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Sample records for deduced polypeptide structure

  1. Complete nucleotide sequence and deduced polypeptide sequence of a nonmuscle myosin heavy chain gene from Acanthamoeba: evidence of a hinge in the rodlike tail

    PubMed Central

    1987-01-01

    We have completely sequenced a gene encoding the heavy chain of myosin II, a nonmuscle myosin from the soil ameba Acanthamoeba castellanii. The gene spans 6 kb, is split by three small introns, and encodes a 1,509-residue heavy chain polypeptide. The positions of the three introns are largely conserved relative to characterized vertebrate and invertebrate muscle myosin genes. The deduced myosin II globular head amino acid sequence shows a high degree of similarity with the globular head sequences of the rat embryonic skeletal muscle and nematode unc 54 muscle myosins. By contrast, there is no unique way to align the deduced myosin II rod amino acid sequence with the rod sequence of these muscle myosins. Nevertheless, the periodicities of hydrophobic and charged residues in the myosin II rod sequence, which dictate the coiled-coil structure of the rod and its associations within the myosin filament, are very similar to those of the muscle myosins. We conclude that this ameba nonmuscle myosin shares with the muscle myosins of vertebrates and invertebrates an ancestral heavy chain gene. The low level of direct sequence similarity between the rod sequences of myosin II and muscle myosins probably reflects a general tolerance for residue changes in the rod domain (as long as the periodicities of hydrophobic and charged residues are largely maintained), the relative evolutionary "ages" of these myosins, and specific differences between the filament properties of myosin II and muscle myosins. Finally, sequence analysis and electron microscopy reveal the presence within the myosin II rodlike tail of a well-defined hinge region where sharp bending can occur. We speculate that this hinge may play a key role in mediating the effect of heavy chain phosphorylation on enzymatic activity. PMID:3040773

  2. Phycobilisome structure of porphyridium cruentum: polypeptide composition

    SciTech Connect

    Redlinger, T.; Gantt, E.

    1981-01-01

    Purified phycobilisomes of porphyridium cruentum were solubilized in sodium dodecyl sulfate and resolved by sodium dodecyl sulfate-acrylamide gel electrophoresis into nine colored and nine colorless polypeptides. The colored polypeptides accounted for about 84% of the total stainable protein, and the colorless polypeptides accounted for the remaining 16%. Five of the colored polypeptides ranging in molecular weight from 13,300 to 19,500 were identified as the ..cap alpha.. and ..beta.. subunits of allophycocyanin, R-phycocyanin, and phycoerythrin. Three others (29,000-30,500) were orange and are probably related to the ..gamma.. subunit of phycoerythrin. Sequential dissociation of phycobilisomes, and analysis of the polypeptides in each fraction, revealed the association of a 32,500 molecular weight colorless polypeptide with a phycoerythrin fraction. The remaining eight colorless polypeptides were in the core fraction of the phycobilisome, which also was enriched in allophycocyanin.

  3. Beta structures of alternating polypeptides and their possible prebiotic significance

    NASA Technical Reports Server (NTRS)

    Brack, A.; Orgel, L. E.

    1975-01-01

    A survey of the commonest amino acids formed in prebiotic conditions suggests that the earliest form of genetic coding may have specified polypeptides with a strong tendency to form stable beta-sheet structures. Poly(Val-Lys), like other polypeptides in which hydrophobic and hydrophilic residues alternate, tends to form beta structures. It is shown that bilayers with a hydrophobic interior and a hydrophilic exterior may be present in aqueous solution.

  4. Deducing chemical structure from crystallographically determined atomic coordinates

    PubMed Central

    Bruno, Ian J.; Shields, Gregory P.; Taylor, Robin

    2011-01-01

    An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures. PMID:21775812

  5. Nucleic-acid Structural Deformability Deduced from Anisotropic Displacement Parameters†

    PubMed Central

    Peckham, Heather E.; Olson, Wilma K.

    2011-01-01

    The growing numbers of very well resolved nucleic-acid crystal structures with anisotropic displacement parameters provide an unprecedented opportunity to learn about the natural motions of DNA and RNA. Here we report a new Monte-Carlo approach that takes direct account of this information to extract the distortions of covalent structure, base pairing, and dinucleotide geometry intrinsic to regularly organized double-helical molecules. We present new methods to test the validity of the anisotropic parameters and examine the apparent deformability of a variety of structures, including several A, B, and Z DNA duplexes, an AB helical intermediate, an RNA, a ligand-DNA complex, and an enzyme-bound DNA. The rigid-body parameters characterizing the positions of the bases in the structures mirror the mean parameters found when atomic motion is taken into account. The base-pair fluctuations intrinsic to a single structure, however, differ from those extracted from collections of nucleic-acid structures, although selected base-pair steps undergo conformational excursions along routes suggested by the ensembles. The computations reveal surprising new molecular insights, such as the stiffening of DNA and concomitant separation of motions of contacted nucleotides on opposite strands by the binding of Escherichia coli endonuclease VIII, that suggest how the protein may direct enzymatic action. PMID:21280021

  6. Nucleic-acid structural deformability deduced from anisotropic displacement parameters.

    PubMed

    Peckham, Heather E; Olson, Wilma K

    2011-04-01

    The growing numbers of very well resolved nucleic-acid crystal structures with anisotropic displacement parameters provide an unprecedented opportunity to learn about the natural motions of DNA and RNA. Here we report a new Monte-Carlo approach that takes direct account of this information to extract the distortions of covalent structure, base pairing, and dinucleotide geometry intrinsic to regularly organized double-helical molecules. We present new methods to test the validity of the anisotropic parameters and examine the apparent deformability of a variety of structures, including several A, B, and Z DNA duplexes, an AB helical intermediate, an RNA, a ligand-DNA complex, and an enzyme-bound DNA. The rigid-body parameters characterizing the positions of the bases in the structures mirror the mean parameters found when atomic motion is taken into account. The base-pair fluctuations intrinsic to a single structure, however, differ from those extracted from collections of nucleic-acid structures, although selected base-pair steps undergo conformational excursions along routes suggested by the ensembles. The computations reveal surprising new molecular insights, such as the stiffening of DNA and concomitant separation of motions of contacted nucleotides on opposite strands by the binding of Escherichia coli endonuclease VIII, which suggest how the protein may direct enzymatic action.

  7. Polypeptide Chirality Influences Multilayer Thin Film Growth and Structure

    NASA Astrophysics Data System (ADS)

    Bell, Zephra; Khadka, Dhan; Haynie, Donald

    2011-03-01

    Polypeptide multilayer thin films are being developed for a variety of applications.These include coatings for implant devices and systems for drug delivery in thebiomedical sciences, and optical coatings. Subsequent polymer adsorption steps involve polymers of opposite polarity. Here, the polymers were polypeptides. This project compared the consequences of changing polypeptide chirality on film growth and structure. The peptides were poly(L-glutamic acid), its right-handed counterpart, poly(D-glutamic acid), and poly(lysine-tyrosine). The first two are negatively charged at neutral pH, the third one is positively charged. Poly(lysine-tyrosine)/poly(L-glutamic acid) films and poly(lysine-tyrosine)/poly(D-glutamic acid) films werefabricated on 1 mm-thick quartz plates. In one experiment, films were grown to 34layers. The UV absorption spectrum was taken after each layer deposited to determinethe rate of polymer self-assembly. Separately, UV or visible wavelength spectra wereobtained for films stained with a dye cooled/heated in the range 4-65 °C. In anotherexperiment, a mixture of poly-L-glutamic acid and poly-D-glutamic acid was used as thepolyanion for film buildup. The data show that poly(lysine-tyrosine)/poly(L-glutamicacid) films built up at a higher rate than the corresponding right-handed films.

  8. Precursor Polypeptides to Structural Proteins of Visna Virus

    PubMed Central

    Vigne, Robert; Filippi, Pierre; Quérat, Gilles; Sauze, Nicole; Vitu, Christian; Russo, Pierre; Delori, Pierre

    1982-01-01

    Visna virus is a retrovirus which replicates in fibroblast-like cells of the sheep choroid plexus through a lytic cycle. Visna virions contain three major low-molecular-weight proteins (p30, p16, and p14) which, together with the genomic RNA and several molecules of reverse transcriptase, constitute the core structure of the virions. The core is surrounded by an envelope containing a major glycoprotein (gp135). By analogy with the oncoviruses, these three groups of structural proteins (i.e., the internal proteins, the envelope glycoprotein, and the reverse transcriptase) are probably encoded by the gag, env, and pol genes, respectively. To elucidate the genetic organization of the visna virus genome and its expression, we studied the synthesis of viral proteins in infected sheep choroid plexus cells. Intracellular viral proteins were detected by immunoprecipitation of pulse-labeled cell extracts with monospecific sera raised against p30, p16, and gp135 and resolution of the proteins by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Immunoprecipitation with anti-p30 and anti-p16 sera allowed the characterization of the 55,000-dalton polypeptide precursor to internal virion proteins p30, p16, and p14 (Pr55gag). Tryptic peptide mapping confirmed the precursor-product relationship between Pr55gag and the three internal proteins. In addition, a gag-related polypeptide of 150,000 daltons was also detected. This polypeptide, which was less abundant than Pr55gag, is a likely precursor to the viral reverse transcriptase (Pr150gag-pol). Pr55gag and Pr150gag-pol are not glycosylated. The precursor related to major envelope protein gp135 is a glycosylated polypeptide with an average molecular weight of 150,000 (gPr150env). Pulse-chase experiments indicated that gPr150env matures into glycoprotein gp135 intracellularly; however, gp135 was never preponderant in cell extracts. The non-glycosylated from of gPr150env, which accumulated in the presence of 2-deoxy

  9. Structural analysis of photosystem I polypeptides using chemical crosslinking

    NASA Technical Reports Server (NTRS)

    Armbrust, T. S.; Odom, W. R.; Guikema, J. A.; Spooner, B. S. (Principal Investigator)

    1994-01-01

    Thylakoid membranes, obtained from leaves of 14 d soybean (Glycine max L. cv. Williams) plants, were treated with the chemical crosslinkers glutaraldehyde or 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) to investigate the structural organization of photosystem I. Polypeptides were resolved using lithium dodecyl sulfate polyacrylamide gel electrophoresis, and were identified by western blot analysis using a library of polyclonal antibodies specific for photosystem I subunits. An electrophoretic examination of crosslinked thylakoids revealed numerous crosslinked products, using either glutaraldehyde or EDC. However, only a few of these could be identified by western blot analysis using subunit-specific polyclonal antibodies. Several glutaraldehyde dependent crosslinked species were identified. A single band was identified minimally composed of PsaC and PsaD, documenting the close interaction between these two subunits. The most interesting aspect of these studies was a crosslinked species composed of the PsaB subunit observed following EDC treatment of thylakoids. This is either an internally crosslinked species, which will provide structural information concerning the topology of the complex PsaB protein, a linkage with a polypeptide for which we do not yet have an immunological probe, or a masking of epitopes by the EDC linkage at critical locations in the peptide which is linked to PsaB.

  10. Structural analysis of photosystem I polypeptides using chemical crosslinking.

    PubMed

    Armbrust, T S; Odom, W R; Guikema, J A

    1994-07-01

    Thylakoid membranes, obtained from leaves of 14 d soybean (Glycine max L. cv. Williams) plants, were treated with the chemical crosslinkers glutaraldehyde or 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) to investigate the structural organization of photosystem I. Polypeptides were resolved using lithium dodecyl sulfate polyacrylamide gel electrophoresis, and were identified by western blot analysis using a library of polyclonal antibodies specific for photosystem I subunits. An electrophoretic examination of crosslinked thylakoids revealed numerous crosslinked products, using either glutaraldehyde or EDC. However, only a few of these could be identified by western blot analysis using subunit-specific polyclonal antibodies. Several glutaraldehyde dependent crosslinked species were identified. A single band was identified minimally composed of PsaC and PsaD, documenting the close interaction between these two subunits. The most interesting aspect of these studies was a crosslinked species composed of the PsaB subunit observed following EDC treatment of thylakoids. This is either an internally crosslinked species, which will provide structural information concerning the topology of the complex PsaB protein, a linkage with a polypeptide for which we do not yet have an immunological probe, or a masking of epitopes by the EDC linkage at critical locations in the peptide which is linked to PsaB.

  11. Structural features that distinguish kinetically distinct biomineralization polypeptides.

    PubMed

    Collino, Sebastiano; Evans, John Spencer

    2007-05-01

    AP7 and AP24 are mollusk shell proteins which are responsible for aragonite polymorph formation and stabilization within the nacre layer of the Pacific red abalone, Haliotis rufescens. It is known that the 30-AA N-terminal mineral modification domains of both proteins (AP7N, AP24N) possess identical multifunctional mineralization capabilities within in vitro assays but differ in terms of rate kinetics, with AP24N > AP7N. In this report, we identify previously unreported molecular features of AP24N and contrast the lowest energy polypeptide backbone structures of AP24N (planar configuration) with that of AP7N ("bent paper clip" configuration) using NMR data and simulated annealing molecular dynamics structure refinement. Like AP7N, we find that AP24N possesses an unfolded conformation, can sequester Ca(II) and other multivalent metal ions, can adsorb onto or within calcite crystals, and possesses anionic and cationic electrostatic "pocket" regions on its molecular surfaces. However, AP24N has some unique features: greater conformational responsiveness to Ca(II), the tendency to form a more planar backbone configuration, and longer anionic and hydrogen-bonding donor/acceptor sequence blocks. We conclude that the presence of unfolded polypeptide conformation, electrostatic surface pockets, and interactive sequence clustering endow both AP7N and AP24N with similar features that lead to comparable effects on crystal morphology and nucleation. However, AP24N possesses longer anionic and hydrogen-bonding sequence clusters and exhibits a tendency to adopt a more planar backbone configuration than AP7N does. We believe that these features facilitate peptide-mineral, peptide-ion, or water cluster interactions, thereby enhancing the mineralization kinetics of AP24N over AP7N.

  12. Crystal structures of a polypeptide processing and secretion transporter.

    PubMed

    Lin, David Yin-wei; Huang, Shuo; Chen, Jue

    2015-07-23

    Bacteria secrete peptides and proteins to communicate, to poison competitors, and to manipulate host cells. Among the various protein-translocation machineries, the peptidase-containing ATP-binding cassette transporters (PCATs) are appealingly simple. Each PCAT contains two peptidase domains that cleave the secretion signal from the substrate, two transmembrane domains that form a translocation pathway, and two nucleotide-binding domains that hydrolyse ATP. In Gram-positive bacteria, PCATs function both as maturation proteases and exporters for quorum-sensing or antimicrobial polypeptides. In Gram-negative bacteria, PCATs interact with two other membrane proteins to form the type 1 secretion system. Here we present crystal structures of PCAT1 from Clostridium thermocellum in two different conformations. These structures, accompanied by biochemical data, show that the translocation pathway is a large α-helical barrel sufficient to accommodate small folded proteins. ATP binding alternates access to the transmembrane pathway and also regulates the protease activity, thereby coupling substrate processing to translocation.

  13. Aspects of structural landscape of human islet amyloid polypeptide

    SciTech Connect

    He, Jianfeng Dai, Jin; Li, Jing; Peng, Xubiao; Niemi, Antti J.

    2015-01-28

    The human islet amyloid polypeptide (hIAPP) co-operates with insulin to maintain glycemic balance. It also constitutes the amyloid plaques that aggregate in the pancreas of type-II diabetic patients. We have performed extensive in silico investigations to analyse the structural landscape of monomeric hIAPP, which is presumed to be intrinsically disordered. For this, we construct from first principles a highly predictive energy function that describes a monomeric hIAPP observed in a nuclear magnetic resonance experiment, as a local energy minimum. We subject our theoretical model of hIAPP to repeated heating and cooling simulations, back and forth between a high temperature regime where the conformation resembles a random walker and a low temperature limit where no thermal motions prevail. We find that the final low temperature conformations display a high level of degeneracy, in a manner which is fully in line with the presumed intrinsically disordered character of hIAPP. In particular, we identify an isolated family of α-helical conformations that might cause the transition to amyloidosis, by nucleation.

  14. Aspects of structural landscape of human islet amyloid polypeptide

    NASA Astrophysics Data System (ADS)

    He, Jianfeng; Dai, Jin; Li, Jing; Peng, Xubiao; Niemi, Antti J.

    2015-01-01

    The human islet amyloid polypeptide (hIAPP) co-operates with insulin to maintain glycemic balance. It also constitutes the amyloid plaques that aggregate in the pancreas of type-II diabetic patients. We have performed extensive in silico investigations to analyse the structural landscape of monomeric hIAPP, which is presumed to be intrinsically disordered. For this, we construct from first principles a highly predictive energy function that describes a monomeric hIAPP observed in a nuclear magnetic resonance experiment, as a local energy minimum. We subject our theoretical model of hIAPP to repeated heating and cooling simulations, back and forth between a high temperature regime where the conformation resembles a random walker and a low temperature limit where no thermal motions prevail. We find that the final low temperature conformations display a high level of degeneracy, in a manner which is fully in line with the presumed intrinsically disordered character of hIAPP. In particular, we identify an isolated family of α-helical conformations that might cause the transition to amyloidosis, by nucleation.

  15. Aspects of structural landscape of human islet amyloid polypeptide.

    PubMed

    He, Jianfeng; Dai, Jin; Li, Jing; Peng, Xubiao; Niemi, Antti J

    2015-01-28

    The human islet amyloid polypeptide (hIAPP) co-operates with insulin to maintain glycemic balance. It also constitutes the amyloid plaques that aggregate in the pancreas of type-II diabetic patients. We have performed extensive in silico investigations to analyse the structural landscape of monomeric hIAPP, which is presumed to be intrinsically disordered. For this, we construct from first principles a highly predictive energy function that describes a monomeric hIAPP observed in a nuclear magnetic resonance experiment, as a local energy minimum. We subject our theoretical model of hIAPP to repeated heating and cooling simulations, back and forth between a high temperature regime where the conformation resembles a random walker and a low temperature limit where no thermal motions prevail. We find that the final low temperature conformations display a high level of degeneracy, in a manner which is fully in line with the presumed intrinsically disordered character of hIAPP. In particular, we identify an isolated family of α-helical conformations that might cause the transition to amyloidosis, by nucleation.

  16. Polypeptide folding-mediated tuning of the optical and structural properties of gold nanoparticle assemblies.

    PubMed

    Aili, Daniel; Gryko, Piotr; Sepulveda, Borja; Dick, John A G; Kirby, Nigel; Heenan, Richard; Baltzer, Lars; Liedberg, Bo; Ryan, Mary P; Stevens, Molly M

    2011-12-14

    Responsive hybrid nanomaterials with well-defined properties are of significant interest for the development of biosensors with additional applications in tissue engineering and drug delivery. Here, we present a detailed characterization using UV-vis spectroscopy and small angle X-ray scattering of a hybrid material comprised of polypeptide-decorated gold nanoparticles with highly controllable assembly properties. The assembly is triggered by a folding-dependent bridging of the particles mediated by the heteroassociation of immobilized helix-loop-helix polypeptides and a complementary nonlinear polypeptide present in solution. The polypeptides are de novo designed to associate and fold into a heterotrimeric complex comprised of two disulfide-linked four-helix bundles. The particles form structured assemblies with a highly defined interparticle gap (4.8±0.4 nm) that correlates to the size of the folded polypeptides. Transitions in particle aggregation dynamics, mass-fractal dimensions and ordering, as a function of particle size and the concentration of the bridging polypeptide, are observed; these have significant effects on the optical properties of the assemblies. The assembly and ordering of the particles are highly complex processes that are affected by a large number of variables including the number of polypeptides bridging the particles and the particle mobility within the aggregates. A fundamental understanding of these processes is of paramount interest for the development of novel hybrid nanomaterials with tunable structural and optical properties and for the optimization of nanoparticle-based colorimetric biodetection strategies.

  17. Polypeptides of Treponema pallidum: progress toward understanding their structural, functional, and immunologic roles. Treponema Pallidum Polypeptide Research Group.

    PubMed Central

    Norris, S J

    1993-01-01

    Treponema pallidum subsp. pallidum, the spirochete that causes syphilis, is unusual in a number of respects, including its small genome size, inability to grow under standard in vitro culture conditions, microaerophilism, apparent paucity of outer membrane proteins, structurally complex periplasmic flagella, and ability to evade the host immune responses and cause disease over a period of years to decades. Many of these attributes are related ultimately to its protein content. Our knowledge of the activities, structure, and immunogenicity of its proteins has been expanded by the application of recombinant DNA, hybridoma, and structural fractionation techniques. The purpose of this monograph is to summarize and correlate this new information by using two-dimensional gel electrophoresis, monoclonal antibody reactivity, sequence data, and other properties as the bases of polypeptide identification. The protein profiles of the T. pallidum subspecies causing syphilis, yaws, and endemic syphilis are virtually indistinguishable but differ considerably from those of other treponemal species. Among the most abundant polypeptides are a group of lipoproteins of unknown function that appear to be important in the immune response during syphilitic infection. The periplasmic flagella of T. pallidum and other spirochetes are unique with regard to their protein content and ultrastructure, as well as their periplasmic location. They are composed of three core proteins (homologous to the other members of the eubacterial flagellin family) and a single, unrelated sheath protein; the functional significance of this arrangement is not understood at present. Although the bacterium contains the chaperonins GroEL and DnaK, these proteins are not under the control of the heat shock regulon as they are in most organisms. Studies of the immunogenicity of T. pallidum proteins indicate that many may be useful for immunodiagnosis and immunoprotection. Future goals in T. pallidum polypeptide

  18. Polypeptides of Treponema pallidum: progress toward understanding their structural, functional, and immunologic roles. Treponema Pallidum Polypeptide Research Group.

    PubMed

    Norris, S J

    1993-09-01

    Treponema pallidum subsp. pallidum, the spirochete that causes syphilis, is unusual in a number of respects, including its small genome size, inability to grow under standard in vitro culture conditions, microaerophilism, apparent paucity of outer membrane proteins, structurally complex periplasmic flagella, and ability to evade the host immune responses and cause disease over a period of years to decades. Many of these attributes are related ultimately to its protein content. Our knowledge of the activities, structure, and immunogenicity of its proteins has been expanded by the application of recombinant DNA, hybridoma, and structural fractionation techniques. The purpose of this monograph is to summarize and correlate this new information by using two-dimensional gel electrophoresis, monoclonal antibody reactivity, sequence data, and other properties as the bases of polypeptide identification. The protein profiles of the T. pallidum subspecies causing syphilis, yaws, and endemic syphilis are virtually indistinguishable but differ considerably from those of other treponemal species. Among the most abundant polypeptides are a group of lipoproteins of unknown function that appear to be important in the immune response during syphilitic infection. The periplasmic flagella of T. pallidum and other spirochetes are unique with regard to their protein content and ultrastructure, as well as their periplasmic location. They are composed of three core proteins (homologous to the other members of the eubacterial flagellin family) and a single, unrelated sheath protein; the functional significance of this arrangement is not understood at present. Although the bacterium contains the chaperonins GroEL and DnaK, these proteins are not under the control of the heat shock regulon as they are in most organisms. Studies of the immunogenicity of T. pallidum proteins indicate that many may be useful for immunodiagnosis and immunoprotection. Future goals in T. pallidum polypeptide

  19. Chiral and structural discrimination in binding of polypeptides with condensed nucleic acid structures.

    PubMed

    Reich, Z; Ittah, Y; Weinberger, S; Minsky, A

    1990-04-05

    In biological systems nucleic acids are invariably found in highly compact forms. These rather intricate forms raise questions of basic importance which are related to the various factors involved in the condensation processes, the chemical, physical, and structural features revealed by the packed species, and the effects of the extremely tight packaging upon interactions of the DNA molecules with proteins and drugs. A means for addressing these questions on a molecular level is provided by various procedures known to induce in vitro condensation of DNA molecules into highly compact species which, in turn, may serve as a model for the in vivo physical organization of nucleic acids. A study of the optical properties of the tightly packed DNA molecules indicates that the interactions of these species with polypeptides are characterized by distinct, hitherto unobserved, chiral and structural discrimination. Specifically, the polypeptides found to be selected against are composed of those amino acids that are not normally used in protein biosynthesis, such as D-lysine or ornithine. These findings provide new clues to long debated topics such as the specific universal chirality of amino acids in proteins or the correlation between conformational flexibility of polypeptides and their ability to form stable compact complexes with nucleic acids.

  20. Structure-function relationship in the antifreeze activity of synthetic alanine-lysine antifreeze polypeptides.

    PubMed

    Wierzbicki, A; Knight, C A; Rutland, T J; Muccio, D D; Pybus, B S; Sikes, C S

    2000-01-01

    Recently antifreeze proteins (AFP) have been the subject of many structure-function relationship studies regarding their antifreeze activity. Attempts have been made to elucidate the structure-function relationship by various amino acid substitutions, but to our knowledge there has been no successful from first principles design of a polypeptide that would bind to designated ice planes along a specific direction. In this paper we show the results of our first attempt on an entirely de novo design of an alanine-lysine-rich antifreeze polypeptide. This 43 residue alanine-lysine peptide exhibits characteristic nonequilibrium freezing point depression and binds to the designated (210) planes of ice along the [122] vector. The structural and thermodynamic properties of this polypeptide were determined using circular dichroism spectroscopy and its nonequilibrium antifreeze properties were investigated using an ice-etching method and nanoliter osmometry.

  1. Structural organization and polypeptide composition of the avian adenovirus core.

    PubMed Central

    Li, P; Bellett, A J; Parish, C R

    1984-01-01

    CELO virus (fowl adenovirus 1) contained three core polypeptides of molecular weights 20,000, 12,000, and 9,500. The core was similar to that of human adenoviruses, with some evidence of compact subcore domains. Micrococcal nuclease digestion of CELO virus cores produced a smear of DNA fragments of gradually decreasing size, with no nucleosome subunit or repeat pattern. Moreover, when digested cores were analyzed without protease treatment, there was again no evidence of a nucleosome substructure; neither DNA fragments nor core proteins entered a 4% polyacrylamide gel. The organization of the core is thus quite unlike that of chromatin. Restriction endonuclease analysis of the DNA from digested cores showed that the right end was on the outside of the core. We suggest that adenovirus DNA is condensed into the core by cross-linking and neutralization by the core proteins, beginning with the packaging sequence at the center of the core and ending with the right end of the DNA on the outside. Images PMID:6092686

  2. Geoelectrical Structure of Ulleung Island, Korea Deduced from 3D MT Interpretations

    NASA Astrophysics Data System (ADS)

    Lee, T. J.; Kim, M. S.; Park, I. H.; Song, Y.

    2016-12-01

    A three-dimensional (3D) magnetotelluric (MT) survey has been carried out to delineate subsurface structures and possible fractures for geothermal development in Ulleung Island, Korea. Quite good quality of MT data could be obtained throughout the survey region by locating the remote reference in Sawauchi, Japan, which is approximately 900 km from the centre of the field site. 3D modelling and inversion are performed taking into account the sea effect in MT measurements near the seashore. The modelling results showed that seawater surrounding the Ulleung Island affected MT data at frequencies below 10 Hz, depending on the distance from the seashore. Two kinds of 3D inversion have been performed with the MT data observed from the area; ordinary 3D inversion, and inversion including the sea as a constraint. The sea-effect constraint inversion gave more reasonable and reliable results and showed clear E-W trend of conductive anomaly along the connection line between the test boreholes GH-1 and GH-2, which showed very high geothermal gradients of about 100 °/km. Comparing the gradients of the other two boreholes in north and south directions are of about 70 °/km, one can deduce that the deep circulation of convective water through the deeply connected fractures, say E-W trends conductive anomaly, carries the heat from the deep to near the surface. This can explain the big gradient differences from site to site in this small island.

  3. Structure of La Primavera caldera, Jalisco, Mexico, deduced from gravity anomalies and drilling results

    NASA Astrophysics Data System (ADS)

    Yokoyama, I.; Mena, M.

    1991-07-01

    Previous studies of La Primavera caldera have mostly been based on surface geology and topography. Since 1980, many wells, exploring for geothermal energy, have reached depths of about 2 to 3 km at the center of the caldera. The results of the drillings, together with those of the gravity surveys, provide information about the subsurface structure of the caldera, and shed light on its formation. The drilling results and gravity anomalies at La Primavera caldera and San Marcos, located at about 40 km distance from the caldera, suggest that regional gravity anomalies can be interpreted in terms of depths of the granitic basements: the basement beneath La Primavera caldera is about 3 km deep and consists of roughly the same horizon as that beneath San Marcos. The drilling results within the caldera reveal that the depth of the caldera fills ranges from 0.3 to 1 km at the drilling sites. The andesite basement, about 1 km deep, remains approximately horizontal, and the granitic basement has a depth of about 3 km. The surface topographies, such as the postcaldera domes, scarcely disturb the subsurface strata. The local gravity anomalies show two lows within the caldera reflecting the configuration of caldera bottom, two funnel-shaped depressions, one of which corresponds to a vent of the Tala tuff deduced from geological observations. The mass deficiency within the caldera estimated from the gravity anomaly, satisfies the general relationship that the mass deficiency is proportional to the caldera diameter cubed. This means that caldera structure is three-dimensional: the larger the diameter, the deeper the funnel-shape. At present this argument may be limited to funnel-shaped calderas.

  4. Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species.

    PubMed

    Smith, Kathrine J; Petit, Chantal M; Aubart, Kelly; Smyth, Martin; McManus, Edward; Jones, Jo; Fosberry, Andrew; Lewis, Ceri; Lonetto, Michael; Christensen, Siegfried B

    2003-02-01

    Polypeptide deformylase (PDF) catalyzes the deformylation of polypeptide chains in bacteria. It is essential for bacterial cell viability and is a potential antibacterial drug target. Here, we report the crystal structures of polypeptide deformylase from four different species of bacteria: Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, and Escherichia coli. Comparison of these four structures reveals significant overall differences between the two Gram-negative species (E. coli and H. influenzae) and the two Gram-positive species (S. pneumoniae and S. aureus). Despite these differences and low overall sequence identity, the S1' pocket of PDF is well conserved among the four enzymes studied. We also describe the binding of nonpeptidic inhibitor molecules SB-485345, SB-543668, and SB-505684 to both S. pneumoniae and E. coli PDF. Comparison of these structures shows similar binding interactions with both Gram-negative and Gram-positive species. Understanding the similarities and subtle differences in active site structure between species will help to design broad-spectrum polypeptide deformylase inhibitor molecules.

  5. Relating secondary structure to the mechanical properties of polypeptide hydrogels

    NASA Astrophysics Data System (ADS)

    Hagan, Sharon Anne

    Biomimetic hydrogels are being developed for use in medicine as drug delivery devices and tissue engineering matrices, and the mechanical properties of the materials play an important role in their performance. For example, in tissue engineering, gene expression and cell adhesion have been closely linked to the mechanical properties of the surrounding hydrogel matrix. In poly-L-lysine hydrogels, a five-fold increase in storage modulus, a 50% increase in equilibrium modulus, and a 62% decrease in swelling degree are shown to occur as the hydrogel network chains transition from an alpha-helix to a beta-sheet conformation. The manipulation of the network's mechanical behavior through changes in the secondary structure of the polymer chains offers an additional design variable in the development of biosynthetic materials. Analogous to poly-L-lysine, elastin-mimetic proteins based on the consensus repeat sequence of elastin (VPGVG) undergo a temperature-dependent secondary structure transition from a random coil to a beta-spiral. In this research, chemically-crosslinked poly[(VPGVG)4(VPGKG)] hydrogels are shown to possess temperature- and pH-dependent swelling. Following scaling law predictions (G ˜ φ2n), the hydrogels have been shown to behave as ideal elastic networks when the crosslink density is varied at synthesis (theory: n = 9/4, experimental: n = 2.0 +/- 0.1), and behave as flexible networks above and below their structural transition temperature of 35°C (theory: n = 1/3, experimental: n = 0.45 +/- 0.06). Evaluation of published data on elastin-mimetic hydrogels shows that the hydrogels behave as ideal elastic networks for all crosslinking techniques, crosslink spacings, and crosslink functionalities reported. As a contrast to chemically-crosslinked hydrogels, a novel elastin-mimetic triblock (EMT) copolymer was evaluated because of its potential use in cell encapsulation without potentially harmful side reactions. Unlike other thermally gelling copolymers

  6. Deducing nanopore structure and growth mechanisms in porogen-templated silsesquioxane thin films

    NASA Astrophysics Data System (ADS)

    Peng, Hua-Gen; Vallery, Richard S.; Liu, Ming; Frieze, William E.; Gidley, David W.; Yim, Jin-Heong; Jeong, Hyun-Dam; Kim, Jongmin

    2005-10-01

    Adjusting the functional group of a porogen is found to have a tremendous effect on the pore structre of porous low dielectric constant films with silsesquioxane as the matrix precursor. The pore size and interconnection length measured by positronium annihilation lifetime spectroscopy can be used to deduce the pore shape and its evolution with porosity from templates of isolated porogen molecules through film percolation. Inert, self-linkable, and amphiphilic porogens are demonstrated to randomly aggregate three-dimensionally, linearly polymerize, and form micelles, respectively.

  7. Induction of human gamma interferon by structurally defined polypeptide fragments of group A streptococcal M protein.

    PubMed Central

    Weigent, D A; Beachey, E H; Huff, T; Peterson, J W; Stanton, G J; Baron, S

    1984-01-01

    The presence of interferon (IFN) has been demonstrated previously (i) in fluids obtained from the middle ears of children with Streptococcus pneumoniae infections, (ii) from the serum of mice injected intraperitoneally with either S. pneumoniae or Streptococcus pyogenes, and (iii) from human lymphoid cell cultures treated with a variety of bacteria. In this study, we showed that highly purified peptic extracts of three different serotypes of group A streptococcal M protein (pep M5, pep M6, and pep M24) stimulated human peripheral leukocytes to produce IFN. IFN production was apparent by 10 h and peaked 24 h after exposure. Dose-response experiments indicated that IFN could be detected in cultures treated with concentrations of M protein as low as 6 micrograms/ml, whereas maximum IFN production occurred at a concentration of 200 micrograms/ml. The IFN had antigenic and physicochemical characteristics of IFN-gamma. Preliminary leukocyte fractionation studies revealed that the IFN-producing cell was a nonadherent lymphocyte with receptors for sheep erythrocytes (T cell). Rabbit antisera specific for these structurally defined polypeptide fragments of streptococcal M protein (pep M5, pep M6, and pep M24) blocked IFN induction by each of the polypeptides. The data suggest that the different serotypes of streptococcal M protein may induce IFN by a common structural determinant shared by each of the polypeptide fragments tested. PMID:6418655

  8. CMB and the elementary particles structure deduced from QFT of non-dot model

    NASA Astrophysics Data System (ADS)

    Chen, Shao-Guang

    In my paper ‘Planck Constant Deduced from Metrical Results of Doppler Effect of Moving Particle —Uncertainty Principle Caused by Collision of a Particle with CMB Photons and Virtual Photons (H05-0036-10)’ the absolute velocity is decided by CMB which as a mark of the vacuum. CMB come from the thermal radiation of stars via gravitational redshift about 10 (13) year (E14- 0032-08). In my paper ‘Quanta turn-advance ism, China Science && Technology Overview 131 192-210 (2011)’, QFT four-dimensional uncertainty principle and momentum-energy conservation law had been generalized as a five-dimensional equations: de Broglie wavelength as a position vector \\underline{q}= (i c t, r, s), momentum \\underline{P} = (i E / c, P, U c), \\underline{q} = i h / \\underline{P}, \\underline{q} \\underline{q} = 0, \\underline{P} \\underline{P} = 0, Sigma∑ \\underline{P} = \\underline{P} (0) . The five-dimensional time-space-spin had been quantized as a non-dot model basic cell, the lowest energy state vertical polarized left spin 1/2 neutrino and right spin 1/2 antineutrino are just the left, right advance unit quanta _{0}nuυ, nuυ _{0} and left, right back unit quanta (0) nuυ, nuυ (0) , it again compose into spin 1 unit advance photons _{0}nuυnuυ _{0} and back (0) nuυnuυ (0) , spin 0 unit rest mass nuυ _{0}nuυ (0) and anti-mass _{0}nuυ (0) nuυ, spin 0 unit positive charge _{0}nuυnuυ (0) and negative charge nuυ _{0} (0) nuυ. It accord to the high energy physics experimental results of the transformation among the photons, masses quanta and charges quanta. The physical vacuum is the even collocation of non-combinational nuυ _{0} or _{0}nuυ. QFT is no longer with divergence difficulty by the non-dot model. It is mathematically easy that from five-dimensional equations deduce out the Dirac, Klein-Gordan, Maxwell equations and Lorentz force formula, but appear some new results. The interactions between _{0}nuυ, nuυ _{0}, (0) nuυ, nuυ (0) , i.e., force f

  9. Temperature structure of active regions deduced from helium-like sulphur lines

    NASA Technical Reports Server (NTRS)

    Watanabe, Tetsuya; Hara, Hirohisa; Shimizu, Toshifumi; Hiei, Eijiro; Bentley, Robert D.; Lang, James; Phillips, Kenneth J. H.; Pike, C. David; Fludra, Andrzej; Bromage, Barbara J. I.

