl)-1H-imidazole-4,5-dicarboxylic acid, bpy = 2,2'-bipyridine, phen = 1,10-phenanthroline), were hydrothermally synthesized and characterized. In compound 1, the adjacent two supramolecular layers are constructed from different types of helical chains with the same pitch. In compound 2, the adjacent 2D water-chloride layers, {[(H2O)10Cl]-}n, are pillared by [Cu(o-H2PIDC)(phen)Cl] units to form the overall 3D supramolecular network with 1D channels through Osbnd H⋯O hydrogen bond interactions. In compound 3, two Cd(II) are linked into a binuclear [Cd2(o-H2PIDC)2(H2O)4Cl2] with a ten-membered ring by two o-H2PIDC- ligands. The three compounds self-assemble into 3D supramolecular structures via hydrogen bond and π-π stacking interactions. The fluorescence properties of compound 3 was also investigated.

  15. Supramolecular isomerism in cadmium (II) coordination polymers from benzene-1,3,5-tribenzoate (BTB): Syntheses, structures and luminescent properties

    Science.gov (United States)

    Zhang, Jian-Yong; Cui, Peng-Hui; Shi, Jun-Xia; Zhang, Na; Deng, Wei

    2017-12-01

    By tuning the solvent mixture, four CdII-based compounds, [Cd3(BTB)2(DMA)4]·2DMA (1α), [Cd3(BTB)2(DMA)4]·2DMA (1β), [Cd3(BTB)2(DMF)4]·2DMF (1γ), Cd2(BTB)(HCOO)(DMF)3 (2) have been successfully separated from H3BTB ligand and Cd(NO3)2 salts. Structural analyses revealed that compounds 1α, 1β and 1γ are iso-structural and have essentially identical local and two-dimensional structures constructed from trinuclear Cd3(OCO)6 unit. Their structural differences only arise from the different packing fashions, which are novel modes of supramolecular isomerism in coordination polymers. Compound 2 displays 3D two-fold interpenetrated network based on 1D infinite Cd3(μ1,1,3-OCO)2(HCOO) chains containing mixed BTB3- and formate ligands. The fluorescence measurements show that compounds 2 exhibit red-shifts (about 25 nm) in the solid state, compared with three iso-structural 1α, 1β and 1γ, and this can be attributed to the cooperative effects of intraligand π-π* transitions and ligand-to-metal charge transfer (LMCT).

  16. Structure-activity relationship of CART peptide fragments

    Czech Academy of Sciences Publication Activity Database

    Maletínská, Lenka; Maixnerová, Jana; Hlaváček, Jan; Blokešová, Darja; Elbert, Tomáš; Šanda, Miloslav; Slaninová, Jiřina; Železná, Blanka

    2007-01-01

    Roč. 88, č. 4 (2007), s. 565 ISSN 0006-3525. [American Peptide Society Symposium /20./. 26.06.2007-30.06.2007, Montreal] Institutional research plan: CEZ:AV0Z40550506 Keywords : cocaine and amphetamine regulated transcript peptide * structure * activity Subject RIV: CE - Biochemistry

  17. Two 8-Hydroxyquinolinate Based Supramolecular Coordination Compounds: Synthesis, Structures and Spectral Properties

    Directory of Open Access Journals (Sweden)

    Chengfeng Zhu

    2017-03-01

    Full Text Available Two new Cr(III complexes based on 2-substituted 8-hydroxyquinoline ligands, namely [Cr(L13] (1, (HL1=(E-2-[2-(4-nitro-phenyl-vinyl]-8-hydroxy-quinoline and [Cr(L23] (2, (HL2=(E-2-[2-(4-chloro-phenylvinyl]-8-hydroxy-quinoline, were prepared by a facile hydrothermal method and characterized thoroughly by single crystal X-ray diffraction, powder X-ray diffraction, FTIR, TGA, ESI-MS, UV-Visible absorption spectra and fluorescence emission spectra. Single crystal X-ray diffraction analyses showed that the two compounds featured 3D supramolecular architectures constructed from noncovalent interactions, such as π···π stacking, C-H···π, C-H···O, C-Cl···π, C-H···Cl interactions. The thermogravimetric analysis and ESI-MS study of compounds 1 and 2 suggested that the Cr(III complexes possessed good stability both in solid and solution. In addition, the ultraviolet and fluorescence response of the HL1 and HL2 shown marked changes upon their complexation with Cr(III ion, which indicated that the two 8-hydroxyquinolinate based ligand are promising heavy metal chelating agent for Cr3+.

  18. Electrostatic Force Microscopy of Self Assembled Peptide Structures

    DEFF Research Database (Denmark)

    Clausen, Casper Hyttel; Dimaki, Maria; Pantagos, Spyros P.

    2011-01-01

    In this report electrostatic force microscopy (EFM) is used to study different peptide self-assembled structures, such as tubes and particles. It is shown that not only geometrical information can be obtained using EFM, but also information about the composition of different structures. In partic...... compared to the radius of the AFM tip used. Finally, an agreement between the detected signal and the structure of the hollow peptide tubes is demonstrated....

  19. Hirshfeld surface analyses and crystal structures of supramolecular self-assembly thiourea derivatives directed by non-covalent interactions

    Science.gov (United States)

    Gumus, Ilkay; Solmaz, Ummuhan; Binzet, Gun; Keskin, Ebru; Arslan, Birdal; Arslan, Hakan

    2018-04-01

    The novel N-(bis(3,5-dimethoxybenzyl)carbamothioyl)-4-R-benzamide (R: H, Cl, CH3 and OCH3) compounds have been synthesized and characterized by FT-IR, 1H NMR and 13C NMR spectroscopy. Their crystal structures were also determined by single-crystal X-ray diffraction studies. Hirshfeld surfaces analysis and their associated two dimensional fingerprint plots of compounds were used as theoretical approach to assess driving force for crystal structure formation via the intermolecular interactions in the crystal lattices of synthesized compounds. The study of X-ray single crystal diffraction and Hirshfeld surfaces analysis of the prepared compounds shows that hydrogen bonding and other weaker interactions such as Nsbnd H⋯S, weak Csbnd H⋯S, Csbnd H⋯O, Csbnd H⋯N and Csbnd H···π intermolecular interactions and π-π stacking, among molecules of synthesized compounds participate in a cooperative way to stabilize the supramolecular structures.

  20. Supramolecular chemistry and crystal engineering

    Indian Academy of Sciences (India)

    recognition and binding, ice structures, and supramolecular chemistry. The traditional view is .... pair-wise leads to synthon control and crystal design in multifunctional molecules. ..... Crystal structure of Na(sac)•1.875H2O (Na pink, O red, N blue, S yellow, C gray, H cream). The regular region on the left side has 10 sac. −.

  1. Synergy in supramolecular chemistry

    CERN Document Server

    Nabeshima, Tatsuya

    2014-01-01

    Synergy and Cooperativity in Multi-metal Supramolecular Systems, T. NabeshimaHierarchically Assembled Titanium Helicates, Markus AlbrechtSupramolecular Hosts and Catalysts Formed by Self-assembly of Multinuclear Zinc Complexes in Aqueous Solution, Shin AokiSupramolecular Assemblies Based on Interionic Interactions, H. MaedaSupramolecular Synergy in the Formation and Function of Guanosine Quadruplexes, Jeffery T. DavisOn-Surface Chirality in Porous Self-Assembled Monolayers at Liquid-Solid Interface, Kazukuni Tahar

  2. Supramolecular structure of a perylene derivative in thin films made by vacuum thermal evaporation; Estrutura supramolecular de um derivado de perileno em filmes finos fabricados por evaporacao termica a vacuo

    Energy Technology Data Exchange (ETDEWEB)

    Fernandes, Jose Diego

    2015-07-01

    The supramolecular arrangement of organic thin films is a factor that influences both optical and electrical properties of these films and, consequently, the technological applications involving organic electronics. In this dissertation, thin films of a perylene derivative (bis butylimido perylene, acronym BuPTCD) were produced by physical vapor deposition (PVD) using vacuum thermal evaporation. The aim of this work was to investigate the supramolecular arrangement of BuPTCD films, which implies to control the thickness at nanometer scale and to determine the molecular organization, the morphology (at nano and micrometer scales) and the crystallinity, besides the stability of this arrangement as a function of the temperature. Optical properties (such as absorption and emission) and electrical properties (such as conductivity and photoconductivity) were also determined. The UV-Vis absorption spectra revealed a controlled growth (uniform) of the BuPTCD films. Atomic force and optical microscopy images showed a homogeneous surface of the film at nano and micrometer scales, respectively. The X-ray diffraction showed that the BuPTCD powder and PVD film have different crystalline structures, with the BuPTCD molecules head-on oriented in the PVD films, supported on the substrate surface by the side group (FTIR). This structure favors the light emission (photoluminescence) by the formation of excimers. The thermal treatment (200°C for 10 min) does not affect the molecular organization of the PVD films, showing a thermal stability of the BuPTCD supramolecular arrangement under these circumstances. The electrical measurements (DC) showed a linear increase of the current as a function of the tension, which is characteristic of ohmic behavior. Also, the films exhibited an increase of current by 2 orders of magnitude when exposed to light (photoconductive properties). Finally, BuPTCD films were exposed to vapor of trifluoroacetic acid (TFA) to verify the sensitivity of the Bu

  3. Internalization of p53(14-29) peptide amphiphiles and subsequent endosomal disruption results in SJSA-1 cell death.

    Science.gov (United States)

    Missirlis, Dimitris; Krogstad, Daniel V; Tirrell, Matthew

    2010-12-06

    In vivo peptide inhibition of tumor suppressor p53 binding to the protein MDM2 is hampered by inefficient delivery of the peptide. Our approach to couple a hydrophobic lipid-like tail on the inhibitory peptide p53(14-29) allowed its intracellular delivery in vitro, in a panel of different cell lines. The constructed chimeric molecules, termed peptide amphiphiles, further self-assembled into supramolecular structures, identified as elongated wormlike micelles. Internalization of peptides occurred following micelle disassembly, partly via clathrin-mediated endocytosis of monomers. Incubation of SJSA-1 cells in hypertonic culture media, aimed to disrupt endocytic vesicles, resulted in peptide amphiphile-mediated cell death. Our results provide the basis for the construction of novel therapeutic supramolecular nanoparticles and suggest hydrophobic modification of peptides as a promising strategy for enhancing delivery of impermeable peptides.

  4. Synthesis, Crystal Structures, and Photoluminescent Properties of Two Supramolecular Architectures Based on Difunctional Ligands Containing Imidazolyl and Carboxyl Groups

    Directory of Open Access Journals (Sweden)

    Mei-An Zhu

    2017-07-01

    Full Text Available Two new supramolecular architectures, namely, [Cd(L12(H2O]n (1 and [Ni(L22(H2O]n (2, were synthesized by the reaction of corresponding metal salts of CdCl2·2.5H2O and NiCl2·6H2O with 2-(1H-imidazol-4-ylbenzoic acid (HL1 and 3-(1H-imidazol-4-ylbenzoic acid (HL2 respectively, and characterized by single-crystal X-ray diffraction, IR spectroscopy, elemental analysis and powder X-ray diffraction (PXRD. Both HL1 and HL2 ligands are deprotonated to be L1- and L2- anions that coordinate with Cd(II and Ni(II atoms to form two-dimensional (2D layer structure. Topologically, complex 1 is a 2D network with (4, 4 sql topology, while 2 is a typical 63-hcb topology net. Complex 1 exhibits intense light blue emission in the solid state at room temperature.

  5. Synthesis and structural investigation of 2-aminomethyl-3-(4-methoxy-phenyl)-propionic acid containing a peptide analogue of the amyloidogenic AS(6-7) sequence: inhibition of fibril formation.

    Science.gov (United States)

    Paikar, Arpita; Debnath, Mintu; Podder, Debasish; Sasmal, Supriya; Haldar, Debasish

    2017-05-16

    The incorporation of a single β-amino acid moiety in a highly amyloidogenic peptide sequence resulted in the complete inhibition of amyloid fibril formation. The Boc-l-Phe-l-Leu-OMe sequence 1, which has sequence identity with the N-terminal AS(6-7) of the non-immunoglobulin amyloid fibril protein AS, which is responsible for rheumatoid arthritis, self-associates to produce fibrils. The d-Phe analogue peptide 2 shows an elongated ribbon-like morphology. However, the 2-aminomethyl-3-(4-methoxy-phenyl)-propionic acid containing analogue peptide 3 exhibits a polydisperse microsphere morphology. Moreover, fibrils from peptides 1 and 2 exhibit typical green-gold birefringence upon Congo red (CR) staining and show an amyloid-like morphological resemblance. However, the 2-aminomethyl-3-(4-methoxy-phenyl)-propionic acid modified peptide 3 does not respond to the Congo red assay. From X-ray crystallography, peptide 1 with the l-Phe residue adopts an extended structure, whereas the d-Phe analogue 2 adopts a kink-like structure. Both peptides 1 and 2 show twisted anti-parallel sheet-like structures at higher order assembly. However, peptide 3 adopts a nine-membered hydrogen bonded δ-turn-like structure in the solid state and self-associates to form a loop-like supramolecular structure through multiple intermolecular hydrogen bonds. The structural analysis presented herein may foster new studies for de novo design and therapeutics.

  6. Triangles and tetrahedra: metal directed self-assembly of metallo-supramolecular structures incorporating bis-beta-diketonato ligands.

    Science.gov (United States)

    Clegg, Jack K; Lindoy, Leonard F; Moubaraki, Boujema; Murray, Keith S; McMurtrie, John C

    2004-08-21

    The interaction of six aryl-linked bis-beta-diketones, including a new naphthylene linked species, with copper(II), iron(III) and, in one instance gallium(III), has been investigated with the aim of obtaining metallo-supramolecular assemblies exhibiting different geometries. New examples of two assembly types incorporating the above bis-beta-diketones (L) were generated. The first type is represented by a range of molecular triangles of formula [Cu(3)(L-H(2))(3)](solvent)(n) while the second is given by a corresponding selection of less-common neutral molecular tetrahedra of formula [Fe(4)(L-H(2))(6)](solvent)(n) as well as [Ga(4)(L-H(2))(6)].8.5THF.0.5H(2)O; an example of each type has been characterised by X-ray crystallography. A magnetochemical investigation of [Fe(4)(-H(2))(6)].6THF is reported. The susceptibility is Curie like and consistent with very weak coupling occurring between the iron(III) d(5)(high spin) centres. The X-ray structures of two trinuclear copper(II) as well as a tetranuclear iron(III) and a tetranuclear gallium(III) assembly confirm their discrete triangular and tetrahedral geometries, respectively. The structure of the gallium(III) species is closely related to that of the corresponding iron(III) species. The tetrahedral structures provide rare examples of such assemblies encapsulating guest solvent molecules--in each case tetrahydrofuran is incorporated in the central cavity.

  7. Structure-activity relationship of crustacean peptide hormones.

    Science.gov (United States)

    Katayama, Hidekazu

    2016-01-01

    In crustaceans, various physiological events, such as molting, vitellogenesis, and sex differentiation, are regulated by peptide hormones. To understanding the functional sites of these hormones, many structure-activity relationship (SAR) studies have been published. In this review, the author focuses the SAR of crustacean hyperglycemic hormone-family peptides and androgenic gland hormone and describes the detailed results of our and other research groups. The future perspectives will be also discussed.

  8. On some problems of inorganic supramolecular chemistry.

    Science.gov (United States)

    Pervov, Vladislav S; Zotova, Anna E

    2013-12-02

    In this study, some features that distinguish inorganic supramolecular host-guest objects from traditional architectures are considered. Crystalline inorganic supramolecular structures are the basis for the development of new functional materials. Here, the possible changes in the mechanism of crystalline inorganic supramolecular structure self-organization at high interaction potentials are discussed. The cases of changes in the host structures and corresponding changes in the charge states under guest intercalation, as well as their impact on phase stability and stoichiometry are considered. It was demonstrated that the deviation from the geometrical and topological complementarity conditions may be due to the additional energy gain from forming inorganic supramolecular structures. It has been assumed that molecular recognition principles can be employed for the development of physicochemical analysis and interpretation of metastable states in inorganic crystalline alloys. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Supramolecular Structure and Functional Analysis of the Type III Secretion System in Pseudomonas fluorescens 2P24.

    Science.gov (United States)

    Liu, Ping; Zhang, Wei; Zhang, Li-Qun; Liu, Xingzhong; Wei, Hai-Lei

    2015-01-01

    The type III secretion system (T3SS) of plant and animal bacterial pathogens directs the secretion and injection of proteins into host cells. Some homologous genes of T3SS were found also in non-pathogenic bacteria, but the organization of its machinery and basic function are still unknown. In this study, we identified a T3SS gene cluster from the plant growth-promoting Pseudomonas fluorescens 2P24 and isolated the corresponding T3SS apparatus. The T3SS gene cluster of strain 2P24 is similar organizationally to that of pathogenic P. syringae, except that it lacks the regulator hrpR and the hrpK1 and hrpH genes, which are involved in translocation of proteins. Electron microscopy revealed that the T3SS supramolecular structure of strain 2P24 was comprised of two distinctive substructures: a long extracellular, filamentous pilus, and a membrane-embedded base. We show that strain 2P24 deploys a harpin homolog protein, RspZ1, to elicit a hypersensitive response when infiltrated into Nicotiana tabacum cv. xanthi leaves with protein that is partially purified, and by complementing the hrpZ1 mutation of pHIR11. The T3SS of strain 2P24 retained ability to secrete effectors, whereas its effector translocation activity appeared to be excessively lost. Mutation of the rscC gene from 2P24 T3SS abolished the secretion of effectors, but the general biocontrol properties were unaffected. Remarkably, strain 2P24 induced functional MAMP-triggered immunity that included a burst of reactive oxygen species, strong suppression of challenge cell death, and disease expansion, while it was not associated with the secretion functional T3SS.

  10. Supramolecular structure and functional analysis of the type III secretion system in Pseudomonas fluorescens 2P24

    Directory of Open Access Journals (Sweden)

    Ping eLiu

    2016-01-01

    Full Text Available The type III secretion system (T3SS of plant and animal bacterial pathogens directs the secretion and injection of proteins into host cells. Some homologous genes of T3SS were found also in nonpathogenic bacteria, but the organization of its machinery and basic function are still unknown. In this study, we identified a T3SS gene cluster from the plant growth-promoting Pseudomonas fluorescens 2P24 and isolated the corresponding T3SS apparatus. The T3SS gene cluster of strain 2P24 is similar organizationally to that of pathogenic P. syringae, except that it lacks the regulator hrpR and the hrpK1 and hrpH genes, which are involved in translocation of proteins. Electron microscopy revealed that the T3SS supramolecular structure of strain 2P24 was comprised of two distinctive substructures: a long extracellular, filamentous pilus and a membrane-embedded base. We show that strain 2P24 deploys a harpin homologue protein, RspZ1, to elicit a hypersensitive response when infiltrated into Nicotiana tabacum cv. xanthi leaves with protein that is partially purified, and by complementing the hrpZ1 mutation of pHIR11. The T3SS of strain 2P24 retained ability to secrete effectors, whereas its effector translocation activity appeared to be excessively lost. Mutation of the rscC gene from 2P24 T3SS abolished the secretion of effectors, but the general biocontrol properties were unaffected. Remarkably, strain 2P24 induced functional MAMP-triggered immunity that included a burst of reactive oxygen species, strong suppression of challenge cell death, and disease expansion, while it was not associated with the secretion functional T3SS.

  11. Supramolecular Assembly of Water-Soluble Poly(ferrocenylsilanes): Multilayer Structures on Flat Interfaces and Permeability of Microcapsules

    NARCIS (Netherlands)

    Ma, Y.; Dong, Wen-Fei; Kooij, Ernst S.; Hempenius, Mark A.; Mohwald, Helmuth; Vancso, Gyula J.

    2007-01-01

    We report on the layer-by-layer (LBL) supramolecular assembly of redox responsive, organometallic polyion films on planar and curved (spherical) substrates. Organometallic poly(ferrocenylsilane) (PFS) polyanions and polycations were first used to assemble multilayers on planar quartz, silicon and

  12. Programming supramolecular biohybrids as precision therapeutics.

    Science.gov (United States)

    Ng, David Yuen Wah; Wu, Yuzhou; Kuan, Seah Ling; Weil, Tanja

    2014-12-16

    chains available for grafting with molecules of interest. Additionally, we are equipped with analytical tools to map the fingerprint of the protein chain, directly elucidating the structure at the molecular level. Contrary to conventional polymers, these biopolymers facilitate a more systematic avenue to investigate engineered macromolecules, with greater detail and accuracy. In this regard, we focus on denaturing serum albumin, an abundant blood protein, and exploit its peptidic array of functionalities to program supramolecular architectures for bioimaging, drug and gene delivery. Ultimately, we seek to assimilate the evolutionary advantage of these protein based biopolymers with the limitless versatility of synthetic chemistry to merge the best of both worlds.

  13. Frog oocytes to unveil the structure and supramolecular organization of human transport proteins.

    Directory of Open Access Journals (Sweden)

    Marc J Bergeron

    Full Text Available Structural analyses of heterologously expressed mammalian membrane proteins remain a great challenge given that microgram to milligram amounts of correctly folded and highly purified proteins are required. Here, we present a novel method for the expression and affinity purification of recombinant mammalian and in particular human transport proteins in Xenopus laevis frog oocytes. The method was validated for four human and one murine transporter. Negative stain transmission electron microscopy (TEM and single particle analysis (SPA of two of these transporters, i.e., the potassium-chloride cotransporter 4 (KCC4 and the aquaporin-1 (AQP1 water channel, revealed the expected quaternary structures within homogeneous preparations, and thus correct protein folding and assembly. This is the first time a cation-chloride cotransporter (SLC12 family member is isolated, and its shape, dimensions, low-resolution structure and oligomeric state determined by TEM, i.e., by a direct method. Finally, we were able to grow 2D crystals of human AQP1. The ability of AQP1 to crystallize was a strong indicator for the structural integrity of the purified recombinant protein. This approach will open the way for the structure determination of many human membrane transporters taking full advantage of the Xenopus laevis oocyte expression system that generally yields robust functional expression.

  14. Molecular and supra-molecular structure of waxy starches developed from cassava (Manihot esculenta Crantz).

    Science.gov (United States)

    Rolland-Sabaté, Agnès; Sanchez, Teresa; Buléon, Alain; Colonna, Paul; Ceballos, Hernan; Zhao, Shan-Shan; Zhang, Peng; Dufour, Dominique

    2013-02-15

    The aim of this work was to characterize the amylopectin of low amylose content cassava starches obtained from transgenesis comparatively with a natural waxy cassava starch (WXN) discovered recently in CIAT (International Center for Tropical Agriculture). Macromolecular features, starch granule morphology, crystallinity and thermal properties of these starches were determined. M¯(w) of amylopectin from the transgenic varieties are lower than WXN. Branched and debranched chain distributions analyses revealed slight differences in the branching degree and structure of these amylopectins, principally on DP 6-9 and DP>37. For the first time, a deep structural characterization of a series of transgenic lines of waxy cassava was carried out and the link between structural features and the mutated gene expression approached. The transgenesis allows to silenced partially or totally the GBSSI, without changing deeply the starch granule ultrastructure and allows to produce clones with similar amylopectin as parental cassava clone. Copyright © 2012 Elsevier Ltd. All rights reserved.

  15. Structures and related properties of helical, disulfide-stabilized peptides

    Energy Technology Data Exchange (ETDEWEB)

    Pagel, Mark D. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1993-11-01

    The three dimensional structure of several peptides were determined by NMR spectroscopy and distance geometry calculations. Each peptide formed a predictable, rigid structure, consisting of an α-helix, a "scaffold" region which packed along one face of the helix, and two disulfide bridges which covalently connect the helix and scaffold regions. The peptide Apa-M5 was designed to constrain the M5 peptide from MLCK in a helical geometry using the apamin disulfide scaffold. This scaffold constrains the N- terminal end of the helix with two disulfide bridges and a reverse turn. Like the M5 peptide, Apa-M5 was found to bind calmodulin in a Ca2+-dependent 1:1 stoichiometry. However, the dissociation constant of the (Apa-M5)-calmodulin complex, 107 nM, was 100-fold higher than the dissociation constant of the M5-calmodulin complex. This difference was due to a putative steric overlap between the Apa-M5 scaffold and calmodulin. The peptide Apa-Cro was designed to replace the large structural protein matrix of λ Cro with the apamin disulfide scaffold. However, Apa-Cro did not bind the consensus DNA operator half-site of λ Cro, probably due to a steric overlap between the Apa-Cro disulfide framework and the DNA. The amino acid sequence of the scaffold-disulfide bridge arrangement of the peptide Max was derived from the core sequence of scyllatoxin, which contains an α-helix constrained at the C-terminal end by two disulfide bridges and a two-stranded βsheet scaffold. Max was shown to fold with >84% yield to form a predictable, stable structure that is similar to scyllatoxin. The folding and stability properties of Max make this scaffold and disulfide bridge arrangement an ideal candidate for the development of hybrid sequence peptides. The dynamics of a fraying C-terminal end of the helix of the peptide Apa-AlaN was determined by analysis of 15N NMR relaxation properties.

  16. Supramolecular structure formation of Langmuir-Blodgett films of comblike precursor and polyimide

    Energy Technology Data Exchange (ETDEWEB)

    Goloudina, S. I., E-mail: goloudina@mail.ru; Luchinin, V. V. [St. Petersburg Electrotechnical University (Russian Federation); Rozanov, V. V. [Russian Academy of Sciences, Institute for Analytical Instrumentation (Russian Federation); Pasyuta, V. M. [St. Petersburg Electrotechnical University (Russian Federation); Gofman, I. V.; Sklizkova, V. P.; Kudryavtsev, V. V. [Russian Academy of Sciences, Institute of Macromolecular Compounds (Russian Federation)

    2013-03-15

    The surface structure of Langmuir-Blodgett films of a comblike polyimide precursor-a rigid-chain polyamic acid alkylamine salt bearing multichains of tertiary amine-and films of the corresponding polyimide were studied by atomic force microscopy (AFM). An analysis of the images of the surface of three-layer films revealed a domain structure. It was found that the Langmuir-Blodgett film formation of the precursor occurs as a result of the layer-by-layer deposition of two-dimensional domains (composed of polyamic acid salt molecules on the water surface) onto a substrate. The formation of domains in a monolayer is associated with the chemical structure of the precursor, to be more precise, with the rigidity of the main chain and the presence of closely spaced aliphatic side chains in the polymer chain, whose total cross-section area is close to the surface area of the projection onto the plane of the repeating unit of the main chain. Polyimide films inherit the domain structure of the precursor films; the inhomogeneity of the film thickness substantially decreases, whereas the domain size and character of their distribution in the film remain unchanged.

  17. From random coil polymers to helical structures induced by carbon nanotubes and supramolecular interactions.

    Science.gov (United States)

    Huang, Kai-Wei; Wu, Yu-Rong; Jeong, Kwang-Un; Kuo, Shiao-Wei

    2013-10-01

    A simple method is reported for the preparation of double-helical structures through a series of achiral random and block copolymers poly(styrene-co-4-vinylbenzyl triazolylmethyl methylthymine) (PS-co-PVBT) with various T units on the side chains through click reactions of poly(styrene-co-4-vinylbenzyl azide) (PS-co-PVBN(3)) with propargyl thymine (PT) and also the synthesis of the A-appended pyrene derivative (A-Py) through click chemistry. This double-helical structure is observed from achiral random-coil polystyrene (PS) main chains, stabilized through the combination of multiple A-T hydrogen bonds, and π-π stacking between pyrene units and single-walled carbon nanotubes (SWCNTs). © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. A supramolecular proposal of lignin structure and its relation with the wood properties.

    Science.gov (United States)

    Abreu, Heber S; Latorraca, João V F; Pereira, Regina P W; Monteiro, Maria Beatriz O; Abreu, Fábio A; Amparado, Kelysson F

    2009-03-01

    In spite of the great importance of cellulose the lignin is considered the second most abundant substance of the wood. However, little attention has been given it, mainly to wood properties. The lignin as well as other structural compounds (cellulose and hemicelluloses), has obviously an important role on the wood properties, probably due its composition and existent bonds. In general lignins have beta-O-4 (Alkyl Aril Ether) as majoritary bond. This bond in a continued structure form big molecules with spiral conformation as virtual model. Based on this idea, lignins that have high/low beta-O-4 content may have differentiated spiraled structures,suggesting different behaviors on the wood properties,which shows that the lignins (Guaicyl:Syringyl (GS)) of angiosperms, for example, which have higher beta-O-4 content would present higher spiral conformation than gymnosperms lignins(HG). On the other hand HG lignins have chance of being more anchored on the matrix compound than GS lignins. In this context, the beta-O-4 bonds of lignins possibly affect the wood properties, therefore, it is considered relevant for wood technology science discussion.

  19. Effect of high hydrostatic pressure on the supramolecular structure of corn starch with different amylose contents.

    Science.gov (United States)

    Yang, Zhi; Swedlund, Peter; Hemar, Yacine; Mo, Guang; Wei, Yanru; Li, Zhihong; Wu, Zhonghua

    2016-04-01

    Corn starches with amylose contents ranging from 0 to 80% were suspended in 60 wt% water or ethanol and subjected to high hydrostatic pressure (HHP) up to 600 MPa. The impact of HHP treatment on the granule morphology, lamellae structures, and crystalline characteristics were examined with a combination of SAXS, WAXS and optical microscopy. All starch dispersed in water showed a decrease in area of the lamellar peak in the SAXS data at q∼0.6 nm(-1). The lamellae thickness (d) increased for pressurized waxy, normal, and Gelose80 corn starches, suggesting water is forced into starch lamellae during HHP. However, for Gelose50 corn starch, the d remained constant over the whole pressure range and light microscopy showed no obvious granule swelling. WAXS studies demonstrated that HHP partially converted A-type starches (waxy and normal corn) to starches with a faint B-type pattern while starches with a B+V-type pattern (Gelose50 and Gelose80), were not affected by HHP. All corn starches suspended in ethanol showed no detectable changes in either granule morphology, or the fractal, the lamellae, and the crystalline structures. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Supramolecular macrocycles based on porphyrins- correlation of molecular structure and biological photoactivity

    International Nuclear Information System (INIS)

    Ion, R. M.; Oprea, F.; Bacinschi, Z.; Scarlat, F.; Scarlat, Fl.; Niculescu, V.I.R.

    2002-01-01

    Porphyrins and phthalocyanines are organic dyes which can be used as highly fluorescent species in laser technology, in photography, as radiation power indicators, as photosensitizers in photodynamic therapy of cancerous disease. Porphyrins constitute a class of the molecules which contain four pyrrole rings linked by the methane carbon bridges whereas the phthalocyanine molecules are composed of four indole units - pyrrole rings linked by nitrogen atoms conjugated with benzene rings. A large group of porphyrins and phthalocyanines can be chemically modified by introducing metal in the center of the pyrrole rings or by attaching the peripheral groups to the outer rings of the methane bridges or isoindole units, respectively. In this study five groups of tetraphenylporphyrins (TPP) and phthalocyanines (Pc) were investigated: - metal (Me)-free dyes without any substitutes, - non-substituted porphyrins and phthalocyanines but complexed with metal (Me) - Zn, Mg, Mn, Co, Cu, Pt, Pd, Pb and others, - metal-complexed dyes substituted with aromatic rings, - metal-complexed dyes substituted with fluorines, - metal-complexed dyes substituted with long organic chains (alkyl or alkyloxy). The difference in the TPP and Pc molecular structure, the kind of metal incorporated into the main molecular core or the variation in the peripheral groups attached to the molecular skeleton are expected to affect the effectiveness of dyes in photocurrent generation. Since there is a competition between the charge separation process and other deactivation processes in the molecule, in our study photochemical investigations (photodynamic action) are usually accompanied with the spectroscopic examinations (absorption, fluorescence- which give information on the (non-) radiative processes) of dyes. In the paper we have presented the review of our study on the correlation between the molecular structure of dyes and their photoactive properties. (authors)

  1. A supramolecular proposal of lignin structure and its relation with the wood properties

    Directory of Open Access Journals (Sweden)

    Heber S. Abreu

    2009-03-01

    Full Text Available In spite of the great importance of cellulose the lignin is considered the second most abundant substance of the wood. However, little attention has been given it, mainly to wood properties. The lignin as well as other structural compounds (cellulose and hemicelluloses, has obviously an important role on the wood properties, probably due its composition and existent bonds. In general lignins have β-O-4 (Alkyl Aril Ether as majoritary bond. This bond in a continued structure form big molecules with spiral conformation as virtual model. Based on this idea, lignins that have high/low β-O-4 content may have differentiated spiraled structures,suggesting different behaviors on the wood properties,which shows that the lignins (Guaicyl:Syringyl (GS of angiosperms, for example, which have higher β-O-4 content would present higher spiral conformation than gymnosperms lignins(HG. On the other hand HG lignins have chance of being more anchored on the matrix compound than GS lignins. In this context, the β-O-4 bonds of lignins possibly affect the wood properties, therefore, it is considered relevant for wood technology science discussion.Apesar da grande importância da celulose a lignina é considerada a segunda substância mais abundante da madeira. Entretanto, pouca atenção tem sido dada a ela, principalmente com relação às propriedades da madeira. A lignina assim como outras substâncias (celulose e hemicelulose, tem obviamente um papel importante sobre as propriedades da madeira, provavelmente devido a sua composição e a existências de ligações. Geralmente as ligninas possuem majoritariamente ligaçõesβ-O-4 (Éter Alquil-Arílico, esta ligação em uma estrutura contínua forma grandes moléculas com conformação em espiral, como visto em modelo virtual. Com base nesta idéia, ligninas que possuem alto/baixo teor de β-O-4, podem ter estruturas espiraladas diferenciadas, sugerindo comportamentos diferentes sobre as propriedades da

  2. Correlation between ionic radii of metals and thermal decomposition of supramolecular structure of azodye complexes

    Science.gov (United States)

    El-Sonbati, A. Z.; Diab, M. A.; El-Bindary, A. A.; Eldesoky, A. M.; Morgan, Sh. M.

    2015-01-01

    An interesting azodye heterocyclic ligand of copper(II), cobalt(II), nickel(II) and uranyl(II) complexes have been synthesized by the reaction of metal salts with 5-(2,3-dimethyl-1-phenylpyrazol-5-one azo)-2-thioxo-4-thiazolidinone (HL) yields 1:1 and 1:2 (M:L) complexes depending on the reaction conditions. The elemental analysis, magnetic moments, spectral (UV-Vis, IR, 1H and 13C NMR and ESR) and thermal studies were used to characterize the isolated complexes. The molecular structures of the ligand tautomers are optimized theoretically and the quantum chemical parameters are calculated. The IR spectra showed that the ligand (HL) act as monobasic tridentate/neutral bidentate through the (sbnd Ndbnd N), enolic (Csbnd O)- and/or oxygen keto moiety groups forming a five/six-membered structures. According to intramolecular hydrogen bond leads to increasing of the complexes stability. The molar conductivities show that all the complexes are non-electrolytes. The ESR spectra indicate that the free electron is in dxy orbital. The calculated bonding parameter indicates that in-plane σ-bonding is more covalent than in-plane π-bonding. The coordination geometry is five/six-coordinated trigonal bipyramidal for complex (1) and octahedral for complexes (2-6). The value of covalency factor β12 and orbital reduction factor K accounts for the covalent nature of the complexes. The activation thermodynamic parameters are calculated using Coats-Redfern and Horowitz-Metzger methods. The synthesized ligand (HL) and its Cu(II) complexes (1, 2 and 4) are screened for their biological activity against bacterial and fungal species. The ligand (HL) showed antimicrobial activities against Escherichia coli. The ligand (HL) and its Cu(II) complexes (2 and 4) have very high antifungal activity against Penicillium italicum. The inhibitive action of ligand (HL), against the corrosion of C-steel in 2 M HCl solution has been investigated using potentiodynamic polarization and electrochemical

  3. Applications of new biophysical techniques to supramolecular structure of ATP synthase

    International Nuclear Information System (INIS)

    Zhu Jie; Wang Guodong

    2007-01-01

    The developing modern physical techniques offer a series of abundant and effective methods to study ATP synthase in structure and function. Firstly we stressed on the dialectic relationship between physical techniques and the improvement of science in history, and introduced a lot of physical techniques in common use in protein researches such as mass spectroscopy, nuclear magnetic resonance, synchronization X-ray diffraction, infrared spectroscopy and ultraviolet spectroscopy, and then reviewed their application status in quo to ATP synthase. Secondly we paid out attention to the burgeoning unconventionally instruments, i.e., the atomic force microscope and the fluorescence resonance energy transform (FRET) which have attracted the professional attention, and introduced latest application and researches' achievements. Compared the development of the techniques in recent years, we have set forth the shortcoming and excellence of all kinds of equipments introduced. And it was ended with the conclusion that it is necessary to manage the possible instruments effectively and sufficient for the personalities, and given out the optimum research routes which emphasized on the new techniques and novel methods, i.e., the atomic force microscope and FRET. (authors)

  4. Structural and thermodynamic characterization of doxycycline/β-cyclodextrin supramolecular complex and its bacterial membrane interactions.

    Science.gov (United States)

    Suárez, Diego F; Consuegra, Jessika; Trajano, Vivianne C; Gontijo, Sávio M L; Guimarães, Pedro P G; Cortés, Maria E; Denadai, Ângelo L; Sinisterra, Rubén D

    2014-06-01

    Doxycycline is a semi-synthetic antibiotic commonly used for the treatment of many aerobic and anaerobic bacteria. It inhibits the activity of matrix metalloproteinases (MMPs) and affects cell proliferation. In this study, the structural and thermodynamic parameters of free DOX and a DOX/βCD complex were investigated, as well as their interactions and effects on Staphylococcus aureus cells and cellular cytotoxicity. Complexation of DOX and βCD was confirmed to be an enthalpy- and entropy-driven process, and a low equilibrium constant was obtained. Treatment of S. aureus with higher concentrations of DOX or DOX/βCD resulted in an exponential decrease in S. aureus cell size, as well as a gradual neutralization of zeta potential. These thermodynamic profiles suggest that ion-pairing and hydrogen bonding interactions occur between DOX and the membrane of S. aureus. In addition, the adhesion of βCD to the cell membrane via hydrogen bonding is hypothesized to mediate a synergistic effect which accounts for the higher activity of DOX/βCD against S. aureus compared to pure DOX. Lower cytotoxicity and induction of osteoblast proliferation was also associated with DOX/βCD compared with free DOX. These promising findings demonstrate the potential for DOX/βCD to mediate antimicrobial activity at lower concentrations, and provides a strategy for the development of other antimicrobial formulations. Copyright © 2014. Published by Elsevier B.V.

  5. Correlation between the structure and biological activity studies of supramolecular coordination azodye compounds

    Directory of Open Access Journals (Sweden)

    M.I. Abou-Dobara

    2017-02-01

    Full Text Available A series of novel bidentate azodye quinoline ligands were synthesized with various p-aromatic amines like p-(OCH3, CH3, H, Cl and NO2. Novel azodye (HLn and complexes [Cu(II/Ni(II] of these ligands have been characterized on the basis of elemental analysis, molar conductance and magnetic measurements, infrared and electronic spectral studies. Suitable structures have been proposed for these complexes. The synthesized ligands and their metal complexes were screened for their antimicrobial activity against four local bacterial species, two Gram positive bacteria (Bacillus cereus and Staphylococcus aureus and two Gram negative bacteria (Escherichia coli and Klebsiella pneumoniae as well as against four local fungal species; namely Aspergillus niger, Alternaria alternata, Penicillium italicum and Fusarium oxysporium. The tested compounds have good antibacterial activity against B. cereus, E. coli and K. pneumoniae. Very low effect was detected against S. aureus and F. oxysporium. We found that the results of antifungal activity of HLn revealed that the complexes are more toxic than ligands against fungi due to the transition metal involved in the coordination. Also Cu2+ complexes are more active than Ni2+ complexes against B. cereus, E. coli and K. pneumoniae. The size of the clear zone was in the following order p-(OCH3 < CH3 < H < Cl < NO2 as expected from Hammett’s constants σR.

  6. Selective adsorption of a supramolecular structure on flat and stepped gold surfaces

    Science.gov (United States)

    Peköz, Rengin; Donadio, Davide

    2018-04-01

    Halogenated aromatic molecules assemble on surfaces forming both hydrogen and halogen bonds. Even though these systems have been intensively studied on flat metal surfaces, high-index vicinal surfaces remain challenging, as they may induce complex adsorbate structures. The adsorption of 2,6-dibromoanthraquinone (2,6-DBAQ) on flat and stepped gold surfaces is studied by means of van der Waals corrected density functional theory. Equilibrium geometries and corresponding adsorption energies are systematically investigated for various different adsorption configurations. It is shown that bridge sites and step edges are the preferred adsorption sites for single molecules on flat and stepped surfaces, respectively. The role of van der Waals interactions, halogen bonds and hydrogen bonds are explored for a monolayer coverage of 2,6-DBAQ molecules, revealing that molecular flexibility and intermolecular interactions stabilize two-dimensional networks on both flat and stepped surfaces. Our results provide a rationale for experimental observation of molecular carpeting on high-index vicinal surfaces of transition metals.

  7. Tunable N-substitution in zwitterionic benzoquinonemonoimine derivatives: metal coordination, tandemlike synthesis of zwitterionic metal complexes, and supramolecular structures.

    Science.gov (United States)

    Yang, Qing-Zheng; Siri, Olivier; Braunstein, Pierre

    2005-12-09

    Full details on a very efficient transamination reaction for the synthesis of zwitterionic N,N-dialkyl-2-amino-5-alcoholate-1,4-benzoquinonemonoiminium derivatives [C6H2(=NHR)2(=O)2] 5-16 are reported. The molecular structures of zwitterions 5 (R=CH3) in 5.H2O, 13 (R=CH2CH2OMe), 15 (R=CH2CH2NMe2), and of the parent, unsubstituted system [C6H2(=NH2)2(=O)2] 4 in 4.H2O have been established by single-crystal X-ray diffraction. This one-pot preparation can be carried out in water, MeOH, or EtOH and allows access to new zwitterions with N-substituents bearing functionalities such as -OMe (13), -OH (9-12), NR1R2 with R1 = or not equal R2 (14-16) or an alkene (8), leading to a rich coordination chemistry and allowing fine-tuning of the supramolecular arrangements in the solid state. As previously described for 15, which reacted with Zn(acac)2 to afford the octahedral Zn(II) complex [Zn[C6H2(NCH2CH2NMe2)O(O)(NHCH2CH2NMe2)]2] (20), ligands 13 and 16 with coordinating "arms" afforded with Zn(acac)2 the 2:1 adducts [Zn[C6H2(NCH2CH2X)O(=O)(NHCH2CH2NX)]2] 19 (X=OMe) and 21 (X=NHEt), with N2O4 and N4O2 donor sets around the octahedral Zn(II) center, respectively. Furthermore, zwitterions 15 and 16 reacted with ZnCl2 to give the stable, crystallographically characterized Zn(II) zwitterionic complexes [ZnCl2[C6H2(NCH2CH2NR1R2)O(=O)(NHCH2CH2NHR1R2)

  8. Novel peptide-specific quantitative structure-activity relationship (QSAR) analysis applied to collagen IV peptides with antiangiogenic activity.

    Science.gov (United States)

    Rivera, Corban G; Rosca, Elena V; Pandey, Niranjan B; Koskimaki, Jacob E; Bader, Joel S; Popel, Aleksander S

    2011-10-13

    Angiogenesis is the growth of new blood vessels from existing vasculature. Excessive vascularization is associated with a number of diseases including cancer. Antiangiogenic therapies have the potential to stunt cancer progression. Peptides derived from type IV collagen are potent inhibitors of angiogenesis. We wanted to gain a better understanding of collagen IV structure-activity relationships using a ligand-based approach. We developed novel peptide-specific QSAR models to study the activity of the peptides in endothelial cell proliferation, migration, and adhesion inhibition assays. We found that the models produced quantitatively accurate predictions of activity and provided insight into collagen IV derived peptide structure-activity relationships.

  9. Primary structure and conformational analysis of peptide methionine-tyrosine, a peptide related to neuropeptide Y and peptide YY isolated from lamprey intestine

    DEFF Research Database (Denmark)

    Conlon, J M; Bjørnholm, B; Jørgensen, Flemming Steen

    1991-01-01

    A peptide belonging to the pancreatic-polypeptide-fold family of regulatory peptides has been isolated from the intestine of an Agnathan, the sea lamprey (Petromyzon marinus). The primary structure of the peptide (termed peptide methionine-tyrosine) was established as Met-Pro-Pro-Lys-Pro-Asp-Asn-......A peptide belonging to the pancreatic-polypeptide-fold family of regulatory peptides has been isolated from the intestine of an Agnathan, the sea lamprey (Petromyzon marinus). The primary structure of the peptide (termed peptide methionine-tyrosine) was established as Met......%) or with pig pancreatic polypeptide (42%). Molecular modelling and dynamic simulation, based upon sequence similarity with turkey pancreatic polypeptide, indicates that the conformations of the polyproline-helix-like region (residues 1-8) and the alpha-helical region (residues 15-30) in turkey pancreatic...... polypeptide are conserved in peptide methionine-tyrosine, and that non-bonded interactions between these domains have preserved the overall polypeptide fold in the molecule. The substitution of the otherwise totally conserved Gly9 residue by serine in lamprey peptide methionine-tyrosine, however, results...

  10. Supramolecular polymers

    National Research Council Canada - National Science Library

    Ciferri, A

    2000-01-01

    ... to the new class of self-assembled polymers that undergo reversible growth by the formation of noncovalent bonds. This class (Part II) is wider than expected: not only mainchain assemblies of hydrogen-bonded repeating units, but also planar organization of S-layer proteins, micellar and related three-dimensional structures of blo...

  11. New five coordinated supramolecular structured cadmium complex as precursor for CdO nanoparticles: Synthesis, crystal structure, theoretical and 3D Hirshfeld surface analyses

    Science.gov (United States)

    Ghanbari Niyaky, S.; Montazerozohori, M.; Masoudiasl, A.; White, J. M.

    2017-03-01

    In this paper, a combined experimental and theoretical study on a new CdLBr2 complex (L = N1-(2-bromobenzylidene)-N2-(2-((E)-(2-bromobenzylidene) amino)ethyl) ethane-1,2-diamine) synthesized via template method, is described. The crystal structure analysis of the complex indicates that, the Cd(II) ion is centered in a distorted square pyramidal space constructed by three iminic nitrogens of the ligand as well as two bromide anions. More analysis of crystal packing proposed a supramolecular structure stabilized by some non-covalent interactions such as Br⋯Br and Xsbnd H⋯Br (X = N and C) in solid state. Furthermore, 3D Hirshfeld surface analyses and DFT studies were applied for theoretical investigation of the complexes. Theoretical achievements were found in a good agreement with respect to the experimental data. To evaluate the nature of bonding and the strength of the intra and inter-molecular interactions a natural bond orbital (NBO) analysis on the complex structure was performed. Time dependent density functional theory (TD-DFT) was also applied to predict the electronic spectral data of the complex as compared with the experimental ones. CdLBr2 complex as nano-structure compound was also prepared under ultrasonic conditions and characterized by scanning electron microscopy (SEM) and X-ray powder diffraction (XRPD). Finally, it was found that the cadmium complex can be used as a suitable precursor for preparation of CdO nanoparticles via calcination process at 600 °C under air atmosphere.

  12. Recognition of GPCRs by peptide ligands and membrane compartments theory: structural studies of endogenous peptide hormones in membrane environment.

    Science.gov (United States)

    Sankararamakrishnan, Ramasubbu

    2006-04-01

    One of the largest family of cell surface proteins, G-protein coupled receptors (GPCRs) regulate virtually all known physiological processes in mammals. With seven transmembrane segments, they respond to diverse range of extracellular stimuli and represent a major class of drug targets. Peptidergic GPCRs use endogenous peptides as ligands. To understand the mechanism of GPCR activation and rational drug design, knowledge of three-dimensional structure of receptor-ligand complex is important. The endogenous peptide hormones are often short, flexible and completely disordered in aqueous solution. According to "Membrane Compartments Theory", the flexible peptide binds to the membrane in the first step before it recognizes its receptor and the membrane-induced conformation is postulated to bind to the receptor in the second step. Structures of several peptide hormones have been determined in membrane-mimetic medium. In these studies, micelles, reverse micelles and bicelles have been used to mimic the cell membrane environment. Recently, conformations of two peptide hormones have also been studied in receptor-bound form. Membrane environment induces stable secondary structures in flexible peptide ligands and membrane-induced peptide structures have been correlated with their bioactivity. Results of site-directed mutagenesis, spectroscopy and other experimental studies along with the conformations determined in membrane medium have been used to interpret the role of individual residues in the peptide ligand. Structural differences of membrane-bound peptides that belong to the same family but differ in selectivity are likely to explain the mechanism of receptor selectivity and specificity of the ligands. Knowledge of peptide 3D structures in membrane environment has potential applications in rational drug design.

  13. Non-equilibrium supramolecular polymerization.

    Science.gov (United States)

    Sorrenti, Alessandro; Leira-Iglesias, Jorge; Markvoort, Albert J; de Greef, Tom F A; Hermans, Thomas M

    2017-09-18

    Supramolecular polymerization has been traditionally focused on the thermodynamic equilibrium state, where one-dimensional assemblies reside at the global minimum of the Gibbs free energy. The pathway and rate to reach the equilibrium state are irrelevant, and the resulting assemblies remain unchanged over time. In the past decade, the focus has shifted to kinetically trapped (non-dissipative non-equilibrium) structures that heavily depend on the method of preparation (i.e., pathway complexity), and where the assembly rates are of key importance. Kinetic models have greatly improved our understanding of competing pathways, and shown how to steer supramolecular polymerization in the desired direction (i.e., pathway selection). The most recent innovation in the field relies on energy or mass input that is dissipated to keep the system away from the thermodynamic equilibrium (or from other non-dissipative states). This tutorial review aims to provide the reader with a set of tools to identify different types of self-assembled states that have been explored so far. In particular, we aim to clarify the often unclear use of the term "non-equilibrium self-assembly" by subdividing systems into dissipative, and non-dissipative non-equilibrium states. Examples are given for each of the states, with a focus on non-dissipative non-equilibrium states found in one-dimensional supramolecular polymerization.

  14. Functional supramolecular polymers for biomedical applications.

    Science.gov (United States)

    Dong, Ruijiao; Zhou, Yongfeng; Huang, Xiaohua; Zhu, Xinyuan; Lu, Yunfeng; Shen, Jian

    2015-01-21

    As a novel class of dynamic and non-covalent polymers, supramolecular polymers not only display specific structural and physicochemical properties, but also have the ability to undergo reversible changes of structure, shape, and function in response to diverse external stimuli, making them promising candidates for widespread applications ranging from academic research to industrial fields. By an elegant combination of dynamic/reversible structures with exceptional functions, functional supramolecular polymers are attracting increasing attention in various fields. In particular, functional supramolecular polymers offer several unique advantages, including inherent degradable polymer backbones, smart responsiveness to various biological stimuli, and the ease for the incorporation of multiple biofunctionalities (e.g., targeting and bioactivity), thereby showing great potential for a wide range of applications in the biomedical field. In this Review, the trends and representative achievements in the design and synthesis of supramolecular polymers with specific functions are summarized, as well as their wide-ranging biomedical applications such as drug delivery, gene transfection, protein delivery, bio-imaging and diagnosis, tissue engineering, and biomimetic chemistry. These achievements further inspire persistent efforts in an emerging interdisciplin-ary research area of supramolecular chemistry, polymer science, material science, biomedical engineering, and nanotechnology. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Supramolecular Photodimerization of Coumarins

    Directory of Open Access Journals (Sweden)

    Koichi Tanaka

    2012-02-01

    Full Text Available Stereoselective photodimerization of coumarin and its derivatives in supra-molecular systems is reviewed. The enantioselective photodimerization of coumarin and thiocoumarin in inclusion crystals with optically active host compounds is also described.

  16. Supramolecular catalysis: Refocusing catalysis

    NARCIS (Netherlands)

    van Leeuwen, P.W.N.M.; Freixa, Z.; van Leeuwen, P.W.N.M.

    2008-01-01

    This chapter contains sections titled: * Introduction: A Brief Personal History * Secondary Phosphines or Phosphites as Supramolecular Ligands * Host-Guest Catalysis * Ionic Interactions as a Means to Form Heterobidentate Assembly Ligands * Ditopic Ligands for the Construction of Bidentate Phosphine

  17. Different conjugated system Zn(ii) Schiff base complexes: supramolecular structure, luminescent properties, and applications in the PMMA-doped hybrid materials.

    Science.gov (United States)

    Dong, Yu-Wei; Fan, Rui-Qing; Chen, Wei; Zhang, Hui-Jie; Song, Yang; Du, Xi; Wang, Ping; Wei, Li-Guo; Yang, Yu-Lin

    2017-01-24

    A series of Zn(ii) complexes with different conjugated systems, [ZnL1Cl 2 ] 2 (Zn1), [ZnL2Cl 2 ] (Zn2), [Zn(L3) 2 ]·(ClO 4 ) 2 (Zn3), [Zn 2 L4Cl 4 ] (Zn4), and [ZnL5Cl 2 ] (Zn5), were synthesized and subsequently characterized via single crystal X-ray diffraction, 1 H and 13 C NMR, FT-IR, elemental analyses, melting point, and PXRD. The X-ray diffraction analyses revealed that the supramolecular frameworks of complexes Zn1-Zn5 are constructed by C-HO/Cl hydrogen bonds and ππ interactions. Complexes Zn1-Zn3 feature 3D 6-connected {4 12 ·6 3 } topological structures, whereas complex Zn4 exhibits a 3D 7-connected supramolecular framework with a {4 17 ·6 4 } topological structure. However, complex Zn5 shows one-dimensional "wave-like" chains. Based on these varied structures, the emission maximum wavelengths of complexes Zn1-Zn5 can be tuned in a wide range of 461-592 nm due to the red shift direction of λ em caused by different conjugated systems and their electron donating abilities. Complex Zn3 shows a strong luminescence in the solid state and in the acetonitrile solution. Therefore, a series of Zn3-poly(methylmethacrylate) (Zn3-PMMA) hybrid materials were obtained by controlling the concentration of complex Zn3 in poly(methylmethacrylate) (PMMA). At an optimal concentration of 4%, the doped polymer film of Zn3-PMMA displays strong green luminescence emissions that are 19-fold in the luminescence intensities and 98 °C higher in the thermal stability temperature compared to the Zn3 film.

  18. How Peptide Molecular Structure and Charge Influence the Nanostructure of Lipid Bicontinuous Cubic Mesophases: Model Synthetic WALP Peptides Provide Insights.

    Science.gov (United States)

    van 't Hag, Leonie; Li, Xu; Meikle, Thomas G; Hoffmann, Søren V; Jones, Nykola C; Pedersen, Jan Skov; Hawley, Adrian M; Gras, Sally L; Conn, Charlotte E; Drummond, Calum J

    2016-07-12

    Nanostructured bicontinuous lipidic cubic phases are used for the encapsulation of proteins in a range of applications such as in meso crystallization of transmembrane proteins and as drug delivery vehicles. The retention of the nanoscale order of the cubic phases subsequent to protein incorporation, as well as retention of the protein structure and function, is essential for all of these applications. Herein synthetic peptides (WALP21, WALPS53, and WALPS73) with a common α-helical hydrophobic domain, but varying hydrophilic loop size, were designed to systematically examine the effect of peptide structure and charge on bicontinuous cubic phases. The effect of the cubic phases on the secondary structure of the peptides was also investigated. The incorporation of the WALP peptides in cubic phases formed by a range of lipids showed that hydrophobic mismatch of the peptides with the lipid bilayers, the hydrophilic domain size, and peptide charge were all significant factors determining the response of the lipid nanomaterial to protein insertion. As charge repulsion had the most significant effect on the phase transitions observed, we suggest that buffer pH and salt concentration must be carefully considered to ensure cubic mesophase retention. Importantly, the WALP peptides were found to have a different conformation depending on the local lipid environment. Such structural changes could potentially affect membrane protein function, which is crucial for both current and prospective applications.

  19. A supramolecular structure based on copper complex of 2,3-pyridinedicarboxylic acid and 1,3-bis(3-aminopropyl)tetramethyldisiloxane chlorohydrate

    Science.gov (United States)

    Soroceanu, Alina; Bargan, Alexandra; Shova, Sergiu; Avadanei, Mihaela; Cazacu, Maria

    2015-03-01

    Having in mind the synthesis of a cooper complex with the product of condensation between an anhydride and a siloxane diamine as a new polydentate ligand, 2,3-pyridinedicarboxylic anhydride (PDCA) was treated first with 1,3-bis(3-aminopropyl)tetramethyldisiloxane (AP0) and then with cooper chloride in alcoholic solution. However, according to single-crystal X-ray crystallography and IR spectroscopy, the reaction resulted in an ionic compound with the charge balance in agreement with the formation of [H2AP0]2[Cu(PDC)2]·Cl2·2H2O species, where PDC is a double deprotonated 2,3-pyridinedicarboxylic acid. The thermal and moisture behaviors of the complex were studied by thermogravimetrical analysis and dynamic vapor sorption, respectively. The stability of the supramolecular structure with temperature and in methanol solution was studied by ATR-FTIR analysis.

  20. Communication: Supramolecular structures in monohydroxy alcohols: Insights from shear-mechanical studies of a systematic series of octanol structural isomers

    DEFF Research Database (Denmark)

    Hecksher, Tina; Jakobsen, Bo

    2014-01-01

    response, also has a mechanical signature. In this work, we apply broadband shear-mechanical spectroscopy to a systematic series of octanol structural isomers, x-methyl-3-heptanol (with x ranging from 2 to 6). We find that the characteristics of the mechanical signature overall follow the systematic...

  1. Synthesis, spectral, crystal structure, thermal behavior, antimicrobial and DNA cleavage potential of two octahedral cadmium complexes: A supramolecular structure

    Czech Academy of Sciences Publication Activity Database

    Montazerozohori, M.; Musavi, S.A.; Masoudiasl, A.; Naghiha, A.; Dušek, Michal; Kučeráková, Monika

    2015-01-01

    Roč. 137, FEB (2015), s. 389-396 ISSN 1386-1425 R&D Projects: GA ČR(CZ) GA14-03276S Institutional support: RVO:68378271 Keywords : Schiff base * Cd(II) * DNA cleavage * TG/DTG analysis * X-ray structure analysis Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.653, year: 2015

  2. The structure of salt bridges between Arg(+) and Glu(-) in peptides investigated with 2D-IR spectroscopy: Evidence for two distinct hydrogen-bond geometries.

    Science.gov (United States)

    Huerta-Viga, Adriana; Amirjalayer, Saeed; Domingos, Sérgio R; Meuzelaar, Heleen; Rupenyan, Alisa; Woutersen, Sander

    2015-06-07

    Salt bridges play an important role in protein folding and in supramolecular chemistry, but they are difficult to detect and characterize in solution. Here, we investigate salt bridges between glutamate (Glu(-)) and arginine (Arg(+)) using two-dimensional infrared (2D-IR) spectroscopy. The 2D-IR spectrum of a salt-bridged dimer shows cross peaks between the vibrational modes of Glu(-) and Arg(+), which provide a sensitive structural probe of Glu(-)⋯Arg(+) salt bridges. We use this probe to investigate a β-turn locked by a salt bridge, an α-helical peptide whose structure is stabilized by salt bridges, and a coiled coil that is stabilized by intra- and intermolecular salt bridges. We detect a bidentate salt bridge in the β-turn, a monodentate one in the α-helical peptide, and both salt-bridge geometries in the coiled coil. To our knowledge, this is the first time 2D-IR has been used to probe tertiary side chain interactions in peptides, and our results show that 2D-IR spectroscopy is a powerful method for investigating salt bridges in solution.

  3. Cytotoxicity and photocytotoxicity of structure-defined water-soluble C{sub 60}/micelle supramolecular nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Metanawin, Tanapak; Tang Tian; Chen Rongjun; Wang Xiaosong [School of Chemistry, University of Leeds, LS2 9TJ (United Kingdom); Vernon, David, E-mail: X.S.Wang@leeds.ac.uk [School of Biological Sciences, University of Leeds, LS2 9TJ (United Kingdom)

    2011-06-10

    Well-defined, water-soluble C{sub 60}/micelle hierarchical colloids with varied amounts of C{sub 60} sitting on the surface of micellar cores were prepared via the self-assembly of PS-b-PDMA block copolymer micelles and C{sub 60}. The composites can generate a significant amount of reactive oxygen upon irradiation with red light. Cell studies showed that the colloids were either strongly associated with, or internalized by, the cells after 2 h incubation, but did not show obvious toxicity in the dark. In contrast, efficient cell killing was observed when the colloid-incubated cells were exposed to red light. This indicates that the supramolecular colloids are promising as photosensitizers for photodynamic cancer therapy.