    1995-01-01

    Solar active-region temperatures have been determined from the full-Sun spectra of helium-like sulfur (S XV) observed by the Bragg Crystal Spectrometer on Board the Yohkoh satellite. The average temperature deduced from S XV is demonstrated to vary with the solar activity level: A temperature of 2.5 x 10(exp 6) K is derived from the spectra taken during low solar activity, similar to the general corona, while 4 x 10(exp 6) K is obtained during a higher activity phase. For the latter, the high- temperature tail of the differential emission measure of active regions is found most likely due to the superposition of numerous flare-like events (micro/nano-flares).

  10. Temperature structure of active regions deduced from helium-like sulphur lines

    NASA Technical Reports Server (NTRS)

    Watanabe, Tetsuya; Hara, Hirohisa; Shimizu, Toshifumi; Hiei, Eijiro; Bentley, Robert D.; Lang, James; Phillips, Kenneth J. H.; Pike, C. David; Fludra, Andrzej; Bromage, Barbara J. I.

    1995-01-01

    Solar active-region temperatures have been determined from the full-Sun spectra of helium-like sulfur (S XV) observed by the Bragg Crystal Spectrometer on Board the Yohkoh satellite. The average temperature deduced from S XV is demonstrated to vary with the solar activity level: A temperature of 2.5 x 10(exp 6) K is derived from the spectra taken during low solar activity, similar to the general corona, while 4 x 10(exp 6) K is obtained during a higher activity phase. For the latter, the high- temperature tail of the differential emission measure of active regions is found most likely due to the superposition of numerous flare-like events (micro/nano-flares).

  11. Atomic structure of the cross-[beta] spine of islet amyloid polypeptide (amylin)

    SciTech Connect

    Wiltzius, J.J.; Sievers, S.A.; Sawaya, M.R.; Cascio, D.; Popov, D.; Riekel, C.; Eisenberg, D.

    2009-03-27

    Human islet amyloid polypeptide (IAPP or amylin) is a 37-residue hormone found as fibrillar deposits in pancreatic extracts of nearly all type II diabetics. Although the cellular toxicity of IAPP has been established, the structure of the fibrillar form found in these deposits is unknown. Here we have crystallized two segments from IAPP, which themselves form amyloid-like fibrils. The atomic structures of these two segments, NNFGAIL and SSTNVG, were determined, and form the basis of a model for the most commonly observed, full-length IAPP polymorph.

  12. Bovine cone photoreceptor cGMP phosphodiesterase structure deduced from a cDNA clone.

    PubMed Central

    Li, T S; Volpp, K; Applebury, M L

    1990-01-01

    A full-length cDNA clone encoding the alpha' subunit of cGMP phosphodiesterase (PDE) from bovine cone photoreceptors was selected by probing a retinal library with a DNA fragment encoding the catalytic core of the rod cGMP PDE alpha subunit. Identity of the clone was confirmed by comparing its deduced sequence with cone PDE peptide sequences determined by Charbonneau et al. [Charbonneau, H., Prusti, R. K., LeTrong, H., Sonnenburg, W. K., Mullaney, P. J., Walsh, K. A. & Beavo, J. A. (1990) Proc. Natl. Acad. Sci. USA, pp. 288-292]. The cone PDE alpha' and the rod PDE alpha and beta subunits are encoded by distinct genes. cGMP PDE subunits share a common ancestry with cAMP PDEs and cyclic nucleotide-binding proteins. Sequence comparisons predict the presence of a catalytic core and possible secondary sites for noncatalytic cGMP binding. The presence of a C-terminal CAAX (Cys-aliphatic-aliphatic-Xaa) motif suggests the cone enzyme may be posttranslationally modified by proteolysis, methylation, and isoprenylation. Images PMID:2153291

  13. Effects of Protein Structure on Iron–Polypeptide Vibrational Dynamic Coupling in Cytochrome c

    DOE PAGES

    Galinato, Mary Grace I.; Bowman, Sarah E. J.; Kleingardner, Jesse G.; ...

    2014-12-22

    Cytochrome c (Cyt c) has a heme covalently bound to the polypeptide via a Cys-X-X-Cys-His (CXXCH) linker that is located in the interface region for protein–protein interactions. To determine whether the polypeptide matrix influences iron vibrational dynamics, nuclear resonance vibrational spectroscopy (NRVS) measurements were performed on 57Fe-labeled ferric Hydrogenobacter thermophilus cytochrome c-552, and variants M13V, M13V/K22M, and A7F, which have structural modifications that alter the composition or environment of the CXXCH pentapeptide loop. Simulations of the NRVS data indicate that the 150–325 cm–1 region is dominated by NHis–Fe–SMet axial ligand and polypeptide motions, while the 325–400 cm–1 region shows dominantmore » contributions from ν(Fe–NPyr) (Pyr = pyrrole) and other heme-based modes. Diagnostic spectral signatures that directly relate to structural features of the heme active site are identified using a quantum chemistry-centered normal coordinate analysis (QCC-NCA). In particular, spectral features that directly correlate with CXXCH loop stiffness, the strength of the Fe–His interaction, and the degree of heme distortion are identified. Cumulative results from our investigation suggest that compared to the wild type (wt), variants M13V and M13V/K22M have a more rigid CXXCH pentapeptide segment, a stronger Fe–NHis interaction, and a more ruffled heme. Conversely, the A7F variant has a more planar heme and a weaker Fe–NHis bond. These results are correlated to the observed changes in reduction potential between wt protein and the variants studied here. Lastly, we discuss the implications of these results for Cyt c biogenesis and electron transfer.« less

  14. Effects of Protein Structure on Iron–Polypeptide Vibrational Dynamic Coupling in Cytochrome c

    PubMed Central

    2015-01-01

    Cytochrome c (Cyt c) has a heme covalently bound to the polypeptide via a Cys-X-X-Cys-His (CXXCH) linker that is located in the interface region for protein–protein interactions. To determine whether the polypeptide matrix influences iron vibrational dynamics, nuclear resonance vibrational spectroscopy (NRVS) measurements were performed on 57Fe-labeled ferric Hydrogenobacter thermophilus cytochrome c-552, and variants M13V, M13V/K22M, and A7F, which have structural modifications that alter the composition or environment of the CXXCH pentapeptide loop. Simulations of the NRVS data indicate that the 150–325 cm–1 region is dominated by NHis–Fe–SMet axial ligand and polypeptide motions, while the 325–400 cm–1 region shows dominant contributions from ν(Fe–NPyr) (Pyr = pyrrole) and other heme-based modes. Diagnostic spectral signatures that directly relate to structural features of the heme active site are identified using a quantum chemistry-centered normal coordinate analysis (QCC-NCA). In particular, spectral features that directly correlate with CXXCH loop stiffness, the strength of the Fe–His interaction, and the degree of heme distortion are identified. Cumulative results from our investigation suggest that compared to the wild type (wt), variants M13V and M13V/K22M have a more rigid CXXCH pentapeptide segment, a stronger Fe–NHis interaction, and a more ruffled heme. Conversely, the A7F variant has a more planar heme and a weaker Fe–NHis bond. These results are correlated to the observed changes in reduction potential between wt protein and the variants studied here. Implications of these results for Cyt c biogenesis and electron transfer are also discussed. PMID:25531247

  15. Structure of the polypeptide crotamine from the Brazilian rattlesnake Crotalus durissus terrificus.

    PubMed

    Coronado, Monika A; Gabdulkhakov, Azat; Georgieva, Dessislava; Sankaran, Banumathi; Murakami, Mario T; Arni, Raghuvir K; Betzel, Christian

    2013-10-01

    The crystal structure of the myotoxic, cell-penetrating, basic polypeptide crotamine isolated from the venom of Crotalus durissus terrificus has been determined by single-wavelength anomalous dispersion techniques and refined at 1.7 Å resolution. The structure reveals distinct cationic and hydrophobic surface regions that are located on opposite sides of the molecule. This surface-charge distribution indicates its possible mode of interaction with negatively charged phospholipids and other molecular targets to account for its diverse pharmacological activities. Although the sequence identity between crotamine and human β-defensins is low, the three-dimensional structures of these functionally related peptides are similar. Since crotamine is a leading member of a large family of myotoxic peptides, its structure will provide a basis for the design of novel cell-penetrating molecules.

  16. Primary structure of pancreatic polypeptide from four species of Perissodactyla (Przewalski's horse, zebra, rhino, tapir).

    PubMed

    Henry, J S; Lance, V A; Conlon, J M

    1991-12-01

    Pancreatic polypeptide (PP) has been purified from extracts of the pancreas of four species of odd-toed ungulates (Perissodactyla): Przewalski's horse, mountain zebra, white rhinoceros, and mountain tapir. The amino acid sequence of Przewalski's horse pancreatic polypeptide was established as Ala-Pro-Met-Glu-Pro-Val-Tyr-Pro-Gly-Asp10-Asn- Ala-Thr-Pro-Glu-Gln-Met-Ala-Gln-Tyr20-Ala-Ala-Glu-Leu-Arg-Arg-Tyr- Ile-Asn-Met30 - Leu-Thr-Arg-Pro-Arg-Tyr.NH2. Zebra PP was identical to Przewalski's horse PP, rhinoceros PP contained three substitutions relative to the horse (Ser for Ala1, Leu for Met3, and Glu for Gln16), and tapir PP contained one substitution relative to the horse (Leu for Met3). On the basis of morphological characteristics and the fossil record, the rhinocerotids are classified with the tapirids in the suborder Ceratomorpha, whereas the horse and zebra belong to a separate suborder, Hippomorpha. On the basis of structural similarity of the PP molecules, however, it would appear that the tapir is more closely related to the horse than to the rhinoceros. These observations provide a further example of the need for extreme caution when inferring taxonomic or phylogenetic relationships between species from the structures of homologous peptides.

  17. Dithiol amino acids can structurally shape and enhance the ligand-binding properties of polypeptides

    NASA Astrophysics Data System (ADS)

    Chen, Shiyu; Gopalakrishnan, Ranganath; Schaer, Tifany; Marger, Fabrice; Hovius, Ruud; Bertrand, Daniel; Pojer, Florence; Heinis, Christian

    2014-11-01

    The disulfide bonds that form between two cysteine residues are important in defining and rigidifying the structures of proteins and peptides. In polypeptides containing multiple cysteine residues, disulfide isomerization can lead to multiple products with different biological activities. Here, we describe the development of a dithiol amino acid (Dtaa) that can form two disulfide bridges at a single amino acid site. Application of Dtaas to a serine protease inhibitor and a nicotinic acetylcholine receptor inhibitor that contain disulfide constraints enhanced their inhibitory activities 40- and 7.6-fold, respectively. X-ray crystallographic and NMR structure analysis show that the peptide ligands containing Dtaas have retained their native tertiary structures. We furthermore show that replacement of two cysteines by Dtaas can avoid the formation of disulfide bond isomers. With these properties, Dtaas are likely to have broad application in the rational design or directed evolution of peptides and proteins with high activity and stability.

  18. Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures

    SciTech Connect

    Lammert, Heiko; Noel, Jeffrey K.; Haglund, Ellinor; Onuchic, José N.; Schug, Alexander

    2015-12-28

    The diversity in a set of protein nuclear magnetic resonance (NMR) structures provides an estimate of native state fluctuations that can be used to refine and enrich structure-based protein models (SBMs). Dynamics are an essential part of a protein’s functional native state. The dynamics in the native state are controlled by the same funneled energy landscape that guides the entire folding process. SBMs apply the principle of minimal frustration, drawn from energy landscape theory, to construct a funneled folding landscape for a given protein using only information from the native structure. On an energy landscape smoothed by evolution towards minimal frustration, geometrical constraints, imposed by the native structure, control the folding mechanism and shape the native dynamics revealed by the model. Native-state fluctuations can alternatively be estimated directly from the diversity in the set of NMR structures for a protein. Based on this information, we identify a highly flexible loop in the ribosomal protein S6 and modify the contact map in a SBM to accommodate the inferred dynamics. By taking into account the probable native state dynamics, the experimental transition state is recovered in the model, and the correct order of folding events is restored. Our study highlights how the shared energy landscape connects folding and function by showing that a better description of the native basin improves the prediction of the folding mechanism.

  19. Comparisons of the immunological properties of two structural polypeptides of type C RNA viruses endogenous to old world monkeys.

    PubMed Central

    Stephenson, J R; Reynolds, R K; Aaronson, S A

    1976-01-01

    Immunologically very closely related type C RNA viruses are endogenous to the domestic cat and to an old world primate, the baboon. In the present studies, radioimmunological techniques have been developed for detection of the 15,000 and 30,000 molecular weight (MW) polypeptides of each virus. The much more pronounced type-specific antigenic determinants of the lower MW polypeptides made it possible to readily differentiate these viruses from each other as well as from a type C virus isolate from a second baboon species. Normal rhesus monkey tissues were partially purified and shown to contain a reactivity with MW and immunological properties similar to that of the baboon virus 30,000 MW polypeptide. Despite a similar degree of purification, antigenic reactivity like that of the baboon virus 15,000 MW polypeptide was undetectable even in the brodest immunological tests available for this polypeptide. The present findings indicate that the immunological properties of two structural polypeptides of closely related viruses endogenous to primate and feline species have undergone different rates of antigenic change in the course of evolution within their respective host cell genome. PMID:56455

  20. Structural Investigations of Afghanistan Deduced from Remote Sensing and Potential Field Data

    NASA Astrophysics Data System (ADS)

    Saibi, Hakim; Azizi, Masood; Mogren, Saad

    2016-08-01

    This study integrates potential gravity and magnetic field data with remotely sensed images and geological data in an effort to understand the subsurface major geological structures in Afghanistan. Integrated analysis of Landsat SRTM data was applied for extraction of geological lineaments. The potential field data were analyzed using gradient interpretation techniques, such as analytic signal (AS), tilt derivative (TDR), horizontal gradient of the tilt derivative (HG-TDR), Euler Deconvolution (ED) and power spectrum methods, and results were correlated with known geological structures. The analysis of remote sensing data and potential field data reveals the regional geological structural characteristics of Afghanistan. The power spectrum analysis of magnetic and gravity data suggests shallow basement rocks at around 1 to 1.5 km depth. The results of TDR of potential field data are in agreement with the location of the major regional fault structures and also the location of the basins and swells, except in the Helmand region (SW Afghanistan) where many high potential field anomalies are observed and attributed to batholiths and near-surface volcanic rocks intrusions. A high-resolution airborne geophysical survey in the data sparse region of eastern Afghanistan is recommended in order to have a complete image of the potential field anomalies.

  1. Comprehensive conformational studies of five tripeptides and a deduced method for efficient determinations of peptide structures.

    PubMed

    Yu, Wenbo; Wu, Zhiqing; Chen, Huibin; Liu, Xu; MacKerell, Alexander D; Lin, Zijing

    2012-02-23

    Thorough searches on the potential energy surfaces of five tripeptides, GGG, GYG, GWG, TGG, and MGG, were performed by considering all possible combinations of the bond rotational degrees of freedom with a semiempirical and ab initio combined computational approach. Structural characteristics of the obtained stable tripeptide conformers were carefully analyzed. Conformers of the five tripeptides were found to be closely connected with conformers of their constituting dipeptides and amino acids. A method for finding all important tripeptide conformers by optimizing a small number of trial structures generated by suitable superposition of the parent amino acid and dipeptide conformers is thus proposed. Applying the method to another five tripeptides, YGG, FGG, WGG, GFA, and GGF, studied before shows that the new approach is both efficient and reliable by providing the most complete ensembles of tripeptide conformers. The method is further generalized for application to larger peptides by introducing the breeding and mutation concepts in a genetic algorithm way. The generalized method is verified to be capable of finding tetrapeptide conformers with secondary structures of strands, helices, and turns, which are highly populated in larger peptides. This show some promise for the proposed method to be applied for the structural determination of larger peptides. © 2012 American Chemical Society

  2. Comprehensive Conformational Studies of Five Tripeptides and a Deduced Method for Efficient Determinations of Peptide Structures

    PubMed Central

    Yu, Wenbo; Wu, Zhiqing; Chen, Huibin; Liu, Xu; MacKerell, Alexander D.

    2012-01-01

    Thorough searches on the potential energy surfaces of five tripeptides, GGG, GYG, GWG, TGG and MGG, were performed by considering all possible combinations of the bond rotational degrees of freedom with a semi-empirical and ab initio combined computational approach. Structural characteristics of the obtained stable tripeptide conformers were carefully analyzed. Conformers of the five tripeptides were found to be closely connected with conformers of their constituting dipeptides and amino acids. A method for finding all important tripeptide conformers by optimizing a small number of trial structures generated by suitable superposition of the parent amino acid and dipeptide conformers is thus proposed. Applying the method to another five tripeptides, YGG, FGG, WGG, GFA and GGF, studied before shows that the new approach is both efficient and reliable by providing the most complete ensembles of tripeptide conformers. The method is further generalized for application to larger peptides by introducing the breeding and mutation concepts in a genetic algorithm way. The generalized method is verified to be capable of finding tetrapeptide conformers with secondary structures of strands, helices and turns which are highly populated in larger peptides. This show some promise for the proposed method to be applied for the structural determination of larger peptides. PMID:22260814

  3. High-resolution polypeptide structure and dynamics in anisotropic environments: The gramicidin channel

    SciTech Connect

    Cross, T.A.; Lee, K.C.; Ketchem, R.R.; Hu, W.; Lazo, N.D.; Huo, S.

    1994-12-01

    To understand the details of macromolecular function, high-resolution structural and dynamic detail is essential. The polypeptide fold of the gramicidin channel has been effectively modeled for the past 20 years, yet the functional changes in conductance and channel lifetime associated with amino acid substitutions cannot be predicted. To accomplish this goal, high-resolution electrostatic modeling and the precise orientation of all dipoles are required. Furthermore, an enhanced knowledge of the complex molecular environment of this membrane-bound peptide is needed. An aqueous environment is relatively uniform and achiral. The membrane environment is very heterogenous and chiral. A knowledge of the interactions, specific and nonspecific, between peptide and lipid will aid in developing a better understanding of this environment. To accomplish this goal, it is necessary to study the peptide in an extended lipid bilayer, rather than in a vesicular or micellar form. These latter environments are likely to possess increased dynamics, increased water penetration, and distorted interactions between the polypeptide and membrane surface. To perform NMR studies on bilayer bound peptides, solid state NMR methods are required, and for specific site information, isotopic labels are incorporated using solid phase peptide synthesis.

  4. The structure of the magnetosphere as deduced from magnetospherically reflected whistlers

    NASA Technical Reports Server (NTRS)

    Edgar, B. C.

    1972-01-01

    Very low frequency (VLF) electromagnetic wave phenomenon called the magnetospherically reflected (MR) whistler was investigated. VLF (0.3 to 12.5 kHz) data obtained from the Orbiting Geophysical Observatories 1 and 3 from October 1964 to December 1966 were used. MR whistlers are produced by the dispersive propagation of energy from atmospheric lightning through the magnetosphere to the satellite along ray paths which undergo one or more reflections due to the presence of ions. The gross features of MR whistler frequency-time spectrograms are explained in terms of propagation through a magnetosphere composed of thermal ions and electrons and having small density gradients across L-shells. Irregularities observed in MR spectra were interpreted in terms of propagation through field-aligned density structures. Trough and enhancement density structures were found to produce unique and easily recognizable signatures in MR spectra. Sharp cross-field density dropoff produces extra traces in MR spectrograms.

  5. Crustal structure deduced from receiver functions via single-scattering migration

    NASA Astrophysics Data System (ADS)

    Bertrand, E.; Deschamps, A.; Virieux, J.

    2002-08-01

    An investigation of the teleseismic P-wave coda is performed using the single-scattering approximation. The method allows one to image short-wavelength scale (<=2 km) velocity and density heterogeneities and structures that are barely detected by traveltime tomography. Source effects are removed by using receiver functions for data interpretation, but the amplitude (especially the sign of the signal) is synthesized. Both broad-band seismological stations in the southwestern Alps (France) and Campanian plain (Italy) are used for the illustration of the proposed method. Because of the large aperture of our arrays, laterally small-scale heterogeneities are difficult to image and we must assume lateral continuity of the detectable structure. If so, we show that this depth migration based on a single-scattering approach can recover both the depth and the geometry of the main discontinuities below the studied areas. In the southwestern Alps, we underline a complex crustal structure and Moho dipping topography. The Moho depth increases from 20 to 30 km between the coastline and the Mercantour range. In the Campanian plain (surrounding Mount Vesuvius) we also find a southeastwards-dipping Moho. Furthermore, the three main discontinuities are imaged, showing a relatively shallow mantle-crust discontinuity and a deeper one near the coastline.

  6. Seismic structure off the Kii Peninsula, Japan, deduced from passive- and active-source seismographic data

    NASA Astrophysics Data System (ADS)

    Yamamoto, Yojiro; Takahashi, Tsutomu; Kaiho, Yuka; Obana, Koichiro; Nakanishi, Ayako; Kodaira, Shuichi; Kaneda, Yoshiyuki

    2017-03-01

    We conduct seismic tomography to model subsurface seismicity between 2010 and 2012 and structural heterogeneity off the Kii Peninsula, southwestern Japan, and to investigate their relationships with segmentation of the Nankai and Tonankai seismogenic zones of the Nankai Trough. In order to constrain both the shallow and deep structure of the offshore seismogenic segments, we use both active- and passive-source data recorded by both ocean-bottom seismometers and land seismic stations. The relocated microearthquakes indicate a lack of seismic activity in the Tonankai seismogenic segment off Kumano, whereas there was active intraslab seismicity in the Kii Channel area of the Nankai seismogenic segment. Based on comparisons among the distribution of seismicity, age, and spreading rate of the subducting Philippine Sea plate, and the slip-deficit distribution, we conclude that seismicity in the subducting slab under the Kii Channel region nucleated from structures in the Philippine Sea slab that pre-date subduction and that fluids released by dehydration are related to decreased interplate coupling of these intraslab earthquakes. Our velocity model clearly shows the areal extent of two key structures reported in previous 2-D active-source surveys: a high-velocity zone beneath Cape Shionomisaki and a subducted seamount off Cape Muroto, both of which are roughly circular and of 15-20 km radius. The epicenters of the 1944 Tonankai and 1946 Nankai earthquakes are near the edge of the high-velocity body beneath Cape Shionomisaki, suggesting that this anomalous structure is related to the nucleation of these two earthquakes. We identify several other high- and low-velocity zones immediately above the plate boundary in the Tonankai and Nankai seismogenic segments. In comparison with the slip-deficit model, some of the low-velocity zones appear to correspond to an area of strong coupling. Our observations suggest that, unlike the Japan Trench subduction zone, in our study area

  7. Elastomeric Polypeptides

    PubMed Central

    van Eldijk, Mark B.; McGann, Christopher L.

    2013-01-01

    Elastomeric polypeptides are very interesting biopolymers and are characterized by rubber-like elasticity, large extensibility before rupture, reversible deformation without loss of energy, and high resilience upon stretching. Their useful properties have motivated their use in a wide variety of materials and biological applications. This chapter focuses on elastin and resilin – two elastomeric biopolymers – and the recombinant polypeptides derived from them (elastin-like polypeptides and resilin-like polypeptides). This chapter also discusses the applications of these recombinant polypeptides in the fields of purification, drug delivery, and tissue engineering. PMID:21826606

  8. Deduced primary structure of rat hepatocyte growth factor and expression of the mRNA in rat tissues.

    PubMed Central

    Tashiro, K; Hagiya, M; Nishizawa, T; Seki, T; Shimonishi, M; Shimizu, S; Nakamura, T

    1990-01-01

    The primary structure of rat hepatocyte growth factor (HGF) was elucidated by determining the base sequence of the complementary DNA (cDNA) of HGF. The cDNA for rat HGF was isolated by screening a liver cDNA library with oligonucleotides based on the partial N-terminal amino acid sequence of the beta subunit of purified rat HGF. HGF is encoded in an mRNA of about 6 kilobases. Both alpha and beta subunits of HGF are specified in a single open reading frame for a 728-amino acid protein with a calculated molecular weight of 82,904. The N-terminal part of HGF has a signal sequence and a prosequence with 30 and 25 amino acid residues, respectively. The mature heterodimer structure is derived proteolytically from this single pre-pro precursor polypeptide. The calculated molecular weights of the alpha and beta subunits are 50,664 and 25,883, respectively, and each subunit has two potential N-linked glycosylation sites. The amino acid sequence of HGF is 38% identical with that of plasminogen. The alpha subunit of HGF contains four "kringle" structures, and the beta subunit has 37% amino acid identity with the serine protease domain of plasmin. Northern blot analysis revealed that HGF mRNA was expressed in rat various tissues, including the liver, kidney, lung, and brain. Images PMID:2139229

  9. Shallow structure and recent evolution of the Aegean Sea deduced from the seismic reflection analysis

    SciTech Connect

    Laure, M.; Mascle, J.

    1988-08-01

    Together with the Tyrrhenian Sea, the Aegean Sea represents one of two marine basins still developing as a consequence of the subduction of the African lithosphere beneath Europe. Despite many geophysical similarities with the Tyrrhenian Sea, the Aegean displays a specific structural segmentation characterized by two distinct domains separated by the central Aegean. To the north of the basin, the so-called North Aegean trough likely represents the western marine extension of the transtensive Anatolian transform fault zone. The northern margin of this area contains a series of disconnected, often thickly sedimented small basins that probably initiated during the late Miocene as a consequence of a dominantly north-south extension; typical uppermost Miocene (Messinian) formations can be observed on seismic grounds. To the south, the Cretan Sea shows clear evidence of important distensive events occurring during two main episodes and following two main trends; a dominantly north-south-directed extension is responsibile for most of the structural features detected along both the Cretan and southern Cyclades margins.

  10. Structure-property relationships in major ampullate spider silk as deduced from polarized FTIR spectroscopy

    NASA Astrophysics Data System (ADS)

    Papadopoulos, P.; Sölter, J.; Kremer, F.

    2007-10-01

    Polarized Fourier Transform Infrared (FTIR) spectroscopy is employed to study structure-property relationships in major ampullate spider silk being exposed to an external mechanical strain. From the measured infrared dichroism of aminoacid-residue - specific bands the molecular order parameter, the frequency width at half-maximum (FWHM) and the spectral position of the absorption maximum are determined in dependence on the external strain. For the highly ordered alanine-rich β sheets a change in the vibrational potential is found for macroscopic strains as low as a few percent. It can be quantitatively described by a quantum-mechanical approach in which the mechanical strain is treated as a weak external perturbation. The immediate microscopic response to the external field proves that β -sheeted crystals are tightly interconnected by pre-stretched chains as suggested recently (Y. Liu et al., Nat. Mater. 4, 901 (2005)).

  11. Jupiter's atmospheric composition and cloud structure deduced from absorption bands in reflected sunlight

    NASA Technical Reports Server (NTRS)

    Sato, M.; Hansen, J. E.

    1979-01-01

    The spectrum of sunlight reflected by Jupiter is analyzed by comparing observations of Woodman (1979) with multiple-scattering computations. The analysis yields information on the vertical cloud structure at several latitudes and on the abundance of CH4 and NH3 in the atmosphere of Jupiter. The abundances of CH4 and NH3 suggest that all ices and rocks are overabundant on Jupiter by a factor of 2 or more, providing an important constraint on models for the formation of Jupiter from the primitive solar nebula. The pressure level of the clouds, the gaseous NH3 abundance, the mean temperature profile, and the Clausius-Clapeyron relation suggest that these clouds are predominantly ammonia crystals with the cloud bottom at 600-700 mb. A diffuse distribution of aerosols exists between 150 and 500 mb, and the spectral variation of albedo reflects a changing bulk absorption coefficient of the material composing the aerosols and is diagnostic of the aerosol composition.

  12. Stoichiometry of lipid interactions with transmembrane proteins--Deduced from the 3D structures.

    PubMed

    Páli, Tibor; Bashtovyy, Denys; Marsh, Derek

    2006-05-01

    The stoichiometry of the first shell of lipids interacting with a transmembrane protein is defined operationally by the population of spin-labeled lipid chains whose motion is restricted directly by the protein. Interaction stoichiometries have been determined experimentally for a wide range of alpha-helical integral membrane proteins by using spin-label ESR spectroscopy. Here, we determine the spatially defined number of first-shell lipids at the hydrophobic perimeter of integral membrane proteins whose 3D structure has been determined by X-ray crystallography and lipid-protein interactions characterized by spin-labeling. Molecular modeling is used to build a single shell of lipids surrounding transmembrane structures derived from the PDB. Constrained energy optimization of the protein-lipid assemblies is performed by molecular mechanics. For relatively small proteins (up to 7-12 transmembrane helices), the geometrical first shell corresponds to that defined experimentally by perturbation of the lipid-chain dynamics. For larger, multi-subunit alpha-helical proteins, the lipids perturbed directly by the protein may either exceed or be less in number than those that can be accommodated at the intramembranous perimeter. In these latter cases, the motionally restricted spin-labeled lipids can be augmented by intercalation, or can correspond to a specific subpopulation at the protein interface, respectively. For monomeric beta-barrel proteins, the geometrical lipid stoichiometry corresponds to that determined from lipid mobility for a 22-stranded barrel, but fewer lipids are motionally restricted than can be accommodated around an eight-stranded barrel. Deviations from the geometrical first shell, in the beta-barrel case, are for the smaller protein with a highly curved barrel.

  13. Crustal structure of the Hecataeus Rise (eastern Mediterranean) deduced by marine gravity and marine magnetic modelling

    NASA Astrophysics Data System (ADS)

    Dehghani, Ali

    2016-04-01

    In the year 2010 extensive geophysical researches were carried out in the area of Hecataeus Rise using the German research vessel Maria S. Merian. Beside the bathymetry, refraction and reflection seismic data, marine gravity and marine magnetic data were acquired during this cruise. The result of the research along one Wide-Angle reflection/refraction seismic line of this cruise is published 2015 by K. Welford et al.. Based on interpretation of reflection seismic and bathymetry data across the Hecataeus Rise, S. Reiche published 2015 the crustal structure and bathymetric features along some seismic profiles of this cruise. The focus of this work is to use the available sediments and crustal structures inferred by seismic information together with real marine gravity and marine magnetic data in order to produce gravity and magnetic 2-D models along all seismic profiles. While Welford et al. used the altimetry gravity data and magnetic data from EMAG3 database for their modelling, the real gravity and magnetic data measured exactly along the seismic profiles will be used in this work. The advantage of the real marine gravity and real marine magnetic data used for the modelling is that they have higher accuracy in the values as well as in the positions. Furthermore, Welford et al. calculated the gravity and Magnetic models along some seismic profiles, while in this work the result of gravity and magnetic modelling along all seismic profiles of this cruise will be presented. The marine gravity and marine magnetic data along all seismic profiles were recorded continuously. The accuracy of marine gravity data is about ± 1 mGal, while the accuracy of Marine magnetic data is in the range of ± 3 nT. The results of 2-D gravity and magnetic modelling will be presented and discussed in this work.

  14. Biomimetic deposition of hydroxyapatite on a synthetic polypeptide with beta sheet structure in a solution mimicking body fluid.

    PubMed

    Takeuchi, Akari; Ohtsuki, Chikara; Kamitakahara, Masanobu; Ogata, Shin-ichi; Miyazaki, Toshiki; Tanihara, Masao

    2008-01-01

    Deposition of a hydroxyapatite layer with similar structure to bone mineral is an attractive approach to the fabrication of bioactive coating layers to achieve direct bonding to living bone. To get successful coating of a hydroxyapatite layer on an organic polymer using a biomimetic solution, it is essential to find organic substrates that can effectively induce heterogeneous nucleation of hydroxyapatite after exposure to the body environment. Our previous study showed that sericin, a type of silk protein, has the ability to induce hydroxyapatite nucleation in a biomimetic solution when the sericin has a beta sheet structure. To confirm the effectiveness of the beta sheet structure in hydroxyapatite nucleation, we focused on investigating hydroxyapatite deposition on a synthetic polypeptide with a beta sheet structure in a biomimetic solution. The beta sheet forming polypeptides with and without carboxyl groups, poly(FE)(3)FG, poly(FQ)(3)FG, poly(LE)(3)LG and poly(LQ)(3)LG, were synthesized in this study. All the polypeptides had mainly beta sheet structure. After soaking the polypeptide films in 1.5SBF, which has 1.5 times the inorganic ion concentrations of human blood plasma, hydroxyapatite formed on the surfaces of the polypeptides with carboxyl groups, poly(FE)(3)FG and poly(LE)(3)LG, within 2 days, but not on those without carboxyl groups, poly(FQ)(3)FG and poly(LQ)(3)LG. We confirmed that the beta sheet structure was effective for hydroxyapatite nucleation even in the synthetic polypeptide. This finding is useful for the future design of organic polymers that can effectively induce nucleation of hydroxyapatite.

  15. A model for the quaternary structure of human placental insulin receptor deduced from electron microscopy.

    PubMed Central

    Christiansen, K; Tranum-Jensen, J; Carlsen, J; Vinten, J

    1991-01-01

    Electrophoretically pure and functionally intact human placental insulin receptor was studied by electron microscopy with negative-staining techniques. The quaternary structure of the detergent-solubilized receptor was determined. The receptor had the shape of a letter T approximately 24 nm in height and 18 nm in width with a thickness of the stem and the crossbar of 3-4 nm. No consistent change in ultrastructure of the receptor could be detected after the addition of insulin alone or insulin and Mn2+/Mg2+/ATP. After partial reduction of the alpha 2 beta 2 heterotetrameric receptor into alpha beta heterodimers, the electron micrographs showed a clear reduction in average size of the molecule with disappearance of the T profiles characteristic of the alpha 2 beta 2 heterotetramers. By incubation of the heterodimers in a phosphorylation medium containing insulin, a reassociation to molecules with molecular weights of the alpha 2 beta 2 heterotetramer took place judged from SDS/PAGE. Electron microscopy showed that the molecule formed larger aggregates, and only a few solitary T-shaped copies were seen. Images PMID:1986371

  16. The structure of the shallow crust beneath Olkaria geothermal field, Kenya, deduced from gravity studies

    NASA Astrophysics Data System (ADS)

    Ndombi, J. M.

    1981-02-01

    The Olkaria region of the Kenya rift valley is a potentially important geothermal area due to the occurrence of young volcanic activity and surface geothermal manifestations which include hot springs, fumaroles and thermally altered ground. In order to determine subsurface structure nearly 255 new gravity measurements, together with existing regional gravity data, were used to propose a subsurface model. A few surface density measurements have been made within Olkaria and in adjoining areas, and these combined with density values inferred from the measured P-wave seismic velocities within Olkaria are used to define the density distribution within the shallow crust. A two-dimensional model to explain the local gravity anomalies indicates that an approximately horizontal three-layer volcanic sequence overlying the basement system is downfaulted on the western part of Olkaria, and is intruded by denser dyke-like bodies of rhyolitic composition along the north-south-trending fractures that occur mainly in the central part of the Olkaria. An increase in the thickness of volcanics in the western part of Olkaria is responsible for the observed negative Bouguer anomaly in that area, while vertical density contrasts between the dyke-like intrusions and the host rock generate model anomalies in good agreement with the observed positive Bouguer anomalies in the central part of Olkaria. The largest and most recent intrusion, which is probably still in a magmatic state, occurs along the Ololbutot fracture zone and is apparently the main heat source for the geothermal phenomena in Olkaria.

  17. Lower mantle thermal structure deduced from seismic tomography, mineral physics and numerical modelling

    NASA Technical Reports Server (NTRS)

    Cadek, O.; Yuen, D. A.; Steinbach, V.; Chopelas, A.; Matyska, C.

    1994-01-01

    The long-wavelength thermal anomalies in the lower mantle have been mapped out using several seismic tomographic models in conjunction with thermodynamic parameters derived from high-pressure mineral physics experiments. These parameters are the depth variations of thermal expansivity and of the proportionality factor between changes in density and seismic velocity. The giant plume-like structures in the lower mantle under the Pacific Ocean and Africa have outer fringes with thermal anomalies around 300-400 K, but very high temperatures are found in the center of the plumes near the base of the core-mantle boundary. These extreme values can exceed +1500 K and may reflect large hot thermal anomalies in the lower mantle, which are supported by recent measurements of high melting temperatures of perovskite and iron. Extremely cold anomalies, around -1500 K, are found for anomalies in the deep mantle around the Pacific rim and under South America. Numerical simulations show that large negative thermal anomalies in the mid-lower mantle have modest magnitudes of around -500 K. correlation pattern exists between the present-day locations of cold masses in the lower mantle and the sites of past subduction since the Cretaceous. Results from correlation analysis show that the slab mass-flux in the lower mantle did not conform to a steady-state nature but exhibited time-dependent behavior.

  18. Lower mantle thermal structure deduced from seismic tomography, mineral physics and numerical modelling

    NASA Technical Reports Server (NTRS)

    Cadek, O.; Yuen, D. A.; Steinbach, V.; Chopelas, A.; Matyska, C.

    1994-01-01

    The long-wavelength thermal anomalies in the lower mantle have been mapped out using several seismic tomographic models in conjunction with thermodynamic parameters derived from high-pressure mineral physics experiments. These parameters are the depth variations of thermal expansivity and of the proportionality factor between changes in density and seismic velocity. The giant plume-like structures in the lower mantle under the Pacific Ocean and Africa have outer fringes with thermal anomalies around 300-400 K, but very high temperatures are found in the center of the plumes near the base of the core-mantle boundary. These extreme values can exceed +1500 K and may reflect large hot thermal anomalies in the lower mantle, which are supported by recent measurements of high melting temperatures of perovskite and iron. Extremely cold anomalies, around -1500 K, are found for anomalies in the deep mantle around the Pacific rim and under South America. Numerical simulations show that large negative thermal anomalies in the mid-lower mantle have modest magnitudes of around -500 K. correlation pattern exists between the present-day locations of cold masses in the lower mantle and the sites of past subduction since the Cretaceous. Results from correlation analysis show that the slab mass-flux in the lower mantle did not conform to a steady-state nature but exhibited time-dependent behavior.

  19. Gene conversion variations generate structurally distinct pilin polypeptides in Neisseria gonorrhoeae.

    PubMed

    Swanson, J; Robbins, K; Barrera, O; Koomey, J M

    1987-04-01

    Pilus+ to pilus- phenotype change occurs in Neisseria gonorrhoeae through gene conversion of the gonococcus' complete, expressed pilin gene by nucleotides homologous to the pilS1 copy 5 partial pilin gene; assembly missense pilin is synthesized but pili are not. Reversion to pilus+ occurs by a subsequent recombinational event that replaces the complete pilin gene's pilS1 copy 5-like sequence with nucleotides from a different partial gene to effect expression of an orthodox (i.e., pilus producing) pilin. Sibling pilus+ revertants of common parentage can carry different sequences in their expressed pilin genes because they have undergone nonidentical gene conversion events such as recombinations with sequences from different partial genes, or recombinations with different length nucleotide stretches of the same partial gene; either can yield structurally and antigenically variant pilin polypeptides.

  20. Effect of O-Linked Glycosylation on the Equilibrium Structural Ensemble of Intrinsically Disordered Polypeptides.

    PubMed

    Zerze, Gül H; Mittal, Jeetain

    2015-12-24

    Glycosylation is one of the most common post-translational modifications (PTMs), which provides a large proteome diversity. Previous work on glycosylation of globular proteins has revealed remarkable effects of glycosylation on protein function, altering the folding stability and structure and/or altering the protein surface which affects their binding characteristics. Intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) of large proteins are also frequently glycosylated, yet how glycosylation affects their function remains to be elucidated. An important open question is, does glycosylation affect IDP structure or binding characteristics or both? In this work, we particularly address the structural effects of O-linked glycosylation by investigating glycosylated and unglycosylated forms of two different IDPs, tau174-183 and human islet amyloid polypeptide (hIAPP), by all-atom explicit solvent simulations. We simulate these IDPs in aqueous solution for O-linked glycosylated and unglycosylated forms by employing two modern all-atom force fields for which glycan parameters are also available. We find that O-linked glycosylation only has a modest effect on equilibrium structural ensembles of IDPs, for the cases studied here, which suggests that the functional role of glycosylation may be primarily exerted by modulation of the protein binding characteristics rather than structure.

  1. Antifungal polypeptides

    DOEpatents

    Altier, Daniel J [Waukee, IA; Ellanskaya, Irina [Kyiv, UA; Ellanskaya, legal representative, Natalia; Gilliam, Jacob T [Norwalk, IA; Hunter-Cevera, Jennie [Elliott City, MD; Presnail, James K [Avondale, PA; Schepers, Eric [Port Deposit, MD; Simmons, Carl R [Des Moines, IA; Torok, Tamas [Richmond, CA; Yalpani, Nasser [Johnston, IA

    2009-09-15

    The invention relates to antifungal compositions and methods for protecting a plant from a fungal pathogen. Compositions including antifungal polypeptides isolated from a fungal fermentation broth are provided.

  2. Proton–proton Overhauser NMR spectroscopy with polypeptide chains in large structures

    PubMed Central

    Horst, Reto; Wider, Gerhard; Fiaux, Jocelyne; Bertelsen, Eric B.; Horwich, Arthur L.; Wüthrich, Kurt

    2006-01-01

    The use of 1H–1H nuclear Overhauser effects (NOE) for structural studies of uniformly deuterated polypeptide chains in large structures is investigated by model calculations and NMR experiments. Detailed analysis of the evolution of the magnetization during 1H–1H NOE experiments under slow-motion conditions shows that the maximal 1H–1H NOE transfer is independent of the overall rotational correlation time, even in the presence of chemical exchange with the bulk water, provided that the mixing time is adjusted for the size of the structure studied. 1H–1H NOE buildup measurements were performed for the 472-kDa complex of the 72-kDa cochaperonin GroES with a 400-kDa single-ring variant of the chaperonin GroEL (SR1). These experiments demonstrate that multidimensional NOESY experiments with cross-correlated relaxation-enhanced polarization transfer and transverse relaxation-optimized spectroscopy elements can be applied to structures of molecular masses up to several hundred kilodaltabs, which opens new possibilities for studying functional interactions in large maromolecular assemblies in solution. PMID:17032756

  3. Antifungal polypeptides

    DOEpatents

    Altier, Daniel J.; Dahlbacka, Glen; Ellanskaya, legal representative, Natalia; Herrmann, Rafael; Hunter-Cevera, Jennie; McCutchen, Billy F.; Presnail, James K.; Rice, Janet A.; Schepers, Eric; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser; Ellanskaya, deceased, Irina

    2007-12-11

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include novel amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from microbial fermentation broths. Nucleic acid molecules comprising nucleotide sequences that encode the antipathogenic polypeptides of the invention are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention, or variant or fragment thereof, are also disclosed.

  4. Antifungal polypeptides

    DOEpatents

    Altier, Daniel J [Granger, IA; Dahlbacka, Glen [Oakland, CA; Ellanskaya, Irina [Kyiv, UA; Ellanskaya, legal representative, Natalia; Herrmann, Rafael [Wilmington, DE; Hunter-Cevera, Jennie [Elliott City, MD; McCutchen, Billy F [College Station, TX; Presnail, James K [Avondale, PA; Rice, Janet A [Wilmington, DE; Schepers, Eric [Port Deposit, MD; Simmons, Carl R [Des Moines, IA; Torok, Tamas [Richmond, CA; Yalpani, Nasser [Johnston, IA

    2012-04-03

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include novel amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from microbial fermentation broths. Nucleic acid molecules comprising nucleotide sequences that encode the antipathogenic polypeptides of the invention are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention, or variant or fragment thereof, are also disclosed.

  5. Antifungal polypeptides

    DOEpatents

    Altier, Daniel J.; Dahlbacka, Glen; Elleskaya, Irina; Ellanskaya, legal representative; Natalia; Herrmann, Rafael; Hunter-Cevera, Jennie; McCutchen, Billy F.; Presnail, James K.; Rice, Janet A.; Schepers, Eric; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2010-08-10

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include novel amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from microbial fermentation broths. Nucleic acid molecules comprising nucleotide sequences that encode the antipathogenic polypeptides of the invention are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention, or variant or fragment thereof, are also disclosed.

  6. Antifungal polypeptides

    DOEpatents

    Altier, Daniel J [Waukee, IA; Dahlbacka, Glen [Oakland, CA; Elleskaya, Irina [Kyiv, UA; Ellanskaya, legal representative, Natalia; Herrmann, Rafael [Wilmington, DE; Hunter-Cevera, Jennie [Elliott City, MD; McCutchen, Billy F [College Station, IA; Presnail, James K [Avondale, PA; Rice, Janet A [Wilmington, DE; Schepers, Eric [Port Deposit, MD; Simmons, Carl R [Des Moines, IA; Torok, Tamas [Richmond, CA; Yalpani, Nasser [Johnston, IA

    2011-04-12

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include novel amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from microbial fermentation broths. Nucleic acid molecules comprising nucleotide sequences that encode the antipathogenic polypeptides of the invention are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention, or variant or fragment thereof, are also disclosed.

  7. Identifying structural features of fibrillar islet amyloid polypeptide using site-directed spin labeling.

    PubMed

    Jayasinghe, Sajith A; Langen, Ralf

    2004-11-12

    Pancreatic amyloid deposits, composed primarily of the 37-residue islet amyloid polypeptide (IAPP), are a characteristic feature found in more than 90% of patients with type II diabetes. Although IAPP amyloid deposits are associated with areas of pancreatic islet beta-cell dysfunction and depletion and are thought to play a role in disease, their structure is unknown. We used electron paramagnetic resonance spectroscopy to analyze eight spin-labeled derivatives of IAPP in an effort to determine structural features of the peptide. In solution, all eight derivatives gave rise to electron paramagnetic resonance spectra with sharp lines indicative of rapid motion on the sub-nanosecond time scale. These spectra are consistent with a rapidly tumbling and highly dynamic peptide. In contrast, spectra for the fibrillar form exhibit reduced mobility and the presence of strong intermolecular spin-spin interactions. The latter implies that the peptide subunits are ordered and that the same residues from neighboring peptides are in close proximity to one another. Our data are consistent with a parallel arrangement of IAPP peptides within the amyloid fibril. Analysis of spin label mobility indicates a high degree of order throughout the peptide, although the N-terminal region is slightly less ordered. Possible similarities with respect to the domain organization and parallelism of Alzheimer's amyloid beta peptide fibrils are discussed.

  8. [Structure, localization and physiologic role of pituitary adenylate cyclase activating polypeptide (PACAP)].

    PubMed

    Vincze, E; Köves, K

    2001-03-11

    PACAP was isolated on the basis of its ability to stimulate adenylate cyclase in primary anterior pituitary cell culture from ovine hypothalami by Miyata et al. in 1989. This peptide is structurally related to the secretin family and shows a 67% sequence homology with vasoactive intestinal polypeptide (VIP). The amino acid sequence of PACAP has been highly preserved during the evolution that may be connected with its important physiological role. Similar to other "brain-gut peptides" PACAP is localized not only in the central but in the peripheral nervous system and in non-neural tissues as well. In addition to its hypophysiotropic effects in the hypothalamo-hypophysial system PACAP exerts its effects on water-salt balance, cardiovascular functions, gastrointestinal motility and secretion and also on the regulation of reproductive functions. PACAP has a role in certain neuro-immuno-endocrine processes, in the differentiation of the nervous system, and it has neuroprotective effects in the case of ischaemia and various toxic agents. Locally PACAP takes its effects as an auto- and paracrine hormone, a neurotransmitter or a neuromodulator in different organs. Besides VIP, PACAP plays an important role in the function of the photo-neuro-endocrine system.

  9. Chaperone activity and structure of monomeric polypeptide binding domains of GroEL

    PubMed Central

    Zahn, Ralph; Buckle, Ashley M.; Perrett, Sarah; Johnson, Christopher M.; Corrales, Fernando J.; Golbik, Ralph; Fersht, Alan R.

    1996-01-01

    The chaperonin GroEL is a large complex composed of 14 identical 57-kDa subunits that requires ATP and GroES for some of its activities. We find that a monomeric polypeptide corresponding to residues 191 to 345 has the activity of the tetradecamer both in facilitating the refolding of rhodanese and cyclophilin A in the absence of ATP and in catalyzing the unfolding of native barnase. Its crystal structure, solved at 2.5 Å resolution, shows a well-ordered domain with the same fold as in intact GroEL. We have thus isolated the active site of the complex allosteric molecular chaperone, which functions as a “minichaperone.” This has mechanistic implications: the presence of a central cavity in the GroEL complex is not essential for those representative activities in vitro, and neither are the allosteric properties. The function of the allosteric behavior on the binding of GroES and ATP must be to regulate the affinity of the protein for its various substrates in vivo, where the cavity may also be required for special functions. PMID:8986757

  10. Structural characteristics of the beta-sheet-like human and rat islet amyloid polypeptides as determined by scanning tunneling microscopy.

    PubMed

    Mao, Xiaobo; Ma, Xiaojing; Liu, Lei; Niu, Lin; Yang, Yanlian; Wang, Chen

    2009-09-01

    We demonstrate in this work that scanning tunneling microscopy (STM) provides a useful approach to obtaining structural information about human islet amyloid polypeptide (hIAPP) and rat islet amyloid polypeptide (rIAPP) assembly on highly oriented pyrolytic graphite (HOPG) with sub-molecular resolution. The observed hIAPP and rIAPP lamellae consisted of parallel stripes. The STM images of hIAPPs show multiple molecular folding structures, with an average of 11 amino acid residues for the core regions. In addition, the STM images also reveal the assembly characteristics of rIAPP lamellae and may indicate a secondary structural conformation from random coil to beta-sheet-like on the graphite surface.

  11. Thermodynamic and structural analysis of phosphotyrosine polypeptide binding to Grb2-SH2.

    PubMed

    McNemar, C; Snow, M E; Windsor, W T; Prongay, A; Mui, P; Zhang, R; Durkin, J; Le, H V; Weber, P C

    1997-08-19

    A thermodynamic analysis using isothermal titration calorimetry (ITC) has been performed to examine the binding interaction between the SH2 (Src homology 2) domain of growth factor receptor binding protein 2 (Grb2-SH2) and one of its phosphotyrosine (pY) polypeptide ligands. Interaction of the Shc-derived phosphotyrosine hexapeptide Ac-SpYVNVQ-NH2 with Grb2-SH2 was both enthalpically and entropically favorable (DeltaH = -7.55 kcal mol-1, -TDeltaS = -1.46 kcal mol-1 , DeltaG = -9.01 kcal mol-1, T = 20 degrees C). ITC experiments using five alanine-substituted peptides were performed to examine the role of each side chain in binding. The results were consistent with homology models of the Grb2-SH2-Shc hexapeptide complex which identified several possible hydrogen bonds between Grb2-SH2 and the phosphotyrosine and conserved asparagine(+2) side chains of the Shc hexapeptide. These studies also demonstrated that the hydrophobic valine(+1) side chain contributes significantly to the favorable entropic component of binding. The thermodynamic and structural data are consistent with a Grb2-SH2 recognition motif of pY-hydrophobic-N-X (where X is any amino acid residue). The measured heat capacity of binding (DeltaCp = -146 cal mol-1 K-1) was very similar to computed values using semiempirical estimates (DeltaCp = -106 to -193 cal mol-1 K-1) derived from apolar and polar accessible surface area values calculated from several homology models of the Grb2-SH2-Shc hexapeptide complex. The homology model which most closely reproduced the measured DeltaCp value is also the model which had the lowest RMS deviation from the subsequently determined crystal structure. Calculations based on the thermodynamic data and these semiempirical estimates indicated that the binding event involves burial of nearly comparable apolar (677 A2) and polar (609 A2) surface areas.

  12. Prediction of polyelectrolyte polypeptide structures using Monte Carlo conformational search methods with implicit solvation modeling.

    PubMed Central

    Evans, J. S.; Chan, S. I.; Goddard, W. A.

    1995-01-01

    Many interesting proteins possess defined sequence stretches containing negatively charged amino acids. At present, experimental methods (X-ray crystallography, NMR) have failed to provide structural data for many of these sequence domains. We have applied the dihedral probability grid-Monte Carlo (DPG-MC) conformational search algorithm to a series of N- and C-capped polyelectrolyte peptides, (Glu)20, (Asp)20, (PSer)20, and (PSer-Asp)10, that represent polyanionic regions in a number of important proteins, such as parathymosin, calsequestrin, the sodium channel protein, and the acidic biomineralization proteins. The atomic charges were estimated from charge equilibration and the valence and van der Waals parameters are from DREIDING. Solvation of the carboxylate and phosphate groups was treated using sodium counterions for each charged side chain (one Na+ for COO-; two Na for CO(PO3)-2) plus a distance-dependent (shielded) dielectric constant, epsilon = epsilon 0 R, to simulate solvent water. The structures of these polyelectrolyte polypeptides were obtained by the DPG-MC conformational search with epsilon 0 = 10, followed by calculation of solvation energies for the lowest energy conformers using the protein dipole-Langevin dipole method of Warshel. These calculations predict a correlation between amino acid sequence and global folded conformational minima: 1. Poly-L-Glu20, our structural benchmark, exhibited a preference for right-handed alpha-helix (47% helicity), which approximates experimental observations of 55-60% helicity in solution. 2. For Asp- and PSer-containing sequences, all conformers exhibited a low preference for right-handed alpha-helix formation (< or = 10%), but a significant percentage (approximately 20% or greater) of beta-strand and beta-turn dihedrals were found in all three sequence cases: (1) Aspn forms supercoil conformers, with a 2:1:1 ratio of beta-turn:beta-strand:alpha-helix dihedral angles; (2) PSer20 features a nearly 1:1 ratio of

  13. Structural characterization of reverse transcriptase and endonuclease polypeptides of the acquired immunodeficiency syndrome retrovirus.

    PubMed Central

    Lightfoote, M M; Coligan, J E; Folks, T M; Fauci, A S; Martin, M A; Venkatesan, S

    1986-01-01

    Automated N-terminal microsequencing of immune affinity-purified acquired immunodeficiency syndrome retrovirus polypeptides from infected cells was used to locate the N termini of 64-, 51-, and 34-kilodalton (kDa) polypeptides within the pol open reading frame (ORF) of the proviral DNA. The 64- and 51-kDa proteins had identical N termini (Pro-Ile-Ser-Pro-IIe-Glu-Thr-Val-) positioned 156 residues from the beginning of the pol ORF. The N terminus of the 34-kDa pol gene product, Phe-Leu-Asp-Gly-Ile-Asp-Lys-, mapped 716 residues into the pol ORF. These polypeptides were absent in an RT-negative, CD4-negative, persistently infected cell line (8E5) carrying a single defective copy of a constitutively expressed, integrated proviral DNA. Images PMID:2430111

  14. Secondary Structure-Induced Micro- and Macro-Phase Separation in Polypeptide Diblock, Triblock and Star-Block Copolymers

    NASA Astrophysics Data System (ADS)

    Sanchez-Ferrer, Antoni; Mezzenga, Raffaele

    2010-03-01

    Self-organized polypeptide block copolymers are of great interest due to their potential uses as materials for nano-devices and bio-engineering. In order to explore the effect of block copolymer topologies on their structures, a series of di-, tri- and tetra-block copolymers has been synthesized. A coil-like soft block based on poly(propylene oxide) chemistry was chosen due to its low glass transition temperature, amorphous nature and immiscibility with biological systems. On the other hand, rod-like block polypeptide based on poly(L-glutamic acid γ-benzyl ester) was selected and grown from the coil soft macroinitiator by ring opening polymerization. Because of the mono-, bi-, or tri-functionality of the coiled blocks, linear di-block, tri-block and star-like tetra-block copolymers could be successfully synthesized. The resulting materials show micro-phase separated liquid-crystalline morphologies, in which the architecture or connectivity of the blocks, the molecular weight of the coil segment, the volume fraction and the secondary structure of the polypeptide blocks all contribute to their micro-phase separated features. These materials can be seen as model reference systems towards the design of biocompatible scaffolds and artificial muscles.

  15. Iron-mediated aggregation and a localized structural change characterize ferritin from a mutant light chain polypeptide that causes neurodegeneration.

    PubMed

    Baraibar, Martin A; Barbeito, Ana G; Muhoberac, Barry B; Vidal, Ruben

    2008-11-14

    Nucleotide insertions in the ferritin light chain (FTL) polypeptide gene cause hereditary ferritinopathy, a neurodegenerative disease characterized by abnormal accumulation of ferritin and iron in the central nervous system. Here we describe for the first time the protein structure and iron storage function of the FTL mutant p.Phe167SerfsX26 (MT-FTL), which has a C terminus altered in sequence and extended in length. MT-FTL polypeptides assembled spontaneously into soluble, spherical 24-mers that were ultrastructurally indistinguishable from those of the wild type. Far-UV CD showed a decrease in alpha-helical content, and 8-anilino-1-naphthalenesulfonate fluorescence revealed the appearance of hydrophobic binding sites. Near-UV CD and proteolysis studies suggested little or no structural alteration outside of the C-terminal region. In contrast to wild type, MT-FTL homopolymers precipitated at much lower iron loading, had a diminished capacity to incorporate iron, and were less thermostable. However, precipitation was significantly reversed by addition of iron chelators both in vitro and in vivo. Our results reveal substantial protein conformational changes localized at the 4-fold pore of MT-FTL homopolymers and imply that the C terminus of the MT-FTL polypeptide plays an important role in ferritin solubility, stability, and iron management. We propose that the protrusion of some portion of the C terminus above the spherical shell allows it to cross-link with other mutant polypeptides through iron bridging, leading to enhanced mutant precipitation by iron. Our data suggest that hereditary ferritinopathy pathogenesis is likely to result from a combination of reduction in iron storage function and enhanced toxicity associated with iron-induced ferritin aggregates.

  16. Structural evolution of lamprophyric dikes in Lailai, northeastern coast of Taiwan, deduced from mesoscopic structures in dikes and country rocks

    NASA Astrophysics Data System (ADS)

    You, Cian-Siang; Huang, Wen-Jeng; Lo, Wei; Wang, Tzu-Bin; Chen, Chien-Chih

    2015-04-01

    Lamprophyric dikes are standing in right-stepping en echelon up to 2.3 meters high within the Oligocene Tatungshan formation on the Lai-Lai wave-cut platform in the northeastern coast of Taiwan. The marine platform composed mainly of argillite is the extension of Hsuehshan range, which has the tallest peak of 3,886 m high in Taiwan. The dikes formed at depth in the late Miocene of 9±1.1 Ma ago are exposed on the marine platform nowadays due to the exhumation and Penglai orogeny resulting from the collision of Eurasian plate and Philippine Sea plate, which began in Pleistocene of 5-6 Ma ago. In consequence, folds, faults, joints and other structures are associated with them. In this study, the distribution of the dikes and fractures were mapped by conducting accurate surveys with a total station theodolite and orthorectifying aerial images taken by an unmanned aerial vehicle in different elevations. Electrical resistivity exploration was performed to decipher the arrangement of the dikes underground and the characteristics of the faults. The associated mesoscopic structures were delineated by mapping at a scale of 1: 40 in the field. We infer that the dikes was formed at depth of approximately 2.4 kilometers according to the thickness of overlaying sedimentary rocks formed from late Oligocene to late Miocene. Thus, it excludes the possibility that fractures existed before the lamprophyric magma intruded into the country rocks. Our observations help restore the original status of the current 19 dike segments. We conclude that the lamprophyric magma forcedly and vertically intruded into the Oligocene rocks and the direction change of maximum principle stress at depth of 2.4 kilometers resulted in three or more right-stepping en-echelon dikes.

  17. Structure of LEP100, a glycoprotein that shuttles between lysosomes and the plasma membrane, deduced from the nucleotide sequence of the encoding cDNA

    PubMed Central

    1988-01-01

    LEP100, a membrane glycoprotein that has the unique property of shuttling from lysosomes to endosomes to plasma membrane and back, was purified from chicken brain. Its NH2-terminal amino acid sequence was determined, and an oligonucleotide encoding part of this sequence was used to clone the encoding cDNA. The deduced amino acid sequence consists of 414 residues of which the NH2-terminal 18 constitute a signal peptide. The sequence includes 17 sites for N-glycosylation in the NH2-terminal 75% of the polypeptide chain followed by a region lacking N-linked oligosaccharides, a single possible membrane-spanning segment, and a cytoplasmic domain of 11 residues, including three potential phosphorylation sites. Eight cysteine residues are spaced in a regular pattern through the lumenal (extracellular) domain, while a 32-residue sequence rich in proline, serine, and threonine occurs at its midpoint. Expression of the cDNA in mouse L cells resulted in targeting of LEP100 primarily to the mouse lysosomes. PMID:3339090

  18. Purification and primary structure of pituitary adenylate cyclase activating polypeptide (PACAP) from the brain of an elasmobranch, stingray, Dasyatis akajei.

    PubMed

    Matsuda, K; Yoshida, T; Nagano, Y; Kashimoto, K; Yatohgo, T; Shimomura, H; Shioda, S; Arimura, A; Uchiyama, M

    1998-01-01

    Pituitary adenylate cyclase activating polypeptide (PACAP) was isolated from ovine hypothalami and found to exist as two amidated forms with 38 (PACAP 38) and 27 (PACAP 27) residues. The amino acid sequences of PACAPs isolated from the vertebrates, such as a bird, a frog and teleost fish, appear to be well conserved. In the present study, we attempted to isolate PACAP from the brain of an elasmobranch fish, Dasyatis akajei (stingray), which belongs to the Chondrichthyes (cartilaginous fish), by extraction of the acetone-dried powder with acetic acid, followed by successive high-performance liquid chromatography (HPLC) on a gel-filtration, a cation-exchange and two reverse-phase columns. Purification was monitored by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) and Western blotting analysis using an anti-PACAP 27 serum. The PACAP thus obtained consisted of 44 residues. The amino acid sequence of the comparable portion of its N-terminal 38 residues showed 92%, 89%, 89%, and 82% identity with those of mammalian, chicken, frog and teleost PACAPs with 38 residues, respectively. The extra six C-terminal residues of the stingray resembled those of tetrapod and teleost PACAP precursors which were deduced from the respective cDNAs. These results indicate that PACAP, which has an amino acid sequence showing high similarity with those of tetrapod and teleost PACAPs, is present in the elasmobranch brain.

  19. Molecular thermodynamic model to predict the alpha-helical secondary structure of polypeptide chains in solution.

    PubMed

    Zhu, Y; Chen, C C; King, J A; Evans, L B

    1992-11-03

    The native state of a protein molecule in aqueous solutions represents one of the lowest states of Gibbs energy [Anfinsen, C.B. (1973) Science 181, 223-230]. Much progress has been made about the rules of protein folding [King, J. (1989) Chem. Eng. News 67, 32-54] and the dominant forces in protein folding [Dill, K.A. (1990) Biochemistry 29, 7133-7155]. However, the quantitative contributions of different Gibbs energy terms to protein stability remains a controversial issue [Moult, J., & Unger, R. (1991) Biochemistry 30, 3816-3824]. A molecular thermodynamic model has been proposed for the Gibbs energy of folding a residue in aqueous homopolypeptides from a random-coiled state to either the alpha-helix state or the beta-sheet state [Chen, C.-C., Zhu, Y., King, J.A., & Evans, L.B. (1992) Biopolymers 32, 1375-1392]. In this work, we present a generalization of the molecular thermodynamic model for the Gibbs energy of folding natural and synthetic heteropolypeptides from random-coiled conformations into alpha-helical conformations. The generalized model incorporates the intrinsic folding potential due to residue-solvent interactions, the cooperative folding effect due to residue-residue interactions, and the location and length of alpha-helices. The utility of the model was demonstrated by examining the stability of alpha-helical conformations of a number of natural polypeptides including C-peptide (residues 1-13) and S-peptide (residues 1-20) of RNase A (bovine pancreatic ribonuclease A), the P alpha fragment in BPTI (bovine pancreatic trypsin inhibitor), and synthetic polypeptides (the copolymers of different amino acid residues) including alanine-based peptides (16 or 17 residues long) in water. The computed Gibbs energies correspond well with the experimental data on helicity. The results also accounted for the effects of amino acid substitution and temperature on the stability of alpha-helical conformations of the test polypeptides.

  20. Nucleotide sequence of Phaseolus vulgaris L. alcohol dehydrogenase encoding cDNA and three-dimensional structure prediction of the deduced protein

    PubMed Central

    Amelia, Kassim; Khor, Chin Yin; Shah, Farida Habib; Bhore, Subhash J.

    2015-01-01

    Background: Common beans (Phaseolus vulgaris L.) are widely consumed as a source of proteins and natural products. However, its yield needs to be increased. In line with the agenda of Phaseomics (an international consortium), work of expressed sequence tags (ESTs) generation from bean pods was initiated. Altogether, 5972 ESTs have been isolated. Alcohol dehydrogenase (AD) encoding gene cDNA was a noticeable transcript among the generated ESTs. This AD is an important enzyme; therefore, to understand more about it this study was undertaken. Objective: The objective of this study was to elucidate P. vulgaris L. AD (PvAD) gene cDNA sequence and to predict the three-dimensional (3D) structure of deduced protein. Materials and Methods: positive and negative strands of the PvAD cDNA clone were sequenced using M13 forward and M13 reverse primers to elucidate the nucleotide sequence. Deduced PvAD cDNA and protein sequence was analyzed for their basic features using online bioinformatics tools. Sequence comparison was carried out using bl2seq program, and tree-view program was used to construct a phylogenetic tree. The secondary structures and 3D structure of PvAD protein were predicted by using the PHYRE automatic fold recognition server. Results: The sequencing results analysis showed that PvAD cDNA is 1294 bp in length. It's open reading frame encodes for a protein that contains 371 amino acids. Deduced protein sequence analysis showed the presence of putative substrate binding, catalytic Zn binding, and NAD binding sites. Results indicate that the predicted 3D structure of PvAD protein is analogous to the experimentally determined crystal structure of s-nitrosoglutathione reductase from an Arabidopsis species. Conclusions: The 1294 bp long PvAD cDNA encodes for 371 amino acid long protein that contains conserved domains required for biological functions of AD. The predicted deduced PvAD protein's 3D structure reflects the analogy with the crystal structure of

  1. Effects of Protein Structure on Iron–Polypeptide Vibrational Dynamic Coupling in Cytochrome c

    SciTech Connect

    Galinato, Mary Grace I.; Bowman, Sarah E. J.; Kleingardner, Jesse G.; Martin, Sherri; Zhao, Jiyong; Sturhahn, Wolfgang; Alp, E. Ercan; Bren, Kara L.; Lehnert, Nicolai

    2014-12-22

    Cytochrome c (Cyt c) has a heme covalently bound to the polypeptide via a Cys-X-X-Cys-His (CXXCH) linker that is located in the interface region for protein–protein interactions. To determine whether the polypeptide matrix influences iron vibrational dynamics, nuclear resonance vibrational spectroscopy (NRVS) measurements were performed on 57Fe-labeled ferric Hydrogenobacter thermophilus cytochrome c-552, and variants M13V, M13V/K22M, and A7F, which have structural modifications that alter the composition or environment of the CXXCH pentapeptide loop. Simulations of the NRVS data indicate that the 150–325 cm–1 region is dominated by NHis–Fe–SMet axial ligand and polypeptide motions, while the 325–400 cm–1 region shows dominant contributions from ν(Fe–NPyr) (Pyr = pyrrole) and other heme-based modes. Diagnostic spectral signatures that directly relate to structural features of the heme active site are identified using a quantum chemistry-centered normal coordinate analysis (QCC-NCA). In particular, spectral features that directly correlate with CXXCH loop stiffness, the strength of the Fe–His interaction, and the degree of heme distortion are identified. Cumulative results from our investigation suggest that compared to the wild type (wt), variants M13V and M13V/K22M have a more rigid CXXCH pentapeptide segment, a stronger Fe–NHis interaction, and a more ruffled heme. Conversely, the A7F variant has a more planar heme and a weaker Fe–NHis bond. These results are correlated to the observed changes in reduction potential between wt protein and the variants studied here. Lastly, we discuss the implications of these results for Cyt c biogenesis and electron transfer.

  2. Structural stability of Amandin, a major allergen from almond (Prunus dulcis), and its acidic and basic polypeptides.

    PubMed

    Albillos, Silvia M; Menhart, Nicholas; Fu, Tong-Jen

    2009-06-10

    Information relating to the resistance of food allergens to thermal and/or chemical denaturation is critical if a reduction in protein allergenicity is to be achieved through food-processing means. This study examined the changes in the secondary structure of an almond allergen, amandin, and its acidic and basic polypeptides as a result of thermal and chemical denaturation. Amandin ( approximately 370 kDa) was purified by cryoprecipitation followed by gel filtration chromatography and subjected to thermal (13-96 degrees C) and chemical (urea and dithiothreitol) treatments. Changes in the secondary structure of the protein were followed using circular dichroism spectroscopy. The secondary structure of the hexameric amandin did not undergo remarkable changes at temperatures up to 90 degrees C, although protein aggregation was observed. In the presence of a reducing agent, irreversible denaturation occurred with the following experimental values: T(m) = 72.53 degrees C (transition temperature), DeltaH = 87.40 kcal/mol (unfolding enthalpy), and C(p) = 2.48 kcal/(mol degrees C) (heat capacity). The concentration of urea needed to achieve 50% denaturation was 2.59 M, and the Gibbs free energy of chemical denaturation was calculated to be DeltaG = 3.82 kcal/mol. The basic and acidic polypeptides of amandin had lower thermal stabilities than the multimeric protein.