  4. Computational analysis and structure predictions of CHH-related peptides from Litopenaeus vannamei.

    Science.gov (United States)

    Nagaraju, G Purna Chandra; Kumari, N Siva; Prasad, G L V; Naik, B Reddya; Borst, D W

    2011-03-01

    The crustaceans produce several related peptides that belong to the crustacean hyperglycemic hormone (CHH) family. While these peptides have similar amino acid sequences, they have diverse biological functions that must arise, in part, from differences in the 3D shape of these peptides. However, it is generally accepted that peptides with a high degree of sequence similarity also have a similar 3-D structure. We used the solution structure of one peptide in the crustacean hyperglycemic hormone family, the molt-inhibiting hormone of the kuruma prawn (Marsupenaeus japonicus), to predict the shape of the five known peptides related to CHH in the Pacific white shrimp, Litopenaeus vannamei. The high similarity of the 3-D structures of these peptides suggests a common fold for the entire family. Nevertheless, minor differences in the shape of these peptides were observed, which may be the basis for their different biological properties.

  5. RFamide Peptides: Structure, Function, Mechanisms and Pharmaceutical Potential

    Directory of Open Access Journals (Sweden)

    Maria Findeisen

    2011-09-01

    Full Text Available Different neuropeptides, all containing a common carboxy-terminal RFamide sequence, have been characterized as ligands of the RFamide peptide receptor family. Currently, five subgroups have been characterized with respect to their N-terminal sequence and hence cover a wide pattern of biological functions, like important neuroendocrine, behavioral, sensory and automatic functions. The RFamide peptide receptor family represents a multiligand/multireceptor system, as many ligands are recognized by several GPCR subtypes within one family. Multireceptor systems are often susceptible to cross-reactions, as their numerous ligands are frequently closely related. In this review we focus on recent results in the field of structure-activity studies as well as mutational exploration of crucial positions within this GPCR system. The review summarizes the reported peptide analogs and recently developed small molecule ligands (agonists and antagonists to highlight the current understanding of the pharmacophoric elements, required for affinity and activity at the receptor family. Furthermore, we address the biological functions of the ligands and give an overview on their involvement in physiological processes. We provide insights in the knowledge for the design of highly selective ligands for single receptor subtypes to minimize cross-talk and to eliminate effects from interactions within the GPCR system. This will support the drug development of members of the RFamide family.

  6. Supramolecular Phase-Selective Gelation by Peptides Bearing Side-Chain Azobenzenes: Effect of Ultrasound and Potential for Dye Removal and Oil Spill Remediation

    Science.gov (United States)

    Bachl, Jürgen; Oehm, Stefan; Mayr, Judith; Cativiela, Carlos; Marrero-Tellado, José Juan; Díaz Díaz, David

    2015-01-01

    Phase selective gelation (PSG) of organic phases from their non-miscible mixtures with water was achieved using tetrapeptides bearing a side-chain azobenzene moiety. The presence of the chromophore allowed PSG at the same concentration as the minimum gelation concentration (MGC) necessary to obtain the gels in pure organic phases. Remarkably, the presence of the water phase during PSG did not impact the thermal, mechanical, and morphological properties of the corresponding organogels. In the case of miscible oil/water mixtures, the entire mixture was gelled, resulting in the formation of quasi-hydrogels. Importantly, PSG could be triggered at room temperature by ultrasound treatment of the mixture or by adding ultrasound-aided concentrated solution of the peptide in an oil-phase to a mixture of the same oil and water. Moreover, the PSG was not affected by the presence of salts or impurities existing in water from natural sources. The process could be scaled-up, and the oil phases (e.g., aromatic solvents, gasoline, diesel fuel) recovered almost quantitatively after a simple distillation process, which also allowed the recovery and reuse of the gelator. Finally, these peptidic gelators could be used to quantitatively remove toxic dyes from aqueous solutions. PMID:26006247

  7. Synthesis, spectroscopy, thermal studies and supramolecular ...

    Indian Academy of Sciences (India)

    TECS

    structures of two new alkali-earth 4-nitrobenzoate complexes containing ... adopt a cis orientation in 2 resulting in different supramolecular structures. Complex 1 .... The compound analysed satisfactorily and exhibited an identical IR spectrum as that of the product from method 1. 2.2 Preparation of anhydrous complexes.

  8. Structural Heterogeneity of Doubly-Charged Peptide b-Ions

    Science.gov (United States)

    Li, Xiaojuan; Huang, Yiqun; O'Connor, Peter B.; Lin, Cheng

    2011-02-01

    Performing collisionally activated dissociation (CAD) and electron capture dissociation (ECD) in tandem has shown great promise in providing comprehensive sequence information that was otherwise unobtainable by using either fragmentation method alone or in duet. However, the general applicability of this MS3 approach in peptide sequencing may be undermined by the formation of non-direct sequence ions, as sometimes observed under CAD, particularly when multiple stages of CAD are involved. In this study, varied-sized doubly-charged b-ions from three tachykinin peptides were investigated by ECD. Sequence scrambling was observed in ECD of all b-ions from neurokinin A (HKTDSFVGLM-NH2), suggesting the presence of N- and C-termini linked macro-cyclic conformers. On the contrary, none of the b-ions from eledoisin (pEPSKDAFIGLM-NH2) produced non-direct sequence ions under ECD, as it does not contain a free N-terminal amino group. ECD of several b-ions from Substance P (RPKPQQFFGLM-NH2) showed series of cm-Lys fragment ions which suggested that the macro-cyclic structure may also be formed by connecting the C-terminal carbonyl group and the ɛ-amino group of the lysine side chain. Theoretical investigation of selected Substance P b-ions revealed several low energy conformers, including both linear oxazolones and macro-ring structures, in corroboration with the experimental observation. This study showed that a b-ion may exist as a mixture of several forms, with their propensities influenced by its N-terminus, length, and certain side-chain groups. Further, the presence of several macro-cyclic structures may result in erroneous sequence assignment when the combined CAD and ECD methods are used in peptide sequencing.

  9. Structural Basis of Rap Phosphatase Inhibition by Phr Peptides

    Science.gov (United States)

    Gallego del Sol, Francisca; Marina, Alberto

    2013-01-01

    Two-component systems, composed of a sensor histidine kinase and an effector response regulator (RR), are the main signal transduction devices in bacteria. In Bacillus, the Rap protein family modulates complex signaling processes mediated by two-component systems, such as competence, sporulation, or biofilm formation, by inhibiting the RR components involved in these pathways. Despite the high degree of sequence homology, Rap proteins exert their activity by two completely different mechanisms of action: inducing RR dephosphorylation or blocking RR binding to its target promoter. However the regulatory mechanism involving Rap proteins is even more complex since Rap activity is antagonized by specific signaling peptides (Phr) through a mechanism that remains unknown at the molecular level. Using X-ray analyses, we determined the structure of RapF, the anti-activator of competence RR ComA, alone and in complex with its regulatory peptide PhrF. The structural and functional data presented herein reveal that peptide PhrF blocks the RapF-ComA interaction through an allosteric mechanism. PhrF accommodates in the C-terminal tetratricopeptide repeat domain of RapF by inducing its constriction, a conformational change propagated by a pronounced rotation to the N-terminal ComA-binding domain. This movement partially disrupts the ComA binding site by triggering the ComA disassociation, whose interaction with RapF is also sterically impaired in the PhrF-induced conformation of RapF. Sequence analyses of the Rap proteins, guided by the RapF-PhrF structure, unveil the molecular basis of Phr recognition and discrimination, allowing us to relax the Phr specificity of RapF by a single residue change. PMID:23526880

  10. Functional and structural characteristics of anticancer peptide Pep27 analogues

    Directory of Open Access Journals (Sweden)

    Seo Youn-Kyung

    2005-07-01

    Full Text Available Abstract Background A secreted peptide Pep27 initiates the cell death program in S. pneumoniae through signal transduction. This study was undertaken to evaluate the relation between the structure and cytotoxic activity of Pep27 and its analogues on cancer cells. Results Pep27anal2 characterized substituting (2R→W, (4E→W, (11S→W and (13Q→W in native Pep27, exhibited greater hydrophobicity and anticancer activity than Pep27 and other analogues. The IC50 values of Pep27anal2 were approximately 10 – 30 μM in a number of cell lines (AML-2, HL-60, Jurkat, MCF-7 and SNU-601. Confocal microscopy showed that Pep27anal2-FITC was localized in the plasma membrane, and then moving from the membrane to subcellular compartments with the initiation of membrane blebbing. Flow cytometric analysis using propidium iodide and Annexin V also revealed that Pep27anal2 induced apoptosis with minor membrane damage. Electron microscopy revealed that Pep27 induced apoptosis in Jurkat cells. The anticancer activity of Pep27anal2 was neither abrogated by pan-caspase inhibitor (Z-VAD-fmk nor related to cytochrome c release from mitochondria. The 3D solution structures of these two Pep27 peptides revealed that both form a random coil conformation in water; however, they adopted stable α-helical conformations in solutions. Conclusion The results indicate that Pep27anal2 can penetrate the plasma membrane, and then induce apoptosis in both caspase-and cytochrome c-independent manner. The hydrophobicity of Pep27anal2 appears to play an important role in membrane permeabilization and/or anticancer properties. The structure-functional relationships of these peptides are also discussed. It is proposed that Pep27anal2 is a potential candidate for anticancer therapeutic agents.

  11. Structure of HLA-A*1101 in complex with a hepatitis B peptide homologue

    DEFF Research Database (Denmark)

    Blicher, Thomas; Kastrup, Jette Sandholm; Pedersen, Lars Østergaard

    2006-01-01

    A high-resolution structure of the human MHC-I molecule HLA-A*1101 is presented in which it forms a complex with a sequence homologue of a peptide that occurs naturally in hepatitis B virus DNA polymerase. The sequence of the bound peptide is AIMPARFYPK, while that of the corresponding natural pe...... peptide is LIMPARFYPK. The peptide does not make efficient use of the middle E pocket for binding, which leads to a rather superficial and exposed binding mode for the central peptide residues. Despite this, the peptide binds with high affinity (IC50 of 31 nM)....

  12. Sound attenuation of polymerizing actin reflects supramolecular structures: viscoelastic properties of actin gels modified by cytochalasin D, profilin and alpha-actinin.

    Science.gov (United States)

    Wagner, O; Schüler, H; Hofmann, P; Langer, D; Dancker, P; Bereiter-Hahn, J

    2001-05-01

    Polymerization and depolymerization of cytoskeletal elements maintaining cytoplasmic stiffness are key factors in the control of cell crawling. Rheometry is a significant tool in determining the mechanical properties of the single elements in vitro. Viscoelasticity of gels formed by these polymers strongly depends on both the length and the associations of the filaments (e.g. entanglements, annealings and side-by-side associations). Ultrasound attenuation is related to viscosity, sound velocity and supramolecular structures in the sample. In combination with a small glass fibre (2 mm x 50 microm), serving as a viscosity sensor, an acoustic microscope was used to measure the elasticity and acoustic attenuation of actin solutions. Changes in acoustic attenuation of polymerizing actin by far exceed the values expected from calculations based on changes in viscosity and sound velocity. During the lag-phase of actin polymerization, attenuation slightly decreases, depending on actin concentration. After the half-maximum viscosity is accomplished and elasticity turns into steady state, attenuation distinctly rises. Changes in ultrasound attenuation depend on actin concentration, and they are modulated by the addition of alpha-actinin, cytochalasin D and profilin. Thus absorption and scattering of sound on the polymerization of actin is related to the packing density of the actin net, entanglements and the length of the actin filaments. Shortening of actin filaments by cytochalasin D was also confirmed by electron micrographs and falling-ball viscosimetry. In addition to viscosity and elasticity, the attenuation of sound proved to be a valuable parameter in characterizing actin polymerization and the supramolecular associations of F-actin.

  13. Exploring the Changes in the Structure of α-Helical Peptides ...

    Indian Academy of Sciences (India)

    sathish

    peptides based on alanine. • Validation of the results with respect to different force fields. • Interaction of long α-helical peptides derived from X-ray crystal structure with CNT. • Assessment of role of different interactions in the stabilization of CNT-peptide complex. K. Balamurugan, R. Gopalakrishnan, S. Sundar Raman, and ...

  14. Cyclic peptide as reference system for b ion structural analysis in the gas phase

    NARCIS (Netherlands)

    Chen, X.; Tirado, M.; Steill, J. D.; Oomens, J.; Polfer, N. C.

    2011-01-01

    Infrared multiple photon dissociation spectroscopy and hydrogen/deuterium exchange methods are used to confirm the macrocylic structure of a b(6) peptide fragment by direct comparison with a synthetically made cyclic peptide. The acetylation of the peptide N-terminus results in the inhibition of the

  15. Cyclic peptide as reference system for b ion structural analysis in the gas phase

    NARCIS (Netherlands)

    Chen, X.; Tirado, M.; Steill, J.D.; Oomens, J.; Polfer, N.C.

    2011-01-01

    Infrared multiple photon dissociation spectroscopy and hydrogen/deuterium exchange methods are used to confirm the macrocylic structure of a b6 peptide fragment by direct comparison with a synthetically made cyclic peptide. The acetylation of the peptide N-terminus results in the inhibition of the

  16. 3D Printing Polymers with Supramolecular Functionality for Biological Applications.

    Science.gov (United States)

    Pekkanen, Allison M; Mondschein, Ryan J; Williams, Christopher B; Long, Timothy E

    2017-09-11

    Supramolecular chemistry continues to experience widespread growth, as fine-tuned chemical structures lead to well-defined bulk materials. Previous literature described the roles of hydrogen bonding, ionic aggregation, guest/host interactions, and π-π stacking to tune mechanical, viscoelastic, and processing performance. The versatility of reversible interactions enables the more facile manufacturing of molded parts with tailored hierarchical structures such as tissue engineered scaffolds for biological applications. Recently, supramolecular polymers and additive manufacturing processes merged to provide parts with control of the molecular, macromolecular, and feature length scales. Additive manufacturing, or 3D printing, generates customizable constructs desirable for many applications, and the introduction of supramolecular interactions will potentially increase production speed, offer a tunable surface structure for controlling cell/scaffold interactions, and impart desired mechanical properties through reinforcing interlayer adhesion and introducing gradients or self-assembled structures. This review details the synthesis and characterization of supramolecular polymers suitable for additive manufacture and biomedical applications as well as the use of supramolecular polymers in additive manufacturing for drug delivery and complex tissue scaffold formation. The effect of supramolecular assembly and its dynamic behavior offers potential for controlling the anisotropy of the printed objects with exquisite geometrical control. The potential for supramolecular polymers to generate well-defined parts, hierarchical structures, and scaffolds with gradient properties/tuned surfaces provides an avenue for developing next-generation biomedical devices and tissue scaffolds.

  17. Structural Diversity and Biological Activities of Fungal Cyclic Peptides, Excluding Cyclodipeptides

    OpenAIRE

    Xiaohan Wang; Minyi Lin; Dan Xu; Daowan Lai; Ligang Zhou

    2017-01-01

    Cyclic peptides are cyclic compounds formed mainly by the amide bonds between either proteinogenic or non-proteinogenic amino acids. This review highlights the occurrence, structures and biological activities of fungal cyclic peptides (excluding cyclodipeptides, and peptides containing ester bonds in the core ring) reported until August 2017. About 293 cyclic peptides belonging to the groups of cyclic tri-, tetra-, penta-, hexa-, hepta-, octa-, nona-, deca-, undeca-, dodeca-, tetradeca-, and ...

  18. Topology-dependent swichability of peptide secondary structures in bioconjugates with complex architectures.

    Science.gov (United States)

    Börner, Hans G; Sütterlin, Romina I; Theato, Patrick; Wiss, Kerstin T

    2014-01-01

    Peptide sequences, which exhibit a reversible pH-responsive coil to α-helix secondary structure transition, are conjugated to polymer precursors to yield linear AB and graft ABA peptide-poly(ethylene oxide) conjugates. While the PEO B-block is comparable, the conjugates differ in topologies of the peptide bearing A-blocks. The influences of topology on the structure transitions in the peptide segments are investigated, comparing linear AB-bioconjugates with graft ABA-bioconjugates having multiple peptide segments combined in star or pom-pom topologies. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Comparison of precursor structures of the GGNG peptides derived from the earthworm Eisenia foetida and the leech Hirudo nipponia.

    Science.gov (United States)

    Minakata, H; Ikeda, T; Nagahama, T; Oumi, T; Ukena, K; Matsushima, O; Kawano, T; Kimura, Y

    1999-02-01

    Earthworm and leech cDNAs encoding the GGNG peptides, a family of myotropic peptides, were cloned and examined in this study. Both of the predicted precursor proteins are of polyprotein structure and contain several putative peptides distinct from the GGNG peptides. However, the precursors show organizations distinct from each other and no sequence similarity except for the GGNG peptides.

  20. X-ray studies on crystalline complexes involving amino acids and peptides. XLII. Adipic acid complexes of L- and DL-arginine and supramolecular association in arginine-dicarboxylic acid complexes.

    Science.gov (United States)

    Roy, Siddhartha; Singh, Desh Deepak; Vijayan, M

    2005-02-01

    The adipic acid complexes of DL-arginine and L-arginine are made up of zwitterionic, singularly positively charged arginium ions and doubly negatively charged adipate ions, with a 2:1 stoichiometry. One of the two crystallographically independent arginium ions in the L-arginine complex has a conformation hitherto unobserved in crystal structures containing the amino acid. In the present study the structural data on arginine complexes of saturated dicarboxylic acids with 0-5 C atoms separating the two carboxyl functions are given. In terms of molecular aggregation, formic and acetic acid complexes behave in a similar way to those involving fairly long carboxylic acids such as adipic acid. By and large, the supramolecular assembly in complexes involving dicarboxylic acids with 3 or more C atoms separating the carboxyl groups (glutaric, adipic and pimelic acids), and those involving formic and acetic acids, have common features. The aggregation patterns in complexes involving oxalic, malonic and maleic acids do not share striking features among themselves (except for the mode of hydrogen-bonded dimerization of arginium ions) or with those involving larger dicarboxylic acids. Complexes of succinic acid, the shortest linear dicarboxylic acid, share features with those involving shorter as well as longer dicarboxylic acids. The difference in the behaviour of long and short dicarboxylic acids and the ambiguous behaviour of succinic acid can be broadly related to their lengths.

  1. Carbohydrates in Supramolecular Chemistry.

    Science.gov (United States)

    Delbianco, Martina; Bharate, Priya; Varela-Aramburu, Silvia; Seeberger, Peter H

    2016-02-24

    Carbohydrates are involved in a variety of biological processes. The ability of sugars to form a large number of hydrogen bonds has made them important components for supramolecular chemistry. We discuss recent advances in the use of carbohydrates in supramolecular chemistry and reveal that carbohydrates are useful building blocks for the stabilization of complex architectures. Systems are presented according to the scaffold that supports the glyco-conjugate: organic macrocycles, dendrimers, nanomaterials, and polymers are considered. Glyco-conjugates can form host-guest complexes, and can self-assemble by using carbohydrate-carbohydrate interactions and other weak interactions such as π-π interactions. Finally, complex supramolecular architectures based on carbohydrate-protein interactions are discussed.

  2. Supramolecular luminescence from oligofluorenol-based supramolecular polymer semiconductors.

    Science.gov (United States)

    Zhang, Guang-Wei; Wang, Long; Xie, Ling-Hai; Lin, Jin-Yi; Huang, Wei

    2013-11-13

    Supramolecular luminescence stems from non-covalent exciton behaviors of active π-segments in supramolecular entities or aggregates via intermolecular forces. Herein, a π-conjugated oligofluorenol, containing self-complementary double hydrogen bonds, was synthesized using Suzuki coupling as a supramolecular semiconductor. Terfluorenol-based random supramolecular polymers were confirmed via concentration-dependent nuclear magnetic resonance (NMR) and dynamic light scattering (DLS). The photoluminescent spectra of the TFOH-1 solution exhibit a green emission band (g-band) at approximately ~520 nm with reversible features, as confirmed through titration experiments. Supramolecular luminescence of TFOH-1 thin films serves as robust evidence for the aggregates of g-band. Our results suggest that the presence of polyfluorene ketone defects is a sufficient condition, rather than a sufficient-necessary condition for the g-band. Supramolecular electroluminescence will push organic devices into the fields of supramolecular optoelectronics, spintronics, and mechatronics.

  3. Quantitative characterization of new supramolecular synthons involving fluorine atoms in the crystal structures of di- and tetrafluorinated benzamides.

    Science.gov (United States)

    Mondal, Pradip Kumar; Yadav, Hare Ram; Choudhury, Angshuman Roy; Chopra, Deepak

    2017-10-01

    Strong hydrogen bonds play a significant role in crystal packing. In particular, the involvement of interactions involving fluorine in controlling the crystal packing requires appropriate attention, especially in the presence of other strong hydrogen bonds. In the present study, a detailed quantitative assessment has been performed of the nature, energetics and topological properties derived from the electron density in model compounds based on fluorinated benzamides (a total of 46 fluorine-substituted benzamides containing multiple fluorine atoms) in the solid state. The primary motivation in the design of such molecules is to enhance the acidity of the interacting H atoms in the presence of an increasing number of F atoms on the molecular scaffold, resulting in increased propensity towards the formation of intermolecular interactions involving organic fluorine. This exercise has resulted in the identification of new and frequently occurring supramolecular synthons involving F atoms in the packing of molecules in the solid state. The energetics associated with short and directional intermolecular Csp 2 -H...F-Csp 2 interactions with significantly high electrostatic contributions is noteworthy, and the topological analysis reveals the bonding character of these ubiquitous interactions in crystal packing in addition to the presence of Csp 2 -F...F-Csp 2 contacts.

  4. Hydrogen bonded supramolecular materials

    CERN Document Server

    Li, Zhan-Ting

    2015-01-01

    This book is an up-to-date text covering topics in utilizing hydrogen bonding for constructing functional architectures and supramolecular materials. The first chapter addresses the control of photo-induced electron and energy transfer. The second chapter summarizes the formation of nano-porous materials. The following two chapters introduce self-assembled gels, many of which exhibit unique functions. Other chapters cover the advances in supramolecular liquid crystals and the versatility of hydrogen bonding in tuning/improving the properties and performance of materials. This book is designed

  5. What Triggers Supramolecular Isomerism in Nonmolecular Solids ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 128; Issue 11. What Triggers ... interpret the phase diagram of a system. The structure-synthesis correlation discussed here provides chemical insight to evolve a synthetic protocol to interpret and predict the possibilityof supramolecular isomers in metal organic solids.

  6. Construction of diverse supramolecular assemblies of dimetal ...

    Indian Academy of Sciences (India)

    Construction of diverse supramolecular assemblies of dimetal subunits differing in coordinated water molecules via strong hydrogen bonding interactions: Synthesis, crystal structures and spectroscopic properties. Sadhika Khullar Sanjay K Mandal. Special issue on Chemical Crystallography Volume 126 Issue 5 September ...

  7. Supramolecular assembly based on a heteropolyanion: Synthesis ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 117; Issue 3. Supramolecular assembly based on a heteropolyanion: Synthesis and crystal structure of Na3(H2O)6[Al(OH)6Mo6O18] ⋅ 2H2O. Vaddypally Shivaiah Samar K Das. Volume 117 Issue 3 May 2005 pp 227-233 ...

  8. Three silver (I) supramolecular compounds constructed from ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 127; Issue 9. Three silver (I) supramolecular compounds constructed from pyridinium or methylimidazolium polycations: Synthesis, crystal structure and properties. Yao Li Wen Li Zhang Hai Juan Du Chao-Hai Wang Ya Bin Lu Yun-Yin Niu. Volume 127 Issue 9 ...

  9. Structural and Functional Studies of Experimental HIV Synthetic Peptide Immunogens

    Science.gov (United States)

    1997-10-01

    Work performed in this grant continues to address 2 major problems in HIV synthetic peptide vaccine development: (1) the ability of synthetic...In technical aim #1, intranasal immunization with HIV synthetic peptide immunogens was found to be effective for the induction of serum anti-peptide

  10. Supramolecular Langmuir monolayers and multilayered vesicles of self-assembling DNA–lipid surface structures and their further implications in polyelectrolyte-based cell transfections

    Energy Technology Data Exchange (ETDEWEB)

    Demirsoy, Fatma Funda Kaya [Ankara University, The Central Laboratory of The Institute of Biotechnology (Turkey); Eruygur, Nuraniye [Gazi University, Department of Pharmacognosy, Faculty of Pharmacy (Turkey); Süleymanoğlu, Erhan, E-mail: erhans@mail.ru [Gazi University, Department of Pharmaceutical Chemistry, Faculty of Pharmacy (Turkey)

    2015-01-15

    The basic interfacial characteristics of DNA–lipid recognitions have been studied. The complex structures of individual unbound DNA molecules and their binary and ternary complexes with zwitterionic lipids and divalent cations were followed by employing lipid monolayers at the air–liquid interfaces, as well as by performing various microscopic, spectroscopic, and thermodynamic measurements with multilayered vesicles. The pressure-area isotherms depicted that Mg{sup 2+}-ions increase the surface pressure of lipid films and thus give rise to electrostatic and hydrophobic lipid–DNA interactions in terms of DNA adsorption, adhesion, and compaction. These features were further approached by using multilamellar vesicles with a mean diameter of 850 nm, where a metal ion-directed nucleic acid compaction and condensation effects were shown. The data obtained show the effectiveness of Langmuir monolayers and lipid multilayers in studying nucleic acid–lipid recognitions. The data provide with further details and support previous reports on mainly structural features of these recognitions. Biomolecular surface recognition events were presented in direct link with spectral and thermodynamic features of lipid vesicle–polynucleotide complex formations. The results serve to build a theoretical model considering the use of neutral lipids in lipoplex designs as a polyelectrolyte alternatives to the currently employed cytotoxic cationic liposomes. The supramolecular structures formed and their possible roles in interfacial electrostatic and hydrophobic mechanisms of endosomal escape in relevant cell transfection assays are particularly emphasized.

  11. Cd (II) and holodirected lead (II) 3D-supramolecular coordination polymers based on nicotinic acid: Structure, fluorescence property and photocatalytic activity

    Science.gov (United States)

    Etaiw, Safaa El-din H.; Abd El-Aziz, Dina M.; Marie, Hassan; Ali, Elham

    2018-05-01

    Two new supramolecular coordination polymers namely {[Cd(NA)2(H2O)]}, SCP 1 and {[Pb(NA)2]}, SCP 2, (NA = nicotinate ligand) were synthesized by self-assembly method and structurally characterized by different analytical and spectroscopic methods. Single-crystal X-ray diffraction showed that SCP 1 extend in three dimensions containing bore structure where the 3D- network is constructed via interweaving zigzag chains. The Cd atom coordinates to (O4N2) atoms forming distorted-octahedral configuration. The structure of SCP 2 extend down the projection of the b-axis creating parallel zigzag 1D-chains connected by μ2-O2 atoms and H-bonds forming a holodirected lead (II) hexagonal bi-pyramid configuration. SCP 2 extend to 3D-network via coordinate and hydrogen bonds. The thermal stability, photoluminescence properties, photocatalytic activity for the degradation of methylene blue dye (MB) under UV-irradiation and sunlight irradiation were also studied.

  12. Gold nanoparticle assemblies through Hydrogen-bonded supramolecular mediators

    NARCIS (Netherlands)

    Kinge, S.S.; Crego Calama, Mercedes; Reinhoudt, David

    2007-01-01

    The synthesis of spherical gold nanoparticle assemblies with multicomponent double rosette molecular boxes as mediators is presented. These nine-component hydrogen-bonded supramolecular structures held together by 36 hydrogen bonds induce gold nanoparticle assembly. The morphologies of the

  13. DFT study and crystal structure analysis of a new nano-structure five coordinated Hg(II) complex involving C-H⋯O, N⋯O and π⋯π interactions in a supra-molecular structure.

    Science.gov (United States)

    Montazerozohori, M; Musavi, S A; Masoudiasl, A; Hojjati, A; Assoud, A

    2015-08-05

    In this research, template synthesis and crystal structure of a new HgLI₂ complex are presented (L=N(1)-(4-nitrobenzylidene)-N(2)-(2-((E)-(4-nitrobenzylidene)amino)ethyl)ethane-1,2-diamine). The mercury complex crystallizes in the triclinic system with space group of P1¯. The crystal structure of the complex shows a distorted trigonal bipyramidal geometry around the mercury(II) center; including two I and an N atoms of Schiff base ligand in equatorial plane and two iminic N atoms in axial positions. Two five membered mercury containing rings [Hg(-N-C-C-N-)] are found in the structure. Some C-H⋯O, N⋯O and π⋯π intermolecular interactions causes a supra-molecular network in the solid-state. In addition to crystal structure analysis, density functional theory (DFT) study at the B3LYP/LanL2DZ level of theory has been also performed on the structure. Thereafter some theoretical structural and spectral data were compared with experimental results. Furthermore, total energy levels of HOMO and LUMO orbitals, molecular electrostatic potential, Mullikan atomic charges, thermodynamic and polarizability properties of the complex were calculated. Finally the mercury complex was prepared in nano-structure size confirmed by SEM and XRD analyses. The particles size of the titled complex was evaluated under 40 nm based on Sherrer's formula. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Supramolecular systems chemistry

    NARCIS (Netherlands)

    Mattia, Elio; Otto, Sijbren

    The field of supramolecular chemistry focuses on the non-covalent interactions between molecules that give rise to molecular recognition and self-assembly processes. Since most non-covalent interactions are relatively weak and form and break without significant activation barriers, many

  15. Structure-Activity Studies and Therapeutic Potential of Host Defense Peptides of Human Thrombin▿

    OpenAIRE

    Kasetty, Gopinath; Papareddy, Praveen; Kalle, Martina; Rydengård, Victoria; Mörgelin, Matthias; Albiger, Barbara; Malmsten, Martin; Schmidtchen, Artur

    2011-01-01

    Peptides of the C-terminal region of human thrombin are released upon proteolysis and identified in human wounds. In this study, we wanted to investigate minimal determinants, as well as structural features, governing the antimicrobial and immunomodulating activity of this peptide region. Sequential amino acid deletions of the peptide GKYGFYTHVFRLKKWIQKVIDQFGE (GKY25), as well as substitutions at strategic and structurally relevant positions, were followed by analyses of antimicrobial activit...

  16. Singlet and triplet energy transfer dynamics in self-assembled axial porphyrin-anthracene complexes: towards supra-molecular structures for photon upconversion.

    Science.gov (United States)

    Gray, Victor; Küçüköz, Betül; Edhborg, Fredrik; Abrahamsson, Maria; Moth-Poulsen, Kasper; Albinsson, Bo

    2018-03-14

    Energy and electron transfer reactions are central to many different processes and research fields, from photosynthesis and solar energy harvesting to biological and medical applications. Herein we report a comprehensive study of the singlet and triplet energy transfer dynamics in porphyrin-anthracene coordination complexes. Seven newly synthesized pyridine functionalized anthracene ligands, five with various bridge lengths and two dendrimer structures containing three and seven anthracene units, were prepared. We found that triplet energy transfer from ruthenium octaethylporphyrin to an axially coordinated anthracene is possible, and is in some cases followed by back triplet energy transfer to the porphyrin. The triplet energy transfer follows an exponential distance dependence with an attenuation factor, β, of 0.64 Å -1 . Further, singlet energy transfer from anthracene to the ruthenium porphyrin appears to follow a R 6 Förster distance dependence. Porphyrin-anthracene complexes are also used as triplet sensitizers for triplet-triplet annihilation (TTA) based photon upconversion, demonstrating their potential for photophysical and photochemical applications. The triplet lifetime of the complex is extended by the anthracene ligands, resulting in a threefold increase in the upconversion efficiency, Φ UC to 4.5%, compared to the corresponding ruthenium porphyrin-pyridine complex. Based on the results herein we discuss the future design of supra-molecular structures for TTA upconversion.

  17. Blends of conjugated rigid-rod polymers: Novel supramolecular materials for electronics, optoelectronics and photonics

    Energy Technology Data Exchange (ETDEWEB)

    Jenekhe, S.A. [Univ. of Rochester, NY (United States)

    1996-12-31

    Selected examples of binary blends of conjugated polymers will be presented to illustrate the vast scope of their supramolecular structures and electronic, optical, nonlinear optical, and optoelectronic properties.

  18. Synthesis, structure and characterization of two copper(II) supramolecular coordination polymers based on a multifunctional ligand 2-amino-4-sulfobenzoic acid.

    Science.gov (United States)

    Wei, Yan; Zhang, Lei; Wang, Meng-Jie; Chen, Si-Chun; Wang, Zi-Hao; Zhang, Kou-Lin

    2015-07-01

    Copper(II) coordination polymers have attracted considerable interest due to their catalytic, adsorption, luminescence and magnetic properties. The reactions of copper(II) with 2-amino-4-sulfobenzoic acid (H(2)asba) in the presence/absence of the auxiliary chelating ligand 1,10-phenanthroline (phen) under ambient conditions yielded two supramolecular coordination polymers, namely (3-amino-4-carboxybenzene-1-sulfonato-κO(1))bis(1,10-phenanthroline-κ(2)N,N')copper(II) 3-amino-4-carboxybenzene-1-sulfonate monohydrate, [Cu(C7H6N2O5S)(C12H8N2)2](C7H6N2O5S)·H2O, (1), and catena-poly[[diaquacopper(II)]-μ-3-amino-4-carboxylatobenzene-1-sulfonato-κ(2)O(4):O(4')], [Cu(C7H6N2O5S)(H2O)2]n, (2). The products were characterized by FT-IR spectroscopy, thermogravimetric analysis (TGA), solid-state UV-Vis spectroscopy and single-crystal X-ray diffraction analysis, as well as by variable-temperature powder X-ray diffraction analysis (VT-PXRD). Intermolecular π-π stacking interactions in (1) link the mononuclear copper(II) cation units into a supramolecular polymeric chain, which is further extended into a supramolecular double chain through interchain hydrogen bonds. Supramolecular double chains are then extended into a two-dimensional supramolecular double layer through hydrogen bonds between the lattice Hasba(-) anions, H2O molecules and double chains. Left- and right-handed 21 helices formed by the Hasba(-) anions are arranged alternately within the two-dimensional supramolecular double layers. Complex (2) exhibits a polymeric chain which is further extended into a three-dimensional supramolecular network through interchain hydrogen bonds. Complex (1) shows a reversible dehydration-rehydration behaviour, while complex (2) shows an irreversible dehydration-rehydration behaviour.

  19. p-halo N4-phenyl substituted thiosemicarbazones: Crystal structure, supramolecular architecture, characterization and bio-assay of their Co(III) and Ni(II) complexes

    Science.gov (United States)

    Kotian, Avinash; Kumara, Karthik; Kamat, Vinayak; Naik, Krishna; Kokare, Dhoolesh G.; Nevrekar, Anupama; Lokanath, Neratur Krishnappagowda; Revankar, Vidyanand K.

    2018-03-01

    In the present work, three potential metal ion chelating ligands, p-halo N4-phenyl substituted thiosemicarbazones are synthesized and characterized. The molecular structure of all (E)-4-(4-halophenyl)-1-(3-hydroxyiminobutan-2-ylidene) thiosemicarbazones (halo = F/Cl/Br) are determined by single crystal X-ray diffraction method. All the molecules have crystallized in monoclinic crystal system with P21/n space group. The ligands show Csbnd H⋯S and Nsbnd H⋯S intermolecular interactions, which are responsible to form the supramolecular self-assemblies through R22(8), R22(12) and R22(14) ring motifs. Hirshfeld surface analysis is carried out to explore the intermolecular interactions. A series of Co(III) and Ni(II) mononuclear transition metal complexes derived from these ligands have been synthesized and characterized by various spectro-analytical methods. The metal to ligand stoichiometry has been found to be 1:2 in all the complexes. The synthesized compounds have been investigated for their in vitro antimicrobial potencies. The compounds are found to be more active than the standard used, in the case of E. coli and A. niger. Additionally, they are also screened for their in vitro antitubercular activity.

  20. Metal-organic and supramolecular networks driven by 5-chloronicotinic acid: Hydrothermal self-assembly synthesis, structural diversity, luminescent and magnetic properties

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Zhu-Qing, E-mail: zqgao2008@163.com [School of Chemical and Biological Engineering, Taiyuan University of Science and Technology, Taiyuan 030021 (China); Li, Hong-Jin [School of Chemical and Biological Engineering, Taiyuan University of Science and Technology, Taiyuan 030021 (China); Gu, Jin-Zhong, E-mail: gujzh@lzu.edu.cn [College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000 (China); Zhang, Qing-Hua [School of Chemical and Biological Engineering, Taiyuan University of Science and Technology, Taiyuan 030021 (China); Kirillov, Alexander M. [Centro de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049–001 Lisbon (Portugal)

    2016-09-15

    Four new crystalline solids, namely [Co{sub 2}(µ{sub 2}-5-Clnic){sub 2}(µ{sub 3}-5-Clnic){sub 2}(µ{sub 2}-H{sub 2}O)]{sub n} (1), [Co(5-Clnic){sub 2}(H{sub 2}O){sub 4}]·2(5-ClnicH) (2), [Pb(µ{sub 2}-5-Clnic){sub 2}(phen)]{sub n} (3), and [Cd(5-Clnic){sub 2}(phen){sub 2}]·3H{sub 2}O (4) were generated by hydrothermal self-assembly methods from the corresponding metal(II) chlorides, 5-chloronicotinic acid (5-ClnicH) as a principal building block, and 1,10-phenanthroline (phen) as an ancillary ligand (optional). All the products 1–4 were characterized by IR spectroscopy, elemental analysis, thermogravimetric (TGA), powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction. Their structures range from an intricate 3D metal-organic network 1 with the 3,6T7 topology to a ladder-like 1D coordination polymer 3 with the 2C1 topology, whereas compounds 2 and 4 are the discrete 0D monomers. The structures of 2 and 4 are further extended (0D→2D or 0D→3D) by hydrogen bonds, generating supramolecular networks with the 3,8L18 and ins topologies, respectively. Synthetic aspects, structural features, thermal stability, magnetic (for 1) and luminescent (for 3 and 4) properties were also investigated and discussed. - Graphical abstract: A new series of crystalline solids was self-assembled and fully characterized; their structural, topological, luminescent and magnetic features were investigated. Display Omitted.

  1. Supramolecular polymers for organocatalysis in water.

    Science.gov (United States)

    Neumann, Laura N; Baker, Matthew B; Leenders, Christianus M A; Voets, Ilja K; Lafleur, René P M; Palmans, Anja R A; Meijer, E W

    2015-07-28

    A water-soluble benzene-1,3,5-tricarboxamide (BTA) derivative that self-assembles into one-dimensional, helical, supramolecular polymers is functionalised at the periphery with one L-proline moiety. In water, the BTA-derivative forms micrometre long supramolecular polymers, which are stabilised by hydrophobic interactions and directional hydrogen bonds. Furthermore, we co-assemble a catalytically inactive, but structurally similar, BTA with the L-proline functionalised BTA to create co-polymers. This allows us to assess how the density of the L-proline units along the supramolecular polymer affects its activity and selectivity. Both the supramolecular polymers and co-polymers show high activity and selectivity as catalysts for the aldol reaction in water when using p-nitrobenzaldehyde and cyclohexanone as the substrates for the aldol reaction. After optimisation of the reaction conditions, a consistent conversion of 92 ± 7%, deanti of 92 ± 3%, and eeanti of 97 ± 1% are obtained with a concentration of L-proline as low as 1 mol%.

  2. Crystal structure of the GLP-1 receptor bound to a peptide agonist.

    Science.gov (United States)

    Jazayeri, Ali; Rappas, Mathieu; Brown, Alastair J H; Kean, James; Errey, James C; Robertson, Nathan J; Fiez-Vandal, Cédric; Andrews, Stephen P; Congreve, Miles; Bortolato, Andrea; Mason, Jonathan S; Baig, Asma H; Teobald, Iryna; Doré, Andrew S; Weir, Malcolm; Cooke, Robert M; Marshall, Fiona H

    2017-06-08

    Glucagon-like peptide 1 (GLP-1) regulates glucose homeostasis through the control of insulin release from the pancreas. GLP-1 peptide agonists are efficacious drugs for the treatment of diabetes. To gain insight into the molecular mechanism of action of GLP-1 peptides, here we report the crystal structure of the full-length GLP-1 receptor bound to a truncated peptide agonist. The peptide agonist retains an α-helical conformation as it sits deep within the receptor-binding pocket. The arrangement of the transmembrane helices reveals hallmarks of an active conformation similar to that observed in class A receptors. Guided by this structural information, we design peptide agonists with potent in vivo activity in a mouse model of diabetes.

  3. Structure and orientation study of Ebola fusion peptide inserted in lipid membrane models.

    Science.gov (United States)

    Agopian, Audrey; Castano, Sabine

    2014-01-01

    The fusion peptide of Ebola virus comprises a highly hydrophobic sequence located downstream from the N-terminus of the glycoprotein GP2 responsible for virus-host membrane fusion. The internal fusion peptide of GP2 inserts into membranes of infected cell to mediate the viral and the host cell membrane fusion. Since the sequence length of Ebola fusion peptide is still not clear, we study in the present work the behavior of two fusion peptides of different lengths which were named EBO17 and EBO24 referring to their amino acid length. The secondary structure and orientation of both peptides in lipid model systems made of DMPC:DMPG:cholesterol:DMPE (6:2:5:3) were investigated using PMIRRAS and polarized ATR spectroscopy coupled with Brewster angle microscopy. The infrared results showed a structural flexibility of both fusion peptides which are able to transit reversibly from an α-helix to antiparallel β-sheets. Ellipsometry results corroborate together with isotherm measurements that EBO peptides interacting with lipid monolayer highly affected the lipid organization. When interacting with a single lipid bilayer, at low peptide content, EBO peptides insert as mostly α-helices mainly perpendicular into the lipid membrane thus tend to organize the lipid acyl chains. Inserted in multilamellar vesicles at higher peptide content, EBO peptides are mostly in β-sheet structures and induce a disorganization of the lipid chain order. In this paper, we show that the secondary structure of the Ebola fusion peptide is reversibly flexible between α-helical and β-sheet conformations, this feature being dependent on its concentration in lipids, eventually inducing membrane fusion. © 2013.

  4. A His-Pro-Aib peptide that exhibits an Asx-Pro-turn-like structure

    Science.gov (United States)

    Blank; Guerin; Miller

    2000-05-04

    [formula: see text] Small peptides 1 and 2, which differ only in that 1 possesses a BOC-Phe residue at the N-terminus, where 2 bears a BOC-(tau-benzyl)His, were found to exhibit very different structures. In both the solid state (X-ray) and in solution (NMR and IR), peptide 1 exists as a beta-turn, whereas peptide 2 exists in a conformation that resembles the Asx-Pro motif.

  5. Structural and Functional Studies of Experimental HIV Synthetic Peptides Immunogens.

    Science.gov (United States)

    1998-09-01

    Work performed in this grant continues to address major hurdles in the development of an effective synthetic peptide HIV vaccine: 1) the ability of...isolates and 2) the design of synthetic peptide immunogens capable of being recognized by MHC Class I and II molecules in outbred populations. In

  6. Nucleic Acid Backbone Structure Variations: Peptide Nucleic Acids

    DEFF Research Database (Denmark)

    Nielsen, Peter E.

    2010-01-01

    Synthetic analogues and mimics of the natural genetic material deoxyribonucleic acid (DNA) are potential gene therapeutic (antisense or antigene) drugs. One of these mimics, peptide nucleic acids (PNAs), are chemically closer to peptides and proteins than to DNA, but nonetheless have retained many...

  7. Structural prediction and analysis of VIH-related peptides from selected crustacean species.

    Science.gov (United States)

    Nagaraju, Ganji Purna Chandra; Kumari, Nunna Siva; Prasad, Ganji Lakshmi Vara; Rajitha, Balney; Meenu, Madan; Rao, Manam Sreenivasa; Naik, Bannoth Reddya

    2009-08-17

    The tentative elucidation of the 3D-structure of vitellogenesis inhibiting hormone (VIH) peptides is conversely underprivileged by difficulties in gaining enough peptide or protein, diffracting crystals, and numerous extra technical aspects. As a result, no structural information is available for VIH peptide sequences registered in the Genbank. In this situation, it is not surprising that predictive methods have achieved great interest. Here, in this study the molt-inhibiting hormone (MIH) of the kuruma prawn (Marsupenaeus japonicus) is used, to predict the structure of four VIHrelated peptides in the crustacean species. The high similarity of the 3D-structures and the calculated physiochemical characteristics of these peptides suggest a common fold for the entire family.

  8. Structural requirements for the interaction between class II MHC molecules and peptide antigens

    DEFF Research Database (Denmark)

    Sette, A; Buus, S; Appella, E

    1990-01-01

    IA(d) and IE(d) molecules and their peptide ligands, we found that some structural characteristics apply to both antigen-MHC interactions. In particular, we found: 1) each MHC molecule is capable of binding many unrelated peptides through the same peptide-binding site; 2) despite this permissiveness......Previous work from our and other laboratories indicates that T cells recognize a complex between the MHC restriction element and peptide antigen fragments. This paper reviews the structural characteristics of the formation of such a complex. By analyzing in detail the interactions between purified...... of binding, it is possible to define certain structural features of peptides that are associated with the capacity to bind to a particular MHC specificity (IA(d) or IE(d)); 3) IA(d) and IE(d) molecules recognize different and independent structures on the antigen molecule; 4) only about 10% of the single...

  9. Rheology of Supramolecular Polymers

    DEFF Research Database (Denmark)

    Shabbir, Aamir

    efficient processes or biomedical areas. Design and development of supramolecular polymers using ionic, hydrogen bonding or transition metal complexes with tailored properties requires deep understanding of dynamics both in linear and non-linear deformations. While linear rheology is important to understand...... the dynamics under equilibrium conditions, extensional rheology is relevant during the processing or in the usage of polymers utilizing supramolecular associations for example, acrylic based pressure sensitive adhesives are subjected to extensional deformations during the peeling where strain hardening......) hydrogen bonding polymers, and (b) ionic bonding polymers (hereafter termed as ionomers). We study linear and non-linear rheology fora model system of entangled pure poly(n-butyl acrylate), PnBA, homopolymer andfour poly(acrylic acid), PnBA-PAA, copolymers with varying AA side groups synthesizedvia...

  10. Applications of supramolecular chemistry

    CERN Document Server

    Schneider, Hans-Jörg

    2012-01-01

    ""The time is ripe for the present volume, which gathers thorough presentations of the numerous actually realized or potentially accessible applications of supramolecular chemistry by a number of the leading figures in the field. The variety of topics covered is witness to the diversity of the approaches and the areas of implementation…a broad and timely panorama of the field assembling an eminent roster of contributors.""-Jean-Marie Lehn, 1987 Noble Prize Winner in Chemistry

  11. Immune Response of Multiparous Hyper-Immunized Sows against Peptides from Non-Structural and Structural Proteins of PRRSV

    Directory of Open Access Journals (Sweden)

    Edgar Rascón-Castelo

    2015-11-01

    Full Text Available The purpose of this study was to evaluate the humoral and cellular responses of commercial multiparous and hyper-immunized sows against peptides from non-structural (nsp and structural proteins of porcine reproductive and respiratory syndrome virus (PRRSV. We selected sows with different numbers of parities from a commercial farm. Management practices on this farm include the use of the MLV commercial vaccine four times per year, plus two vaccinations during the acclimation period. The humoral response was evaluated via the antibody recognition of peptides from nsp and structural proteins, and the cellular response was assessed by measuring the frequency of peptide and PRRSV-specific IFN-gamma-secreting cells (IFNγ-SC. Our results show that sows with six parities have more antibodies against peptides from structural proteins than against peptides from nsp. The analysis of the cellular response revealed that the number of immunizations did not affect the frequency of IFNγ-SC and that the response was stronger against peptides from structural proteins (M protein than against nsp (nsp2. In summary, these results demonstrate that multiparous, hyper-immunized sows have a stronger immune humoral response to PRRSV structural peptides than nsp, but no differences in IFNγ-SC against the same peptides were observed.

  12. Thermally bisignate supramolecular polymerization

    Science.gov (United States)

    Venkata Rao, Kotagiri; Miyajima, Daigo; Nihonyanagi, Atsuko; Aida, Takuzo

    2017-11-01

    One of the enticing characteristics of supramolecular polymers is their thermodynamic reversibility, which is attractive, in particular, for stimuli-responsive applications. These polymers usually disassemble upon heating, but here we report a supramolecular polymerization that occurs upon heating as well as cooling. This behaviour arises from the use of a metalloporphyrin-based tailored monomer bearing eight amide-containing side chains, which assembles into a highly thermostable one-dimensional polymer through π-stacking and multivalent hydrogen-bonding interactions, and a scavenger, 1-hexanol, in a dodecane-based solvent. At around 50 °C, the scavenger locks the monomer into a non-polymerizable form through competing hydrogen bonding. On cooling, the scavenger preferentially self-aggregates, unlocking the monomer for polymerization. Heating also results in unlocking the monomer for polymerization, by disrupting the dipole and hydrogen-bonding interactions with the scavenger. Analogous to 'upper and lower critical solution temperature phenomena' for covalently bonded polymers, such a thermally bisignate feature may lead to supramolecular polymers with tailored complex thermoresponsive properties.

  13. Pathways to Structure-Property Relationships of Peptide-Materials Interfaces: Challenges in Predicting Molecular Structures.

    Science.gov (United States)

    Walsh, Tiffany R

    2017-07-18

    An in-depth appreciation of how to manipulate the molecular-level recognition between peptides and aqueous materials interfaces, including nanoparticles, will advance technologies based on self-organized metamaterials for photonics and plasmonics, biosensing, catalysis, energy generation and harvesting, and nanomedicine. Exploitation of the materials-selective binding of biomolecules is pivotal to success in these areas and may be particularly key to producing new hierarchically structured biobased materials. These applications could be accomplished by realizing preferential adsorption of a given biomolecule onto one materials composition over another, one surface facet over another, or one crystalline polymorph over another. Deeper knowledge of the aqueous abiotic-biotic interface, to establish clear structure-property relationships in these systems, is needed to meet this goal. In particular, a thorough structural characterization of the surface-adsorbed peptides is essential for establishing these relationships but can often be challenging to accomplish via experimental approaches alone. In addition to myriad existing challenges associated with determining the detailed molecular structure of any molecule adsorbed at an aqueous interface, experimental characterization of materials-binding peptides brings new, complex challenges because many materials-binding peptides are thought to be intrinsically disordered. This means that these peptides are not amenable to experimental techniques that rely on the presence of well-defined secondary structure in the peptide when in the adsorbed state. To address this challenge, and in partnership with experiment, molecular simulations at the atomistic level can bring complementary and critical insights into the origins of this abiotic/biotic recognition and suggest routes for manipulating this phenomenon to realize new types of hybrid materials. For the reasons outlined above, molecular simulation approaches also face

  14. Structures of peptide families by nuclear magnetic resonance spectroscopy and distance geometry

    Energy Technology Data Exchange (ETDEWEB)

    Pease, J.H.

    1989-12-01

    The three dimensional structures of several small peptides were determined using a combination of {sup 1}H nuclear magnetic resonance (NMR) and distance geometry calculations. These techniques were found to be particularly helpful for analyzing structural differences between related peptides since all of the peptides' {sup 1}H NMR spectra are very similar. The structures of peptides from two separate classes are presented. Peptides in the first class are related to apamin, an 18 amino acid peptide toxin from honey bee venom. The {sup 1}H NMR assignments and secondary structure determination of apamin were done previously. Quantitative NMR measurements and distance geometry calculations were done to calculate apamin's three dimensional structure. Peptides in the second class are 48 amino acid toxins from the sea anemone Radianthus paumotensis. The {sup 1}H NMR assignments of toxin II were done previously. The {sup 1}H NMR assignments of toxin III and the distance geometry calculations for both peptides are presented.

  15. Structural Diversity and Biological Activities of Fungal Cyclic Peptides, Excluding Cyclodipeptides.

    Science.gov (United States)

    Wang, Xiaohan; Lin, Minyi; Xu, Dan; Lai, Daowan; Zhou, Ligang

    2017-11-27

    Cyclic peptides are cyclic compounds formed mainly by the amide bonds between either proteinogenic or non-proteinogenic amino acids. This review highlights the occurrence, structures and biological activities of fungal cyclic peptides (excluding cyclodipeptides, and peptides containing ester bonds in the core ring) reported until August 2017. About 293 cyclic peptides belonging to the groups of cyclic tri-, tetra-, penta-, hexa-, hepta-, octa-, nona-, deca-, undeca-, dodeca-, tetradeca-, and octadecapeptides as well as cyclic peptides containing ether bonds in the core ring have been isolated from fungi. They were mainly isolated from the genera Aspergillus , Penicillium , Fusarium , Acremonium and Amanita . Some of them were screened to have antimicrobial, antiviral, cytotoxic, phytotoxic, insecticidal, nematicidal, immunosuppressive and enzyme-inhibitory activities to show their potential applications. Some fungal cyclic peptides such as the echinocandins, pneumocandins and cyclosporin A have been developed as pharmaceuticals.

  16. Structural Diversity and Biological Activities of Fungal Cyclic Peptides, Excluding Cyclodipeptides

    Directory of Open Access Journals (Sweden)

    Xiaohan Wang

    2017-11-01

    Full Text Available Cyclic peptides are cyclic compounds formed mainly by the amide bonds between either proteinogenic or non-proteinogenic amino acids. This review highlights the occurrence, structures and biological activities of fungal cyclic peptides (excluding cyclodipeptides, and peptides containing ester bonds in the core ring reported until August 2017. About 293 cyclic peptides belonging to the groups of cyclic tri-, tetra-, penta-, hexa-, hepta-, octa-, nona-, deca-, undeca-, dodeca-, tetradeca-, and octadecapeptides as well as cyclic peptides containing ether bonds in the core ring have been isolated from fungi. They were mainly isolated from the genera Aspergillus, Penicillium, Fusarium, Acremonium and Amanita. Some of them were screened to have antimicrobial, antiviral, cytotoxic, phytotoxic, insecticidal, nematicidal, immunosuppressive and enzyme-inhibitory activities to show their potential applications. Some fungal cyclic peptides such as the echinocandins, pneumocandins and cyclosporin A have been developed as pharmaceuticals.

  17. Peptides actively transported across the tympanic membrane: Functional and structural properties.

    Directory of Open Access Journals (Sweden)

    Arwa Kurabi

    Full Text Available Otitis media (OM is the most common infectious disease of children under six, causing more antibiotic prescriptions and surgical procedures than any other pediatric condition. By screening a bacteriophage (phage library genetically engineered to express random peptides on their surfaces, we discovered unique peptides that actively transport phage particles across the intact tympanic membrane (TM and into the middle ear (ME. Herein our goals were to characterize the physiochemical peptide features that may underlie trans-TM phage transport; assess morphological and functional effects of phage peptides on the ME and inner ear (IE; and determine whether peptide-bearing phage transmigrate from the ME into the IE. Incubation of five peptide-bearing phage on the TM for over 4hrs resulted in demonstrably superior transport of one peptide, in level and in exponential increase over time. This suggests a preferred peptide motif for TM active transport. Functional and structural comparisons revealed unique features of this peptide: These include a central lysine residue, isoelectric point of 0.0 at physiological pH and a hydrophobic C-terminus. When the optimal peptide was applied to the TM independent of phage, similar transport was observed, indicating that integration into phage is not required. When 109 particles of the four different trans-TM phage were applied directly into the ME, no morphological effects were detected in the ME or IE when compared to saline or wild-type (WT phage controls. Comparable, reversible hearing loss was observed for saline controls, WT phage and trans-TM peptide phage, suggesting a mild conductive hearing loss due to ME fluid. Perilymph titers after ME incubation established that few copies of trans-TM peptide phage crossed into the IE. The results suggest that, within the parameters tested, trans-TM peptides are safe and could be used as potential agents for noninvasive delivery of drugs, particles and gene therapy

  18. Structure-CaSR-Activity Relation of Kokumi γ-Glutamyl Peptides.

    Science.gov (United States)

    Amino, Yusuke; Nakazawa, Masakazu; Kaneko, Megumi; Miyaki, Takashi; Miyamura, Naohiro; Maruyama, Yutaka; Eto, Yuzuru

    2016-01-01

    Modulation of the calcium sensing receptor (CaSR) is one of the physiological activities of γ-glutamyl peptides such as glutathione (γ-glutamylcysteinylglycine). γ-Glutamyl peptides also possess a flavoring effect, i.e., sensory activity of kokumi substances, which modifies the five basic tastes when added to food. These activities have been shown to be positively correlated, suggesting that kokumi γ-glutamyl peptides are perceived through CaSRs in humans. Our research is based on the hypothesis that the discovery of highly active CaSR agonist peptides will lead to the creation of practical kokumi peptides. Through continuous study of the structure-CaSR-activity relation of a large number of γ-glutamyl peptides, we have determined that the structural requirements for intense CaSR activity of γ-glutamyl peptides are as follows: existence of an N-terminal γ-L-glutamyl residue; existence of a moderately sized, aliphatic, neutral substituent at the second residue in an L-configuration; and existence of a C-terminal carboxylic acid, preferably with the existence of glycine as the third constituent. By the sensory analysis of γ-glutamyl peptides selected by screening using the CaSR activity assay, γ-glutamylvalylglycine was found to be a potent kokumi peptide. Furthermore, norvaline-containing γ-glutamyl peptides, i.e., γ-glutamylnorvalylglycine and γ-glutamylnorvaline, possessed excellent sensory activity of kokumi substances. A novel, practical industrial synthesis of regiospecific γ-glutamyl peptides is also required for their commercialization, which was achieved through the ring opening reaction of N-α-carbobenzoxy-L-glutamic anhydride and amino acids or peptides in the presence of N-hydroxysuccinimide.

  19. Novel metal-organic and supramolecular 3D frameworks constructed from flexible biphenyl-2,5,3‧-tricarboxylate blocks: Synthesis, structural features and properties

    Science.gov (United States)

    You, Ao; Li, Yu; Zhang, Ze-Min; Zou, Xun-Zhong; Gu, Jin-Zhong; Kirillov, Alexander M.; Chen, Jin-Wei; Chen, Yun-Bo

    2017-10-01

    Biphenyl-2,5,3‧-tricarboxylic acid (H3L) was selected as an unexplored tricarboxylate building block and applied for the hydrothermal synthesis of three novel coordination compounds, namely a 0D tetramer [Co4(HL)2(μ3-HL)2(phen)6(H2O)2]·3H2O (1) and two 3D metal-organic frameworks (MOFs) [Cd3(μ5-L)(μ6-L)(py)(μ-H2O)2(H2O)]n·H2O (2) and [Zn3(μ4-L)2(2,2‧-bpy)(μ-4,4‧-bpy)]n·2H2O (3). These products were easily generated in aqueous medium from the corresponding metal(II) chlorides, H3L, and various N-donor ancillary ligands, selected from 1,10-phenanthroline (phen), pyridine (py), 2,2‧-bipyridine (2,2‧-bpy), and 4,4‧-bipyridine (4,4‧-bpy). Compounds 1-3 were isolated as stable crystalline solids and were fully characterized by IR and UV-vis spectroscopy, elemental, thermogravimetric (TGA), powder (PXRD) and single-crystal X-ray diffraction analyses. Compound 1 possesses a discrete tetracobalt(II) structure, which is extended into a 3D H-bonded network with the pcu topology. In contrast, MOF 2 discloses a very complex trinodal 4,5,12-connected net with an undocumented topology, while MOF 3 features the nce/I topological framework. The magnetic (for 1) and luminescence (for 2 and 3) properties were also studied and discussed. The present study thus widens a still very limited family of metal-organic and supramolecular frameworks driven by flexible biphenyl-2,5,3‧-tricarboxylate building blocks.

  20. Antimicrobial activity, DNA cleavage, thermal analysis data and crystal structure of some new CdLX.sub.2./sub. complexes: a supramolecular network

    Czech Academy of Sciences Publication Activity Database

    Montazerozohori, M.; Nazaripour, A.; Masoudiasl, A.; Naghiha, R.; Dušek, Michal; Kučeráková, Monika

    2015-01-01

    Roč. 55, Oct (2015), s. 462-470 ISSN 0928-4931 R&D Projects: GA ČR(CZ) GA14-03276S Institutional support: RVO:68378271 Keywords : cadmium(II) * Schiff base * supramolecular * antimicrobial * tetrahedral * x-ray Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.420, year: 2015

  1. Phase behavior and nanoscale structure of phospholipid membranes incorporated with acylated C-14-peptides

    DEFF Research Database (Denmark)

    Pedersen, T.B.; Kaasgaard, Thomas; Jensen, M.O.

    2005-01-01

    The thermotropic phase behavior and lateral structure of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers containing an acylated peptide has been characterized by differential scanning calorimetry (DSC) on vesicles and atomic force microscopy (AFM) on mica-supported bilayers. The acylated...... peptide, which is a synthetic decapeptide N-terminally linked to a C-14 acyl chain (C-14-peptide), is incorporated into DPPC bilayers in amounts ranging from 0-20 mol %. The calorimetric scans of the two-component system demonstrate a distinct influence of the C-14-peptide on the lipid bilayer...... gel phase DPPC bilayers, inserts preferentially into preexisting defect regions and has a noticeable influence on the organization of the surrounding lipids. The presence of the C-14-peptide gives rise to a laterally heterogeneous bilayer structure with coexisting lipid domains characterized by a 10...