  3. Comprehensive structural analysis of designed incomplete polypeptide chains of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus

    PubMed Central

    Vazquez, Leonardo; e Lima, Luis Mauricio Trambaioli da Rocha

    2017-01-01

    The cotranslational folding is recognized as a very cooperative process that occurs after the nearly completion of the polypeptide sequence of a domain. Here we investigated the challenges faced by polypeptide segments of a non-vectorial β-barrel fold. Besides the biological interest behind the SARS coronavirus non-structural protein 1 (nsp1, 117 amino acids), this study model has two structural features that motivated its use in this work: 1- its recombinant production is dependent on the temperature, with greater solubility when expressed at low temperatures. This is an indication of the cotranslational guidance to the native protein conformation. 2- Conversely, nsp1 has a six-stranded, mixed parallel/antiparallel β-barrel with intricate long-range interactions, indicating it will need the full-length protein to fold properly. We used non-denaturing purification conditions that allowed the characterization of polypeptide chains of different lengths, mimicking the landscape of the cotranslational fold of a β-barrel, and avoiding the major technical hindrances of working with the nascent polypeptide bound to the ribosome. Our results showed partially folded states formed as soon as the amino acids of the second β-strand were present (55 amino acids). These partially folded states are different based on the length of polypeptide chain. The native α-helix (amino acids 24–37) was identified as a transient structure (~20–30% propensity). We identified the presence of regular secondary structure after the fourth native β-strand is present (89 amino acids), in parallel to the collapse to a non-native 3D structure. Interestingly the polypeptide sequences of the native strands β2, β3 and β4 have characteristics of α-helices. Our comprehensive analyses support the idea that incomplete polypeptide chains, such as the ones of nascent proteins much earlier than the end of the translation, adopt an abundance of specific transient folds, instead of disordered

  4. Comprehensive structural analysis of designed incomplete polypeptide chains of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus.

    PubMed

    Vazquez, Leonardo; E Lima, Luis Mauricio Trambaioli da Rocha; Almeida, Marcius da Silva

    2017-01-01

    The cotranslational folding is recognized as a very cooperative process that occurs after the nearly completion of the polypeptide sequence of a domain. Here we investigated the challenges faced by polypeptide segments of a non-vectorial β-barrel fold. Besides the biological interest behind the SARS coronavirus non-structural protein 1 (nsp1, 117 amino acids), this study model has two structural features that motivated its use in this work: 1- its recombinant production is dependent on the temperature, with greater solubility when expressed at low temperatures. This is an indication of the cotranslational guidance to the native protein conformation. 2- Conversely, nsp1 has a six-stranded, mixed parallel/antiparallel β-barrel with intricate long-range interactions, indicating it will need the full-length protein to fold properly. We used non-denaturing purification conditions that allowed the characterization of polypeptide chains of different lengths, mimicking the landscape of the cotranslational fold of a β-barrel, and avoiding the major technical hindrances of working with the nascent polypeptide bound to the ribosome. Our results showed partially folded states formed as soon as the amino acids of the second β-strand were present (55 amino acids). These partially folded states are different based on the length of polypeptide chain. The native α-helix (amino acids 24-37) was identified as a transient structure (~20-30% propensity). We identified the presence of regular secondary structure after the fourth native β-strand is present (89 amino acids), in parallel to the collapse to a non-native 3D structure. Interestingly the polypeptide sequences of the native strands β2, β3 and β4 have characteristics of α-helices. Our comprehensive analyses support the idea that incomplete polypeptide chains, such as the ones of nascent proteins much earlier than the end of the translation, adopt an abundance of specific transient folds, instead of disordered

  5. α-Helical Structures Drive Early Stages of Self-Assembly of Amyloidogenic Amyloid Polypeptide Aggregate Formation in Membranes

    PubMed Central

    Pannuzzo, Martina; Raudino, Antonio; Milardi, Danilo; La Rosa, Carmelo; Karttunen, Mikko

    2013-01-01

    The human islet amyloid polypeptide (hIAPP) is the primary component in the toxic islet amyloid deposits in type-2 diabetes. hIAPP self-assembles to aggregates that permeabilize membranes and constitutes amyloid plaques. Uncovering the mechanisms of amyloid self-assembly is the key to understanding amyloid toxicity and treatment. Although structurally similar, hIAPP's rat counterpart, the rat islet amyloid polypeptide (rIAPP), is non-toxic. It has been a puzzle why these peptides behave so differently. We combined multiscale modelling and theory to explain the drastically different dynamics of hIAPP and rIAPP: The differences stem from electrostatic dipolar interactions. hIAPP forms pentameric aggregates with the hydrophobic residues facing the membrane core and stabilizing water-conducting pores. We give predictions for pore sizes, the number of hIAPP peptides, and aggregate morphology. We show the importance of curvature-induced stress at the early stages of hIAPP assembly and the α-helical structures over β-sheets. This agrees with recent fluorescence spectroscopy experiments. PMID:24071712

  6. Hydrophilic Silica-Polypeptide Composite Particles

    NASA Astrophysics Data System (ADS)

    Soto-Cantu, Erick; Russo, Paul

    2007-03-01

    Composite, pH-responsive particles have been synthesized by covalently attaching a simple polypeptide to a silica core. The synthesis begins with the production of organophilic poly(benzylglutamate)-coated silica particles. The particles are rendered hydrophilic by cleaving the benzyl side group by treatment with hydrogen bromide in benzene. The resulting poly(glutamic acid)-coated silica spheres exhibit a change in hydrodynamic radius in response to pH stimulus. The size transition is due to a change in the polypeptide conformation, as deduced from circular dichroism measurements. Fong,B.; Russo, P.S. Organophilic Colloidal Particles with a Synthetic Polypeptide Coating. Langmuir 1999, 15, 4421-4426.

  7. Structure and Thermodynamic Stability of Islet Amyloid Polypeptide Monomers and Small Aggregates

    NASA Astrophysics Data System (ADS)

    Chiu, Chi-Cheng; Singh, Sadanand; de Pablo, Juan

    2013-03-01

    Human islet amyloid polypeptide (hIAPP, also known as human amylin) is associated with the development of type II diabetes. It is known to form amyloid fibrils that are found in pancreatic islets. Pramlintide, a synthetic analog of hIAPP with three proline substitutions, is not amyloidogenic and has been applied in amylin replacement treatments. In this work, we use molecular simulations with advanced sampling techniques to examine the effect of these proline substitutions on hIAPP monomer conformations. We find that all three proline substitutions are required to attenuate the formation of β-sheets encountered in amylin. Furthermore, we investigate the formation of hIAPP dimers and trimers, and investigate how that process is affected by the presence of various additives. Our simulations show that hIAPP can form a β-sheet at the N-terminus and the C-terminus independently, in agreement with experimental observations. Our results provide valuable insights into the mechanism of hIAPP early aggregation and the design of fibril formation inhibitors.

  8. Two Different Structures of the Oxygen-Evolving Complex in the Same Polypeptide Frameworks of Photosystem II.

    PubMed

    Tanaka, Ayako; Fukushima, Yoshimasa; Kamiya, Nobuo

    2017-02-08

    The oxygen-evolving complex (OEC) forms the heart of photosystem II (PSII) in photosynthesis. The crystal structure of PSII from Thermosynechococcus vulcanus has been reported at a resolution of 1.9 Å and at an averaged X-ray dose of 0.43 MGy. The OEC structure is suggested to be partially reduced to Mn(II) by EXAFS and DFT computational studies. Recently, the "radiation-damage-free" structures have been published at 1.95 Å resolution using XFEL, but reports continued to appear that the OEC is reduced to the S0-state of the Kok cycle. To elucidate much more precise structure of the OEC, in this study two structures were determined at extremely low X-ray doses of 0.03 and 0.12 MGy using conventional synchrotron radiation source. The results indicated that the X-ray reduction effects on the OEC were very small in the low dose region below 0.12 MGy, that is, a threshold existed for the OEC structural changes caused by X-ray exposure. The OEC structures of the two identical monomers in the crystal were clearly different under the threshold of the radiation dose, although the surrounding polypeptide frameworks of PSII were the same. The assumption that the OECs in the crystal were in the dark-stable S1-state of the Kok cycle should be re-evaluated.

  9. Structural and Functional Analysis of Cell Wall-anchored Polypeptide Adhesin BspA in Streptococcus agalactiae.

    PubMed

    Rego, Sara; Heal, Timothy J; Pidwill, Grace R; Till, Marisa; Robson, Alice; Lamont, Richard J; Sessions, Richard B; Jenkinson, Howard F; Race, Paul R; Nobbs, Angela H

    2016-07-29

    Streptococcus agalactiae (group B Streptococcus, GBS) is the predominant cause of early-onset infectious disease in neonates and is responsible for life-threatening infections in elderly and immunocompromised individuals. Clinical manifestations of GBS infection include sepsis, pneumonia, and meningitis. Here, we describe BspA, a deviant antigen I/II family polypeptide that confers adhesive properties linked to pathogenesis in GBS. Heterologous expression of BspA on the surface of the non-adherent bacterium Lactococcus lactis confers adherence to scavenger receptor gp340, human vaginal epithelium, and to the fungus Candida albicans Complementary crystallographic and biophysical characterization of BspA reveal a novel β-sandwich adhesion domain and unique asparagine-dependent super-helical stalk. Collectively, these findings establish a new bacterial adhesin structure that has in effect been hijacked by a pathogenic Streptococcus species to provide competitive advantage in human mucosal infections. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Structural and Functional Analysis of Cell Wall-anchored Polypeptide Adhesin BspA in Streptococcus agalactiae*

    PubMed Central

    Rego, Sara; Heal, Timothy J.; Pidwill, Grace R.; Till, Marisa; Robson, Alice; Lamont, Richard J.; Sessions, Richard B.; Jenkinson, Howard F.; Race, Paul R.; Nobbs, Angela H.

    2016-01-01

    Streptococcus agalactiae (group B Streptococcus, GBS) is the predominant cause of early-onset infectious disease in neonates and is responsible for life-threatening infections in elderly and immunocompromised individuals. Clinical manifestations of GBS infection include sepsis, pneumonia, and meningitis. Here, we describe BspA, a deviant antigen I/II family polypeptide that confers adhesive properties linked to pathogenesis in GBS. Heterologous expression of BspA on the surface of the non-adherent bacterium Lactococcus lactis confers adherence to scavenger receptor gp340, human vaginal epithelium, and to the fungus Candida albicans. Complementary crystallographic and biophysical characterization of BspA reveal a novel β-sandwich adhesion domain and unique asparagine-dependent super-helical stalk. Collectively, these findings establish a new bacterial adhesin structure that has in effect been hijacked by a pathogenic Streptococcus species to provide competitive advantage in human mucosal infections. PMID:27311712

  11. Crust and mantle lithospheric structure of the South China Sea and adjacent regions deduced from geophysical potential data

    NASA Astrophysics Data System (ADS)

    Fang, J.

    2016-12-01

    In order to investigate the lithospheric structure of the South China Sea and adjacent regions and it's lateral crustal density variations, we using a two-step approach. First the crustal and lithospheric mantle structure is calculated from the geoid height and elevation data combined with thermal analysis further constrained by seismic data. We then compute the 3D gravity effect of the resulting lithospheric structure to separate the measured Bouguer anomaly into its regional and local components. Our results show that for the majority of the study area the crustal thickness does correlate with the regional topography pattern. Moho depth varies from ˜10 km at the Central basin to ˜35 km at the continental shelf and slope zones. The lithosphere is thinner beneath the Central basin (˜70 km) and thicker underneath the continental shelf and slope zones (˜100 km). The residual gravity anomaly, obtained by subtraction of the regional components to the measured field, is analyzed in terms of the dominating upper crustal structures. Central basins and areas with high velocity layer are characterized by positive values (20 100 mGal), whereas the negative values are related to the Trough and Trench, such as Nansha Trough and Manila Trench and shallow basement depths(-100 -20 mGal). The transform boundary of continental-oceanic is consistent with the residual gravity anomaly gradient zone and is proposed accordingly. The variation of Moho and the residual gravity anomaly exists between the conjugate margins which demonstrated the asymmetric crustal extension of the South China Sea margin.

  12. Donut-shaped fingerprint in homologous polypeptide relationships--a topological feature related to pathogenic structural changes in conformational disease.

    PubMed

    Liu, Xin; Zhao, Ya-Pu

    2009-05-21

    Features of homologous relationship of proteins can provide us a general picture of protein universe, assist protein design and analysis, and further our comprehension of the evolution of organisms. Here we carried out a study of the evolution of protein molecules by investigating homologous relationships among residue segments. The motive was to identify detailed topological features of homologous relationships for short residue segments in the whole protein universe. Based on the data of a large number of non-redundant proteins, the universe of non-membrane polypeptide was analyzed by considering both residue mutations and structural conservation. By connecting homologous segments with edges, we obtained a homologous relationship network of the whole universe of short residue segments, which we named the graph of polypeptide relationships (GPR). Since the network is extremely complicated for topological transitions, to obtain an in-depth understanding, only subgraphs composed of vital nodes of the GPR were analyzed. Such analysis of vital subgraphs of the GPR revealed a donut-shaped fingerprint. Utilization of this topological feature revealed the switch sites (where the beginning of exposure of previously hidden "hot spots" of fibril-forming happens, in consequence a further opportunity for protein aggregation is provided; 188-202) of the conformational conversion of the normal alpha-helix-rich prion protein PrP(C) to the beta-sheet-rich PrP(Sc) that is thought to be responsible for a group of fatal neurodegenerative diseases, transmissible spongiform encephalopathies. Efforts in analyzing other proteins related to various conformational diseases are also introduced.

  13. Extrapolating surface structures to depth in transpressional systems: the role of rheology and convergence angle deduced from analogue experiments

    NASA Astrophysics Data System (ADS)

    Hsieh, Shang Yu; Neubauer, Franz; Cloetingh, Sierd; Willingshofer, Ernst; Sokoutis, Dimitrios

    2014-05-01

    The internal structure of major strike-slip faults is still poorly understood, particularly how the deep structure could be inferred from its surface expression (Molnar and Dayem, 2011 and references therein). Previous analogue experiments suggest that the convergence angle is the most influential factor (Leever et al., 2011). Further analogue modeling may allow a better understanding how to extrapolate surface structures to the subsurface geometry of strike-slip faults. Various scenarios of analogue experiments were designed to represent strike-slip faults in nature from different geological settings. As such key parameters, which are investigated in this study include: (a) the angle of convergence, (b) the thickness of brittle layer, (c) the influence of a rheological weak layer within the crust, and (d) influence of a thick and rheologically weak layer at the base of the crust. The latter aimed to simulate the effect of a hot metamorphic core complex or an alignment of uprising plutons bordered by a transtensional/transpressional strike-slip fault. The experiments are aimed to explain first order structures along major transcurrent strike-slip faults such as the Altyn, Kunlun, San Andrea and Greendale (Darfield earthquake 2010) faults. The preliminary results show that convergence angle significantly influences the overall geometry of the transpressive system with greater convergence angles resulting in wider fault zones and higher elevation. Different positions, densities and viscosities of weak rheological layers have not only different surface expressions but also affect the fault geometry in the subsurface. For instance, rheological weak material in the bottom layer results in stretching when experiment reaches a certain displacement and a buildup of a less segmented, wide positive flower structure. At the surface, a wide fault valley in the middle of the fault zone is the reflection of stretching along the velocity discontinuity at depth. In models with a

  14. Seismic velocity structure around the shallow megathrust zone of the 2011 Tohoku earthquake deduced from onshore and offshore seismic observations

    NASA Astrophysics Data System (ADS)

    Yamamoto, Y.; Obana, K.; Machida, Y.; Nakahigashi, K.; Shinohara, M.; Suzuki, K.; Ito, Y.; Hino, R.; Kodaira, S.; Kaneda, Y.; Murai, Y.; Sato, T.; Uehira, K.; Yakiwara, H.; Hirata, K.; Sugioka, H.; Ito, A.; Suetsugu, D.

    2012-12-01

    The coseismic rupture area of the 2011 Tohoku Earthquake has been estimated to be over the wide region from the coastline to near the Japan Trench. Several kinds of studies, such as tsunami source inversion [e.g., Fujii et al., 2011], coseismic slip inversion [e.g., Ide et al., 2011], submarine topography change [Fujiwara et al., 2011] and seafloor displacement observation [Sato et al., 2011; Ito et al., 2011; Kido et al., 2011], share the common feature that the largest coseismic slip occurred at the shallow plate boundary in close vicinity to the Japan Trench. However, the structural image just beneath the largest coseismic slip area was unclear since the observation areas of previous ocean bottom seismographs (OBSs) in this region were limited and there were few OBSs near the Japan Trench [e.g., Yamamoto et al., 2011]. To understand the relationship between the coseismic rupture behavior and structural heterogeneities, it is necessary to know the seismic velocity structure around the plate boundary near the trench axis. After the occurrence of the 2011 earthquake, some National Universities (Hokkaido, Tohoku, Chiba, Tokyo, Kyushu, and Kagoshima), JAMSTEC, and Meteorological Research Institute together have conducted the aftershock observations along the landward slope of the Japan Trench to obtain detail hypocenter distribution [Shinohara et al., 2012]. Tohoku University has performed the other OBS observation off Miyagi prefecture from 2010 to 2011. During this observation, a sequence of foreshocks, the mainshock, and aftershocks of the 2011 Tohoku earthquake were recorded [Suzuki et al., 2012]. In addition, JAMSTEC has conducted the aftershock observation at outer slope of Japan Trench, around the epicenter of a Mw 7.6 earthquake that occurred about 40 minutes after the 2011 mainshock, from May to June in 2011[Obana et al., 2012]. In this study, we attempt to obtain the three-dimensional seismic velocity structure around the largest coseismic slip zone of the

  15. Geometry of plate boundary and seismic structure beneath the southern Ryukyu Trench subduction zone deduced from passive seismic observation

    NASA Astrophysics Data System (ADS)

    Yamamoto, Y.; Takahashi, T.; Ishihara, Y.; Kaiho, Y.; Arai, R.; Nakanishi, A.; Obana, K.; Miura, S.; Kodaira, S.; Kaneda, Y.

    2016-12-01

    In the Ryukyu Trench subduction zone, many large earthquakes occurred historically. In particular, plausible seismogenic zone of the 1771 Yaeyama earthquake (Mw 8.0) is located near the trench [Nakamura, 2009]. However, the plane geometry is uncertain due to the sparse seismic observation network. To investigate the subducted plate geometry, we have conducted the passive seismic observation around the southern Ryukyu Trench using 6 land stations and 30 ocean bottom seismographs from Nov. 2013 to Mar. 2014. By using the newly detected events from continuous seismic records in addition to Japan Meteorological Agency catalogued events, we performed a seismic tomography to estimate the seismic velocity structure and precious hypocenter locations. Then, we estimated the focal mechanisms of relocated earthquakes and searched the repeating earthquakes (REs) according to the catalogue of Igarashi (2010). Finally, we estimated the depth variation of the subducted Philippine Sea plate beneath the Ryukyu arc by following assumptions: 1) low-angle thrust-type earthquakes (LTEs) and REs occur along the plate boundary, 2) landward dipping low velocity layer indicates the oceanic crust between landward and slab mantles. The consistency of our plate geometry model and the result of active source survey [Arai et al., 2016] indicated the validity of above assumptions. Our plate model indicates local variation between Ishigaki to Miyako Islands, whereas plate geometry western Ishigaki seems to be smooth. In this area, plate boundary estimated shallower than slab1.0 model [Hayes et al., 2012], and it seems to have a convex structure beneath the Tarama Island. Besides, LTEs and REs estimated in this study located the outside of the dominant area of short-term slow slip [Nishimura, 2014]. Our velocity model also indicated that the landward mantle is serpentinized, which might be corresponding to the occurrence of slow slip events.

  16. Active site properties of monomeric triosephosphate isomerase (monoTIM) as deduced from mutational and structural studies.

    PubMed

    Schliebs, W; Thanki, N; Eritja, R; Wierenga, R

    1996-02-01

    MonoTIM is a stable monomeric variant of the dimeric trypanosomal enzyme triose phosphate isomerase (TIM) with less, but significant, catalytic activity. It is known that in TIM, three residues, Lys 13 (loop 1), His 95 (loop 4), and Glu 167 (loop 6) are the crucial catalytic residues. In the wild-type TIM dimer, loop 1 and loop 4 are very rigid because of tight interactions with residues of the other subunit. Previous structural studies indicate that Lys 13 and His 95 have much increased conformational flexibility in monoTIM. Using site-directed mutagenesis, it is shown here that Lys 13 and His 95 are nevertheless essential for optimal catalysis by monoTIM: monoTIM-K13A is completely inactive, although it can still bind substrate analogues, and monoTIM-H95A is 50 times less active. The best inhibitors of wild-type TIM are phosphoglycolohydroxamate (PGH) and 2-phosphoglycolate (2PG), with KI values of 8 microM and 26 microM, respectively. The affinity of the monoTIM active site for PGH has been reduced approximately 60-fold, whereas for 2PG, only a twofold weakening of affinity is observed. The mode of binding, as determined by protein crystallographic analysis of these substrate analogues, shows that, in particular, 2PG interacts with Lys 13 and His 95 in a way similar but not identical to that observed for the wild-type enzyme. This crystallographic analysis also shows that Glu 167 has the same interactions with the substrate analogues as in the wild type. The data presented suggest that, despite the absence of the second subunit, monoTIM catalyzes the interconversion of D-glyceraldehyde-3-phosphate and dihydroxyacetone phosphate via the same mechanism as in the wild type.

  17. The susceptibility of α-helical secondary structure to steric strain: Coarse-grained simulation of dendronized polypeptides.

    PubMed

    Browne, William; Geissler, Phillip L

    2010-10-14

    The propensity of a peptide chain for adopting helical secondary structure can be modulated not only through the solvation properties of its side chains but also through their size and shape. Here we examine a coarse-grained model for dendronized polypeptides that focuses on the susceptibility of α-helical structure to the steric strain exerted by hydrophilic pendant groups. Undecorated molecules exhibit a pronounced transition from random coil to helix upon cooling [J. P. Kemp and J. Z. Y. Chen, Biomacromolecules 2, 389 (2001)]. As gauged by specific heat and by order parameters characterizing helicity at several length scales, this transition is quite robust to the introduction of first- and second-generation dendron side chains. More highly branched side chains, however, reduce the entropy of compact states so severely that helical ordering is undetectable over the entire temperature range accessible to our importance sampling methods. Consistent with experimental observations for side chains comparable to those of our model in volume-excluding size and shape, we find the backbone of these third-generation molecules to assume a distended rodlike state that is both stiff and achiral.

  18. Role of monomer sequence and backbone structure in polypeptoid and polypeptide polymers for anti-fouling applications

    NASA Astrophysics Data System (ADS)

    Patterson, Anastasia; Rizis, Georgios; Wenning, Brandon; Finlay, John; Ober, Christopher; Segalman, Rachel

    Polymeric coatings rely on a fine balance of surface properties to achieve biofouling resistance. Bioinsipired polymers and oligomers provide a modular strategy for the inclusion of multiple functionalities with controlled architecture, sequence and surface properties. In this work, polypeptoid and polypeptide functionalized coatings based on PEO and PDMS block copolymers were compared with respect to surface presentation and fouling by Ulva linza. While polypeptoids and polypeptides are simple isomers of each other, the lack of backbone chirality and hydrogen bonding in polypeptoids leads to surprisingly different surface behavior. Specifically, the polypeptoids surface segregate much more strongly than analogous polypeptide functionalized polymers, which in turn affects the performance of the coating. Indeed, polypeptoid functionalized surfaces were significantly better both in terms of anti-fouling and fouling release than the corresponding polypeptide-bearing polymers. The role of specific monomer sequence and backbone chemistry will be further discussed in this poster.

  19. The four hexamerin genes in the honey bee: structure, molecular evolution and function deduced from expression patterns in queens, workers and drones.

    PubMed

    Martins, Juliana R; Nunes, Francis M F; Cristino, Alexandre S; Simões, Zilá L P; Bitondi, Márcia M G

    2010-03-26

    Hexamerins are hemocyanin-derived proteins that have lost the ability to bind copper ions and transport oxygen; instead, they became storage proteins. The current study aimed to broaden our knowledge on the hexamerin genes found in the honey bee genome by exploring their structural characteristics, expression profiles, evolution, and functions in the life cycle of workers, drones and queens. The hexamerin genes of the honey bee (hex 70a, hex 70b, hex 70c and hex 110) diverge considerably in structure, so that the overall amino acid identity shared among their deduced protein subunits varies from 30 to 42%. Bioinformatics search for motifs in the respective upstream control regions (UCRs) revealed six overrepresented motifs including a potential binding site for Ultraspiracle (Usp), a target of juvenile hormone (JH). The expression of these genes was induced by topical application of JH on worker larvae. The four genes are highly transcribed by the larval fat body, although with significant differences in transcript levels, but only hex 110 and hex 70a are re-induced in the adult fat body in a caste- and sex-specific fashion, workers showing the highest expression. Transcripts for hex 110, hex 70a and hex70b were detected in developing ovaries and testes, and hex 110 was highly transcribed in the ovaries of egg-laying queens. A phylogenetic analysis revealed that HEX 110 is located at the most basal position among the holometabola hexamerins, and like HEX 70a and HEX 70c, it shares potential orthology relationship with hexamerins from other hymenopteran species. Striking differences were found in the structure and developmental expression of the four hexamerin genes in the honey bee. The presence of a potential binding site for Usp in the respective 5' UCRs, and the results of experiments on JH level manipulation in vivo support the hypothesis of regulation by JH. Transcript levels and patterns in the fat body and gonads suggest that, in addition to their primary

  20. The four hexamerin genes in the honey bee: structure, molecular evolution and function deduced from expression patterns in queens, workers and drones

    PubMed Central

    2010-01-01

    Background Hexamerins are hemocyanin-derived proteins that have lost the ability to bind copper ions and transport oxygen; instead, they became storage proteins. The current study aimed to broaden our knowledge on the hexamerin genes found in the honey bee genome by exploring their structural characteristics, expression profiles, evolution, and functions in the life cycle of workers, drones and queens. Results The hexamerin genes of the honey bee (hex 70a, hex 70b, hex 70c and hex 110) diverge considerably in structure, so that the overall amino acid identity shared among their deduced protein subunits varies from 30 to 42%. Bioinformatics search for motifs in the respective upstream control regions (UCRs) revealed six overrepresented motifs including a potential binding site for Ultraspiracle (Usp), a target of juvenile hormone (JH). The expression of these genes was induced by topical application of JH on worker larvae. The four genes are highly transcribed by the larval fat body, although with significant differences in transcript levels, but only hex 110 and hex 70a are re-induced in the adult fat body in a caste- and sex-specific fashion, workers showing the highest expression. Transcripts for hex 110, hex 70a and hex70b were detected in developing ovaries and testes, and hex 110 was highly transcribed in the ovaries of egg-laying queens. A phylogenetic analysis revealed that HEX 110 is located at the most basal position among the holometabola hexamerins, and like HEX 70a and HEX 70c, it shares potential orthology relationship with hexamerins from other hymenopteran species. Conclusions Striking differences were found in the structure and developmental expression of the four hexamerin genes in the honey bee. The presence of a potential binding site for Usp in the respective 5' UCRs, and the results of experiments on JH level manipulation in vivo support the hypothesis of regulation by JH. Transcript levels and patterns in the fat body and gonads suggest that

  1. Polypeptide having an amino acid replaced with N-benzylglycine

    DOEpatents

    Mitchell, Alexander R.; Young, Janis D.

    1996-01-01

    The present invention relates to one or more polypeptides having useful biological activity in a mammal, which comprise: a polypeptide related to bradykinin of four to ten amino acid residues wherein one or more specific amino acids in the polypeptide chain are replaced with achiral N-benzylglycine. These polypeptide analogues have useful potent agonist or antagonist pharmacological properties depending upon the structure. A preferred polypeptide is (N-benzylglycine.sup.7)-bradykinin.

  2. Structural and Pharmacological Characterization of Novel Potent and Selective Monoclonal Antibody Antagonists of Glucose-dependent Insulinotropic Polypeptide Receptor

    PubMed Central

    Ravn, Peter; Madhurantakam, Chaithanya; Kunze, Susan; Matthews, Evelyn; Priest, Claire; O'Brien, Siobhan; Collinson, Andie; Papworth, Monika; Fritsch-Fredin, Maria; Jermutus, Lutz; Benthem, Lambertus; Gruetter, Markus; Jackson, Ronald H.

    2013-01-01

    Glucose-dependent insulinotropic polypeptide (GIP) is an endogenous hormonal factor (incretin) that, upon binding to its receptor (GIPr; a class B G-protein-coupled receptor), stimulates insulin secretion by beta cells in the pancreas. There has been a lack of potent inhibitors of the GIPr with prolonged in vivo exposure to support studies on GIP biology. Here we describe the generation of an antagonizing antibody to the GIPr, using phage and ribosome display libraries. Gipg013 is a specific competitive antagonist with equally high potencies to mouse, rat, dog, and human GIP receptors with a Ki of 7 nm for the human GIPr. Gipg013 antagonizes the GIP receptor and inhibits GIP-induced insulin secretion in vitro and in vivo. A crystal structure of Gipg013 Fab in complex with the human GIPr extracellular domain (ECD) shows that the antibody binds through a series of hydrogen bonds from the complementarity-determining regions of Gipg013 Fab to the N-terminal α-helix of GIPr ECD as well as to residues around its highly conserved glucagon receptor subfamily recognition fold. The antibody epitope overlaps with the GIP binding site on the GIPr ECD, ensuring competitive antagonism of the receptor. This well characterized antagonizing antibody to the GIPr will be useful as a tool to further understand the biological roles of GIP. PMID:23689510

  3. Structural and pharmacological characterization of novel potent and selective monoclonal antibody antagonists of glucose-dependent insulinotropic polypeptide receptor.

    PubMed

    Ravn, Peter; Madhurantakam, Chaithanya; Kunze, Susan; Matthews, Evelyn; Priest, Claire; O'Brien, Siobhan; Collinson, Andie; Papworth, Monika; Fritsch-Fredin, Maria; Jermutus, Lutz; Benthem, Lambertus; Gruetter, Markus; Jackson, Ronald H

    2013-07-05

    Glucose-dependent insulinotropic polypeptide (GIP) is an endogenous hormonal factor (incretin) that, upon binding to its receptor (GIPr; a class B G-protein-coupled receptor), stimulates insulin secretion by beta cells in the pancreas. There has been a lack of potent inhibitors of the GIPr with prolonged in vivo exposure to support studies on GIP biology. Here we describe the generation of an antagonizing antibody to the GIPr, using phage and ribosome display libraries. Gipg013 is a specific competitive antagonist with equally high potencies to mouse, rat, dog, and human GIP receptors with a Ki of 7 nm for the human GIPr. Gipg013 antagonizes the GIP receptor and inhibits GIP-induced insulin secretion in vitro and in vivo. A crystal structure of Gipg013 Fab in complex with the human GIPr extracellular domain (ECD) shows that the antibody binds through a series of hydrogen bonds from the complementarity-determining regions of Gipg013 Fab to the N-terminal α-helix of GIPr ECD as well as to residues around its highly conserved glucagon receptor subfamily recognition fold. The antibody epitope overlaps with the GIP binding site on the GIPr ECD, ensuring competitive antagonism of the receptor. This well characterized antagonizing antibody to the GIPr will be useful as a tool to further understand the biological roles of GIP.

  4. Analogies between solitonic bio-energy transport along polypeptide chains and nonautonomous optical solitons in structurated nonuniform fibers

    NASA Astrophysics Data System (ADS)

    Morales-Lara, L.; Peña-Moreno, R.; Mena-Contla, A.; Serkin, V. N.; Belyaeva, T. L.

    2015-01-01

    The interpenetration of the main ideas and methods being used in different fields of science and technology has become one of the decisive factors in the progress of science as a whole. Mathematical analogies between different physical systems can be extremely fruitful in understanding the novel physical concepts. Accordingly to the new theory of bio-energy transport along protein molecules in living systems and modified Davydov molecular soliton theory, we propose a nonautonomous model that can be considered as a candidate of the bio-energy transport mechanism in protein molecules. Based on the generalized nonlinear Schrödinger equation model with varying-intime harmonic oscillator potential, we show that conditions of its exact integrability in one-dimensional case indicate conclusively the way for solitonlike pulse generation in polypeptide molecular systems. The most important properties of this soliton transport of bio-energy are related with periodically changed energy-release conditions and the influences of structure nonuniformity in protein molecules. By analogy with the corresponding optical phenomena in inhomogeneous optical fibers with varying properties along the length, we study the main features of modified Davydov soliton on the basis of the unified nonautonomous nonlinear Schrodinger model in the parameters region of the exact integrability of the model under consideration.

  5. Sensitive radioimmunoassay of. cap alpha. human atrial natriuretic polypeptide using monoclonal antibody recognizing human form ring structure

    SciTech Connect

    Naomi, S.; Umeda, T.; Iwaoka, T.; Miura, F.; Ohno, M.; Sasaki, M.; Oishi, S.; Sato, T.; Takatsu, K.

    1988-01-01

    A monoclonal antibody (C351) against ..cap alpha.. human atrial natriuretic polypeptide (..cap alpha..hANP) recognizing human form ring structure was established and applied to a radioimmunoassay of plasma ..cap alpha..hANP. The minimum detectable amount in terms of 10 % radioligand displacement relative to zero dose were 0.28 fmol/tube, corresponding to 0.7 fmol/ml in plasma after extraction using Sep-Pak C18 cartridges. When the mean plasma levels at recumbent position in fasted morning were compared in 10 young (<30 years) and 10 elderly (greater than or equal to50 years) healthy subjects taking normal sodium diet, it was slightly higher in the latter. After i.v. infusion of hypertonic saline at a rate of 0.24 ml/kg/min for 20 min in 6 normal subjects (26 to 35 years), it was increased from 4.1 +/- 0.4 to 5.9 +/- 0.7 fmol/ml (p<0.01). In 6 patients with essential hypertension (34 to 57 years), it was elevated with high salt intake. From these results, the radioimmunoassay of plasma IR-..cap alpha..hANP using MAb C351 seems to be quite suitable to detect rather small changes at low plasma concentrations and to investigate a physiological importance of ..cap alpha..hANP in man.

  6. Function of Bacterial Spore Coat Polypeptides in Structure, Resistance and Germination

    DTIC Science & Technology

    1990-12-20

    fragment from the glutamine synthetase structural gene. E 11 (Strauch et al .. 1988) to RNA from exponential cells (lane 4). Marks to the right of lane 4... glutamine synthetase gene region. Gene 71 : 257-265. Thomas. P.S. (1980) Hybridization of denatured RNA and small DNA fragments transferred to

  7. Complete primary structure of vertebrate smooth muscle myosin heavy chain deduced from its complementary DNA sequence. Implications on topography and function of myosin.

    PubMed

    Yanagisawa, M; Hamada, Y; Katsuragawa, Y; Imamura, M; Mikawa, T; Masaki, T

    1987-11-20

    The 1979 amino acid sequence of embryonic chicken gizzard smooth muscle myosin heavy chain (MHC) have been determined by cloning and sequencing its cDNA. Genomic Southern analysis and Northern analysis with the cDNA sequence show that gizzard MHC is encoded by a single-copy gene, and this gene is expressed in the gizzard and aorta. The encoded protein has a calculated Mr of 229 X 10(3), and can be divided into a long alpha-helical rod and a globular head. Only 32 to 33% of the amino acid residues in the rod and 48 to 49% in the head are conserved when compared with nematode or vertebrate sarcomeric MHC sequences. However, the seven residue hydrophobic periodicity, together with the 28 and 196 residue repeat of charge distribution previously described in nematode myosin rod, are all present in the gizzard myosin rod. Two of the trypsin-sensitive sites in gizzard light meromyosin have been mapped by partial peptide sequencing to 99 nm and 60 nm from the tip of the myosin tail, where these sites coincide with the two "hinges" for the 6 S/10 S transition. In the head sequence, several polypeptide segments, including the regions around the putative ATP-binding site and the reactive thiol groups, are highly conserved. These areas presumably reflect conserved structural elements important for the function of myosin. A multi-domain folding model of myosin head is proposed on the basis of the conserved sequences, information on the topography of myosin in the literature, and the predicted secondary structures. In this model, Mg2+ ATP is bound to a pocket between two opposing alpha/beta domains, while actin undergoes electrostatic interactions with lysine-rich surface loops on two other domains. The actin-myosin interactions are thought to be modulated through relative movements of the domains induced by the binding of ATP.