  2. Synthesis, structural characterization, thermal analysis, and DFT calculation of a novel zinc (II)-trifluoro-β-diketonate 3D supramolecular nano organic-inorganic compound with 1,3,5-triazine derivative

    Energy Technology Data Exchange (ETDEWEB)

    Mirtamizdoust, Babak, E-mail: babakm.tamizdoust@gmail.com [Department of Chemistry, Yasouj University, Yasouj, 75918-74831 (Iran, Islamic Republic of); Department of Chemistry, Faculty of Science, University of Qom, PO Box 37185-359, Qom, Islamic Republic of Iran (Iran, Islamic Republic of); Ghaedi, Mehrorang [Department of Chemistry, Yasouj University, Yasouj, 75918-74831 (Iran, Islamic Republic of); Hanifehpour, Younes, E-mail: y_hanifehpour@yu.ac.kr [School of Mechanical Engineering, WCU Nano Research Center, Yeungnam University, Gyongsan, 712-749 (Korea, Republic of); Mague, Joel T. [Department of Chemistry, Tulane University, New Orleans (United States); Joo, Sang Woo, E-mail: swjoo1@gmail.com [School of Mechanical Engineering, WCU Nano Research Center, Yeungnam University, Gyongsan, 712-749 (Korea, Republic of)

    2016-10-01

    A sonochemical method was used to synthesize a novel nano-structure of a zinc(II) organic-inorganic compound [Zn(dapt){sub 2}(ttfa){sub 2}] (1) [dapt = 2,4-diamino-6-phenyl-1,3,5-triazine and ttfa = 2-thenoyltrifluoroacetonate]. The new nanostructure was characterized by scanning electron microscopy, X-ray powder diffraction, elemental analysis, and thermal analysis. The single-crystal X-ray structure shows that 1 is a discrete coordination compound. Strong intra- and intermolecular hydrogen bonds are observed in the structure with the latter forming chains of molecules running parallel to (110). The chains are further extended into a three-dimensional supramolecular structure by intermolecular C−F⋯π interactions between trifluoromethyl and triazine moieties. The coordination number of the zinc(II) ion is six (ZnN{sub 2}O{sub 4}), and the coordination sphere is tetragonally elongated octahedral. The structure of the title complex was optimized by DFT calculations. - Highlights: • A new zinc(II) 3D coordination supramolecular compound was synthesized. • Ultrasound synthesis of nano coordination compound have been reported. • The X-ray crystal structure of the compound is reported.

  3. Structural organization and spectroscopy of peptide-actinide(IV) complexes

    International Nuclear Information System (INIS)

    Dahou, S.

    2010-01-01

    The contamination of living organisms by actinide elements is at the origin of both radiological and chemical toxicity that may lead to severe dysfunction. Most of the data available on the actinide interaction with biological systems are macroscopic physiological measurements and are lacking a molecular description of the systems. Because of the intricacy of these systems, classical biochemical methods are difficult to implement. Our strategy consisted in designing simplified biomimetic peptides, and describing the corresponding intramolecular interactions with actinides. A carboxylic pentapeptide of the form DDPDD has been at the starting point of this work in order to further assess the influence of the peptide sequence on the topology of the complexes.To do so, various linear (Asp/Ala permutations, peptoids) and cyclic analogues have been synthesized. Furthermore, in order to include the hydroxamic function (with a high affinity for Fe(III)) in the peptide, both desferrioxamine and acetohydroxamic acid have been investigated. However because of difficulties in synthesis, we have not been able to test these peptides. Three actinide cations have been considered at oxidation state +IV (Th, Np, Pu) and compared to Fe(III), often considered as a biological surrogate of Pu(IV). The spatial arrangement of the peptide around the cation has been probed by spectrophotometry and X-ray Absorption Spectroscopy. The spectroscopic data and EXAFS data adjustment lead us to rationalize the topology of the complexes as a function of the peptide sequence: mix hydroxy polynuclear species for linear and cyclic peptides, mononuclear for the desferrioxamine complexes. Furthermore, significant differences have appeared between Fe(III) and actinide(IV), related to differences of reactivity in aqueous medium. (author)

  4. Structural and Pharmacological Effects of Ring-Closing Metathesis in Peptides

    Directory of Open Access Journals (Sweden)

    Pål Rongved

    2010-09-01

    Full Text Available Applications of ring-closing alkene metathesis (RCM in acyclic α- and β-peptides and closely related systems are reviewed, with a special emphasis on the structural and pharmacological effects of cyclization by RCM.

  5. Primary structure of the signal peptide of tropoelastin b.

    Science.gov (United States)

    Karr, S R; Foster, J A

    1981-06-25

    Elastin is a major protein of compliant connective tissue and is characterized by an amino acid composition abundant in nonpolar residues. The soluble precursor to elastin tropoelastin, is extractable in organic solvents and possesses an extensive clustering of nonpolar amino acid residues in the immediate NH2-terminal region (Foster, J. A., Shapiro, R., Voynow, P., Crombie, G., Faris, B., and Franzblau, C. (1975) Biochemistry 14, 857-864). It was, therefore, of special interest to determine whether tropoelastin requires a hydrophobic signal peptide for vectorial transport of the nascent polypeptide. The possibility that the initial tropoelastin translation product possesses a short signal peptide was examined in a cell-free translation system. Total RNA, isolated from aortae of 1-day-old chicks, was translated in an mRNA-dependent reticulocyte lysate translation assay. The translation products were then immunoprecipitated and subjected to automated radiosequencing. Comparison of the NH2-terminal sequence of tropoelastin b synthesized in the cell-free system versus that synthesized in organ culture demonstrated the presence of a signal peptide 24 amino acid residues in length. The signal peptide sequence is as follows: Met-Arg-Gln-Ala-Ala-Ala-Pro-Leu-Leu-Pro-Gly-Val-Leu-Leu-Leu-Phe-Ser-Ile-Leu-Pro -Ala-Ser-Gln-Gln. The preponderance of hydrophobic amino acid residues as well as the polar residues adjacent to the initiator methionine and the carboxyl termini found in the signal peptide is similar to that reported for other secreted proteins.

  6. Cation-pi interactions stabilize the structure of the antimicrobial peptide indolicidin near membranes: molecular dynamics simulations

    DEFF Research Database (Denmark)

    Khandelia, Himanshu; Kaznessis, Yiannis N

    2007-01-01

    to the sulfate groups leads to an extended peptide structure. To the best of our knowledge, this is the first time that a cation-pi interaction between peptide side chains has been shown to stabilize the structure of a small antimicrobial peptide. The simulations are in excellent agreement with available...

  7. Quantitative Structure-Activity Relationships and Docking Studies of Calcitonin Gene-Related Peptide Antagonists

    DEFF Research Database (Denmark)

    Jenssen, Håvard; Mehrabian, Mohadeseh; Kyani, Anahita

    2012-01-01

    of calcitonin gene-related peptide antagonists was performed using a panel of physicochemical descriptors. The computational studies evaluated different variable selection techniques and demonstrated shuffling stepwise multiple linear regression to be superior over genetic algorithm-multiple linear regression....... The linear quantitative structure-activity relationship model revealed better statistical parameters of cross-validation in comparison with the non-linear support vector regression technique. Implementing only five peptide descriptors into this linear quantitative structure-activity relationship model...

  8. Antimicrobial Dendrimeric Peptides: Structure, Activity and New Therapeutic Applications

    Directory of Open Access Journals (Sweden)

    Mariano A. Scorciapino

    2017-03-01

    Full Text Available Microbial resistance to conventional antibiotics is one of the most outstanding medical and scientific challenges of our times. Despite the recognised need for new anti-infective agents, however, very few new drugs have been brought to the market and to the clinic in the last three decades. This review highlights the properties of a new class of antibiotics, namely dendrimeric peptides. These intriguing novel compounds, generally made of multiple peptidic sequences linked to an inner branched core, display an array of antibacterial, antiviral and antifungal activities, usually coupled to low haemolytic activity. In addition, several peptides synthesized in oligobranched form proved to be promising tools for the selective treatment of cancer cells.

  9. Supramolecular polymers constructed from macrocycle-based host-guest molecular recognition motifs.

    Science.gov (United States)

    Dong, Shengyi; Zheng, Bo; Wang, Feng; Huang, Feihe

    2014-07-15

    CONSPECTUS: Supramolecular polymers, fabricated via the combination of supramolecular chemistry and polymer science, are polymeric arrays of repeating units held together by reversible, relatively weak noncovalent interactions. The introduction of noncovalent interactions, such as hydrogen bonding, aromatic stacking interactions, metal coordination, and host-guest interactions, endows supramolecular polymers with unique stimuli responsiveness and self-adjusting abilities. As a result, diverse monomer structures have been designed and synthesized to construct various types of supramolecular polymers. By changing the noncovalent interaction types, numbers, or chemical structures of functional groups in these monomers, supramolecular polymeric materials can be prepared with tailored chemical and physical properties. In recent years, the interest in supramolecular polymers has been extended from the preparation of intriguing topological structures to the discoveries of potential applications as functional materials. Compared with traditional polymers, supramolecular polymers show some advantages in the fabrication of reversible or responsive materials. The development of supramolecular polymers also offers a platform to construct complex and sophisticated materials with a bottom-up approach. Macrocylic hosts, including crown ethers, cyclodextrins, calixarenes, cucurbiturils, and pillararenes, are the most commonly used building blocks in the fabrication of host-guest interaction-based supramolecular polymers. With the introduction of complementary guest molecules, macrocylic hosts demonstrate selective and stimuli-responsive host-guest complexation behaviors. By elaborate molecular design, the resultant supramolecular polymers can exhibit diverse structures based on the self-selectivity of host-guest interactions. The introduction of reversible host-guest interactions can further endow these supramolecular polymers with interesting and fascinating chemical

  10. Supramolecular Structure, Physical Properties, and Langmuir-Blodgett Film Formation of an Optically Active Liquid-Crystalline Phthalocyanine

    NARCIS (Netherlands)

    Nostrum, Cornelus F. van; Bosman, Anton W.; Gelinck, Gerwin H.; Schouten, Pieter G.; Warman, John M.; Devillers, Marinus A.C.; Meijerink, Andries; Picken, Stephen J.; Sohling, Ulrich; Schouten, Arend-Jan; Nolte, Roeland J.M.

    The structure and physical properties of optically active, metal-free 2,3,9,10,16,17,23,24-octa(S-3,7-dimethyloctoxy)phthalocyanine ((S)-Pc(8,2)) are reported and compared with those of the phthalocyanine with (R,S) side chains (mixture of 43 stereoisomers). Unlike the latter compound, (S)-Pc(8,2)

  11. A triaxial supramolecular weave

    Science.gov (United States)

    Lewandowska, Urszula; Zajaczkowski, Wojciech; Corra, Stefano; Tanabe, Junki; Borrmann, Ruediger; Benetti, Edmondo M.; Stappert, Sebastian; Watanabe, Kohei; Ochs, Nellie A. K.; Schaeublin, Robin; Li, Chen; Yashima, Eiji; Pisula, Wojciech; Müllen, Klaus; Wennemers, Helma

    2017-11-01

    Despite recent advances in the synthesis of increasingly complex topologies at the molecular level, nano- and microscopic weaves have remained difficult to achieve. Only a few diaxial molecular weaves exist—these were achieved by templation with metals. Here, we present an extended triaxial supramolecular weave that consists of self-assembled organic threads. Each thread is formed by the self-assembly of a building block comprising a rigid oligoproline segment with two perylene-monoimide chromophores spaced at 18 Å. Upon π stacking of the chromophores, threads form that feature alternating up- and down-facing voids at regular distances. These voids accommodate incoming building blocks and establish crossing points through CH-π interactions on further assembly of the threads into a triaxial woven superstructure. The resulting micrometre-scale supramolecular weave proved to be more robust than non-woven self-assemblies of the same building block. The uniform hexagonal pores of the interwoven network were able to host iridium nanoparticles, which may be of interest for practical applications.

  12. Supramolecular analytical chemistry.

    Science.gov (United States)

    Anslyn, Eric V

    2007-02-02

    A large fraction of the field of supramolecular chemistry has focused in previous decades upon the study and use of synthetic receptors as a means of mimicking natural receptors. Recently, the demand for synthetic receptors is rapidly increasing within the analytical sciences. These classes of receptors are finding uses in simple indicator chemistry, cellular imaging, and enantiomeric excess analysis, while also being involved in various truly practical assays of bodily fluids. Moreover, one of the most promising areas for the use of synthetic receptors is in the arena of differential sensing. Although many synthetic receptors have been shown to yield exquisite selectivities, in general, this class of receptor suffers from cross-reactivities. Yet, cross-reactivity is an attribute that is crucial to the success of differential sensing schemes. Therefore, both selective and nonselective synthetic receptors are finding uses in analytical applications. Hence, a field of chemistry that herein is entitled "Supramolecular Analytical Chemistry" is emerging, and is predicted to undergo increasingly rapid growth in the near future.

  13. A fluorescent protein scaffold for presenting structurally constrained peptides provides an effective screening system to identify high affinity target-binding peptides.

    Directory of Open Access Journals (Sweden)

    Tetsuya Kadonosono

    Full Text Available Peptides that have high affinity for target molecules on the surface of cancer cells are crucial for the development of targeted cancer therapies. However, unstructured peptides often fail to bind their target molecules with high affinity. To efficiently identify high-affinity target-binding peptides, we have constructed a fluorescent protein scaffold, designated gFPS, in which structurally constrained peptides are integrated at residues K131-L137 of superfolder green fluorescent protein. Molecular dynamics simulation supported the suitability of this site for presentation of exogenous peptides with a constrained structure. gFPS can present 4 to 12 exogenous amino acids without a loss of fluorescence. When gFPSs presenting human epidermal growth factor receptor type 2 (HER2-targeting peptides were added to the culture medium of HER2-expressing cells, we could easily identify the peptides with high HER2-affinity and -specificity based on gFPS fluorescence. In addition, gFPS could be expressed on the yeast cell surface and applied for a high-throughput screening. These results demonstrate that gFPS has the potential to serve as a powerful tool to improve screening of structurally constrained peptides that have a high target affinity, and suggest that it could expedite the one-step identification of clinically applicable cancer cell-binding peptides.

  14. Structure-activity study of the antibacterial peptide fallaxin

    DEFF Research Database (Denmark)

    Søndergaard, Sandra Lerche; Frimodt-Møller, Niels; Kragelund, Birthe Brandt

    2007-01-01

    Fallaxin is a 25-mer antibacterial peptide amide, which was recently isolated from the West Indian mountain chicken frog Leptodactylus fallax. Fallaxin has been shown to inhibit the growth of several Gram-negative bacteria including Enterobacter cloacae, Escherichia coli, Klebsiella pneumoniae...

  15. Structural features of the ionic self-complementary amyloidogenic peptide

    Science.gov (United States)

    Egorov, V. V.; Zabrodskaya, Ya A.; Lebedev, D. V.; Gorshkov, A. N.; Kuklin, A. I.

    2017-05-01

    In this study we investigate the effect of triazavirine on ionic self-complementary (iSCM) containing peptides fibrils with transmission electron microscopy (TEM), small-angle neutron scattering (SANS) and MALDI mass-spectrometry (MS). It was shown that triazavirine is capable to dissociate iSCM amyloid fibrils. The mechanism of such an action is proposed.

  16. Combining UV photodissociation with electron transfer for peptide structure analysis

    Czech Academy of Sciences Publication Activity Database

    Shaffer, C. J.; Marek, Aleš; Pepin, R.; Slováková, K.; Tureček, F.

    2015-01-01

    Roč. 50, č. 3 (2015), s. 470-475 ISSN 1076-5174 Institutional support: RVO:61388963 Keywords : electron transfer dissociation * laser photodissociation * peptide ions * cation radical * chromophores * isomer distinction Subject RIV: CE - Biochemistry Impact factor: 2.541, year: 2015

  17. NMR and structural data for Connexin 32 and Connexin 26 N-terminal peptides

    Directory of Open Access Journals (Sweden)

    Yuksel Batir

    2016-12-01

    Full Text Available In this article we present 1H and 13C chemical shift assignments, secondary structural propensity data and normalized temperature coefficient data for N-terminal peptides of Connexin 26 (Cx26, Cx26G12R and Cx32G12R mutants seen in syndromic deafness and Charcot Marie Tooth Disease respectively, published in “Structural Studies of N-Terminal Mutants of Connexin 26 and Connexin 32 Using 1H NMR Spectroscopy” (Y. Batir, T.A. Bargiello, T.L. Dowd, 2016 [1]. The mutation G12R affects the structure of both Cx26 and Cx32 peptides differently. We present data from secondary structure propensity chemical shift analysis which calculates a secondary structure propensity (SSP score for both disordered or folded peptides and proteins using the difference between the 13C secondary chemical shifts of the Cα and Cβ protons. This data supplements the calculated NMR structures from NOESY data [1]. We present and compare the SSP data for the Cx26 vs Cx26G12R peptides and the Cx32 and Cx32G12R peptides. In addition, we present plots of temperature coefficients obtained for Cx26, Cx26G12R and Cx32G12R peptides collected previously [1] and normalized to their random coil temperature coefficients, “Random coil 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG” (G. Merutka, H.J. Dyson, P.E. Wright, 1995 [2]. Reductions in these normalized temperature coefficients are directly observable for residues in different segments of the peptide and this data informs on solvent accessibility of the NH protons and NH protons which may be more constrained due to the formation of H bonds.

  18. A novel asymmetric chair-like hydroxyl-bridged tetra-copper compound: Synthesis, supramolecular structure and magnetic property

    Science.gov (United States)

    Wang, Xiao-Feng; Du, Ke-Jie; Wang, Hong-Qing; Zhang, Xue-Li; Nie, Chang-Ming

    2017-06-01

    A new polynuclear Cu(II) compound, [Cu4(bpy)4(OH)4(H2O)(BTC)]NO3·8H2O (1), was prepared by self-assembly from the solution of copper(II) nitrate and two kinds of ligands, 2,2‧-bipyridine (bpy) and benzene-tricarboxylic acid (H3BTC). Single crystal structure analysis reveals that 1 features a rare asymmetric chair-like hydroxyl-bridged tetra-copper cluster: [Cu4(OH)4] core along with one H2O and one BTC3- occupied each terminal coordinated site. In addition, the magnetic property has been investigated.

  19. Structure-Activity Relationship of Chlorotoxin-Like Peptides

    Directory of Open Access Journals (Sweden)

    Syed Abid Ali

    2016-02-01

    Full Text Available Animal venom (e.g., scorpion is a rich source of various protein and peptide toxins with diverse physio-/pharmaco-logical activities, which generally exert their action via target-specific modulation of different ion channel functions. Scorpion venoms are among the most widely-known source of peptidyl neurotoxins used for callipering different ion channels, such as; Na+, K+, Ca+, Cl−, etc. A new peptide of the chlorotoxin family (i.e., Bs-Tx7 has been isolated, sequenced and synthesized from scorpion Buthus sindicus (family Buthidae venom. This peptide demonstrates 66% with chlorotoxin (ClTx and 82% with CFTR channel inhibitor (GaTx1 sequence identities reported from Leiurus quinquestriatus hebraeus venom. The toxin has a molecular mass of 3821 Da and possesses four intra-chain disulphide bonds. Amino acid sequence analysis of Bs-Tx7 revealed the presence of a scissile peptide bond (i.e., Gly-Ile for human MMP2, whose activity is increased in the case of tumour malignancy. The effect of hMMP2 on Bs-Tx7, or vice versa, observed using the FRET peptide substrate with methoxycoumarin (Mca/dinitrophenyl (Dnp as fluorophore/quencher, designed and synthesized to obtain the lowest Km value for this substrate, showed approximately a 60% increase in the activity of hMMP2 upon incubation of Bs-Tx7 with the enzyme at a micromolar concentration (4 µM, indicating the importance of this toxin in diseases associated with decreased MMP2 activity.

  20. Nuclear Magnetic Resonance structural studies of peptides and proteins from the vaso-regulatory System

    International Nuclear Information System (INIS)

    Sizun, Philippe

    1991-01-01

    The aim of the present work is to show how Nuclear Magnetic Resonance (NMR) allows to determine the 3D structure of peptides and proteins in solution. A comparative study of peptides involved in the vaso-regulatory System (form small hormonal peptide to the 65 amido-acid protein hirudin) has allowed to design most efficient NMR 1D and 2D strategies. It rapidly appeared that the size of the peptide plays a key role in the structuration of the molecule, smallest peptides being weakly structured owing to the lack of cooperative effects. As the molecular size increases or if conformational locks are present (disulfide bridges) the probability of stable secondary structure increases. For the protein hirudin, a combination of ail available NMR parameters deduced form dedicated experiments (chemical shifts, coupling constants, overhauser effects, accessibility of amide protons) and molecular modelling under constraints allows a clear 3D structure to be proposed for this protein in solution. Finally, a comparative study of the experimental structures and of those deduced form prediction rules has shed light on the concept of structural predisposition, the latter being of high value for a better understanding of structure-activity relationships. (author) [fr

  1. Light-Switchable Hemithioindigo-Hemistilbene-Containing Peptides : Ultrafast Spectroscopy of the Z -> E Isomerization of the Chromophore and the Structural Dynamics of the Peptide Moiety

    NARCIS (Netherlands)

    Regner, N.; Herzog, T. T.; Haiser, K.; Hoppmann, C.; Beyermann, M.; Sauermann, J.; Engelhard, M.; Cordes, T.; Rueck-Braun, K.; Zinth, W.; Rück-Braun, K.

    2012-01-01

    Two hemithioindigo-hemistilbene (HTI) derivatives, designed to operate as structural switches in peptides, as well as two HTI peptides are characterized by ultrafast spectroscopy in the visible and the infrared. The two HTI switches follow the reaction scheme published for other HTI compounds with a

  2. Structural basis for antibacterial peptide self-immunity by the bacterial ABC transporter McjD.

    Science.gov (United States)

    Bountra, Kiran; Hagelueken, Gregor; Choudhury, Hassanul G; Corradi, Valentina; El Omari, Kamel; Wagner, Armin; Mathavan, Indran; Zirah, Séverine; Yuan Wahlgren, Weixiao; Tieleman, D Peter; Schiemann, Olav; Rebuffat, Sylvie; Beis, Konstantinos

    2017-10-16

    Certain pathogenic bacteria produce and release toxic peptides to ensure either nutrient availability or evasion from the immune system. These peptides are also toxic to the producing bacteria that utilize dedicated ABC transporters to provide self-immunity. The ABC transporter McjD exports the antibacterial peptide MccJ25 in Escherichia coli Our previously determined McjD structure provided some mechanistic insights into antibacterial peptide efflux. In this study, we have determined its structure in a novel conformation, apo inward-occluded and a new nucleotide-bound state, high-energy outward-occluded intermediate state, with a defined ligand binding cavity. Predictive cysteine cross-linking in E. coli membranes and PELDOR measurements along the transport cycle indicate that McjD does not undergo major conformational changes as previously proposed for multi-drug ABC exporters. Combined with transport assays and molecular dynamics simulations, we propose a novel mechanism for toxic peptide ABC exporters that only requires the transient opening of the cavity for release of the peptide. We propose that shielding of the cavity ensures that the transporter is available to export the newly synthesized peptides, preventing toxic-level build-up. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

  3. Buckwheat trypsin inhibitor with helical hairpin structure belongs to a new family of plant defence peptides.

    Science.gov (United States)

    Oparin, Peter B; Mineev, Konstantin S; Dunaevsky, Yakov E; Arseniev, Alexander S; Belozersky, Mikhail A; Grishin, Eugene V; Egorov, Tsezi A; Vassilevski, Alexander A

    2012-08-15

    A new peptide trypsin inhibitor named BWI-2c was obtained from buckwheat (Fagopyrum esculentum) seeds by sequential affinity, ion exchange and reversed-phase chromatography. The peptide was sequenced and found to contain 41 amino acid residues, with four cysteine residues involved in two intramolecular disulfide bonds. Recombinant BWI-2c identical to the natural peptide was produced in Escherichia coli in a form of a cleavable fusion with thioredoxin. The 3D (three-dimensional) structure of the peptide in solution was determined by NMR spectroscopy, revealing two antiparallel α-helices stapled by disulfide bonds. Together with VhTI, a trypsin inhibitor from veronica (Veronica hederifolia), BWI-2c represents a new family of protease inhibitors with an unusual α-helical hairpin fold. The linker sequence between the helices represents the so-called trypsin inhibitory loop responsible for direct binding to the active site of the enzyme that cleaves BWI-2c at the functionally important residue Arg(19). The inhibition constant was determined for BWI-2c against trypsin (1.7×10(-1)0 M), and the peptide was tested on other enzymes, including those from various insect digestive systems, revealing high selectivity to trypsin-like proteases. Structural similarity shared by BWI-2c, VhTI and several other plant defence peptides leads to the acknowledgement of a new widespread family of plant peptides termed α-hairpinins.

  4. Amyloid-β peptides time-dependent structural modifications: AFM and voltammetric characterization.

    Science.gov (United States)

    Enache, Teodor Adrian; Chiorcea-Paquim, Ana-Maria; Oliveira-Brett, Ana Maria

    2016-07-05

    The human amyloid beta (Aβ) peptides, Aβ1-40 and Aβ1-42, structural modifications, from soluble monomers to fully formed fibrils through intermediate structures, were investigated, and the results were compared with those obtained for the inverse Aβ40-1 and Aβ42-1, mutant Aβ1-40Phe(10) and Aβ1-40Nle(35), and rat Aβ1-40Rat peptide sequences. The aggregation was followed at a slow rate, in chloride free media and room temperature, and revealed to be a sequence-structure process, dependent on the physicochemical properties of each Aβ peptide isoforms, and occurring at different rates and by different pathways. The fibrilization process was investigated by atomic force microscopy (AFM), via changes in the adsorption morphology from: (i) initially random coiled structures of ∼0.6 nm height, corresponding to the Aβ peptide monomers in random coil or in α-helix conformations, to (ii) aggregates and protofibrils of 1.5-6.0 nm height and (iii) two types of fibrils, corresponding to the Aβ peptide in a β-sheet configuration. The reactivity of the carbon electrode surface was considered. The hydrophobic surface induced rapid changes of the Aβ peptide conformations, and differences between the adsorbed fibrils, formed at the carbon surface (beaded, thin, 2.0 nm height), were detected. Differential pulse voltammetry showed that, according to their primary structure, the Aβ peptides undergo oxidation in one or two steps, the first step corresponding to the tyrosine amino acids oxidation, and the second one to the histidine and methionine amino acids oxidation. The fibrilization process was electrochemically detected via the decrease of the Aβ peptide oxidation peak currents that occurred in a time dependent manner. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Differential Interaction of Antimicrobial Peptides with Lipid Structures Studied by Coarse-Grained Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Galo E. Balatti

    2017-10-01

    Full Text Available In this work; we investigated the differential interaction of amphiphilic antimicrobial peptides with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC lipid structures by means of extensive molecular dynamics simulations. By using a coarse-grained (CG model within the MARTINI force field; we simulated the peptide–lipid system from three different initial configurations: (a peptides in water in the presence of a pre-equilibrated lipid bilayer; (b peptides inside the hydrophobic core of the membrane; and (c random configurations that allow self-assembled molecular structures. This last approach allowed us to sample the structural space of the systems and consider cooperative effects. The peptides used in our simulations are aurein 1.2 and maculatin 1.1; two well-known antimicrobial peptides from the Australian tree frogs; and molecules that present different membrane-perturbing behaviors. Our results showed differential behaviors for each type of peptide seen in a different organization that could guide a molecular interpretation of the experimental data. While both peptides are capable of forming membrane aggregates; the aurein 1.2 ones have a pore-like structure and exhibit a higher level of organization than those conformed by maculatin 1.1. Furthermore; maculatin 1.1 has a strong tendency to form clusters and induce curvature at low peptide–lipid ratios. The exploration of the possible lipid–peptide structures; as the one carried out here; could be a good tool for recognizing specific configurations that should be further studied with more sophisticated methodologies.

  6. Cellular uptake: lessons from supramolecular organic chemistry.

    Science.gov (United States)

    Gasparini, Giulio; Bang, Eun-Kyoung; Montenegro, Javier; Matile, Stefan

    2015-07-04

    The objective of this Feature Article is to reflect on the importance of established and emerging principles of supramolecular organic chemistry to address one of the most persistent problems in life sciences. The main topic is dynamic covalent chemistry on cell surfaces, particularly disulfide exchange for thiol-mediated uptake. Examples of boronate and hydrazone exchange are added for contrast, comparison and completion. Of equal importance are the discussions of proximity effects in polyions and counterion hopping, and more recent highlights on ring tension and ion pair-π interactions. These lessons from supramolecular organic chemistry apply to cell-penetrating peptides, particularly the origin of "arginine magic" and the "pyrenebutyrate trick," and the currently emerging complementary "disulfide magic" with cell-penetrating poly(disulfide)s. They further extend to the voltage gating of neuronal potassium channels, gene transfection, and the delivery of siRNA. The collected examples illustrate that the input from conceptually innovative chemistry is essential to address the true challenges in biology beyond incremental progress and random screening.

  7. Software-aided approach to investigate peptide structure and metabolic susceptibility of amide bonds in peptide drugs based on high resolution mass spectrometry.

    Directory of Open Access Journals (Sweden)

    Tatiana Radchenko

    Full Text Available Interest in using peptide molecules as therapeutic agents due to high selectivity and efficacy is increasing within the pharmaceutical industry. However, most peptide-derived drugs cannot be administered orally because of low bioavailability and instability in the gastrointestinal tract due to protease activity. Therefore, structural modifications peptides are required to improve their stability. For this purpose, several in-silico software tools have been developed such as PeptideCutter or PoPS, which aim to predict peptide cleavage sites for different proteases. Moreover, several databases exist where this information is collected and stored from public sources such as MEROPS and ExPASy ENZYME databases. These tools can help design a peptide drug with increased stability against proteolysis, though they are limited to natural amino acids or cannot process cyclic peptides, for example. We worked to develop a new methodology to analyze peptide structure and amide bond metabolic stability based on the peptide structure (linear/cyclic, natural/unnatural amino acids. This approach used liquid chromatography / high resolution, mass spectrometry to obtain the analytical data from in vitro incubations. We collected experimental data for a set (linear/cyclic, natural/unnatural amino acids of fourteen peptide drugs and four substrate peptides incubated with different proteolytic media: trypsin, chymotrypsin, pepsin, pancreatic elastase, dipeptidyl peptidase-4 and neprilysin. Mass spectrometry data was analyzed to find metabolites and determine their structures, then all the results were stored in a chemically aware manner, which allows us to compute the peptide bond susceptibility by using a frequency analysis of the metabolic-liable bonds. In total 132 metabolites were found from the various in vitro conditions tested resulting in 77 distinct cleavage sites. The most frequent observed cleavage sites agreed with those reported in the literature. The

  8. Software-aided approach to investigate peptide structure and metabolic susceptibility of amide bonds in peptide drugs based on high resolution mass spectrometry

    Science.gov (United States)

    Fontaine, Fabien; Morettoni, Luca; Zamora, Ismael

    2017-01-01

    Interest in using peptide molecules as therapeutic agents due to high selectivity and efficacy is increasing within the pharmaceutical industry. However, most peptide-derived drugs cannot be administered orally because of low bioavailability and instability in the gastrointestinal tract due to protease activity. Therefore, structural modifications peptides are required to improve their stability. For this purpose, several in-silico software tools have been developed such as PeptideCutter or PoPS, which aim to predict peptide cleavage sites for different proteases. Moreover, several databases exist where this information is collected and stored from public sources such as MEROPS and ExPASy ENZYME databases. These tools can help design a peptide drug with increased stability against proteolysis, though they are limited to natural amino acids or cannot process cyclic peptides, for example. We worked to develop a new methodology to analyze peptide structure and amide bond metabolic stability based on the peptide structure (linear/cyclic, natural/unnatural amino acids). This approach used liquid chromatography / high resolution, mass spectrometry to obtain the analytical data from in vitro incubations. We collected experimental data for a set (linear/cyclic, natural/unnatural amino acids) of fourteen peptide drugs and four substrate peptides incubated with different proteolytic media: trypsin, chymotrypsin, pepsin, pancreatic elastase, dipeptidyl peptidase-4 and neprilysin. Mass spectrometry data was analyzed to find metabolites and determine their structures, then all the results were stored in a chemically aware manner, which allows us to compute the peptide bond susceptibility by using a frequency analysis of the metabolic-liable bonds. In total 132 metabolites were found from the various in vitro conditions tested resulting in 77 distinct cleavage sites. The most frequent observed cleavage sites agreed with those reported in the literature. The main advantages of

  9. Supramolecular patterns and Hirshfeld surface analysis in the crystal structure of bis(2-amino-4-methoxy-6-methylpyrimidinium isophthalate

    Directory of Open Access Journals (Sweden)

    Muthaiah Jeevaraj

    2017-10-01

    Full Text Available In the title molecular salt, 2C6H10N3O+·C8H4O42−, the N atom of each of the two 2-amino-4-methoxy-6-methylpyrimidine molecules lying between the amine and methyl groups has been protonated. The dihedral angles between the pyrimidine rings of the cations and the benzene ring of the succinate dianion are 5.04 (8 and 7.95 (8°. Each of the cations is linked to the anion through a pair of N—H...O(carboxylate hydrogen bonds, forming cyclic R22(8 ring motifs which are then linked through inversion-related N—H...O hydrogen bonds, giving a central R24(8 motif. Peripheral amine N—H...O hydrogen-bonding interactions on either side of the succinate anion, also through centrosymmetric R22(8 extensions, form one-dimensional ribbons extending along [211]. The crystal structure also features π–π stacking interactions between the aromatic rings of the pyrimidine cations [minimum ring centroid separation = 3.6337 (9 Å]. The intermolecular interactions were also investigated using Hirshfeld surface studies and two-dimensional fingerprint images.

  10. Synthesis, crystal structure, physicochemical properties of hydrogen bonded supramolecular assembly of N,N-diethylanilinium-3, 5-dinitrosalicylate crystal

    Science.gov (United States)

    Rajkumar, M.; Chandramohan, A.

    2017-12-01

    An organic salt, N,N-diethylanilinium 3,5-dinitrosalicylate was synthesized and single crystals grown by employing the slow solvent evaporation solution growth technique in methanol-acetone (1:1) mixture. The electronic transitions of the salt crystal were studied by UV-Visible spectrum. The optical transmittance window and lower wavelength cut-off of grown crystal have been identified by UV-Vis-NIR studies. The FT-IR spectrum was recorded to confirm the presence of various functional groups in the grown crystal. 1H and 13C NMR spectrum were recorded to establish the molecular structure of the title crystal. Single crystal X-ray diffraction data indicated that the crystal belongs to monoclinic crystal system with P21/n space group. The thermal stability of the crystal was established by TG/DTA studies. The mechanical properties of the grown crystal were studied by Vickers' microhardness technique. The dielectric studies indicated that the dielectric constant and dielectric loss decrease exponentially with frequency at different temperatures.

  11. Membrane interaction and secondary structure of de novo designed arginine-and tryptophan peptides with dual function

    KAUST Repository

    Rydberg, Hanna A.

    2012-10-01

    Cell-penetrating peptides and antimicrobial peptides are two classes of positively charged membrane active peptides with several properties in common. The challenge is to combine knowledge about the membrane interaction mechanisms and structural properties of the two classes to design peptides with membrane-specific actions, useful either as transporters of cargo or as antibacterial substances. Membrane active peptides are commonly rich in arginine and tryptophan. We have previously designed a series of arg/trp peptides and investigated how the position and number of tryptophans affect cellular uptake. Here we explore the antimicrobial properties and the interaction with lipid model membranes of these peptides, using minimal inhibitory concentrations assay (MIC), circular dichroism (CD) and linear dichroism (LD). The results show that the arg/trp peptides inhibit the growth of the two gram positive strains Staphylococcus aureus and Staphylococcus pyogenes, with some individual variations depending on the position of the tryptophans. No inhibition of the gram negative strains Proteus mirabilis or Pseudomonas aeruginosa was noticed. CD indicated that when bound to lipid vesicles one of the peptides forms an α-helical like structure, whereas the other five exhibited rather random coiled structures. LD indicated that all six peptides were somehow aligned parallel with the membrane surface. Our results do not reveal any obvious connection between membrane interaction and antimicrobial effect for the studied peptides. By contrast cell-penetrating properties can be coupled to both the secondary structure and the degree of order of the peptides. © 2012 Elsevier Inc.

  12. Supramolecular photochemistry of drugs in biomolecular environments.

    Science.gov (United States)

    Monti, Sandra; Manet, Ilse

    2014-06-21

    In this tutorial review we illustrate how the interaction of photoactive drugs/potential drugs with proteins or DNA in supramolecular complexes can determine the course of the reactions initiated by the drug absorbed photons, evidencing the mechanistic differences with respect to the solution conditions. We focus on photoprocesses, independent of oxygen, that lead to chemical modification of the biomolecules, with formation of new covalent bonds or cleavage of existing bonds. Representative systems are mainly selected from the literature of the last decade. The photoreactivity of some aryl propionic acids, (fluoro)quinolones, furocoumarins, metal coordination complexes, quinine-like compounds, naphthaleneimides and pyrenyl-peptides with proteins or DNA is discussed. The use of light for biomolecule photomodification, historically relevant to biological photosensitization processes and some forms of photochemotherapy, is nowadays becoming more and more important in the development of innovative methods in nanomedicine and biotechnology.

  13. Polymeric peptide pigments with sequence-encoded properties

    Energy Technology Data Exchange (ETDEWEB)

    Lampel, Ayala; McPhee, Scott A.; Park, Hang-Ah; Scott, Gary G.; Humagain, Sunita; Hekstra, Doeke R.; Yoo, Barney; Frederix, Pim W. J. M.; Li, Tai-De; Abzalimov, Rinat R.; Greenbaum, Steven G.; Tuttle, Tell; Hu, Chunhua; Bettinger, Christopher J.; Ulijn, Rein V.

    2017-06-08

    Melanins are a family of heterogeneous polymeric pigments that provide ultraviolet (UV) light protection, structural support, coloration, and free radical scavenging. Formed by oxidative oligomerization of catecholic small molecules, the physical properties of melanins are influenced by covalent and noncovalent disorder. We report the use of tyrosine-containing tripeptides as tunable precursors for polymeric pigments. In these structures, phenols are presented in a (supra-)molecular context dictated by the positions of the amino acids in the peptide sequence. Oxidative polymerization can be tuned in a sequence-dependent manner, resulting in peptide sequence–encoded properties such as UV absorbance, morphology, coloration, and electrochemical properties over a considerable range. Short peptides have low barriers to application and can be easily scaled, suggesting near-term applications in cosmetics and biomedicine.

  14. Single molecule studies of surface-induced secondary structure in a model peptide

    Science.gov (United States)

    English, Douglas S.; Cunningham, Joy A.; Wehri, Sarah C.; Petrik, Amy F.; Okamoto, Kenji

    2004-10-01

    We have proposed using single molecule fluorescence resonant energy transfer (SM-FRET) to investigate the induction of secondary structure in model, surface-active peptides upon binding at an interface. The ability for SM-FRET to distinguish structural heterogeneity will offer a distinct advantage over traditional biophysical methods in these types of studies. Ensemble methods mask heterogeneity and only provide an average measure of secondary structural features. Because secondary structure contributes greatly to the energetics of dehydrating the amide backbone, detailed information of conformational distributions is crucial to the understanding of the thermodynamic cycle involved. Here we present results from our first efforts at using SM-FRET to study an amphipathic α-helix forming peptide immobilized at the solid-liquid interface between an aqueous solution and an octadecylsilane modified glass surface. This system serves as a model for future studies of peptide partitioning to lipid bilayers and other relevant interfaces.

  15. Constitutional dynamic chemistry: bridge from supramolecular chemistry to adaptive chemistry.

    Science.gov (United States)

    Lehn, Jean-Marie

    2012-01-01

    Supramolecular chemistry aims at implementing highly complex chemical systems from molecular components held together by non-covalent intermolecular forces and effecting molecular recognition, catalysis and transport processes. A further step consists in the investigation of chemical systems undergoing self-organization, i.e. systems capable of spontaneously generating well-defined functional supramolecular architectures by self-assembly from their components, thus behaving as programmed chemical systems. Supramolecular chemistry is intrinsically a dynamic chemistry in view of the lability of the interactions connecting the molecular components of a supramolecular entity and the resulting ability of supramolecular species to exchange their constituents. The same holds for molecular chemistry when the molecular entity contains covalent bonds that may form and break reversibility, so as to allow a continuous change in constitution by reorganization and exchange of building blocks. These features define a Constitutional Dynamic Chemistry (CDC) on both the molecular and supramolecular levels.CDC introduces a paradigm shift with respect to constitutionally static chemistry. The latter relies on design for the generation of a target entity, whereas CDC takes advantage of dynamic diversity to allow variation and selection. The implementation of selection in chemistry introduces a fundamental change in outlook. Whereas self-organization by design strives to achieve full control over the output molecular or supramolecular entity by explicit programming, self-organization with selection operates on dynamic constitutional diversity in response to either internal or external factors to achieve adaptation.The merging of the features: -information and programmability, -dynamics and reversibility, -constitution and structural diversity, points to the emergence of adaptive and evolutive chemistry, towards a chemistry of complex matter.

  16. Determining peptide sequence effects that control the size, structure, and function of nanoparticles.

    Science.gov (United States)

    Coppage, Ryan; Slocik, Joseph M; Briggs, Beverly D; Frenkel, Anatoly I; Naik, Rajesh R; Knecht, Marc R

    2012-02-28

    The ability to tune the size, shape, and composition of nanomaterials at length scales particle morphology through controlling the biotic/abiotic interface. Here we demonstrate the ability to finely tune the size, surface structure, and functionality of single-crystal Pd nanoparticles between 2 and 3 nm using materials directing peptides. This was achieved by selectively altering the peptide sequence to change the binding motif, which in turn modifies the surface structure of the particles. The materials were fully characterized before and after reduction using atomically resolved spectroscopic and microscopic analyses, which indicated that the coordination environment prior to reduction significantly affects the structure of the final nanoparticles. Additionally, changes to the particle surface structure, as a function of peptide sequence, can allow for chloride ion coordination that alters the catalytic abilities of the materials for the C-C coupling Stille reaction. These results suggest that peptide-based approaches may be able to achieve control over the structure/function relationship of nanomaterials where the peptide sequence could be used to selectivity tune such capabilities.

  17. Morphogenesis and Optoelectronic Properties of Supramolecular Assemblies of Chiral Perylene Diimides in a Binary Solvent System.

    Science.gov (United States)

    Shang, Xiaobo; Song, Inho; Ohtsu, Hiroyoshi; Tong, Jiaqi; Zhang, Haoke; Oh, Joon Hak

    2017-07-14

    Chiral supramolecular structures are attracting great attention due to their specific properties and high potential in chiral sensing and separation. Herein, supramolecular assembling behaviors of chiral perylene diimides have been systematically investigated in a mixed solution of tetrahydrofuran and water. They exhibit remarkably different morphologies and chiral aggregation behaviors depending on the mixing ratio of the solvents, i.e., the fraction of water. The morphogenesis and optoelectronic properties of chiral supramolecular structures have been thoroughly studied using a range of experimental and theoretical methods to investigate the morphological effects of chiral supramolecular assemblies on the electrical performances and photogenerated charge-carrier behaviors. In addition, chiral perylene diimides have been discriminated by combining vibrational circular dichroism with theoretical calculations, for the first time. The chiral supramolecular nanostructures developed herein strongly absorb visible spectral region and exhibit high photoresponsivity and detectivity, opening up new opportunities for practical applications in optoelectronics.

  18. Cell death versus cell survival instructed by supramolecular cohesion of nanostructures

    Science.gov (United States)

    Newcomb, Christina J.; Sur, Shantanu; Ortony, Julia H.; Lee, One-Sun; Matson, John B.; Boekhoven, Job; Yu, Jeong Min; Schatz, George C.; Stupp, Samuel I.

    2014-02-01

    Many naturally occurring peptides containing cationic and hydrophobic domains have evolved to interact with mammalian cell membranes and have been incorporated into materials for non-viral gene delivery, cancer therapy or treatment of microbial infections. Their electrostatic attraction to the negatively charged cell surface and hydrophobic interactions with the membrane lipids enable intracellular delivery or cell lysis. Although the effects of hydrophobicity and cationic charge of soluble molecules on the cell membrane are well known, the interactions between materials with these molecular features and cells remain poorly understood. Here we report that varying the cohesive forces within nanofibres of supramolecular materials with nearly identical cationic and hydrophobic structure instruct cell death or cell survival. Weak intermolecular bonds promote cell death through disruption of lipid membranes, while materials reinforced by hydrogen bonds support cell viability. These findings provide new strategies to design biomaterials that interact with the cell membrane.

  19. Rational design of anti-microbial peptides with enhanced activity and low cytotoxicity based on the structure of the arginine/histidine-rich peptide, chensinin-1.

    Science.gov (United States)

    Shang, D; Sun, Y; Wang, C; Ma, L; Li, J; Wang, X

    2012-09-01

    To understand the structure-activity relationship of chensinin-1, a anti-microbial peptide (AMP) with an unusual structure, and to develop novel AMPs as therapeutic agents. A series of chensinin-1 analogues were designed and synthesized by one to three replacement of glycines with leucines at the hydrophilic face of chensinin-1 or rearrangement of some of the residues in its sequence. Circular dichroism spectroscopy showed that the analogues adopted α-helical-type conformations in 50% trifluoroethanol/water but adopted β-strand-type conformations in 30 mmol l(-1) sodium dodecyl sulphate. The anti-microbial activities of the peptides against Gram-positive bacteria increased 5- to 30-fold, and these increases paralleled the increases in the peptides' hydrophobicities. Their haemolytic activities also increased. Amphipathicities had little influence on the bactericidal activity of chensinin-1. All peptides caused leakage of calcein entrapped in negatively charged liposomes although with different efficiencies. The peptides did not induce leakage of calcein from uncharged liposomes. Peptide adopted an aperiodic structure can improve the anti-microbial potency by increasing peptide hydrophobicity. Its target is bacteria plasma membrane. Chensinin-1 can act as a new lead molecule for the study of AMPs with atypical structures. © 2012 The Authors Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

  20. Crystal structure of a TAPBPR–MHC I complex reveals the mechanism of peptide editing in antigen presentation

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Jiansheng; Natarajan, Kannan; Boyd, Lisa F.; Morozov, Giora I.; Mage, Michael G.; Margulies, David H. (NIH); (Hebrew)

    2017-10-12

    Central to CD8+ T cell–mediated immunity is the recognition of peptide–major histocompatibility complex class I (p–MHC I) proteins displayed by antigen-presenting cells. Chaperone-mediated loading of high-affinity peptides onto MHC I is a key step in the MHC I antigen presentation pathway. However, the structure of MHC I with a chaperone that facilitates peptide loading has not been determined. We report the crystal structure of MHC I in complex with the peptide editor TAPBPR (TAP-binding protein–related), a tapasin homolog. TAPBPR remodels the peptide-binding groove of MHC I, resulting in the release of low-affinity peptide. Changes include groove relaxation, modifications of key binding pockets, and domain adjustments. This structure captures a peptide-receptive state of MHC I and provides insights into the mechanism of peptide editing by TAPBPR and, by analogy, tapasin.

  1. Structurally Ordered Nanowire Formation from Co-Assembly of DNA Origami and Collagen-Mimetic Peptides

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Tao [Department; Meyer, Travis A. [Wallace; Modlin, Charles [Department; Zuo, Xiaobing [X-ray; Conticello, Vincent P. [Department; Ke, Yonggang [Wallace

    2017-10-02

    We describe the co-assembly of two different building units: collagen-mimetic peptides and DNA origami. Two peptides CP++ and sCP(++) are designed with a sequence comprising a central block (Pro-Hyp-Gly) and two positively charged domains (Pro-Arg-Gly) at both N- and C-termini. Co-assembly of peptides and DNA origami two-layer (TL) nanosheets affords the formation of one-dimensional nanowires with repeating periodicity of similar to 10 nm. Structural analyses suggest a face-to-face stacking of DNA nanosheets with peptides aligned perpendicularly to the sheet surfaces. We demonstrate the potential of selective peptide-DNA association between face-to-face and edge-to-edge packing by tailoring the size of DNA nanostructures. This study presents an attractive strategy to create hybrid biomolecular assemblies from peptide and DNA-based building blocks that takes advantage of the intrinsic chemical and physical properties of the respective components to encode structural and, potentially, functional complexity within readily accessible biomimetic materials.

  2. High-resolution structure of HLA-A*1101 in complex with SARS nucleocapsid peptide

    DEFF Research Database (Denmark)

    Blicher, Thomas; Kastrup, Jette Sandholm; Buus, Søren

    2005-01-01

    The structure of the human MHC-I molecule HLA-A*1101 in complex with a nonameric peptide (KTFPPTEPK) has been determined by X-ray crystallography to 1.45 A resolution. The peptide is derived from the SARS-CoV nucleocapsid protein positions 362-370 (SNP362-370). It is conserved in all known isolates...... of SARS-CoV and has been verified by in vitro peptide-binding studies to be a good to intermediate binder to HLA-A*0301 and HLA-A*1101, with IC50 values of 70 and 186 nM, respectively [Sylvester-Hvid et al. (2004), Tissue Antigens, 63, 395-400]. In terms of the residues lining the peptide-binding groove...

  3. Structural requirements for the interaction between peptide antigens and I-Ed molecules

    DEFF Research Database (Denmark)

    Sette, A; Adorini, L; Appella, E

    1989-01-01

    We have analyzed the structural characteristics of the interaction between I-Ed molecules and their peptide ligands. It was found that unrelated good I-Ed binders share structurally similar "core" regions that were experimentally demonstrated to be crucial for binding to I-Ed molecules. Single am...

  4. Supramolecular Nanoparticles for Molecular Diagnostics and Therapeutics

    Science.gov (United States)

    Chen, Kuan-Ju

    Over the past decades, significant efforts have been devoted to explore the use of various nanoparticle-based systems in the field of nanomedicine, including molecular imaging and therapy. Supramolecular synthetic approaches have attracted lots of attention due to their flexibility, convenience, and modularity for producing nanoparticles. In this dissertation, the developmental story of our size-controllable supramolecular nanoparticles (SNPs) will be discussed, as well as their use in specific biomedical applications. To achieve the self-assembly of SNPs, the well-characterized molecular recognition system (i.e., cyclodextrin/adamantane recognition) was employed. The resulting SNPs, which were assembled from three molecular building blocks, possess incredible stability in various physiological conditions, reversible size-controllability and dynamic disassembly that were exploited for various in vitro and in vivo applications. An advantage of using the supramolecular approach is that it enables the convenient incorporation of functional ligands onto SNP surface that confers functionality ( e.g., targeting, cell penetration) to SNPs. We utilized SNPs for molecular imaging such as magnetic resonance imaging (MRI) and positron emission tomography (PET) by introducing reporter systems (i.e., radio-isotopes, MR contrast agents, and fluorophores) into SNPs. On the other hand, the incorporation of various payloads, including drugs, genes and proteins, into SNPs showed improved delivery performance and enhanced therapeutic efficacy for these therapeutic agents. Leveraging the powers of (i) a combinatorial synthetic approach based on supramolecular assembly and (ii) a digital microreactor, a rapid developmental pathway was developed that is capable of screening SNP candidates for the ideal structural and functional properties that deliver optimal performance. Moreover, SNP-based theranostic delivery systems that combine reporter systems and therapeutic payloads into a

  5. Solution structures of proteins from NMR data and modeling: Alternative folds for neutrophil peptide 5

    International Nuclear Information System (INIS)

    Levy, R.M.; Bassolino, D.A.; Kitchen, D.B.; Pardi, A.

    1989-01-01

    The structure of neutrophil peptide 5 in solution has recently reported. The structure determination was accomplished by using a distance geometry algorithm and 107 interproton distances constrains obtained from 2D NMR data. In each of the eight independent solutions to the distance geometry equations, the overall fold of the polypeptide backbone was identical and the root mean square (rms) deviation between backbone atoms of the superimposed structures was small. In this paper the authors report additional NP-5 structures obtained by using a new structure generation algorithm: a Monte Carlo search in torsion angle space. These structures have a large rms backbone deviation from the distance geometry structures. The backbone topologies differ in significant respects from the distance geometry structures and from each other. Structures are found that are pseudo mirror images of part or all of the fold corresponding to that first obtained with the distance geometry procedure. The results demonstrate that the previously accepted criteria for defining the accuracy and precision of a peptide structure generated from NMR data are inadequate. An energetic analysis of structures corresponding to the different folding topologies has been carried out. The molecular mechanics energies obtained by minimization and molecular dynamics refinement provide sufficient information to eliminate certain alternative structures. On the basis of a careful comparison of the different trial structures with the experimental data, it is concluded that the NP-5 peptide fold which was originally reported is most consistent with the data

  6. Structure-based prediction of MHC-peptide association: algorithm comparison and application to cancer vaccine design.

    Science.gov (United States)

    Schiewe, Alexandra J; Haworth, Ian S

    2007-10-01

    Peptide vaccination for cancer immunotherapy requires identification of peptide epitopes derived from antigenic proteins associated with the tumor. Such peptides can bind to MHC proteins (MHC molecules) on the tumor-cell surface, with the potential to initiate a host immune response against the tumor. Computer prediction of peptide epitopes can be based on known motifs for peptide sequences that bind to a certain MHC molecule, on algorithms using experimental data as a training set, or on structure-based approaches. We have developed an algorithm, which we refer to as PePSSI, for flexible structural prediction of peptide binding to MHC molecules. Here, we have applied this algorithm to identify peptide epitopes (of nine amino acids, the common length) from the sequence of the cancer-testis antigen KU-CT-1, based on the potential of these peptides to bind to the human MHC molecule HLA-A2. We compared the PePSSI predictions with those of other algorithms and found that several peptides predicted to be strong HLA-A2 binders by PePSSI were similarly predicted by another structure-based algorithm, PREDEP. The results show how structure-based prediction can identify potential peptide epitopes without known binding motifs and suggest that side chain orientation in binding peptides may be obtained using PePSSI.

  7. Collagencin, an antibacterial peptide from fish collagen: Activity, structure and interaction dynamics with membrane

    Energy Technology Data Exchange (ETDEWEB)

    Ennaas, Nadia [STELA Dairy Research Centre, Institute of Nutrition and Functional Foods, Université Laval, G1V 0A6 Québec, QC (Canada); Hammami, Riadh, E-mail: riadh.hammami@fsaa.ulaval.ca [STELA Dairy Research Centre, Institute of Nutrition and Functional Foods, Université Laval, G1V 0A6 Québec, QC (Canada); Gomaa, Ahmed [STELA Dairy Research Centre, Institute of Nutrition and Functional Foods, Université Laval, G1V 0A6 Québec, QC (Canada); Bédard, François; Biron, Éric [Faculty of Pharmacy, Université Laval and Laboratory of Medicinal Chemistry, CHU de Québec Research Centre, G1V 4G2 Québec, QC (Canada); Subirade, Muriel [STELA Dairy Research Centre, Institute of Nutrition and Functional Foods, Université Laval, G1V 0A6 Québec, QC (Canada); Beaulieu, Lucie, E-mail: lucie.beaulieu@fsaa.ulaval.ca [STELA Dairy Research Centre, Institute of Nutrition and Functional Foods, Université Laval, G1V 0A6 Québec, QC (Canada); Department of Biology, Chemistry and Geography, Université du Québec à Rimouski (UQAR), 300 Allée des Ursulines, Rimouski, QC G5L 3A1 (Canada); Fliss, Ismail, E-mail: ismail.fliss@fsaa.ulaval.ca [STELA Dairy Research Centre, Institute of Nutrition and Functional Foods, Université Laval, G1V 0A6 Québec, QC (Canada)

    2016-04-29

    In this study, we first report characterization of collagencin, an antimicrobial peptide identified from fish collagen hydrolysate. The peptide completely inhibited the growth of Staphylococcus aureus at 1.88 mM. Although non-toxic up to 470 μM, collagencin was hemolytic at higher concentrations. The secondary structure of collagencin was mainly composed by β-sheet and β-turn as determined by CD measurements and molecular dynamics. The peptide is likely to form β-sheet structure under hydrophobic environments and interacts with both anionic (phosphatidylglycerol) and zwitterionic (phosphoethanolamine and phosphatidylcholine) lipids as shown with CD spectroscopy and molecular dynamics. The peptide formed several hydrogen bonds with both POPG and POPE lipids and remained at membrane–water interface, suggesting that collagencin antibacterial action follows a carpet mechanism. Collagenous fish wastes could be processed by enzymatic hydrolysis and transformed into products of high value having functional or biological properties. Marine collagens are a promising source of antimicrobial peptides with new implications in food safety and human health. - Highlights: • Collagencin, an antibacterial (G+ & G-) peptide identified from fish collagen hydrolysate. • The peptide completely inhibited the growth of S. aureus at 1.88 mM and non-toxic at 470 μM. • The secondary structure was mainly composed by β-sheet and turn as determined by CD and MD. • Collagencin interacts with both anionic and zwitterionic lipids as shown with CD and MD. • Collagencin antibacterial action probably follows a carpet mechanism.

  8. Predicting binding within disordered protein regions to structurally characterised peptide-binding domains.

    Directory of Open Access Journals (Sweden)

    Waqasuddin Khan

    Full Text Available Disordered regions of proteins often bind to structured domains, mediating interactions within and between proteins. However, it is difficult to identify a priori the short disordered regions involved in binding. We set out to determine if docking such peptide regions to peptide binding domains would assist in these predictions.We assembled a redundancy reduced dataset of SLiM (Short Linear Motif containing proteins from the ELM database. We selected 84 sequences which had an associated PDB structures showing the SLiM bound to a protein receptor, where the SLiM was found within a 50 residue region of the protein sequence which was predicted to be disordered. First, we investigated the Vina docking scores of overlapping tripeptides from the 50 residue SLiM containing disordered regions of the protein sequence to the corresponding PDB domain. We found only weak discrimination of docking scores between peptides involved in binding and adjacent non-binding peptides in this context (AUC 0.58.Next, we trained a bidirectional recurrent neural network (BRNN using as input the protein sequence, predicted secondary structure, Vina docking score and predicted disorder score. The results were very promising (AUC 0.72 showing that multiple sources of information can be combined to produce results which are clearly superior to any single source.We conclude that the Vina docking score alone has only modest power to define the location of a peptide within a larger protein region known to contain it. However, combining this information with other knowledge (using machine learning methods clearly improves the identification of peptide binding regions within a protein sequence. This approach combining docking with machine learning is primarily a predictor of binding to peptide-binding sites, and is not intended as a predictor of specificity of binding to particular receptors.

  9. Correlation of charge, hydrophobicity, and structure with antimicrobial activity of S1 and MIRIAM peptides.

    Science.gov (United States)

    Leptihn, Sebastian; Har, Jia Yi; Wohland, Thorsten; Ding, Jeak Ling

    2010-11-02

    Antimicrobial peptides are key elements of the innate immune system. Many of them interact with membranes of bacteria leading to perturbation of the lipid bilayer and eventually to inactivation of the pathogen. The emergence of multidrug-resistant bacteria has necessitated innovations of new and more powerful classes of antimicrobials. Here we present the in-depth study of an antimicrobial peptide, MIRIAM, derived from Sushi1 (S1), a well-characterized peptide from the horseshoe crab. MIRIAM interacts strongly with negatively charged lipids, forming an α-helical structure. MIRIAM was found to neutralize LPS and kill Gram-negative bacteria with high efficiency, while not releasing LPS. The promising therapeutic potential of MIRIAM is shown by hemolytic assays, which demonstrate that eukaryotic membranes are unaffected at bactericidal concentrations. Nanoparticle-conjugated MIRIAM used in single-molecule fluorescence and electron microscopy experiments showed that MIRIAM targets bacterial membranes to kill bacteria similarly to parental S1. Furthermore, fragments derived from MIRIAM and S1 provided insights on their molecular mechanisms of action, in particular, the relationships of functional motifs comprised by charge, hydrophobicity, and structure within each peptide. We conclude that the combination of charge, hydrophobicity, and length of the peptide is important. A close interaction of amino acids in a single molecule in a carefully balanced ensemble of sequence position and secondary structure is crucial.

  10. β-hairpin-mediated formation of structurally distinct multimers of neurotoxic prion peptides.

    Directory of Open Access Journals (Sweden)

    Andrew C Gill

    Full Text Available Protein misfolding disorders are associated with conformational changes in specific proteins, leading to the formation of potentially neurotoxic amyloid fibrils. During pathogenesis of prion disease, the prion protein misfolds into β-sheet rich, protease-resistant isoforms. A key, hydrophobic domain within the prion protein, comprising residues 109-122, recapitulates many properties of the full protein, such as helix-to-sheet structural transition, formation of fibrils and cytotoxicity of the misfolded isoform. Using all-atom, molecular simulations, it is demonstrated that the monomeric 109-122 peptide has a preference for α-helical conformations, but that this peptide can also form β-hairpin structures resulting from turns around specific glycine residues of the peptide. Altering a single amino acid within the 109-122 peptide (A117V, associated with familial prion disease increases the prevalence of β-hairpin formation and these observations are replicated in a longer peptide, comprising residues 106-126. Multi-molecule simulations of aggregation yield different assemblies of peptide molecules composed of conformationally-distinct monomer units. Small molecular assemblies, consistent with oligomers, comprise peptide monomers in a β-hairpin-like conformation and in many simulations appear to exist only transiently. Conversely, larger assemblies are comprised of extended peptides in predominately antiparallel β-sheets and are stable relative to the length of the simulations. These larger assemblies are consistent with amyloid fibrils, show cross-β structure and can form through elongation of monomer units within pre-existing oligomers. In some simulations, assemblies containing both β-hairpin and linear peptides are evident. Thus, in this work oligomers are on pathway to fibril formation and a preference for β-hairpin structure should enhance oligomer formation whilst inhibiting maturation into fibrils. These simulations provide an

  11. β-Hairpin-Mediated Formation of Structurally Distinct Multimers of Neurotoxic Prion Peptides

    Science.gov (United States)

    Gill, Andrew C.

    2014-01-01

    Protein misfolding disorders are associated with conformational changes in specific proteins, leading to the formation of potentially neurotoxic amyloid fibrils. During pathogenesis of prion disease, the prion protein misfolds into β-sheet rich, protease-resistant isoforms. A key, hydrophobic domain within the prion protein, comprising residues 109–122, recapitulates many properties of the full protein, such as helix-to-sheet structural transition, formation of fibrils and cytotoxicity of the misfolded isoform. Using all-atom, molecular simulations, it is demonstrated that the monomeric 109–122 peptide has a preference for α-helical conformations, but that this peptide can also form β-hairpin structures resulting from turns around specific glycine residues of the peptide. Altering a single amino acid within the 109–122 peptide (A117V, associated with familial prion disease) increases the prevalence of β-hairpin formation and these observations are replicated in a longer peptide, comprising residues 106–126. Multi-molecule simulations of aggregation yield different assemblies of peptide molecules composed of conformationally-distinct monomer units. Small molecular assemblies, consistent with oligomers, comprise peptide monomers in a β-hairpin-like conformation and in many simulations appear to exist only transiently. Conversely, larger assemblies are comprised of extended peptides in predominately antiparallel β-sheets and are stable relative to the length of the simulations. These larger assemblies are consistent with amyloid fibrils, show cross-β structure and can form through elongation of monomer units within pre-existing oligomers. In some simulations, assemblies containing both β-hairpin and linear peptides are evident. Thus, in this work oligomers are on pathway to fibril formation and a preference for β-hairpin structure should enhance oligomer formation whilst inhibiting maturation into fibrils. These simulations provide an important new

  12. Structural heterogeneity in familial Alzheimer's disease mutants of amyloid-beta peptides.

    Science.gov (United States)

    Chong, Song-Ho; Yim, Janghyun; Ham, Sihyun

    2013-05-01

    Alzheimer's disease is a neurodegenerative disorder characterized by progressive deposition of amyloid-beta (Aβ) peptides in brain parenchyma and cerebral blood vessels. Several pathogenic familial mutations of Aβ peptides have been identified that exhibit enhanced neurotoxicity and aggregative ability. However, knowledge of the structural characteristics of those Aβ mutants is still limited. Here, we report multiple all-atom molecular dynamics simulations of the wild-type 42-residue Aβ peptide (Aβ42) and its Flemish (A21G), Arctic (E22G), Dutch (E22Q), Italian (E22K), and Iowa (D23N) familial mutants in explicit water. After validating our simulations by comparison with available experimental data, we examined common/different features in the secondary and tertiary structures of the wild-type and five familial mutants of Aβ42. We found that Aβ42 peptides display quite heterogeneous secondary and tertiary structure ensembles. Such structural heterogeneity in the monomeric state would facilitate interconversions between various secondary structures during the formation of a β-sheet-rich amyloid fibril, and may also serve as a structural basis of the amyloid polymorphism.

  13. Potential of acylated peptides to target the influenza A virus

    Directory of Open Access Journals (Sweden)

    Daniel Lauster

    2015-04-01

    Full Text Available For antiviral drug design, especially in the field of influenza virus research, potent multivalent inhibitors raise high expectations for combating epidemics and pandemics. Among a large variety of covalent and non-covalent scaffold systems for a multivalent display of inhibitors, we created a simple supramolecular platform to enhance the antiviral effect of our recently developed antiviral Peptide B (PeBGF, preventing binding of influenza virus to the host cell. By conjugating the peptide with stearic acid to create a higher-order structure with a multivalent display, we could significantly enhance the inhibitory effect against the serotypes of both human pathogenic influenza virus A/Aichi/2/1968 H3N2, and avian pathogenic A/FPV/Rostock/34 H7N1 in the hemagglutination inhibition assay. Further, the inhibitory potential of stearylated PeBGF (C18-PeBGF was investigated by infection inhibition assays, in which we achieved low micromolar inhibition constants against both viral strains. In addition, we compared C18-PeBGF to other published amphiphilic peptide inhibitors, such as the stearylated sugar receptor mimicking peptide (Matsubara et al. 2010, and the “Entry Blocker” (EB (Jones et al. 2006, with respect to their antiviral activity against infection by Influenza A Virus (IAV H3N2. However, while this strategy seems at a first glance promising, the native situation is quite different from our experimental model settings. First, we found a strong potential of those peptides to form large amyloid-like supramolecular assemblies. Second, in vivo, the large excess of cell surface membranes provides an unspecific target for the stearylated peptides. We show that acylated peptides insert into the lipid phase of such membranes. Eventually, our study reveals serious limitations of this type of self-assembling IAV inhibitors.

  14. A Novel MS-Cleavable Azo Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS)

    Science.gov (United States)

    Iacobucci, Claudio; Hage, Christoph; Schäfer, Mathias; Sinz, Andrea

    2017-10-01

    The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers. The ABI-linker possesses an innovative modular scaffold combining the benefits of collisional activation lability with open shell chemistry. This MS-cleavable cross-linker can be efficiently operated via free radical initiated peptide sequencing (FRIPS) in positive ionization mode. Our proof-of-principle study challenges the gas phase behavior of the ABI-linker for the three amino acids, lysine, leucine, and isoleucine, as well as the model peptide thymopentin. The isomeric amino acids leucine and isoleucine could be discriminated by their characteristic side chain fragments. Collisional activation experiments were conducted via positive electrospray ionization (ESI) on two Orbitrap mass spectrometers. The ABI-mediated formation of odd electron product ions in MS/MS and MS3 experiments was evaluated and compared with a previously described azo-based cross-linker. All cross-linked products were amenable to automated analysis by the MeroX software, underlining the future potential of the ABI-linker for structural proteomics studies. [Figure not available: see fulltext.

  15. Structural studies and anticancer activity of a novel class of β-peptides.

    Science.gov (United States)

    Kudryavtsev, Konstantin V; Yu, Chia-Chun; Ivantcova, Polina M; Polshakov, Vladimir I; Churakov, Andrei V; Bräse, Stefan; Zefirov, Nikolay S; Guh, Jih-Hwa

    2015-02-01

    Functionalized oligomeric organic compounds with well-defined β-proline scaffold have been synthesized by a cycloadditive oligomerization approach in racemic and enantiopure forms. The structure of the novel β-peptides was investigated by NMR spectroscopic and X-ray methods determining the conformational shapes of the β-proline oligomers in solution and solid states. The main structural elements subject to conformational switches are β-peptide bonds between 5-arylpyrrolidine-2-carboxylic acid units existing in Z/E configurations. The whole library of short β-peptides and intermediate acrylamides has been tested on antiproliferative activity towards the hormone-refractory prostate cancer cell line PC-3 revealing several oligomeric compounds with low micromolar and submicromolar activities. Bromine-substituted dimeric and trimeric acrylamides induced caspase-dependent apoptosis of PC-3 cells through cell-cycle arrest and mitochondrial damage. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Structural analysis of a functional DIAP1 fragment bound to grim and hid peptides.

    Science.gov (United States)

    Wu, J W; Cocina, A E; Chai, J; Hay, B A; Shi, Y

    2001-07-01

    The inhibitor of apoptosis protein DIAP1 suppresses apoptosis in Drosophila, with the second BIR domain (BIR2) playing an important role. Three proteins, Hid, Grim, and Reaper, promote apoptosis, in part by binding to DIAP1 through their conserved N-terminal sequences. The crystal structures of DIAP1-BIR2 by itself and in complex with the N-terminal peptides from Hid and Grim reveal that these peptides bind a surface groove on DIAP1, with the first four amino acids mimicking the binding of the Smac tetrapeptide to XIAP. The next 3 residues also contribute to binding through hydrophobic interactions. Interestingly, peptide binding induces the formation of an additional alpha helix in DIAP1. Our study reveals the structural conservation and diversity necessary for the binding of IAPs by the Drosophila Hid/Grim/Reaper and the mammalian Smac proteins.

  17. A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement.

    Science.gov (United States)

    García-Iriepa, Cristina; Gueye, Moussa; Léonard, Jérémie; Martínez-López, David; Campos, Pedro J; Frutos, Luis Manuel; Sampedro, Diego; Marazzi, Marco

    2016-03-07

    In spite of considerable interest in the design of molecular switches towards photo-controllable (bio)materials, few studies focused on the major influence of the surrounding environment on the switch photoreactivities. We present a combined experimental and computational study of a retinal-like molecular switch linked to a peptide, elucidating the effects on the photoreactivity and on the α-helix secondary structure. Temperature-dependent, femtosecond UV-vis transient absorption spectroscopy and high-level hybrid quantum mechanics/molecular mechanics methods were applied to describe the photoisomerization process and the subsequent peptide rearrangement. It was found that the conformational heterogeneity of the ground state peptide controls the excited state potential energy surface and the thermally activated population decay. Still, a reversible α-helix to α-hairpin conformational change is predicted, paving the way for a fine photocontrol of different secondary structure elements, hence (bio)molecular functions, using retinal-inspired molecular switches.

  18. Carborane–β-cyclodextrin complexes as a supramolecular connector for bioactive surfaces

    NARCIS (Netherlands)

    Neirynck, Pauline; Neirynck, P.; Schimer, J.; Jonkheijm, Pascal; Milroy, L.G.; Cigler, P.; Brunsveld, Luc

    2015-01-01

    Supramolecular chemistry provides an attractive entry to generate dynamic and well-controlled bioactive surfaces. Novel host–guest systems are urgently needed to provide a broader affinity and applicability portfolio. A synthetic strategy to carborane–peptide bioconjugates was therefore developed to

  19. Structural Requirements and Biological Significance of Interactions between Peptides and the Major Histocompatibility Complex

    Science.gov (United States)

    Grey, H. M.; Buus, S.; Colon, S.; Miles, C.; Sette, A.

    1989-06-01

    Previous studies indicate that T cells recognize a complex between the major histocompatibility complex (MHC) restriction-element and peptide-antigen fragments. Two aspects of this complex formation are considered in this paper: (1) what is the nature of the specificity of the interactions that allows a few MHC molecules to serve as restriction elements for a large universe of antigens; and (2) what is the relative contribution of determinant selection (i.e. antigen-MHC complex formation) and Tcell repertoire in determining the capacity of an individual to respond to an antigen? By analysing single amino acid substitution analogues of a peptide antigen (Ova 325-335) as well as by analysing the structural similarities between unrelated peptides capable of binding to the same MHC molecule, we have been able to document the very permissive nature of the antigen--MHC interaction. Despite this permissiveness of binding, it is possible to define certain structural features of peptides that are associated with the capacity to bind to a particular MHC specificity. With respect to the question of the relative role of determinant selection' and 'holes in the T-cell repertoire' in determining immune responsiveness, we present data that suggest both mechanisms operate in concert with one another. Thus only about 30% of a collection of peptides that in sum represent the sequence of a protein molecule were found to bind to Ia. Although immunogenicity was restricted to those peptides that were capable of binding to Ia (i.e. determinant selection was operative), we found that about 40% of Ia-binding peptides were not immunogenic (i.e. there were also 'holes in the T-cell repertoire').

  20. Accurate Structure Prediction of Peptide-MHC Complexes for Identifying Highly Immunogenic Antigens

    Science.gov (United States)

    Park, Min-Sun; Park, Sung Yong; Miller, Keith R.; Collins, Edward J.; Lee, Ha Youn

    2013-01-01

    Designing an optimal HIV-1 vaccine faces the challenge of identifying antigens that induce a broad immune capacity. One factor to control the breadth of T cell responses is the surface morphology of a peptide-MHC complex. Here, we present an in silico protocol for predicting peptide-MHC structure. A robust signature of a conformational transition was identified during all-atom molecular dynamics, which results in a model with high accuracy. A large test set was used in constructing our protocol and we went another step further using a blind test with a wild-type peptide and two highly immunogenic mutants, which predicted substantial conformational changes in both mutants. The center residues at position five of the analogs were configured to be accessible to solvent, forming a prominent surface, while the residue of the wild-type peptide was to point laterally towards the side of the binding cleft. We then experimentally determined the structures of the blind test set, using high resolution of X-ray crystallography, which verified predicted conformational changes. Our observation strongly supports a positive association of the surface morphology of a peptide-MHC complex to its immunogenicity. Our study offers the prospect of enhancing immunogenicity of vaccines by identifying MHC binding immunogens. PMID:23688437

  1. Active Hydrogenation Catalyst with a Structured, Peptide-Based Outer-Coordination Sphere

    Energy Technology Data Exchange (ETDEWEB)

    Jain, Avijita; Buchko, Garry W.; Reback, Matthew L.; O' Hagan, Molly J.; Ginovska-Pangovska, Bojana; Linehan, John C.; Shaw, Wendy J.

    2012-10-05

    The synthesis, catalytic activity, and structural features of a rhodium-based hydrogenation catalyst containing a phosphine ligand coupled to a 14-residue peptide are reported. Both CD and NMR spectroscopy show that the peptide adopts a helical structure in 1:1:1 TFE/MeCN/H2O that is maintained when the peptide is attached to the ligand and when the ligand is attached to the metal complex. The metal complex hydrogenates aqueous solutions of 3-butenol to 1-butanol at 360 ± 50 turnovers/Rh/h at 294 K. This peptide- based catalyst represents a starting point for developing and characterizing a peptide-based outer-coordination sphere that can be used to introduce enzyme-like features into molecular catalysts. This work was funded by the US DOE Basic Energy Sciences, Chemical Sciences, Geoscience and Biosciences Division (AJ, JCL and WJS), the Office of Science Early Career Research Program through the Office of Basic Energy Sciences (GWB, MLR and WJS). Part of the research was conducted at the W.R. Wiley Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by U.S. Department of Energy’s Office of Biolog-ical and Environmental Research (BER) program located at Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for the U.S. Department of Energy.

  2. PEPTIDE SOLUBILITY, STRUCTURE AND CHARGE POSITION EFFECT ON ADSORPTION BY ALUMINIUM HYDROXIDE

    Directory of Open Access Journals (Sweden)

    Mary Trujillo

    2008-04-01

    Full Text Available Solubility, structure and position of charges in a peptide antigen sequence can be mentioned as being amongst the basic features of adsorption. In order to study their effect on adsorption, seven analogue series were synthesized from a MSP-1 peptide sequence by systematically replacing each one of the positions in the peptide sequence by aspartic acid, glutamic acid, serine, alanine, asparagine, glutamine or lysine. Such modifications in analogue peptide sequences showed a non-regular tendency regarding solubility and adsorption data. Aspartic acid and Glutamic acid analogue series showed great improvements in adsorption, especially in peptides where Lysine in position 6 and Arginine in position 13 were replaced. Solubility of position 5 analogue was greater than the position 6 analogue in Aspartic acid series; however, the position 6 analogue showed best adsorption results whilst the Aspartic acid in position 5 analogue showed no adsorption in the same conditions. Nuclear Magnetic Resonance structural analysis revealed differences in the -helical structureextension between these analogues. The Aspartic acid in position 6, located in the polar side of the helix, may allow this analogueto fit better onto the adsorption regions suggesting that the local electrostatic charge is responsible for this behavior.

  3. Thermodynamics of engineered gold binding peptides: establishing the structure-activity relationships.

    Science.gov (United States)

    Seker, Urartu Ozgur Safak; Wilson, Brandon; Kulp, John L; Evans, John S; Tamerler, Candan; Sarikaya, Mehmet

    2014-07-14

    Adsorption behavior of a gold binding peptide was experimentally studied to achieve kinetics and thermodynamics parameters toward understanding of the binding of an engineered peptide onto a solid metal surface. The gold-binding peptide, GBP1, was originally selected using a cell surface display library and contains 14 amino acid residues. In this work, single- and three-repeats of GBP1 were used to assess the effects of two parameters: molecular architecture versus secondary structure on adsorption on to gold substrate. The adsorption measurements were carried out using surface plasmon resonance (SPR) spectroscopy at temperatures ranging from 10 to 55 °C. At all temperatures, two different regimes of peptide adsorption were observed, which, based on the model, correspond to two sets of thermodynamics values. The values of enthalpy, ΔH(ads), and entropy, ΔS(ads), in these two regimes were determined using the van't Hoff approach and Gibbs-Helmholtz relationship. In general, the values of enthalpy for both peptides are negative indicating GBP1 binding to gold is an exothermic phenomenon and that the binding of three repeat gold binding peptide (3l-GBP1) is almost 5 times tighter than that for the single repeat (l-GBP1). More intriguing result is that the entropy of adsorption for the 3l-GBP1 is negative (-43.4 ± 8.5 cal/(mol K)), while that for the l-GBP1 is positive (10.90 ± 1.3 cal/(mol K)). Among a number of factors that synergistically contribute to the decrease of entropy, long-range ordered self-assembly of the 3l-GBP1 on gold surface is the most effective, probably through both peptide-solid and peptide-peptide intermolecular interactions. Additional adsorption experiments were conducted in the presence of 2,2,2-trifluoroethanol (TFE) to determine how the conformational structures of the biomolecules responded to the environmental perturbation. We found that the peptides differ in their conformational responses to the change in solution conditions; while

  4. Peptide inhibitors of botulinum neurotoxin serotype A: design, inhibition, cocrystal structures, structure-activity relationship and pharmacophore modeling

    Energy Technology Data Exchange (ETDEWEB)

    Kumar G.; Swaminathan S.; Kumaran, D.; Ahmed, S. A.

    2012-05-01

    Clostridium botulinum neurotoxins are classified as Category A bioterrorism agents by the Centers for Disease Control and Prevention (CDC). The seven serotypes (A-G) of the botulinum neurotoxin, the causative agent of the disease botulism, block neurotransmitter release by specifically cleaving one of the three SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins and induce flaccid paralysis. Using a structure-based drug-design approach, a number of peptide inhibitors were designed and their inhibitory activity against botulinum serotype A (BoNT/A) protease was determined. The most potent peptide, RRGF, inhibited BoNT/A protease with an IC{sub 50} of 0.9 {micro}M and a K{sub i} of 358 nM. High-resolution crystal structures of various peptide inhibitors in complex with the BoNT/A protease domain were also determined. Based on the inhibitory activities and the atomic interactions deduced from the cocrystal structures, the structure-activity relationship was analyzed and a pharmacophore model was developed. Unlike the currently available models, this pharmacophore model is based on a number of enzyme-inhibitor peptide cocrystal structures and improved the existing models significantly, incorporating new features.

  5. A chiral Mn (IV) complex and its supramolecular assembly ...

    Indian Academy of Sciences (India)

    Singlecrystal X-ray analysis revealed that compound 1 crystallises in the monoclinic 21 space group with six mononuclear [MnIVL2] units in the asymmetric unit along with three solvent DMF molecules. In the crystal structure, each Mn(IV) complex, acting as the building unit, undergoes supramolecular linking through C-H ...

  6. Supramolecular network formed through OH $\\cdots $ O and - ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 121; Issue 4. Supramolecular network formed through O-H ⋯ O and - stacking interactions: Hydrothermal syntheses and crystal structures of M(H2O)6](optp)2 (M = Mg, Ni, Zn, and optp = 1-oxopyridinium-2-thiopropionate). Murugan Indrani Ramasamy ...

  7. Peptide amphiphile self-assembly

    Science.gov (United States)

    Iscen, Aysenur; Schatz, George C.

    2017-08-01

    Self-assembly is a process whereby molecules organize into structures with hierarchical order and complexity, often leading to functional materials. Biomolecules such as peptides, lipids and DNA are frequently involved in self-assembly, and this leads to materials of interest for a wide variety of applications in biomedicine, photonics, electronics, mechanics, etc. The diversity of structures and functions that can be produced provides motivation for developing theoretical models that can be used for a molecular-level description of these materials. Here we overview recently developed computational methods for modeling the self-assembly of peptide amphiphiles (PA) into supramolecular structures that form cylindrical nanoscale fibers using molecular-dynamics simulations. Both all-atom and coarse-grained force field methods are described, and we emphasize how these calculations contribute insight into fiber structure, including the importance of β-sheet formation. We show that the temperature at which self-assembly takes place affects the conformations of PA chains, resulting in cylindrical nanofibers with higher β-sheet content as temperature increases. We also present a new high-density PA model that shows long network formation of β-sheets along the long axis of the fiber, a result that correlates with some experiments. The β-sheet network is mostly helical in nature which helps to maintain strong interactions between the PAs both radially and longitudinally. Contribution to Focus Issue Self-assemblies of Inorganic and Organic Nanomaterials edited by Marie-Paule Pileni.

  8. Structural properties of a peptide derived from H+-V-ATPase subunit a

    NARCIS (Netherlands)

    Vermeer, L.S.; Reat, V.; Hemminga, M.A.; Milon, A.

    2009-01-01

    The 3D structure of a peptide derived from the putative transmembrane segment 7 (TM7) of subunit a from H+-V-ATPase from Saccharomyces cerevisiae has been determined by solution state NMR in SDS. A stable helix is formed from L736 up to and including Q745, the lumenal half of the putative TM7. The

  9. Contribution to the study of proteins and peptides structure by hydrogen isotopic exchange

    International Nuclear Information System (INIS)

    Nabedryk-Viala, Eliane.

    1978-01-01

    Development of hydrogen exchange measurement methods to study the structure and the molecular interaction of globular protein molecules in aqueous solution (ribonuclease A, cytochrome c, coupling factors of chloroplasts), in peptide hormones in trifluoroethanol solution (angiotensin II, corticotropin) and in proteins of membranes (rhodopsin) [fr

  10. Deamidation of asparagine and glutamine residues in proteins and peptides: structural determinants and analytical methodology

    NARCIS (Netherlands)

    Bischoff, Rainer; Kolbe, H.V.

    1994-01-01

    Non-enzymatic deamidation of asparagine and glutamine residues in proteins and peptides are reviewed by first outlining the well-described reaction mechanism involving cyclic imide intermediates, followed by a discussion of structural features which influence the reaction rate. The second and major

  11. The Structure and Stability of the Monomorphic HLA-G Are Influenced by the Nature of the Bound Peptide

    Energy Technology Data Exchange (ETDEWEB)

    Walpole, Nicholas G.; Kjer-Nielsen, Lars; Kostenko, Lyudmila; McCluskey, James; Brooks, Andrew G.; Rossjohn, Jamie; Clements, Craig S. (Monash); (Melbourne)

    2010-03-26

    The highly polymorphic major histocompatibility complex class Ia (MHC-Ia) molecules present a broad array of peptides to the clonotypically diverse {alpha}{beta} T-cell receptors. In contrast, MHC-Ib molecules exhibit limited polymorphism and bind a more restricted peptide repertoire, in keeping with their major role in innate immunity. Nevertheless, some MHC-Ib molecules do play a role in adaptive immunity. While human leukocyte antigen E (HLA-E), the MHC-Ib molecule, binds a very restricted repertoire of peptides, the peptide binding preferences of HLA-G, the class Ib molecule, are less stringent, although the basis by which HLA-G can bind various peptides is unclear. To investigate how HLA-G can accommodate different peptides, we compared the structure of HLA-G bound to three naturally abundant self-peptides (RIIPRHLQL, KGPPAALTL and KLPQAFYIL) and their thermal stabilities. The conformation of HLA-G{sup KGPPAALTL} was very similar to that of the HLA-G{sup RIIPRHLQL} structure. However, the structure of HLA-G{sup KLPQAFYIL} not only differed in the conformation of the bound peptide but also caused a small shift in the {alpha}2 helix of HLA-G. Furthermore, the relative stability of HLA-G was observed to be dependent on the nature of the bound peptide. These peptide-dependent effects on the substructure of the monomorphic HLA-G are likely to impact on its recognition by receptors of both innate and adaptive immune systems.

  12. Structure of the antimicrobial beta-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation

    DEFF Research Database (Denmark)

    Khandelia, Himanshu; Kaznessis, Yiannis N

    2007-01-01

    -18 to extend perpendicular to the beta-hairpin plane. This bend was driven by a highly persistent hydrogen-bond between the polar peptide side-chain of TYR7 and the unshielded backbone carbonyl oxygen atom of GLY17. The H-bond formation relieves the unfavorable free energy of insertion of polar groups......All atom molecular dynamics simulations of the 18-residue beta-hairpin antimicrobial peptide protegrin-1 (PG-1, RGGRLCYCRRRFCVCVGR-NH(2)) in a fully hydrated dilauroylphosphatidylcholine (DLPC) lipid bilayer have been implemented. The goal of the reported work is to investigate the structure......-550]), and to delineate specific peptide-membrane interactions which are responsible for the peptide's membrane binding properties. A novel, previously unknown, "kick" shaped conformation of the peptide was detected, where a bend at the C-terminal beta-strand of the peptide caused the peptide backbone at residues 16...

  13. Molecular Design, Structures, and Activity of Antimicrobial Peptide-Mimetic Polymers

    Science.gov (United States)

    Takahashi, Haruko; Palermo, Edmund F.; Yasuhara, Kazuma; Caputo, Gregory A.

    2014-01-01

    There is an urgent need for new antibiotics which are effective against drug-resistant bacteria without contributing to resistance development. We have designed and developed antimicrobial copolymers with cationic amphiphilic structures based on the mimicry of naturally occurring antimicrobial peptides. These copolymers exhibit potent antimicrobial activity against a broad spectrum of bacteria including methicillin-resistant Staphylococcus aureus with no adverse hemolytic activity. Notably, these polymers also did not result in any measurable resistance development in E. coli. The peptide-mimetic design principle offers significant flexibility and diversity in the creation of new antimicrobial materials and their potential biomedical applications. PMID:23832766

  14. Structural aspects of phenylglycines, their biosynthesis and occurrence in peptide natural products.

    Science.gov (United States)

    Al Toma, Rashed S; Brieke, Clara; Cryle, Max J; Süssmuth, Roderich D

    2015-08-01

    Phenylglycine-type amino acids occur in a wide variety of peptide natural products, including glycopeptide antibiotics and biologically active linear and cyclic peptides. Sequencing of biosynthesis gene clusters of chloroeremomycin, balhimycin and pristinamycin paved the way for intensive investigations on the biosynthesis of 4-hydroxyphenylglycine (Hpg), 3,5-dihydroxyphenylglycine (Dpg) and phenylglycine (Phg) in recent years. The significance and importance of this type of unusual non-proteinogenic aromatic amino acids also for medicinal chemistry has drawn the attention of many research groups and pharmaceutical companies. Herein structures and properties of phenylglycine containing natural products as well as the biosynthetic origin and incorporation of phenylglycines are discussed.

  15. Two Zn and Hg bromide salts based on 1-ethyl-3-methyl imidazolium ionic liquid: Ionothermal synthesis, structures and supramolecular organization

    Directory of Open Access Journals (Sweden)

    Xiu-Cheng Zhang

    2012-12-01

    Full Text Available Two Zn(II and Hg(II bromide salts, [EMI]2[ZnBr4] (1 and [EMI][HgBr3] (2, have been synthesized under ionothermal conditions using 1-ethyl-3-methyl imidazolium bromide ([EMI]Br as solvents. 1 consists of tetrahedral anion [ZnBr4]2− and 2 consists of 1D double chain locating in the cavities surrounded by [EMI]+ cations. Both compounds exhibit 3D supramolecular architectures organized by the C-H•••Br hydrogen bondings and alkyl-alkyl interactions.DOI: http://dx.doi.org/10.4314/bcse.v26i3.9

  16. Structural and Thermodynamic Properties of Amyloid-β Peptides: Impact of Fragment Size

    Science.gov (United States)

    Kitahara, T.; Wise-Scira, O.; Coskuner, O.

    2010-10-01

    Alzheimer's disease is a progressive neurodegenerative disease whose physiological characteristics include the accumulation of amyloid-containing deposits in the brain and consequent synapse and neuron loss. Unfortunately, most widely used drugs for the treatment can palliate the outer symptoms but cannot cure the disease itself. Hence, developing a new drug that can cure it. Most recently, the ``early aggregation and monomer'' hypothesis has become popular and a few drugs have been developed based on this hypothesis. Detailed understanding of the amyloid-β peptide structure can better help us to determine more effective treatment strategies; indeed, the structure of Amyloid has been studied extensively employing experimental and theoretical tools. Nevertheless, those studies have employed different fragment sizes of Amyloid and characterized its conformational nature in different media. Thus, the structural properties might be different from each other and provide a reason for the existing debates in the literature. Here, we performed all-atom MD simulations and present the structural and thermodynamic properties of Aβ1-16, Aβ1-28, and Aβ1-42 in the gas phase and in aqueous solution. Our studies show that the overall structures, secondary structures, and the calculated thermodynamic properties change with increasing peptide size. In addition, we find that the structural properties of those peptides are different from each other in the gas phase and in aqueous solution.

  17. Three-dimensional structure of the two-peptide bacteriocin plantaricin JK.

    Science.gov (United States)

    Rogne, Per; Haugen, Christofer; Fimland, Gunnar; Nissen-Meyer, Jon; Kristiansen, Per Eugen

    2009-09-01

    The three-dimensional structures of the two peptides, PlnJ and PlnK, that constitutes the two-peptide bacteriocin plantaricin JK have been solved in water/TFE and water/DPC-micellar solutions using nuclear magnetic resonance (NMR) spectroscopy. PlnJ, a 25 residue peptide, has an N-terminal amphiphilic alpha-helix between Trp-3 and Tyr-15. The 32 residues long PlnK forms a central amphiphilic alpha-helix between Gly-9 and Leu-24. Measurements of the effect on anti-microbial activity of single glycine replacements in PlnJ and PlnK show that Gly-13 and Gly-17 in both peptides are very sensitive, giving more than a 100-fold reduction in activity when large residues replace glycine. In variants where other glycine residues, Gly-20 in PlnJ and Gly-7, Gly-9, Gly-24 and Gly-25 in PlnK, were replaced, the activity was reduced less than 10-fold. It is proposed that the detrimental effect on activity when exchanging Gly-13 and Gly-17 in PlnJ and PlnK is a result of reduced ability of the two peptides to interact through the GxxxG-motifs constituting Gly-13 and Gly-17.

  18. Prospects in the use of aptamers for characterizing the structure and stability of bioactive proteins and peptides in food.

    Science.gov (United States)

    Agyei, Dominic; Acquah, Caleb; Tan, Kei Xian; Hii, Hieng Kok; Rajendran, Subin R C K; Udenigwe, Chibuike C; Danquah, Michael K

    2018-01-01

    Food-derived bioactive proteins and peptides have gained acceptance among researchers, food manufacturers and consumers as health-enhancing functional food components that also serve as natural alternatives for disease prevention and/or management. Bioactivity in food proteins and peptides is determined by their conformations and binding characteristics, which in turn depend on their primary and secondary structures. To maintain their bioactivities, the molecular integrity of bioactive peptides must remain intact, and this warrants the study of peptide form and structure, ideally with robust, highly specific and sensitive techniques. Short single-stranded nucleic acids (i.e. aptamers) are known to have high affinity for cognate targets such as proteins and peptides. Aptamers can be produced cost-effectively and chemically derivatized to increase their stability and shelf life. Their improved binding characteristics and minimal modification of the target molecular signature suggests their suitability for real-time detection of conformational changes in both proteins and peptides. This review discusses the developmental progress of systematic evolution of ligands by exponential enrichment (SELEX), an iterative technology for generating cost-effective aptamers with low dissociation constants (K d ) for monitoring the form and structure of bioactive proteins and peptides. The review also presents case studies of this technique in monitoring the structural stability of bioactive peptide formulations to encourage applications in functional foods. The challenges and potential of aptamers in this research field are also discussed. Graphical abstract Advancing bioactive proteins and peptide functionality via aptameric ligands.

  19. The structure and function of the glucagon-like peptide-1 receptor and its ligands.

    Science.gov (United States)

    Donnelly, Dan

    2012-05-01

    Glucagon-like peptide-1(7-36)amide (GLP-1) is a 30-residue peptide hormone released from intestinal L cells following nutrient consumption. It potentiates the glucose-induced secretion of insulin from pancreatic beta cells, increases insulin expression, inhibits beta-cell apoptosis, promotes beta-cell neogenesis, reduces glucagon secretion, delays gastric emptying, promotes satiety and increases peripheral glucose disposal. These multiple effects have generated a great deal of interest in the discovery of long-lasting agonists of the GLP-1 receptor (GLP-1R) in order to treat type 2 diabetes. This review article summarizes the literature regarding the discovery of GLP-1 and its physiological functions. The structure, function and sequence-activity relationships of the hormone and its natural analogue exendin-4 (Ex4) are reviewed in detail. The current knowledge of the structure of GLP-1R, a Family B GPCR, is summarized and discussed, before its known interactions with the principle peptide ligands are described and summarized. Finally, progress in discovering non-peptide ligands of GLP-1R is reviewed. GLP-1 is clearly an important hormone linking nutrient consumption with blood sugar control, and therefore knowledge of its structure, function and mechanism of action is of great importance. © 2011 The Author. British Journal of Pharmacology © 2011 The British Pharmacological Society.

  20. The structure and function of the glucagon-like peptide-1 receptor and its ligands

    Science.gov (United States)

    Donnelly, Dan

    2012-01-01

    Glucagon-like peptide-1(7-36)amide (GLP-1) is a 30-residue peptide hormone released from intestinal L cells following nutrient consumption. It potentiates the glucose-induced secretion of insulin from pancreatic beta cells, increases insulin expression, inhibits beta-cell apoptosis, promotes beta-cell neogenesis, reduces glucagon secretion, delays gastric emptying, promotes satiety and increases peripheral glucose disposal. These multiple effects have generated a great deal of interest in the discovery of long-lasting agonists of the GLP-1 receptor (GLP-1R) in order to treat type 2 diabetes. This review article summarizes the literature regarding the discovery of GLP-1 and its physiological functions. The structure, function and sequence–activity relationships of the hormone and its natural analogue exendin-4 (Ex4) are reviewed in detail. The current knowledge of the structure of GLP-1R, a Family B GPCR, is summarized and discussed, before its known interactions with the principle peptide ligands are described and summarized. Finally, progress in discovering non-peptide ligands of GLP-1R is reviewed. GLP-1 is clearly an important hormone linking nutrient consumption with blood sugar control, and therefore knowledge of its structure, function and mechanism of action is of great importance. LINKED ARTICLES This article is part of a themed section on Secretin Family (Class B) G Protein-Coupled Receptors. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2012.166.issue-1 PMID:21950636

  1. Structural determinants for selective recognition of peptide ligands for endothelin receptor subtypes ETA and ETB.

    Science.gov (United States)

    Lättig, Jens; Oksche, Alexander; Beyermann, Michael; Rosenthal, Walter; Krause, Gerd

    2009-07-01

    The molecular basis for recognition of peptide ligands endothelin-1, -2 and -3 in endothelin receptors is poorly understood. Especially the origin of ligand selectivity for ET(A) or ET(B) is not clearly resolved. We derived sequence-structure-function relationships of peptides and receptors from mutational data and homology modeling. Our major findings are the dissection of peptide ligands into four epitopes and the delineation of four complementary structural portions on receptor side explaining ligand recognition in both endothelin receptor subtypes. In addition, structural determinants for ligand selectivity could be described. As a result, we could improve the selectivity of BQ3020 about 10-fold by a single amino acid substitution, validating our hypothesis for ligand selectivity caused by different entrances to the receptors' transmembrane binding sites. A narrow tunnel shape in ET(A) is restrictive for a selected group of peptide ligands' N-termini, whereas a broad funnel-shaped entrance in ET(B) accepts a variety of different shapes and properties of ligands.

  2. Structure-activity relationship of Trp-containing analogs of the antimicrobial peptide gomesin.

    Science.gov (United States)

    Domingues, Tatiana M; Buri, Marcus V; Daffre, Sirlei; Campana, Patricia T; Riske, Karin A; Miranda, Antonio

    2014-06-01

    Gomesin (Gm) has a broad antimicrobial activity making it of great interest for development of drugs. In this study, we analyzed three Gm analogs, [Trp(1) ]-Gm, [Trp(7) ]-Gm, and [Trp(9) ]-Gm, in an attempt to gain insight into the contributions of different regions of the peptide sequence to its activity. The incorporation of the tryptophan residue in different positions has no effect on the antimicrobial and hemolytic activities of the Gm analogs in relation to Gm. Spectroscopic studies (circular dichroism, fluorescence and absorbance) of Gm and its analogs were performed in the presence of SDS, below and above its critical micelle concentration (CMC) (~8 mM), in order to monitor structural changes induced by the interaction with this anionic surfactant (0-15 mM). Interestingly, we found that the analogs interact more strongly with SDS at low concentrations (0.3-6.0 mM) than close to or above its CMC. This suggests that SDS monomers are able to cover the whole peptide, forming large detergent-peptide aggregates. On the other hand, the peptides interact differently with SDS micelles, inserting partially into the micelle core. Among the peptides, Trp in position 1 becomes more motionally-restricted in the presence of SDS, probably because this residue is located at the N-terminal region, which presents higher conformational freedom to interact stronger with SDS molecules. Trp residues in positions 7 and 9, close to and in the region of the turn of the molecule, respectively, induced a more constrained structure and the compounds cannot insert deeper into the micelle core or be completely buried by SDS monomers. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.

  3. Total synthesis, structure, and oral absorption of a thiazole cyclic peptide, sanguinamide A

    DEFF Research Database (Denmark)

    Nielsen, Daniel S; Hoang, Huy N; Lohman, Rink-Jan

    2012-01-01

    The first total synthesis and three-dimensional solution structure are reported for sanguinamide A, a thiazole-containing cyclic peptide from the sea slug H. sanguineus. Solution phase fragment synthesis, solid phase fragment assembly, and solution macrocyclization were combined to give (1) in 10......% yield. Spectral properties were identical for the natural product, requiring revision of its structure from (2) to (1). Intramolecular transannular hydrogen bonds help to bury polar atoms, which enables oral absorption from the gut....

  4. Solution Structure and Constrained Molecular Dynamics Study of Vitamin B12 Conjugates of the Anorectic Peptide PYY(3-36).

    Science.gov (United States)

    Henry, Kelly E; Kerwood, Deborah J; Allis, Damian G; Workinger, Jayme L; Bonaccorso, Ron L; Holz, George G; Roth, Christian L; Zubieta, Jon; Doyle, Robert P

    2016-05-06

    Vitamin B12 -peptide conjugates have considerable therapeutic potential through improved pharmacokinetic and/or pharmacodynamic properties imparted on the peptide upon covalent attachment to vitamin B12 (B12 ). There remains a lack of structural studies investigating the effects of B12 conjugation on peptide secondary structure. Determining the solution structure of a B12 -peptide conjugate or conjugates and measuring functions of the conjugate(s) at the target peptide receptor may offer considerable insight concerning the future design of fully optimized conjugates. This methodology is especially useful in tandem with constrained molecular dynamics (MD) studies, such that predictions may be made about conjugates not yet synthesized. Focusing on two B12 conjugates of the anorectic peptide PYY(3-36), one of which was previously demonstrated to have improved food intake reduction compared with PYY(3-36), we performed NMR structural analyses and used the information to conduct MD simulations. The study provides rare structural insight into vitamin B12 conjugates and validates the fact that B12 can be conjugated to a peptide without markedly affecting peptide secondary structure. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Structure of the nociceptin/orphanin FQ receptor in complex with a peptide mimetic

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Aaron A.; Liu, Wei; Chun, Eugene; Katritch, Vsevolod; Wu, Huixian; Vardy, Eyal; Huang, Xi-Ping; Trapella, Claudio; Guerrini, Remo; Calo, Girolamo; Roth, Bryan L.; Cherezov, Vadim; Stevens, Raymond C. (Ferrara); (Scripps); (UNC)

    2012-07-11

    Members of the opioid receptor family of G-protein-coupled receptors (GPCRs) are found throughout the peripheral and central nervous system, where they have key roles in nociception and analgesia. Unlike the 'classical' opioid receptors, {delta}, {kappa} and {mu} ({delta}-OR, {kappa}-OR and {mu}-OR), which were delineated by pharmacological criteria in the 1970s and 1980s, the nociceptin/orphanin FQ (N/OFQ) peptide receptor (NOP, also known as ORL-1) was discovered relatively recently by molecular cloning and characterization of an orphan GPCR. Although it shares high sequence similarity with classical opioid GPCR subtypes ({approx}60%), NOP has a markedly distinct pharmacology, featuring activation by the endogenous peptide N/OFQ, and unique selectivity for exogenous ligands. Here we report the crystal structure of human NOP, solved in complex with the peptide mimetic antagonist compound-24 (C-24) (ref. 4), revealing atomic details of ligand-receptor recognition and selectivity. Compound-24 mimics the first four amino-terminal residues of the NOP-selective peptide antagonist UFP-101, a close derivative of N/OFQ, and provides important clues to the binding of these peptides. The X-ray structure also shows substantial conformational differences in the pocket regions between NOP and the classical opioid receptors {kappa} (ref. 5) and {mu} (ref. 6), and these are probably due to a small number of residues that vary between these receptors. The NOP-compound-24 structure explains the divergent selectivity profile of NOP and provides a new structural template for the design of NOP ligands.

  6. Secondary structure of cell-penetrating peptides during interaction with fungal cells.

    Science.gov (United States)

    Gong, Zifan; Ikonomova, Svetlana P; Karlsson, Amy J

    2018-03-01

    Cell-penetrating peptides (CPPs) are peptides that cross cell membranes, either alone or while carrying molecular cargo. Although their interactions with mammalian cells have been widely studied, much less is known about their interactions with fungal cells, particularly at the biophysical level. We analyzed the interactions of seven CPPs (penetratin, Pep-1, MPG, pVEC, TP-10, MAP, and cecropin B) with the fungal pathogen Candida albicans using experiments and molecular simulations. Circular dichroism (CD) of the peptides revealed a structural transition from a random coil or weak helix to an α-helix occurs for all peptides when the solvent is changed from aqueous to hydrophobic. However, CD performed in the presence of C. albicans cells showed that proximity to the cell membrane is not necessarily sufficient to induce this structural transition, as penetratin, Pep-1, and MPG did not display a structural shift in the presence of cells. Monte Carlo simulations were performed to further probe the molecular-level interaction with the cell membrane, and these simulations suggested that pVEC, TP-10, MAP, and cecropin B strongly penetrate into the hydrophobic domain of the membrane lipid bilayer, inducing a transition to an α-helical conformation. In contrast, penetratin, Pep-1 and MPG remained in the hydrophilic region without a shift in conformation. The experimental data and MC simulations combine to explain how peptide structure affects their interaction with cells and their mechanism of translocation into cells (direct translocation vs. endocytosis). Our work also highlights the utility of combining biophysical experiments, biological experiments, and molecular modeling to understand biological phenomena. © 2017 The Protein Society.

  7. Structural Basis For Antigenic Peptide Precursor Processing by the Endoplasmic Reticulum Aminopeptidase ERAP1

    Energy Technology Data Exchange (ETDEWEB)

    T Nguyen; S Chang; I Evnouchidou; I York; C Zikos; K Rock; A Goldberg; E Stratikos; L Stern

    2011-12-31

    ERAP1 trims antigen precursors to fit into MHC class I proteins. To fulfill this function, ERAP1 has unique substrate preferences, trimming long peptides but sparing shorter ones. To identify the structural basis for ERAP1's unusual properties, we determined the X-ray crystal structure of human ERAP1 bound to bestatin. The structure reveals an open conformation with a large interior compartment. An extended groove originating from the enzyme's catalytic center can accommodate long peptides and has features that explain ERAP1's broad specificity for antigenic peptide precursors. Structural and biochemical analyses suggest a mechanism for ERAP1's length-dependent trimming activity, whereby binding of long rather than short substrates induces a conformational change with reorientation of a key catalytic residue toward the active site. ERAP1's unique structural elements suggest how a generic aminopeptidase structure has been adapted for the specialized function of trimming antigenic precursors.

  8. Structure and antimicrobial activity of platypus 'intermediate' defensin-like peptide.

    Science.gov (United States)

    Torres, Allan M; Bansal, Paramjit; Koh, Jennifer M S; Pagès, Guilhem; Wu, Ming J; Kuchel, Philip W

    2014-05-02

    The three-dimensional structure of a chemically synthesized peptide that we have called 'intermediate' defensin-like peptide (Int-DLP), from the platypus genome, was determined by nuclear magnetic resonance (NMR) spectroscopy; and its antimicrobial activity was investigated. The overall structural fold of Int-DLP was similar to that of the DLPs and β-defensins, however the presence of a third antiparallel β-strand makes its structure more similar to the β-defensins than the DLPs. Int-DLP displayed potent antimicrobial activity against Staphylococcus aureus and Pseudomonas aeruginosa. The four arginine residues at the N-terminus of Int-DLP did not affect the overall fold, but were important for its antimicrobial potency. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

  9. Star-shaped tetrathiafulvalene oligomers towards the construction of conducting supramolecular assembly.

    Science.gov (United States)

    Iyoda, Masahiko; Hasegawa, Masashi

    2015-01-01

    The construction of redox-active supramolecular assemblies based on star-shaped and radially expanded tetrathiafulvalene (TTF) oligomers with divergent and extended conjugation is summarized. Star-shaped TTF oligomers easily self-aggregate with a nanophase separation to produce supramolecular structures, and their TTF units stack face-to-face to form columnar structures using the fastener effect. Based on redox-active self-organizing supramolecular structures, conducting nanoobjects are constructed by doping of TTF oligomers with oxidants after the formation of such nanostructures. Although radical cations derived from TTF oligomers strongly interact in solution to produce a mixed-valence dimer and π-dimer, it seems to be difficult to produce nanoobjects of radical cations different from those of neutral TTF oligomers. In some cases, however, radical cations form nanostructured fibers and rods by controlling the supramolecular assembly, oxidation states, and counter anions employed.

  10. Structure-Based Peptide Design to Modulate Amyloid Beta Aggregation and Reduce Cytotoxicity.

    Directory of Open Access Journals (Sweden)

    Jitendra Kumar

    Full Text Available The deposition of Aβ peptide in the brain is the key event in Alzheimer disease progression. Therefore, the prevention of Aβ self assembly into disease-associated oligomers is a logical strategy for treatment. π stacking is known to provide structural stability to many amyloids; two phenylalanine residues within the Aβ 14-23 self recognition element are in such an arrangement in many solved structures. Therefore, we targeted this structural stacking by substituting these two phenylalanine residues with their D-enantiomers. The resulting peptides were able to modulate Aβ aggregation in vitro and reduce Aβ cytotoxicity in primary neuronal cultures. Using kinetic analysis of fibril formation, electron microscopy and dynamic light scattering characterization of oligomer size distributions, we demonstrate that, in addition to altering fibril structural characteristics, these peptides can induce the formation of larger amorphous aggregates which are protective against toxic oligomers, possibly because they are able to sequester the toxic oligomers during co-incubation. Alternatively, they may alter the surface structure of the oligomers such that they can no longer interact with cells to induce toxic pathways.

  11. Single Molecule Force Spectroscopy of self complementary hydrogen-bonded supramolecular systems: dimers, polymers and solvent effects

    NARCIS (Netherlands)

    Embrechts, A.

    2011-01-01

    The work described in this Thesis aimed at a better understanding of the structure-property relationships of supramolecular assemblies with a specific focus on hydrogen-bond dimers and polymers. The hydrogen-bond strength of (supra)molecular complexes in different solvents is usually determined by

  12. Structural Basis for Degenerate Recognition of Natural HIV Peptide Variants by Cytotoxic Lymphocytes

    International Nuclear Information System (INIS)

    Martinez-Hackert, E.; Anikeeva, N.; Kalams, S.; Walker, B.; Hendrickson, W.; Sykulev, Y.

    2006-01-01

    It is well established that even small changes in amino acid side chains of antigenic peptide bound to MHC protein may completely abrogate recognition of the peptide-MHC (pMHC) complex by the T-cell receptor (TCR). Often, however, several non-conservative substitutions in the peptide antigen are accommodated and do not impair its recognition by TCR. For example, a preponderance of natural sequence variants of the HIV p17 Gag-derived peptide SLYNTVATL (SL9) are recognized by cytotoxic T lymphocytes (CTL), which implies that interactions with SL9 variants are degenerate both with respect to the class I MHC molecule and with respect to TCR. Here we study the molecular basis for this degenerate recognition of SL9 variants. We show that several SL9 variants bind comparably well to soluble HLA-A2 and to a particular soluble TCR and that these variants are active in the cognate cytotoxicity assay. Natural SL9 variation is restricted by its context in the HIV p17 matrix protein, and we have used synthetic variants to explore the wider spectrum of recognition. High-resolution crystal structures of seven selected SL9 variants bound to HLA-A2 all have remarkably similar peptide conformations and side-chain dispositions outside sites of substitution. This preservation of the peptide conformation despite epitope variations suggests a mechanism for the observed degeneracy in pMHC recognition by TCR, and may contribute to the persistence of SL9-mediated immune responses in chronically infected individuals

  13. Structure and dynamics of the peptide strand KRFK from the thrombospondin TSP-1 in water.

    Science.gov (United States)

    Taleb Bendiab, W; Benomrane, B; Bounaceur, B; Dauchez, M; Krallafa, A M

    2018-02-14

    Theoretical investigations of a solute in liquid water at normal temperature and pressure can be performed at different levels of theory. Static quantum calculations as well as classical and ab initio molecular dynamics are used to completely explore the conformational space for large solvated molecular systems. In the classical approach, it is essential to describe all of the interactions of the solute and the solvent in detail. Water molecules are very often described as rigid bodies when the most commonly used interaction potentials, such as the SPCE and the TIP4P models, are employed. Recently, a physical model based upon a cluster of rigid water molecules with a tetrahedral architecture (AB 4 ) was proposed that describes liquid water as a mixture of both TIP4P and SPCE molecular species that occur in the proportions implied by the tetrahedral architecture (one central molecule versus four outer molecules; i.e., 20% TIP4P versus 80% SPCE molecules). In this work, theoretical spectroscopic data for a peptide strand were correlated with the structural properties of the peptide strand solvated in water, based on data calculated using different theoretical approaches and physical models. We focused on a particular peptide strand, KRFK (lysine-arginine-phenylalanine-lysine), found in the thrombospondin TSP-1, due to its interesting properties. As the activity and electronic structure of this system is strongly linked to its structure, we correlated its structure with charge-density maps obtained using different semi-empirical charge Q eq equations. The structural and thermodynamic properties obtained from classical simulations were correlated with ab initio molecular dynamics (AIMD) data. Structural changes in the peptide strand were rationalized in terms of the motions of atoms and groups of atoms. To achieve this, conformational changes were investigated using calculated infrared spectra for the peptide in the gas phase and in water solvent. The calculated AIMD

  14. Cloning and Genomic Characterization of a Natural Insecticidal Peptide LaIT1 with Unique DDH Structural Fold.

    Science.gov (United States)

    Chen, Jing; Xu, Yue; San, Mingkui; Cao, Zhijian; Li, Wenxin; Wu, Yingliang; Chen, Zongyun

    2015-05-01

    Two native peptides with disulfide-directed hairpin (DDH) fold, LaIT1 and LITX, were recently isolated from scorpion venom, a development that offered insights into exploring the evolutionary linkage between DDH and inhibitor cystine knot (ICK) peptides. In this work, we isolated and identified the full-length cDNAs of LaTI1, a representative member with DDH fold, and further determined its complete gene structure. The precursor organization of LaIT1 is similar to that of ICK peptides. The LaIT1 gene contains four exons interrupted by three unique introns and differed from ICK peptides, suggesting divergent genomic organizations of DDH peptides and ICK peptides. Phylogenetic analysis further showed that the "simple" DDH peptide originates from the "complex" ICK peptide, rather than the reverse. To the best of our knowledge, this is the first report on the genomic organization of DDH-fold peptides, and it presents new evidence of an evolutionary linkage between ICK and DDH peptides. © 2015 Wiley Periodicals, Inc.

  15. Crystal structures of two peptide-HLA-B*1501 complexes; structural characterization of the HLA-B62 supertype

    DEFF Research Database (Denmark)

    Roder, G; Blicher, Thomas; Justesen, Sune Frederik Lamdahl

    2006-01-01

    -pocket in HLA-B*1501. The residues most important for the specificity of this pocket are Tyr74, Leu81, Leu95, Tyr123 and Trp147. These residues create a hydrophobic interior in the F-pocket and their spatial arrangement makes the pocket capable of containing large, bulky peptide side chains. Ser116 is located...... at the bottom of the F-pocket and makes the bottom of this pocket hydrophilic. Ser116, may act as a hydrogen-bonding partner and as such is a perfect place for binding of a Tyr9 peptide residue. Thus, based on structure information it is now possible to explain the peptide sequence specificity of HLA-B*1501...... and it would be a major undertaking to address each of these specificities individually. Based upon their peptide binding specificity, they are currently subdivided into 12 supertypes. Several of these HLA supertypes have not yet been described at the structural level. To support a comprehensive understanding...

  16. Biological and mechanical properties of novel composites based on supramolecular polycaprolactone and functionalized hydroxyapatite.

    Science.gov (United States)

    Shokrollahi, Parvin; Mirzadeh, Hamid; Scherman, Oren A; Huck, Wilhelm T S

    2010-10-01

    Supramolecular polymers based on quadruple hydrogen-bonding ureido-pyrimidinone (UPy) moieties hold promise as dynamic/stimuli-responsive materials in applications such as tissue engineering. Here, a new class of materials is introduced: supramolecular polymer composites. We show that despite the highly ordered structure and tacticity-dependent nature of hydrogen-bonded supramolecular polymers, the bioactivity of these polymers can be tuned through composite preparation with bioceramics. These novel supramolecular composites combine the superior processability of supramolecular polymers with the excellent bioactivity and mechanical characteristics of bioceramics. In particular, the bioactive composites prepared from supramolecular polycaprolactone and UPy-grafted hydroxyapatite (HApUPy) are described that can be easily formed into microporous biomaterials. The compression moduli increased about 40 and 90% upon composite preparation with HAp and HApUPy, respectively, as an indication to improved mechanical properties. These new materials show excellent potential as microporous composite scaffolds for the adhesion and proliferation of rat mesenchymal stem cells (rMSCs) as a first step toward bone regeneration studies; rMSCs proliferate about 2 and 2.7 times faster on the conventional composite with HAp and the supramolecular composite with (HApUPy) than on the neat PCL1250(UPy)(2). Copyright 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2010.

  17. Supramolecular chemistry-general principles and selected examples from anion recognition and metallosupramolecular chemistry.

    Science.gov (United States)

    Albrecht, Markus

    2007-12-01

    This review gives an introduction into supramolecular chemistry describing in the first part general principles, focusing on terms like noncovalent interaction, molecular recognition, self-assembly, and supramolecular function. In the second part those will be illustrated by simple examples from our laboratories. Supramolecular chemistry is the science that bridges the gap between the world of molecules and nanotechnology. In supramolecular chemistry noncovalent interactions occur between molecular building blocks, which by molecular recognition and self-assembly form (functional) supramolecular entities. It is also termed the "chemistry of the noncovalent bond." Molecular recognition is based on geometrical complementarity based on the "key-and-lock" principle with nonshape-dependent effects, e.g., solvatization, being also highly influential. Self-assembly leads to the formation of well-defined aggregates. Hereby the overall structure of the target ensemble is controlled by the symmetry features of the certain building blocks. Finally, the aggregates can possess special properties or supramolecular functions, which are only found in the ensemble but not in the participating molecules. This review gives an introduction on supramolecular chemistry and illustrates the fundamental principles by recent examples from our group.

  18. Structure, signaling mechanism and regulation of the natriuretic peptide receptor guanylate cyclase.

    Energy Technology Data Exchange (ETDEWEB)

    Misono, K. S.; Philo, J. S.; Arakawa, T.; Ogata, C. M.; Qiu, Y.; Ogawa, H.; Young, H. S. (Biosciences Division); (Univ. of Nevada); (Alliance Protein Labs.)

    2011-06-01

    Atrial natriuretic peptide (ANP) and the homologous B-type natriuretic peptide are cardiac hormones that dilate blood vessels and stimulate natriuresis and diuresis, thereby lowering blood pressure and blood volume. ANP and B-type natriuretic peptide counterbalance the actions of the renin-angiotensin-aldosterone and neurohormonal systems, and play a central role in cardiovascular regulation. These activities are mediated by natriuretic peptide receptor-A (NPRA), a single transmembrane segment, guanylyl cyclase (GC)-linked receptor that occurs as a homodimer. Here, we present an overview of the structure, possible chloride-mediated regulation and signaling mechanism of NPRA and other receptor GCs. Earlier, we determined the crystal structures of the NPRA extracellular domain with and without bound ANP. Their structural comparison has revealed a novel ANP-induced rotation mechanism occurring in the juxtamembrane region that apparently triggers transmembrane signal transduction. More recently, the crystal structures of the dimerized catalytic domain of green algae GC Cyg12 and that of cyanobacterium GC Cya2 have been reported. These structures closely resemble that of the adenylyl cyclase catalytic domain, consisting of a C1 and C2 subdomain heterodimer. Adenylyl cyclase is activated by binding of G{sub s}{alpha} to C2 and the ensuing 7{sup o} rotation of C1 around an axis parallel to the central cleft, thereby inducing the heterodimer to adopt a catalytically active conformation. We speculate that, in NPRA, the ANP-induced rotation of the juxtamembrane domains, transmitted across the transmembrane helices, may induce a similar rotation in each of the dimerized GC catalytic domains, leading to the stimulation of the GC catalytic activity.

  19. Evolution of mechanics in α-helical peptide conjugated linear- and star-block PEG.

    Science.gov (United States)

    O'Neill, S C; Bhuiyan, Z H; Tu, R S

    2017-10-25

    We have designed a peptide conjugated poly-ethylene glycol (PEG) bioconjugate system that allows us to examine the intra- and inter-molecular dynamics of gelation. We measure the kinetics of gelation for end-functionalized linear- and star-architectures, and we correlate the gelation behavior with the molecular structure and self-association. The 23-amino acid peptide sequence is known to form a coiled-coil structure as a function of the solution's electrolyte concentration, and the two topologies of the PEG are peptide end-functionalized to examine formation of supramolecular assemblies. Subsequently, microrheology is used to evaluate the dynamics of self-assembly and the gelation time-scales. This study shows that the dynamics of peptide folding and assembly for linear-PEG conjugated systems yield a percolated network, but the star-PEG conjugated systems yield discrete assemblies and remain viscous. The results suggest that the degree of intra- and inter-molecular folding defines the critical gel behavior of the supramolecular system.

  20. Supramolecular structures of Ni(II) and Pt(II) based on the substituted 2, 2‧: 6‧, 2″-terpyridine: Synthesis, structural characterization, luminescence and thermal properties

    Science.gov (United States)

    Momeni, Badri Z.; Rahimi, Farzaneh; Jebraeil, S. Mohammad; Janczak, Jan

    2017-12-01

    Three new d8 transitions metal complexes containing substituted-2,2‧:6‧,2″-terpyridine ligands of [NiII(pytpy)2]Cl2. H2O (pytpy = 4‧- (4-pyridyl)-2,2‧:6‧,2″-terpyridine) (1), [Pt(tpyOH)Cl]+Cl-. 2H2O (2) (tpyOH = 4‧-hydroxy-2,2‧:6‧,2″-terpyridine) and [Pt(tpySH)Cl]+Cl-.2H2O (3) (tpySH = 4‧-mercapto-2,2‧:6‧,2″-terpyridine) have been prepared. The crystal structure of 1 reveals that the nickel(II) is six-coordinated by six nitrogen atoms of pytpy in a distorted octahedral geometry NiN6, while the platinum complex (2) is four-coordinated by one Cl- and three nitrogen atoms of tpyOH in a distorted square planar geometry PtClN3. The lattice crystal water molecule plays a significant structure directing role in the complexes 1 and 2. Many strong noncovalent interactions are present in the crystal structure of 1 and 2. For example, the supramolecular network of Csbnd H⋯Cl, Osbnd H⋯Cl and Cl⋯Cl interactions connected molecules and ions in the crystalline 1, while there are several Pt⋯Pt, Csbnd H⋯Cl, H2O⋯H2O, Csbnd OH⋯H2O, Cl⋯H2O and π-π interactions in 2. The solution luminescence properties of 2 and 3 have been investigated. The emissions of the platinum complexes 2 and 3 exhibit the high-energy intense π→π* intraligand and low-energy MLCT transitions in solution. The solid-state emissions of complexes 1-3 due to the MLCT and π-π interactions are also observed in the solid state. The thermal stability of all complexes reveals that the loss of terpyridine ligand is observed at higher temperatures due to the strong metal-nitrogen bonds of terpyridine ligands.

  1. Structural specificity of mucosal-cell transport and metabolism of peptide drugs: implication for oral peptide drug delivery

    Science.gov (United States)

    Bai, J. P.; Amidon, G. L.