  8. Solution structure of murine epidermal growth factor: determination of the polypeptide backbone chain-fold by nuclear magnetic resonance and distance geometry

    SciTech Connect

    Montelione, G.T.; Wuethrich, K.; Nice, E.C.; Burgess, A.W.; Scheraga, H.A.

    1987-08-01

    The polypeptide backbone fold in the solution structure of murine epidermal growth factor has been determined by nuclear magnetic resonance spectroscopy and distance geometry calculations. The results are based on nearly complete sequence-specific resonance assignments and on 333 distance and dihedral-angle constraints; these were determined from nuclear Overhauser effect measurements, identification of hydrogen-bonded amide protons, the known locations of disulfide bonds, and backbone vicinal spin-spin coupling constants. The polypeptide chains of the protein is arranged into two distinct domains. The structures of these domains were determined independently in separate calculations and then combined to obtain an overall view of the protein. The backbone fold thus determined includes the regular backbone structure elements that were previously identified using different techniques for the analysis of the nuclear magnetic resonance data. The distance geometry calculations also provided additional details about the conformations of bends and loops and about the twists of the ..beta..-sheets.

  9. Targeted polypeptide degradation

    DOEpatents

    Church, George M [Brookline, MA; Janse, Daniel M [Brookline, MA

    2008-05-13

    This invention pertains to compositions, methods, cells and organisms useful for selectively localizing polypeptides to the proteasome for degradation. Therapeutic methods and pharmaceutical compositions for treating disorders associated with the expression and/or activity of a polypeptide by targeting these polypeptides for degradation, as well as methods for targeting therapeutic polypeptides for degradation and/or activating therapeutic polypeptides by degradation are provided. The invention provides methods for identifying compounds that mediate proteasome localization and/or polypeptide degradation. The invention also provides research tools for the study of protein function.

  10. Structural polymorphism of human islet amyloid polypeptide (hIAPP) oligomers highlights the importance of interfacial residue interactions.

    PubMed

    Zhao, Jun; Yu, Xiang; Liang, Guizhao; Zheng, Jie

    2011-01-10

    A 37-residue of human islet amyloid polypeptide (hIAPP or amylin) is a main component of amyloid plaques found in the pancreas of ∼90% of type II diabetes patients. It is reported that hIAPP oligomers, rather than mature fibrils, are major toxic species responsible for pancreatic islet β-cell dysfunction and even cell death, but molecular structures of these oligomers remain elusive. In this work, on the basis of recent solid-state NMR and mass-per-length (MPL) data, we model a series of hIAPP oligomers with different β-layers (one, two, and three layers), symmetries (symmetry and asymmetry), and associated interfaces using molecular dynamics simulations. Three distinct interfaces formed by C-terminal β-sheet and C-terminal β-sheet (CC), N-terminal β-sheet and N-terminal β-sheet (NN), and C-terminal β-sheet and N-terminal β-sheet (CN) are identified to drive multiple cross-β-layers laterally associated together to form different amyloid organizations via different intermolecular interactions, in which the CC interface is dominated by polar interactions, the NN interface is dominated by hydrophobic interactions, and the CN interface is dominated by mixed polar and hydrophobic interactions. Overall, the structural stability of the proposed hIAPP oligomers is a result of delicate balance between maximization of favorable peptide-peptide interactions at the interfaces and optimization of solvation energy with globular structure. Different hIAPP oligomeric models indicate a general and intrinsic nature of amyloid polymorphism, driven by different interfacial side-chain interactions. The proposed models are compatible with recent experimental data in overall size, cross-section area, and molecular weight. A general hIAPP aggregation mechanism is proposed on the basis of our simulated models and experimental data.

  11. The crystal structure of the human nascent polypeptide-associated complex domain reveals a nucleic acid-binding region on the NACA subunit .

    PubMed

    Liu, Yiwei; Hu, Yingxia; Li, Xu; Niu, Liwen; Teng, Maikun

    2010-04-06

    In archaea and eukaryotes, the nascent polypeptide-associated complex (NAC) is one of the cytosolic chaperones that contact the nascent polypeptide chains as they emerge from the ribosome and assist in post-translational processes. The eukaryotic NAC is a heterodimer, and its two subunits form a stable complex through a dimerizing domain called the NAC domain. In addition to acting as a protein translation chaperone, the NAC subunits also function individually in transcriptional regulation. Here we report the crystal structure of the human NAC domain, which reveals the manner of human NAC dimerization. On the basis of the structure, we identified a region in the NAC domain of the human NAC alpha-subunit as a new nucleic acid-binding region, which is blocked from binding nucleic acids in the heterodimeric complex by a helix region in the beta-subunit.

  12. Bodian's Silver Method Stains Neurofilament Polypeptides

    NASA Astrophysics Data System (ADS)

    Gambetti, P.; Autilio-Gambetti, L.; Papasozomenos, S. Ch.

    1981-09-01

    Bodian's silver method was used to stain polypeptides of rat spinal cord or peripheral nerve separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The bands corresponding to the three polypeptide subunits of the neurofilaments were intensely impregnated. Two other polypeptides were stained inconsistently and less intensely. The tubulin band was stained weakly or not at all; other polypeptides, including glial fibrillary acidic protein, actin, and vimentin, remained unstained. This novel application of Bodian's method provides indirect proof that neurofilaments are the neuronal subcellular structure stained by the technique.

  13. Primary structure of 6.5k-arginine/glutamate-rich polypeptide from the seeds of sponge gourd (Luffa cylindrica).

    PubMed

    Kimura, M; Park, S S; Sakai, R; Yamasaki, N; Funatsu, G

    1997-06-01

    The amino acid sequence of 6.5k-arginine/glutamate rich polypeptide (6.5k-AGRP) from the seeds of sponge gourd (Luffa cylindrica) has been determined. The 6.5k-AGRP consists of a 47-residue polypeptide chain containing two disulfide bonds, and a molecular mass calculated to be 5695 Da, which fully coincides with a value of [M+H]+ = m/zeta 5693.39 obtained by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). The mass spectrometric evidence indicated that 6.5k-AGRP is also present partially truncated at the C-terminus. In our preparations, approximately half of the polypeptide molecules have the C-terminal sequence Arg-Arg-Glu-Val-Asp; the other half lack Val-Asp and end with the glutamic acid, making a total of 45 residues in the polypeptide chain. The two disulfide bonds connect Cys12 to Cys33 and Cys16 to Cys29. Comparison of the amino acid sequence of 6.5k-AGRP with those of the other known proteins included in the PIR protein sequence database showed that it is related to the amino acid sequence of the N-terminal region encoded by the first exon of the cocoa (Theobroma cacao) and cotton seeds vicilin genes, sharing a characteristic two Cys-Xaa-Xaa-Xaa-Cys motif.

  14. Elastin as a self-organizing biomaterial: use of recombinantly expressed human elastin polypeptides as a model for investigations of structure and self-assembly of elastin.

    PubMed

    Keeley, Fred W; Bellingham, Catherine M; Woodhouse, Kimberley A

    2002-02-28

    Elastin is the major extracellular matrix protein of large arteries such as the aorta, imparting characteristics of extensibility and elastic recoil. Once laid down in tissues, polymeric elastin is not subject to turnover, but is able to sustain its mechanical resilience through thousands of millions of cycles of extension and recoil. Elastin consists of ca. 36 domains with alternating hydrophobic and cross-linking characteristics. It has been suggested that these hydrophobic domains, predominantly containing glycine, proline, leucine and valine, often occurring in tandemly repeated sequences, are responsible for the ability of elastin to align monomeric chains for covalent cross-linking. We have shown that small, recombinantly expressed polypeptides based on sequences of human elastin contain sufficient information to self-organize into fibrillar structures and promote the formation of lysine-derived cross-links. These cross-linked polypeptides can also be fabricated into membrane structures that have solubility and mechanical properties reminiscent of native insoluble elastin. Understanding the basis of the self-organizational ability of elastin-based polypeptides may provide important clues for the general design of self-assembling biomaterials.

  15. Structural and dynamic aspects of binding of prototype lexitropsin to the decadeoxyribonucleotide d(CGCAATTGCC)/sub 2/ deduced from high-resolution /sup 1/H NMR studies

    SciTech Connect

    Lee, M.; Chang, D.K.; Hartley, J.A.; Pon, R.T.; Krowicki, K.; Lown, J.W.

    1988-01-12

    Structural and dynamic properties of the self-complementary decadeoxyribonucleotide d-(CGCAATTGCC)/sub 2/ and the interaction between a prototype lexitropsin, or information-reading oligopeptide, and the decadeoxyribonucleotide and are deduced by using high-resolution /sup 1/H NMR techniques. The nonexchangeable and imino proton resonances of d(CGCAATTGCG)/sub 2/ have been completely assigned by two-dimensional NMR studies. The decadeoxyribonucleotide exists as a right-handed B-DNA. In the /sup 1/H NMR spectrum of the l:1 complex, the selective chemical shifts and removal of degeneracy of AH2(4), AH2(5), T-CH/sub 3/(6), and T-CH/sub 3/(7) due to the anisotropy effects of the heterocyclic moieties of the ligand, and with lesser effects at the flanking base sites C(3) and G(8), locate the drug centrally in the decadeoxyribonucleotide. This conclusion is supported by plots of individual chemical shift changes across the decadeoxyribonucleotide. Strong nuclear Overhauser effects (NOEs) between pyrrol H5 and AH2(5), and weaker NOEs to AH1'(5), TH3'(6), and AH2'(5), firmly locate the ligand in the minor groove. Intraligand NOEs between the adjacent heterocyclic moieties indicate that the lexitropsin is subject to propeller twisting about the N6-C9 bond in both the bound and free forms. Nuclear Overhauser effect spectroscopy (NOESY) and correlated spectroscopy (COSY) experiments also indicate that the removal of degeneracy of the C16 methylene protons upon complexation may arise from restricted rotation about the C15-N9, C15-C16, and C16-C17 bonds. NOE measurements on the decadeoxyribonucleotide in the 1:1 complex confirm it exists as a right-handed helix and belongs to the B family. Alternative mechanisms for this exchange process are considered.

  16. Polypeptide toxins from animal venoms.

    PubMed

    Kozlov, Sergey A

    2007-01-01

    In the course of evolution, venomous animals developed highly specialized venomous systems that provided for drastic increase in hunting and defense efficiency. Venoms of a vast number of animal species represent complex mixtures of compounds such as ions, biogenic amines, polyamines, polypeptide neurotoxins, cytolytic peptides, enzymes, etc. that exert different functions. Natural toxins are sequentially variable molecules that are very stable structurally and produce pronounced biological effects on molecular targets. High activity made them very attractive in terms of novel structure discovery and characterization. In the present review we draw attention to the structure of polypeptide molecules preferably in the 2-12 kDa molecular mass range produced by various venomous animals that were published in patent literature. The structures were reviewed on the basis of functional relation to molecular targets. We also compared the sequence information from patents with Uniprot and other protein databanks to define structures that were patented but missing from the public databases.

  17. Organic Anion Transporting Polypeptides

    PubMed Central

    Stieger, Bruno; Hagenbuch, Bruno

    2013-01-01

    Organic anion transporting polypeptides or OATPs are central transporters in the disposition of drugs and other xenobiotics. In addition, they mediate transport of a wide variety of endogenous substrates. The critical role of OATPs in drug disposition has spurred research both in academia and in the pharmaceutical industry. Translational aspects with clinical questions are the focus in academia, while the pharmaceutical industry tries to define and understand the role these transporters play in pharmacotherapy. The present overview summarizes our knowledge on the interaction of food constituents with OATPs, and on the OATP transport mechanisms. Further, it gives an update on the available information on the structure-function relationship of the OATPs, and finally, covers the transcriptional and posttranscriptional regulation of OATPs. PMID:24745984

  18. Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the β-solenoid structure formed by a silk-like polypeptide.

    PubMed

    Zhao, Binwu; Cohen Stuart, Martien A; Hall, Carol K

    2017-03-01

    The β roll molecules with sequence (GAGAGAGQ)10 stack via hydrogen bonding to form fibrils which have been themselves been used to make viral capsids of DNA strands, supramolecular nanotapes and pH-responsive gels. Accelerated molecular dynamics (aMD) simulations are used to investigate the unfolding of a stack of two β roll molecules, (GAGAGAGQ)10, to shed light on the folding mechanism by which silk-inspired polypeptides form fibrils and to identify the dominant forces that keep the silk-inspired polypeptide in a β roll configuration. Our study shows that a molecule in a stack of two β roll molecules unfolds in a step-wise fashion mainly from the C terminal. The bottom template is found to play an important role in stabilizing the β roll structure of the molecule on top by strengthening the hydrogen bonds in the layer that it contacts. Vertical hydrogen bonds within the β roll structure are considerably weaker than lateral hydrogen bonds, signifying the importance of lateral hydrogen bonds in stabilizing the β roll structure. Finally, an intermediate structure was found containing a β hairpin and an anti-parallel β sheet consisting of strands from the top and bottom molecules, revealing the self-healing ability of the β roll stack.

  19. Characterization of the viral ribonucleic acids and structural polypeptides of Anopheles A, Bunyamwera, Group C, California, Capim, Guama, Patois, and Simbu bunyaviruses.

    PubMed

    Ushijima, H; Klimas, R; Kim, S; Cash, P; Bishop, D H

    1980-11-01

    Analyses of the viral ribonucleic acids and structural polypeptides of 17-22 of the 119 accepted or proposed members of the Bunyavirus genus of arboviruses (family Bunyaviridae), have shown that from the standpoint of their structural components these viruses are highly comparable to each other. The average molecular weights for the three viral RNA species (L, large, M, medium, S, small) of 17 bunyaviruses were 2.93 X 10(6) (L, range 2.7-3.1 X 10(6)), 2.0 X 10(6) (M, range 1.8-2.3 X 10(6)), and 0.435 X 10(6) (Sm range 0.28-0.50 X 10(6)). The average molecular weights of the three major virion polypeptides (glycoproteins G1 and G2, and nucleocapsid protein, N) of 22 bunyaviruses were 115 X 10(3) (G1, range 108-120 X 10(3)), 37 X 10(3) (G2, range 20-41 X 10(3)) and 22 X 10(3) (N, range 19-25 X 10(3)). These results indicate that the structural components of bunyaviruses are different from those reported for Phlebotomus fever, Uukuniemi, and Crimean-Congo hemorrhagic fever, and other members of the Bunyaviridae family that are not currently assigned to a genus.

  20. Covalent structures of BmK AS and BmK AS-1, two novel bioactive polypeptides purified from Chinese scorpion Buthus martensi Karsch.

    PubMed

    Ji, Y H; Li, Y J; Zhang, J W; Song, B L; Yamaki, T; Mochizuki, T; Hoshino, M; Yanaihara, N

    1999-03-01

    Complete amino acid sequences of two novel bioactive polypeptides, each containing 66 amino acid residues, BmK AS and BmK AS-1 purified from the venom of Chinese scorpion Buthus martensi Karsch, have been determined by Edman sequencing and mass spectrometry on native proteins, reduced and S-carboxymethylated proteins and their peptides obtained after cleavage with proteolytic enzymes. Sequence analysis showed 86.4% structural identity between BmK AS and BmK AS-1 and also a high sequence similarity between BmK ASs and AaH IT4, a unique anti-insect toxin and a ligand of Na+ channels obtained from Sahara scorpion A. australis Hector, but poor sequence homology between BmK ASs and those of the known alpha-, beta-type and long-chain insect-selective type scorpion neurotoxins. The positions of four disulfide bridges in BmK AS-1 were established as Cys-12 and Cys-62, Cys-16 and Cys-37, Cys-23 and Cys-44, and Cys-27 and Cys-46, which are the same as those in alpha- and beta-scorpion neurotoxins. These results suggest that BmK ASs and AaH IT4 may form a new group sharing similar structural and functional properties in the family of scorpion neurotoxic polypeptides.

  1. Single amino acid substitutions in the B870 alpha and beta light-harvesting polypeptides of Rhodobacter capsulatus. Structural and spectral effects.

    PubMed

    Babst, M; Albrecht, H; Wegmann, I; Brunisholz, R; Zuber, H

    1991-12-05

    To obtain information on the structural and functional role of highly conserved amino acid residues in the B870 alpha and beta light-harvesting polypeptides of Rhodobacter capsulatus, site-directed mutagenesis was performed. 18 mutants with single amino acid substitutions at nine different positions in the B870 antenna polypeptides were prepared in a B800-850-lacking strain. The characterization of the resulting phenotypes was based on a quantification of the core-complex elements (reaction center, light-harvesting polypeptides, bacteriochlorophyll a and carotenoid) and the core-complex spectral characteristics (absorption maximum, absorption coefficient and fluorescence intensity). These data generally showed that strong structural effects were caused by the amino acid substitutions. Thus, the three tryptophan exchanges at the position alpha 8 resulted in either the absence of a core complex (alpha Trp8----Leu), the absence of the core antenna (alpha Trp8----Ala) or a reduction in the carotenoid content (alpha Trp8----Tyr). Likewise, the mutants alpha Pro13Gly (i.e. alpha Pro13----Gly), beta Gly10Val and alpha Phe23Ala demonstrated an abnormal protein/pigment ratio in the core antenna, while a drastically reduced antenna size resulted from the amino acid exchange beta Arg45Asp. In contrast to the structural effects, the absorption maxima and the fluorescence intensities of the mutant antennae differed only slightly from the wild type. The strongest blue shift of the bacteriochlorophyll a (8-11 nm) was induced by substitutions of the Trp at position alpha 43 (alpha Trp43----Ala, Leu or Tyr). Contrary to the other spectral effects, the absorption coefficient of bacteriochlorophyll a was strongly influenced by the amino acid substitutions and varied by 1.6-times less (beta Arg45Asp) and 1.3-times greater (alpha Phe25Ala) than normal. The antenna-free mutant, alpha Trp8Ala, yielded a high rate of B800-850 revertants during phototrophic growth, indicating a direct

  2. Elastomeric polypeptide-based biomaterials

    PubMed Central

    Li, Linqing; Charati, Manoj B.; Kiick, Kristi L.

    2011-01-01

    Elastomeric proteins are characterized by their large extensibility before rupture, reversible deformation without loss of energy, and high resilience upon stretching. Motivated by their unique mechanical properties, there has been tremendous research in understanding and manipulating elastomeric polypeptides, with most work conducted on the elastins but more recent work on an expanded set of polypeptide elastomers. Facilitated by biosynthetic strategies, it has been possible to manipulate the physical properties, conformation, and mechanical properties of these materials. Detailed understanding of the roles and organization of the natural structural proteins has permitted the design of elastomeric materials with engineered properties, and has thus expanded the scope of applications from elucidation of the mechanisms of elasticity to the development of advanced drug delivery systems and tissue engineering substrates. PMID:21637725

  3. Electrospun Synthetic Polypeptide Nanofibrous Biomaterials

    NASA Astrophysics Data System (ADS)

    Khadka, Dhan; Haynie, Donald

    2011-03-01

    Water-insoluble nanofiber mats of synthetic polypeptides of defined composition have been prepared from fibers electrospun from aqueous solution in the absence of organic co-solvents. 20-50 kDa poly(L-glutamate, L-tyrosine) 4:1 (PLGY) but not 15-50 kDa or 50-100 kDa poly(L-glutamate) was spinnable at 20-55% (w/v) polymer in water. Applied voltage and needle-collector distance were crucial for spinnability. Attractive fibers were obtained at 50% polymer. Fiber diameter and mat morphology have been characterized by electron microscopy. Exposure of spun fiber mats to 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC), which reacts with carboxylate, decreased fiber solubility. Fluorescein-conjugated poly(L-lysine) (FITC-PLL) but not the fluorophore alone was able bind PLGY fiber mats electrostatically, judging by fluorescence microscopy. Key advances of this work are the avoidance of an animal source of peptides and of an inorganic co-solvent to achieve polypeptide spinnability. Polypeptide fiber mats are a promising type of nano-structured biomaterial for applications in biomedicine and biotechnology.

  4. Finite pure integer programming algorithms employing only hyperspherically deduced cuts

    NASA Technical Reports Server (NTRS)

    Young, R. D.

    1971-01-01

    Three algorithms are developed that may be based exclusively on hyperspherically deduced cuts. The algorithms only apply, therefore, to problems structured so that these cuts are valid. The algorithms are shown to be finite.

  5. Structural Characterization of Fibrils from Recombinant Human Islet Amyloid Polypeptide by Solid-State NMR: The Central FGAILS Segment Is Part of the β-Sheet Core

    PubMed Central

    Weirich, Franziska; Gremer, Lothar; Mirecka, Ewa A.; Schiefer, Stephanie; Hoyer, Wolfgang; Heise, Henrike

    2016-01-01

    Amyloid deposits formed from islet amyloid polypeptide (IAPP) are a hallmark of type 2 diabetes mellitus and are known to be cytotoxic to pancreatic β-cells. The molecular structure of the fibrillar form of IAPP is subject of intense research, and to date, different models exist. We present results of solid-state NMR experiments on fibrils of recombinantly expressed and uniformly 13C, 15N-labeled human IAPP in the non-amidated, free acid form. Complete sequential resonance assignments and resulting constraints on secondary structure are shown. A single set of chemical shifts is found for most residues, which is indicative of a high degree of homogeneity. The core region comprises three to four β-sheets. We find that the central 23-FGAILS-28 segment, which is of critical importance for amyloid formation, is part of the core region and forms a β-strand in our sample preparation. The eight N-terminal amino acid residues of IAPP, forming a ring-like structure due to a disulfide bridge between residues C2 and C7, appear to be well defined but with an increased degree of flexibility. This study supports the elucidation of the structural basis of IAPP amyloid formation and highlights the extent of amyloid fibril polymorphism. PMID:27607147

  6. Structural Characterization of Fibrils from Recombinant Human Islet Amyloid Polypeptide by Solid-State NMR: The Central FGAILS Segment Is Part of the β-Sheet Core.

    PubMed

    Weirich, Franziska; Gremer, Lothar; Mirecka, Ewa A; Schiefer, Stephanie; Hoyer, Wolfgang; Heise, Henrike

    2016-01-01

    Amyloid deposits formed from islet amyloid polypeptide (IAPP) are a hallmark of type 2 diabetes mellitus and are known to be cytotoxic to pancreatic β-cells. The molecular structure of the fibrillar form of IAPP is subject of intense research, and to date, different models exist. We present results of solid-state NMR experiments on fibrils of recombinantly expressed and uniformly 13C, 15N-labeled human IAPP in the non-amidated, free acid form. Complete sequential resonance assignments and resulting constraints on secondary structure are shown. A single set of chemical shifts is found for most residues, which is indicative of a high degree of homogeneity. The core region comprises three to four β-sheets. We find that the central 23-FGAILS-28 segment, which is of critical importance for amyloid formation, is part of the core region and forms a β-strand in our sample preparation. The eight N-terminal amino acid residues of IAPP, forming a ring-like structure due to a disulfide bridge between residues C2 and C7, appear to be well defined but with an increased degree of flexibility. This study supports the elucidation of the structural basis of IAPP amyloid formation and highlights the extent of amyloid fibril polymorphism.

  7. Peppytides: Interactive Models of Polypeptide Chains

    SciTech Connect

    Zuckermann, Ron; Chakraborty, Promita; Derisi, Joe

    2014-01-21

    Peppytides are scaled, 3D-printed models of polypeptide chains that can be folded into accurate protein structures. Designed and created by Berkeley Lab Researcher, Promita Chakraborty, and Berkeley Lab Senior Scientist, Dr. Ron Zuckermann, Peppytides are accurate physical models of polypeptide chains that anyone can interact with and fold intro various protein structures - proving to be a great educational tool, resulting in a deeper understanding of these fascinating structures and how they function. Build your own Peppytide model and learn about how nature's machines fold into their intricate architectures!

  8. Peppytides: Interactive Models of Polypeptide Chains

    ScienceCinema

    Zuckermann, Ron; Chakraborty, Promita; Derisi, Joe

    2016-07-12

    Peppytides are scaled, 3D-printed models of polypeptide chains that can be folded into accurate protein structures. Designed and created by Berkeley Lab Researcher, Promita Chakraborty, and Berkeley Lab Senior Scientist, Dr. Ron Zuckermann, Peppytides are accurate physical models of polypeptide chains that anyone can interact with and fold intro various protein structures - proving to be a great educational tool, resulting in a deeper understanding of these fascinating structures and how they function. Build your own Peppytide model and learn about how nature's machines fold into their intricate architectures!

  9. Stereodependent and solvent-specific formation of unusual β-structure through side chain-backbone H-bonding in C4(S)-(NH2 /OH/NHCHO)-L-prolyl polypeptides.

    PubMed

    Bansode, Nitin D; Madhanagopal, B; Sonar, Mahesh V; Ganesh, Krishna N

    2017-01-01

    It is shown that C4(S)-NH2 /OH/NHCHO-prolyl polypeptides exhibit PPII conformation in aqueous medium, but in a relatively hydrophobic solvent trifluoroethanol (TFE) transform into an unusual β-structure. The stereospecific directing effect of H-bonding in defining the specific structure is demonstrated by the absence of β-structure in the corresponding C4(S)-guanidinyl/(NH/O)-acetyl derivatives and retention of β-structure in C4(S)-(NHCHO)-prolyl polypeptides in TFE. The distinct conformations are identified by the characteristic CD patterns and supported by Raman spectroscopic data. The solvent dependent conformational effects are interpreted in terms of intraresidue H-bonding that promotes PPII conformation in water, switching over to interchain H-bonding in TFE. The present observations add a new design principle to the growing repertoire of strategies for engineering peptide secondary structural motifs for innovative nanoassemblies and new biomaterials.

  10. Deducing the subsurface geological conditions and structural framework of the NE Gulf of Suez area, using 2-D and 3-D seismic data

    NASA Astrophysics Data System (ADS)

    Zahra, Hesham Shaker; Nakhla, Adel Mokhles

    2015-06-01

    An interpretation of the seismic data of Ras Budran and Abu Zenima oil fields, northern central Gulf of Suez, is carried out to evaluate its subsurface tectonic setting. The structural configuration, as well as the tectonic features of the concerned area is criticized through the study of 2D and 3D seismic data interpretation with the available geological data, in which the geo-seismic depth maps for the main interesting levels (Kareem, Nukhul, Matulla, Raha and Nubia Formations) are depicted. Such maps reflect that, the Miocene structure of Ras Budran area is a nearly NE-SW trending anticlinal feature, which broken into several panels by a set of NWSE and NE-SW trending faults. The Pre-Miocene structure of the studied area is very complex, where Ras Budran area consists of step faults down stepping to the south and southwest, which have been subjected to cross faults of NE-SW trend with lateral and vertical displacements.

  11. Deducing the functional characteristics of the human selenoprotein SELK from the structural properties of its intrinsically disordered C-terminal domain.

    PubMed

    Polo, Andrea; Colonna, Giovanni; Guariniello, Stefano; Ciliberto, Gennaro; Costantini, Susan

    2016-03-01

    The intrinsically disordered proteins (IDPs) cannot be described by a single structural representation but, due to their high structural fluctuation, through conformational ensembles. Certainly, molecular dynamics (MD) simulations represent a useful tool to study their different conformations capturing the conformational distribution. Our group is focusing on the structural characterization of proteins belonging to the seleno-proteome due to their involvement in cancer. They present disordered domains central for their biological function, and, in particular, SELK is a single-pass transmembrane protein that resides in the endoplasmic reticulum membrane (ER) with a C-terminal domain exposed to the cytoplasm that is known to interact with different components of the endoplasmic reticulum associated to the protein degradation (ERAD) pathway. This protein is found to be up-expressed in hepatocellular carcinoma and in other cancers. In this work we performed a detailed analysis of the C-terminal domain sequence of SELK and discovered that it is characterized by many prolines, and four negatively and eleven positively charged residues, which are crucial for its biological activity. This region can be considered as a weak polyelectrolyte and, specifically, a polycation, with high disordered propensity and different phosphorylation sites dislocated along the sequence. Then, we modeled its three-dimensional structure by performing MD simulations in water at neutral pH to analyze the structural stability as well as to identify the presence of HUB residues that play a key structural role as evidenced by the residue-residue interaction network analysis. Through this approach, we demonstrate that the C-terminal domain of SELK (i) presents a poor content of regular secondary structure elements, (ii) is dynamically stabilized by a network of intra-molecular H-bonds and H-bonds with water molecules, (iii) is highly fluctuating and, therefore, can be described only through a

  12. Structural basis for the inhibition of truncated islet amyloid polypeptide aggregation by Cu(II): insights into the bioinorganic chemistry of type II diabetes.

    PubMed

    Rivillas-Acevedo, Lina; Sánchez-López, Carolina; Amero, Carlos; Quintanar, Liliana

    2015-04-20

    Type 2 diabetes (T2D) is one of the most common chronic diseases, affecting over 300 million people worldwide. One of the hallmarks of T2D is the presence of amyloid deposits of human islet amyloid polypeptide (IAPP) in the islets of Langerhans of pancreatic β-cells. Recent reports indicate that Cu(II) can inhibit the aggregation of human IAPP, although the mechanism for this inhibitory effect is not clear. In this study, different spectroscopic techniques and model fragments of IAPP were employed to shed light on the structural basis for the interaction of Cu(II) with human IAPP. Our results show that Cu(II) anchors to His18 and the subsequent amide groups toward the C-terminal, forming a complex with an equatorial coordination mode 3N1O at physiological pH. Cu(II) binding to truncated IAPP at the His18 region is the key event for its inhibitory effect in amyloid aggregation. Electron paramagnetic resonance studies indicate that the monomeric Cu(II)-IAPP(15-22) complex differs significantly from Cu(II) bound to mature IAPP(15-22) fibers, suggesting that copper binding to monomeric IAPP(15-22) competes with the conformation changes needed to form β-sheet structures, thus delaying fibril formation. A general mechanism is proposed for the inhibitory effect of copper and other imidazole-binding metal ions in IAPP amyloid formation, providing further insights into the bioinorganic chemistry of T2D.

  13. Exon organization of the mouse entactin gene corresponds to the structural domains of the polypeptide and has regional homology to the low-density lipoprotein receptor gene

    SciTech Connect

    Durkin, M.E.; Chung, A.E.; Wewer, U.M.

    1995-03-20

    Entactin is a widespread basement membrane protein of 150 kDa that binds to type IV collagen and laminin. The complete exon-intron structure of the mouse entactin gene has been determined from {lambda} genomic DNA clones. The gene spans at least 65 kb and contains 20 exons. The exon organization of the mouse entactin gene closely corresponds to the organization of the polypeptide into distinct structural and functional domains. The two amino-terminal globular domains are encoded by three exons each. Single exons encode the two protease-sensitive, O-glycosylated linking regions. The six EGF-like repeats and the single thyroglobulin-type repeat are each encoded by separate exons. The carboxyl-terminal half of entactin displays sequence homology to the growth factor-like region of the low-density lipoprotein receptor, and in both genes this region is encoded by eight exons. The positions of four introns are also conserved in the homologous region of the two genes. These observations suggest that the entactin gene has evolved via exon shuffling. Finally, several sequence polymorphisms useful for gene linkage analysis were found in the 3{prime} noncoding region of the last exon. 52 refs., 8 figs.

  14. Variations on the GFP chromophore: A polypeptide fragmentation within the chromophore revealed in the 2.1-A crystal structure of a nonfluorescent chromoprotein from Anemonia sulcata.

    PubMed

    Wilmann, Pascal G; Petersen, Jan; Devenish, Rodney J; Prescott, Mark; Rossjohn, Jamie

    2005-01-28

    We have determined to 2.1 A resolution the crystal structure of a dark state, kindling fluorescent protein isolated from the sea anemone, Anemonia sulcata. The chromophore sequence Met(63)-Tyr(64)-Gly(65) of the A. sulcata chromoprotein was previously proposed to comprise a 6-membered pyrazine-type heterocycle (Martynov, V. I., Savitsky, A. P., Martynova, N. Y., Savitsky, P. A., Lukyanov, K. A., and Lukyanov, S. A. (2001) J. Biol. Chem. 276, 21012-21016). However, our crystallographic data revealed the chromophore to comprise a 5-membered p-hydroxybenzylideneimidazolinone moiety that adopts a non-coplanar trans conformation within the interior of the GFP beta-can fold. Unexpectedly, fragmentation of the polypeptide was found to occur within the chromophore moiety, at the bond between Cys(62C) and Met(63N1.) Our structural data reveal that fragmentation of the chromophore represents an intrinsic, autocatalytic step toward the formation of the mature chromophore within the specific GFP-like proteins.

  15. CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure

    PubMed Central

    2012-01-01

    Background One aim of the in silico characterization of proteins is to identify all residue-positions, which are crucial for function or structure. Several sequence-based algorithms exist, which predict functionally important sites. However, with respect to sequence information, many functionally and structurally important sites are hard to distinguish and consequently a large number of incorrectly predicted functional sites have to be expected. This is why we were interested to design a new classifier that differentiates between functionally and structurally important sites and to assess its performance on representative datasets. Results We have implemented CLIPS-1D, which predicts a role in catalysis, ligand-binding, or protein structure for residue-positions in a mutually exclusive manner. By analyzing a multiple sequence alignment, the algorithm scores conservation as well as abundance of residues at individual sites and their local neighborhood and categorizes by means of a multiclass support vector machine. A cross-validation confirmed that residue-positions involved in catalysis were identified with state-of-the-art quality; the mean MCC-value was 0.34. For structurally important sites, prediction quality was considerably higher (mean MCC = 0.67). For ligand-binding sites, prediction quality was lower (mean MCC = 0.12), because binding sites and structurally important residue-positions share conservation and abundance values, which makes their separation difficult. We show that classification success varies for residues in a class-specific manner. This is why our algorithm computes residue-specific p-values, which allow for the statistical assessment of each individual prediction. CLIPS-1D is available as a Web service at http://www-bioinf.uni-regensburg.de/. Conclusions CLIPS-1D is a classifier, whose prediction quality has been determined separately for catalytic sites, ligand-binding sites, and structurally important sites. It generates hypotheses about

  16. A bio-inspired two-layer sensing structure of polypeptide and multiple-walled carbon nanotube to sense small molecular gases.

    PubMed

    Wang, Li-Chun; Su, Tseng-Hsiung; Ho, Cheng-Long; Yang, Shang-Ren; Chiu, Shih-Wen; Kuo, Han-Wen; Tang, Kea-Tiong

    2015-03-05

    In this paper, we propose a bio-inspired, two-layer, multiple-walled carbon nanotube (MWCNT)-polypeptide composite sensing device. The MWCNT serves as a responsive and conductive layer, and the nonselective polypeptide (40 mer) coating the top of the MWCNT acts as a filter into which small molecular gases pass. Instead of using selective peptides to sense specific odorants, we propose using nonselective, peptide-based sensors to monitor various types of volatile organic compounds. In this study, depending on gas interaction and molecular sizes, the randomly selected polypeptide enabled the recognition of certain polar volatile chemical vapors, such as amines, and the improved discernment of low-concentration gases. The results of our investigation demonstrated that the polypeptide-coated sensors can detect ammonia at a level of several hundred ppm and barely responded to triethylamine.

  17. Tectonic Signals Deduced from Quantitative Analysis of Geomorphic Parameters in Bedrock Rivers and Structural Mapping: A case study from the Surai Khola Siwalik Section, Nepalese Himalaya

    NASA Astrophysics Data System (ADS)

    Bhattarai, I.; Gani, N. D.

    2016-12-01

    The Nepalese Himalaya is one of the most active regions within the Himalayan Mountain Belt, which is characterized by a thick succession of Siwalik sedimentary rocks deposited at its foreland basin. To date, much of the tectonic geomorphologic study in the Nepalese Siwalik is poorly understood, particularly in the Surai Khola section. Thus, the study of quantitative analysis of bedrock river parameters will provide crucial information regarding tectonic activities in the area. This study investigates geomorphic parameters of longitudinal river profiles from 54 watersheds within the Siwalik section of the Nepalese Himalaya. We extracted a total of 140 bedrock rivers from these watersheds using stream power-law function and 30-meter resolution ASTER DEM. In addition, we used 90-meter resolution SRTM DEM for structural mapping within the Surai Khola section. Our new results show presence of major and minor knickpoints that were classified on the basis of relief of the longitudinal profiles. We identified 180 major knickpoints out of 305 total knickpoints. Normalized steepness index (ksn) and concavity index values vary above and below these knicpoints. The ksn values range from 5.3 to 140.6 while concavity index of the streams in the study area ranges from as low as -12.1 to as high as 31.1. We also identified a total of 133 structural lineations that were mapped for the first time using various sun illumination angles and azimuths, and slope. Most of these structural lineations are likely faults that follow the similar east-west trends of the Main Frontal Thrust (MFT) Fault. The length of these faults ranges from 0.5 km to 8 km. We interpreted that a few measured knickpoints might be associated with our mapped mesoscale faults, while the majority of the knickpoints in the river profiles are locally adjusting to the MFT related uplift.

  18. Inferring the subsurface basement depth and the structural trends as deduced from aeromagnetic data at West Beni Suef area, Western Desert, Egypt

    NASA Astrophysics Data System (ADS)

    Khalil, Ahmed; Abdel Hafeez, Tharwat H.; Saleh, Hassan S.; Mohamed, Waheed H.

    2016-12-01

    The present work aimed to delineate the subsurface structures and to estimate the magnetic source depth at the selected area lying in West Beni Suef area, Western Desert, Egypt, following different geomagnetic techniques. The analysis of aeromagnetic data demonstrates five significant tectonic faults trending to NW-SE, ENE-WSW, NE-SW, E-W and NNW-SSE directions constructed using Euler deconvolution techniques. The execution of this study is initiated by transformation of the total intensity aeromagnetic data to the reduced to pole (RTP) magnetic intensity. This is followed by applying several transformation techniques and various filtering processes through qualitative and quantitative analyses on magnetic data. The reduced to the northern magnetic pole (RTP) data are separated spectrally into regional and residual magnetic components using the computed power spectrum of the magnetic data. The estimated mean depths of both regional and residual sources are found to be 5.27 km and 2.78 km respectively. Also, depth estimations have been conducted by application of the Euler deconvolution and 2-D modeling techniques. The results indicate that the eastern and northern parts of the study area discriminate deeper basement relief and the depth of basement surface reaches to 5095 m. While the southern and western parts of the study area discriminate shallower basement relief and the depth of basement surface reaches to 227 m. This study has given a clear picture of the geologic structures beneath the study area.

  19. Properties of a large-scale interplanetary loop structure as deduced from low-energy proton anisotropy and magnetic field measurements

    NASA Technical Reports Server (NTRS)

    Tranquille, C.; Sanderson, T. R.; Marsden, R. G.; Wenzel, K.-P.; Smith, E. J.

    1987-01-01

    Correlated particle and magnetic field measurements by the ISEE 3 spacecraft are presented for the loop structure behind the interplanetary traveling shock event of Nov. 12, 1978. Following the passage of the turbulent shock region, strong bidirectional streaming of low-energy protons is observed for approximately 6 hours, corresponding to a loop thickness of about 0.07 AU. This region is also characterized by a low relative variance of the magnetic field, a depressed proton intensity, and a reduction in the magnetic power spectral density. Using quasi-linear theory applied to a slab model, a value of 3 AU is derived for the mean free path during the passage of the closed loop. It is inferred from this observation that the proton regime associated with the loop structure is experiencing scatter-free transport and that either the length of the loop is approximately 3 AU between the sun and the earth or else the protons are being reflected at both ends of a smaller loop.

  20. Properties of a large-scale interplanetary loop structure as deduced from low-energy proton anisotropy and magnetic field measurements

    NASA Technical Reports Server (NTRS)

    Tranquille, C.; Sanderson, T. R.; Marsden, R. G.; Wenzel, K.-P.; Smith, E. J.

    1987-01-01

    Correlated particle and magnetic field measurements by the ISEE 3 spacecraft are presented for the loop structure behind the interplanetary traveling shock event of Nov. 12, 1978. Following the passage of the turbulent shock region, strong bidirectional streaming of low-energy protons is observed for approximately 6 hours, corresponding to a loop thickness of about 0.07 AU. This region is also characterized by a low relative variance of the magnetic field, a depressed proton intensity, and a reduction in the magnetic power spectral density. Using quasi-linear theory applied to a slab model, a value of 3 AU is derived for the mean free path during the passage of the closed loop. It is inferred from this observation that the proton regime associated with the loop structure is experiencing scatter-free transport and that either the length of the loop is approximately 3 AU between the sun and the earth or else the protons are being reflected at both ends of a smaller loop.

  1. Topography of a binding site for small amnestic peptides deduced from structure-activity studies: relation to amnestic effect of amyloid beta protein.

    PubMed

    Flood, J F; Roberts, E; Sherman, M A; Kaplan, B E; Morley, J E

    1994-01-04

    Four peptides homologous to amyloid beta protein containing the Val-Phe-Phe (VFF) sequence administered intracerebroventricularly after training caused amnesia for footshock active avoidance training in mice. Results with VFF and other peptides containing VFF or portions thereof were used to generate a topographic map for a hypothetical binding surface for amnestic peptides, termed Z. Effects on retention of footshock active avoidance training were rationalized in terms of fit to Z, making possible design of potential memory-modulating peptidic and nonpeptidic substances. Three peptides that neither improved nor impaired retention blocked the amnestic effects of beta-(12-28), a peptide homologous to amyloid beta protein, opening the way to development of substances that can antagonize the neurotoxic effects of amyloid beta protein on neural structures and thus attenuate symptoms and progression of Alzheimer disease.

  2. Topography of a binding site for small amnestic peptides deduced from structure-activity studies: relation to amnestic effect of amyloid beta protein.

    PubMed Central

    Flood, J F; Roberts, E; Sherman, M A; Kaplan, B E; Morley, J E

    1994-01-01

    Four peptides homologous to amyloid beta protein containing the Val-Phe-Phe (VFF) sequence administered intracerebroventricularly after training caused amnesia for footshock active avoidance training in mice. Results with VFF and other peptides containing VFF or portions thereof were used to generate a topographic map for a hypothetical binding surface for amnestic peptides, termed Z. Effects on retention of footshock active avoidance training were rationalized in terms of fit to Z, making possible design of potential memory-modulating peptidic and nonpeptidic substances. Three peptides that neither improved nor impaired retention blocked the amnestic effects of beta-(12-28), a peptide homologous to amyloid beta protein, opening the way to development of substances that can antagonize the neurotoxic effects of amyloid beta protein on neural structures and thus attenuate symptoms and progression of Alzheimer disease. Images Fig. 1 PMID:8278398

  3. Metamorphic fluids and uplift-erosion history of a portion of the Kapuskasing structural zone, Ontario, as deduced from fluid inclusions

    NASA Technical Reports Server (NTRS)

    Rudnick, R. L.; Ashwal, L. D.; Henry, D. J.

    1983-01-01

    Fluid inclusions can be used to determine the compositional evolution of fluids present in high grade metamorphic rocks (Touret, 1979) along with the general P-T path followed by the rocks during uplift and erosion (Hollister et al., 1979). In this context, samples of high grade gneisses from the Kapuskasing structural zone (KSZ, Fig. 1) of eastern Ontario were studied in an attempt to define the composition of syn- and post-metamorphic fluids and help constrain the uplift and erosion history of the KSZ. Recent work by Percival (1980), Percival and Card (1983) and Percival and Krogh (1983) shows that the KSZ represents lower crustal granulites that form the lower portion of an oblique cross section through the Archean crust, which was up faulted along a northeast striking thrust fault. The present fluid inclusion study places constraints upon the P-T path which the KSZ followed during uplift and erosion.

  4. Spatial heterogeneity of the structure and stress field in Hyuga-nada region, southwest Japan, deduced from onshore and offshore seismic observations

    NASA Astrophysics Data System (ADS)

    Uehira, K.; Yakiwara, H.; Yamada, T.; Umakoshi, K.; Nakao, S.; Kobayashi, R.; Goto, K.; Miyamachi, H.; Mochizuki, K.; Nakahigashi, K.; Shinohara, M.; Kanazawa, T.; Hino, R.; Goda, M.; Shimizu, H.

    2010-12-01

    In Hyuga-nada region, the Philippine Sea (PHS) plate is subducting beneath the Eurasian (EU) plate (the southwest Japan arc) along the Nankai trough at a rate of about 5 cm per year. The seismic activity in the boundary between the PHS and the Eurasian (EU) plates varies spatially along the Nankai trough. Especially the region from off coast of Shikoku to the Bungo channel and Hyuga-nada has large variation of seismicity. Although usual microearthquake activity is active in Hyuga-nada, it is inactive near Shikoku. On the other hand, although the great earthquake (M>8) has occurred repeatedly in near Shikoku at intervals of about 100 years, in Hyuga-nada, smaller earthquakes (M7 class) has occurred at intervals of about dozens of years, and so plate coupling varies dozens of kilometers specially. Big earthquakes (M7 class) have occurred in the north region from latitude 31.6 degrees north, but it has not occurred in the south region from latitude 31.6 degrees north. The largest earthquake ever recorded in Hyuga-nada region is the 1968 Hyuga-nada earthquake (Mw 7.5). And microseismicity varies spatially. It is important to understand seismic activity, stress field, and structure in such region in order to understand seismic cycle. We performed extraordinary seismic observation in and around Hyuga-nada region. More than 20 pop-up type OBSs were deployed above hypocentral region of Hyuga-nada using Nagasaki-maru and several data loggers were deployed in order to compensate a regular seismic network on land. We detected earthquakes more than 2 times of JMA. Seismic activity in source region of the 1961 Hyuga-nada Earthquake (M7.0) is low, but around its source region, seismic activity is very high. In order to obtain a 3D seismic velocity structure and precise hypocenter distribution and focal mechanisms around the Hyuga-nada region, we used Double-Difference (DD) Tomography method developed by Zhang and Thurber (2003). We could detect the structure of subduction of

  5. Solution structure and mutational analysis of pituitary adenylate cyclase-activating polypeptide binding to the extracellular domain of PAC1-RS

    PubMed Central

    Sun, Chaohong; Song, Danying; Davis-Taber, Rachel A.; Barrett, Leo W.; Scott, Victoria E.; Richardson, Paul L.; Pereda-Lopez, Ana; Uchic, Marie E.; Solomon, Larry R.; Lake, Marc R.; Walter, Karl A.; Hajduk, Philip J.; Olejniczak, Edward T.

    2007-01-01

    The pituitary adenylate cyclase-activating polypeptide (PACAP) receptor is a class II G protein-coupled receptor that contributes to many different cellular functions including neurotransmission, neuronal survival, and synaptic plasticity. The solution structure of the potent antagonist PACAP (residues 6′–38′) complexed to the N-terminal extracellular (EC) domain of the human splice variant hPAC1-R-short (hPAC1-RS) was determined by NMR. The PACAP peptide adopts a helical conformation when bound to hPAC1-RS with a bend at residue A18′ and makes extensive hydrophobic and electrostatic interactions along the exposed β-sheet and interconnecting loops of the N-terminal EC domain. Mutagenesis data on both the peptide and the receptor delineate the critical interactions between the C terminus of the peptide and the C terminus of the EC domain that define the high affinity and specificity of hormone binding to hPAC1-RS. These results present a structural basis for hPAC1-RS selectivity for PACAP versus the vasoactive intestinal peptide and also differentiate PACAP residues involved in binding to the N-terminal extracellular domain versus other parts of the full-length hPAC1-RS receptor. The structural, mutational, and binding data are consistent with a model for peptide binding in which the C terminus of the peptide hormone interacts almost exclusively with the N-terminal EC domain, whereas the central region makes contacts to both the N-terminal and other extracellular parts of the receptor, ultimately positioning the N terminus of the peptide to contact the transmembrane region and result in receptor activation. PMID:17470806

  6. Open reading frame sequencing and structure-based alignment of polypeptides encoded by RT1-Bb, RT1-Ba, RT1-Db, and RT1-Da alleles.

    PubMed

    Ettinger, Ruth A; Moustakas, Antonis K; Lobaton, Suzanne D

    2004-11-01

    MHC class II genes are major genetic components in rats developing autoimmunity. The majority of rat MHC class II sequencing has focused on exon 2, which forms the first external domain. Sequence of the complete open reading frame for rat MHC class II haplotypes and structure-based alignment is lacking. Herein, the complete open reading frame for RT1-Bbeta, RT1-Balpha, RT1-Dbeta, and RT1-Dalpha was sequenced from ten different rat strains, covering eight serological haplotypes, namely a, b, c, d, k, l, n, and u. Each serological haplotype was unique at the nucleotide level of the sequenced RT1-B/D region. Within individual genes, the number of alleles identified was seven, seven, six, and three and the degree of amino-acid polymorphism between allotypes for each gene was 22%, 16%, 19%, and 0.4% for RT1-Bbeta, RT1-Balpha, RT1-Dbeta, and RT1-Dalpha, respectively. The extent and distribution of amino-acid polymorphism was comparable with mouse and human MHC class II. Structure-based alignment identified the beta65-66 deletion, the beta84a insertion, the alpha9a insertion, and the alpha1a-1c insertion in RT1-B previously described for H2-A. Rat allele-specific deletions were found at RT1-Balpha76 and RT1-Dbeta90-92. The mature RT1-Dbeta polypeptide was one amino acid longer than HLA-DRB1 due to the position of the predicted signal peptide cleavage site. These data are important to a comprehensive understanding of MHC class II structure-function and for mechanistic studies of rat models of autoimmunity.

  7. Formation of highly oxidized multifunctional compounds: autoxidation of peroxy radicals formed in the ozonolysis of alkenes - deduced from structure-product relationships

    NASA Astrophysics Data System (ADS)

    Mentel, T. F.; Springer, M.; Ehn, M.; Kleist, E.; Pullinen, I.; Kurtén, T.; Rissanen, M.; Wahner, A.; Wildt, J.

    2015-06-01

    It has been postulated that secondary organic particulate matter plays a pivotal role in the early growth of newly formed particles in forest areas. The recently detected class of extremely low volatile organic compounds (ELVOC) provides the missing organic vapors and possibly contributes a significant fraction to atmospheric SOA (secondary organic aerosol). The sequential rearrangement of peroxy radicals and subsequent O2 addition results in ELVOC which are highly oxidized multifunctional molecules (HOM). Key for efficiency of such HOM in early particle growth is that their formation is induced by one attack of the oxidant (here O3), followed by an autoxidation process involving molecular oxygen. Similar mechanisms were recently observed and predicted by quantum mechanical calculations e.g., for isoprene. To assess the atmospheric importance and therewith the potential generality, it is crucial to understand the formation pathway of HOM. To elucidate the formation path of HOM as well as necessary and sufficient structural prerequisites of their formation we studied homologous series of cycloalkenes in comparison to two monoterpenes. We were able to directly observe highly oxidized multifunctional peroxy radicals with 8 or 10 O atoms by an Atmospheric Pressure interface High Resolution Time of Flight Mass Spectrometer (APi-TOF-MS) equipped with a NO3--chemical ionization (CI) source. In the case of O3 acting as an oxidant, the starting peroxy radical is formed on the so-called vinylhydroperoxide path. HOM peroxy radicals and their termination reactions with other peroxy radicals, including dimerization, allowed for analyzing the observed mass spectra and narrowing down the likely formation path. As consequence, we propose that HOM are multifunctional percarboxylic acids, with carbonyl, hydroperoxy, or hydroxy groups arising from the termination steps. We figured that aldehyde groups facilitate the initial rearrangement steps. In simple molecules like cycloalkenes

  8. Formation of highly oxidized multifunctional compounds: autoxidation of peroxy radicals formed in the ozonolysis of alkenes - deduced from structure-product relationships

    NASA Astrophysics Data System (ADS)

    Mentel, T. F.; Springer, M.; Ehn, M.; Kleist, E.; Pullinen, I.; Kurtén, T.; Rissanen, M.; Wahner, A.; Wildt, J.

    2015-01-01

    It has been postulated that secondary organic particulate matter plays a pivotal role in the early growth of newly formed particles in forest areas. The recently detected class of extremely low volatile organic compounds (ELVOC) provides the missing organic vapours and possibly contributes a~significant fraction to atmospheric SOA. ELVOC are highly oxidized multifunctional molecules (HOM), formed by sequential rearrangement of peroxy radicals and subsequent O2 addition. Key for efficiency in early particle growth is that formation of HOM is induced by one attack of the oxidant (here O3) and followed by an autoxidation process involving molecular oxygen. Similar mechanisms were recently observed and predicted by quantum mechanical calculations e.g. for isoprene. To assess the atmospheric importance and therewith the potential generality, it is crucial to understand the formation pathway of HOM. To elucidate the formation path of HOM as well as necessary and sufficient structural prerequisites of their formation we studied homologues series of cycloalkenes in comparison to two monoterpenes. We were able to directly observe highly oxidized multifunctional peroxy radicals with 8 or 10 O-atoms by an Atmospheric Pressure interface High Resolution Time of Flight Mass Spectrometer equipped with a NO3--Chemical Ionization (CI) source. In case of O3 acting as oxidant the starting peroxy radical is formed on the so called vinylhydroperoxide path. HOM peroxy radicals and their termination reactions with other peroxy radicals, including dimerization, allowed for analysing the observed mass spectra and narrow down the likely formation path. As consequence we propose that HOM are multifunctional percarboxylic acids; with carbonyl-, hydroperoxy-, or hydroxy-groups arising from the termination steps. We figured that aldehyde groups facilitate the initial rearrangement steps. In simple molecules like cyloalkenes autoxidation was limited to both terminal C-atoms and two further C

  9. The relationship between seismic velocity structure and the seismic coupling in the Hyuga-nada region, southwest Japan, deduced from onshore and offshore seismic observations

    NASA Astrophysics Data System (ADS)

    Uehira, K.; Yakiwara, H.; Yamada, T.; Umakoshi, K.; Nakao, S.; Kobayashi, R.; Goto, K.; Miyamachi, H.; Mochizuki, K.; Nakahigashi, K.; Shinohara, M.; Kanazawa, T.; Hino, R.; Goda, M.; Shimizu, H.

    2011-12-01

    In Hyuga-nada region, the Philippine Sea (PHS) plate is subducting beneath the Eurasian (EU) plate (the southwest Japan arc) along the Nankai trough at a rate of about 5 cm per year. Big earthquakes (M7 class) have occurred in the north region from latitude 31.6 degrees north, but it has not occurred in the south region from latitude 31.6 degrees north. The largest earthquake ever recorded in Hyuga-nada region is the 1968 Hyuga-nada earthquake (Mw 7.5). And microseismicity varies spatially. There are non-seismic slip events in Hyuga-nada region. For example, the after-slips associated with events for 19 October 1996 and 3 December 1996 were observed (Yagi et al., 2001), and in the same region, the slow-slip events were also observed by GPS measurements (GSI, 2011). We performed extraordinary seismic observations for 75 days from April to July 2006, for 73 days from April to July 2008, and for 77 days from April to July 2009. About 25 pop-up type ocean-bottom seismometers were deployed above hypocentral region in Hyuga-nada using Nagasaki-maru. And three data loggers were deployed on land in order to compensate a regular seismic network. We used these data and permanent stations for this analysis. In order to obtain precise hypocenter distribution, focal mechanisms, and a 3D seismic velocity structure around the Hyuga-nada region, we used Double-Difference (DD) Tomography method developed by Zhang and Thurber (2003). In northern part of Hyuga-nada, Vp/Vs ratio is high along the upper part of PHS slab, and this layer is interpreted as the subducting oceanic crust. On the other hand, Vp/Vs ratio is about 1.73 in southern part of Hyuga-nada, and this is interpreted as the subducted Kyushu-Palau Ridge, old island arc, which is made by granitic rock. More over, there is a difference of Poisson's ratio at mantle wedge. This value is high (> 0.3) in northern part of Hyuga-nada. The high Poisson's mantle wedge is suggesting that the zone probably corresponds to a

  10. The evolutionary pathway from a biologically inactive polypeptide sequence to a folded, active structural mimic of DNA

    PubMed Central

    Kanwar, Nisha; Roberts, Gareth A.; Cooper, Laurie P.; Stephanou, Augoustinos S.; Dryden, David T.F.

    2016-01-01

    The protein Ocr (overcome classical restriction) from bacteriophage T7 acts as a mimic of DNA and inhibits all Type I restriction/modification (RM) enzymes. Ocr is a homodimer of 116 amino acids and adopts an elongated structure that resembles the shape of a bent 24 bp DNA molecule. Each monomer includes 34 acidic residues and only six basic residues. We have delineated the mimicry of Ocr by focusing on the electrostatic contribution of its negatively charged amino acids using directed evolution of a synthetic form of Ocr, termed pocr, in which all of the 34 acidic residues were substituted for a neutral amino acid. In vivo analyses confirmed that pocr did not display any antirestriction activity. Here, we have subjected the gene encoding pocr to several rounds of directed evolution in which codons for the corresponding acidic residues found in Ocr were specifically re-introduced. An in vivo selection assay was used to detect antirestriction activity after each round of mutation. Our results demonstrate the variation in importance of the acidic residues in regions of Ocr corresponding to different parts of the DNA target which it is mimicking and for the avoidance of deleterious effects on the growth of the host. PMID:27095198

  11. The evolutionary pathway from a biologically inactive polypeptide sequence to a folded, active structural mimic of DNA.

    PubMed

    Kanwar, Nisha; Roberts, Gareth A; Cooper, Laurie P; Stephanou, Augoustinos S; Dryden, David T F

    2016-05-19

    The protein Ocr (overcome classical restriction) from bacteriophage T7 acts as a mimic of DNA and inhibits all Type I restriction/modification (RM) enzymes. Ocr is a homodimer of 116 amino acids and adopts an elongated structure that resembles the shape of a bent 24 bp DNA molecule. Each monomer includes 34 acidic residues and only six basic residues. We have delineated the mimicry of Ocr by focusing on the electrostatic contribution of its negatively charged amino acids using directed evolution of a synthetic form of Ocr, termed pocr, in which all of the 34 acidic residues were substituted for a neutral amino acid. In vivo analyses confirmed that pocr did not display any antirestriction activity. Here, we have subjected the gene encoding pocr to several rounds of directed evolution in which codons for the corresponding acidic residues found in Ocr were specifically re-introduced. An in vivo selection assay was used to detect antirestriction activity after each round of mutation. Our results demonstrate the variation in importance of the acidic residues in regions of Ocr corresponding to different parts of the DNA target which it is mimicking and for the avoidance of deleterious effects on the growth of the host.

  12. Polypeptide models to understand misfolding and amyloidogenesis and their relevance in protein design and therapeutics.

    PubMed

    Zurdo, Jesús

    2005-02-01

    The study of amyloid polypeptide models (polypeptides able to generate amyloid structures not necessarily connected with any pathology) provides an excellent tool to increase the understanding of the generic aspects of misfolding and aggregation as well as the details of the mechanism of polypeptide deposition in disease. This knowledge can be integrated and applied to different problems in therapy and biotechnology, and in particular to re-designing bio-active polypeptides (biopharmaceuticals) with improved properties.

  13. Chirality-selected phase behaviour in ionic polypeptide complexes

    DOE PAGES

    Perry, Sarah L.; Leon, Lorraine; Hoffmann, Kyle Q.; ...

    2015-01-14

    In this study, polyelectrolyte complexes present new opportunities for self-assembled soft matter. Factors determining whether the phase of the complex is solid or liquid remain unclear. Ionic polypeptides enable examination of the effects of stereochemistry on complex formation. Here we demonstrate that chirality determines the state of polyelectrolyte complexes, formed from mixing dilute solutions of oppositely charged polypeptides, via a combination of electrostatic and hydrogen-bonding interactions. Fluid complexes occur when at least one of the polypeptides in the mixture is racemic, which disrupts backbone hydrogen-bonding networks. Pairs of purely chiral polypeptides, of any sense, form compact, fibrillar solids with amore » β-sheet structure. Analogous behaviour occurs in micelles formed from polypeptide block copolymers with polyethylene oxide, where assembly into aggregates with either solid or fluid cores, and eventually into ordered phases at high concentrations, is possible. Chirality is an exploitable tool for manipulating material properties in polyelectrolyte complexation.« less

  14. Chirality-selected phase behaviour in ionic polypeptide complexes

    NASA Astrophysics Data System (ADS)

    Perry, Sarah L.; Leon, Lorraine; Hoffmann, Kyle Q.; Kade, Matthew J.; Priftis, Dimitrios; Black, Katie A.; Wong, Derek; Klein, Ryan A.; Pierce, Charles F.; Margossian, Khatcher O.; Whitmer, Jonathan K.; Qin, Jian; de Pablo, Juan J.; Tirrell, Matthew

    2015-01-01

    Polyelectrolyte complexes present new opportunities for self-assembled soft matter. Factors determining whether the phase of the complex is solid or liquid remain unclear. Ionic polypeptides enable examination of the effects of stereochemistry on complex formation. Here we demonstrate that chirality determines the state of polyelectrolyte complexes, formed from mixing dilute solutions of oppositely charged polypeptides, via a combination of electrostatic and hydrogen-bonding interactions. Fluid complexes occur when at least one of the polypeptides in the mixture is racemic, which disrupts backbone hydrogen-bonding networks. Pairs of purely chiral polypeptides, of any sense, form compact, fibrillar solids with a β-sheet structure. Analogous behaviour occurs in micelles formed from polypeptide block copolymers with polyethylene oxide, where assembly into aggregates with either solid or fluid cores, and eventually into ordered phases at high concentrations, is possible. Chirality is an exploitable tool for manipulating material properties in polyelectrolyte complexation.

  15. Chirality-selected phase behaviour in ionic polypeptide complexes

    PubMed Central

    Perry, Sarah L.; Leon, Lorraine; Hoffmann, Kyle Q.; Kade, Matthew J.; Priftis, Dimitrios; Black, Katie A.; Wong, Derek; Klein, Ryan A.; Pierce, Charles F.; Margossian, Khatcher O.; Whitmer, Jonathan K.; Qin, Jian; de Pablo, Juan J.; Tirrell, Matthew

    2015-01-01

    Polyelectrolyte complexes present new opportunities for self-assembled soft matter. Factors determining whether the phase of the complex is solid or liquid remain unclear. Ionic polypeptides enable examination of the effects of stereochemistry on complex formation. Here we demonstrate that chirality determines the state of polyelectrolyte complexes, formed from mixing dilute solutions of oppositely charged polypeptides, via a combination of electrostatic and hydrogen-bonding interactions. Fluid complexes occur when at least one of the polypeptides in the mixture is racemic, which disrupts backbone hydrogen-bonding networks. Pairs of purely chiral polypeptides, of any sense, form compact, fibrillar solids with a β-sheet structure. Analogous behaviour occurs in micelles formed from polypeptide block copolymers with polyethylene oxide, where assembly into aggregates with either solid or fluid cores, and eventually into ordered phases at high concentrations, is possible. Chirality is an exploitable tool for manipulating material properties in polyelectrolyte complexation. PMID:25586861

  16. Chirality-selected phase behaviour in ionic polypeptide complexes

    SciTech Connect

    Perry, Sarah L.; Leon, Lorraine; Hoffmann, Kyle Q.; Kade, Matthew J.; Priftis, Dimitrios; Black, Katie A.; Wong, Derek; Klein, Ryan A.; Pierce, III, Charles F.; Margossian, Khatcher O.; Whitmer, Jonathan K.; Qin, Jian; de Pablo, Juan J.; Tirrell, Matthew

    2015-01-14

    In this study, polyelectrolyte complexes present new opportunities for self-assembled soft matter. Factors determining whether the phase of the complex is solid or liquid remain unclear. Ionic polypeptides enable examination of the effects of stereochemistry on complex formation. Here we demonstrate that chirality determines the state of polyelectrolyte complexes, formed from mixing dilute solutions of oppositely charged polypeptides, via a combination of electrostatic and hydrogen-bonding interactions. Fluid complexes occur when at least one of the polypeptides in the mixture is racemic, which disrupts backbone hydrogen-bonding networks. Pairs of purely chiral polypeptides, of any sense, form compact, fibrillar solids with a β-sheet structure. Analogous behaviour occurs in micelles formed from polypeptide block copolymers with polyethylene oxide, where assembly into aggregates with either solid or fluid cores, and eventually into ordered phases at high concentrations, is possible. Chirality is an exploitable tool for manipulating material properties in polyelectrolyte complexation.

  17. Drosophila melanogaster paramyosin: developmental pattern, mapping and properties deduced from its complete coding sequence.

    PubMed

    Vinós, J; Maroto, M; Garesse, R; Marco, R; Cervera, M

    1992-02-01

    Several cDNA clones encoding the complete Drosophila paramyosin sequence, including two potential polyadenylation sites, have been obtained. Southern analysis and in situ hybridization to polytene chromosomes indicate that in Drosophila the paramyosin gene is single copy, located on the left arm of the third chromosome at region 66D14. Northern analyses show predominantly two different RNAs which are the products of the choice between the two alternative polyadenylation sites. The two species begin to be synthesized around 10 h of development when embryonic muscles are formed, expression peaking at the end of embryogenesis. The protein is first expressed at germ band shortening in association with muscle precursor cells. A second maximum of paramyosin RNA expression occurs at late pupal stages when the higher molecular weight form becomes more abundant. In young adults this species becomes the main transcript detected. The 102 kDa polypeptide sequence is highly similar to that of Caenorhabditis elegans paramyosin. The protein has a central alpha-helical coiled-coil rod, organized in 29 groups of four typical seven-residue repeats and flanked by two short non-alpha-helical regions. Several leucine zippers are located on the hydrophobic face of the alpha-helix in paramyosin which, together with disulfide bonds between cysteines, are probably involved in the stabilization of the dimer. The structural and functional properties of Drosophila paramyosin deduced from the sequence are compared with those of known invertebrate myosins and paramyosins.

  18. Structural properties of the D1 and surrounding photosystem II polypeptides as revealed by their interaction with cross-linking reagents.

    PubMed

    Adir, N; Ohad, I

    1988-01-05

    Treatment of Chlamydomonas reinhardtii thylakoids with cross-linking reagents including glutaraldehyde causes polymerization of all thylakoid polypeptides, but not of the reaction center II polypeptide D1 unless the thylakoids are presolubilized by octyl beta-D-glucoside (Adir, N., and Ohad, I. (1986) Biochim. Biophys. Acta 850, 264-274). The results presented here show that this is a general property of D1 as it can be demonstrated in thylakoids of cyanophytes, Dasicladaceae, green algae, and C3 and C4 plants. Solubilization of the membranes by ionic detergents, deoxycholate, lauryl sucrose, or dodecyl beta-D-maltoside is not effective in inducing cross-linking of the D1 polypeptides by glutaraldehyde. The most effective alkyl glucosides were those with 7-9 carbon alkyl chains. The same behavior toward glutaraldehyde was exhibited by the unprocessed D1 precursor and by the palmitoylated D1 protein. Based on the refractility of the D1 protein to cross-linking reagents, a procedure was developed for its isolation from cross-linked thylakoids by lithium dodecyl sulfate-polyacrylamide gel electrophoresis. Isolated D1 retained its behavior toward cross-linking by glutaraldehyde and generated tryptic fragments similar to those obtained following trypsin treatment of intact thylakoids. Denaturation of isolated D1 protein by acetone facilitates cross-linking by glutaraldehyde and extensive degradation by trypsin. The photosystem II polypeptides are differentially cross-linked with increasing concentrations of glutaraldehyde, the most susceptible being the 28- and 23-kDa components of the light-harvesting chlorophyll a-b protein complex and the core complex 44- and 51-kDa polypeptides, and the least affected being the cytochrome b559, the D2 protein, and a 24-kDa component of the light-harvesting chlorophyll a-b protein complex. These results reflect the relative position and interaction of the photosystem II polypeptides within the complex and suggest that strong and

  19. Identification of viral structural polypeptides of Thogoto virus (a tick-borne orthomyxo-like virus) and functions associated with the glycoprotein.

    PubMed

    Portela, A; Jones, L D; Nuttall, P

    1992-11-01

    Thogoto (THO) virus is a tick-borne virus which shares morphological and genetic features with members of the Orthomyxoviridae family although the viral glycoprotein appears to be related to gp64 of baculoviruses. Characterization of THO virus was undertaken to clarify its taxonomic position. Purified virus preparations contained at least six virus-encoded polypeptides with apparent M(r) values ranging from 29K to 92K. A 75K polypeptide was identified as an envelope-associated glycoprotein by Triton X-100 and salt dissociation studies, and by proteolytic degradation of the exposed proteins of the virion. By the same criteria, the nucleoprotein and the matrix protein were identified as the 52K and 29K polypeptides, respectively. Immunofluorescence studies using monoclonal antibodies (MAbs) located the glycoprotein on the external cell membrane and the nucleoprotein in the nucleus of infected cells indicating that virus replication involved a nuclear phase. In addition, the virus displayed haemagglutination and haemolytic activities with an optimum at pH 6. These activities are functions of the viral glycoprotein since they were inhibited by anti-glycoprotein MAbs. The data reported here support the notion that THO virus is a member of the Orthomyxoviridae family but that it should be classified in a group distinct from the other influenza viruses.

  20. Methods for producing secreted polypeptides

    SciTech Connect

    Maiyuran, Suchindra; Fidantsef, Ana; Brody, Howard

    2008-07-01

    The present invention relates to methods for producing a polypeptide, comprising: (a) cultivating a fungal host cell in a medium conducive for the production of the polypeptide, wherein the fungal host cell comprises a nucleic acid construct comprising a first nucleotide sequence encoding a signal peptide operably linked to a second nucleotide sequence encoding the polypeptide, wherein the first nucleotide sequence is foreign to the second nucleotide sequence and the 3' end of the first nucleotide sequence is immediately upstream of the initiator codon of the second nucleotide sequence. The present invention also relates to the isolated signal peptide sequences and to constructs, vectors, and fungal host cells comprising the signal peptide sequences operably linked to nucleotide sequences encoding polypeptides.

  1. Methods for producing secreted polypeptides

    SciTech Connect

    Maiyuran, Suchindra; Fidantsef, Ana; Brody, Howard

    2013-07-30

    The present invention relates to methods for producing a polypeptide, comprising: (a) cultivating a fungal host cell in a medium conducive for the production of the polypeptide, wherein the fungal host cell comprises a nucleic acid construct comprising a first nucleotide sequence encoding a signal peptide operably linked to a second nucleotide sequence encoding the polypeptide, wherein the first nucleotide sequence is foreign to the second nucleotide sequence and the 3' end of the first nucleotide sequence is immediately upstream of the initiator codon of the second nucleotide sequence. The present invention also relates to the isolated signal peptide sequences and to constructs, vectors, and fungal host cells comprising the signal peptide sequences operably linked to nucleotide sequences encoding polypeptides.