    1992-01-01

    The brush border membrane of intestinal mucosal cells contains a peptide carrier system with rather broad substrate specificity and various endo- and exopeptidase activities. Small peptide (di-/tripeptide)-type drugs with or without an N-terminal alpha-amino group, including beta-lactam antibiotics and angiotensin-converting enzyme (ACE) inhibitors, are transported by the peptide transporter. Polypeptide drugs are hydrolyzed by brush border membrane proteolytic enzymes to di-/tripeptides and amino acids. Therefore, while the intestinal brush border membrane has a carrier system facilitating the absorption of di-/tripeptide drugs, it is a major barrier limiting oral availability of polypeptide drugs. In this paper, the specificity of peptide transport and metabolism in the intestinal brush border membrane is reviewed.

  2. Supramolecular Assembly of Complementary Cyanine Salt J-Aggregates

    KAUST Repository

    Li, Zhong’an

    2015-09-09

    An understanding of structure–property relationships in cyanine dyes is critical for their design and application. Anionic and cationic cyanines can be organized into complementary cyanine salts, offering potential building blocks to modulate their intra/intermolecular interactions in the solid state. Here, we demonstrate how the structures of these complementary salts can be tuned to achieve highly ordered J-type supramolecular aggregate structures of heptamethine dyes in crystalline solids.

  3. Topological dynamics in supramolecular rotors.

    Science.gov (United States)

    Palma, Carlos-Andres; Björk, Jonas; Rao, Francesco; Kühne, Dirk; Klappenberger, Florian; Barth, Johannes V

    2014-08-13

    Artificial molecular switches, rotors, and machines are set to establish design rules and applications beyond their biological counterparts. Herein we exemplify the role of noncovalent interactions and transient rearrangements in the complex behavior of supramolecular rotors caged in a 2D metal-organic coordination network. Combined scanning tunneling microscopy experiments and molecular dynamics modeling of a supramolecular rotor with respective rotation rates matching with 0.2 kcal mol(-1) (9 meV) precision, identify key steps in collective rotation events and reconfigurations. We notably reveal that stereoisomerization of the chiral trimeric units entails topological isomerization whereas rotation occurs in a topology conserving, two-step asynchronous process. In supramolecular constructs, distinct displacements of subunits occur inducing a markedly lower rotation barrier as compared to synchronous mechanisms of rigid rotors. Moreover, the chemical environment can be instructed to control the system dynamics. Our observations allow for a definition of mechanical cooperativity based on a significant reduction of free energy barriers in supramolecules compared to rigid molecules.

  4. Use of tritium labeled compounds in peptide chemistry. Part 3. Influence of structure of peptide coupling amino acids on the extent of racemization

    International Nuclear Information System (INIS)

    Kolodziejczyk, A.M.; Arendt, A.

    1979-01-01

    A modified radiochromatographic method has been used to determine the degree of racemization in synthesis reactions of 12 peptides varying in amino acid composition and kind of protection. The degree of racemization in these reactions was not only found to depend on the kind of protection of the acylating amino acid and the reaction conditions as, e.g., the kind of method used in the synthesis, but also, and to a high degree, on the structure of amino acids, both acylating and acylated, concerned with the coupling stage in peptide synthesis. (author)

  5. Ideally amphipathic beta-sheeted peptides at interfaces: structure, orientation, affinities for lipids and hemolytic activity of (KL)(m)K peptides.

    Science.gov (United States)

    Castano, S; Desbat, B; Dufourcq, J

    2000-01-15

    Designed to model ideally amphipathic beta-sheets, the minimalist linear (KL)(m)K peptides (m=4-7) were synthesized and proved to form stable films at the air/water interface, they insert into compressed dimyristoylphosphatidylcholine monolayers and interact with egg phosphatidylcholine vesicles. Whatever the interface or the lateral pressure applied to the films, FT-IR and polarization-modulated IRRAS spectroscopy developed in situ on the films indicated that all the peptides totally fold into intermolecular antiparallel beta-sheets. Calculated spectra of the amide region allowed us to define the orientation of the beta-strands compared to the interface. It is concluded that such beta-sheets remain flat-oriented without deep perturbation of zwitterionic phospholipids. Dansyl labelling at the N-terminus indicates that all the peptides are monomeric at a low concentration in aqueous buffer and bind to lipids with similar Dns burying. The affinities for zwitterionic lecithin mono- and bilayers, quantitatively estimated from buffer to lipid partition constants, monotonically increased with peptide length, indicating that hydrophobicity is a limiting parameter for lipid and membrane affinities. Peptides induced permeability increases on zwitterionic liposomes, they are strongly hemolytic towards human erythrocytes and their activity increases concurrently with length. Taking into account the lipid affinity, a hemolytic efficiency can be defined: at the same amount of peptide bound, this efficiency strongly increases with the peptide length. It is proposed that the first determinant step of membrane disturbance is the invasion of the outer membrane leaflet by these ideally amphipathic beta-sheeted structures lying flat at the interface, like large rafts depending on the number of beta-strands.

  6. Is it biologically relevant to measure the structures of small peptides in the gas-phase?

    Science.gov (United States)

    Barran, Perdita E.; Polfer, Nick C.; Campopiano, Dominic J.; Clarke, David J.; Langridge-Smith, Patrick R. R.; Langley, Ross J.; Govan, John R. W.; Maxwell, Alison; Dorin, Julia R.; Millar, Robert P.; Bowers, Michael T.

    2005-02-01

    Recent developments in sample introduction of biologically relevant molecules have heralded a new era for gas-phase methods of structural determination. One of the biggest challenges is to relate gas-phase structures, often measured in the absence of water and counter ions, with in vivo biologically active structures. An advantage of gas-phase based techniques is that a given peptide can be analysed in a variety of different forms, for example, as a function of charge state, or with additional water molecules. Molecular modelling can provide insight into experimental findings and help elucidate the differences between structural forms. Combining experiment and theory provides a thorough interrogation of candidate conformations. Here two important naturally occurring peptide systems have been examined in detail and results are assessed in terms of their biological significance. The first of these is gonadotropin-releasing hormone (GnRH), a decapeptide which is the central regulator of the reproductive system in vertebrates. We have examined several naturally occurring variants of this peptide using Ion Mobility Mass Spectrometry and Electron Capture Dissociation (ECD) in conjunction with Fourier Transform Ion Cyclotron Mass Spectrometry (FT-ICR-MS). Candidate conformations are modelled using the AMBER force field. Single amino acid changes, for example Gly6 --> Ala6, or Ala6 --> D-Ala6, have observable effects on the gas phase structure of GnRH. It has been shown that evolutionary primary sequence variations are key to the biological activity of GnRH, and it is thought that this is due to different binding affinities at target receptors. This work provides strong evidence that this activity is structurally based. The second system examined is the relationship between the quaternary structure and activity of two novel [beta]-defensins. FT-ICR mass spectrometry has been employed to characterize di-sulphide bridging and dissociation based experiments utilised to

  7. Structural insights into Cn-AMP1, a short disulfide-free multifunctional peptide from green coconut water.

    Science.gov (United States)

    Santana, Mábio J; de Oliveira, Aline L; Queiroz Júnior, Luiz H K; Mandal, Santi M; Matos, Carolina O; Dias, Renata de O; Franco, Octavio L; Lião, Luciano M

    2015-02-27

    Multifunctional and promiscuous antimicrobial peptides (AMPs) can be used as an efficient strategy to control pathogens. However, little is known about the structural properties of plant promiscuous AMPs without disulfide bonds. CD and NMR were used to elucidate the structure of the promiscuous peptide Cn-AMP1, a disulfide-free peptide isolated from green coconut water. Data here reported shows that peptide structure is transitory and could be different according to the micro-environment. In this regard, Cn-AMP1 showed a random coil in a water environment and an α-helical structure in the presence of SDS-d25 micelles. Moreover, deuterium exchange experiments showed that Gly4, Arg5 and Met9 residues are less accessible to solvent, suggesting that flexibility and cationic charges seem to be essential for Cn-AMP1 multiple activities. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  8. Solution conformational features and interfacial properties of an intrinsically disordered peptide coupled to alkyl chains: a new class of peptide amphiphiles.

    Science.gov (United States)

    Accardo, Antonella; Leone, Marilisa; Tesauro, Diego; Aufiero, Rosa; Bénarouche, Anaïs; Cavalier, Jean-François; Longhi, Sonia; Carriere, Frederic; Rossi, Filomena

    2013-06-01

    Owing to the large panel of biological functions of peptides and their high specificity and potency, the development of peptide-based therapeutic and diagnostic tools has received increasing interest. Peptide amphiphiles (PAs) are an emerging class of molecules in which a bioactive peptide is covalently conjugated to a hydrophobic moiety. Due to the coexistence in the molecule of a hydrophilic peptide sequence and a hydrophobic group, PAs are able to self-assemble spontaneously into a variety of nanostructures, such as monolayers, bilayers, and vesicles. In this work we have synthesized a disordered peptide, henceforth called R11, and two lipophilic derivatives of R11 bearing two alkyl chains, connected or not to R11 by an ethoxylic-based linker. The structural properties in solution of these new PAs were investigated using CD and NMR. R11 lipophilic derivatives display typical features of PAs, such as the formation of micelles and unilamellar vesicles. In addition, their surface properties were studied using Langmuir monomolecular films and the results obtained support the formation of molecular aggregates upon compression of the PA films. The presence of the alkyl chains induces not only the self-assembly of these new PAs into supramolecular aggregates but also a gain of structure within the disordered peptide.

  9. Correlations between structure, material properties and bioproperties in self-assembled beta-hairpin peptide hydrogels.

    Science.gov (United States)

    Hule, Rohan A; Nagarkar, Radhika P; Altunbas, Aysegul; Ramay, Hassna R; Branco, Monica C; Schneider, Joel P; Pochan, Darrin J

    2008-01-01

    A de novo designed beta-hairpin peptide (MAX8), capable of undergoing intramolecular folding and consequent intermolecular self-assembly into a cytocompatible hydrogel, has been studied. A combination of small angle neutron scattering (SANS) and cryogenic-transmission electron microscopy (cryo-TEM) have been used to quantitatively investigate the MAX8 nanofibrillar hydrogel network morphology. A change in the peptide concentration from 0.5 to 2 wt% resulted in a denser fibrillar network as revealed via SANS by a change in the high q (q = (4 pi/lambda) x sin (theta/2), where lambda = wavelength of incident neutrons and theta = scattering angle) mass fractal exponent from 2.5 to 3 and by a decrease in the measured correlation length from 23 to 16 A. A slope of -4 in the USANS regime indicates well-defined gel microporosity, an important characteristic for cellular substrate applications. These changes, both at the network as well as the individual fibril lengthscales, can be directly visualized in situ by cryo-TEM. Fibrillar nanostructures and network properties are directly related to bulk hydrogel stiffness via oscillatory rheology. Preliminary cell viability and anchorage studies at varying hydrogel stiffness confirm cell adhesion at early stages of cell culture within the window of stiffness investigated. Knowledge of the precise structure spanning length scales from the nanoscale up to the microscale can help in the formation of future, specific structure-bioproperty relationships when studying in vitro and in vivo behavior of these new peptide scaffolds.

  10. Structure of the human MHC-I peptide-loading complex.

    Science.gov (United States)

    Blees, Andreas; Januliene, Dovile; Hofmann, Tommy; Koller, Nicole; Schmidt, Carla; Trowitzsch, Simon; Moeller, Arne; Tampé, Robert

    2017-11-23

    The peptide-loading complex (PLC) is a transient, multisubunit membrane complex in the endoplasmic reticulum that is essential for establishing a hierarchical immune response. The PLC coordinates peptide translocation into the endoplasmic reticulum with loading and editing of major histocompatibility complex class I (MHC-I) molecules. After final proofreading in the PLC, stable peptide-MHC-I complexes are released to the cell surface to evoke a T-cell response against infected or malignant cells. Sampling of different MHC-I allomorphs requires the precise coordination of seven different subunits in a single macromolecular assembly, including the transporter associated with antigen processing (TAP1 and TAP2, jointly referred to as TAP), the oxidoreductase ERp57, the MHC-I heterodimer, and the chaperones tapasin and calreticulin. The molecular organization of and mechanistic events that take place in the PLC are unknown owing to the heterogeneous composition and intrinsically dynamic nature of the complex. Here, we isolate human PLC from Burkitt's lymphoma cells using an engineered viral inhibitor as bait and determine the structure of native PLC by electron cryo-microscopy. Two endoplasmic reticulum-resident editing modules composed of tapasin, calreticulin, ERp57, and MHC-I are centred around TAP in a pseudo-symmetric orientation. A multivalent chaperone network within and across the editing modules establishes the proofreading function at two lateral binding platforms for MHC-I molecules. The lectin-like domain of calreticulin senses the MHC-I glycan, whereas the P domain reaches over the MHC-I peptide-binding pocket towards ERp57. This arrangement allows tapasin to facilitate peptide editing by clamping MHC-I. The translocation pathway of TAP opens out into a large endoplasmic reticulum lumenal cavity, confined by the membrane entry points of tapasin and MHC-I. Two lateral windows channel the antigenic peptides to MHC-I. Structures of PLC captured at distinct

  11. Structure-based optimization of non-peptidic Cathepsin D inhibitors.

    Science.gov (United States)

    Grädler, Ulrich; Czodrowski, Paul; Tsaklakidis, Christos; Klein, Markus; Werkmann, Daniela; Lindemann, Sven; Maskos, Klaus; Leuthner, Birgitta

    2014-09-01

    We discovered a novel series of non-peptidic acylguanidine inhibitors of Cathepsin D as target for osteoarthritis. The initial HTS-hits were optimized by structure-based design using CatD X-ray structures resulting in single digit nanomolar potency in the biochemical CatD assay. However, the most potent analogues showed only micromolar activities in an ex vivo glycosaminoglycan (GAG) release assay in bovine cartilage together with low cellular permeability and suboptimal microsomal stability. This new scaffold can serve as a starting point for further optimization towards in vivo efficacy. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Impact of the antimicrobial peptide Novicidin on membrane structure and integrity

    DEFF Research Database (Denmark)

    Nielsen, Søren B; Otzen, Daniel Erik

    2010-01-01

    We have studied the impact of an 18-residue cationic antimicrobial peptide Novicidin (Nc) on the structure and integrity of partially anionic lipid membranes using oriented circular dichroism (OCD), quartz crystal microbalance with dissipation (QCM-D), dual polarization interferometry (DPI......), calcein dye leakage and fluorescence spectroscopy. OCD consistently showed that Nc is bound in an alpha-helical, surface bound state over a range of peptide to lipid (P/L) ratios up to approximately 1:15. Realignment of Nc at higher P/L ratios correlates to loss of membrane integrity as shown by Laurdan...... concentration, probably through formation of transient pores or transient disruption of the membrane integrity, followed by more extensive membrane disintegration at higher P/L ratios....

  13. Synthesis, structure, and properties of supramolecular charge-transfer complexes between bis(18-crown-6)stilbene and ammonioalkyl derivatives of 4,4'-bipyridine and 2,7-diazapyrene.

    Science.gov (United States)

    Vedernikov, Artem I; Ushakov, Evgeny N; Efremova, Asya A; Kuz'mina, Lyudmila G; Moiseeva, Anna A; Lobova, Natalia A; Churakov, Andrei V; Strelenko, Yuri A; Alfimov, Michael V; Howard, Judith A K; Gromov, Sergey P

    2011-08-19

    4,4'-Bipyridine and 2,7-diazapyrene derivatives (A) having two ammonioalkyl N-substituents were synthesized. The complex formation of these compounds with bis(18-crown-6)stilbene (D) was studied by spectrophotometry, cyclic voltammetry, (1)H NMR spectroscopy, and X-ray diffraction analysis. In MeCN, π-donor D and π-acceptors A form supramolecular 1:1 (D·A) and 2:1 (D·A·D) charge-transfer complexes. The D·A complexes have a pseudocyclic structure as a result of ditopic binding of the ammonium groups to the crown-ether fragments. The better the geometric matching between the components, the higher the stability of the D·A complexes (log K up to 9.39). A key driving force of the D·A·D complex formation is the excessive steric strain in the precursor D·A complexes. The pseudocyclic D·A complexes involving the ammoniopropyl derivative of 4,4'-bipyridine were obtained as single crystals. Crystallization of the related ammonioethyl derivative was accompanied by transition of the D·A complexes to a structure of the (D·A)(m) coordination polymer type.

  14. DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides.

    Science.gov (United States)

    Pirtskhalava, Malak; Gabrielian, Andrei; Cruz, Phillip; Griggs, Hannah L; Squires, R Burke; Hurt, Darrell E; Grigolava, Maia; Chubinidze, Mindia; Gogoladze, George; Vishnepolsky, Boris; Alekseyev, Vsevolod; Rosenthal, Alex; Tartakovsky, Michael

    2016-01-04

    Antimicrobial peptides (AMPs) are anti-infectives that may represent a novel and untapped class of biotherapeutics. Increasing interest in AMPs means that new peptides (natural and synthetic) are discovered faster than ever before. We describe herein a new version of the Database of Antimicrobial Activity and Structure of Peptides (DBAASPv.2, which is freely accessible at http://dbaasp.org). This iteration of the database reports chemical structures and empirically-determined activities (MICs, IC50, etc.) against more than 4200 specific target microbes for more than 2000 ribosomal, 80 non-ribosomal and 5700 synthetic peptides. Of these, the vast majority are monomeric, but nearly 200 of these peptides are found as homo- or heterodimers. More than 6100 of the peptides are linear, but about 515 are cyclic and more than 1300 have other intra-chain covalent bonds. More than half of the entries in the database were added after the resource was initially described, which reflects the recent sharp uptick of interest in AMPs. New features of DBAASPv.2 include: (i) user-friendly utilities and reporting functions, (ii) a 'Ranking Search' function to query the database by target species and return a ranked list of peptides with activity against that target and (iii) structural descriptions of the peptides derived from empirical data or calculated by molecular dynamics (MD) simulations. The three-dimensional structural data are critical components for understanding structure-activity relationships and for design of new antimicrobial drugs. We created more than 300 high-throughput MD simulations specifically for inclusion in DBAASP. The resulting structures are described in the database by novel trajectory analysis plots and movies. Another 200+ DBAASP entries have links to the Protein DataBank. All of the structures are easily visualized directly in the web browser. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Structural and functional characterization of hBD-1(Ser35), a peptide deduced from a DEFB1 polymorphism.

    Science.gov (United States)

    Circo, Raffaella; Skerlavaj, Barbara; Gennaro, Renato; Amoroso, Antonio; Zanetti, Margherita

    2002-04-26

    beta-Defensins are mammalian antimicrobial peptides that share a unique disulfide-bonding motif of six conserved cysteines. An intragenic polymorphism of the DEFB1 gene that changes a highly conserved Cys to Ser in the peptide coding region has recently been described. The deduced peptide cannot form three disulfide bonds, as one of the cysteines is unpaired. We have determined the cysteine connectivities of a corresponding synthetic hBD-1(Ser35) peptide, investigated the structure by circular dichroism spectroscopy, and assayed the in vitro antimicrobial activity. Despite a different arrangement of the disulfides, hBD-1(Ser35) proved as active as hBD-1 against the microorganisms tested. This activity likely depends on the ability of hBD-1(Ser35) to adopt an amphipathic conformation in hydrophobic environment, similar to the wild type peptide, as suggested by CD spectroscopy.

  16. Multivalency in supramolecular chemistry and nanofabrication

    NARCIS (Netherlands)

    Mulder, A.; Huskens, Jurriaan; Reinhoudt, David

    2004-01-01

    Multivalency is a powerful and versatile self-assembly pathway that confers unique thermodynamic and kinetic behavior onto supramolecular complexes. The diversity of the examples of supramolecular multivalent systems discussed in this perspective shows that the concept of multivalency is a general

  17. Regenerative electronic biosensors using supramolecular approaches

    NARCIS (Netherlands)

    Duan, X.; Rajan, N.; Routenberg, D.; Huskens, Jurriaan; Reed, M.

    2013-01-01

    A supramolecular interface for Si nanowire FETs has been developed with the aim of creating regenerative electronic biosensors. The key to the approach is Si-NWs functionalized with β-cyclodextrin (β-CD), to which receptor moieties can be attached with an orthogonal supramolecular linker. Here we

  18. 3D Printing of Biocompatible Supramolecular Polymers and their Composites.

    Science.gov (United States)

    Hart, Lewis R; Li, Siwei; Sturgess, Craig; Wildman, Ricky; Jones, Julian R; Hayes, Wayne

    2016-02-10

    A series of polymers capable of self-assembling into infinite networks via supramolecular interactions have been designed, synthesized, and characterized for use in 3D printing applications. The biocompatible polymers and their composites with silica nanoparticles were successfully utilized to deposit both simple cubic structures, as well as a more complex twisted pyramidal feature. The polymers were found to be not toxic to a chondrogenic cell line, according to ISO 10993-5 and 10993-12 standard tests and the cells attached to the supramolecular polymers as demonstrated by confocal microscopy. Silica nanoparticles were then dispersed within the polymer matrix, yielding a composite material which was optimized for inkjet printing. The hybrid material showed promise in preliminary tests to facilitate the 3D deposition of a more complex structure.

  19. Collagen-binding VEGF mimetic peptide: Structure, matrix interaction, and endothelial cell activation

    Science.gov (United States)

    Chan, Tania R.

    Long term survival of artificial tissue constructs depends greatly on proper vascularization. In nature, differentiation of endothelial cells and formation of vasculature are directed by dynamic spatio-temporal cues in the extracellular matrix that are difficult to reproduce in vitro. In this dissertation, we present a novel bifunctional peptide that mimics matrix-bound vascular endothelial growth factor (VEGF), which can be used to encode spatially controlled angiogenic signals in collagen-based scaffolds. The peptide, QKCMP, contains a collagen mimetic domain (CMP) that binds to type I collagen by a unique triple helix hybridization mechanism and a VEGF mimetic domain (QK) with pro-angiogenic activity. We demonstrate QKCMP's ability to hybridize with native and heat denatured collagens through a series of binding studies on collagen and gelatin substrates. Circular dichroism experiments show that the peptide retains the triple helical structure vital for collagen binding, and surface plasmon resonance study confirms the molecular interaction between the peptide and collagen strands. Cell culture studies demonstrate QKCMP's ability to induce endothelial cell morphogenesis and network formation as a matrix-bound factor in 2D and 3D collagen scaffolds. We also show that the peptide can be used to spatially modify collagen-based substrates to promote localized endothelial cell activation and network formation. To probe the biological events that govern these angiogenic cellular responses, we investigated the cell signaling pathways activated by collagen-bound QKCMP and determined short and long-term endothelial cell response profiles for p38, ERK1/2, and Akt signal transduction cascades. Finally, we present our efforts to translate the peptide's in vitro bioactivity to an in vivo burn injury animal model. When implanted at the wound site, QKCMP functionalized biodegradable hydrogels induce enhanced neovascularization in the granulation tissue. The results show QKCMP

  20. Analysis of HLA-A24-restricted peptides of carcinoembryonic antigen using a novel structure-based peptide-HLA docking algorithm.

    Science.gov (United States)

    Nakamura, Yoji; Tai, Sachiko; Oshita, Chie; Iizuka, Akira; Ashizawa, Tadashi; Saito, Shuji; Yamaguchi, Shigeki; Kondo, Haruhiko; Yamaguchi, Ken; Akiyama, Yasuto

    2011-04-01

    Carcinoembryonic antigen (CEA) is a very common tumor marker because many types of solid cancer usually produce a variety of CEA and a highly sensitive measuring kit has been developed. However, immunological responses associated with CEA have not been fully characterized, and specifically a weak immunogenicity of CEA protein as a tumor antigen is reported in human leukocyte antigen (HLA)-A24-restricted CEA peptide-based cancer immunotherapy. These observations demonstrated that immunogenic and potent HLA-A24-restricted CTL epitope peptides derived from CEA protein are seemingly difficult to predict using a conventional bioinformatics approach based on primary amino acid sequence. In the present study, we developed an in silico docking simulation assay system of binding affinity between HLA-A24 protein and A24-restricted peptides using two software packages, AutoDock and MODELLER, and a crystal structure of HLA-A24 protein obtained from the Protein Data Bank. We compared the current assay system with HLA-peptide binding predictions of the bioinformatics and molecular analysis section (BIMAS) in terms of the prediction capability using MHC stabilization and peptide-stimulated CTL induction assays for CEA and other HLA-A24 peptides. The MHC stabilization score was inversely correlated with the affinity calculated in the docking simulation alone (r = -0.589, P = 0.015), not with BIMAS score or the IFN-γ production index. On the other hand, BIMAS was not significantly correlated with any other parameters. These results suggested that our in silico assay system has potential advantages in efficiency of epitope prediction over BIMAS and ease of use for bioinformaticians. © 2011 Japanese Cancer Association.

  1. Recent Advances in Supramolecular Gels and Catalysis.

    Science.gov (United States)

    Fang, Weiwei; Zhang, Yang; Wu, Jiajie; Liu, Cong; Zhu, Haibo; Tu, Tao

    2018-04-04

    Over the past two decades, supramolecular gels have attracted significant attention from scientists in diverse research fields and have been extensively developed. This review mainly focuses on the significant achievements in supramolecular gels and catalysis. First, by incorporating diverse catalytic sites and active organic functional groups into gelator molecules, supramolecular gels have been considered as a novel matrix for catalysis. In addition, these rationally designed supramolecular gels also provide a variety of templates to access metal nanocomposites, which may function as catalysts and exhibit high activity in diverse catalytic transformations. Finally, as a new kind of biomaterial, supramolecular gels formed in situ by self-assembly triggered by catalytic transformations are also covered herein. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Structure-based design of peptides against HER2 with cytotoxicity on colon cancer.

    Science.gov (United States)

    Cha, Nier; Han, Xiuhua; Jia, Baoqing; Liu, Yanheng; Wang, Xiaoli; Gao, Yanwei; Ren, Jun

    2017-05-01

    In this study, we found that four novel peptides designed by molecular modeling techniques were successfully applicated with cytotoxicity on colon cancer cells sw620. First, the interactions between the Herstatin and the HER2 were explored by ational-designed approaches, which were combined with homology modeling, protein/protein docking, and structural superimposition analysis. Then, based on the results derived from theoretical analysis, four novel peptides were designed, synthesized, and experimentally evaluated for biological function; it was found that they showed a remarkable enhancement on Herceptin to inhibit the genesis and development of colon cancers, and no significant side effects on normal colon cells NCM460 were observed but Doxorubicin had. These results indicated that it is a feasible way to use the well-designed peptides derived from Herstatin to enhance the efficacy of clinical drugs Herceptin and to kill colon cancer cells selectively without harming normal colon cells. We believe that our research might provide a new way to develop the potential therapies for colon cancers.

  3. Structure-property relationships in self-assembling peptide hydrogels, homopolypeptides and polysaccharides

    Science.gov (United States)

    Hule, Rohan A.

    The main objective of this dissertation is to investigate quantitative structure-property relationships in a variety of molecular systems including de novo designed peptides, peptide amphiphiles, polysaccharides and high molecular weight polypeptides. Peptide molecules consisting of 20 amino acids were designed to undergo thermally triggered intramolecular folding into asymmetric beta-hairpins and intermolecular self-assembly via a strand swapping mechanism into physically crosslinked fibrillar hydrogels. The self-assembly mechanism was confirmed by multiple characterization techniques such as circular dichroism and FITR spectroscopy, atomic force and transmission electron microscopy and small angle neutron scattering. Three distinct fibrillar nanostructures, i.e. non-twisted, twisted and laminated were produced, depending on the degree of strand asymmetry and peptide registry. Differences in the fibrillar morphology have a direct consequence on the mechanical properties of the hydrogels, with the laminated hydrogels exhibiting a significantly higher elastic modulus as compared to the twisted or non-twisted fibrillar hydrogels. SANS and cryo-TEM data reveal that the self-assembled fibrils form networks that are fractal in nature. Models employed to elucidate the fractal behavior can relate changes in the correlation lengths, low q (network), and high q (fibrillar) fractal exponents to the distinct fibrillar nanomorphology. The fractal dimension of the networks varies significantly, from a mass to a surface fractal and can be directly related to the local fibrillar morphology and changes in the peptide concentration. Transitions in the fractal behavior seen in the high q regime can be attributed to self-assembly kinetics. An identical model can be used to establish a direct correlation between the bulk properties and changes in both, the network density and underlying morphology, of a modified peptide-based hydrogel. As in the case of asymmetric peptides, changes in

  4. Systematic Moiety Variations of Ultrashort Peptides Produce Profound Effects on Self-Assembly, Nanostructure Formation, Hydrogelation, and Phase Transition

    KAUST Repository

    Chan, Kiat Hwa

    2017-10-04

    Self-assembly of small biomolecules is a prevalent phenomenon that is increasingly being recognised to hold the key to building complex structures from simple monomeric units. Small peptides, in particular ultrashort peptides containing up to seven amino acids, for which our laboratory has found many biomedical applications, exhibit immense potential in this regard. For next-generation applications, more intricate control is required over the self-assembly processes. We seek to find out how subtle moiety variation of peptides can affect self-assembly and nanostructure formation. To this end, we have selected a library of 54 tripeptides, derived from systematic moiety variations from seven tripeptides. Our study reveals that subtle structural changes in the tripeptides can exert profound effects on self-assembly, nanostructure formation, hydrogelation, and even phase transition of peptide nanostructures. By comparing the X-ray crystal structures of two tripeptides, acetylated leucine-leucine-glutamic acid (Ac-LLE) and acetylated tyrosine-leucine-aspartic acid (Ac-YLD), we obtained valuable insights into the structural factors that can influence the formation of supramolecular peptide structures. We believe that our results have major implications on the understanding of the factors that affect peptide self-assembly. In addition, our findings can potentially assist current computational efforts to predict and design self-assembling peptide systems for diverse biomedical applications.

  5. Functional and structural characterization of recombinant dermcidin-1L, a human antimicrobial peptide

    International Nuclear Information System (INIS)

    Lai Yuping; Peng Yifei; Zuo Yi; Li Jun; Huang Jing; Wang Linfa; Wu Zirong

    2005-01-01

    Antimicrobial peptides from human skin are an important component of the innate immune response and play a key role as a first line of defense against infections. One such peptide is the recently discovered dermcidin-1L. To better understand its mechanism and to further investigate its antimicrobial spectrum, recombinant dermcidin-1L was expressed in Escherichia coli as a fusion protein and purified by affinity chromatography. The fusion protein was cleaved by factor Xa protease to produce recombinant dermcidin-1L. Antimicrobial and hemolytic assays demonstrated that dermcidin-1L displayed microbicidal activity against several opportunistic nosocomial pathogens, but no hemolytic activity against human erythrocytes even at concentrations up to 100 μM. Structural studies performed by circular dichroism spectroscopy indicated that the secondary structure of dermcidin-1L was very flexible, and both α-helix and β-sheet structures might be required for the antimicrobial activity. Our results confirmed previous findings indicating that dermcidin-1L could have promising therapeutic potentials and shed new light on the structure-function relationship of dermcidin-1L

  6. Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide

    Science.gov (United States)

    Singh, Krishna P.; Baweja, Lokesh; Wolkenhauer, Olaf; Rahman, Qamar; Gupta, Shailendra K.

    2018-03-01

    Graphene-based nanomaterials (GBNMs) are widely used in various industrial and biomedical applications. GBNMs of different compositions, size and shapes are being introduced without thorough toxicity evaluation due to the unavailability of regulatory guidelines. Computational toxicity prediction methods are used by regulatory bodies to quickly assess health hazards caused by newer materials. Due to increasing demand of GBNMs in various size and functional groups in industrial and consumer based applications, rapid and reliable computational toxicity assessment methods are urgently needed. In the present work, we investigate the impact of graphene and graphene oxide nanomaterials on the structural conformations of small hepcidin peptide and compare the materials for their structural and conformational changes. Our molecular dynamics simulation studies revealed conformational changes in hepcidin due to its interaction with GBMNs, which results in a loss of its functional properties. Our results indicate that hepcidin peptide undergo severe structural deformations when superimposed on the graphene sheet in comparison to graphene oxide sheet. These observations suggest that graphene is more toxic than a graphene oxide nanosheet of similar area. Overall, this study indicates that computational methods based on structural deformation, using molecular dynamics (MD) simulations, can be used for the early evaluation of toxicity potential of novel nanomaterials.

  7. Molecular and crystal structure of nido-9-C5H5N-11-I-7,8-C2B9H10: supramolecular architecture via hydrogen bonding X-H...I (X = B, C)

    International Nuclear Information System (INIS)

    Polyanskaya, T.M.

    2006-01-01

    A monocrystal X-ray diffraction study of a new iodine-containing cluster compound 9-(pyridine)-11-iodo-decahydro-7,8-dicarba-nido-undecaborane [9-C 5 H 5 N-11-I-7,8-C 2 B 9 H 10 ] has been performed. Crystal data: C 7 H 15 B 9 NI, M = 337.39, monoclinic, space group P2 1 /c, unit cell parameters: a=9.348(1) A, b=11.159(1) A, c=13.442(2) A, β=98.13(1) deg, V=1388.1(5) A 3 , Z=4, d calc = 1.614 g/cm 3 , T = 295 K, F(000)=648, μ=2.276 mm -1 . The structure was solved by a direct method and refined in the full-matrix anisotropic approximation (isotropic for hydrogen atoms) to final agreement factors R 1 = 0.0254, wR 2 = 0.0454 for 2437 I hkl >2σ I from 3590 measured I hkl (an Enraf-Nonius CAD-4 diffractometer, λMoK α , graphite monochromator, θ/2θ-scanning). The molecules are joined into a supramolecular assembly by hydrogen bonds X-H...I (X = B, C) [ru

  8. pH-Directed assembly of four polyoxometalate-based supramolecular hybrids by using tritopic bridging ligand 1, 3, 5-tris-(1-imidazolyl)-benzene: Structures and electrocatalytic properties

    Science.gov (United States)

    Zhang, Zhuanfang; Pang, Haijun; Ma, Huiyuan; Li, Shaobin; Zhao, Chunyan

    2018-01-01

    Four new inorganic-organic supramolecular compounds, namely, (H2tib)2[GeW12O40] (1), [Mn(Htib)4][HGeW12O40]2·4H2O (2), [Mn(tib)]2(H2O)6[GeW12O40]·4H2O (3) and [Mn(tib)]2(H2O)6[GeW12O40]·2H2O (4) (tib = 1, 3, 5-tris-(1-imidazolyl)-benzene), have been synthesized through the hydrothermal reaction of [GeW12O40]4- anions, MnII cations and tib ligands under different pH conditions. Compounds 1 and 2 were prepared at lower pH (pH ≈ 2.0 for 1 and 3.2 for 2). Compound 1 exhibits a simple monomer structure. In 2, the Mn cation is coordinated with four tib ligands and two [GeW12 O40]4- anions to form a dimer, in which each of [GeW12 O40]4- anion connects with one Mn cation. Compounds 3 and 4 were pr

  9. Structural Basis for Receptor Activity-Modifying Protein-Dependent Selective Peptide Recognition by a G Protein-Coupled Receptor.

    Science.gov (United States)

    Booe, Jason M; Walker, Christopher S; Barwell, James; Kuteyi, Gabriel; Simms, John; Jamaluddin, Muhammad A; Warner, Margaret L; Bill, Roslyn M; Harris, Paul W; Brimble, Margaret A; Poyner, David R; Hay, Debbie L; Pioszak, Augen A

    2015-06-18

    Association of receptor activity-modifying proteins (RAMP1-3) with the G protein-coupled receptor (GPCR) calcitonin receptor-like receptor (CLR) enables selective recognition of the peptides calcitonin gene-related peptide (CGRP) and adrenomedullin (AM) that have diverse functions in the cardiovascular and lymphatic systems. How peptides selectively bind GPCR:RAMP complexes is unknown. We report crystal structures of CGRP analog-bound CLR:RAMP1 and AM-bound CLR:RAMP2 extracellular domain heterodimers at 2.5 and 1.8 Å resolutions, respectively. The peptides similarly occupy a shared binding site on CLR with conformations characterized by a β-turn structure near their C termini rather than the α-helical structure common to peptides that bind related GPCRs. The RAMPs augment the binding site with distinct contacts to the variable C-terminal peptide residues and elicit subtly different CLR conformations. The structures and accompanying pharmacology data reveal how a class of accessory membrane proteins modulate ligand binding of a GPCR and may inform drug development targeting CLR:RAMP complexes. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  10. How Does Amino Acid Ligand Modulate Au Core Structure and Characteristics in Peptide Coated Au Nanocluster?

    Science.gov (United States)

    Li, Nan; Li, Xu; Zhao, Hongkang; Zhao, Lina

    2018-03-01

    The atomic structures and the corresponding physicochemical properties of peptide coated Au nanoclusters determine their distinctive biological targeting applications. To learn the modulation of amino acid ligand on the atomic structure and electronic characteristics of coated Au core is the fundamental knowledge for peptide coated Au nanocluster design and construction. Based on our recent coated Au nanocluster configuration study (Nanoscale, 2016, 8, 11454), we built the typically simplified Au13(Cys-Au-Cys) system to more clearly learn the basic modulation information of amino acid ligand on Au core by the density functional theory (DFT) calculations. There are two isomers as ligand adjacent bonding (Iso1) and diagonal bonding (Iso2) to Au13 cores. The geometry optimizations indicate the adjacent bonding Iso1 is more stable than Iso2. More important, the Au13 core of Iso1 distorts much more significantly than that of Iso2 by Cys-Au-Cys bonding through the root-mean-square deviation (RMSD) analysis, which modulate their electronic characteristics in different ways. In addition, the frontier molecular orbital results of Au13(Cys-Au-Cys) isomers confirm that the Au cores mainly determine the blue shifts of Au13(Cys-Au-Cys) systems versus the original Au13 core in their UV-visible absorption spectrum studies. The configuration of Au13 core performs deformation under Cys-Au-Cys ligand modulation to reach new stability with distinct atomic structure and electronic properties, which could be the theory basis for peptide coated AuNCs design and construction.

  11. Structure-Based Design of a New Scaffold for Cell-Penetrating Peptidic Inhibitors of the Histone Demethylase PHF8

    DEFF Research Database (Denmark)

    Dorosz, Jerzy; Olsen, Lars; Seger, Signe Teuber

    2017-01-01

    and a PHD reader domain. The latter specifically recognizes tri-methylated Ly4 on histone H3. A fragment of the histone H3 tail with tri-methylated Lys4 was used as a template for the structure-based design of a cyclic, cell-penetrating peptide that exhibits micromolar binding affinity to PHF8......, thus implying that the free N terminus is not part of the KDM5 enzyme substrate recognition machinery. The cyclic peptide's ability to penetrate cells is achieved by incorporation of a sequence derived from HIV Tat. The derived cyclic peptide can be used as a starting compound in the search for potent...

  12. Mapping the antigenic structure of porcine parvovirus at the level of peptides

    DEFF Research Database (Denmark)

    Kamstrup, Søren; Langeveld, Jan; Bøtner, Anette

    1998-01-01

    The antigenic structure of the capsid proteins of porcine parvovirus (PPV) was investigated. A total of nine linear epitopes were identified by Pepscan using porcine or rabbit anti-PPV antisera. No sites were identified with a panel of neutralising monoclonal antibodies (MAbs). All epitopes were...... located in the region corresponding to the major capsid protein VP2. Based on this information, and on analogy to other autonomous parvoviruses, 24 different peptides were synthesised, coupled to keyhole limpet haemocyanin (KLH) and used to immunise rabbits. Most antisera were able to bind viral protein...

  13. Two Supramolecular Inorganic–Organic Hybrid Crystals Based on Keggin Polyoxometalates and Crown Ethers

    Directory of Open Access Journals (Sweden)

    Jun Xiong

    2018-01-01

    Full Text Available New supramolecular structures were designed in this work using large-sized polyoxometalates (POMs and crown-ether-based supramolecular cations selected as building blocks. Two novel supramolecular inorganic–organic hybrids [(3-F-4-MeAnis([18]crown-6]2[SMo12O40]•CH3CN (1 and [(4-IAnis([18]crown-6]3[PMo12O40]•4CH3CN (2 (3-F-4-MeAnis = 3-fluoro-4-methylanilinium and 4-IAnis = 4-iodoanilinium were synthesized. Crystals 1 and 2 have been characterized by infrared spectroscopy (IR and elemental analysis (EA. Based on X-ray diffraction analysis, Crystals 1 and 2 were constructed through noncovalent bonding interactions and belong to different space groups due to the difference of the building blocks used. Supramolecular cations formed due to strong N–H···O hydrogen bonding interactions between the six oxygen atoms of [18]crown-6 molecules and nitrogen atoms of anilinium derivatives. Crystal 1 has two different supramolecular cations with an anti-paralleled arrangement that forms a dimer through weak hydrogen bonding interactions between adjacent [18]crown-6 molecules. Crystal 2 has three independent supramolecular cations that fill large spaces between the [PMo12O40] polyoxoanions forming a rhombus-shape packing arrangement in the ac plane. Crystals 1 and 2 are unstable at room temperature.

  14. Structural insight into antibody-mediated antagonism of the Glucagon-like peptide-1 Receptor

    DEFF Research Database (Denmark)

    Hennen, Stephanie; Kodra, János T; Soroka, Vladyslav

    2016-01-01

    The Glucagon-like peptide-1 receptor (GLP-1R) is a member of the class B G protein-coupled receptor (GPCR) family and a well-established target for the treatment of type 2 diabetes. The N-terminal extracellular domain (ECD) of GLP-1R is important for GLP-1 binding and the crystal structure...... of the GLP-1/ECD complex was reported previously. The first structure of a class B GPCR transmembrane (TM) domain was solved recently, but the full length receptor structure is still not well understood. Here we describe the molecular details of antibody-mediated antagonism of the GLP-1R using both in vitro...... pharmacology and x-ray crystallography. We showed that the antibody Fab fragment (Fab 3F52) blocked the GLP-1 binding site of the ECD directly and thereby acts as a competitive antagonist of native GLP-1. Interestingly, Fab 3F52 also blocked a short peptide agonist believed to engage primarily...

  15. Phosphorylation regulates the secondary structure and function of dentin phosphoprotein peptides

    Energy Technology Data Exchange (ETDEWEB)

    Villarreal-Ramirez, Eduardo; Eliezer, David; Garduño-Juarez, Ramon; Gericke, Arne; Perez-Aguilar, Jose Manuel; Boskey, Adele

    2017-02-01

    Dentin phosphoprotein (DPP) is the most acidic protein in vertebrates and structurally is classified as an intrinsically disordered protein. Functionally, DPP is related to dentin and bone formation, however the specifics of such association remain unknown. Here, we used atomistic molecular dynamics simulations to screen selected binding domains of DPP onto hydroxyapatite (HA), which is one of its important interacting partners. From these results, we selected a functionally relevant peptide, Ace-SSDSSDSSDSSDSSD-NH2 (named P5) and its phosphorylated form (named P5P), for experimental characterization. SAXS experiments indicated that in solution P5 was disordered, possibly in an extended conformation while P5P displayed more compact globular conformations. Circular dichroism and FTIR confirmed that, either in the presence or absence of Ca2 +/HA, P5 adopts a random coil structure, whereas its phosphorylated counterpart, P5P, has a more compact arrangement associated with conformations that display β-sheet and α-helix motifs when bound to HA. In solution, P5 inhibited HA crystal growth, whereas at similar concentrations, P5P stimulated it. These findings suggest that phosphorylation controls the transient formation of secondary and tertiary structure of DPP peptides, and, most likely of DPP itself, which in turn controls HA growth in solution and possibly HA growth in mineralized tissues.

  16. Supramolecular chemistry: from molecular information towards self-organization and complex matter

    International Nuclear Information System (INIS)

    Lehn, Jean-Marie

    2004-01-01

    Molecular chemistry has developed a wide range of very powerful procedures for constructing ever more sophisticated molecules from atoms linked by covalent bonds. Beyond molecular chemistry lies supramolecular chemistry, which aims at developing highly complex chemical systems from components interacting via non-covalent intermolecular forces. By the appropriate manipulation of these interactions, supramolecular chemistry became progressively the chemistry of molecular information, involving the storage of information at the molecular level, in the structural features, and its retrieval, transfer, and processing at the supramolecular level, through molecular recognition processes operating via specific interactional algorithms. This has paved the way towards apprehending chemistry also as an information science. Numerous receptors capable of recognizing, i.e. selectively binding, specific substrates have been developed, based on the molecular information stored in the interacting species. Suitably functionalized receptors may perform supramolecular catalysis and selective transport processes. In combination with polymolecular organization, recognition opens ways towards the design of molecular and supramolecular devices based on functional (photoactive, electroactive, ionoactive, etc) components. A step beyond preorganization consists in the design of systems undergoing self-organization, i.e. systems capable of spontaneously generating well-defined supramolecular architectures by self-assembly from their components. Self-organization processes, directed by the molecular information stored in the components and read out at the supramolecular level through specific interactions, represent the operation of programmed chemical systems. They have been implemented for the generation of a variety of discrete functional architectures of either organic or inorganic nature. Self-organization processes also give access to advanced supramolecular materials, such as

  17. Azobenzene-based supramolecular polymers for processing MWCNTs.

    Science.gov (United States)

    Maggini, Laura; Marangoni, Tomas; Georges, Benoit; Malicka, Joanna M; Yoosaf, K; Minoia, Andrea; Lazzaroni, Roberto; Armaroli, Nicola; Bonifazi, Davide

    2013-01-21

    Photothermally responsive supramolecular polymers containing azobenzene units have been synthesised and employed as dispersants for multi-walled carbon nanotubes (MWCNTs) in organic solvents. Upon triggering the trans-cis isomerisation of the supramolecular polymer intermolecular interactions between MWCNTs and the polymer are established, reversibly affecting the suspensions of the MWCNTs, either favouring it (by heating, i.e. cis→trans isomerisation) or inducing the CNTs' precipitation (upon irradiation, trans→cis isomerisation). Taking advantage of the chromophoric properties of the molecular subunits, the solubilisation/precipitation processes have been monitored by UV-Vis absorption spectroscopy. The structural properties of the resulting MWCNT-polymer hybrid materials have been thoroughly investigated via thermogravimetric analysis (TGA), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM) and atomic force microscopy (AFM) and modelled with molecular dynamics simulations.

  18. Supramolecular photochemistry and solar cells

    Directory of Open Access Journals (Sweden)

    IHA NEYDE YUKIE MURAKAMI

    2000-01-01

    Full Text Available Supramolecular photochemistry as well as solar cells are fascinating topics of current interest in Inorganic Photochemistry and very active research fields which have attracted wide attention in last two decades. A brief outline of the investigations in these fields carried out in our Laboratory of Inorganic Photochemistry and Energy Conversion is given here with no attempt of an exhaustive coverage of the literature. The emphasis is placed on recent work and information on the above mentioned subjects. Three types of supramolecular systems have been the focus of this work: (i cage-type coordination compounds; (ii second-sphere coordination compounds, exemplified by ion-pair photochemistry of cobalt complexes and (iii covalently-linked systems. In the latter, modulation of the photoluminescence and photochemistry of some rhenium complexes are discussed. Solar energy conversion and development of thin-layer photoelectrochemical solar cells based on sensitization of nanocrystalline semiconductor films by some ruthenium polypyridyl complexes are presented as an important application that resulted from specifically engineered artificial assemblies.

  19. Correlations between structure, material properties and bioproperties in self-assembled β-hairpin peptide hydrogels

    Science.gov (United States)

    Hule, Rohan A.; Nagarkar, Radhika P.; Altunbas, Aysegul; Ramay, Hassna R.; Branco, Monica C.; Schneider, Joel P.; Pochan, Darrin J.

    2009-01-01

    A de novo designed β-hairpin peptide (MAX8), capable of undergoing intramolecular folding and consequent intermolecular self-assembly into a cytocompatible hydrogel, has been studied. A combination of small angle neutron scattering (SANS) and cryogenic-transmission electron microscopy (cryo-TEM) have been used to quantitatively investigate the MAX8 nanofibrillar hydrogel network morphology. A change in the peptide concentration from 0.5 to 2 wt% resulted in a denser fibrillar network as revealed via SANS by a change in the high q (q = (4π/λ) × sin (θ/2), where λ = wavelength of incident neutrons and θ = scattering angle) mass fractal exponent from 2.5 to 3 and by a decrease in the measured correlation length from 23 to 16 A. Å slope of −4 in the USANS regime indicates well-defined gel microporosity, an important characteristic for cellular substrate applications. These changes, both at the network as well as the individual fibril lengthscales, can be directly visualized in situ by cryo-TEM. Fibrillar nanostructures and network properties are directly related to bulk hydrogel stiffness via oscillatory rheology. Preliminary cell viability and anchorage studies at varying hydrogel stiffness confirm cell adhesion at early stages of cell culture within the window of stiffness investigated. Knowledge of the precise structure spanning length scales from the nanoscale up to the microscale can help in the formation of future, specific structure-bioproperty relationships when studying in vitro and in vivo behavior of these new peptide scaffolds. PMID:19048999

  20. Molecular structure and diversity of PBAN/Pyrokinin family peptides in ants

    Directory of Open Access Journals (Sweden)

    Man-Yeon eChoi

    2012-02-01

    Full Text Available Neuropeptides are the largest group of insect hormones. They are produced in the central and peripheral nervous systems and affect insect development, reproduction, feeding and behavior. A variety of neuropeptide families have been identified in insects. One of these families is the PBAN/pyrokinin family defined by a common FXPRLamide or similar amino acid fragment at the C-terminal end. These peptides, found in all insects studied thus far, have been conserved throughout evolution. The most well studied physiological function is regulation of moth sex pheromone biosynthesis through the Pheromone Biosynthesis Activating Neurohormone (PBAN, although several developmental functions have also been reported. Over the past years we have extended knowledge of the PBAN/pyrokinin family of peptides to ants, focusing mainly on the fire ant, Solenopsis invicta. The fire ant is one of the most studied social insects and over the last 60 years a great deal has been learned about many aspects of this ant, including the behaviors and chemistry of pheromone communication. However, virtually nothing is known about the regulation of these pheromone systems. Recently, we demonstrated the presence of PBAN/pyrokinin immunoreactive neurons in the fire ant, and identified and characterized PBAN and additional neuropeptides. We have mapped the fire ant PBAN gene structure and determined the tissue expression level in the central nervous system of the ant. We review here our research to date on the molecular structure and diversity of ant PBAN/pyrokinin peptides in preparation for determining the function of the neuropeptides in ants and other social insects.

  1. Glucosamine-Based Supramolecular Nanotubes for Human Mesenchymal Cell Therapy.

    Science.gov (United States)

    Talloj, Satish Kumar; Cheng, Bill; Weng, Jen-Po; Lin, Hsin-Chieh

    2018-04-23

    Herein, we demonstrate an example of glucosamine-based supramolecular hydrogels that can be used for human mesenchymal cell therapy. We designed and synthesized a series of amino acid derivatives based on a strategy of capping d-glucosamine moiety at the C-terminus and fluorinated benzyl group at the N-terminus. From a systematic study on chemical structures, we discovered that the glucosamine-based supramolecular hydrogel [pentafluorobenzyl (PFB)-F-Glu] self-assembled with one-dimensional nanotubular structures at physiological pH. The self-assembly of a newly discovered PFB-F-Glu motif is attributed to the synergistic effect of π-π stacking and extensive intermolecular hydrogen bonding network in aqueous medium. Notably, PFB-F-Glu nanotubes are proven to be nontoxic to human mesenchymal stem cells (hMSCs) and have been shown to enhance hMSC proliferation while maintaining their pluripotency. Retaining of pluripotency capabilities provides potentially unlimited source of undifferentiated cells for the treatment of future cell therapies. Furthermore, hMSCs cultured on PFB-F-Glu are able to secrete paracrine factors that downregulate profibrotic gene expression in lipopolysaccharide-treated human skin fibroblasts, which demonstrates that PFB-F-Glu nanotubes have the potential to be used for wound healing applications. Overall, this article addresses the importance of chemical design to generate supramolecular biomaterials for stem cell therapy.

  2. Peptide secondary structures in the gas phase: consensus motif of N-linked glycoproteins.

    Science.gov (United States)

    Cocinero, Emilio J; Stanca-Kaposta, E Cristina; Gamblin, David P; Davis, Benjamin G; Simons, John P

    2009-01-28

    The possibility of secondary structure acting as a primary determinant in nature's choice of the consensus sequon, NXS/T in all N-linked glycoproteins, has been addressed by determining the intrinsic secondary structures of the capped oligopeptide, Ac-NGS-NHBn, and two "mutants", Ac-QGS-NHBn and Ac-NPS-NHBn, by use of infrared laser ion dip spectroscopy in the gas phase coupled with ab initio and density functional theory calculation. Their global minimum energy conformations, exclusively or preferentially populated in all three peptides, display marked differences. NGS adopts an open, S-shaped backbone conformation rather than the C(10) "Asx" turn structure that all previous measurements have identified in solution; the difference can be related to the high dipole moment of the "Asx" conformation and structural selection in a polar environment. QGS adopts a similar but more rigid backbone structure, supported by markedly stronger hydrogen bonds. NPS adopts an Asx turn coupled with a C(10) beta-turn backbone conformation, a structure also adopted in a crystal environment. These and other more subtle structural differences, particularly those involving interactions with the carboxamide side chain, provide strong evidence for the operation of structural constraints, and a potential insight into the unique reactivity of the asparagine side chain toward enzymatic glycosylation.

  3. Structure and interaction with lipid membrane models of Semliki Forest virus fusion peptide.

    Science.gov (United States)

    Agopian, A; Quetin, M; Castano, S

    2016-11-01

    Semliki Forest virus (SFV) is a well-characterized alphavirus that infects cells via endocytosis and an acid-triggered fusion step using class II fusion proteins. Membrane fusion is mediated by the viral spike protein, a heterotrimer of two transmembrane subunits, E1 and E2, and a peripheral protein, E3. Sequence analysis of the E1 ectodomain of a number of alphaviruses demonstrated the presence of a highly conserved hydrophobic domain on the E1 ectodomain. This sequence was proposed to be the fusion peptide of SFV and is believed to be the domain of E1 that interacts with the target membrane and triggers fusion. Here, we investigate the structure and the interaction with lipid membrane models of 76 YQCKVYTGVYPFMWGGAYCFC 96 sequence from SFV, named SFV21, using optical method (ellipsometry) and vibrational spectroscopiy approaches (Polarization Modulation infra-Red Reflection Absorption Spectroscopy, PMIRRAS, and polarized ATR-FTIR). We demonstrate a structural flexibility of SFV21 sequence whether the lateral pressure and the lipid environment. In a lipid environment that mimics eukaryotic cell membranes, a conformational transition from an α-helix to a β-sheet is induced in the presence of lipid by increasing the peptide to lipid ratio, which leads to important perturbations in the membrane organisation. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Multivalent supramolecular dendrimer-based drugs.

    Science.gov (United States)

    Galeazzi, Simone; Hermans, Thomas M; Paolino, Marco; Anzini, Maurizio; Mennuni, Laura; Giordani, Antonio; Caselli, Gianfranco; Makovec, Francesco; Meijer, E W; Vomero, Salvatore; Cappelli, Andrea

    2010-01-11

    Supramolecular complexes consisting of a hydrophobic dendrimer host [DAB-dendr-(NHCONH-Ad)(64)] as well as solubilizing and bioactive guest molecules have been synthesized using a noncovalent approach. The guest-host supramolecular assembly is first preassembled in chloroform and transferred via the neat phase to aqueous solution. The bioactive guest molecules can bind to a natural (serotonin 5-HT(3)) receptor with nanomolar affinity as well as to the synthetic dendrimer receptor in aqueous solution, going toward a dynamic multivalent supramolecular construct capable of adapting itself to a multimeric receptor motif.

  5. Dielectric properties of barium titanate supramolecular nanocomposites.

    Science.gov (United States)

    Lee, Keun Hyung; Kao, Joseph; Parizi, Saman Salemizadeh; Caruntu, Gabriel; Xu, Ting

    2014-04-07

    Nanostructured dielectric composites can be obtained by dispersing high permittivity fillers, barium titanate (BTO) nanocubes, within a supramolecular framework. Thin films of BTO supramolecular nanocomposites exhibit a dielectric permittivity (εr) as high as 15 and a relatively low dielectric loss of ∼0.1 at 1 kHz. These results demonstrate a new route to control the dispersion of high permittivity fillers toward high permittivity dielectric nanocomposites with low loss. Furthermore, the present study shows that the size distribution of nanofillers plays a key role in their spatial distribution and local ordering and alignment within supramolecular nanostructures.

  6. Main-chain supramolecular block copolymers.

    Science.gov (United States)

    Yang, Si Kyung; Ambade, Ashootosh V; Weck, Marcus

    2011-01-01

    Block copolymers are key building blocks for a variety of applications ranging from electronic devices to drug delivery. The material properties of block copolymers can be tuned and potentially improved by introducing noncovalent interactions in place of covalent linkages between polymeric blocks resulting in the formation of supramolecular block copolymers. Such materials combine the microphase separation behavior inherent to block copolymers with the responsiveness of supramolecular materials thereby affording dynamic and reversible materials. This tutorial review covers recent advances in main-chain supramolecular block copolymers and describes the design principles, synthetic approaches, advantages, and potential applications.

  7. Self-assembly of amphiphilic Janus dendrimers into mechanically robust supramolecular hydrogels for sustained drug release.

    Science.gov (United States)

    Nummelin, Sami; Liljeström, Ville; Saarikoski, Eve; Ropponen, Jarmo; Nykänen, Antti; Linko, Veikko; Seppälä, Jukka; Hirvonen, Jouni; Ikkala, Olli; Bimbo, Luis M; Kostiainen, Mauri A

    2015-10-05

    Compounds that can gelate aqueous solutions offer an intriguing toolbox to create functional hydrogel materials for biomedical applications. Amphiphilic Janus dendrimers with low molecular weights can readily form self-assembled fibers at very low mass proportion (0.2 wt %) to create supramolecular hydrogels (G'≫G'') with outstanding mechanical properties and storage modulus of G'>1000 Pa. The G' value and gel melting temperature can be tuned by modulating the position or number of hydrophobic alkyl chains in the dendrimer structure; thus enabling exquisite control over the mesoscale material properties in these molecular assemblies. The gels are formed within seconds by simple injection of ethanol-solvated dendrimers into an aqueous solution. Cryogenic TEM, small-angle X-ray scattering, and SEM were used to confirm the fibrous structure morphology of the gels. Furthermore, the gels can be efficiently loaded with different bioactive cargo, such as active enzymes, peptides, or small-molecule drugs, to be used for sustained release in drug delivery. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Structure of Calmodulin Bound to a Calcineurin Peptide: A New Way of Making an Old Binding Mode

    International Nuclear Information System (INIS)

    Ye, Q.; Li, X.; Wong, A.; Wei, Q.; Jia, Z.

    2006-01-01

    Calcineurin is a calmodulin-binding protein in brain and the only serine/threonine protein phosphatase under the control of Ca 2+ /calmodulin (CaM), which plays a critical role in coupling Ca 2+ signals to cellular responses. CaM up-regulates the phosphatase activity of calcineurin by binding to the CaM-binding domain (CBD) of calcineurin subunit A. Here, we report crystal structural studies of CaM bound to a CBD peptide. The chimeric protein containing CaM and the CBD peptide forms an intimate homodimer, in which CaM displays a native-like extended conformation and the CBD peptide shows -helical structure. Unexpectedly, the N-terminal lobe from one CaM and the C-terminal lobe from the second molecule form a combined binding site to trap the peptide. Thus, the dimer provides two binding sites, each of which is reminiscent of the fully collapsed conformation of CaM commonly observed in complex with, for example, the myosin light chain kinase (MLCK) peptide. The interaction between the peptide and CaM is highly specific and similar to MLCK

  9. Interaction of the chaperone calreticulin with proteins and peptides of different structural classes

    DEFF Research Database (Denmark)

    Duus, K; Sandhu, N; Jørgensen, C S

    2009-01-01

    The interaction of calreticulin with native and denatured forms and polypeptides in proteolytic digests of proteins representing structural classes of all-alpha-helix (hemoglobin, serum albumin), all-beta-sheet (IgG) and alpha-helix + beta-sheets (lysozyme, ovalbumin) was investigated. The binding...... of calreticulin to denatured proteins was found to depend on conformation and structural class of the protein. No interaction was observed with the native proteins, whereas binding was seen for the denatured proteins, the order of interaction being lysozyme = IgG > ovalbumin >> hemoglobin = serum albumin....... Moreover, the interaction between calreticulin and the heat-denatured proteins depended on the temperature and time used for denaturation and the degree of proteolytic fragmentation. Calreticulin bound well to peptides in proteolytic digests from protease K or chymotrypsin treatment of lysozyme, Ig...

  10. Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide

    Science.gov (United States)

    Wang, Yukun; Chen, Charles H.; Hu, Dan; Ulmschneider, Martin B.; Ulmschneider, Jakob P.

    2016-11-01

    Many antimicrobial peptides (AMPs) selectively target and form pores in microbial membranes. However, the mechanisms of membrane targeting, pore formation and function remain elusive. Here we report an experimentally guided unbiased simulation methodology that yields the mechanism of spontaneous pore assembly for the AMP maculatin at atomic resolution. Rather than a single pore, maculatin forms an ensemble of structurally diverse temporarily functional low-oligomeric pores, which mimic integral membrane protein channels in structure. These pores continuously form and dissociate in the membrane. Membrane permeabilization is dominated by hexa-, hepta- and octamers, which conduct water, ions and small dyes. Pores form by consecutive addition of individual helices to a transmembrane helix or helix bundle, in contrast to current poration models. The diversity of the pore architectures--formed by a single sequence--may be a key feature in preventing bacterial resistance and could explain why sequence-function relationships in AMPs remain elusive.

  11. Novel Concepts of MS-Cleavable Cross-linkers for Improved Peptide Structure Analysis

    Science.gov (United States)

    Hage, Christoph; Falvo, Francesco; Schäfer, Mathias; Sinz, Andrea

    2017-10-01

    The chemical cross-linking/mass spectrometry (MS) approach is gaining increasing importance as an alternative method for studying protein conformation and for deciphering protein interaction networks. This study is part of our ongoing efforts to develop innovative cross-linking principles for a facile and efficient assignment of cross-linked products. We evaluate two homobifunctional, amine-reactive, and MS-cleavable cross-linkers regarding their potential for automated analysis of cross-linked products. We introduce the bromine phenylurea (BrPU) linker that possesses a unique structure yielding a distinctive fragmentation pattern on collisional activation. Moreover, BrPU delivers the characteristic bromine isotope pattern and mass defect for all cross-linker-decorated fragments. We compare the fragmentation behavior of the BrPU linker with that of our previously described MS-cleavable TEMPO-Bz linker (which consists of a 2,2,6,6-tetramethylpiperidine-1-oxy moiety connected to a benzyl group) that was developed to perform free-radical-initiated peptide sequencing. Comparative collisional activation experiments (collision-induced dissociation and higher-energy collision-induced dissociation) with both cross-linkers were conducted in negative electrospray ionization mode with an Orbitrap Fusion mass spectrometer using five model peptides. As hypothesized in a previous study, the presence of a cross-linked N-terminal aspartic acid residue seems to be the prerequisite for the loss of an intact peptide from the cross-linked products. As the BrPU linker combines a characteristic mass shift with an isotope signature, it presents a more favorable combination for automated assignment of cross-linked products compared with the TEMPO-Bz linker. [Figure not available: see fulltext.

  12. Detergent-like actions of linear amphipathic cationic antimicrobial peptides.

    Science.gov (United States)

    Bechinger, Burkhard; Lohner, Karl

    2006-09-01

    Antimicrobial peptides have raised much interest as pathogens become resistant against conventional antibiotics. We review biophysical studies that have been performed to better understand the interactions of linear amphipathic cationic peptides such as magainins, cecropins, dermaseptin, delta-lysin or melittin. The amphipathic character of these peptides and their interactions with membranes resemble the properties of detergent molecules and analogies between membrane-active peptide and detergents are presented. Several models have been suggested to explain the pore-forming, membrane-lytic and antibiotic activities of these peptides. Here we suggest that these might be 'special cases' within complicated phase diagrams describing the morphological plasticity of peptide/lipid supramolecular assemblies.

  13. The native structure of annexin A2 peptides in hydrophilic environment determines their anti-angiogenic effects.

    Science.gov (United States)

    Raddum, Aase M; Hollås, Hanne; Shumilin, Igor A; Henklein, Petra; Kretsinger, Robert; Fossen, Torgils; Vedeler, Anni

    2015-05-01

    The progression of aggressive cancer occurs via angiogenesis and metastasis makes these processes important targets for the development of anti-cancer agents. However, recent studies have raised the concern that selective inhibition of angiogenesis results in a switch towards increased tumour growth and metastasis. Since Annexin A2 (AnxA2) is involved in both angiogenesis and metastasis, it may serve as an ideal target for the simultaneous inhibition of both processes. Based on the discovery that domains I (D(I)) and IV (D(IV)) of AnxA2 are potent inhibitors of angiogenesis, we designed seven peptides derived from these domains based on AnxA2 crystal structures. The peptides were expressed as fusion peptides to increase their folding and solubility. Light scattering, far-UV circular dichroism and thermal transition analyses were employed to investigate their aggregation tendencies, α-helical propensity and stability, respectively. 2,2,2-trifluoroethanol (50%) increased the α-helical propensities of all peptides, indicating that they may favour a hydrophobic environment, but did not enhance their thermal stability. D(I)-P2 appears to be the most stable and folded peptide in a hydrophilic environment. The secondary structure of D(I)-P2 was confirmed by nuclear magnetic resonance spectra. The effect of the seven AnxA2 peptides on the formation and integrity of capillary-like networks was studied in a co-culture system mimicking many of the angiogenesis-related processes. Notably, D(I)-P2 inhibited significantly network formation in this system, indicating that the folded D(I)-P2 peptide interferes with vascular endothelial growth factor-dependent pro-angiogenic processes. Thus, this peptide has the potential of being developed further as an anti-angiogenic drug. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  14. Self-assembling supramolecular systems of different symmetry formed by wedged macromolecular dendrons

    Energy Technology Data Exchange (ETDEWEB)

    Shcherbina, M. A., E-mail: shcherbina@ispm.ru; Bakirov, A. V. [Russian Academy of Sciences, Institute of Synthetic Polymer Materials (Russian Federation); Yakunin, A. N. [Karpov Institute of Physical Chemistry (Russian Federation); Percec, V. [University of Pennsylvania (United States); Beginn, U. [Universitaet Osnabrueck, Institut fuer Chemie (Germany); Moeller, M. [Institute for Technical and Macromolecular Chemistry (Germany); Chvalun, S. N. [Russian Academy of Sciences, Institute of Synthetic Polymer Materials (Russian Federation)

    2012-03-15

    The main stages of the self-assembling of supramolecular ensembles have been revealed by studying different functional wedged macromolecules: polymethacrylates with tapered side chains based on gallic acid, their macromonomers, and salts of 2,3,4- and 3,4,5-tris(dodecyloxy)benzenesulphonic acid. The first stage is the formation of individual supramolecular aggregates (long cylinders or spherical micelles) due to the weak noncovalent interactions of mesogenic groups and the subsequent ordering in these aggregates, which is accompanied by a decrease in the free energy of the system. Supramolecular aggregates, in turn, form 2D or 3D lattices. The shape of supramolecular aggregates and its change with temperature are delicate functions of the mesogen chemical structure; this circumstance makes it possible to rationally design complex self-assembling systems with the ability to respond smartly to external stimuli. X-ray diffraction analysis allows one to study the structure of supramolecular systems with different degrees of order, determine the type of mesophases formed by these systems, and reveal the phase behavior of the material. Particular attention has been paid to the method for reconstruction of electron density distribution from the relative reflection intensity. The application of a suite of experimental methods, including wide- and small-angle X-ray diffraction, molecular modeling, differential scanning calorimetry, and polarization optical microscopy, allows one to establish the relationship between the shape of the structural unit (molecule or molecular aggregate), the nature of the interaction, and the phase behavior of the material.

  15. Self-assembling supramolecular systems of different symmetry formed by wedged macromolecular dendrons

    Science.gov (United States)

    Shcherbina, M. A.; Bakirov, A. V.; Yakunin, A. N.; Percec, V.; Beginn, U.; Möller, M.; Chvalun, S. N.

    2012-03-01

    The main stages of the self-assembling of supramolecular ensembles have been revealed by studying different functional wedged macromolecules: polymethacrylates with tapered side chains based on gallic acid, their macromonomers, and salts of 2,3,4- and 3,4,5-tris(dodecyloxy)benzenesulphonic acid. The first stage is the formation of individual supramolecular aggregates (long cylinders or spherical micelles) due to the weak noncovalent interactions of mesogenic groups and the subsequent ordering in these aggregates, which is accompanied by a decrease in the free energy of the system. Supramolecular aggregates, in turn, form 2D or 3D lattices. The shape of supramolecular aggregates and its change with temperature are delicate functions of the mesogen chemical structure; this circumstance makes it possible to rationally design complex self-assembling systems with the ability to respond smartly to external stimuli. X-ray diffraction analysis allows one to study the structure of supramolecular systems with different degrees of order, determine the type of mesophases formed by these systems, and reveal the phase behavior of the material. Particular attention has been paid to the method for reconstruction of electron density distribution from the relative reflection intensity. The application of a suite of experimental methods, including wide- and small-angle X-ray diffraction, molecular modeling, differential scanning calorimetry, and polarization optical microscopy, allows one to establish the relationship between the shape of the structural unit (molecule or molecular aggregate), the nature of the interaction, and the phase behavior of the material.

  16. Supramolecular protein immobilization on lipid bilayers

    NARCIS (Netherlands)

    Bosmans, R.P.G.; Hendriksen, W.E.; Verheijden, Mark Lloyd; Eelkema, R.; Jonkheijm, Pascal; van Esch, J.H.; Brunsveld, Luc

    2015-01-01

    Protein immobilization on surfaces, and on lipid bilayers specifically, has great potential in biomolecular and biotechnological research. Of current special interest is the immobilization of proteins using supramolecular noncovalent interactions. This allows for a reversible immobilization and

  17. Enhanced intermolecular forces in supramolecular polymer nanocomposites

    Directory of Open Access Journals (Sweden)

    F. Lin

    2017-09-01

    Full Text Available Ureido-pyrimidone (Upy can dimerize in a self-complementary array of quadruple hydrogen bonds. In this paper, supramolecular polymer composites were prepared by blending Upy functionalized nanosilica with Upy end-capped polycarbonatediol. Surface characteristics of Upy functionalized nanosilica and influences of supramolecular forces on interfacial binding were researched. Fourier transform infrared spectroscopy (FTIR, Nuclear magnetic resonance (NMR and Gel permeation chromatography (GPC were used to characterize the synthesized molecules. Grafting ratio of Upy segments on the surface of nanosilica was analysed by Thermogravimetic analysis (TGA. Hydrophobicity and morphology of Upy modified nanosilica were analysed by Contact angle tester and Scanning electron microscope (SEM. Furthermore, dynamic thermo mechanical properties, mechanical properties and distribution of nanosilica in supramolecular polymer composites were also researched. Compared with the matrix resin, tensile stress and young's modulus of supramolecular polymer composites containing 5 wt% modified nanosilica were increased by 292 and 198% respectively.

  18. Supramolecular chemistry - interdisciplinary branch of science

    International Nuclear Information System (INIS)

    Radecka-Paryzek, W.

    1997-01-01

    The scientific problems connected with supramolecular chemistry have been reviewed. The basic concepts have been defined as well as rules governed of macromolecules formation. The special emphasize has been put on present and possible in future application of such systems

  19. Solvent induced supramolecular anisotropy in molecular gels

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, Michael A., E-mail: mroger09@uoguelph.ca [Department of Food Science, University of Guelph, Guelph, Ontario, N3C3X9 (Canada); Corradini, Maria G. [Department of Food Science, University of Massachusetts Amherst, Amherst, MA, 01003 (United States); Emge, Thomas [Department of Chemistry and Biochemistry, Rutgers University, New Brunswick, NJ, 08901 (United States)

    2017-06-15

    Herein is the first report of solvent induced anisotropy in 12-hydroxystearic acid self-assembled fibrillar networks. Increasing the chain length of polar solvent, such as nitriles and ketones, tailored the anisotropy of the fibrillar aggregates. 12HSA molecular gels, comprised of alkanes, exhibited an isotropic fibrillar network irrespective of the alkane chain length. In polar solvents, anisotropy, observed using 2D powder x-ray diffraction profiles, is correlated to a fibrillar supramolecular morphologies in long chain nitriles and ketones while sphereulitic crystals are correlated to x-ray diffraction patterns with an isotropic scatter intensity in short chain ketones and nitriles. These changes directly modify the final physical properties of the gels. - Highlights: • 12-HSA self-assembles into crystalline supramolecular morphologies depending on the solvent. • Alkanes, short chain nitriles and ketones led to 12-HSA displaying supramolecular isotropy. • In long chain nitriles and ketones, 12-HSA displays supramolecular anisotropy.

  20. Solvent induced supramolecular anisotropy in molecular gels

    International Nuclear Information System (INIS)

    Rogers, Michael A.; Corradini, Maria G.; Emge, Thomas

    2017-01-01

    Herein is the first report of solvent induced anisotropy in 12-hydroxystearic acid self-assembled fibrillar networks. Increasing the chain length of polar solvent, such as nitriles and ketones, tailored the anisotropy of the fibrillar aggregates. 12HSA molecular gels, comprised of alkanes, exhibited an isotropic fibrillar network irrespective of the alkane chain length. In polar solvents, anisotropy, observed using 2D powder x-ray diffraction profiles, is correlated to a fibrillar supramolecular morphologies in long chain nitriles and ketones while sphereulitic crystals are correlated to x-ray diffraction patterns with an isotropic scatter intensity in short chain ketones and nitriles. These changes directly modify the final physical properties of the gels. - Highlights: • 12-HSA self-assembles into crystalline supramolecular morphologies depending on the solvent. • Alkanes, short chain nitriles and ketones led to 12-HSA displaying supramolecular isotropy. • In long chain nitriles and ketones, 12-HSA displays supramolecular anisotropy.

  1. Structural determination of nanomolar quantities of neuroactive peptides by nuclear magnetic resonance

    Science.gov (United States)

    Matei, Elena

    The specificity of the conotoxin is one of the attributes that make them a valuable diagnostic tool in the characterization of neuronal mechanisms, or therapeutic agents in medicine. It appears that Nature has provided us with a pharmaceutical tool in the form of Conus peptides. Further studies will only enhance our understanding, and use, of these molecules in medicine and science. The study of three-dimensional structure in relation to the function of cone snail peptides is an area of increasing interest. The venom of a single cone snail can contain as many as 300 different chemical components. Individual cone snail venom components, or conopeptides, can have powerful neurological effects. For many interesting species, not enough venom collected from the natural origin is available for experimental investigations. After a laborious separation procedure, only nanomole quantities of these native conopeptides are able to be obtained. Therefore, several experimental applications, such as NMR spectroscopy, are difficult to carry out using traditional methods. The research was focused on using nanoNMR spectroscopy as an alternative method to the conventional NMR spectroscopy method in order to analyze small quantities of novel peptides with unknown three-dimensional conformational arrangement. The experimental results obtained using the HR-MAS NMR technique, in addition to the use of a 3mm gHCN (with 1.7mm inserts) NMR probes, proved the capability of conformational analysis of different types of natural products at sample levels down to nanomole range. Understanding the interaction between agonist or antagonist ligands and their target receptors, at a molecular level, offer promise for the development of pharmacological therapeutics for the central nervous system. Conopeptides are of great interest as ligands in neuroscience and are valuable leads in drug design, based on their specificity and potency for therapeutically relevant receptors and ion channels. For

  2. Detection of trans-cis flips and peptide-plane flips in protein structures

    NARCIS (Netherlands)

    Touw, W.G.; Joosten, R.P.; Vriend, G.

    2015-01-01

    A coordinate-based method is presented to detect peptide bonds that need correction either by a peptide-plane flip or by a trans-cis inversion of the peptide bond. When applied to the whole Protein Data Bank, the method predicts 4617 trans-cis flips and many thousands of hitherto unknown

  3. Polarization switching and patterning in self-assembled peptide tubular structures

    Science.gov (United States)

    Bdikin, Igor; Bystrov, Vladimir; Delgadillo, Ivonne; Gracio, José; Kopyl, Svitlana; Wojtas, Maciej; Mishina, Elena; Sigov, Alexander; Kholkin, Andrei L.

    2012-04-01

    Self-assembled peptide nanotubes are unique nanoscale objects that have great potential for a multitude of applications, including biosensors, nanotemplates, tissue engineering, biosurfactants, etc. The discovery of strong piezoactivity and polar properties in aromatic dipeptides [A. Kholkin, N. Amdursky, I. Bdikin, E. Gazit, and G. Rosenman, ACS Nano 4, 610 (2010)] opened up a new perspective for their use as biocompatible nanoactuators, nanomotors, and molecular machines. Another, as yet unexplored functional property is the ability to switch polarization and create artificial polarization patterns useful in various electronic and optical applications. In this work, we demonstrate that diphenylalanine peptide nanotubes are indeed electrically switchable if annealed at a temperature of about 150 °C. The new orthorhombic antipolar structure that appears after annealing allows for the existence of a radial polarization component, which is directly probed by piezoresponse force microscopy (PFM) measurements. Observation of the relatively stable polarization patterns and hysteresis loops via PFM testifies to the local reorientation of molecular dipoles in the radial direction. The experimental results are complemented with rigorous molecular calculations and create a solid background of electric-field induced deformation of aromatic rings and corresponding polarization switching in this emergent material.

  4. The gp41659 - 671 HIV-1 antibody epitope: a structurally challenging small peptide

    Science.gov (United States)

    Zhang, Yuan; Sagui, Celeste

    2014-03-01

    We present the results of extensive Molecular Dynamics (MD) simulations of the tridecapeptide corresponding to residues 659-671 of the envelope glycoprotein gp41 of HIV-1, which spans the 2F5 monoclonal antibody epitope ELDKWA. The most recent AMBER force fields ff99SB and ff12SB in both implicit and explicit solvents have been used for a cumulative time longer than 7.2 μs . We have analyzed the conformational ensembles of the peptide both with and without applied tensile restraints, and found that: (1) The amount of helical populations is important in aqueous solution, but this structure forms part of a flexible conformational ensemble with a rugged free energy landscape with shallow minima, which agrees well with the bulk of the experimental observations; (2) our results are more consistent with the experimental results than those from previous simulations; (3) under uniaxial tension, the disordered peptide first becomes fully helical before melting into turns, loops and 310-helices.

  5. Role of Charge and Solvation in the Structure and Dynamics of Alanine-Rich Peptide AKA2 in AOT Reverse Micelles.

    Science.gov (United States)

    Martinez, Anna Victoria; Małolepsza, Edyta; Domínguez, Laura; Lu, Qing; Straub, John E

    2015-07-23

    The propensity of peptides to form α-helices has been intensely studied using theory, computation, and experiment. Important model peptides for the study of the coil-to-helix transition have been alanine-lysine (AKA) peptides in which the lysine residues are placed on opposite sides of the helix avoiding charge repulsion while enhancing solubility. In this study, the effects of capped versus zwitterionic peptide termini on the secondary structure of alanine-rich peptides in reverse micelles are explored. The reverse micelles are found to undergo substantial shape fluctuations, a property observed in previous studies of AOT reverse micelles in the absence of solvated peptide. The peptides are observed to interact with water, as well as the AOT surfactant, including interactions between the nonpolar residues and the aliphatic surfactant tails. Computation of IR spectra for the amide I band of the peptide allows for direct comparison with experimental spectra. The results demonstrate that capped AKA2 peptides form more stable α helices than zwitterionic AKA2 peptides in reverse micelles. The rotational anisotropy decay of water is found to be distinctly different in the presence or absence of peptide within the reverse micelle, suggesting that the introduction of peptide significantly alters the number of free waters within the reverse micelle nanopool. However, neither the nature of the peptide termini (capped or charged) nor the degree of peptide helicity is found to significantly alter the balance of interactions between the peptides and the environment. Observed changes in the degree of helicity in AKA2 peptides in bulk solution and in reverse micelle environments result from changes in peptide confinement and hydration as well as direct nonpolar and polar interactions with the water-surfactant interface.

  6. Ligand-induced changes in the structure and dynamics of Escherichia coli peptide deformylase.

    Science.gov (United States)

    Amero, Carlos D; Byerly, Douglas W; McElroy, Craig A; Simmons, Amber; Foster, Mark P

    2009-08-18

    Peptide deformylase (PDF) is an enzyme that is responsible for removing the formyl group from nascently synthesized polypeptides in bacteria, attracting much attention as a potential target for novel antibacterial agents. Efforts to develop potent inhibitors of the enzyme have progressed on the basis of classical medicinal chemistry, combinatorial chemistry, and structural approaches, yet the validity of PDF as an antibacterial target hangs, in part, on the ability of inhibitors to selectively target this enzyme in favor of structurally related metallohydrolases. We have used (15)N NMR spectroscopy and isothermal titration calorimetry to investigate the high-affinity interaction of EcPDF with actinonin, a naturally occurring potent EcPDF inhibitor. Backbone amide chemical shifts, residual dipolar couplings, hydrogen-deuterium exchange, and (15)N relaxation reveal structural and dynamic effects of ligand binding in the immediate vicinity of the ligand-binding site as well as at remote sites. A comparison of the crystal structures of free and actinonin-bound EcPDF with the solution data suggests that most of the consequences of the ligand binding to the protein are lost or obscured during crystallization. The results of these studies improve our understanding of the thermodynamic global minimum and have important implications for structure-based drug design.

  7. Novel Formulations for Antimicrobial Peptides

    Directory of Open Access Journals (Sweden)

    Ana Maria Carmona-Ribeiro

    2014-10-01

    Full Text Available Peptides in general hold much promise as a major ingredient in novel supramolecular assemblies. They may become essential in vaccine design, antimicrobial chemotherapy, cancer immunotherapy, food preservation, organs transplants, design of novel materials for dentistry, formulations against diabetes and other important strategical applications. This review discusses how novel formulations may improve the therapeutic index of antimicrobial peptides by protecting their activity and improving their bioavailability. The diversity of novel formulations using lipids, liposomes, nanoparticles, polymers, micelles, etc., within the limits of nanotechnology may also provide novel applications going beyond antimicrobial chemotherapy.

  8. Structural and antigenic features of the synthetic SF23 peptide corresponding to the receptor binding fragment of diphtheria toxin.

    Science.gov (United States)

    Khrustaleva, Tatyana Aleksandrovna; Khrustalev, Vladislav Victorovich; Barkovsky, Eugene Victorovich; Kolodkina, Valentina Leonidovna; Astapov, Anatoly Archipovich

    2015-02-01

    The SF23 peptide corresponding to the receptor binding fragment of diphtheria toxin (residues 508-530) has been synthesized. This fragment forming a protruding beta hairpin has been chosen because it is the less mutable B-cell epitope. Affine chromatography and ELISA show that antibodies from the sera of persons infected by toxigenic Corynebacterium diphtheriae and those immunized by diphtheria toxoid are able to bind the synthetic SF23 peptide. There are antibodies recognizing the SF23 peptide in the serum of horses hyperimmunized with diphtheria toxoid. Analysis of circular dichroism spectra show formation of beta hairpin by the peptide. Taken together, the results showed that the structure of the less mutable epitope of C. diphtheriae toxin was reproduced by the short SF23 peptide. Since antibodies against that epitope should block its interactions with cellular receptor (heparin-binding epidermal growth factor), the SF23 peptide can be considered as a promising candidate for synthetic vaccine development. Fluorescence quenching studies showed the existence of chloride and phosphate binding sites on the SF23 molecule. Phosphate containing adjuvants (aluminum hydroxyphosphate or aluminum hydroxyphosphate sulfate) are recommended to increase the SF23 immunogenic properties. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Sequence-Dependent Structure/Function Relationships of Catalytic Peptide-Enabled Gold Nanoparticles Generated under Ambient Synthetic Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Bedford, Nicholas M.; Hughes, Zak E.; Tang, Zhenghua; Li, Yue; Briggs, Beverly D.; Ren, Yang; Swihart, Mark T.; Petkov, Valeri G.; Naik, Rajesh R.; Knecht, Mark R.; Walsh, Tiffany R.

    2016-01-20

    Peptide-enabled nanoparticle (NP) synthesis routes can create and/or assemble functional nanomaterials under environmentally friendly conditions, with properties dictated by complex interactions at the biotic/abiotic interface. Manipulation of this interface through sequence modification can provide the capability for material properties to be tailored to create enhanced materials for energy, catalysis, and sensing applications. Fully realizing the potential of these materials requires a comprehensive understanding of sequence-dependent structure/function relationships that is presently lacking. In this work, the atomic-scale structures of a series of peptide-capped Au NPs are determined using a combination of atomic pair distribution function analysis of high-energy X-ray diffraction data and advanced molecular dynamics (MD) simulations. The Au NPs produced with different peptide sequences exhibit varying degrees of catalytic activity for the exemplar reaction 4-nitrophenol reduction. The experimentally derived atomic-scale NP configurations reveal sequence-dependent differences in structural order at the NP surface. Replica exchange with solute-tempering MD simulations are then used to predict the morphology of the peptide overlayer on these Au NPs and identify factors determining the structure/catalytic properties relationship. We show that the amount of exposed Au surface, the underlying surface structural disorder, and the interaction strength of the peptide with the Au surface all influence catalytic performance. A simplified computational prediction of catalytic performance is developed that can potentially serve as a screening tool for future studies. Our approach provides a platform for broadening the analysis of catalytic peptide-enabled metallic NP systems, potentially allowing for the development of rational design rules for property enhancement.

  10. STUDY OF DOUBLE PROTONS MIGRATION MECHANISM IN SUPRAMOLECULAR STRUCTURES OF ACETIC ACID-WATER AND ACETIC ACID-AMMONIA BY AB INITIO METHOD

    Directory of Open Access Journals (Sweden)

    Karna Wijaya

    2010-06-01

    Full Text Available The theoretical study of double protons migration mechanism on acetic acid-water and acetic acid-ammonia associations has been carried out. The research covered determinations the reactant, transition state and product structures. To gain the goal, the research was conducted in three steps, i.e. (i designing the reactant, transition state and product models, (ii optimizing of structures, and (iii calculating of their uncorrected total energy and frequencies with ab initio methods (basis set 6-31G**. All calculations were performed using Hyperchem ver 5.0 for Windows and Gaussian 94W package program. The computational study result showed that the calculated structures were in good agreement with the hypothetical structures.   Keywords: double protons migration, acetic acid, water, ammonia, molecular mechanics and ab-initio

  11. Conjugation of a cell-penetrating peptide to parathyroid hormone affects its structure, potency, and transepithelial permeation

    DEFF Research Database (Denmark)

    Kristensen, Mie; de Groot, Anne Marit; Berthelsen, Jens

    2015-01-01

    to covalent conjugation was compared with regards to the transepithelial permeation. CPP-conjugated PTH(1-34) fusion peptides were successfully expressed in Escherichia coli and purified from inclusion bodies. No clear correlation between the degree of secondary structure of the CPP-conjugated PTH(1......Delivery of therapeutic peptides and proteins by the use of cell-penetrating peptides (CPPs) as carriers has been suggested as a feasible strategy. The aim of the present study was to investigate the effect of conjugating a series of well-known CPPs to the biologically active part of parathyroid...... hormone, i.e. PTH(1-34), and to evaluate the effect with regards to secondary structure, potency in Saos-2 cells, immunogenicity, safety as well as the transepithelial permeation across monolayers by using the Caco-2 cell culture model. Further, co-administration of CPP and PTH(1-34) as an alternative...

  12. Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach

    Energy Technology Data Exchange (ETDEWEB)

    Economou, Nicoleta J.; Zentner, Isaac J. [Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102 (United States); Lazo, Edwin; Jakoncic, Jean; Stojanoff, Vivian [Brookhaven National Laboratory, Upton, NY 11973 (United States); Weeks, Stephen D.; Grasty, Kimberly C.; Cocklin, Simon; Loll, Patrick J. [Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102 (United States)

    2013-04-01

    Using a carrier-protein strategy, the structure of teicoplanin bound to its bacterial cell-wall target has been determined. The structure reveals the molecular determinants of target recognition, flexibility in the antibiotic backbone and intrinsic radiation sensitivity of teicoplanin. Multidrug-resistant bacterial infections are commonly treated with glycopeptide antibiotics such as teicoplanin. This drug inhibits bacterial cell-wall biosynthesis by binding and sequestering a cell-wall precursor: a d-alanine-containing peptide. A carrier-protein strategy was used to crystallize the complex of teicoplanin and its target peptide by fusing the cell-wall peptide to either MBP or ubiquitin via native chemical ligation and subsequently crystallizing the protein–peptide–antibiotic complex. The 2.05 Å resolution MBP–peptide–teicoplanin structure shows that teicoplanin recognizes its ligand through a combination of five hydrogen bonds and multiple van der Waals interactions. Comparison of this teicoplanin structure with that of unliganded teicoplanin reveals a flexibility in the antibiotic peptide backbone that has significant implications for ligand recognition. Diffraction experiments revealed an X-ray-induced dechlorination of the sixth amino acid of the antibiotic; it is shown that teicoplanin is significantly more radiation-sensitive than other similar antibiotics and that ligand binding increases radiosensitivity. Insights derived from this new teicoplanin structure may contribute to the development of next-generation antibacterials designed to overcome bacterial resistance.

  13. Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach

    International Nuclear Information System (INIS)

    Economou, Nicoleta J.; Zentner, Isaac J.; Lazo, Edwin; Jakoncic, Jean; Stojanoff, Vivian; Weeks, Stephen D.; Grasty, Kimberly C.; Cocklin, Simon; Loll, Patrick J.

    2013-01-01

    Using a carrier-protein strategy, the structure of teicoplanin bound to its bacterial cell-wall target has been determined. The structure reveals the molecular determinants of target recognition, flexibility in the antibiotic backbone and intrinsic radiation sensitivity of teicoplanin. Multidrug-resistant bacterial infections are commonly treated with glycopeptide antibiotics such as teicoplanin. This drug inhibits bacterial cell-wall biosynthesis by binding and sequestering a cell-wall precursor: a d-alanine-containing peptide. A carrier-protein strategy was used to crystallize the complex of teicoplanin and its target peptide by fusing the cell-wall peptide to either MBP or ubiquitin via native chemical ligation and subsequently crystallizing the protein–peptide–antibiotic complex. The 2.05 Å resolution MBP–peptide–teicoplanin structure shows that teicoplanin recognizes its ligand through a combination of five hydrogen bonds and multiple van der Waals interactions. Comparison of this teicoplanin structure with that of unliganded teicoplanin reveals a flexibility in the antibiotic peptide backbone that has significant implications for ligand recognition. Diffraction experiments revealed an X-ray-induced dechlorination of the sixth amino acid of the antibiotic; it is shown that teicoplanin is significantly more radiation-sensitive than other similar antibiotics and that ligand binding increases radiosensitivity. Insights derived from this new teicoplanin structure may contribute to the development of next-generation antibacterials designed to overcome bacterial resistance

  14. Structural dynamic of a self-assembling peptide d-EAK16 made of only D-amino acids.

    Directory of Open Access Journals (Sweden)

    Zhongli Luo

    Full Text Available We here report systematic study of structural dynamics of a 16-residue self-assembling peptide d-EAK16 made of only D-amino acids. We compare these results with its chiral counterpart L-form, l-EAK16. Circular dichroism was used to follow the structural dynamics under various temperature and pH conditions. At 25 degrees C the d-EAK16 peptide displayed a typical beta-sheet spectrum. Upon increasing the temperature above 70 degrees C, there was a spectrum shift as the 218 nm valley widens toward 210 nm. Above 80 degrees C, the d-EAK16 peptide transformed into a typical alpha-helix CD spectrum without going through a detectable random-coil intermediate. When increasing the temperature from 4 degrees C to 110 degrees C then cooling back from 110 degrees C to 4 degrees C, there was a hysteresis: the secondary structure from beta-sheet to alpha-helix and then from alpha-helix to beta-sheet occurred. d-EAK16 formed an alpha-helical conformation at pH0.76 and pH12 but formed a beta-sheet at neutral pH. The effects of various pH conditions, ionic strength and denaturing agents were also noted. Since D-form peptides are resistant to natural enzyme degradation, such drastic structural changes may be exploited for fabricating molecular sensors to detect minute environmental changes. This provides insight into the behaviors of self-assembling peptides made of D-amino acids and points the way to designing new peptide materials for biomedical engineering and nanobiotechnology.

  15. Peptide Targeted by Human Antibodies Associated with HIV Vaccine-Associated Protection Assumes a Dynamic α-Helical Structure.

    Science.gov (United States)

    Aiyegbo, Mohammed S; Shmelkov, Evgeny; Dominguez, Lorenzo; Goger, Michael; Battacharya, Shibani; deCamp, Allan C; Gilbert, Peter B; Berman, Phillip W; Cardozo, Timothy

    2017-01-01

    The only evidence of vaccine-induced protection from HIV acquisition in humans was obtained in the RV144 HIV vaccine clinical trial. One immune correlate of risk in RV144 was observed to be higher titers of vaccine-induced antibodies (Abs) reacting with a 23-mer non-glycosylated peptide with the same amino acid sequence as a segment in the second variable (V2) loop of the MN strain of HIV. We used NMR to analyze the dynamic 3D structure of this peptide. Distance restraints between spatially proximate inter-residue protons were calculated from NOE cross peak intensities and used to constrain a thorough search of all possible conformations of the peptide. α-helical folding was strongly preferred by part of the peptide. A high-throughput structure prediction of this segment in all circulating HIV strains demonstrated that α-helical conformations are preferred by this segment almost universally across all subtypes. Notably, α-helical conformations of this segment of the V2 loop cluster cross-subtype-conserved amino acids on one face of the helix and the variable amino acid positions on the other in a semblance of an amphipathic α-helix. Accordingly, some Abs that protected against HIV in RV144 may have targeted a specific, conserved α-helical peptide epitope in the V2 loop of HIV's surface envelope glycoprotein.

  16. Synthesis, structure, and properties of a series of chiral tweezer-diamine complexes consisting of an achiral zinc(II) bisporphyrin host and chiral diamine guest: induction and rationalization of supramolecular chirality.

    Science.gov (United States)

    Brahma, Sanfaori; Ikbal, Sk Asif; Rath, Sankar Prasad

    2014-01-06

    We report here the synthesis, structure, and spectroscopic properties of a series of supramolecular chiral 1:1 tweezer-diamine complexes consisting of an achiral Zn(II) bisporphyrin (Zn2DPO) host and five different chiral diamine guests, namely, (R)-diaminopropane (DAP), (1S,2S)-diaminocyclohexane (CHDA), (S)-phenylpropane diamine (PPDA), (S)-phenyl ethylenediamine (PEDA), and (1R,2R)-diphenylethylene diamine (DPEA). The solid-state structures are preserved in solution, as reflected in their (1)H NMR spectra, which also revealed the remarkably large upfield shifts of the NH2 guest protons with the order Zn2DPO·DAP > Zn2DPO·CHDA > Zn2DPO·PPDA> Zn2DPO·PEDA ≫ Zn2DPO·DPEA, which happens to be the order of binding constants of the respective diamines with Zn2DPO. As the bulk of the substituent at the chiral center of the guest ligand increases, the Zn-Nax distance of the tweezer-diamine complex also increases, which eventually lowers the binding of the guest ligand toward the host. Also, the angle between the two porphyrin rings gradually increases with increasing bulk of the guest in order to accommodate the guest within the bisporphyrin cavity with minimal steric clash. The notably high amplitude bisignate CD signal response by Zn2DPO·DAP, Zn2DPO·CHDA, and Zn2DPO·PPDA can be ascribed to the complex's high stability and the formation of a unidirectional screw as observed in the X-ray structures of the complexes. A relatively lower value of CD amplitude shown by Zn2DPO·PEDA is due to the lower stability of the complex. The projection of the diamine binding sites of the chiral guest would make the two porphyrin macrocycles oriented in either a clockwise or anticlockwise direction in order to minimize host-guest steric clash. In sharp contrast, Zn2DPO·DPEA shows a very low amplitude bisignate CD signal due to the presence of both left- (dictated by the pre-existing chirality of (1R,2R)-DPEA) and right-handed screws (dictated by the steric differentiation at

  17. Basic amphipathic model peptides: Structural investigations in solution, studied by circular dichroism, fluorescence, analytical ultracentrifugation and molecular modelling

    Science.gov (United States)

    Mangavel, C.; Sy, D.; Reynaud, J. A.

    1999-05-01

    A twenty amino acid residue long amphipathic peptide made of ten leucine and ten lysine residues and four derivatives, in which a tryptophan, as a fluorescent probe, is substituted for a leucine, are studied. The peptides in water are mainly in an unordered conformation (~90%), and undergo a two state reversible transition upon heating, leading to a partially helical conformation (cold denaturation). Time resolved fluorescence results show that fluorescence decay for the four Trp containing peptides is best described by triple fluorescence decay kinetics. In TFE/water mixture, peptides adopt a single α-helix conformation but the Leu-Trp9 substitution leads to an effective helix destabilizing effect. In salted media, the peptides are fully helical and present a great tendency to self associate by bringing the hydrophobic faces of helices into close contact. This proceeds in non-cooperative multisteps leading to the formation of α helix aggregates with various degrees of complexation. Using modelling, the relative hydrophobic surface areas accessible to water molecules in n-mer structures are calculated and discussed. Nous avons étudié un peptide amphipathique composé de dix lysine et dix leucine, ainsi que quatre dérivés comportant un résidu tryptophane pour les études par fluorescence. Dans l'eau, les peptides ne sont pas structurés (~90%), et se structurent partiellement en hélice α par chauffage (dénaturation froide). Les mesures de déclin de fluorescence font apparaître une cinétique à trois temps de vie. Dans un mélange eau/TFE, les peptides adoptent une conformation en hélice α, mais la substitution Leu-Trp9 possède un effet déstabilisant. En mileu salin, les peptides sont totalement hélicoïdaux et ont tendance à s'agréger de façon à regrouper leur face hydrophobe. Ce processus se fait en plusieurs étapes avec des agrégats de taille variable. L'existence de tels agrégats est discutée sur la base de la modélisation mol

  18. Functional and structural characterization of a synthetic peptide representing the N-terminal domain of prokaryotic pyruvate dehydrogenase

    NARCIS (Netherlands)

    Hengeveld, A.F.; Mierlo, van C.P.M.; Hooven, van den H.W.; Visser, A.J.W.G.; Kok, de A.

    2002-01-01

    A synthetic peptide (Nterm-E1p) is used to characterize the structure and function of the N-terminal region (amino acid residues 4-45) of the pyruvate dehydrogenase component (E1p) from the pyruvate dehydrogenase multienzyme complex (PDHC) from Azotobacter vinelandii. Activity and binding studies

  19. Simulation of Major Histocompatibility Complex (MHC Structure and Peptide Loading into an MHC Binding Pocket with Teachers’Hands

    Directory of Open Access Journals (Sweden)

    Mojtaba Sankian

    2013-10-01

    Full Text Available Molecular understanding of three-dimensional (3D peptide: MHC models require both basic knowledge of computational modeling and skilled visual perception, which are not possessed by all students. The present model aims to simulate MHC molecular structure with the hands and make a profound impression on the students.

  20. "Supramolecular" assembly of gold nanorods end-terminated with polymer "pom-poms": effect of pom-pom structure on the association modes.

    Science.gov (United States)

    Nie, Zhihong; Fava, Daniele; Rubinstein, Michael; Kumacheva, Eugenia

    2008-03-19

    We report a predefined self-organization of gold nanorods (NRs) end-terminated with multiple polymer arms ("pom-poms") in higher-order structures. The assembly of polymer-tethered NRs was controlled by changing the structure of the polymer pom-poms. We show that the variation in the molecular weight of the polymer molecules and their relative location with respect to the long side of the NRs resulted in two competing association modes of the nanorods, that is, their side-by-side and end-to-end assembly, and produced bundles, chains, rings, and bundled chains of the NRs. The superposition of the two variables controlling the organization of NRs allowed us to create a map showing the variation in the longitudinal plasmonic bands of the NRs achieved by their self-assembly.

  1. Stabilization of reactive species by supramolecular encapsulation.

    Science.gov (United States)

    Galan, Albano; Ballester, Pablo

    2016-03-21

    Molecular containers have attracted the interest of supramolecular chemists since the early beginnings of the field. Cavitands' inner cavities were quickly exploited by Cram and Warmuth to construct covalent containers able to stabilize and assist the characterization of short-lived reactive species such as cyclobutadiene or o-benzyne. Since then, more complex molecular architectures have been prepared able to store and isolate a myriad of fleeting species (i.e. organometallic compounds, cationic species, radical initiators…). In this review we cover selected examples of the stabilization of reactive species by encapsulation in molecular containers from the first reports of covalent containers described by Cram et al. to the most recent examples of containers with self-assembled structure (metal coordination cages and hydrogen bonded capsules). Finally, we briefly review examples reported by Rebek et al. in which elusive reaction intermediates could be detected in the inner cavities of self-folding resorcin[4]arene cavitands by the formation of covalent host-guest complexes. The utilization of encapsulated reactive species in catalysis or synthesis is not covered.

  2. Structural analysis of peptides capable of binding to more than one Ia antigen

    DEFF Research Database (Denmark)

    Sette, A; Buus, S; Colon, S

    1989-01-01

    The Ia binding regions were analyzed for three unrelated peptide Ag (sperm whale myoglobin 106-118, influenza hemagglutinin 130-142, and lambda repressor protein 12-26) for which binding to more than one Ia molecule has previously been demonstrated. By determining the binding profile of three...... separate series of truncated synthetic peptides, it was found that in all three cases the different Ia reactivities mapped to largely overlapping regions of the peptides; although, for two of the peptides, the regions involved in binding the different Ia specificities were distinct. Moreover, subtle...... differences were found to dramatically influence some, but not other, Ia reactivities. Using a large panel of synthetic peptides it was found that a significant correlation exists between the capacity of peptides to interact with different alleles of the same molecule (i.e., IAd and IAk), but no correlation...

  3. Catalytic Features of the Botulinum Neurotoxin A Light Chain Revealed by High Resolution Structure of an Inhibitory Peptide Complex

    Energy Technology Data Exchange (ETDEWEB)

    Silvaggi,N.; Wilson, D.; Tzipori, S.; Allen, K.

    2008-01-01

    The Clostridium botulinum neurotoxin serotype A light chain (BoNT/A-LC) is a Zn(II)-dependent metalloprotease that blocks the release of acetylcholine at the neuromuscular junction by cleaving SNAP-25, one of the SNARE proteins required for exocytosis. Because of the potential for use of the toxin in bioterrorism and the increasingly widespread application of the toxin in the medical field, there is significant interest in the development of small-molecule inhibitors of the metalloprotease. Efforts to design such inhibitors have not benefited from knowledge of how peptides bind to the active site since the enzyme-peptide structures available previously either were not occupied in the vicinity of the catalytic Zn(II) ion or did not represent the product of SNAP-25 substrate cleavage. Herein we report the 1.4 Angstroms-resolution X-ray crystal structure of a complex between the BoNT/A-LC and the inhibitory peptide N-Ac-CRATKML, the first structure of the light chain with an inhibitory peptide bound at the catalytic Zn(II) ion. The peptide is bound with the Cys S? atom coordinating the metal ion. Surprisingly, the cysteine sulfur is oxidized to the sulfenic acid form. Given the unstable nature of this species in solution, is it likely that oxidation occurs on the enzyme. In addition to the peptide-bound structure, we report two structures of the unliganded light chain with and without the Zn(II) cofactor bound at 1.25 and 1.20 Angstroms resolution, respectively. The two structures are nearly identical, confirming that the Zn(II) ion plays a purely catalytic role. Additionally, the structure of the Zn(II)-bound uncomplexed enzyme allows identification of the catalytic water molecule and a second water molecule that occupies the same position as the peptidic oxygen in the tetrahedral intermediate. This observation suggests that the enzyme active site is prearranged to stabilize the tetrahedral intermediate of the protease reaction.

  4. Hemin and bile pigments are the secondary structure regulators of intrinsically disordered antimicrobial peptides.

    Science.gov (United States)

    Zsila, Ferenc; Juhász, Tünde; Bősze, Szilvia; Horváti, Kata; Beke-Somfai, Tamás

    2018-02-01

    The interaction of protoporphyrin compounds of human origin with the major bee venom component melittin (26 a.a., Z +6) and its hybrid derivative (CM15, 15 a.a., Z +6) were studied by a combination of various spectroscopic methods. Throughout a two-state, concentration-dependent process, hemin and its metabolites (biliverdin, bilirubin, bilirubin ditaurate) increase the parallel β-sheet content of the natively unfolded melittin, suggesting the oligomerization of the peptide chains. In contrast, α-helix promoting effect was observed with the also disordered but more cationic CM15. According to fluorescence quenching experiments, the sole Trp residue of melittin is the key player during the binding, in the vicinity of which the first pigment molecule is accommodated presumably making indole-porphyrin π-π stacking interaction. As circular dichroism titration data suggest, cooperative association of additional ligands subsequently occurs, resulting in multimeric complexes with an apparent dissociation constant ranged from 20 to 65 μM. Spectroscopic measurements conducted with the bilirubin catabolite urobilin and stercobilin refer to the requirement of intact dipyrrinone moieties for inducing secondary structure transformations. The binding topography of porphyrin rings on a model parallel β-sheet motif was evaluated by absorption spectroscopy and computational modeling showing a slipped-cofacial binding mode responsible for the red shift and hypochromism of the Soret band. Our results may aid to recognize porphyrin-responsive binding motifs of biologically relevant, intrinsically disordered peptides and proteins, where transient conformations play a vital role in their functions. © 2017 Wiley Periodicals, Inc.

  5. A bioartificial environment for kidney epithelial cells based on a supramolecular polymer basement membrane mimic and an organotypical culture system.

    Science.gov (United States)

    Mollet, Björne B; Bogaerts, Iven L J; van Almen, Geert C; Dankers, Patricia Y W

    2017-06-01

    Renal applications in healthcare, such as renal replacement therapies and nephrotoxicity tests, could potentially benefit from bioartificial kidney membranes with fully differentiated and functional human tubular epithelial cells. A replacement of the natural environment of these cells is required to maintain and study cell functionality cell differentiation in vitro. Our approach was based on synthetic supramolecular biomaterials to mimic the natural basement membrane (BM) on which these cells grow and a bioreactor to provide the desired organotypical culture parameters. The BM mimics were constructed from ureidopyrimidinone (UPy)-functionalized polymer and bioactive peptides by electrospinning. The resultant membranes were shown to have a hierarchical fibrous BM-like structure consisting of self-assembled nanofibres within the electrospun microfibres. Human kidney-2 (HK-2) epithelial cells were cultured on the BM mimics under organotypical conditions in a custom-built bioreactor. The bioreactor facilitated in situ monitoring and functionality testing of the cultures. Cell viability and the integrity of the epithelial cell barrier were demonstrated inside the bioreactor by microscopy and transmembrane leakage of fluorescently labelled inulin, respectively. Furthermore, HK-2 cells maintained a polarized cell layer and showed modulation of both gene expression of membrane transporter proteins and metabolic activity of brush border enzymes when subjected to a continuous flow of culture medium inside the new bioreactor for 21 days. These results demonstrated that both the culture and study of renal epithelial cells was facilitated by the bioartificial in vitro environment that is formed by synthetic supramolecular BM mimics in our custom-built bioreactor. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  6. Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence

    Directory of Open Access Journals (Sweden)

    Leitner Dietmar

    2005-04-01

    Full Text Available Abstract Background A reliable prediction of the Xaa-Pro peptide bond conformation would be a useful tool for many protein structure calculation methods. We have analyzed the Protein Data Bank and show that the combined use of sequential and structural information has a predictive value for the assessment of the cis versus trans peptide bond conformation of Xaa-Pro within proteins. For the analysis of the data sets different statistical methods such as the calculation of the Chou-Fasman parameters and occurrence matrices were used. Furthermore we analyzed the relationship between the relative solvent accessibility and the relative occurrence of prolines in the cis and in the trans conformation. Results One of the main results of the statistical investigations is the ranking of the secondary structure and sequence information with respect to the prediction of the Xaa-Pro peptide bond conformation. We observed a significant impact of secondary structure information on the occurrence of the Xaa-Pro peptide bond conformation, while the sequence information of amino acids neighboring proline is of little predictive value for the conformation of this bond. Conclusion In this work, we present an extensive analysis of the occurrence of the cis and trans proline conformation in proteins. Based on the data set, we derived patterns and rules for a possible prediction of the proline conformation. Upon adoption of the Chou-Fasman parameters, we are able to derive statistically relevant correlations between the secondary structure of amino acid fragments and the Xaa-Pro peptide bond conformation.

  7. NMR structure of a biologically active peptide containing the RNA-binding domain of human immunodeficiency virus type 1 Tat.

    Science.gov (United States)

    Mujeeb, A; Bishop, K; Peterlin, B M; Turck, C; Parslow, T G; James, T L

    1994-01-01

    The Tat protein of human immunodeficiency virus type 1 enhances transcription by binding to a specific RNA element on nascent viral transcripts. Binding is mediated by a 10-amino acid basic domain that is rich in arginines and lysines. Here we report the three-dimensional peptide backbone structure of a biologically active 25-mer peptide that contains the human immunodeficiency virus type 1 Tat basic domain linked to the core regulatory domain of another lentiviral Tat--i.e., that from equine infectious anemia virus. Circular dichroism and two-dimensional proton NMR studies of this hybrid peptide indicate that the Tat basic domain forms a stable alpha-helix, whereas the adjacent regulatory sequence is mostly in extended form. These findings suggest that the tendency to form stable alpha-helices may be a common property of arginine- and lysine-rich RNA-binding domains. Images PMID:8058789

  8. Simulations of the pore structures for a M2G1yR derived channel forming peptide in membrane

    Science.gov (United States)

    Al-Rawi, Ahlam N.; Al-Rawi, Asma; Chen, Jianhan; Herrera, Alvaro; Tomich, John; Rahman, Talat S.

    2008-03-01

    In an effort to develop a peptide-based compound suitable for clinical use as a channel replacement therapeutic for treating channelopathies such as cystic fibrosis, we present a reductionist model that appears to capture many of the biophysical properties of an intact ion channel using short channel-forming peptides. We have developed two anion selective channel-forming peptides with near native and altered properties from the peptides derived from the glycine receptor: NK4-M2GlyR-p22 WT (KKKKPAR-VGLGITTVLTMTTQS) and NK4-M2GlyR-p22 S22W (KKKKPARVGLGITTVLTMTTQW), respectively. Starting with the two structures determined by solution multidimensional NMR (800 MHz) in SDS, we used CHARMM and NAMD to perform molecular dynamics simulations on the monomers. Using the existing experimental data, we then built an initial 5- helix assembly by altering the tilted angle, rotational angle and pore radius. We investigated the impact of the single mutation at position 22 on the structure and dynamics of the pore formed in a membrane build in a hydrated POPC lipid bilayer. Probable structures for both assemblies are presented.

  9. Structure-activity study of macropin, a novel antimicrobial peptide from the venom of solitary bee Macropis fulvipes (Hymenoptera: Melittidae).

    Science.gov (United States)

    Monincová, Lenka; Veverka, Václav; Slaninová, Jiřina; Buděšínský, Miloš; Fučík, Vladimír; Bednárová, Lucie; Straka, Jakub; Ceřovský, Václav

    2014-06-01

    A novel antimicrobial peptide, designated macropin (MAC-1) with sequence Gly-Phe-Gly-Met-Ala-Leu-Lys-Leu-Leu-Lys-Lys-Val-Leu-NH2 , was isolated from the venom of the solitary bee Macropis fulvipes. MAC-1 exhibited antimicrobial activity against both Gram-positive and Gram-negative bacteria, antifungal activity, and moderate hemolytic activity against human red blood cells. A series of macropin analogs were prepared to further evaluate the effect of structural alterations on antimicrobial and hemolytic activities and stability in human serum. The antimicrobial activities of several analogs against pathogenic Pseudomonas aeruginosa were significantly increased while their toxicity against human red blood cells was decreased. The activity enhancement is related to the introduction of either l- or d-lysine in selected positions. Furthermore, all-d analog and analogs with d-amino acid residues introduced at the N-terminal part of the peptide chain exhibited better serum stability than did natural macropin. Data obtained by CD spectroscopy suggest a propensity of the peptide to adopt an amphipathic α-helical secondary structure in the presence of trifluoroethanol or membrane-mimicking sodium dodecyl sulfate. In addition, the study elucidates the structure-activity relationship for the effect of d-amino acid substitutions in MAC-1 using NMR spectroscopy. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.

  10. Insights into MHC class I peptide loading from the structure of the Tapasin-ERp57 thiol oxidoreductase heterodimer

    Energy Technology Data Exchange (ETDEWEB)

    Dong, G.; Wearsch, P.A.; Peaper, D.R.; Cresswell, P.; Reinisch, K.M.; (Yale-MED)

    2009-03-02

    Tapasin is a glycoprotein critical for loading major histocompatibility complex (MHC) class I molecules with high-affinity peptides. It functions within the multimeric peptide-loading complex (PLC) as a disulfide-linked, stable heterodimer with the thiol oxidoreductase ERp57, and this covalent interaction is required to support optimal PLC activity. Here, we present the 2.6 {angstrom} resolution structure of the tapasin-ERp57 core of the PLC. The structure revealed that tapasin interacts with both ERp57 catalytic domains, accounting for the stability of the heterodimer, and provided an example of a protein disulfide isomerase family member interacting with substrate. Mutational analysis identified a conserved surface on tapasin that interacted with MHC class I molecules and was critical for peptide loading and editing functions of the tapasin-ERp57 heterodimer. By combining the tapasin-ERp57 structure with those of other defined PLC components, we present a molecular model that illuminates the processes involved in MHC class I peptide loading.

  11. Supramolecular [60]fullerene liquid crystals formed by self-organized two-dimensional crystals.

    Science.gov (United States)

    Zhang, Xiaoyan; Hsu, Chih-Hao; Ren, Xiangkui; Gu, Yan; Song, Bo; Sun, Hao-Jan; Yang, Shuang; Chen, Erqiang; Tu, Yingfeng; Li, Xiaohong; Yang, Xiaoming; Li, Yaowen; Zhu, Xiulin

    2015-01-02

    Fullerene-based liquid crystalline materials have both the excellent optical and electrical properties of fullerene and the self-organization and external-field-responsive properties of liquid crystals (LCs). Herein, we demonstrate a new family of thermotropic [60]fullerene supramolecular LCs with hierarchical structures. The [60]fullerene dyads undergo self-organization driven by π-π interactions to form triple-layer two-dimensional (2D) fullerene crystals sandwiched between layers of alkyl chains. The lamellar packing of 2D crystals gives rise to the formation of supramolecular LCs. This design strategy should be applicable to other molecules and lead to an enlarged family of 2D crystals and supramolecular liquid crystals. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Seeded on-surface supramolecular growth for large area conductive donor-acceptor assembly.

    Science.gov (United States)

    Goudappagouda; Chithiravel, Sundaresan; Krishnamoorthy, Kothandam; Gosavi, Suresh W; Babu, Sukumaran Santhosh

    2015-07-04

    Charge transport features of organic semiconductor assemblies are of paramount importance. However, large-area extended supramolecular structures of donor-acceptor combinations with controlled self-assembly pathways are hardly accessible. In this context, as a representative example, seeded on-surface supramolecular growth of tetrathiafulvalene and tetracyano-p-quinodimethane (TTF-TCNQ) using active termini of solution-formed sheaves has been introduced to form an extended assembly. We demonstrate for the first time, the creation of a large-area donor-acceptor assembly on the surface, which is practically very tedious, using a seeded, evaporation-assisted growth process. The excellent molecular ordering in this assembly is substantiated by its good electrical conductivity (~10⁻² S cm⁻¹). The on-surface assembly via both internally formed and externally added sheaf-like seeds open new pathways in supramolecular chemistry and device applications.

  13. TOPICAL REVIEW: Metallo-supramolecular modules as a paradigm for materials science

    Directory of Open Access Journals (Sweden)

    Dirk G Kurth

    2008-01-01

    Full Text Available Metal ion coordination in discrete or extended metallo-supramolecular assemblies offers ample opportunity to fabricate and study devices and materials that are equally important for fundamental research and new technologies. Metal ions embedded in a specific ligand field offer diverse thermodynamic, kinetic, chemical, physical and structural properties that make these systems promising candidates for active components in functional materials. A key challenge is to improve and develop methodologies for placing these active modules in suitable device architectures, such as thin films or mesophases. This review highlights recent developments in extended, polymeric metallo-supramolecular systems and discrete polyoxometalates with an emphasis on materials science.

  14. Preface: special topic on supramolecular self-assembly at surfaces.

    Science.gov (United States)

    Bartels, Ludwig; Ernst, Karl-Heinz; Gao, Hong-Jun; Thiel, Patricia A

    2015-03-14

    Supramolecular self-assembly at surfaces is one of the most exciting and active fields in Surface Science today. Applications can take advantage of two key properties: (i) versatile pattern formation over a broad length scale and (ii) tunability of electronic structure and transport properties, as well as frontier orbital alignment. It provides a new frontier for Chemical Physics as it uniquely combines the versatility of Organic Synthesis and the Physics of Interfaces. The Journal of Chemical Physics is pleased to publish this Special Topic Issue, showcasing recent advances and new directions.

  15. Protein and Peptide Gas-phase Structure Investigation Using Collision Cross Section Measurements and Hydrogen Deuterium Exchange

    Science.gov (United States)

    Khakinejad, Mahdiar

    Protein and peptide gas-phase structure analysis provides the opportunity to study these species outside of their explicit environment where the interaction network with surrounding molecules makes the analysis difficult [1]. Although gas-phase structure analysis offers a unique opportunity to study the intrinsic behavior of these biomolecules [2-4], proteins and peptides exhibit very low vapor pressures [2]. Peptide and protein ions can be rendered in the gas-phase using electrospray ionization (ESI) [5]. There is a growing body of literature that shows proteins and peptides can maintain solution structures during the process of ESI and these structures can persist for a few hundred milliseconds [6-9]. Techniques for monitoring gas-phase protein and peptide ion structures are categorized as physical probes and chemical probes. Collision cross section (CCS) measurement, being a physical probe, is a powerful method to investigate gas-phase structure size [3, 7, 10-15]; however, CCS values alone do not establish a one to one relation with structure(i.e., the CCS value is an orientationally averaged value [15-18]. Here we propose the utility of gas-phase hydrogen deuterium exchange (HDX) as a second criterion of structure elucidation. The proposed approach incudes extensive MD simulations to sample biomolecular ion conformation space with the production of numerous, random in-silico structures. Subsequently a CCS can be calculated for these structures and theoretical CCS values are compared with experimental values to produce a pool of candidate structures. Utilizing a chemical reaction model based on the gas-phase HDX mechanism, the HDX kinetics behavior of these candidate structures are predicted and compared to experimental results to nominate the best in-silico structures which match (chemically and physically) with experimental observations. For the predictive approach to succeed, an extensive technique and method development is essential. To combine CCS

  16. Probing the outer mouth structure of the HERG channel with peptide toxin footprinting and molecular modeling.

    Science.gov (United States)

    Tseng, Gea-Ny; Sonawane, Kailas D; Korolkova, Yuliya V; Zhang, Mei; Liu, Jie; Grishin, Eugene V; Guy, H Robert

    2007-05-15

    Previous studies have shown that the unusually long S5-P linker lining human ether a-go-go related gene's (hERG's) outer vestibule is critical for its channel function: point mutations at high-impact positions here can interfere with the inactivation process and, in many cases, also reduce the pore's K+ selectivity. Because no data are available on the equivalent region in the available K channel crystal structures to allow for homology modeling, we used alternative approaches to model its three-dimensional structure. The first part of this article describes mutant cycle analysis used to identify residues on hERG's outer vestibule that interact with specific residues on the interaction surface of BeKm-1, a peptide toxin with known NMR structure and a high binding affinity to hERG. The second part describes molecular modeling of hERG's pore domain. The transmembrane region was modeled after the crystal structure of KvAP pore domain. The S5-P linker was docked to the transmembrane region based on data from previous NMR and mutagenesis experiments, as well as a set of modeling criteria. The models were further restrained by contact points between hERG's outer vestibule and the bound BeKm-1 toxin molecule deduced from the mutant cycle analysis. Based on these analyses, we propose a working model for the open conformation of the outer vestibule of the hERG channel, in which the S5-P linkers interact with the pore loops to influence ion flux through the pore.

  17. Effects of the KIF2C neck peptide on microtubules: lateral disintegration of microtubules and β-structure formation.

    Science.gov (United States)

    Shimizu, Youské; Shimizu, Takashi; Nara, Masayuki; Kikumoto, Mahito; Kojima, Hiroaki; Morii, Hisayuki

    2013-04-01

    Members of the kinesin-13 sub-family, including KIF2C, depolymerize microtubules. The positive charge-rich 'neck' region extending from the N-terminus of the catalytic head is considered to be important in the depolymerization activity. Chemically synthesized peptides, covering the basic region (A182-E200), induced a sigmoidal increase in the turbidity of a microtubule suspension. The increase was suppressed by salt addition or by reduction of basicity by amino acid substitutions. Electron microscopic observations revealed ring structures surrounding the microtubules at high peptide concentrations. Using the peptide A182-D218, we also detected free thin straight filaments, probably protofilaments disintegrated from microtubules. Therefore, the neck region, even without the catalytic head domain, may induce lateral disintegration of microtubules. With microtubules lacking anion-rich C-termini as a result of subtilisin treatment, addition of the peptide induced only a moderate increase in turbidity, and rings and protofilaments were rarely detected, while aggregations, also thought to be caused by lateral disintegration, were often observed in electron micrographs. Thus, the C-termini are not crucial for the action of the peptides in lateral disintegration but contribute to structural stabilization of the protofilaments. Previous structural studies indicated that the neck region of KIF2C is flexible, but our IR analysis suggests that the cation-rich region (K190-A204) forms β-structure in the presence of microtubules, which may be of significance with regard to the action of the neck region. Therefore, the neck region of KIF2C is sufficient to cause disintegration of microtubules into protofilaments, and this may contribute to the ability of KIF2C to cause depolymerization of microtubules. © 2013 The Authors Journal compilation © 2013 FEBS.