  2. Hydrogenase polypeptide and methods of use

    DOEpatents

    Adams, Michael W.W.; Hopkins, Robert C.; Jenney, JR, Francis E.; Sun, Junsong

    2016-02-02

    Provided herein are polypeptides having hydrogenase activity. The polypeptide may be multimeric, and may have hydrogenase activity of at least 0.05 micromoles H.sub.2 produced min.sup.-1 mg protein.sup.-1. Also provided herein are polynucleotides encoding the polypeptides, genetically modified microbes that include polynucleotides encoding one or more subunits of the multimeric polypeptide, and methods for making and using the polypeptides.

  3. Probing the role of the C-H...O hydrogen bond stabilized polypeptide chain reversal at the C-terminus of designed peptide helices. Structural characterization of three decapeptides.

    PubMed

    Aravinda, Subrayashastry; Shamala, Narayanaswamy; Bandyopadhyay, Abhishek; Balaram, Padmanabhan

    2003-12-10

    The structural characterization in crystals of three designed decapeptides containing a double d-segment at the C-terminus is described. The crystal structures of the peptides Boc-Leu-Aib-Val-Xxx-Leu-Aib-Val-(D)Ala-(D)Leu-Aib-OMe, (Xxx = Gly 2, (D)Ala 3, Aib 4) have been determined and compared with those reported earlier for peptide 1 (Xxx = Ala) and the all l analogue Boc-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe, which yielded a perfect right-handed alpha-helical structure. Peptides 1 and 2 reveal a right-handed helical segment spanning residues 1 to 7, ending in a Schellman motif with (D)Ala(8) functioning as the terminating residue. Polypeptide chain reversal occurs at residue 9, a novel feature that appears to be the consequence of a C-H.O hydrogen bond between residue 4 C(alpha)H and residue 9 CO groups. The structures of peptides 3 and 4, which lack the pro R hydrogen at the C(alpha) atom of residue 4, are dramatically different. Peptide 3 adopts a right-handed helical conformation over the 1 to 7 segment. Residues 8 and 9 adopt alpha(L) conformations forming a C-terminus type I' beta-turn, corresponding to an incipient left-handed twist of the polypeptide chain. In peptide 4, helix termination occurs at Aib(6), with residues 6 to 9 forming a left-handed helix, resulting in a structure that accommodates direct fusion of two helical segments of opposite twist. Peptides 3 and 4 provide examples of chiral residues occurring in the less favored sense of helical twist; (D)Ala(4) in peptide 3 adopts an alpha(R) conformation, while (L)Val(7) in 4 adopts an alpha(L) conformation. The structural comparison of the decapeptides reported here provides evidence for the role of specific C-H.O hydrogen bonds in stabilizing chain reversals at helix termini, which may be relevant in aligning contiguous helical and strand segments in polypeptide structures.

  4. Biosynthetic Polypeptides as Templates in Materials Design

    NASA Astrophysics Data System (ADS)

    Kiick, Kristi

    2007-03-01

    Biosynthetic routes to protein-based polymeric materials offer important opportunities for the production of well-defined macromolecular templates, owing to the control of sequence and molecular weight inherent in the biosynthesis of proteins. In particular, the biosynthesis of polypeptides with controlled presentation of functional groups in multiple positions, coupled with their subsequent chemical modification with biologically relevant ligands, will permit the production of well-defined, bioactive macromolecules that may provide insight into biological binding events in which multivalent binding is important. Modification of the well-defined macromolecules with ligands such as saccharides has application in the study of events such as toxin neutralization and mediation of the immune and inflammatory responses. In this work, alanine-rich polypeptides of both random coil and helical conformations, equipped with glutamic acid residues to impart chemical versatility, have been produced via biosynthetic strategies. Analysis via spectroscopic and calorimetric methods indicates that the polypeptides adopt helical, beta-sheet, or random-coil conformations that can be controlled with variations in temperature, pH, and salt concentration; the conformational behavior of the polypeptides is not compromised upon chemical modification with saccharides. The binding of these macromolecules to bacterial toxins has been characterized via immunochemical and spectroscopic methods; results indicate that specific architectural features of the glycopolymer scaffold cause changes in the binding of these molecules to multivalent receptors. Given the chemical flexibility in the design of such scaffolds, they can be modified with many different moieties in addition to saccharides, so multiple opportunities exist for their application in areas where control of active side chains is important, such as in biomaterials, electronic devices, and bioinorganic structures.

  5. Ordered Nanostructures Made Using Chaperonin Polypeptides

    NASA Technical Reports Server (NTRS)

    Trent, Jonathan; McMillan, Robert; Paavola, Chad; Mogul, Rakesh; Kagawa, Hiromi

    2004-01-01

    A recently invented method of fabricating periodic or otherwise ordered nanostructures involves the use of chaperonin polypeptides. The method is intended to serve as a potentially superior and less expensive alternative to conventional lithographic methods for use in the patterning steps of the fabrication of diverse objects characterized by features of the order of nanometers. Typical examples of such objects include arrays of quantum dots that would serve as the functional building blocks of future advanced electronic and photonic devices. A chaperonin is a double-ring protein structure having a molecular weight of about 60 plus or minus 5 kilodaltons. In nature, chaperonins are ubiquitous, essential, subcellular structures. Each natural chaperonin molecule comprises 14, 16, or 18 protein subunits, arranged as two stacked rings approximately 16 to 18 nm tall by approximately 15 to 17 nm wide, the exact dimensions depending on the biological species in which it originates. The natural role of chaperonins is unknown, but they are believed to aid in the correct folding of other proteins, by enclosing unfolded proteins and preventing nonspecific aggregation during assembly. What makes chaperonins useful for the purpose of the present method is that under the proper conditions, chaperonin rings assemble themselves into higher-order structures. This method exploits such higher-order structures to define nanoscale devices. The higher-order structures are tailored partly by choice of chemical and physical conditions for assembly and partly by using chaperonins that have been mutated. The mutations are made by established biochemical techniques. The assembly of chaperonin polypeptides into such structures as rings, tubes, filaments, and sheets (two-dimensional crystals) can be regulated chemically. Rings, tubes, and filaments of some chaperonin polypeptides can, for example, function as nano vessels if they are able to absorb, retain, protect, and release gases or

  6. Self-assembly of high molecular weight polypeptide copolymers studied via diffusion limited aggregation.

    PubMed

    Meier, Christoph; Wu, Yuzhou; Pramanik, Goutam; Weil, Tanja

    2014-01-13

    The assembly of high molecular weight polypeptides into complex architectures exhibiting structural complexity ranging from the nano- to the mesoscale is of fundamental importance for various protein-related diseases but also hold great promise for various nano- and biotechnological applications. Here, the aggregation of partially unfolded high molecular weight polypeptides into multiscale fractal structures is investigated by means of diffusion limited aggregation and atomic force microscopy. The zeta potential, the hydrodynamic radius, and the obtained fractal morphologies were correlated with the conformation of the polypeptide backbones as obtained from circular dichroism measurements. The polypeptides are modified with polyethylene oxide side chains to stabilize the polypeptides and to normalize intermolecular interactions. The modification with the hydrophobic thioctic acid alters the folding of the polypeptide backbone, resulting in a change in solution aggregation and fractal morphology. We found that a more compact folding results in dense and highly branched structures, whereas a less compact folded polypeptide chain yields a more directional assembly. Our results provide first evidence for the role of compactness of polypeptide folding on aggregation. Furthermore, the mesoscale-structured biofilms were used to achieve a hierarchical protein assembly, which is demonstrated by deposition of Rhodamine-labeled HSA with the preassembled fractal structures. These results contribute important insights to the fundamental understanding of the aggregation of high molecular weight polypeptides in general and provide opportunities to study nanostructure-related effects on biological systems such as adhesion, proliferation, and the development of, for example, neuronal cells.

  7. Aqueous cholesteric liquid crystals using uncharged rodlike polypeptides. Polypeptide vesicles by conformation-specific assembly. Ordered chiral macroporous hybrid silica-polypeptide composites

    NASA Astrophysics Data System (ADS)

    Bellomo, Enrico Giuseppe

    2005-07-01

    Aqueous cholesteric liquid crystals using uncharged rodlike polypeptides . The aqueous, lyotropic liquid-crystalline phase behavior of an alpha helical polypeptide, has been studied using optical microscopy and X-ray scattering. Solutions of optically pure polypeptide were found to form cholesteric liquid crystals at volume fractions that decreased with increasing average chain length. At very high volume fractions, the formation of a hexagonal mesophase was observed. The pitch of the cholesteric phase could be varied by a mixture of enantiomeric samples, where the pitch increased as the mixture approached equimolar. The cholesteric phases could be untwisted, using either magnetic field or shear flow, into nematic phases, which relaxed into cholesterics upon removal of field or shear. We have found that the phase diagram of this polypeptide in aqueous solution parallels that of poly(gamma-benzyl glutamate) in organic solvents, thus providing a useful system for liquid-crystal applications requiring water as solvent. Polypeptide vesicles by conformation-specific assembly. We have found that block copolymers composed of polypeptide segments provide significant advantages in controlling both the function and supramolecular structure of bioinspired self-assemblies. Incorporation of the stable chain conformations found in proteins into block copolymers was found to provide an additional element of control, beyond amphiphilicity and composition that defines self-assembled architecture. The abundance of functionality present in amino acids, and the ease by which they can be incorporated into these materials, also provides a powerful mechanism to impart block copolypeptides with function. This combination of structure and function work synergistically to enable significant advantages in the preparation of therapeutic agents as well as provide insight into design of self-assemblies beginning to approach the complexity of natural structures such as virus capsids. Ordered

  8. Pulsed ELDOR in spin-labeled polypeptides

    NASA Astrophysics Data System (ADS)

    Milov, Alexander D.; Maryasov, Alexander G.; Tsvetkov, Yuri D.; Raap, Jan

    1999-04-01

    The pulsed electron-electron double-resonance (PELDOR) technique was applied to obtain information about the structure of the synthetic polypeptide-biradical in a frozen glassy solution. From the concentration dependence of the PELDOR signal, the effects of intermolecular and intramolecular interactions were separated. It was found that the intramolecular dipole-dipole interactions in the biradical peptide led to the modulation effects in the PELDOR signal decay. This may be attributed to the existence of a conformational population having a distance between the two unpaired electrons of ˜20 Å with a distribution of (˜2 Å). Its fraction is estimated as about 25%.

  9. The Structure of the Poliovirus 135S Cell Entry Intermediate at 10-Angstrom Resolution Reveals the Location of an Externalized Polypeptide That Binds to Membranes†

    PubMed Central

    Bubeck, Doryen; Filman, David J.; Cheng, Naiqian; Steven, Alasdair C.; Hogle, James M.; Belnap, David M.

    2005-01-01

    Poliovirus provides a well-characterized system for understanding how nonenveloped viruses enter and infect cells. Upon binding its receptor, poliovirus undergoes an irreversible conformational change to the 135S cell entry intermediate. This transition involves shifts of the capsid protein β barrels, accompanied by the externalization of VP4 and the N terminus of VP1. Both polypeptides associate with membranes and are postulated to facilitate entry by forming a translocation pore for the viral RNA. We have calculated cryo-electron microscopic reconstructions of 135S particles that permit accurate placement of the β barrels, loops, and terminal extensions of the capsid proteins. The reconstructions and resulting models indicate that each N terminus of VP1 exits the capsid though an opening in the interface between VP1 and VP3 at the base of the canyon that surrounds the fivefold axis. Comparison with reconstructions of 135S particles in which the first 31 residues of VP1 were proteolytically removed revealed that the externalized N terminus is located near the tips of propeller-like features surrounding the threefold axes rather than at the fivefold axes, as had been proposed in previous models. These observations have forced a reexamination of current models for the role of the 135S particle in transmembrane pore formation and suggest testable alternatives. PMID:15919927

  10. Lack of coupling between secondary structure formation and collapse in a model polypeptide that mimics early folding intermediates, the F2 fragment of the Escherichia coli tryptophan-synthase beta chain.

    PubMed Central

    Gast, K.; Chaffotte, A. F.; Zirwer, D.; Guillou, Y.; Mueller-Frohne, M.; Cadieux, C.; Hodges, M.; Damaschun, G.; Goldberg, M. E.

    1997-01-01

    The isolated, 101-residue long C-terminal (so called F2) fragment of the beta chain from Escherichia coli tryptophan synthase was shown previously to fold into an ensemble of conformations that are condensed, to contain large amounts of highly dynamic secondary structures, and to behave as a good model of structured intermediates that form at the very early stages of protein folding. Here, solvent perturbations were used to investigate the forces that are involved in stabilizing the secondary structure (monitored by far-UV CD) and the condensation of the polypeptide chain (monitored by dynamic light scattering) in isolated F2. It was observed that neither the ionic strength, nor the pH (between 7 and 10), nor salts of the Hofmeister series affected the global secondary structure contents of F2, whereas some of these salts affected the collapse slightly. Addition of trifluoroethanol resulted in a large increase in both the amount of secondary structure and the Stokes radius of F2. Conversely, F2 became more condensed upon raising the temperature from 4 to 60 degrees C, whereas in this temperature range, the secondary structure undergoes significant melting. These observations lead to the conclusion that, in isolated F2, there is no coupling between the hydrophobic collapse and the secondary structure. This finding will be discussed in terms of early events in protein folding. PMID:9416607

  11. Methods for using polypeptides having cellobiohydrolase activity

    DOEpatents

    Morant, Marc D; Harris, Paul

    2016-08-23

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  12. Surface active complexes formed between keratin polypeptides and ionic surfactants.

    PubMed

    Pan, Fang; Lu, Zhiming; Tucker, Ian; Hosking, Sarah; Petkov, Jordan; Lu, Jian R

    2016-12-15

    Keratins are a group of important proteins in skin and hair and as biomaterials they can provide desirable properties such as strength, biocompatibility, and moisture regaining and retaining. The aim of this work is to develop water-soluble keratin polypeptides from sheep wool and then explore how their surface adsorption behaves with and without surfactants. Successful preparation of keratin samples was demonstrated by identification of the key components from gel electrophoresis and the reproducible production of gram scale samples with and without SDS (sodium dodecylsulphate) during wool fibre dissolution. SDS micelles could reduce the formation of disulphide bonds between keratins during extraction, reducing inter-molecular crosslinking and improving keratin polypeptide solubility. However, Zeta potential measurements of the two polypeptide batches demonstrated almost identical pH dependent surface charge distributions with isoelectric points around pH 3.5, showing complete removal of SDS during purification by dialysis. In spite of different solubility from the two batches of keratin samples prepared, very similar adsorption and aggregation behavior was revealed from surface tension measurements and dynamic light scattering. Mixing of keratin polypeptides with SDS and C12TAB (dodecyltrimethylammonium bromide) led to the formation of keratin-surfactant complexes that were substantially more effective at reducing surface tension than the polypeptides alone, showing great promise in the delivery of keratin polypeptides via the surface active complexes. Neutron reflection measurements revealed the coexistence of surfactant and keratin polypeptides at the interface, thus providing the structural support to the observed surface tension changes associated with the formation of the surface active complexes.

  13. Self-assembly of polypeptide-based copolymers into diverse aggregates.

    PubMed

    Cai, Chunhua; Wang, Liquan; Lin, Jiaping

    2011-10-28

    Recently, increasing attention has been given to the self-assembly behavior of polypeptide-based copolymers. Polypeptides can serve as either shell-forming or core-forming blocks in the formation of various aggregates. The solubility and rigidity of polypeptide blocks have been found to have a profound effect on the self-assembly behavior of polypeptide-based copolymers. Polypeptide graft copolymers combine the advantages of a grafting strategy and the characteristics of polypeptide chains and their self-assembly behavior can be easily adjusted by choosing different polymer chains and copolymer architectures. Fabricating hierarchical structures is one of the attractive topics of self-assembly research of polypeptide copolymers. These hierarchical structures are promising for use in preparing functional materials and, thus, attract increasing attention. Computer simulations have emerged as powerful tools to investigate the self-assembly behavior of polymers, such as polypeptides. These simulations not only support the experimental results, but also provide information that cannot be directly obtained from experiments. In this feature article, recent advances in both experimental and simulation studies for the self-assembly behavior of polypeptide-based copolymers are reviewed.

  14. Simplified lattice model for polypeptide fibrillar transitions

    NASA Astrophysics Data System (ADS)

    Xiao, Xuhui; Wu, Ming-Chya

    2014-10-01

    Polypeptide fibrillar transitions are studied using a simplified lattice model, modified from the three-state Potts model, where uniform residues as spins, placed on a cubic lattice, can interact with neighbors to form coil, helical, sheet, or fibrillar structure. Using the transfer matrix method and numerical calculations, we analyzed the partition function and construct phase diagrams. The model manifests phase transitions among coil, helix, sheet, and fibril through parameterizing bond coupling energy ɛh,ɛs,ɛf, structural entropies sh,ss,sf of helical, sheet, and fibrillar states, and number density ρ. The phase diagrams show the transition sequence is basically governed by ɛh, ɛs, and ɛf, while the transition temperature is determined by the competition among ɛh, ɛs, and ɛf, as well as sh, ss, sf, and ρ. Furthermore, the fibrillation is accompanied with an abrupt phase transition from coil, helix, or sheet to fibril even for short polypeptide length, resembling the feature of nucleation-growth process. The finite-size effect in specific heat at transitions for the nonfibrillation case can be described by the scaling form of lattice model. With rich phase-transition properties, our model provides a useful reference for protein aggregation experiments and modeling.

  15. Nano polypeptide particles reinforced polymer composite fibers.

    PubMed

    Li, Jiashen; Li, Yi; Zhang, Jing; Li, Gang; Liu, Xuan; Li, Zhi; Liu, Xuqing; Han, Yanxia; Zhao, Zheng

    2015-02-25

    Because of the intensified competition of land resources for growing food and natural textile fibers, there is an urgent need to reuse and recycle the consumed/wasted natural fibers as regenerated green materials. Although polypeptide was extracted from wool by alkaline hydrolysis, the size of the polypeptide fragments could be reduced to nanoscale. The wool polypeptide particles were fragile and could be crushed down to nano size again and dispersed evenly among polymer matrix under melt extrusion condition. The nano polypeptide particles could reinforce antiultraviolet capability, moisture regain, and mechanical properties of the polymer-polypeptide composite fibers.

  16. Identification of the polypeptide encoded by the URF-1 gene of Neurospora crassa mtDNA.

    PubMed

    Zauner, R; Christner, J; Jung, G; Borchart, U; Machleidt, W; Videira, A; Werner, S

    1985-08-01

    Two peptides, potentially representing antigenic determinants of a proposed gene product, were synthesized. The peptide sequences were deduced from the nucleotide sequence of the unidentified reading frame (URF)1 of the Neurospora crassa mitochondrial genome. Specific antisera to the synthetic peptides were produced. The antibodies recognized a single polypeptide species with an apparent relative molecular mass of about 30 000. The mitochondrial origin of this polypeptide was verified by in vivo labelling experiments in the presence of cycloheximide, as well as by in vitro translation using isolated mitochondria. The chemical identification of the protein was performed by partial radiosequencing of the N-terminal portion of the immunoprecipitated URF-1 product. The amount of URF-1 polypeptide present in N. crassa mitochondria is in the range of 1-2%. The protein is a constituent of the inner envelope of the organelle and probably part of a more complex membrane unit.

  17. Interplay between electrophoretic mobility and intrinsic viscosity of polypeptide chains.

    PubMed

    Deiber, Julio A; Peirotti, Marta B; Piaggio, María V

    2012-03-01

    The present work is motivated specifically by the need to find a simple interplay between experimental values of electrophoretic mobility and intrinsic viscosity (IV) of polypeptides. The connection between these two properties, as they are evaluated experimentally in a formulated dilute solution, may provide relevant information concerning the physicochemical characterization and separation of electrically charged chains such as polypeptides. Based on this aspect, a study on the relation between the effective electrophoretic mobility and the IV of the following globular proteins is carried out: bovine carbonic anhydrase, staphylococcal nuclease, human carbonic anhydrase, lysozyme, human serum albumin. The basic interpretation of the IV through polypeptide chain conformations involves two unknowns: one is the Flory characteristic ratio involving short-range intramolecular interactions and the other is the Mark-Houwink exponent associated with large-range intramolecular interactions. Here, it will be shown via basic and well-established electrokinetic theories and scaling concepts that the IV and global chain flexibility of polypeptides in dilute solutions may be estimated from capillary zone electrophoresis, in addition to classical transport properties. The polypeptide local chain flexibility may change due to electrostatic interactions among closer chain ionizing groups and the hindrance effect of their associated structural water.

  18. DNA clone encoding a photosystem I protein with homology to photosystem II chlorophyll a/b-binding polypeptides

    SciTech Connect

    Hoffman, N.E.; Pichersky, E.; Malik, V.S.; Castresana, C.; Ko, K.; Darr, S.C.; Cashmore, A.R.

    1987-12-01

    The authors report here the isolation and nucleotide sequence of a complete cDNA clone encoding a photosystem I (PS I) polypeptide that is recognized by a monoclonal antibody made against photosystem II (PS II) chlorophyll a/b-binding (CAB) proteins. The deduced sequence of this PS I protein shows 30% overall identity to PS II CAB sequences, and two long segments within this protein show 50% and 65% identity to the corresponding segments in the PS II CAB polypeptides. Even though the sequence of this PS I CAB protein is substantially divergent from PS II CAB sequences, their hydropathy plots are very similar and suggest they all traverse the thylakoid membrane three times. A segment of the PS I CAB polypeptide shows similarity to the functionally analogous ..beta.. subunits of the antenna proteins of purple bacteria. In contrast, no homology was observed between these bacterial proteins and PS II CAB polypeptides.

  19. Polypeptide having swollenin activity and uses thereof

    DOEpatents

    Schoonneveld-Bergmans, Margot Elizabeth Francoise; Heijne, Wilbert Herman Marie; Vlasie, Monica D; Damveld, Robbertus Antonius

    2015-11-04

    The invention relates to a polypeptide comprising the amino acid sequence set out in SEQ ID NO: 2 or an amino acid sequence encoded by the nucleotide sequence of SEQ ID NO: 1, or a variant polypeptide or variant polynucleotide thereof, wherein the variant polypeptide has at least 73% sequence identity with the sequence set out in SEQ ID NO: 2 or the variant polynucleotide encodes a polypeptide that has at least 73% sequence identity with the sequence set out in SEQ ID NO: 2. The invention features the full length coding sequence of the novel gene as well as the amino acid sequence of the full-length functional polypeptide and functional equivalents of the gene or the amino acid sequence. The invention also relates to methods for using the polypeptide in industrial processes. Also included in the invention are cells transformed with a polynucleotide according to the invention suitable for producing these proteins.

  20. Polypeptide having cellobiohydrolase activity and uses thereof

    DOEpatents

    Sagt, Cornelis Maria Jacobus; Schooneveld-Bergmans, Margot Elisabeth Francoise; Roubos, Johannes Andries; Los, Alrik Pieter

    2015-09-15

    The invention relates to a polypeptide comprising the amino acid sequence set out in SEQ ID NO: 2 or an amino acid sequence encoded by the nucleotide sequence of SEQ ID NO: 1, or a variant polypeptide or variant polynucleotide thereof, wherein the variant polypeptide has at least 93% sequence identity with the sequence set out in SEQ ID NO: 2 or the variant polynucleotide encodes a polypeptide that has at least 93% sequence identity with the sequence set out in SEQ ID NO: 2. The invention features the full length coding sequence of the novel gene as well as the amino acid sequence of the full-length functional polypeptide and functional equivalents of the gene or the amino acid sequence. The invention also relates to methods for using the polypeptide in industrial processes. Also included in the invention are cells transformed with a polynucleotide according to the invention suitable for producing these proteins.

  1. Investigation of genetically-engineered beta-sheet polypeptides for nanoelectronics

    NASA Astrophysics Data System (ADS)

    Rana, Narender

    2007-12-01

    Ongoing miniaturization in integrated circuit (IC) device fabrication via conventional lithography faces increasing technical challenges and imposes significant performance limitations on devices and interconnects stemming from the fundamental physics of electron transport. This drives the need to explore other nanofabrication approaches, such as self-assembly, and alternate device or interconnect structures with novel electron transport mechanisms, such as ballistic electron transport. Molecular self-assembly, ubiquitous in biology and bio-inspired materials, might have tremendous potential for nanoelectronic applications. Specifically, genetically-engineered beta-sheet polypeptides offer certain key attributes for nanoelectronic applications. These attributes include: controllable self-assembly, potential to form one dimensional quantum channels for ballistic electron transport, and substrate-specific interactions for interfacial engineering. This dissertation explores and evaluates the nanowire self-assembly characteristics of several de novo genetically-engineered beta-sheet polypeptides (synthesized by our group) on various substrates for applications in nanoelectronic interconnect schemes. In addition, substrate-attachment of the beta-sheet polypeptide nanowire structures is investigated and preliminary electrical testing of a polypeptide nanowire fibril is presented. Chapters 1 and 2 provide an overall introduction and discuss the characterization techniques utilized in the experimental work. Chapter 3 describes a detailed self-assembly study of various polypeptides and documents the formulation and deposition of controlled, linear self-assemblies of polypeptides. It was determined that control of the concentration and deposition-time enables the deposition of linear ordered polypeptide assemblies on substrates. A predominance of bilayer stacking of polypeptide sheets in the solution-formed linear assemblies has been observed. Template-directed self

  2. Simulating Massive Conformation Changes within Polypeptide Systems

    NASA Astrophysics Data System (ADS)

    Singh, Jaspinder Paul

    In this dissertation I employ all-atom structure based models with stable energy basins to several existing and novel polypeptide systems (postulated conformation changes of the mammalian prion protein and structurally dual proteins). The common themes are finding unfolding and refolding pathways between highly dissimilar protein structures as a means of understanding exactly how and why a protein may misfold. The modeling is based on the energy funnel landscape theory of protein conformation space. The principle of minimal frustration is considered as the model includes parameters which vary the roughness of the landscape and give rise to off-pathway misfoldings. The dual basin model is applied to the C-terminal (residues 166-226) of the mammalian prion protein. One basin represents the known alpha-helical (aH) structure while the other represents the same residues in a lefthanded beta-helical (LHBH) conformation. The LHBH structure has been proposed to help describe one class of in vitro grown fibrils, as well as possibly self-templating the conversion of normal cellular prion protein to the infectious form. Yet, it is unclear how the protein may make this global rearrangement. Our results demonstrate that the conformation changes are not strongly limited by large-scale geometry modification and that there may exist an overall preference for the LHBH conformation. Furthermore, our model presents novel intermediate trapping conformations with twisted LHBH structure. Polypeptides that display structural duality have primary structures that can give rise to different potential native conformations. We apply the structure-based all-atom model to a leucine zipper protein template with a stable aH structure that has been shown in experiment to switch to a β hairpin structure when exposed to a low-pH environment. We show that the model can be used to perform large-scale temperature-dependent conformational switching by simulating this switching behavior. We augmented

  3. Protein encapsulation via polypeptide complex coacervation.

    SciTech Connect

    Black, Katie A.; Priftis, Dimitrios; Perry, Sarah L.; Yip, Jeremy; Byun, William Y.; Tirrell, Matthew

    2014-10-01

    Proteins have gained increasing success as therapeutic agents; however, challenges exist in effective and efficient delivery. In this work, we present a simple and versatile method for encapsulating proteins via complex coacervation with oppositely charged polypeptides, poly(L-lysine) (PLys) and poly(D/L-glutamic acid) (PGlu). A model protein system, bovine serum albumin (BSA), was incorporated efficiently into coacervate droplets via electrostatic interaction up to a maximum loading of one BSA per PLys/PGlu pair and could be released under conditions of decreasing pH. Additionally, encapsulation within complex coacervates did not alter the secondary structure of the protein. Lastly the complex coacervate system was shown to be biocompatible and interact well with cells in vitro. A simple, modular system for encapsulation such as the one presented here may be useful in a range of drug delivery applications.

  4. cDNA encoding a polypeptide including a hevein sequence

    DOEpatents

    Raikhel, N.V.; Broekaert, W.F.; Chua, N.H.; Kush, A.

    1999-05-04

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74--79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli. 12 figs.

  5. CDNA encoding a polypeptide including a hevein sequence

    DOEpatents

    Raikhel, Natasha V.; Broekaert, Willem F.; Chua, Nam-Hai; Kush, Anil

    1995-03-21

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74-79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

  6. cDNA encoding a polypeptide including a hevein sequence

    DOEpatents

    Raikhel, Natasha V.; Broekaert, Willem F.; Chua, Nam-Hai; Kush, Anil

    1999-05-04

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74-79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

  7. cDNA encoding a polypeptide including a hevein sequence

    DOEpatents

    Raikhel, N.V.; Broekaert, W.F.; Chua, N.H.; Kush, A.

    1995-03-21

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1,018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74--79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli. 11 figures.

  8. cDNA encoding a polypeptide including a hevein sequence

    SciTech Connect

    Raikhel, N.V.; Broekaert, W.F.; Chua, N.H.; Kush, A.

    2000-07-04

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74--79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

  9. Methods for engineering polypeptide variants via somatic hypermutation and polypeptide made thereby

    DOEpatents

    Tsien, Roger Y; Wang, Lei

    2015-01-13

    Methods using somatic hypermutation (SHM) for producing polypeptide and nucleic acid variants, and nucleic acids encoding such polypeptide variants are disclosed. Such variants may have desired properties. Also disclosed are novel polypeptides, such as improved fluorescent proteins, produced by the novel methods, and nucleic acids, vectors, and host cells comprising such vectors.

  10. [Mechanisms of formation and action of polypeptide bio-regulators-- cytomedins ].

    PubMed

    Kaĭdashev, I P

    1994-01-01

    Possible mechanism of synthesis and effects of polypeptide bioregulative molecules (cytomedines) have been shown. This polypeptide has been obtained from different organs and tissues of animals. Its effects are supposed to be based on the processes of intercellular exchange and the cross-membrane transference of information signals. Synthesis of these molecules is considered as the limited proteolysis of protein structures. The information molecules of this kind will be found both inside and outside the cells. The evolution of regulative polypeptides was shown from the organisms of prebiotic era till contemporary organisms. The possibility of interaction between entigenic--endogenic peptides and regulative peptides is described. A hypothetic scheme of the effect of polypeptide molecules on the cell populations is suggested. Space interactions between proteins and polypeptides on the basis of the recognition codes of aminoacids can be most important factors.

  11. Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments.

    PubMed

    Gradišar, Helena; Božič, Sabina; Doles, Tibor; Vengust, Damjan; Hafner-Bratkovič, Iva; Mertelj, Alenka; Webb, Ben; Šali, Andrej; Klavžar, Sandi; Jerala, Roman

    2013-06-01

    Protein structures evolved through a complex interplay of cooperative interactions, and it is still very challenging to design new protein folds de novo. Here we present a strategy to design self-assembling polypeptide nanostructured polyhedra based on modularization using orthogonal dimerizing segments. We designed and experimentally demonstrated the formation of the tetrahedron that self-assembles from a single polypeptide chain comprising 12 concatenated coiled coil-forming segments separated by flexible peptide hinges. The path of the polypeptide chain is guided by a defined order of segments that traverse each of the six edges of the tetrahedron exactly twice, forming coiled-coil dimers with their corresponding partners. The coincidence of the polypeptide termini in the same vertex is demonstrated by reconstituting a split fluorescent protein in the polypeptide with the correct tetrahedral topology. Polypeptides with a deleted or scrambled segment order fail to self-assemble correctly. This design platform provides a foundation for constructing new topological polypeptide folds based on the set of orthogonal interacting polypeptide segments.

  12. Thermodynamic stability of polypeptides folding within modeled ribosomal exit tunnel: a density functional study.

    PubMed

    Xu, Xiaofei; Cao, Dapeng

    2010-07-01

    The mechanism of polypeptide folding, especially for the formation of tertiary structures, within the ribosomal exit tunnel, remains one of the most important unsolved problems in biophysical chemistry and molecular biology. In this work, we use a density functional theory (DFT) to explore the polypeptide folding within a modified nanopore, which mimics the confined environment of ribosomal exit tunnel. Results indicate that too long polypeptides (N>100 cannot fold into a helix state within the nanopore, and the helix polypeptides favor folding into a negative coiled coil rather than a positive one, because the negative coiled coil has a lower grand potential than the positive one, and the polypeptide folding into the negative coiled coil therefore needs less driving force than the positive one. To fold into the positive coiled coil, the helix polypeptides must have a small minor radius or a short chain length, which provides helpful insights into the design of nanodevices for manipulating the positive coiled coil. In the presence of attractive interaction, helices need more driving force to fold into coiled coil. Importantly, we have also proposed a scaling relation to understand the folding behavior. The scaling relation gives a good estimate for the computational results, and provides a reasonable explanation for the folding behavior. In summary, it is expected that the proposed DFT approach and the scaling relation provide alternative means for the investigation of polypeptide folding in confined environment, and these impressive results could give useful insights into nascent polypeptide folding.

  13. Structural Similarities and Differences between Amyloidogenic and Non-Amyloidogenic Islet Amyloid Polypeptide (IAPP) Sequences and Implications for the Dual Physiological and Pathological Activities of These Peptides

    PubMed Central

    Wu, Chun; Shea, Joan-Emma

    2013-01-01

    IAPP, a 37 amino-acid peptide hormone belonging to the calcitonin family, is an intrinsically disordered protein that is coexpressed and cosecreted along with insulin by pancreatic islet β-cells in response to meals. IAPP plays a physiological role in glucose regulation; however, in certain species, IAPP can aggregate and this process is linked to β-cell death and Type II Diabetes. Using replica exchange molecular dynamics with extensive sampling (16 replicas per sequence and 600 ns per replica), we investigate the structure of the monomeric state of two species of aggregating peptides (human and cat IAPP) and two species of non-aggregating peptides (pig and rat IAPP). Our simulations reveal that the pig and rat conformations are very similar, and consist of helix-coil and helix-hairpin conformations. The aggregating sequences, on the other hand, populate the same helix-coil and helix-hairpin conformations as the non-aggregating sequence, but, in addition, populate a hairpin structure. Our exhaustive simulations, coupled with available peptide-activity data, leads us to a structure-activity relationship (SAR) in which we propose that the functional role of IAPP is carried out by the helix-coil conformation, a structure common to both aggregating and non-aggregating species. The pathological role of this peptide may have multiple origins, including the interaction of the helical elements with membranes. Nonetheless, our simulations suggest that the hairpin structure, only observed in the aggregating species, might be linked to the pathological role of this peptide, either as a direct precursor to amyloid fibrils, or as part of a cylindrin type of toxic oligomer. We further propose that the helix-hairpin fold is also a possible aggregation prone conformation that would lead normally non-aggregating variants of IAPP to form fibrils under conditions where an external perturbation is applied. The SAR relationship is used to suggest the rational design of therapeutics

  14. Ice Growth Inhibition in Antifreeze Polypeptide Solution by Short-Time Solution Preheating

    PubMed Central

    Nishi, Naoto; Miyamoto, Takuya; Waku, Tomonori; Tanaka, Naoki; Hagiwara, Yoshimichi

    2016-01-01

    The objective of this study is to enhance the inhibition of ice growth in the aqueous solution of a polypeptide, which is inspired by winter flounder antifreeze protein. We carried out measurements on unidirectional freezing of the polypeptide solution. The thickness of the solution was 0.02 mm, and the concentration of polypeptide was varied from 0 to 2 mg/mL. We captured successive microscopic images of ice/solution interfaces, and measured the interface velocity from the locations of tips of the pectinate interface in the images. We also simultaneously measured the temperature by using a small thermocouple. The ice/solution interface temperature was defined by the temperature at the tips. It was found that the interface temperature was decreased with an increasing concentration of polypeptide. To try varying the activity of the polypeptide, we preheated the polypeptide solution and cooled it before carrying out the measurements. Preheating for 1–5 hours was found to cause a further decrease in the interface temperature. Furthermore, wider regions of solution and ice with inclined interfaces in the pectinate interface structure were observed, compared with the case where the solution was not preheated. Thus, the ice growth inhibition was enhanced by this preheating. To investigate the reason for this enhancement, we measured the conformation and aggregates of polypeptide in the solution. We also measured the local concentration of polypeptide. It was found that the polypeptide aggregates became larger as a result of preheating, although the polypeptide conformation was unchanged. These large aggregates caused both adsorption to the interface and the wide regions of supercooled solution in the pectinate interface structure. PMID:27152720

  15. Ice Growth Inhibition in Antifreeze Polypeptide Solution by Short-Time Solution Preheating.

    PubMed

    Nishi, Naoto; Miyamoto, Takuya; Waku, Tomonori; Tanaka, Naoki; Hagiwara, Yoshimichi

    2016-01-01

    The objective of this study is to enhance the inhibition of ice growth in the aqueous solution of a polypeptide, which is inspired by winter flounder antifreeze protein. We carried out measurements on unidirectional freezing of the polypeptide solution. The thickness of the solution was 0.02 mm, and the concentration of polypeptide was varied from 0 to 2 mg/mL. We captured successive microscopic images of ice/solution interfaces, and measured the interface velocity from the locations of tips of the pectinate interface in the images. We also simultaneously measured the temperature by using a small thermocouple. The ice/solution interface temperature was defined by the temperature at the tips. It was found that the interface temperature was decreased with an increasing concentration of polypeptide. To try varying the activity of the polypeptide, we preheated the polypeptide solution and cooled it before carrying out the measurements. Preheating for 1-5 hours was found to cause a further decrease in the interface temperature. Furthermore, wider regions of solution and ice with inclined interfaces in the pectinate interface structure were observed, compared with the case where the solution was not preheated. Thus, the ice growth inhibition was enhanced by this preheating. To investigate the reason for this enhancement, we measured the conformation and aggregates of polypeptide in the solution. We also measured the local concentration of polypeptide. It was found that the polypeptide aggregates became larger as a result of preheating, although the polypeptide conformation was unchanged. These large aggregates caused both adsorption to the interface and the wide regions of supercooled solution in the pectinate interface structure.