  18. Simulations of the Pore Structures for a M2GlyR Derived Channel Forming Peptide in Different Membrane Environments

    Science.gov (United States)

    Al-Rawi, A.; Herrera, A.; Tomich, J.; Rahman, T.

    2007-03-01

    As part of an effort to develop a peptide-based compound suitable for clinical use as a channel replacement therapeutic for treating channelopathies such as cystic fibrosis, we present a reductionist model that appears to grasp the characteristics of ion channeling peptides. In particular we present the observed changes in the functional characteristics of NK4-M2GlyR p22 (KKKKPARVGLGITTVLTMTTQS), a M2 GlyR derived channel forming peptide. Starting with a structure determined by multidimensional NMR (800 MHz) in SDS, a potential from CHARMM force-field was used to relax the structure of NK4-M2GlyR p22. Following the relaxation, numerous pore structures were generated for the symmetric five-helix assembly with geometries varying from cylindrical to conical. As it is difficult a priori to assign accurately the orientation of the hydrophilic portion of M2GlyR derived amphipath towards the inside of the pore, we tilted and rotated the helical structure by five different angles about the backbone axis before forming the pore. Energy minimization of the channel was performed in vacuum, in phosphotidylcholine (POPC) membrane, and 60% POPC 30% phosphotidylethanolamine (POPE) in order to determine the effect of the environment surrounding on the structure on its energy minimization. We will present the various pore assemblies, in the different membrane environments, used to predict the most probably membrane bound structure.

  19. Influence of hydrophobic Teflon particles on the structure of amyloid beta-peptide

    NARCIS (Netherlands)

    Giacomelli, C.E.; Norde, W.

    2003-01-01

    The amyloid beta-protein (Abeta) constitutes the major peptide component of the amyloid plaque deposits of Alzheimer's disease in humans. The Abeta changes from a nonpathogenic to a pathogenic conformation resulting in self-aggregation and deposition of the peptide. It has been established that

  20. Structural study of a novel antimicrobial peptide isolated from the venom of bee Anthophora plumipes

    Czech Academy of Sciences Publication Activity Database

    Čujová, Sabína; Veverka, Václav; Buděšínský, Miloš; Bednárová, Lucie; Čeřovský, Václav

    2014-01-01

    Roč. 20, Suppl S1 (2014), S263-S264 ISSN 1075-2617. [European Peptide Symposium /33./. 31.08.2014-05.09.2014, Sofia] Institutional support: RVO:61388963 Keywords : antimicrobial peptides * membranes * CD-spectroscopy * NMR spectroscopy Subject RIV: CC - Organic Chemistry

  1. Comparative structural studies of potent neuroprotective peptides of the Humanin family

    Czech Academy of Sciences Publication Activity Database

    Benaki, D.; Zikos, C.; Evangelou, A.; Slaninová, Jiřina; Vlassi, M.; Livaniou, E.; Mikros, E.; Pelecanou, M.

    2008-01-01

    Roč. 14, č. 8 (2008), s. 108-108 ISSN 1075-2617. [European Peptide Symposium /30./. 31.08.2008-05.09.2008, Helsinki] Institutional research plan: CEZ:AV0Z40550506 Keywords : neuroprotective peptides * analogues of humanin e * synthesis * activity Subject RIV: CC - Organic Chemistry

  2. The presence of food-derived collagen peptides in human body-structure and biological activity.

    Science.gov (United States)

    Sato, Kenji

    2017-12-13

    It has been demonstrated that the ingestion of some protein hydrolysates exerts health-promoting effects. For understanding the underlying mechanisms responsible for these effects, the identification of bioactive peptides in the target organ is crucial. For this purpose, in vitro activity-guided fractionation for peptides in the protein hydrolysate has been performed. However, the peptides in the hydrolysate may be further degraded during digestion. The concentration of the active peptides, which were identified by in vitro activity-guided fractionation, in human blood is frequently very low (nanomolar levels). In contrast, micromolar levels of food-derived collagen peptides are present in human blood. Pro-Hyp, one of the major food-derived collagen peptides, enhances the growth of fibroblasts and synthesis of hyaluronic acid. These observations partially explain the beneficial effects of collagen hydrolysate ingestion on the enhancement of wound healing and improvement in the skin condition. The recent advancement involving liquid chromatography and mass spectrometry coupled with a pre-column derivatization technique has enabled the identification of food-derived peptides at nanomolar levels in the body post-ingestion of protein hydrolysates. Thus, this technique can be used for the identification of bioactive food-derived peptides in the body.

  3. Supramolecular self-assembly of a coumarine-based acylthiourea synthon directed by π-stacking interactions: Crystal structure and Hirshfeld surface analysis

    Science.gov (United States)

    Saeed, Aamer; Ashraf, Saba; Flörke, Ulrich; Delgado Espinoza, Zuly Yuliana; Erben, Mauricio F.; Pérez, Hiram

    2016-05-01

    The structure of 1-(2-oxo-2H-chromene-3-carbonyl)-3-(2-methoxy-phenyl)thiourea (1) has been determined by single-crystal X-ray crystallography. This compound crystallizes in the monoclinic space group P21/c with a = 7.455 (2) Å, b = 12.744 (3) Å, c = 16.892 (4) Å, β = 90.203 (6)° and Z = 4. Both, the coumarin and the phenyl rings are nearly coplanar with the central 1-acylthiourea group, with the Cdbnd O and Cdbnd S bonds adopting an opposite orientation. Intramolecular N-H···O, C-H···O, and C-H···S hydrogen bonds are favored by the planar conformation. The molecules are packed through C-H···O, C-H···S and C-H···C hydrogen bonds, and two π···π interactions with offset arrangement. Inter-centroid distance of 3.490 (2) Å, slip angles of 18.5 and 20.9°, and vertical displacements of 1.10 and 1.24 Å are the stacking parameters corresponding to the stronger π···π interaction. Hirshfeld surface analysis was performed for visualizing, exploring and quantifying intermolecular interactions in the crystal lattice of compound 1, and compared with two closely related species. Shape index and Curvedness surfaces indicated π-stacking with different features in opposed sides of the molecule. Fingerprint plot showed C···C contacts with similar contributions to the crystal packing in comparison with those associated to hydrogen bonds. Enrichment ratios for H···H, O···H, S···H and C···C contacts revealed a high propensity to form in the crystal.

  4. DFT/TD-semiempirical study on the structural and electronic properties and absorption spectra of supramolecular fullerene-porphyrine-metalloporphyrine triads based dye-sensitized solar cells

    Science.gov (United States)

    Rezvani, M.; Darvish Ganji, M.; Jameh-Bozorghi, S.; Niazi, A.

    2018-04-01

    In the present work density functional theory (DFT) and time-dependent semiempirical ZNIDO/S (TD-ZNIDO/S) methods have been used to investigate the ground state geometries, electronic structures and excited state properties of triad systems. The influences of the type of metal in the porphyrin ring, change in bridge position and porphyrine-ZnP duplicate on the energies of frontier molecular orbital and UV-Vis spectra has been studied. Geometry optimization, the energy levels and electron density of the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO), chemical hardness (η), electrophilicity index (ω), electron accepting power (ω+) were calculated using ZINDO/S method to predict which molecule is the most efficient with a great capability to be used as a triad molecule in solar industry. Moreover the light harvesting efficiency (LHE) was calculated by means of the oscillator strengths which are obtained by TD-ZINDO/S calculation. Theoretical studies of the electronic spectra by ZINDO/S method were helpful in interpreting the observed electronic transitions. This aspect was systematically explored in a series of C60-Porphyrine-Metalloporphyrine (C60-P-Mp) triad system with M being Fe, Co, Ni, Ti, and Zn. Generally, transition metal coordination compounds are used as effective sensitizers, due to their intense charge-transfer absorption over the whole visible range and highly efficient metal-to-ligand charge transfer. We aim to optimize the performance of the title solar cells by altering the frontier orbital energy gaps. The results reveal that cell efficiency can be enhanced by metal functionalization of the free base porphyrin. Ti-porphyrin was found to be the most efficient dye sensitizer for dye sensitized solar cells (DSSCs) based on C60-P-Mptriad system due to C60-Por-TiP complex has lower chemical hardness, gap energy and chemical potential as well as higher electron accepting power among other complexes. In

  5. Solution structure of the first SH3 domain of human vinexin and its interaction with vinculin peptides

    International Nuclear Information System (INIS)

    Zhang, Jiahai; Li, Xiang; Yao, Bo; Shen, Weiqun; Sun, Hongbin; Xu, Chao; Wu, Jihui; Shi, Yunyu

    2007-01-01

    Solution structure of the first Src homology (SH) 3 domain of human vinexin (V S H3 1 ) was determined using nuclear magnetic resonance (NMR) method and revealed that it was a canonical SH3 domain, which has a typical β-β-β-β-α-β fold. Using chemical shift perturbation and surface plasmon resonance experiments, we studied the binding properties of the SH3 domain with two different peptides from vinculin hinge regions: P856 and P868. The observations illustrated slightly different affinities of the two peptides binding to V S H3 1 . The interaction between P868 and V S H3 1 belonged to intermediate exchange with a modest binding affinity, while the interaction between P856 and V S H3 1 had a low binding affinity. The structure and ligand-binding interface of V S H3 1 provide a structural basis for the further functional study of this important molecule

  6. Exploring biological effects of MoS{sub 2} nanosheets on native structures of α-helical peptides

    Energy Technology Data Exchange (ETDEWEB)

    Gu, Zonglin; Li, Weifeng, E-mail: wfli@suda.edu.cn, E-mail: ruhong@us.ibm.com [School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123 (China); Hong, Linbi [Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Zhou, Ruhong, E-mail: wfli@suda.edu.cn, E-mail: ruhong@us.ibm.com [School for Radiological and Interdisciplinary Sciences (RAD-X) and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123 (China); Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Department of Chemistry, Columbia University, New York, New York 10027 (United States)

    2016-05-07

    Recent reports of mono- and few-layer molybdenum disulfide (MoS{sub 2}), a representative transition metal dichacogenide (TMD), as antibacterial and anticancer agents have shed light on their potential in biomedical applications. To better facilitate these promising applications, one needs to understand the biological effects of these TMDs as well, such as their potential adverse effects on protein structure and function. Here, we sought to understand the interaction of MoS{sub 2} nanosheets with peptides using molecular dynamics simulations and a simple model polyalanine with various lengths (PA{sub n}, n = 10, 20, 30, and 40; mainly α − helices). Our results demonstrated that MoS{sub 2} monolayer has an exceptional capability to bind all peptides in a fast and strong manner. The strong attraction from the MoS{sub 2} nanosheet is more than enough to compensate the energy needed to unfold the peptide, regardless of the length, which induces drastic disruptions to the intra-peptide hydrogen bonds and subsequent secondary structures of α − helices. This universal phenomenon may point to the potential nanotoxicity of MoS{sub 2} when used in biological systems. Moreover, these results aligned well with previous findings on the potential cytotoxicity of TMD nanomaterials.

  7. Exploring biological effects of MoS2 nanosheets on native structures of α-helical peptides

    International Nuclear Information System (INIS)

    Gu, Zonglin; Li, Weifeng; Hong, Linbi; Zhou, Ruhong

    2016-01-01

    Recent reports of mono- and few-layer molybdenum disulfide (MoS 2 ), a representative transition metal dichacogenide (TMD), as antibacterial and anticancer agents have shed light on their potential in biomedical applications. To better facilitate these promising applications, one needs to understand the biological effects of these TMDs as well, such as their potential adverse effects on protein structure and function. Here, we sought to understand the interaction of MoS 2 nanosheets with peptides using molecular dynamics simulations and a simple model polyalanine with various lengths (PA n , n = 10, 20, 30, and 40; mainly α − helices). Our results demonstrated that MoS 2 monolayer has an exceptional capability to bind all peptides in a fast and strong manner. The strong attraction from the MoS 2 nanosheet is more than enough to compensate the energy needed to unfold the peptide, regardless of the length, which induces drastic disruptions to the intra-peptide hydrogen bonds and subsequent secondary structures of α − helices. This universal phenomenon may point to the potential nanotoxicity of MoS 2 when used in biological systems. Moreover, these results aligned well with previous findings on the potential cytotoxicity of TMD nanomaterials.

  8. Oligonuclear 3d-4f complexes as tectons in designing supramolecular solid-state architectures: impact of the nature of linkers on the structural diversity.

    Science.gov (United States)

    Gheorghe, Ruxandra; Cucos, Paula; Andruh, Marius; Costes, Jean-Pierre; Donnadieu, Bruno; Shova, Sergiu

    2005-12-16

    Heteronuclear cationic complexes, [LCuLn]3+ and [(LCu)2Ln]3+, were employed as nodes in designing high-nuclearity complexes and coordination polymers with a rich variety of network topologies (L is the dianion of the Schiff base resulting from the 2:1 condensation of 3-methoxysalycilaldehyde with 1,3-propanediamine). Two families of linkers have been chosen: the first consists of exo-dentate ligands bearing nitrogen-donor atoms (bipyridine (bipy), dicyanamido (dca)), whereas the second consists of exo-dentate ligands with oxygen-donor atoms (anions derived from the acetylenedicarboxylic (H2acdca), fumaric (H2fum), trimesic (H3trim), and oxalic (H2ox) acids). The ligands belonging to the first family prefer copper(II) ions, whereas the ligands from the second family interact preferentially with oxophilic rare-earth cations. The following complexes have been obtained and crystallographically characterized: [LCu(II)(OH2)Gd(III)(NO3)3] (1), [{LCu(II)Gd(III)(NO3)3}2(mu-4,4'-bipy)] (2), 1infinity[LCu(II)Gd(III)(acdca)(1.5)(H2O)2].13H2O (3), 2infinity[LCu(II)Gd(III)(fum)(1.5)(H2O)2].4H2O.C2H5OH (4), 1infinity[LCu(II)Sm(III)(H2O)(Hfum)(fum)] (5), 1infinity[LCu(II)Er(III)(H2O)2(fum)]NO3.3H2O (6), 2infinity[LCu(II)Sm(III)(fum)(1.5)(H2O)2].4H2O.C2H5OH (7), [{(LCu(II))2Sm(III)}2fum2](OH)2 (8), 1infinity[LCu(II)Gd(III)(trim)(H2O)2].H2O (9), 2infinity[{(LCu(II))2Pr(III)}(C2O4)(0.5)(dca)]dca.2H2O (10), [LCu(II)Gd(III)(ox)(H2O)3][Cr(III)(2,2'-bipy)(ox)2].9H2O (11), and [LCuGd(H2O)4{Cr(CN)6}].3H2O (12). Compound 1 is representative of the whole family of binuclear Cu(II)-Ln(III) complexes which have been used as precursors in constructing heteropolymetallic complexes. The rich variety of the resulting structures is due to several factors: 1) the nature of the donor atoms of the linkers, 2) the preference of the copper(II) ion for nitrogen atoms, 3) the oxophilicity of the lanthanides, 4) the degree of deprotonation of the polycarboxylic acids, 5) the various connectivity modes

  9. Structural and Functional Elucidation of Peptide Ts11 Shows Evidence of a Novel Subfamily of Scorpion Venom Toxins

    Science.gov (United States)

    Cremonez, Caroline M.; Maiti, Mohitosh; Peigneur, Steve; Cassoli, Juliana Silva; Dutra, Alexandre A. A.; Waelkens, Etienne; Lescrinier, Eveline; Herdewijn, Piet; de Lima, Maria Elena; Pimenta, Adriano M. C.; Arantes, Eliane C.; Tytgat, Jan

    2016-01-01

    To date, several families of peptide toxins specifically interacting with ion channels in scorpion venom have been described. One of these families comprise peptide toxins (called KTxs), known to modulate potassium channels. Thus far, 202 KTxs have been reported, belonging to several subfamilies of KTxs (called α, β, γ, κ, δ, and λ-KTxs). Here we report on a previously described orphan toxin from Tityus serrulatus venom, named Ts11. We carried out an in-depth structure-function analysis combining 3D structure elucidation of Ts11 and electrophysiological characterization of the toxin. The Ts11 structure is highlighted by an Inhibitor Cystine Knot (ICK) type scaffold, completely devoid of the classical secondary structure elements (α-helix and/or β-strand). This has, to the best of our knowledge, never been described before for scorpion toxins and therefore represents a novel, 6th type of structural fold for these scorpion peptides. On the basis of their preferred interaction with voltage-gated K channels, as compared to all the other targets tested, it can be postulated that Ts11 is the first member of a new subfamily, designated as ε-KTx. PMID:27706049

  10. Thin molecular films of supramolecular porphyrins

    Directory of Open Access Journals (Sweden)

    KOITI ARAKI

    2000-03-01

    Full Text Available A relevant series of symmetric supramolecular porphyrins has been obtained by attaching four [Ru II(bipy2Cl] groups to the pyridyl substituents of meso-tetra(4-pyridylporphyrin and its metallated derivatives. These compounds display a rich electrochemistry and versatile catalytic, electrocatalytic and photochemical properties, associated with the ruthenium-bipyridine and the porphyrin complexes. These properties can be transferred to the electrodes by attaching thin molecular films of the compounds, by dip-coating, electrostatic assembly or electropolymerization. In this way, the interesting properties of those supermolecules and supramolecular assemblies can be used to prepare molecular devices and sensors.

  11. Switching surface chemistry with supramolecular machines.

    Energy Technology Data Exchange (ETDEWEB)

    Dunbar, Timothy D.; Kelly, Michael James; Jeppesen, Jan O. (University of California, Los Angeles, CA); Bunker, Bruce Conrad; Matzke, Carolyn M.; Stoddart, J. Fraser; Huber, Dale L.; Kushmerick, James G.; Flood, Amar H. (University of California, Los Angeles, CA); Perkins, Julie (University of California, Los Angeles, CA); Cao, Jianguo (University of California, Los Angeles, CA)

    2005-07-01

    Tethered supramolecular machines represent a new class of active self-assembled monolayers in which molecular configurations can be reversibly programmed using electrochemical stimuli. We are using these machines to address the chemistry of substrate surfaces for integrated microfluidic systems. Interactions between the tethered tetracationic cyclophane host cyclobis(paraquat-p-phenylene) and dissolved {pi}-electron-rich guest molecules, such as tetrathiafulvalene, have been reversibly switched by oxidative electrochemistry. The results demonstrate that surface-bound supramolecular machines can be programmed to adsorb or release appropriately designed solution species for manipulating surface chemistry.

  12. From metal-organic squares to porous zeolite-like supramolecular assemblies

    KAUST Repository

    Wang, Shuang

    2010-12-29

    We report the synthesis, structure, and characterization of two novel porous zeolite-like supramolecular assemblies, ZSA-1 and ZSA-2, having zeolite gis and rho topologies, respectively. The two compounds were assembled from functional metal-organic squares (MOSs) via directional hydrogen-bonding interactions and exhibited permanent microporosity and thermal stability up to 300 °C. © 2010 American Chemical Society.

  13. Dynamic diversity of synthetic supramolecular polymers in water as revealed by hydrogen/deuterium exchange

    Science.gov (United States)

    Lou, Xianwen; Lafleur, René P. M.; Leenders, Christianus M. A.; Schoenmakers, Sandra M. C.; Matsumoto, Nicholas M.; Baker, Matthew B.; van Dongen, Joost L. J.; Palmans, Anja R. A.; Meijer, E. W.

    2017-05-01

    Numerous self-assembling molecules have been synthesized aiming at mimicking both the structural and dynamic properties found in living systems. Here we show the application of hydrogen/deuterium exchange (HDX) mass spectrometry (MS) to unravel the nanoscale organization and the structural dynamics of synthetic supramolecular polymers in water. We select benzene-1,3,5-tricarboxamide (BTA) derivatives that self-assemble in H2O to illustrate the strength of this technique for supramolecular polymers. The BTA structure has six exchangeable hydrogen atoms and we follow their exchange as a function of time after diluting the H2O solution with a 100-fold excess of D2O. The kinetic H/D exchange profiles reveal that these supramolecular polymers in water are dynamically diverse; a notion that has previously not been observed using other techniques. In addition, we report that small changes in the molecular structure can be used to control the dynamics of synthetic supramolecular polymers in water.

  14. D-amino acid residue in a defensin-like peptide from platypus venom: effect on structure and chromatographic properties.

    Science.gov (United States)

    Torres, Allan M; Tsampazi, Chryssanthi; Geraghty, Dominic P; Bansal, Paramjit S; Alewood, Paul F; Kuchel, Philip W

    2005-10-15

    The recent discovery that the natriuretic peptide OvCNPb (Ornithorhynchus venom C-type natriuretic peptide B) from platypus (Ornithorynchus anatinus) venom contains a D-amino acid residue suggested that other D-amino-acid-containing peptides might be present in the venom. In the present study, we show that DLP-2 (defensin-like peptide-2), a 42-amino-acid residue polypeptide in the platypus venom, also contains a D-amino acid residue, D-methionine, at position 2, while DLP-4, which has an identical amino acid sequence, has all amino acids in the L-form. These findings were supported further by the detection of isomerase activity in the platypus gland venom extract that converts DLP-4 into DLP-2. In the light of this new information, the tertiary structure of DLP-2 was recalculated using a new structural template with D-Met2. The structure of DLP-4 was also determined in order to evaluate the effect of a D-amino acid at position 2 on the structure and possibly to explain the large retention time difference observed for the two molecules in reverse-phase HPLC. The solution structures of the DLP-2 and DLP-4 are very similar to each other and to the earlier reported structure of DLP-2, which assumed that all amino acids were in the L-form. Our results suggest that the incorporation of the D-amino acid at position 2 has minimal effect on the overall fold in solution.

  15. Mesoscale characterization of supramolecular transient networks using SAXS and rheology.

    Science.gov (United States)

    Pape, A C H; Bastings, Maartje M C; Kieltyka, Roxanne E; Wyss, Hans M; Voets, Ilja K; Meijer, E W; Dankers, Patricia Y W

    2014-01-16

    Hydrogels and, in particular, supramolecular hydrogels show promising properties for application in regenerative medicine because of their ability to adapt to the natural environment these materials are brought into. However, only few studies focus on the structure-property relationships in supramolecular hydrogels. Here, we study in detail both the structure and the mechanical properties of such a network, composed of poly(ethylene glycol), end-functionalized with ureido-pyrimidinone fourfold hydrogen bonding units. This network is responsive to triggers such as concentration, temperature and pH. To obtain more insight into the sol-gel transition of the system, both rheology and small-angle X-ray scattering (SAXS) are used. We show that the sol-gel transitions based on these three triggers, as measured by rheology, coincide with the appearance of a structural feature in SAXS. We attribute this feature to the presence of hydrophobic domains where cross-links are formed. These results provide more insight into the mechanism of network formation in these materials, which can be exploited for tailoring their behavior for biomedical applications, where one of the triggers discussed might be used.

  16. Structure-Based Drug Design of Small Molecule Peptide Deformylase Inhibitors to Treat Cancer

    Directory of Open Access Journals (Sweden)

    Jian Gao

    2016-03-01

    Full Text Available Human peptide deformylase (HsPDF is an important target for anticancer drug discovery. In view of the limited HsPDF, inhibitors were reported, and high-throughput virtual screening (HTVS studies based on HsPDF for developing new PDF inhibitors remain to be reported. We reported here on diverse small molecule inhibitors with excellent anticancer activities designed based on HTVS and molecular docking studies using the crystal structure of HsPDF. The compound M7594_0037 exhibited potent anticancer activities against HeLa, A549 and MCF-7 cell lines with IC50s of 35.26, 29.63 and 24.63 μM, respectively. Molecular docking studies suggested that M7594_0037 and its three derivatives could interact with HsPDF by several conserved hydrogen bonds. Moreover, the pharmacokinetic and toxicity properties of M7594_0037 and its derivatives were predicted using the OSIRIS property explorer. Thus, M7594_0037 and its derivatives might represent a promising scaffold for the further development of novel anticancer drugs.

  17. Ligand and Structure-Based Approaches for the Identification of Peptide Deformylase Inhibitors as Antibacterial Drugs.

    Science.gov (United States)

    Gao, Jian; Liang, Li; Zhu, Yasheng; Qiu, Shengzhi; Wang, Tao; Zhang, Ling

    2016-07-15

    Peptide deformylase (PDF) is a metalloprotease catalyzing the removal of a formyl group from newly synthesized proteins, which makes it an important antibacterial drug target. Given the importance of PDF inhibitors like actinonin in antibacterial drug discovery, several reported potent PDF inhibitors were used to develop pharmacophore models using the Galahad module of Sybyl 7.1 software. Generated pharmacophore models were composed of two donor atom centers, four acceptor atom centers and two hydrophobic groups. Model-1 was screened against the Zinc database and several compounds were retrieved as hits. Compounds with Qfit values of more than 60 were employed to perform a molecular docking study with the receptor Escherichia coli PDF, then compounds with docking score values of more than 6 were used to predict the in silico pharmacokinetic and toxicity risk via OSIRIS property explorer. Two known PDF inhibitors were also used to perform a molecular docking study with E. coli PDF as reference molecules. The results of the molecular docking study were validated by reproducing the crystal structure of actinonin. Molecular docking and in silico pharmacokinetic and toxicity prediction studies suggested that ZINC08740166 has a relatively high docking score of 7.44 and a drug score of 0.78.

  18. Studies on the supramolecular shape memory polyurethane containing pyridine moieties

    Science.gov (United States)

    Shaojun, Chen

    Fabricating smart materials with supramolecular switch is an attractive research topic. In this study, supramolecular polyurethane networks containing pyridine moieties (PUPys) were synthesized from N,N-bis(2-hydroxylethyl)isonicotinamide (BINA), hexamethylene diisocyanate (HDI), 4, 4-diphenylmethane diisocyanate (MDI) and 1,4-butanediol (BDO). A series of studies were carried out to investigate the supramolecular structure, morphology and shape memory properties including of thermal-induced shape memory effect and moisture-sensitive shape memory effect. Results show that hydrogen-bonded supramolecular structure and phase separation morphology are formed in the PUPys. The glass transition temperature (Tg) of soft phase is controlled by the hydrogen bonding while the hard phase grows up from amorphous phase to crystalline phase as the BINA content increases. The addition of MDI-BDO promotes the formation of amorphous hard phase. PUPys have high shape fixity and high shape recovery with the recovery temperature of 45 °C-55 °C. To achieve satisfying shape recovery, 30wt% BINA contents are required. The addition of MDI-BDO improves the shape recovery force. In addition, PUPys have high moisture absorption which increases with the increase of temperature, relative humidity, BINA content as well as the decrease of MDI-BDO content. The final shape recovery decreases with the decrease of BINA content significantly and the strain recovery start time, strain recovery time, strain recovery end time and the time length are also short in the higher BINA content PUPys. Moreover, it is found that the low critical value of BINA unit for PUPys having moisture-sensitive SME is still 30wt%. The addition of MDI-BDO improves the moisture-sensitive shape recovery. Finally, it is proposed that the hydrogen bonding present in the pyridine ring serves as "switch" whereas the formed hard phase via hydrogen bonding present in the urethane groups acts as the physical netpoints for the both

  19. Structure of a SARS coronavirus-derived peptide bound to the human major histocompatibility complex class I molecule HLA-B*1501

    DEFF Research Database (Denmark)

    Røder, Gustav; Kristensen, Ole; Kastrup, Jette S

    2008-01-01

    , the crystal structure of HLA-B*1501 in complex with a SARS coronavirus-derived nonapeptide (VQQESSFVM) has been determined at high resolution (1.87 A). The peptide is deeply anchored in the B and F pockets, but with the Glu4 residue pointing away from the floor in the peptide-binding groove, making...

  20. Progress Toward the Clinical Translation of Bioinspired Peptide and Protein Assemblies.

    Science.gov (United States)

    Hainline, Kelly M; Fries, Chelsea N; Collier, Joel H

    2018-03-01

    Supramolecular materials composed of proteins and peptides have been receiving considerable attention toward a range of diseases and conditions from vaccines to drug delivery. Owing to the relative newness of this class of materials, the bulk of work to date has been preclinical. However, examples of approved treatments particularly in vaccines, dentistry, and hemostasis demonstrate the translational potential of supramolecular polypeptides. Critical milestones in the clinical development of this class of materials and currently approved supramolecular polypeptide therapies are described in this study. Additional examples of not-yet-approved materials that are steadily advancing toward clinical use are also featured. Spherical assemblies such as virus-like particles, designed protein nanoparticles, and spherical peptide amphiphiles are highlighted, followed by fiber-forming systems such as fibrillizing peptides, fiber-forming peptide-amphiphiles, and filamentous bacteriophages. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Effect of secondary structure on the interactions of peptide T4 LYS (11-36) in mixtures of aqueous sodium chloride and 2,2,2,-Trifluoroethanol

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Camille O.; Spiegelberg, Susanne; Prausnitz, John M.; Blanch, Harvey W.

    2001-10-01

    The potential of mean force for protein-protein interactions is key to the development of a statistical-mechanical model for salt-induced protein precipitation and crystallization, and for understanding certain disease states, including cataract formation and {beta}-amyloid pathology in Alzheimer's disease. Fluorescence anisotropy provides a method for quantitative characterization of intermolecular interactions due to reversible association. Monomer-dimer equilibria for the peptide T4 LYS(11-36) were studied by fluorescence anisotropy. This peptide, derived from the {beta}-sheet region of the T4 lysozyme molecule, has the potential to form amyloid fibrils. 2,2,2-trifluoroethanol (TFE) induces a change in peptide secondary structure, and was used in aqueous solutions at concentrations from 0 to 50% (v/v) at 25 and 37 C to examine the role of peptide conformation on peptide-peptide interactions. The association constant for dimerization increased with rising TFE concentration and with falling temperature. The peptide-peptide potential of mean force was computed from these association constants. Circular-dichroism measurements showed that the secondary structure of the peptide plays an important role in these strong attractive interactions due to intermolecular hydrogen-bond formation and hydrophobic interactions.

  2. Structural characterization of the α-mating factor prepro-peptide for secretion of recombinant proteins in Pichia pastoris.

    Science.gov (United States)

    Chahal, Sabreen; Wei, Peter; Moua, Pachai; Park, Sung Pil James; Kwon, Janet; Patel, Arth; Vu, Anthony T; Catolico, Jason A; Tsai, Yu Fang Tina; Shaheen, Nadia; Chu, Tiffany T; Tam, Vivian; Khan, Zill-E-Huma; Joo, Hyun Henry; Xue, Liang; Lin-Cereghino, Joan; Tsai, Jerry W; Lin-Cereghino, Geoff P

    2017-01-20

    The methylotrophic yeast Pichia pastoris has been used extensively for expressing recombinant proteins because it combines the ease of genetic manipulation, the ability to provide complex posttranslational modifications and the capacity for efficient protein secretion. The most successful and commonly used secretion signal leader in Pichia pastoris has been the alpha mating factor (MATα) prepro secretion signal. However, limitations exist as some proteins cannot be secreted efficiently, leading to strategies to enhance secretion efficiency by modifying the secretion signal leader. Based on a Jpred secondary structure prediction and knob-socket modeling of tertiary structure, numerous deletions and duplications of the MATα prepro leader were engineered to evaluate the correlation between predicted secondary structure and the secretion level of the reporters horseradish peroxidase (HRP) and Candida antarctica lipase B. In addition, circular dichroism analyses were completed for the wild type and several mutant pro-peptides to evaluate actual differences in secondary structure. The results lead to a new model of MATα pro-peptide signal leader, which suggests that the N and C-termini of MATα pro-peptide need to be presented in a specific orientation for proper interaction with the cellular secretion machinery and for efficient protein secretion. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Structures of a Nonribosomal Peptide Synthetase Module Bound to MbtH-like Proteins Support a Highly Dynamic Domain Architecture.

    Science.gov (United States)

    Miller, Bradley R; Drake, Eric J; Shi, Ce; Aldrich, Courtney C; Gulick, Andrew M

    2016-10-21

    Nonribosomal peptide synthetases (NRPSs) produce a wide variety of peptide natural products. During synthesis, the multidomain NRPSs act as an assembly line, passing the growing product from one module to the next. Each module generally consists of an integrated peptidyl carrier protein, an amino acid-loading adenylation domain, and a condensation domain that catalyzes peptide bond formation. Some adenylation domains interact with small partner proteins called MbtH-like proteins (MLPs) that enhance solubility or activity. A structure of an MLP bound to an adenylation domain has been previously reported using a truncated adenylation domain, precluding any insight that might be derived from understanding the influence of the MLP on the intact adenylation domain or on the dynamics of the entire NRPS module. Here, we present the structures of the full-length NRPS EntF bound to the MLPs from Escherichia coli and Pseudomonas aeruginosa These new structures, along with biochemical and bioinformatics support, further elaborate the residues that define the MLP-adenylation domain interface. Additionally, the structures highlight the dynamic behavior of NRPS modules, including the module core formed by the adenylation and condensation domains as well as the orientation of the mobile thioesterase domain. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Structures of a Nonribosomal Peptide Synthetase Module Bound to MbtH-like Proteins Support a Highly Dynamic Domain Architecture

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Bradley R.; Drake, Eric J.; Shi, Ce; Aldrich, Courtney C.; Gulick, Andrew M. (UMM); (HWMRI)

    2016-09-05

    Nonribosomal peptide synthetases (NRPSs) produce a wide variety of peptide natural products. During synthesis, the multidomain NRPSs act as an assembly line, passing the growing product from one module to the next. Each module generally consists of an integrated peptidyl carrier protein, an amino acid-loading adenylation domain, and a condensation domain that catalyzes peptide bond formation. Some adenylation domains interact with small partner proteins called MbtH-like proteins (MLPs) that enhance solubility or activity. A structure of an MLP bound to an adenylation domain has been previously reported using a truncated adenylation domain, precluding any insight that might be derived from understanding the influence of the MLP on the intact adenylation domain or on the dynamics of the entire NRPS module. Here, we present the structures of the full-length NRPS EntF bound to the MLPs from Escherichia coli and Pseudomonas aeruginosa. These new structures, along with biochemical and bioinformatics support, further elaborate the residues that define the MLP-adenylation domain interface. Additionally, the structures highlight the dynamic behavior of NRPS modules, including the module core formed by the adenylation and condensation domains as well as the orientation of the mobile thioesterase domain.

  5. Structural Insights into the Mechanisms of Action of Short-Peptide HIV-1 Fusion Inhibitors Targeting the Gp41 Pocket

    Directory of Open Access Journals (Sweden)

    Xiujuan Zhang

    2018-02-01

    Full Text Available The deep hydrophobic pocket of HIV-1 gp41 has been considered a drug target, but short-peptides targeting this site usually lack potent antiviral activity. By applying the M-T hook structure, we previously generated highly potent short-peptide fusion inhibitors that specifically targeted the pocket site, such as MT-SC22EK, HP23L, and LP-11. Here, the crystal structures of HP23L and LP-11 bound to the target mimic peptide N36 demonstrated the critical intrahelical and interhelical interactions, especially verifying that the hook-like conformation was finely adopted while the methionine residue was replaced by the oxidation-less prone residue leucine, and that addition of an extra glutamic acid significantly enhanced the binding and inhibitory activities. The structure of HP23L bound to N36 with two mutations (E49K and L57R revealed the critical residues and motifs mediating drug resistance and provided new insights into the mechanism of action of inhibitors. Therefore, the present data help our understanding for the structure-activity relationship (SAR of HIV-1 fusion inhibitors and facilitate the development of novel antiviral drugs.

  6. Understanding the structure, dynamics, and mass transport properties of self assembling peptide hydrogels for injectable, drug delivery applications

    Science.gov (United States)

    Branco, Monica Cristina

    hydrogels as a function of peptide sequence and concentration. Changes in nanoscale dynamics and structure inherently lead to substantial differences in bulk properties, such as the elastic modulus and network mesh size. Learning how the material properties of the gels influence the transport rate of therapeutics through the hydrogel is essential to the development of delivery vehicles. The remainder of the thesis focuses on correlating the mesh sizes of MAX1 and MAX8 gels to the diffusion and mass transport properties of model dextran and protein probes. Here, work is centered on how peptide charge and concentration, as well as probe structure, in particular hydrodynamic diameter and charge, dictate the temporal release of model probes from the peptide hydrogels. Experiments include self diffusion studies and bulk release experiments with model dextrans and proteins from gels before and after syringe delivery. Overall, this thesis will demonstrate the importance of understanding material properties from the nanoscale up to the macroscale for application based design. With this approach, better and specific development of self-assembling peptide materials can be achieved, allowing for the rational engineering of peptide sequences to form hydrogels appropriate for specific drug delivery applications.

  7. Synthesis, spectroscopy and supramolecular structures of two ...

    Indian Academy of Sciences (India)

    TECS

    2007-05-16

    May 16, 2007 ... Abstract. The aqueous reaction of [Mg(H2O)6]Cl2 with the in situ generated sodium salt of 4-nitro- benzoic acid (4-nbaH) and N-methylimidazole (N-MeIm) results in the formation of the dinuclear complex. [Mg(H2O)(N-MeIm)2(4-nba)2]2 1 (4-nba = 4-nitro benzoate), while the direct reaction of [Mg(H2O)6] ...

  8. Supramolecular Structures for Photochemical Energy Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Gust, Devens; Moore, Thomas A.; Moore, Ana L.

    2003-08-26

    OAK B188 The goal of this project is to mimic the energy transduction processes by which photosynthetic organisms harvest sunlight and convert it to forms of energy that are more easily used and stored. The results may lead to new technologies for solar energy harvesting based on the natural photosynthetic process. They may also enrich our understanding and control of photosynthesis in living organisms, and lead to methods for increasing natural biomass production, carbon dioxide removal, and oxygen generation. In our work to date, we have learned how to make synthetic antenna and reaction center molecules that absorb light and undergo photoinduced electron transfer to generate long-lived, energetic charge-separated states. We have assembled a prototype system in which artificial reaction centers are inserted into liposomes (artificial cell-like constructs), where they carry out light-driven transmembrane translocation of hydrogen ions to generate proton motive force. By insertion of natural ATP synthase into the liposomal bilayer, this proton motive force has been used to power the synthesis of ATP. ATP is a natural biological energy currency. We are carrying out a systematic investigation of these artificial photosynthetic energy harvesting constructs in order to understand better how they operate. In addition, we are exploring strategies for reversing the direction of the light-powered proton pumping. Most recently, we have extended these studies to develop a light-powered transmembrane calcium ion pump that converts sunlight into energy stored as a calcium ion concentration gradient across a lipid bilayer.

  9. Synthesis, spectroscopy and supramolecular structures of two ...

    Indian Academy of Sciences (India)

    Author Affiliations. Bikshandarkoil R Srinivasan1 Jyoti V Sawant1 Christian Näther2 Wolfgang Bensch2. Department of Chemistry, Goa University, Goa 403 206; Institut für Anorganische Chemie, Christian-Albrechts-Universität Kiel, Olshausenstraße 40, D-24098 Kiel, Germany ...

  10. Supramolecular coordination polymers using a close to 'V-shaped' fluorescent 4-amino-1,8-naphthalimide Tröger's base scaffold.

    Science.gov (United States)

    Shanmugaraju, Sankarasekaran; Hawes, Chris S; Savyasachi, Aramballi J; Blasco, Salvador; Kitchen, Jonathan A; Gunnlaugsson, Thorfinnur

    2017-11-21

    A V-shaped 4-amino-1,8-naphthalimide derived dipyridyl ligand comprising the Tröger's base structural motif has been synthesised and subsequently used in the formation of two new supramolecular coordination polymers.

  11. Structure-activity relationship study of tachykinin peptides for the development of novel neurokinin-3 receptor selective agonists.

    Science.gov (United States)

    Misu, Ryosuke; Noguchi, Taro; Ohno, Hiroaki; Oishi, Shinya; Fujii, Nobutaka

    2013-04-15

    Neurokinin B (NKB) is a potential regulator of pulsatile gonadotropin-releasing hormone (GnRH) secretion via activation of the neurokinin-3 receptor (NK3R). NKB with the consensus sequence of the tachykinin peptide family also binds to other tachykinin receptors [neurokinin-1 receptor (NK1R) and neurokinin-2 receptor (NK2R)] with low selectivity. In order to identify the structural requirements for the development of novel potent and selective NK3R agonists, a structure-activity relationship (SAR) study of [MePhe(7)]-NKB and other naturally occurring tachykinin peptides was performed. The substitutions to naturally occurring tachykinins with Asp and MePhe improved the receptor binding and agonistic activity for NK3R. The corresponding substitutions to NKB provided an NK3R selective analog. Copyright © 2013 Elsevier Ltd. All rights reserved.

  12. The peptide-receptive transition state of MHC-1 molecules: Insight from structure and molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Robinson H.; Mage, M.; Dolan, M.; Wang, R.; Boyd, L.; Revilleza, M.; Natarajan, K.; Myers, N.; Hansen, T.; Margulies, D.

    2012-05-01

    MHC class I (MHC-I) proteins of the adaptive immune system require antigenic peptides for maintenance of mature conformation and immune function via specific recognition by MHC-I-restricted CD8(+) T lymphocytes. New MHC-I molecules in the endoplasmic reticulum are held by chaperones in a peptide-receptive (PR) transition state pending release by tightly binding peptides. In this study, we show, by crystallographic, docking, and molecular dynamics methods, dramatic movement of a hinged unit containing a conserved 3(10) helix that flips from an exposed 'open' position in the PR transition state to a 'closed' position with buried hydrophobic side chains in the peptide-loaded mature molecule. Crystallography of hinged unit residues 46-53 of murine H-2L(d) MHC-I H chain, complexed with mAb 64-3-7, demonstrates solvent exposure of these residues in the PR conformation. Docking and molecular dynamics predict how this segment moves to help form the A and B pockets crucial for the tight peptide binding needed for stability of the mature peptide-loaded conformation, chaperone dissociation, and Ag presentation.

  13. Two new supramolecular compounds induced by novel ...

    Indian Academy of Sciences (India)

    Min Xiao

    2017-09-19

    Sep 19, 2017 ... Our group has been devoted to the construction of inorganic–organic hybrid compounds ... supramolecular construction has been rarely reported.23. The introduction of C=C bonds in ..... Figure 8. (a) IR spectra of the as-synthesized and solid residue samples of 1 after the photocatalytic degradation of MB.

  14. Supramolecular liquid crystal displays : construction and applications

    NARCIS (Netherlands)

    Hoogboom, Joannes Theodorus Valentinus

    2004-01-01

    This thesis describes chemical methodologies, which can be ued to construct alignment layers for liquid crystal display purposes in a non-clean room environment, by making use of supramolecular chemistry. These techniques are subsequently used to attain control over LCD-properties, both pre- and

  15. Supramolecular assemblies based on glycoconjugated dyes

    NARCIS (Netherlands)

    Schmidt, B.

    2016-01-01

    Supramolecular assemblies of glycoconjugated dyes can be tailored with properties that make them attractive for use in biomedical applications. For example, when assemblies of glycoconjugated dyes are displaying carbohydrates on their periphery in a polyvalent manner, these assemblies can be used to

  16. Strong and Reversible Monovalent Supramolecular Protein Immobilization

    NARCIS (Netherlands)

    Young, Jacqui F.; Nguyen, Hoang D.; Yang, Lanti; Huskens, Jurriaan; Jonkheijm, Pascal; Brunsveld, Luc

    2010-01-01

    Proteins with an iron clasp: Site-selective incorporation of a ferrocene molecule into a protein allows for easy, strong, and reversible supramolecular protein immobilization through a selective monovalent interaction of the ferrocene with a cucurbit[7]uril immobilized on a gold surface. The

  17. Self-assembly of a supramolecular hexagram and a supramolecular pentagram

    Science.gov (United States)

    Jiang, Zhilong; Li, Yiming; Wang, Ming; Song, Bo; Wang, Kun; Sun, Mingyu; Liu, Die; Li, Xiaohong; Yuan, Jie; Chen, Mingzhao; Guo, Yuan; Yang, Xiaoyu; Zhang, Tong; Moorefield, Charles N.; Newkome, George R.; Xu, Bingqian; Li, Xiaopeng; Wang, Pingshan

    2017-05-01

    Five- and six-pointed star structures occur frequently in nature as flowers, snow-flakes, leaves and so on. These star-shaped patterns are also frequently used in both functional and artistic man-made architectures. Here following a stepwise synthesis and self-assembly approach, pentagonal and hexagonal metallosupramolecules possessing star-shaped motifs were prepared based on the careful design of metallo-organic ligands (MOLs). In the MOL design and preparation, robust ruthenium-terpyridyl complexes were employed to construct brominated metallo-organic intermediates, followed by a Suzuki coupling reaction to achieve the required ensemble. Ligand LA (VRu2+X, V=bisterpyridine, X=tetraterpyridine, Ru=Ruthenium) was initially used for the self-assembly of an anticipated hexagram upon reaction with Cd2+ or Fe2+ however, unexpected pentagonal structures were formed, that is, [Cd5LA5]30+ and [Fe5LA5]30+. In our redesign, LB [V(Ru2+X)2] was synthesized and treated with 60° V-shaped bisterpyridine (V) and Cd2+ to create hexagonal hexagram [Cd12V3LB3]36+ along with traces of the triangle [Cd3V3]6+. Finally, a pure supramolecular hexagram [Fe12V3LB3]36+ was successfully isolated in a high yield using Fe2+ with a higher assembly temperature.

  18. Synthetic peptide monolayers: Probing structure, attachment, and hydration conduction with STM

    Science.gov (United States)

    Bergeron, David Joseph

    2000-10-01

    Although the scanning tunneling microscope (STM) has been used in many studies of proteins and other biological molecules, the interpretation of the data has been hampered by a limited understanding of image contrast and tip-sample interactions. It has been recognized that adsorbed water can carry the currents necessary for STM imaging, and it has been speculated that the mechanism of charge transport is based on the exchange of protons along hydrogen-bonded networks. While a water film facilitates the imaging of proteins, it hampers efforts to use STM to probe the electronic structure of redox proteins. The physics of charge transfer in proteins and the intricacies of imaging large molecules with STM can be studied using synthetic proteins. A protein designed with engineerable electron transfer properties, a hydrophilic exterior and mechanisms for attachment to surfaces has been studied using both STM and fixed-electrode conductivity measurements. The effects of immobilization strategy on image quality were investigated by preparing monolayers using self-assembly, Langmuir-Blodgett and monolayer insertion techniques and imaging these films in both humid air and vacuum. The molecules were easily imaged in humid air due to the adsorbed water film, but dehydration in vacuum introduced a conductance gap which prevented the proteins from being imaged within a wide voltage range. The molecules were subjected to large forces when the tip scanned over them without retracting from the surface and peptides were displaced in ways which reflected the strength of their attachment to the surface. In the course of these studies, new STM imaging phenomena have been observed including meniscus-limited lateral resolution, and intermittent imaging of covalently attached molecules. The conductivity of protein films deposited between fixed electrodes depended strongly on hydration, and the experimental arrangement provides a platform for further study of the mechanism of conduction

  19. Structures of MART-126/27-35Peptide/HLA-A2 Complexes Reveal a Remarkable Disconnect between Antigen Structural Homology and T Cell Recognition

    Energy Technology Data Exchange (ETDEWEB)

    Borbulevych, Oleg Y; Insaidoo, Francis K; Baxter, Tiffany K; Powell, Jr., Daniel J.; Johnson, Laura A; Restifo, Nicholas P; Baker, Brian M [NIH; (Notre)

    2008-09-17

    Small structural changes in peptides presented by major histocompatibility complex (MHC) molecules often result in large changes in immunogenicity, supporting the notion that T cell receptors are exquisitely sensitive to antigen structure. Yet there are striking examples of TCR recognition of structurally dissimilar ligands. The resulting unpredictability of how T cells will respond to different or modified antigens impacts both our understanding of the physical bases for TCR specificity as well as efforts to engineer peptides for immunomodulation. In cancer immunotherapy, epitopes and variants derived from the MART-1/Melan-A protein are widely used as clinical vaccines. Two overlapping epitopes spanning amino acid residues 26 through 35 are of particular interest: numerous clinical studies have been performed using variants of the MART-1 26-35 decamer, although only the 27-35 nonamer has been found on the surface of targeted melanoma cells. Here, we show that the 26-35 and 27-35 peptides adopt strikingly different conformations when bound to HLA-A2. Nevertheless, clonally distinct MART-1{sub 26/27-35}-reactive T cells show broad cross-reactivity towards these ligands. Simultaneously, however, many of the cross-reactive T cells remain unable to recognize anchor-modified variants with very subtle structural differences. These dichotomous observations challenge our thinking about how structural information on unligated peptide/MHC complexes should be best used when addressing questions of TCR specificity. Our findings also indicate that caution is warranted in the design of immunotherapeutics based on the MART-1 26/27-35 epitopes, as neither cross-reactivity nor selectivity is predictable based on the analysis of the structures alone.

  20. Crystal Structure of Glucagon-like Peptide-1 in Complex with the Extracellular Domain of the Glucagon-like Peptide-1 Receptor*

    Science.gov (United States)

    Underwood, Christina Rye; Garibay, Patrick; Knudsen, Lotte Bjerre; Hastrup, Sven; Peters, Günther H.; Rudolph, Rainer; Reedtz-Runge, Steffen

    2010-01-01

    GLP-1 (glucagon-like peptide-1) is an incretin released from intestinal L-cells in response to food intake. Activation of the GLP-1 receptor potentiates the synthesis and release of insulin from pancreatic β-cells in a glucose-dependent manner. The GLP-1 receptor belongs to class B of the G-protein-coupled receptors, a subfamily characterized by a large N-terminal extracellular ligand binding domain. Exendin-4 and GLP-1 are 50% identical, and exendin-4 is a full agonist with similar affinity and potency for the GLP-1 receptor. We recently solved the crystal structure of the GLP-1 receptor extracellular domain in complex with the competitive antagonist exendin-4(9–39). Interestingly, the isolated extracellular domain binds exendin-4 with much higher affinity than the endogenous agonist GLP-1. Here, we have solved the crystal structure of the extracellular domain in complex with GLP-1 to 2.1 Åresolution. The structure shows that important hydrophobic ligand-receptor interactions are conserved in agonist- and antagonist-bound forms of the extracellular domain, but certain residues in the ligand-binding site adopt a GLP-1-specific conformation. GLP-1 is a kinked but continuous α-helix from Thr13 to Val33 when bound to the extracellular domain. We supplemented the crystal structure with site-directed mutagenesis to link the structural information of the isolated extracellular domain with the binding properties of the full-length receptor. The data support the existence of differences in the binding modes of GLP-1 and exendin-4 on the full-length GLP-1 receptor. PMID:19861722

  1. Crystal structure of glucagon-like peptide-1 in complex with the extracellular domain of the glucagon-like peptide-1 receptor.

    Science.gov (United States)

    Underwood, Christina Rye; Garibay, Patrick; Knudsen, Lotte Bjerre; Hastrup, Sven; Peters, Günther H; Rudolph, Rainer; Reedtz-Runge, Steffen

    2010-01-01

    GLP-1 (glucagon-like peptide-1) is an incretin released from intestinal L-cells in response to food intake. Activation of the GLP-1 receptor potentiates the synthesis and release of insulin from pancreatic beta-cells in a glucose-dependent manner. The GLP-1 receptor belongs to class B of the G-protein-coupled receptors, a subfamily characterized by a large N-terminal extracellular ligand binding domain. Exendin-4 and GLP-1 are 50% identical, and exendin-4 is a full agonist with similar affinity and potency for the GLP-1 receptor. We recently solved the crystal structure of the GLP-1 receptor extracellular domain in complex with the competitive antagonist exendin-4(9-39). Interestingly, the isolated extracellular domain binds exendin-4 with much higher affinity than the endogenous agonist GLP-1. Here, we have solved the crystal structure of the extracellular domain in complex with GLP-1 to 2.1 Aresolution. The structure shows that important hydrophobic ligand-receptor interactions are conserved in agonist- and antagonist-bound forms of the extracellular domain, but certain residues in the ligand-binding site adopt a GLP-1-specific conformation. GLP-1 is a kinked but continuous alpha-helix from Thr(13) to Val(33) when bound to the extracellular domain. We supplemented the crystal structure with site-directed mutagenesis to link the structural information of the isolated extracellular domain with the binding properties of the full-length receptor. The data support the existence of differences in the binding modes of GLP-1 and exendin-4 on the full-length GLP-1 receptor.

  2. Syntheses and structures of technetium(V) and rhenium(V) oxo complexes of peptide having KYC-sequence

    International Nuclear Information System (INIS)

    Takayama, T.; Suzuki, K.; Sekine, T.; Kudo, H.

    2000-01-01

    Technetium(V) and rhenium(V) oxo complexes of a peptide having a KYC-sequence such as KYCAR (H 3 L 5 ) and KYCAREPPTRTNAYQGQG-NH 2 (H 3 L 18 ) were synthesized, and structures of the complexes were characterized by spectroscopic techniques. All of the complexes were synthesized by the ligand exchange reaction of [(n-C 4 H 9 ) 4 N][MOCl 4 ] (M = 99 Tc, Re) with peptide in methanol or dimethylformamide solution. These complexes have a square pyramidal structure with an oxo ligand at the apical position. The peptide is coordinated to a metal atom through N amine of lysine. S thiol of cysteine, and N amide of tyrosine and cysteine in the equatorial plane. A lysine (CH 2 ) 4 NH 2 group of the L 5 ligand has the syn conformation with respect to metal-oxo bonding in the complex. The syn isomer was selectively formed in the ligand exchange reaction. The conversion of the syn isomer to the anti isomer was observed only for syn-[ReO(L 5 )], in which the coordination of water to the trans position of the oxo ligand was involved. (orig.)

  3. Syntheses and structures of technetium(V) and rhenium(V) oxo complexes of peptide having KYC-sequence

    Energy Technology Data Exchange (ETDEWEB)

    Takayama, T.; Suzuki, K.; Sekine, T.; Kudo, H. [Dept. of Chemistry, Tohoku Univ., Sendai (Japan)

    2000-07-01

    Technetium(V) and rhenium(V) oxo complexes of a peptide having a KYC-sequence such as KYCAR (H{sub 3}L{sup 5}) and KYCAREPPTRTNAYQGQG-NH{sub 2} (H{sub 3}L{sup 18}) were synthesized, and structures of the complexes were characterized by spectroscopic techniques. All of the complexes were synthesized by the ligand exchange reaction of [(n-C{sub 4}H{sub 9}){sub 4}N][MOCl{sub 4}] (M = {sup 99}Tc, Re) with peptide in methanol or dimethylformamide solution. These complexes have a square pyramidal structure with an oxo ligand at the apical position. The peptide is coordinated to a metal atom through N{sub amine} of lysine. S{sub thiol} of cysteine, and N{sub amide} of tyrosine and cysteine in the equatorial plane. A lysine (CH{sub 2}){sub 4}NH{sub 2} group of the L{sup 5} ligand has the syn conformation with respect to metal-oxo bonding in the complex. The syn isomer was selectively formed in the ligand exchange reaction. The conversion of the syn isomer to the anti isomer was observed only for syn-[ReO(L{sup 5})], in which the coordination of water to the trans position of the oxo ligand was involved. (orig.)

  4. Crystal Structure of Glucagon-like Peptide-1 in Complex with the Extracellular Domain of the Glucagon-like Peptide-1 Receptor

    DEFF Research Database (Denmark)

    Underwood, Christina Rye; Garibay, P.; Knudsen, L.B.

    2010-01-01

    GLP-1 (glucagon-like peptide-1) is an incretin released from intestinal L-cells in response to food intake. Activation of the GLP-1 receptor potentiates the synthesis and release of insulin from pancreatic beta-cells in a glucose-dependent manner. The GLP-1 receptor belongs to class B of the G-protein....... The structure shows that important hydrophobic ligand-receptor interactions are conserved in agonist-and antagonist-bound forms of the extracellular domain, but certain residues in the ligand-binding site adopt a GLP-1-specific conformation. GLP-1 is a kinked but continuous alpha-helix from Thr(13) to Val(33......-coupled receptors, a subfamily characterized by a large N-terminal extracellular ligand binding domain. Exendin-4 and GLP-1 are 50% identical, and exendin-4 is a full agonist with similar affinity and potency for the GLP-1 receptor. We recently solved the crystal structure of the GLP-1 receptor extracellular domain...

  5. Dependence of Self-Assembled Peptide Hydrogel Network Structure on Local Fibril Nanostructure

    Science.gov (United States)

    Hule, Rohan A.; Nagarkar, Radhika P.; Hammouda, Boualem; Schneider, Joel P.; Pochan, Darrin J.

    2011-01-01

    Physically cross-linked, fibrillar hydrogel networks are formed by the self-assembly of β-hairpin peptide molecules with varying degrees of strand asymmetry. The peptide registry in the self-assembled state can be used as a design element to generate fibrils with twisting, nontwisting, or laminated morphology. The mass density of the networks varies significantly, and can be directly related to the local fibrillar morphology as evidenced by small angle neutron scattering (SANS) and in situ substantiation using cryogenic transmission electron microscopy (cryo-TEM) under identical concentrations and conditions. Similarly, the density of the network is dependent on changes in the peptide concentration. Bulk rheological properties of the hydrogels can be correlated to the fibrillar nanostructure, with the stiffer, laminated fibrils forming networks with a higher G′ as compared to the flexible, singular fibrillar networks. PMID:21566682

  6. Tryptophan-Containing Non-Cationizable Opioid Peptides - a new chemotype with unusual structure and in vivo activity.

    Science.gov (United States)

    Marco, Rossella De; Gentilucci, Luca

    2017-11-01

    Recently, a new family of opioid peptides containing tryptophan came to the spotlight for the absence of the fundamental protonable tyramine 'message' pharmacophore. Structure-activity relationship investigations led to diverse compounds, characterized by different selectivity profiles and agonist or antagonist effects. Substitution at the indole of Trp clearly impacted peripheral/central antinociceptivity. These peculiarities prompted to gather all the compounds in a new class, and to coin the definition 'Tryptophan-Containing Non-Cationizable Opioid Peptides', in short 'TryCoNCOPs'. Molecular docking analysis suggested that the TryCoNCOPs can still interact with the receptors in an agonist-like fashion. However, most TryCoNCOPs showed significant differences between the in vitro and in vivo activities, suggesting that opioid activity may be elicited also via alternative mechanisms.

  7. X-ray structures of human neutrophil collagenase complexed with peptide hydroxamate and peptide thiol inhibitors. Implications for substrate binding and rational drug design.

    Science.gov (United States)

    Grams, F; Reinemer, P; Powers, J C; Kleine, T; Pieper, M; Tschesche, H; Huber, R; Bode, W

    1995-03-15

    Matrix metalloproteinases (MMPs) are a family of zinc endopeptidases involved in tissue remodeling. They have also been implicated in various disease processes including tumour invasion and joint destruction and are therefore attractive targets for inhibitor design. For rational drug design, information of inhibitor binding at the atomic level is essential. Recently, we have published the refined high-resolution crystal structure of the catalytic domain of human neutrophil collagenase (HNC) complexed with the inhibitor Pro-Leu-Gly-NHOH, which is a mimic for the unprimed (P3-P1) residues of a bound peptide substrate. We have now determined two additional HNC complexes formed with the thiol inhibitor HSCH2CH(CH2Ph)CO-L-Ala-Gly-NH2 and another hydroxamate inhibitor, HONHCOCH(iBu)CO-L-Ala-Gly-NH2, which were both refined to R-values of 0.183/0.198 at 0.240/0.225-nm resolution. The inhibitor thiol and hydroxamate groups ligand the catalytic zinc, giving rise to a slightly distorted tetrahedral and trigonal-bipyramidal coordination sphere, respectively. The thiol inhibitor diastereomer with S-configuration at the P1' residue (corresponding to an L-amino acid analog) binds to HNC. Its peptidyl moiety mimics binding of primed (P1'-P3') residues of the substrate. In combination with our first structure a continuous hexapeptide corresponding to a peptide substrate productively bound to HNC was constructed and energy-minimized. Proteolytic cleavage of this Michaelis complex is probably general base-catalyzed as proposed for thermolysin, i.e. a glutamate assists nucleophilic attack of a water molecule. Although there are many structural and mechanistic similarities to thermolysin, substrate binding to MMPs differs due to the interactions beyond S1'-P1'. While thermolysin binds substrates with a kink at P1', substrates are bound in an extended conformation in the collagenases. This property explains the tolerance of thermolysin for D-amino acid residues at the P1' position, in

  8. Structure-Based Design of Peptidic Inhibitors of the Interaction between CC Chemokine Ligand 5 (CCL5) and Human Neutrophil Peptides 1 (HNP1)

    NARCIS (Netherlands)

    Wichapong, Kanin; Alard, Jean-Eric; Ortega-Gomez, Almudena; Weber, Christian; Hackeng, Tilman M.; Soehnlein, Oliver; Nicolaes, Gerry A. F.

    2016-01-01

    Protein-protein interactions (PPIs) are receiving increasing interest, much sparked by the realization that they represent druggable targets. Recently, we successfully developed a peptidic inhibitor, RRYGTSKYQ ("SKY" peptide), that shows high potential in vitro and in vivo to interrupt a PPI between

  9. Structural studies and SH3 domain binding properties of a human antiviral salivary proline-rich peptide.

    Science.gov (United States)

    Righino, Benedetta; Pirolli, Davide; Radicioni, Giorgia; Marzano, Valeria; Longhi, Renato; Arcovito, Alessandro; Sanna, Maria Teresa; De Rosa, Maria Cristina; Paoluzi, Serena; Cesareni, Gianni; Messana, Irene; Castagnola, Massimo; Vitali, Alberto

    2016-09-01

    Human saliva contains hundreds of small proline-rich peptides originated by the proteolytic cleavage of the salivary basic Proline-Rich Proteins. Nevertheless only for few of them a specific biological activity has been assigned to date. Among them, the 1932 Da peptide (p1932) has been patented as an anti-HIV agent. In order to shed light on the possible mechanism of action of this peptide, we assessed in this study, by means of molecular dynamics calculations, circular dichroism and FTIR spectroscopic techniques, that p1932 has an intrinsic propensity to adopt a polyproline-II helix arrangement. This structural feature combined with the presence of PxxP motifs in its primary structure, represents an essential property for the exploitation of several biological activities. Next to these findings, we recently demonstrated the ability of this peptide to be internalized within cells of the oral mucosa, thus we focused onto a possible intracellular target, represented by the SH3 domains family. Its ability to interact with selected SH3 domains was finally assayed by Surface Plasmon Resonance spectroscopy. As a result, only Fyn, Hck, and c-Src SH3 domains gave positive results in terms of interaction, showing dissociation constants ranging from nanomolar to micromolar values having the best performer a KD of 148 nM. It is noteworthy that all the interacting domains belong to the Src kinases family, suggesting a role for p1932 as a modulator of the signal transduction pathways mediated by these kinases. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 714-725, 2016. © 2016 Wiley Periodicals, Inc.

  10. Analysis of supramolecular surface nanostructures using secondary ion mass spectrometry (poster)

    International Nuclear Information System (INIS)

    Halaszova, S.; Velic, D.

    2013-01-01

    Our system consists of host molecules β-cyclodextrin (C 42 H 70 O 35 ), of implemented Iron nanoparticles (guest). Whole supramolecular complex is placed on a gold substrate. In our project we work with monotiolated β-cyclodextrin (C 42 H 70 O 34 S), consisting of seven α-D-1-4 glucopyranose units. Cyclodextrins have been selected deliberately because of their ability to form inclusion complexes .They are also capable of forming structures similar to self-assembly monolayers. To study the formation of these supramolecular surface nanostructures mass secondary ion spectrometry is used. With this technique fragmentation of monotiolated β-cyclodextrin and the presence of the supramolecular complex on a gold surface can be examined. The observed fragments of monotiolated cyclodextrines films can be divided into three groups: Au X H Y S Z , fragments originating from cyclodextrin molecules associated with Au. Fragments as (C 42 H 70 O 34 S)Na + , (C 42 H 70 O 35 )Na + and (AuC 42 H 69 O 34 S)Na + were identified as well as fragments thereof in cationized form with K + . The main objective of the project is a detailed study and preparation of supramolecular nanostructures consisting of complex guest-host monotiolated β-cyclodextrin host-iron), and a gold substrate. (Authors)

  11. Structural and antimicrobial properties of human pre-elafin/trappin-2 and derived peptides against Pseudomonas aeruginosa

    Directory of Open Access Journals (Sweden)

    Gagné Stéphane M

    2010-10-01

    Full Text Available Abstract Background Pre-elafin/trappin-2 is a human innate defense molecule initially described as a potent inhibitor of neutrophil elastase. The full-length protein as well as the N-terminal "cementoin" and C-terminal "elafin" domains were also shown to possess broad antimicrobial activity, namely against the opportunistic pathogen P. aeruginosa. The mode of action of these peptides has, however, yet to be fully elucidated. Both domains of pre-elafin/trappin-2 are polycationic, but only the structure of the elafin domain is currently known. The aim of the present study was to determine the secondary structures of the cementoin domain and to characterize the antibacterial properties of these peptides against P. aeruginosa. Results We show here that the cementoin domain adopts an α-helical conformation both by circular dichroism and nuclear magnetic resonance analyses in the presence of membrane mimetics, a characteristic shared with a large number of linear polycationic antimicrobial peptides. However, pre-elafin/trappin-2 and its domains display only weak lytic properties, as assessed by scanning electron micrography, outer and inner membrane depolarization studies with P. aeruginosa and leakage of liposome-entrapped calcein. Confocal microscopy of fluorescein-labeled pre-elafin/trappin-2 suggests that this protein possesses the ability to translocate across membranes. This correlates with the finding that pre-elafin/trappin-2 and elafin bind to DNA in vitro and attenuate the expression of some P. aeruginosa virulence factors, namely the biofilm formation and the secretion of pyoverdine. Conclusions The N-terminal cementoin domain adopts α-helical secondary structures in a membrane mimetic environment, which is common in antimicrobial peptides. However, unlike numerous linear polycationic antimicrobial peptides, membrane disruption does not appear to be the main function of either cementoin, elafin or full-length pre-elafin/trappin-2 against

  12. Folding Topology of a Short Coiled-Coil Peptide Structure Templated by an Oligonucleotide Triplex

    DEFF Research Database (Denmark)

    Lou, Chenguang; Christensen, Niels Johan; Martos Maldonado, Manuel Cristo

    2017-01-01

    by oligonucleotide duplex and triplex formation. POC synthesis was achieved by copper-free alkyne-azide cycloaddition between three oligonucleotides and a 23-mer peptide, which by itself exhibited multiple oligomeric states in solution. The oligonucleotide domain was designed to furnish a stable parallel triplex...

  13. Vibrational spectral simulation for peptides of mixed secondary structure: Method comparisons with the Trpzip model hairpin

    Czech Academy of Sciences Publication Activity Database

    Bouř, Petr; Keiderling, T. A.

    2005-01-01

    Roč. 109, - (2005), 23687-23697 ISSN 1089-5647 R&D Projects: GA AV ČR(CZ) IAA4055104 Grant - others:NSF(US) CHE03-16014 Institutional research plan: CEZ:AV0Z40550506 Keywords : VCD * trpzin model hairpin * peptides Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.679, year: 2003

  14. Structure-activity relationship of CART (cocaine- and amphetamine-regulated transcript) peptide fragments

    Czech Academy of Sciences Publication Activity Database

    Maixnerová, Jana; Hlaváček, Jan; Blokešová, Darja; Kowalczyk, W.; Elbert, Tomáš; Šanda, Miloslav; Blechová, Miroslava; Železná, Blanka; Slaninová, Jiřina; Maletínská, Lenka

    2007-01-01

    Roč. 28, č. 10 (2007), s. 1945-1953 ISSN 0196-9781 R&D Projects: GA ČR GA303/05/0614 Institutional research plan: CEZ:AV0Z40550506 Keywords : CART peptide * fragments * binding * PC12 cells Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.368, year: 2007

  15. Biofilms from Klebsiella pneumoniae: Matrix Polysaccharide Structure and Interactions with Antimicrobial Peptides

    Directory of Open Access Journals (Sweden)

    Monica Benincasa

    2016-08-01

    Full Text Available Biofilm matrices of two Klebsiella pneumoniae clinical isolates, KpTs101 and KpTs113, were investigated for their polysaccharide composition and protective effects against antimicrobial peptides. Both strains were good biofilm producers, with KpTs113 forming flocs with very low adhesive properties to supports. Matrix exopolysaccharides were isolated and their monosaccharide composition and glycosidic linkage types were defined. KpTs101 polysaccharide is neutral and composed only of galactose, in both pyranose and furanose ring configurations. Conversely, KpTs113 polysaccharide is anionic due to glucuronic acid units, and also contains glucose and mannose residues. The susceptibility of the two strains to two bovine cathelicidin antimicrobial peptides, BMAP-27 and Bac7(1–35, was assessed using both planktonic cultures and biofilms. Biofilm matrices exerted a relevant protection against both antimicrobials, which act with quite different mechanisms. Similar protection was also detected when antimicrobial peptides were tested against planktonic bacteria in the presence of the polysaccharides extracted from KpTs101 and KpTs113 biofilms, suggesting sequestering adduct formation with antimicrobials. Circular dichroism experiments on BMAP-27 in the presence of increasing amounts of either polysaccharide confirmed their ability to interact with the peptide and induce an α-helical conformation.

  16. Structural features of peptoid-peptide hybrids in lipid-water interfaces

    DEFF Research Database (Denmark)

    Uggerhøj, Lars Erik; Munk, Jens K.; Hansen, Paul Robert

    2014-01-01

    The inclusion of peptoid monomers into antimicrobial peptides (AMPs) increases their proteolytic resistance, but introduces conformational flexibility (reduced hydrogen bonding ability and cis/trans isomerism). We here use NMR spectroscopy to answer how the insertion of a peptoid monomer influenc...

  17. Chemical construction and structural permutation of potent cytotoxin polytheonamide B: discovery of artificial peptides with distinct functions.

    Science.gov (United States)

    Itoh, Hiroaki; Inoue, Masayuki

    2013-07-16

    Polytheonamide B (1), isolated from the marine sponge Theonella swinhoei, is a posttranslationally modified ribosomal peptide (MW 5030 Da) that displays extraordinary cytotoxicity. Among its 48 amino acid residues, this peptide includes a variety D- and L-amino acids that do not occur in proteins, and the chiralities of these amino acids alternate in sequence. These structural features induce the formation of a stable β6.3-helix, giving rise to a tubular structure of over 4 nm in length. In the biological setting, this fold is believed to transport cations across the lipid bilayer through a pore, thereby acting as an ion channel. In this Account, we discuss the construction and structural permutations of this potent cytotoxin. First we describe the 161-step chemical construction of this unusual peptide 1. By developing a synthetic route to 1, we established the chemical basis for subsequent SAR studies to pinpoint the proteinogenic and nonproteinogenic building blocks within the molecule that confer its toxicity and channel function. Using fully synthetic 1, we generated seven analogues with point mutations, and studies of their activity revealed the importance of the N-terminal moiety. Next, we simplified the structure of 1 by substituting six amino acid residues of 1 to design a more synthetically accessible analogue 9. This dansylated polytheonamide mimic 9 was synthesized in 127 total steps, and we evaluated its function to show that it can emulate the toxic and ion channel activities of 1 despite its multiple structural modifications. Finally, we applied a highly automated synthetic route to 48-mer 9 to generate 13 substructures of 27-39-mers. The 37-mer 12 exhibited nanomolar level toxicity through a potentially distinct mode of action from 1 and 9. The SAR studies of polytheonamide B and the 21 artificial analogues have deepened our understanding of the precise structural requirements for the biological functions of 1. They have also led to the discovery of

  18. High-Resolution Structure of a Self-Assembly-Competent Form of a Hydrophobic Peptide Captured in a Soluble [beta]-Sheet Scaffold

    Energy Technology Data Exchange (ETDEWEB)

    Makabe, Koki; Biancalana, Matthew; Yan, Shude; Tereshko, Valentina; Gawlak, Grzegorz; Miller-Auer, Hélène; Meredith, Stephen C.; Koide, Shohei (UC)

    2010-02-08

    {beta}-Rich self-assembly is a major structural class of polypeptides, but still little is known about its atomic structures and biophysical properties. Major impediments for structural and biophysical studies of peptide self-assemblies include their insolubility and heterogeneous composition. We have developed a model system, termed peptide self-assembly mimic (PSAM), based on the single-layer {beta}-sheet of Borrelia outer surface protein A. PSAM allows for the capture of a defined number of self-assembly-like peptide repeats within a water-soluble protein, making structural and energetic studies possible. In this work, we extend our PSAM approach to a highly hydrophobic peptide sequence. We show that a penta-Ile peptide (Ile{sub 5}), which is insoluble and forms {beta}-rich self-assemblies in aqueous solution, can be captured within the PSAM scaffold in a form capable of self-assembly. The 1.1-{angstrom} crystal structure revealed that the Ile{sub 5} stretch forms a highly regular {beta}-strand within this flat {beta}-sheet. Self-assembly models built with multiple copies of the crystal structure of the Ile5 peptide segment showed no steric conflict, indicating that this conformation represents an assembly-competent form. The PSAM retained high conformational stability, suggesting that the flat {beta}-strand of the Ile{sub 5} stretch primed for self-assembly is a low-energy conformation of the Ile{sub 5} stretch and rationalizing its high propensity for self-assembly. The ability of the PSAM to 'solubilize' an otherwise insoluble peptide stretch suggests the potential of the PSAM approach to the characterization of self-assembling peptides.

  19. Structural changes of the ligand and of the receptor alters the receptor preference for neutrophil activating peptides starting with a 3 formylmethionyl group

    DEFF Research Database (Denmark)

    Forsman, Huamei; Winther, Malene; Gabl, Michael

    2015-01-01

    Pathogenic Staphylococcus aureus strains produce N-formylmethionyl containing peptides, of which the tetrapeptide fMIFL is a potent activator of the neutrophil formyl peptide receptor 1 (FPR1) and the PSMα2 peptide is a potent activator of the closely related FPR2. Variants derived from these two...... peptide activators were used to disclose the structural determinants for receptor interaction. Removal of five amino acids from the C-terminus of PSMα2 gave rise to a peptide that had lost the receptor-independent neutrophil permeabilizing effect, whereas neutrophil activation capacity as well as its...... preference for FPR2 was retained. Shorter peptides, PSMα21–10 and PSMα21–5, activate neutrophils, but the receptor preference for these peptides was switched to FPR1. The fMIFL-PSM5–16 peptide, in which the N-terminus of PSMα21–16 was replaced by the sequence fMIFL, was a dual agonist for FPR1/FPR2, whereas...

  20. Static Electricity-Responsive Supramolecular Assembly.

    Science.gov (United States)

    Jintoku, Hirokuni; Ihara, Hirotaka; Matsuzawa, Yoko; Kihara, Hideyuki

    2017-12-01

    Stimuli-responsive materials can convert between molecular scale and macroscopic scale phenomena. Two macroscopic static electricity-responsive phenomena based on nanoscale supramolecular assemblies of a zinc porphyrin derivative are presented. One example involves the movement of supramolecular assemblies in response to static electricity. The assembly of a pyridine (Py) complex of the above-mentioned derivative in cyclohexane is drawn to a positively charged material, whereas the assembly of a 3,5-dimethylpyridine complex is drawn to a negatively charged material. The second phenomenon involves the movement of a non-polar solvent in response to static electrical stimulation. A cyclohexane solution containing a small quantity of the Py-complexed assembly exhibited a strong movement response towards negatively charged materials. Based on spectroscopic measurements and electron microscope observations, it was revealed that the assembled formation generates the observed response to static electricity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Supramolecular interactions in the solid state

    Directory of Open Access Journals (Sweden)

    Giuseppe Resnati

    2015-11-01

    Full Text Available In the last few decades, supramolecular chemistry has been at the forefront of chemical research, with the aim of understanding chemistry beyond the covalent bond. Since the long-range periodicity in crystals is a product of the directionally specific short-range intermolecular interactions that are responsible for molecular assembly, analysis of crystalline solids provides a primary means to investigate intermolecular interactions and recognition phenomena. This article discusses some areas of contemporary research involving supramolecular interactions in the solid state. The topics covered are: (1 an overview and historical review of halogen bonding; (2 exploring non-ambient conditions to investigate intermolecular interactions in crystals; (3 the role of intermolecular interactions in morphotropy, being the link between isostructurality and polymorphism; (4 strategic realisation of kinetic coordination polymers by exploiting multi-interactive linker molecules. The discussion touches upon many of the prerequisites for controlled preparation and characterization of crystalline materials.

  2. Metallo-supramolecular Architectures based on Multifunctional N-Donor Ligands

    OpenAIRE

    Tanh Jeazet, Harold Brice

    2010-01-01

    Self-assembly processes were used to construct supramolecular architectures based on metal-ligand interactions. The structures formed strongly depend on the used metal ion, the ligand type, the chosen counter ion and solvent as well as on the experimental conditions. The focus of the studies was the design of multifunctional N-donor ligands and the characterization of their complexing and structural properties. This work was divided into three distinct main parts: The bis(2-pyridylimine), the...

  3. Graphene controlled H- and J-stacking of perylene dyes into highly stable supramolecular nanostructures for enhanced photocurrent generation

    DEFF Research Database (Denmark)

    Gan, Shiyu; Zhong, Lijie; Engelbrekt, Christian

    2014-01-01

    We report a new method for controlling H- and J-stacking in supramolecular self-assembly. Graphene nanosheets act as structure inducers to direct the self-assembly of a versatile organic dye, perylene into two distinct types of functional nanostructures, i.e. one-dimensional nanotubes via J-stack......-junction solar cells.......We report a new method for controlling H- and J-stacking in supramolecular self-assembly. Graphene nanosheets act as structure inducers to direct the self-assembly of a versatile organic dye, perylene into two distinct types of functional nanostructures, i.e. one-dimensional nanotubes via J......-stacking and two-dimensional branched nanobuds through H-stacking. Graphene integrated supramolecular nanocomposites are highly stable and show significant enhancement of photocurrent generation in these two configurations of photosensing devices, i.e. solid-state optoelectronic constructs and liquid...

  4. Supramolecular gel electrophoresis of large DNA fragments.

    Science.gov (United States)

    Tazawa, Shohei; Kobayashi, Kazuhiro; Oyoshi, Takanori; Yamanaka, Masamichi

    2017-10-01

    Pulsed-field gel electrophoresis is a frequent technique used to separate exceptionally large DNA fragments. In a typical continuous field electrophoresis, it is challenging to separate DNA fragments larger than 20 kbp because they migrate at a comparable rate. To overcome this challenge, it is necessary to develop a novel matrix for the electrophoresis. Here, we describe the electrophoresis of large DNA fragments up to 166 kbp using a supramolecular gel matrix and a typical continuous field electrophoresis system. C 3 -symmetric tris-urea self-assembled into a supramolecular hydrogel in tris-boric acid-EDTA buffer, a typical buffer for DNA electrophoresis, and the supramolecular hydrogel was used as a matrix for electrophoresis to separate large DNA fragments. Three types of DNA marker, the λ-Hind III digest (2 to 23 kbp), Lambda DNA-Mono Cut Mix (10 to 49 kbp), and Marker 7 GT (10 to 165 kbp), were analyzed in this study. Large DNA fragments of greater than 100 kbp showed distinct mobility using a typical continuous field electrophoresis system. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Antimicrobial Peptides in 2014

    Directory of Open Access Journals (Sweden)

    Guangshun Wang

    2015-03-01

    Full Text Available This article highlights new members, novel mechanisms of action, new functions, and interesting applications of antimicrobial peptides reported in 2014. As of December 2014, over 100 new peptides were registered into the Antimicrobial Peptide Database, increasing the total number of entries to 2493. Unique antimicrobial peptides have been identified from marine bacteria, fungi, and plants. Environmental conditions clearly influence peptide activity or function. Human α-defensin HD-6 is only antimicrobial under reduced conditions. The pH-dependent oligomerization of human cathelicidin LL-37 is linked to double-stranded RNA delivery to endosomes, where the acidic pH triggers the dissociation of the peptide aggregate to release its cargo. Proline-rich peptides, previously known to bind to heat shock proteins, are shown to inhibit protein synthesis. A model antimicrobial peptide is demonstrated to have multiple hits on bacteria, including surface protein delocalization. While cell surface modification to decrease cationic peptide binding is a recognized resistance mechanism for pathogenic bacteria, it is also used as a survival strategy for commensal bacteria. The year 2014 also witnessed continued efforts in exploiting potential applications of antimicrobial peptides. We highlight 3D structure-based design of peptide antimicrobials and vaccines, surface coating, delivery systems, and microbial detection devices involving antimicrobial peptides. The 2014 results also support that combination therapy is preferred over monotherapy in treating biofilms.

  6. Membrane-Active Epithelial Keratin 6A Fragments (KAMPs Are Unique Human Antimicrobial Peptides with a Non-αβ Structure

    Directory of Open Access Journals (Sweden)

    Judy Tsz Ying Lee

    2016-11-01

    Full Text Available Antibiotic resistance is a pressing global health problem that threatens millions of lives each year. Natural antimicrobial peptides and their synthetic derivatives, including peptoids and peptidomimetics, are promising candidates as novel antibiotics. Recently, the C-terminal glycine-rich fragments of human epithelial keratin 6A were found to have bactericidal and cytoprotective activities. Here, we used an improved 2-dimensional NMR method coupled with a new protocol for structural refinement by low temperature simulated annealing to characterize the solution structure of these kerain-derived antimicrobial peptides (KAMPs. Two specific KAMPs in complex with membrane mimicking sodium dodecyl sulfate (SDS micelles displayed amphipathic conformations with only local bends and turns, and a central 10-residue glycine-rich hydrophobic strip that is central to bactericidal activity. To our knowledge, this is the first report of non-αβ structure for human antimicrobial peptides. Direct observation of Staphylococcus aureus and Pseudomonas aeruginosa by scanning and transmission electron microscopy showed that KAMPs deformed bacterial cell envelopes and induced pore formation. Notably, in competitive binding experiments, KAMPs demonstrated binding affinities to LPS and LTA that did not correlate with their bactericidal activities, suggesting peptide-LPS and peptide-LTA interactions are less important in their mechanisms of action. Moreover, immunoprecipitation of KAMPs-bacterial factor complexes indicated that membrane surface lipoprotein SlyB and intracellular machineries NQR sodium pump and ribosomes are potential molecular targets for the peptides. Results of this study improve our understanding of the bactericidal function of epithelial cytokeratin fragments, and highlight an unexplored class of human antimicrobial peptides, which may serve as non-αβ peptide scaffolds for the design of novel peptide-based antibiotics.

  7. Synthesis and supramolecular assembly of biomimetic polymers

    Science.gov (United States)

    Marciel, Amanda Brittany

    oligopeptides nanostructures using microscale extensional flows. This strategy enabled reproducible, reliable fabrication of aligned hierarchical constructs that do not form spontaneously in solution. In this way, fluidic-directed assembly of supramolecular structures allows for unprecedented manipulation at the nano- and mesoscale, which has the potential to provide rapid and efficient control of functional materials properties.

  8. Structure/Function Analysis of Cotton-Based Peptide-Cellulose Conjugates: Spatiotemporal/Kinetic Assessment of Protease Aerogels Compared to Nanocrystalline and Paper Cellulose

    Directory of Open Access Journals (Sweden)

    J. Vincent Edwards

    2018-03-01

    Full Text Available Nanocellulose has high specific surface area, hydration properties, and ease of derivatization to prepare protease sensors. A Human Neutrophil Elastase sensor designed with a nanocellulose aerogel transducer surface derived from cotton is compared with cotton filter paper, and nanocrystalline cellulose versions of the sensor. X-ray crystallography was employed along with Michaelis–Menten enzyme kinetics, and circular dichroism to contrast the structure/function relations of the peptide-cellulose conjugate conformation to enzyme/substrate binding and turnover rates. The nanocellulosic aerogel was found to have a cellulose II structure. The spatiotemporal relation of crystallite surface to peptide-cellulose conformation is discussed in light of observed enzyme kinetics. A higher substrate binding affinity (Km of elastase was observed with the nanocellulose aerogel and nanocrystalline peptide-cellulose conjugates than with the solution-based elastase substrate. An increased Km observed for the nanocellulosic aerogel sensor yields a higher enzyme efficiency (kcat/Km, attributable to binding of the serine protease to the negatively charged cellulose surface. The effect of crystallite size and β-turn peptide conformation are related to the peptide-cellulose kinetics. Models demonstrating the orientation of cellulose to peptide O6-hydroxymethyl rotamers of the conjugates at the surface of the cellulose crystal suggest the relative accessibility of the peptide-cellulose conjugates for enzyme active site binding.

  9. Structure/Function Analysis of Cotton-Based Peptide-Cellulose Conjugates: Spatiotemporal/Kinetic Assessment of Protease Aerogels Compared to Nanocrystalline and Paper Cellulose

    Science.gov (United States)

    Edwards, J. Vincent; Fontenot, Krystal; Liebner, Falk; Pircher, Nicole Doyle nee; French, Alfred D.; Condon, Brian D.

    2018-01-01

    Nanocellulose has high specific surface area, hydration properties, and ease of derivatization to prepare protease sensors. A Human Neutrophil Elastase sensor designed with a nanocellulose aerogel transducer surface derived from cotton is compared with cotton filter paper, and nanocrystalline cellulose versions of the sensor. X-ray crystallography was employed along with Michaelis–Menten enzyme kinetics, and circular dichroism to contrast the structure/function relations of the peptide-cellulose conjugate conformation to enzyme/substrate binding and turnover rates. The nanocellulosic aerogel was found to have a cellulose II structure. The spatiotemporal relation of crystallite surface to peptide-cellulose conformation is discussed in light of observed enzyme kinetics. A higher substrate binding affinity (Km) of elastase was observed with the nanocellulose aerogel and nanocrystalline peptide-cellulose conjugates than with the solution-based elastase substrate. An increased Km observed for the nanocellulosic aerogel sensor yields a higher enzyme efficiency (kcat/Km), attributable to binding of the serine protease to the negatively charged cellulose surface. The effect of crystallite size and β-turn peptide conformation are related to the peptide-cellulose kinetics. Models demonstrating the orientation of cellulose to peptide O6-hydroxymethyl rotamers of the conjugates at the surface of the cellulose crystal suggest the relative accessibility of the peptide-cellulose conjugates for enzyme active site binding. PMID:29534033

  10. Supramolecular Pharmaceutical Sciences: A Novel Concept Combining Pharmaceutical Sciences and Supramolecular Chemistry with a Focus on Cyclodextrin-Based Supermolecules.

    Science.gov (United States)

    Higashi, Taishi; Iohara, Daisuke; Motoyama, Keiichi; Arima, Hidetoshi

    2018-01-01

    Supramolecular chemistry is an extremely useful and important domain for understanding pharmaceutical sciences because various physiological reactions and drug activities are based on supramolecular chemistry. However, it is not a major domain in the pharmaceutical field. In this review, we propose a new concept in pharmaceutical sciences termed "supramolecular pharmaceutical sciences," which combines pharmaceutical sciences and supramolecular chemistry. This concept could be useful for developing new ideas, methods, hypotheses, strategies, materials, and mechanisms in pharmaceutical sciences. Herein, we focus on cyclodextrin (CyD)-based supermolecules, because CyDs have been used not only as pharmaceutical excipients or active pharmaceutical ingredients but also as components of supermolecules.

  11. Supramolecular chemistry and crystal engineering

    Indian Academy of Sciences (India)

    ... of elusive saccharin hydrate, Na16(sac)16 . 30H2O, which contains regular and irregular domains in the same structure, and by the Aufbau build up of zinc phosphate framework structures, e.g. ladder motif in [C3N2H12][Zn(HPO4)2] to layer structure in [C3N2H12][Zn2(HPO4)3] upon prolonged hydrothermal conditions.

  12. Construction of nanostructures for selective lithium ion conduction using self-assembled molecular arrays in supramolecular solids.

    Science.gov (United States)

    Moriya, Makoto

    2017-01-01

    In the development of innovative molecule-based materials, the identification of the structural features in supramolecular solids and the understanding of the correlation between structure and function are important factors. The author investigated the development of supramolecular solid electrolytes by constructing ion conduction paths using a supramolecular hierarchical structure in molecular crystals because the ion conduction path is an attractive key structure due to its ability to generate solid-state ion diffusivity. The obtained molecular crystals exhibited selective lithium ion diffusion via conduction paths consisting of lithium bis(trifluoromethanesulfonyl)amide (LiTFSA) and small molecules such as ether or amine compounds. In the present review, the correlation between the crystal structure and ion conductivity of the obtained molecular crystals is addressed based on the systematic structural control of the ionic conduction paths through the modification of the component molecules. The relationship between the crystal structure and ion conductivity of the molecular crystals provides a guideline for the development of solid electrolytes based on supramolecular solids exhibiting rapid and selective lithium ion conduction.

  13. Molecular dynamics investigation of the influence of anionic and zwitterionic interfaces on antimicrobial peptides' structure: implications for peptide toxicity and activity

    DEFF Research Database (Denmark)

    Khandelia, Himanshu; Kaznessis, Yiannis N

    2006-01-01

    Molecular dynamics simulations of three related helical antimicrobial peptides have been carried out in zwitterionic diphosphocholine (DPC) micelles and anionic sodiumdodecylsulfate (SDS) micelles. These systems can be considered as model mammalian and bacterial membrane interfaces, respectively...

  14. Muraymycin nucleoside-peptide antibiotics: uridine-derived natural products as lead structures for the development of novel antibacterial agents

    Directory of Open Access Journals (Sweden)

    Daniel Wiegmann

    2016-04-01

    Full Text Available Muraymycins are a promising class of antimicrobial natural products. These uridine-derived nucleoside-peptide antibiotics inhibit the bacterial membrane protein translocase I (MraY, a key enzyme in the intracellular part of peptidoglycan biosynthesis. This review describes the structures of naturally occurring muraymycins, their mode of action, synthetic access to muraymycins and their analogues, some structure–activity relationship (SAR studies and first insights into muraymycin biosynthesis. It therefore provides an overview on the current state of research, as well as an outlook on possible future developments in this field.

  15. Sustained and controlled release of lipophilic drugs from a self-assembling amphiphilic peptide hydrogel

    DEFF Research Database (Denmark)

    Briuglia, Maria-Lucia; Urquhart, Andrew; Lamprou, Dimitrios A.

    2014-01-01

    . In this work, we have investigated the diffusion properties of Pindolol, Quinine and Timolol maleate from RADA16 in PBS and in BSS-PLUS at 37°C. A sustained, controlled, reproducible and efficient drug release has been detected for all the systems, which allows to understand the dependence of release kinetics......Materials which undergo self-assembly to form supramolecular structures can provide alternative strategies to drug loading problems in controlled release application. RADA 16 is a simple and versatile self-assembling peptide with a designed structure formed of two distinct surfaces, one hydrophilic...... and one hydrophobic that are positioned in such a well-ordered fashion allowing precise assembly into a predetermined organization. A "smart" architecture in nanostructures can represent a good opportunity to use RADA16 as a carrier system for hydrophobic drugs solving problems of drugs delivery...

  16. Small Amphipathic Molecules Modulate Secondary Structure and Amyloid Fibril-forming Kinetics of Alzheimer Disease Peptide Aβ1–42

    Science.gov (United States)

    Ryan, Timothy M.; Friedhuber, Anna; Lind, Monica; Howlett, Geoffrey J.; Masters, Colin; Roberts, Blaine R.

    2012-01-01

    Amyloid fibril formation is associated with a number of debilitating systemic and neurodegenerative diseases. One of the most prominent is Alzheimer disease in which aggregation and deposition of the Aβ peptide occur. Aβ is widely considered to mediate the extensive neuronal loss observed in this disease through the formation of soluble oligomeric species, with the final fibrillar end product of the aggregation process being relatively inert. Factors that influence the aggregation of these amyloid-forming proteins are therefore very important. We have screened a library of 96 amphipathic molecules for effects on Aβ1–42 aggregation and self-association. We find, using thioflavin T fluorescence and electron microscopy assays, that 30 of the molecules inhibit the aggregation process, whereas 36 activate fibril formation. Several activators and inhibitors were subjected to further analysis using analytical ultracentrifugation and circular dichroism. Activators typically display a 1:10 peptide:detergent stoichiometry for maximal activation, whereas the inhibitors are effective at a 1:1 stoichiometry. Analytical ultracentrifugation and circular dichroism experiments show that activators promote a mixture of unfolded and β-sheet structures and rapidly form large aggregates, whereas inhibitors induce α-helical structures that form stable dimeric/trimeric oligomers. The results suggest that Aβ1–42 contains at least one small molecule binding site, which modulates the secondary structure and aggregation processes. Further studies of the binding of these compounds to Aβ may provide insight for developing therapeutic strategies aimed at stabilizing Aβ in a favorable conformation. PMID:22461629

  17. Small amphipathic molecules modulate secondary structure and amyloid fibril-forming kinetics of Alzheimer disease peptide Aβ(1-42).

    Science.gov (United States)

    Ryan, Timothy M; Friedhuber, Anna; Lind, Monica; Howlett, Geoffrey J; Masters, Colin; Roberts, Blaine R

    2012-05-11

    Amyloid fibril formation is associated with a number of debilitating systemic and neurodegenerative diseases. One of the most prominent is Alzheimer disease in which aggregation and deposition of the Aβ peptide occur. Aβ is widely considered to mediate the extensive neuronal loss observed in this disease through the formation of soluble oligomeric species, with the final fibrillar end product of the aggregation process being relatively inert. Factors that influence the aggregation of these amyloid-forming proteins are therefore very important. We have screened a library of 96 amphipathic molecules for effects on Aβ(1-42) aggregation and self-association. We find, using thioflavin T fluorescence and electron microscopy assays, that 30 of the molecules inhibit the aggregation process, whereas 36 activate fibril formation. Several activators and inhibitors were subjected to further analysis using analytical ultracentrifugation and circular dichroism. Activators typically display a 1:10 peptide:detergent stoichiometry for maximal activation, whereas the inhibitors are effective at a 1:1 stoichiometry. Analytical ultracentrifugation and circular dichroism experiments show that activators promote a mixture of unfolded and β-sheet structures and rapidly form large aggregates, whereas inhibitors induce α-helical structures that form stable dimeric/trimeric oligomers. The results suggest that Aβ(1-42) contains at least one small molecule binding site, which modulates the secondary structure and aggregation processes. Further studies of the binding of these compounds to Aβ may provide insight for developing therapeutic strategies aimed at stabilizing Aβ in a favorable conformation.

  18. Differential CLE peptide perception by plant receptors implicated from structural and functional analyses of TDIF-TDR interactions

    Energy Technology Data Exchange (ETDEWEB)

    Li, Zhijie; Chakraborty, Sayan; Xu, Guozhou; Kobe, Bostjan

    2017-04-06

    Tracheary Element Differentiation Inhibitory Factor (TDIF) belongs to the family of post-translationally modified CLE (CLAVATA3/embryo surrounding region (ESR)-related) peptide hormones that control root growth and define the delicate balance between stem cell proliferation and differentiation in SAM (shoot apical meristem) or RAM (root apical meristem). In Arabidopsis, Tracheary Element Differentiation Inhibitory Factor Receptor (TDR) and its ligand TDIF signaling pathway is involved in the regulation of procambial cell proliferation and inhibiting its differentiation into xylem cells. Here we present the crystal structures of the extracellular domains (ECD) of TDR alone and in complex with its ligand TDIF resolved at 2.65 Åand 2.75 Å respectively. These structures provide insights about the ligand perception and specific interactions between the CLE peptides and their cognate receptors. Our in vitro biochemical studies indicate that the interactions between the ligands and the receptors at the C-terminal anchoring site provide conserved binding. While the binding interactions occurring at the N-terminal anchoring site dictate differential binding specificities between different ligands and receptors. Our studies will open different unknown avenues of TDR-TDIF signaling pathways that will enhance our knowledge in this field highlighting the receptor ligand interaction, receptor activation, signaling network, modes of action and will serve as a structure function relationship model between the ligand and the receptor for various similar leucine-rich repeat receptor-like kinases (LRR-RLKs).

  19. Structural and functional characterization of EIAV gp45 fusion peptide proximal region and asparagine-rich layer

    International Nuclear Information System (INIS)

    Duan, Liangwei; Du, Jiansen; Wang, Xuefeng; Zhou, Jianhua; Wang, Xiaojun; Liu, Xinqi

    2016-01-01

    Equine infectious anaemia virus (EIAV) and human immunodeficiency virus (HIV) are members of the lentiviral genus. Similar to HIV gp41, EIAV gp45 is a fusogenic protein that mediates fusion between the viral particle and the host cell membrane. The crystal structure of gp45 reported reveals a different conformation in the here that includes the fusion peptide proximal region (FPPR) and neighboring asparagine-rich layer compared with previous HIV-1 gp41 structures. A complicated hydrogen-bond network containing a cluster of solvent molecules appears to be critical for the stability of the gp45 helical bundle. Interestingly, viral replication was relatively unaffected by site-directed mutagenesis of EIAV, in striking contrast to that of HIV-1. Based on these observations, we speculate that EIAV is more adaptable to emergent mutations, which might be important for the evolution of EIAV as a quasi-species, and could potentially contribute to the success of the EIAV vaccine. - Highlights: • The crystal structure of EIAV gp45 was determined. • The fusion peptide proximal region adopts a novel conformation different to HIV-1. • The asparagine-rich layer includes an extensive hydrogen-bond network. • These regions of EIAV are highly tolerant to mutations. • The results provide insight into the mechanism of gp41/gp45-mediated membrane fusion.

  20. Structural and functional characterization of EIAV gp45 fusion peptide proximal region and asparagine-rich layer

    Energy Technology Data Exchange (ETDEWEB)

    Duan, Liangwei; Du, Jiansen [State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071 (China); Wang, Xuefeng; Zhou, Jianhua; Wang, Xiaojun [State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001 (China); Liu, Xinqi, E-mail: liu2008@nankai.edu.cn [State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071 (China)

    2016-04-15

    Equine infectious anaemia virus (EIAV) and human immunodeficiency virus (HIV) are members of the lentiviral genus. Similar to HIV gp41, EIAV gp45 is a fusogenic protein that mediates fusion between the viral particle and the host cell membrane. The crystal structure of gp45 reported reveals a different conformation in the here that includes the fusion peptide proximal region (FPPR) and neighboring asparagine-rich layer compared with previous HIV-1 gp41 structures. A complicated hydrogen-bond network containing a cluster of solvent molecules appears to be critical for the stability of the gp45 helical bundle. Interestingly, viral replication was relatively unaffected by site-directed mutagenesis of EIAV, in striking contrast to that of HIV-1. Based on these observations, we speculate that EIAV is more adaptable to emergent mutations, which might be important for the evolution of EIAV as a quasi-species, and could potentially contribute to the success of the EIAV vaccine. - Highlights: • The crystal structure of EIAV gp45 was determined. • The fusion peptide proximal region adopts a novel conformation different to HIV-1. • The asparagine-rich layer includes an extensive hydrogen-bond network. • These regions of EIAV are highly tolerant to mutations. • The results provide insight into the mechanism of gp41/gp45-mediated membrane fusion.

  1. Crystal structure of a complete ternary complex of T-cell receptor, peptide-MHC, and CD4

    Energy Technology Data Exchange (ETDEWEB)

    Yin, Yiyuan; Wang, Xin Xiang; Mariuzza, Roy A [Maryland

    2012-07-11

    Adaptive immunity depends on specific recognition by a T-cell receptor (TCR) of an antigenic peptide bound to a major histocompatibility complex (pMHC) molecule on an antigen-presenting cell (APC). In addition, T-cell activation generally requires binding of this same pMHC to a CD4 or CD8 coreceptor. Here, we report the structure of a complete TCR-pMHC-CD4 ternary complex involving a human autoimmune TCR, a myelin-derived self-peptide bound to HLA-DR4, and CD4. The complex resembles a pointed arch in which TCR and CD4 are each tilted ~65° relative to the T-cell membrane. By precluding direct contacts between TCR and CD4, the structure explains how TCR and CD4 on the T cell can simultaneously, yet independently, engage the same pMHC on the APC. The structure, in conjunction with previous mutagenesis data, places TCR-associated CD3εγ and CD3εδ subunits, which transmit activation signals to the T cell, inside the TCR-pMHC-CD4 arch, facing CD4. By establishing anchor points for TCR and CD4 on the T-cell membrane, the complex provides a basis for understanding how the CD4 coreceptor focuses TCR on MHC to guide TCR docking on pMHC during thymic T-cell selection.

  2. An electron induced two-dimensional switch made of azobenzene derivatives anchored in supramolecular assemblies.

    Science.gov (United States)

    Henzl, Jörg; Morgenstern, Karina

    2010-06-21

    Supramolecular assemblies of 4-anilino-4'-nitroazobenzene are investigated on the Au(111) surface by low temperature scanning tunneling microscopy and spectroscopy with submolecular resolution. Adsorption at 250 K leads to three different structures that are formed via hydrogen bonds: a star structure and two types of line structures: a meandering and a zigzag line. The formation of these supramolecular assemblies is affected by the available space on the fcc domains of the reconstructed Au(111) substrate as well as by the two-dimensional chirality of the molecules on the surface. The star structure is enantiomerically pure, while both types of lines consist of a racemic mixture. Bonding between homochiral pairs differ from the one between heterochiral pairs in the position of the hydrogen bonds. Inside these supramolecular assemblies two configurations of the molecules are identified: An almost straight trans-configuration and a slightly bent cis*-configuration. The trans-configuration largely reflects the structure of this isomer in gas phase, while the cis*-configuration is two-dimensional on the surface in contrast to the three-dimensional gas phase cis-configuration. The reversible trans-cis* isomerization is induced by electron tunneling through the LUMO+1 state of the molecule, which is located at +2.9 V.

  3. A review of solute encapsulating nanoparticles used as delivery systems with emphasis on branched amphipathic peptide capsules.

    Science.gov (United States)

    Barros, Sheila M; Whitaker, Susan K; Sukthankar, Pinakin; Avila, L Adriana; Gudlur, Sushanth; Warner, Matt; Beltrão, Eduardo I C; Tomich, John M

    2016-04-15

    Various strategies are being developed to improve delivery and increase the biological half-lives of pharmacological agents. To address these issues, drug delivery technologies rely on different nano-sized molecules including: lipid vesicles, viral capsids and nano-particles. Peptides are a constituent of many of these nanomaterials and overcome some limitations associated with lipid-based or viral delivery systems, such as tune-ability, stability, specificity, inflammation, and antigenicity. This review focuses on the evolution of bio-based drug delivery nanomaterials that self-assemble forming vesicles/capsules. While lipid vesicles are preeminent among the structures; peptide-based constructs are emerging, in particular peptide bilayer delimited capsules. The novel biomaterial-Branched Amphiphilic Peptide Capsules (BAPCs) display many desirable properties. These nano-spheres are comprised of two branched peptides-bis(FLIVI)-K-KKKK and bis(FLIVIGSII)-K-KKKK, designed to mimic diacyl-phosphoglycerides in molecular architecture. They undergo supramolecular self-assembly and form solvent-filled, bilayer delineated capsules with sizes ranging from 20 nm to 2 μm depending on annealing temperatures and time. They are able to encapsulate different fluorescent dyes, therapeutic drugs, radionuclides and even small proteins. While sharing many properties with lipid vesicles, the BAPCs are much more robust. They have been analyzed for stability, size, cellular uptake and localization, intra-cellular retention and, bio-distribution both in culture and in vivo. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. Supramolecular effects in dendritic systems containing photoactive groups

    Directory of Open Access Journals (Sweden)

    GIANLUCA CAMILLO AZZELLINI

    2000-03-01

    Full Text Available In this article are described dendritic structures containing photoactive groups at the surface or in the core. The observed supramolecular effects can be attributed to the nature of the photoactive group and their location in the dendritic architecture. The peripheric azobenzene groups in these dendrimeric compounds can be regarded as single residues that retain the spectroscopic and photochemical properties of free azobenzene moiety. The E and Z forms of higher generation dendrimer, functionalized with azobenzene groups, show different host ability towards eosin dye, suggesting the possibility of using such dendrimer in photocontrolled host-guest systems. The photophysical properties of many dendritic-bipyridine ruthenium complexes have been investigated. Particularly in aerated medium more intense emission and a longer excited-state lifetime are observed as compared to the parent unsubstituted bipyridine ruthenium complexes. These differences can be attributed to a shielding effect towards dioxygen quenching originated by the dendritic branches.

  5. Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation

    Directory of Open Access Journals (Sweden)

    Pero Stephanie C

    2007-09-01

    Full Text Available Abstract Background Human growth factor receptor bound protein 7 (Grb7 is an adapter protein that mediates the coupling of tyrosine kinases with their downstream signaling pathways. Grb7 is frequently overexpressed in invasive and metastatic human cancers and is implicated in cancer progression via its interaction with the ErbB2 receptor and focal adhesion kinase (FAK that play critical roles in cell proliferation and migration. It is thus a prime target for the development of novel anti-cancer therapies. Recently, an inhibitory peptide (G7-18NATE has been developed which binds specifically to the Grb7 SH2 domain and is able to attenuate cancer cell proliferation and migration in various cancer cell lines. Results As a first step towards understanding how Grb7 may be inhibited by G7-18NATE, we solved the crystal structure of the Grb7 SH2 domain to 2.1 Å resolution. We describe the details of the peptide binding site underlying target specificity, as well as the dimer interface of Grb 7 SH2. Dimer formation of Grb7 was determined to be in the μM range using analytical ultracentrifugation for both full-length Grb7 and the SH2 domain alone, suggesting the SH2 domain forms the basis of a physiological dimer. ITC measurements of the interaction of the G7-18NATE peptide with the Grb7 SH2 domain revealed that it binds with a binding affinity of Kd = ~35.7 μM and NMR spectroscopy titration experiments revealed that peptide binding causes perturbations to both the ligand binding surface of the Grb7 SH2 domain as well as to the dimer interface, suggesting that dimerisation of Grb7 is impacted on by peptide binding. Conclusion Together the data allow us to propose a model of the Grb7 SH2 domain/G7-18NATE interaction and to rationalize the basis for the observed binding specificity and affinity. We propose that the current study will assist with the development of second generation Grb7 SH2 domain inhibitors, potentially leading to novel inhibitors of

  6. Structure of the Paramyxovirus Parainfluenza Virus 5 Nucleoprotein in Complex with an Amino-Terminal Peptide of the Phosphoprotein

    Energy Technology Data Exchange (ETDEWEB)

    Aggarwal, Megha; Leser, George P.; Kors, Christopher A.; Lamb, Robert A.; Sundquist, Wesley I.

    2017-12-13

    Parainfluenza virus 5 (PIV5) belongs to the familyParamyxoviridae, which consists of enveloped viruses with a nonsegmented negative-strand RNA genome encapsidated by the nucleoprotein (N). Paramyxovirus replication is regulated by the phosphoprotein (P) through protein-protein interactions with N and the RNA polymerase (L). The chaperone activity of P is essential to maintain the unassembled RNA-free form of N in order to prevent nonspecific RNA binding and premature N oligomerization. Here, we determined the crystal structure of unassembled PIV5 N in complex with a P peptide (N0P) derived from the N terminus of P (P50) at 2.65 Å. The PIV5 N0P consists of two domains: an N-terminal domain (NTD) and a C-terminal domain (CTD) separated by a hinge region. The cleft at the hinge region of RNA-bound PIV5 N was previously shown to be an RNA binding site. The N0P structure shows that the P peptide binds to the CTD of N and extends toward the RNA binding site to inhibit N oligomerization and, hence, RNA binding. Binding of P peptide also keeps the PIV5 N in the open form. A molecular dynamics (MD) analysis of both the open and closed forms of N shows the flexibility of the CTD and the preference of the N protein to be in an open conformation. The gradual opening of the hinge region, to release the RNA, was also observed. Together, these results advance our knowledge of the conformational swapping of N required for the highly regulated paramyxovirus replication.

    IMPORTANCEParamyxovirus replication is regulated by the interaction of P with N and L proteins. Here, we report the crystal structure of unassembled parainfluenza virus 5 (PIV5) N chaperoned with P peptide. Our results provide a detailed understanding of the binding of P to N. The conformational switching of N between closed and open forms during its initial interaction with P, as well as

  7. Self-assembly of pi-conjugated peptides in aqueous environments leading to energy-transporting bioelectronic nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Tavor, John [Johns Hopkins Univ., Baltimore, MD (United States)

    2016-12-06

    The realization of new supramolecular pi-conjugated organic structures inspired and driven by peptide-based self-assembly will offer a new approach to interface with the biotic environment in a way that will help to meet many DOE-recognized grand challenges. Previously, we developed pi-conjugated peptides that undergo supramolecular self-assembly into one-dimensional (1-D) organic electronic nanomaterials under benign aqueous conditions. The intermolecular interactions among the pi-conjugated organic segments within these nanomaterials lead to defined perturbations of their optoelectronic properties and yield nanoscale conduits that support energy transport within individual nanostructures and throughout bulk macroscopic collections of nanomaterials. Our objectives for future research are to construct and study biomimetic electronic materials for energy-related technology optimized for harsher non-biological environments where peptide-driven self-assembly enhances pi-stacking within nanostructured biomaterials, as detailed in the following specific tasks: (1) synthesis and detailed optoelectronic characterization of new pi-electron units to embed within homogeneous self assembling peptides, (2) molecular and data-driven modeling of the nanomaterial aggregates and their higher-order assemblies, and (3) development of new hierarchical assembly paradigms to organize multiple electronic subunits within the nanomaterials leading to heterogeneous electronic properties (i.e. gradients and localized electric fields). These intertwined research tasks will lead to the continued development and fundamental mechanistic understanding of a powerful bioinspired materials set capable of making connections between nanoscale electronic materials and macroscopic bulk interfaces, be they those of a cell, a protein or a device.

  8. Temperature-Induced, Selective Assembly of Supramolecular Colloids in Water

    NARCIS (Netherlands)

    Van Ravensteijn, Bas G.P.; Vilanova, Neus; De Feijter, Isja; Kegel, Willem K.; Voets, Ilja K.

    2017-01-01

    In this article, we report the synthesis and physical characterization of colloidal polystyrene particles that carry water-soluble supramolecular N,N′,N″,-trialkyl-benzene-1,3,5-tricarboxamides (BTAs) on their surface. These molecules are known to assemble into one-dimensional supramolecular

  9. Supramolecular materials based on hydrogen-bonded polymers

    NARCIS (Netherlands)

    ten Brinke, Gerrit; Ruokolainen, Janne; Ikkala, Olli; Binder, W

    2007-01-01

    Combining supramolecular principles with block copolymer self-assembly offers unique possibilities to create materials with responsive and/or tunable properties. The present chapter focuses on supramolecular materials based on hydrogen bonding and (block co-) polymers. Several cases will be

  10. Alternation and tunable composition in hydrogen bonded supramolecular copolymers.

    Science.gov (United States)

    Felder, Thorsten; de Greef, Tom F A; Nieuwenhuizen, Marko M L; Sijbesma, Rint P

    2014-03-07

    Sequence control in supramolecular copolymers is limited by the selectivity of the associating monomer end groups. Here we introduce the use of monomers with aminopyrimidinone and aminohydroxynaphthyridine quadruple hydrogen bonding end groups, which both homodimerize, but form even stronger heterodimers. These features allow the formation of supramolecular copolymers with a tunable composition and a preference for alternating sequences.

  11. Directed Supramolecular Surface Assembly of SNAP-tag Fusion Proteins

    NARCIS (Netherlands)

    Uhlenheuer, D.A.; Wasserberg, D.; Haase, C.; Nguyen, Hoang D.; Schenkel, J.H.; Huskens, Jurriaan; Ravoo, B.J.; Jonkheijm, Pascal; Brunsveld, Luc

    2012-01-01

    Supramolecular assembly of proteins on surfaces and vesicles was investigated by site-selective incorporation of a supramolecular guest element on proteins. Fluorescent proteins were site-selectively labeled with bisadamantane by SNAP-tag technology. The assembly of the bisadamantane functionalized

  12. Supramolecular effects as driving force of dipyrrin based functional materials engineering

    Science.gov (United States)

    Banakova, E.; Bobrov, A.; Kazak, A.; Marfin, Yu; Merkushev, D.; Molchanov, E.; Rumyantsev, E.; Shipalova, M.; Usoltsev, S.; Vodyanova, O.

    2018-01-01

    Dipyrrin based luminophores are of major interest in different areas of chemistry, material science and molecular biology. Vast variety of the structures with dipyrrin motif were synthesized and investigated up to date. Modern trend in the dipyrrin chemistry is the aimed functionalization of the ligand or complex structure allowing to gain the mechanism based on supramolecular interactions for controlling spectral and photophysical characteristics of compounds for tuning practically valuable properties for specific tasks. Presented paper summarize the results of our research group, working in the field of dipyrrin complexes with p-elements: synthesis, spectral characteristics evaluation and possibilities of practical application investigation. Discussion is focused on the opportunities of molecules preorganization for achieving the supramolecular interactions causing the tuning of fluorescence of the compounds in solutions, polymeric matrices and thin films.

  13. Molecular dynamics study of zinc binding to cysteines in a peptide mimic of the alcohol dehydrogenase structural zinc site.

    Science.gov (United States)

    Brandt, Erik G; Hellgren, Mikko; Brinck, Tore; Bergman, Tomas; Edholm, Olle

    2009-02-14

    The binding of zinc (Zn) ions to proteins is important for many cellular events. The theoretical and computational description of this binding (as well as that of other transition metals) is a challenging task. In this paper the binding of the Zn ion to four cysteine residues in the structural site of horse liver alcohol dehydrogenase (HLADH) is studied using a synthetic peptide mimic of this site. The study includes experimental measurements of binding constants, classical free energy calculations from molecular dynamics (MD) simulations and quantum mechanical (QM) electron structure calculations. The classical MD results account for interactions at the molecular level and reproduce the absolute binding energy and the hydration free energy of the Zn ion with an accuracy of about 10%. This is insufficient to obtain correct free energy differences. QM correction terms were calculated from density functional theory (DFT) on small clusters of atoms to include electronic polarisation of the closest waters and covalent contributions to the Zn-S coordination bond. This results in reasonably good agreement with the experimentally measured binding constants and Zn ion hydration free energies in agreement with published experimental values. The study also includes the replacement of one cysteine residue to an alanine. Simulations as well as experiments showed only a small effect of this upon the binding free energy. A detailed analysis indicate that the sulfur is replaced by three water molecules, thereby changing the coordination number of Zn from four (as in the original peptide) to six (as in water).

  14. Antimicrobial Peptides

    Directory of Open Access Journals (Sweden)

    Ali Adem Bahar

    2013-11-01

    Full Text Available The rapid increase in drug-resistant infections has presented a serious challenge to antimicrobial therapies. The failure of the most potent antibiotics to kill “superbugs” emphasizes the urgent need to develop other control agents. Here we review the history and new development of antimicrobial peptides (AMPs, a growing class of natural and synthetic peptides with a wide spectrum of targets including viruses, bacteria, fungi, and parasites. We summarize the major types of AMPs, their modes of action, and the common mechanisms of AMP resistance. In addition, we discuss the principles for designing effective AMPs and the potential of using AMPs to control biofilms (multicellular structures of bacteria embedded in extracellular matrixes and persister cells (dormant phenotypic variants of bacterial cells that are highly tolerant to antibiotics.

  15. Covalent Tethering and Residues with Bulky Hydrophobic Side Chains Enable Self-Assembly of Distinct Amyloid Structures.

    Science.gov (United States)

    Ruiz, Jérémy; Boehringer, Régis; Grogg, Marcel; Raya, Jésus; Schirer, Alicia; Crucifix, Corinne; Hellwig, Petra; Schultz, Patrick; Torbeev, Vladimir

    2016-12-02

    Polymorphism is a common property of amyloid fibers that complicates their detailed structural and functional studies. Here we report experiments illustrating the chemical principles that enable the formation of amyloid polymorphs with distinct stoichiometric composition. Using appropriate covalent tethering we programmed self-assembly of a model peptide corresponding to the [20-41] fragment of human β2-microglobulin into fibers with either trimeric or dimeric amyloid cores. Using a set of biophysical and biochemical methods we demonstrated their distinct structural, morphological, and templating properties. Furthermore, we showed that supramolecular approaches in which the peptide is modified with bulky substituents can also be applied to modulate the formation of different fiber polymorphs. Such strategies, when applied to disease-related peptides and proteins, will greatly help in the evaluation of the biological properties of structurally distinct amyloids. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Structure-Related Roles for the Conservation of the HIV-1 Fusion Peptide Sequence Revealed by Nuclear Magnetic Resonance.

    Science.gov (United States)

    Serrano, Soraya; Huarte, Nerea; Rujas, Edurne; Andreu, David; Nieva, José L; Jiménez, María Angeles

    2017-10-17

    Despite extensive characterization of the human immunodeficiency virus type 1 (HIV-1) hydrophobic fusion peptide (FP), the structure-function relationships underlying its extraordinary degree of conservation remain poorly understood. Specifically, the fact that the tandem repeat of the FLGFLG tripeptide is absolutely conserved suggests that high hydrophobicity may not suffice to unleash FP function. Here, we have compared the nuclear magnetic resonance (NMR) structures adopted in nonpolar media by two FP surrogates, wtFP-tag and scrFP-tag, which had equal hydrophobicity but contained wild-type and scrambled core sequences LFLGFLG and FGLLGFL, respectively. In addition, these peptides were tagged at their C-termini with an epitope sequence that folded independently, thereby allowing Western blot detection without interfering with FP structure. We observed similar α-helical FP conformations for both specimens dissolved in the low-polarity medium 25% (v/v) 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), but important differences in contact with micelles of the membrane mimetic dodecylphosphocholine (DPC). Thus, whereas wtFP-tag preserved a helix displaying a Gly-rich ridge, the scrambled sequence lost in great part the helical structure upon being solubilized in DPC. Western blot analyses further revealed the capacity of wtFP-tag to assemble trimers in membranes, whereas membrane oligomers were not observed in the case of the scrFP-tag sequence. We conclude that, beyond hydrophobicity, preserving sequence order is an important feature for defining the secondary structures and oligomeric states adopted by the HIV FP in membranes.

  17. Anion-switchable supramolecular gels for controlling pharmaceutical crystal growth

    Science.gov (United States)

    Foster, Jonathan A.; Piepenbrock, Marc-Oliver M.; Lloyd, Gareth O.; Clarke, Nigel; Howard, Judith A. K.; Steed, Jonathan W.

    2010-12-01

    We describe the use of low-molecular-weight supramolecular gels as media for the growth of molecular crystals. Growth of a range of crystals of organic compounds, including pharmaceuticals, was achieved in bis(urea) gels. Low-molecular-weight supramolecular gelators allow access to an unlimited range of solvent systems, in contrast to conventional aqueous gels such as gelatin and agarose. A detailed study of carbamazepine crystal growth in four different bis(urea) gelators, including a metallogelator, is reported. The crystallization of a range of other drug substances, namely sparfloxacin, piroxicam, theophylline, caffeine, ibuprofen, acetaminophen (paracetamol), sulindac and indomethacin, was also achieved in supramolecular gel media without co-crystal formation. In many cases, crystals can be conveniently recovered from the gels by using supramolecular anion-triggered gel dissolution; however, crystals of substances that themselves bind to anions are dissolved by them. Overall, supramolecular gel-phase crystallization offers an extremely versatile new tool in pharmaceutical polymorph screening.

  18. Solution structure of the human BTK SH3 domain complexed with a proline-rich peptide from p120cbl

    Energy Technology Data Exchange (ETDEWEB)

    Tzeng, S.-R.; Lou, Y.-C.; Pai, M.-T.; Jain, Moti L.; Cheng, J.-W. [National Tsing Hua University, Division of Structural Biology and Biomedical Science, Department of Life Science (China)

    2000-04-15

    X-linked agammaglobulinemia (XLA), an inherited disease, is caused by mutations in the Bruton's tyrosine kinase (BTK). The absence of functional BTK leads to failure of B cell differentiation which incapacitates antibody production in XLA patients leading to, sometimes lethal, bacterial infections. Point mutation in the BTK gene that leads to deletion of C-terminal 14 aa residues of BTK SH3 domain was found in one patient family. To understand the role of BTK in B cell development, we have determined the solution structure of BTK SH3 domain complexed with a proline-rich peptide from the protein product of c-cbl protooncogene (p120{sup cbl}). Like other SH3 domains, BTK SH3 domain consists of five {beta}-strands packed in two {beta}-sheets forming a {beta}-barrel-like structure. The rmsd calculated from the averaged coordinates for the BTK SH3 domain residues 218-271 and the p120{sup cbl} peptide residues 6-12 of the complex was 0.87 A ({+-}0.16 A) for the backbone heavy atoms (N, C, and C{sub {alpha}}) and 1.64 A ({+-}0.16 A) for all heavy atoms. Based on chemical shift changes and inter-molecular NOEs, we have found that the residues located in the RT loop, n-Src loop and helix-like loop between {beta}4 and {beta}5 of BTK SH3 domain are involved in ligand binding. We have also determined that the proline-rich peptide from p120{sup cbl} binds to BTK SH3 domain in a class I orientation. These results correlate well with our earlier observation that the truncated BTK SH3 domain (deletion of {beta}4, {beta}5 and the helix-like loop) exhibits weaker affinity for the p120{sup cbl} peptide. It is likely that the truncated SH3 domain fails to present to the ligand the crucial residues in the correct context and hence the weaker binding. These results delineate the importance of the C-terminus in the binding of SH3 domains and also indicate that improper folding and the altered binding behavior of mutant BTK SH3 domain likely lead to XLA.

  19. Structural requirements and biological significance of interactions between peptides and the major histocompatibility complex

    DEFF Research Database (Denmark)

    Grey, H M; Buus, S; Colon, S

    1989-01-01

    Previous studies indicate that T cells recognize a complex between the major histocompatibility complex (MHC) restriction-element and peptide-antigen fragments. Two aspects of this complex formation are considered in this paper: (1) what is the nature of the specificity of the interactions...... that allows a few MHC molecules to serve as restriction elements for a large universe of antigens; and (2) what is the relative contribution of determinant selection (i.e. antigen-MHC complex formation) and T-cell repertoire in determining the capacity of an individual to respond to an antigen? By analysing...

  20. Supramolecular chemistry and crystal engineering*

    Indian Academy of Sciences (India)

    Administrator

    separating 4,4′-bipyridine base). A novel feature of self-assembled termolecular organic host ... Hydrothermal synthesis of zinc phosphate frame- work structures starting from amine, phosphoric acid and ZnII in .... synthesis, the classification of synthons as homosyn- thons (those between like functional groups) and.