  16. Two-dimensional (2D) infrared correlation study of the structural characterization of a surface immobilized polypeptide film stimulated by pH

    NASA Astrophysics Data System (ADS)

    Chae, Boknam; Son, Seok Ho; Kwak, Young Jun; Jung, Young Mee; Lee, Seung Woo

    2016-11-01

    The pH-induced structural changes to surface immobilized poly (L-glutamic acid) (PLGA) films were examined by Fourier transform infrared (FTIR) spectroscopy and two-dimensional (2D) correlation analysis. Significant spectral changes were observed in the FTIR spectra of the surface immobilized PLGA film between pH 6 and 7. The 2D correlation spectra constructed from the pH-dependent FTIR spectra of the surface immobilized PLGA films revealed the spectral changes induced by the alternations of the protonation state of the carboxylic acid group in the PLGA side chain. When the pH was increased from 6 to 8, weak spectral changes in the secondary structure of the PLGA main chain were induced by deprotonation of the carboxylic acid side group.

  17. Alanine polypeptide structural fingerprints at room temperature: what can be gained from non-harmonic Car-Parrinello molecular dynamics simulations.

    PubMed

    Gaigeot, M-P

    2008-12-25

    Structural infrared fingerprints of neutral gas phase alanine peptides of increasing size and complexity (dipeptide, octapeptide, and beta-strand peptide) are characterized through DFT-based Car-Parrinello molecular dynamics simulations. Harmonic and nonharmonic vibrational signatures are calculated from the time correlation of the dipole moment of the gas phase peptide in a direct way (without any approximation) respectively from low temperature (20 K) and room temperature (300 K) molecular dynamics. Our main purpose is to answer the two following questions: (i) Is the direct inclusion of temperature for the calculation of infrared spectra mandatory for the comprehension of the vibrational signatures experimentally recorded at room temperature? (ii) To what extent is the amide I, II, and III domain sensitive enough to the local structure of the peptides, to provide vibrational signatures that can be definitely used to assess the peptide conformation at 300 K?

  18. Ordered biological nanostructures formed from chaperonin polypeptides

    NASA Technical Reports Server (NTRS)

    Trent, Jonathan D. (Inventor); McMillan, R. Andrew (Inventor); Kagawa, Hiromi (Inventor); Paavola, Chad D. (Inventor)

    2010-01-01

    The following application relates to nanotemplates, nanostructures, nanoarrays and nanodevices formed from wild-type and mutated chaperonin polypeptides, methods of producing such compositions, methods of using such compositions and particular chaperonin polypeptides that can be utilized in producing such compositions.

  19. The properties of bio-energy transport and influence of structure nonuniformity and temperature of systems on energy transport along polypeptide chains.

    PubMed

    Pang, Xiao-feng

    2012-01-01

    A new theory of bio-energy transport along protein molecules in living systems, where the energy is released by hydrolysis of adenosine triphosphate (ATP), is proposed based on some physical and biological reasons. In the new theory, the Davydov's Hamiltonian and wave function of the systems are simultaneously modified and extended. A new interaction has been added into Davydov's Hamiltonian. The wave function of the excitation state of single particles for the excitons in the Davydov model is replaced by a new wave function of two-quanta quasicoherent state. In such a case, the bio-energy is transported by the new soliton, which differs from the Davydov's soliton. The soliton is formed through self- trapping of two excitons interacting amino acid residues. The exciton is generated by vibrations of amide-I (CO stretching) arising from the energy of hydrolysis of ATP. The properties of the new soliton are extensively studied by analytical method and its lifetime is calculated using the nonlinear quantum perturbation theory and a wide ranges of parameter values relevant to protein molecules. The lifetime of the new soliton at the biological temperature 300 K is enough large and belongs to the order of 10⁻¹⁰ s, or τ/τ₀≥700, in which the soliton can transports over several hundreds amino acid residues. These studied results show clearly that the new soliton is thermally stable and has so larger lifetime that it can play an important role in biological processes. Thus the new model is a candidate of the bio-energy transport mechanism in protein molecules. In the meanwhile, the influences of structure nonuniformity in protein molecules and temperature of the systems on the states and properties of the soliton transport of bio-energy are numerically simulated and studied by the fourth-order Runge-Kutta method. The structure nonuniformity arises from the disorder distributions of masses of amino acid residues, side groups and impurities, which results also in

  20. Polypeptides having cellobiohydrolase activitiy and polynucleotides encoding same

    SciTech Connect

    Liu, Ye; Tang, Lan; Duan, Junxin

    2015-12-15

    The present invention provides isolated polypeptides having cellobiohydrolase activity and isolated polynucleotides encoding the polypeptides. The invention also provides nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  1. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2016-06-28

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  2. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2015-11-17

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  3. Polypeptides having xylanase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2015-10-27

    The present invention relates to isolated polypeptides having xylanase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  4. Polypeptides having catalase activity and polynucleotides encoding same

    DOEpatents

    Liu, Ye; Duan, Junxin; Zhang, Yu; Tang, Lan

    2017-05-02

    Provided are isolated polypeptides having catalase activity and polynucleotides encoding the polypeptides. Also provided are nucleic acid constructs, vectors and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  5. Hybrid polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    SciTech Connect

    Liu, Ye; Shaghasi, Tarana

    2016-11-01

    The present invention provides hybrid polypeptides having cellobiohydrolase activity. The present invention also provides polynucleotides encoding the hybrid polypeptides; nucleic acid constructs, vectors and host cells comprising the polynucleotides; and processes of using the hybrid polypeptides.

  6. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    SciTech Connect

    Zhang, Yu; Duan, Junxin; Tang, Lan; Wu, Wenping

    2015-06-09

    Provided are isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. Also provided are nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  7. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2015-03-31

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  8. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2014-07-15

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  9. Polypeptides having endoglucanase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2015-11-17

    The present invention relates to isolated polypeptides having endoglucanase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  10. Isolation of Polypeptide Sample and Measurement of Its Concentration.

    ERIC Educational Resources Information Center

    Beanan, Maureen J.

    2000-01-01

    Introduces a laboratory experiment that isolates a bacterial polypeptide sample and measures the concentration of polypeptides in the sample. Uses Escherichia coli strain MM294 and performs a bio-rad assay to determine the concentration of polypeptides. (YDS)

  11. Polypeptides having endoglucanase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2015-02-10

    The present invention relates to isolated polypeptides having endoglucanase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  12. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2015-07-14

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  13. Polypeptides having xylanase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2015-08-18

    The present invention relates to isolated polypeptides having xylanase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  14. Polypeptides having endoglucanase activity and polynucleotides encoding same

    DOEpatents

    Liu, Ye; Duan, Junxin; Tang, Lan

    2015-09-22

    The present invention provides isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. The invention also provides nucleic acid constructs, vectors, and host cell comprising the polynucleotides as well as methods of producing and using the polypeptides.

  15. Polypeptides having endoglucanase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2014-07-15

    The present invention relates to isolated polypeptides having endoglucanase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  16. Polypeptides having endoglucanse activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2014-07-08

    The present invention relates to isolated polypeptides having endoglucanase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  17. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2014-06-24

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  18. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2014-07-15

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  19. Polypeptides having xylanase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2014-06-24

    The present invention relates to isolated polypeptides having xylanase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  20. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2014-07-08

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  1. Polypeptides having xylanase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2014-10-14

    The present invention relates to isolated polypeptides having xylanase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  2. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    SciTech Connect

    Zhang, Yu; Tang, Lan; Henriksen, Svend Hostgaard Bang

    2016-05-17

    The present invention provides isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also provides nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  3. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    SciTech Connect

    Spodsberg, Nikolaj

    2016-12-13

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  4. Isolation of Polypeptide Sample and Measurement of Its Concentration.

    ERIC Educational Resources Information Center

    Beanan, Maureen J.

    2000-01-01

    Introduces a laboratory experiment that isolates a bacterial polypeptide sample and measures the concentration of polypeptides in the sample. Uses Escherichia coli strain MM294 and performs a bio-rad assay to determine the concentration of polypeptides. (YDS)

  5. Glycosphingolipid-facilitated membrane insertion and internalization of cobra cardiotoxin. The sulfatide.cardiotoxin complex structure in a membrane-like environment suggests a lipid-dependent cell-penetrating mechanism for membrane binding polypeptides.

    PubMed

    Wang, Chia-Hui; Liu, Jyung-Hurng; Lee, Shao-Chen; Hsiao, Chwan-Deng; Wu, Wen-Guey

    2006-01-06

    Cobra cardiotoxins, a family of basic polypeptides having lipid- and heparin-binding capacities similar to the cell-penetrating peptides, induce severe tissue necrosis and systolic heart arrest in snakebite victims. Whereas cardiotoxins are specifically retained on the cell surface via heparan sulfate-mediated processes, their lipid binding ability appears to be responsible, at least in part, for cardiotoxin-induced membrane leakage and cell death. Although the exact role of lipids involved in toxin-mediated cytotoxicity remains largely unknown, monoclonal anti-sulfatide antibody O4 has recently been shown to inhibit the action of CTX A3, the major cardiotoxin from Taiwan cobra venom, on cardiomyocytes by preventing cardiotoxin-induced membrane leakage and CTX A3 internalization into mitochondria. Here, we show that anti-sulfatide acts by blocking the binding of CTX A3 to the sulfatides in the plasma membrane to prevent sulfatide-dependent CTX A3 membrane pore formation and internalization. We also describe the crystal structure of a CTX A3-sulfatide complex in a membrane-like environment at 2.3 angstroms resolution. The unexpected orientation of the sulfatide fatty chains in the structure allows prediction of the mode of toxin insertion into the plasma membrane. CTX A3 recognizes both the headgroup and the ceramide interfacial region of sulfatide to induce a lipid conformational change that may play a key role in CTX A3 oligomerization and cellular internalization. This proposed lipid-mediated toxin translocation mechanism may also shed light on the cellular uptake mechanism of the amphiphilic cell-penetrating peptides known to involve multiple internalization pathways.

  6. Novel polypeptide toxins with crab lethality from the sea anemone Anemonia erythraea.

    PubMed

    Shiomi, K; Qian, W H; Lin, X Y; Shimakura, K; Nagashima, Y; Ishida, M

    1997-04-17

    The sea anemone Anemonia erythraea was found to contain polypeptide toxins with crab lethality as well as hemolysins. Three polypeptide toxins (AETX I, II and III) were isolated by gel filtration on Sephadex G-50 and reverse-phase HPLC on TSKgel ODS-120T. A geographic variation in toxin composition was suggested. The LD50 against crabs of AETX I, II and III were estimated to be 2.2, 0.53 and 0.28 microg/kg, respectively, but none of the toxins showed lethality in mice. The amino acid sequences of the three toxins were deduced from sequencings of the whole molecules and their enzymatic fragments. Amino acid analyses and molecular mass determinations supported the accuracy of the deduced sequences. AETX I, comprising 47 amino acid residues including 6 half-Cys residues, is an analog of sea anemone type I toxins. On the other hand, AETX II and III, which are highly homologous with each other, are quite distinct from the known sea anemone polypeptide toxins in that they are composed of 59 residues including 10 half-Cys residues. Interestingly, both toxins have sequence similarities with neurotoxins isolated from the Brazilian 'armed' spider Phoneutria nigriventer.

  7. Deducing a mechanism of all musculoskeletal injuries

    PubMed Central

    Verrall, Geoffrey; Dolman, Bronwyn

    2016-01-01

    Summary Background The mechanism of musculoskeletal (MSK) injuries is not well understood. This research applies principles of elastic motion to the anatomy and movement patterns of MSK structures. From this an insight into the application and timing of forces on MSK structures can be established and the mechanism/s of injury derived. Methods (Current Knowledge) All MSK structures demonstrate varying degrees of elasticity. Movement occurs primarily as a consequence of Muscle Tendon Unit (MTU) shortening. The application of an applied external force results in MSK structure lengthening. Results The MTU acts as a non-idealised Hookean Spring. The resting length of MSK structures is the minimum distance between attachment points. The anatomical constraints results in MSK structures having adequate compressive strength during shortening. Thus MSK injuries only occur during lengthening of the MSK structure. From this with knowledge of MSK movement cycles, we can derive the mechanism of injury. Conclusions MSK injuries result from an inability to counter applied forces whilst lengthening. Muscles, tendons and ligaments can only injure during their lengthening contraction phase. Insertional tendons and bone near attachment points injure during the MTU shortening phase. Injuries to other MSK structures can occur independent of the lengthening and shortening phases such as direct contact injuries. PMID:27900289

  8. Complexes of Negatively Charged Polypeptides with Cationic Lipids

    NASA Astrophysics Data System (ADS)

    Subramanian, G.; Li, Youli; Safinya, Cyrus R.

    1997-03-01

    Complexes of cationic lipids with oppositely charged proteins are promising candidates for new biomolecular materials. In addition to being used as a direct vehicle for protein transfection, they also find applications as templates for synthesis of molecular sieves. In spite of these wide ranging applications, the structure and interactions in these complexes have largely remained unclear. Here we report on the study of complexes formed between the cationic lipid didodecyldimethylammonium bromide (DDAB) with negatively charged polypeptide poly glutamic acid (PGA) both in the presence and absence of the neutral lipid dilauroylglycerophosphocholine (DLPC). X-ray diffraction of the complexes indicates a condensed lamellar lipid structure with the polypeptide intercalated between the layers. We present a comprehensive phase diagram on this system based on X-ray diffraction data. This work is supported in part by grants NSF DMR-9624091, PRF-31352 AC7, and CU LAR STP/UC 96-118.

  9. The geometry of the ribosomal polypeptide exit tunnel.

    PubMed

    Voss, N R; Gerstein, M; Steitz, T A; Moore, P B

    2006-07-21

    The geometry of the polypeptide exit tunnel has been determined using the crystal structure of the large ribosomal subunit from Haloarcula marismortui. The tunnel is a component of a much larger, interconnected system of channels accessible to solvent that permeates the subunit and is connected to the exterior at many points. Since water and other small molecules can diffuse into and out of the tunnel along many different trajectories, the large subunit cannot be part of the seal that keeps ions from passing through the ribosome-translocon complex. The structure referred to as the tunnel is the only passage in the solvent channel system that is both large enough to accommodate nascent peptides, and that traverses the particle. For objects of that size, it is effectively an unbranched tube connecting the peptidyl transferase center of the large subunit and the site where nascent peptides emerge. At no point is the tunnel big enough to accommodate folded polypeptides larger than alpha-helices.

  10. Fabrication and characterization of non-volatile transistor memory based on polypeptide as gate dielectric

    NASA Astrophysics Data System (ADS)

    Liang, Lijuan; Li, LianFang; Wei, Xianfu; Huang, Beiqing; Wei, Yen

    2017-01-01

    The organic thin film transistor (OTFT) fabricated with the polypeptide as a dielectric layer shows memory function. In order to investigate the effect of polypeptide structure on the performance of non-volatile transistor memory, the Fourier-transform IR (FT- IR) and Circular Dichiroism (CD) spectral of PMLG film has been applied, respectively. In conclusion, the memory transistor device fabricated with polypeptide as the ferroelectric exhibit promising behavior such as a large memory window, and the dipole moment of the amide group was considered as the main source of the memory function.

  11. Characterization of an amidated form of pancreatic polypeptide from the daddy sculpin (Cottus scorpius).

    PubMed

    Conlon, J M; Schmidt, W E; Gallwitz, B; Falkmer, S; Thim, L

    1986-12-30

    The primary structure of pancreatic polypeptide from the teleostean fish, Cottus scorpius (daddy sculpin) was established as: YPPQPESPGGNASPEDWAKYHAAVRHYVNLITRQRYNH2 The presence of a COOH-terminally alpha-amidated amino acid was established using an HPLC method of general applicability. Although the peptide shows strong homology towards anglerfish pancreatic polypeptide (86%), homology towards porcine peptide YY (PYY) (61%) and porcine neuropeptide Y (NPY) (61%) was greater than towards porcine pancreatic polypeptide (PP) (47%). This result supports suggestions that the gene duplication events which led to PP, NPY and PYY formation took place after the time of divergence of fish and mammals.

  12. Biophysical analyses of synthetic amyloid-beta(1-42) aggregates before and after covalent cross-linking. Implications for deducing the structure of endogenous amyloid-beta oligomers.

    PubMed

    Moore, Brenda D; Rangachari, Vijayaraghavan; Tay, William M; Milkovic, Nicole M; Rosenberry, Terrone L

    2009-12-15

    A neuropathological hallmark of Alzheimer's disease (AD) is the presence of large numbers of senile plaques in the brain. These deposits are rich in fibrils that are composed of 40- and 42-residue amyloid-beta (Abeta) peptides. Several lines of evidence indicate that soluble Abeta aggregates as well as fibrils are important in the etiology of AD. Low levels of endogenous soluble Abeta aggregates make them difficult to characterize, but several species in extracts of AD brains have been detected by gel electrophoresis in sodium dodecyl sulfate (SDS) and immunoblotting. Individual Abeta oligomers ranging in size from dimers through dodecamers of 4 kDa monomeric Abeta have been resolved in other laboratories as discrete species by size exclusion chromatography (SEC). In an effort to reconstitute soluble Abeta aggregates in vitro that resemble the endogenous soluble Abeta aggregates, we previously found that monomeric Abeta(1-42) rapidly forms soluble oligomers in the presence of dilute SDS micelles. Here we extend this work in two directions. First, we contrast the size and secondary structure of these oligomers with those of synthetic Abeta(1-42) fibrils. SEC and multiangle light scattering were used to obtain a molecular mass of 150 kDa for the isolated oligomers. The oligomers partially dissociated to monomers through nonamers when incubated with SDS, but in contrast to endogenous oligomers, we saw no evidence of these discrete species prior to SDS treatment. One hypothesis to explain this difference is that endogenous oligomers are stabilized by covalent cross-linking induced by unknown cellular agents. To explore this hypothesis, optimal mass spectrometry (MS) analysis procedures need to be developed for Abeta cross-linked in vitro. In our second series of studies, we began this process by treating monomeric and aggregated Abeta(1-42) with three cross-linking agents: transglutaminase, glutaraldehyde, and Cu(II) with peroxide. We compared the efficiency of

  13. Maple syrup urine disease. Complete primary structure of the E1 beta subunit of human branched chain alpha-ketoacid dehydrogenase complex deduced from the nucleotide sequence and a gene analysis of patients with this disease.

    PubMed Central

    Nobukuni, Y; Mitsubuchi, H; Endo, F; Akaboshi, I; Asaka, J; Matsuda, I

    1990-01-01

    A defect in the E1 beta subunit of the branched chain alpha-ketoacid dehydrogenase (BCKDH) complex is one cause of maple syrup urine disease (MSUD). In an attempt to elucidate the molecular basis of MSUD, we isolated and characterized a 1.35 kbp cDNA clone encoding the entire precursor of the E1 beta subunit of BCKDH complex from a human placental cDNA library. Nucleotide sequence analysis revealed that the isolated cDNA clone (lambda hBE1 beta-1) contained a 5'-untranslated sequence of four nucleotides, the translated sequence of 1,176 nucleotides and the 3'-untranslated sequence of 169 nucleotides. Comparison of the amino acid sequence predicted from the nucleotide sequence of the cDNA insert of the clone with the NH2-terminal amino acid sequence of the purified mature bovine BCKDH-E1 beta subunit showed that the cDNA insert encodes for a 342-amino acid subunit with a Mr = 37,585. The subunit is synthesized as the precursor with a leader sequence of 50 amino acids and is processed at the NH2 terminus. A search for protein homology revealed that the primary structure of human BCKDH-E1 beta was similar to the bovine BCKDH-E1 beta and to the E1 beta subunit of human pyruvate dehydrogenase complex, in all regions. The structures and functions of mammalian alpha-ketoacid dehydrogenase complexes are apparently highly conserved. Genomic DNA from lymphoblastoid cell lines derived from normal and five MSUD patients, in whom E1 beta was not detected by immunoblot analysis, gave the same restriction maps on Southern blot analysis. The gene has at least 80 kbp. Images PMID:2365818

  14. Photochromic polypeptides as synthetic models of biological photoreceptors: a spectroscopic study.

    PubMed Central

    Angelini, N; Corrias, B; Fissi, A; Pieroni, O; Lenci, F

    1998-01-01

    L-Glutamic acid polypeptides containing photochromic nitrospiropyran bound to the side chains at various percentages ("local" concentration) have been synthesized and investigated as possible artificial models of biological photoreceptors. Absorption and fluorescence spectroscopy have been utilized to investigate the photophysical and photochemical properties of nitrospiropyrans, both inserted in the polypeptide chain and in solution as "free" dye. Conformational variations produced by dark storage and light exposure of the photochromic polypeptides have been studied by means of circular dichroism. Dark-kept "free" dyes in hexafluoro-2-propanol solution in the merocyanine form ("open" form) give rise to molecular aggregates, which have been characterized as merocyanine dimers. The equilibrium constant between the monomer and the dimer, K, and their molar extinction coefficients, epsilon, at several wavelengths have been determined. Fluorescence measurements on "free" and polypeptide-bound nitrospiropyrans suggest that the dimerization process between merocyanines is favored when the photochromic units are inserted in the polypeptide chain and that under these conditions an efficient energy transfer from the monomer (donor) to the dimer (acceptor) occurs. By varying "local" as well as total nitrospiropyran concentration, it has been shown that the dimeric species result from intermolecular interactions between photochromic groups inserted in the same polypeptide chain. The alpha-helix --> random coil transition of the polypeptide structure after dark storage has eventually been shown to be the result of the dimerization process and not of the dark isomerization per se from the "closed" spiropyran form to the "open" merocyanine form of the dye. PMID:9591684

  15. Refined Genetic Algorithms for Polypeptide Structure Prediction.

    DTIC Science & Technology

    1996-12-01

    fo cused ev olution program. 2.5 Parallel Genetic Algorithms General information ab out parallel computing is a v ailable in App endix C. There are t w...to generate a more t \\feasible" candidate, and th us, escap e the lo cal minim a. T able 14. Final minim um energies (k cal/mol) for [Met]-enk...prop osed the tec hnique kno wn as ev olutionary programming. Ev olu- tionary programmi ng tries to generate computational biological ev olution

  16. Theoretical investigations on model ternary polypeptides using genetic algorithm—Some new results

    NASA Astrophysics Data System (ADS)

    Arora, Vinita; Bakhshi, A. K.

    2011-04-01

    Using genetic algorithm (GA) model ternary polypeptides containing glycine, alanine and serine in β-pleated conformation have been theoretically investigated. In designing, the criterion to attain the optimum solution at the end of GA run is minimum band gap and maximum delocalization in the polypeptide chain. Ab initio results obtained using Clementi's minimal basis set are used as input. Effects of (i) change of basis set from minimal to double zeta, (ii) change in secondary structure from β-pleated to α-helical, (iii) presence of solvation shell and (iv) binding of H + and Li + ions to peptide group on the resulting solution as well as on electronic structure and conduction properties of polypeptides are investigated. A comparison is drawn between results obtained for the two cationic adducts. The protonated adduct is expected to withdraw more negative charge from the polypeptide chain due to smaller size of H + and is found to have high electron affinity compared to Li + adduct.

  17. Structure, dynamics, and hydration of a collagen model polypeptide, (L-prolyl-L-prolylglycyl)10, in aqueous media: a chemical equilibrium analysis of triple helix-to-single coil transition.

    PubMed

    Shikata, Toshiyuki; Minakawa, Ayako; Okuyama, Kenji

    2009-10-29

    The structure, dynamics, and hydration behavior of a collagen model polypeptide, (L-prolyl-L-prolylglycyl)(10) (PPG10), were investigated in pure water and dilute acetic acid over a wide temperature range using broadband dielectric relaxation (DR) techniques that spanned frequencies from 1 kHz to 20 GHz. All samples showed pronounced dielectric dispersion with two major relaxation processes around 3 MHz and 20 GHz. Because DR measurements sensitively probe dipoles and their dynamics, the structures and ionization states of the carboxy and amino termini of aqueous PPG10 were precisely determined from the relaxation times and strengths in the 3 MHz frequency range. In solution, PPG10 formed mixtures of monodisperse rods as triple helices with lengths and diameters of 8.6 and 1.5 nm, respectively, and monomeric random coils with radii of approximately 1.4 nm. Ionization of the C-terminus was suppressed by the addition of acetic acid in both states. The fraction of random coils (f(coil)) was found to be a function of temperature (T) and the concentration of PPG10 (c). At low temperatures, small f(coil) values were found, which increased with temperature to reach f(coil) = 1 at approximately 60 degrees C, irrespective of c. This phenomenon, well-known as a triple helix-to-single coil transition, is discussed on the basis of the chemical reaction, (PPG10)(3) <==> 3PPG10, with an equilibrium constant of K = 3(c/55.6)(2)f(coil)(3)(1 - f(coil))(-1). The standard enthalpy change evaluated from Arrhenius plots (ln K versus T(-1)) was found to change dramatically at the same transition temperature that was previously determined by using optical rotation experiments. The other major DR process, observed at approximately 20 GHz, was assigned to free and hydrated water molecules and used to determine the average hydration number (m) per PPG10. The m values for the triple helix and random coil state at 25 degrees C were evaluated to be m(th) = 60-70 and m(coil) = 250-270. The m

  18. Restriction/modification polypeptides, polynucleotides, and methods

    DOEpatents

    Westpheling, Janet; Chung, DaeHwan; Huddleston, Jennifer; Farkas, Joel A

    2015-02-24

    The present invention relates to the discovery of a novel restriction/modification system in Caldicellulosiruptor bescii. The discovered restriction enzyme is a HaeIII-like restriction enzyme that possesses a thermophilic activity profile. The restriction/modification system also includes a methyltransferase, M.CbeI, that methylates at least one cytosine residue in the CbeI recognition sequence to m.sup.4C. Thus, the invention provides, in various aspects, isolated CbeI or M.CbeI polypeptides, or biologically active fragments thereof; isolated polynucleotides that encode the CbeI or M.CbeI polypeptides or biologically active fragments thereof, including expression vectors that include such polynucleotide sequences; methods of digesting DNA using a CbeI polypeptide; methods of treating a DNA molecule using a M.CbeI polypeptide; and methods of transforming a Caldicellulosiruptor cell.

  19. Structure of the N- and O-glycans of the A-chain of human plasma alpha 2HS-glycoprotein as deduced from the chemical compositions of the derivatives prepared by stepwise degradation with exoglycosidases.

    PubMed

    Watzlawick, H; Walsh, M T; Yoshioka, Y; Schmid, K; Brossmer, R

    1992-12-08

    The structure of the glycans of the A-chain of human plasma alpha 2HS-glycoprotein was established from the chemical compositions of its derivatives prepared by sequential enzymatic degradation of the carbohydrate moiety, from the determination of the kind and amount of the monosaccharides liberated after each step of the enzymatic digestion, and from the distinct specificity of the highly purified exoglycosidases. The exoglycosidases were three sialidases (Vibrio cholerae, fowl plague virus, and Arthrobacter ureafaciens), two beta-galactosidases (Streptococcus pneumoniae and bovine testis), one alpha-N-acetylgalactosaminidase, one beta-N-acetylglucosaminidase, and one alpha-mannosidase. Utilizing sialidases with different cleavage specificities, the number of alpha 2-3- and alpha 2-6-linked sialic acid residues could be separately determined. As to the beta-galactosidases, the enzyme isolated from S. pneumoniae cleaves only beta 1-4-linked galactose residues, whereas the bovine testes enzyme acts on both the beta 1-4- and beta 1-3-linked galactose residues. Jack bean beta-N-acetylglucosaminidase cleaves beta 1-2, beta 1-4, and beta 1-6 GlcNAc with higher activity for the beta 1-2. Jack bean alpha-mannosidase cleaves alpha 1-2, alpha 1-6, and alpha 1-3 Man with greater activity for alpha 1-2 and alpha 1-6. Bovine liver alpha-N-acetylgalactosaminidase cleaves O-linked GalNAc. On the basis of these results, the A-chain of alpha 2 HS-glycoprotein was found to possess two biantennary N-glycans and two O-linked trisaccharides.

  20. Polypeptides of the Maize Amyloplast Stroma1

    PubMed Central

    Yu, Ying; He Mu, Helen; Mu-Forster, Chen; Wasserman, Bruce P.

    1998-01-01

    In the developing endosperm of monocotyledonous plants, starch granules are synthesized and deposited within the amyloplast. A soluble stromal fraction was isolated from amyloplasts of immature maize (Zea mays L.) endosperm and analyzed for enzyme activities and polypeptide content. Specific activities of starch synthase and starch-branching enzyme (SBE), but not the cytosolic marker alcohol dehydrogenase, were strongly enhanced in soluble amyloplast stromal fractions relative to soluble extracts obtained from homogenized kernels or endosperms. Immunoblot analysis demonstrated that starch synthase I, SBEIIb, and sugary1, the putative starch-debranching enzyme, were each highly enriched in the amyloplast stroma, providing direct evidence for the localization of starch-biosynthetic enzymes within this compartment. Analysis of maize mutants shows the deficiency of the 85-kD SBEIIb polypeptide in the stroma of amylose extender cultivars and that the dull mutant lacks a >220-kD stromal polypeptide. The stromal fraction is distinguished by differential enrichment of a characteristic group of previously undocumented polypeptides. N-terminal sequence analysis revealed that an abundant 81-kD stromal polypeptide is a member of the Hsp70 family of stress-related proteins. Moreover, the 81-kD stromal polypeptide is strongly recognized by antibodies specific for an Hsp70 of the chloroplast stroma. These findings are discussed in light of implications for the correct folding and assembly of soluble, partially soluble, and granule-bound starch-biosynthetic enzymes during import into the amyloplast. PMID:9536063

  1. Polypeptides having laccase activity and polynucleotides encoding same

    DOEpatents

    Liu, Ye; Tang, Lan; Duan, Junxin; Zhang, Yu

    2017-08-22

    The present invention relates to isolated polypeptides having laccase activity and polynucleotides encoding the polypeptides and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  2. Factors Governing Fibrillogenesis of Polypeptide Chains Revealed by Lattice Models

    NASA Astrophysics Data System (ADS)

    Li, Mai Suan; Co, Nguyen Truong; Reddy, Govardhan; Hu, Chin-Kun; Straub, J. E.; Thirumalai, D.

    2010-11-01

    Using lattice models we explore the factors that determine the tendencies of polypeptide chains to aggregate by exhaustively sampling the sequence and conformational space. The morphologies of the fibril-like structures and the time scales (τfib) for their formation depend on a balance between hydrophobic and Coulomb interactions. The extent of population of an ensemble of N* structures, which are fibril-prone structures in the spectrum of conformations of an isolated protein, is the major determinant of τfib. This observation is used to determine the aggregating sequences by exhaustively exploring the sequence space, thus providing a basis for genome wide search of fragments that are aggregation prone.

  3. Isolation of proteins related to the Rh polypeptides from nonhuman erythrocytes.

    PubMed Central

    Saboori, A M; Denker, B M; Agre, P

    1989-01-01

    It is thought that the Rh antigens may be important in maintaining normal erythrocyte membrane integrity. Despite their name, Rh antigens are serologically present only on human erythrocytes. Rh structural polymorphisms are known to reside within a family of nonglycosylated Mr 32,000 integral membrane proteins that can be purified by hydroxylapatite chromatography. Mr 32,000 integral membrane proteins were purified similarly from erythrocyte membrane vesicles prepared from rhesus monkeys, cows, cats, and rats, but could not be purified from human Rhmod erythrocytes, a rare syndrome lacking Rh antigens. The purified Mr 32,000 polypeptides were labeled with 125I, digested with chymotrypsin, and found to be 30-60% identical to human Rh polypeptides when compared by two-dimensional iodopeptide mapping. The physiologic function of the Rh polypeptides remains to be identified; however, the existence of related proteins in nonhuman erythrocytes supports the concept that the Rh polypeptides are erythrocyte membrane components of fundamental significance. Images PMID:2492035

  4. Deducing spectroscopic factors from wave-function asymptotics

    SciTech Connect

    Capel, P.; Danielewicz, P.; Nunes, F. M.

    2010-11-15

    In a coupled-channel model, we explore the effects of coupling between configurations on the radial behavior of the wave function and, in particular, on the spectroscopic factor (SF) and the asymptotic normalization coefficient (ANC). We evaluate the extraction of a SF from the ratio of the ANC of the coupled-channel model to that of a single-particle approximation of the wave function. We perform this study within a core+n collective model, which includes two states of the core that connect by a rotational coupling. To get additional insights, we also use a simplified model that takes a {delta} function for the coupling potential. Calculations are performed for {sup 11}Be. Fair agreement is obtained between the SF inferred from the single-particle approximation and the one obtained within the coupled-channel models. Significant discrepancies are observed only for large coupling strength and/or large admixture, that is, a small SF. This suggests that reliable SFs can be deduced from the wave-function asymptotics when the structure is dominated by one configuration, that is, for a large SF.

  5. Carbohydrate degrading polypeptide and uses thereof

    DOEpatents

    Sagt, Cornelis Maria Jacobus; Schooneveld-Bergmans, Margot Elisabeth Francoise; Roubos, Johannes Andries; Los, Alrik Pieter

    2015-10-20

    The invention relates to a polypeptide having carbohydrate material degrading activity which comprises the amino acid sequence set out in SEQ ID NO: 2 or an amino acid sequence encoded by the nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO: 4, or a variant polypeptide or variant polynucleotide thereof, wherein the variant polypeptide has at least 96% sequence identity with the sequence set out in SEQ ID NO: 2 or the variant polynucleotide encodes a polypeptide that has at least 96% sequence identity with the sequence set out in SEQ ID NO: 2. The invention features the full length coding sequence of the novel gene as well as the amino acid sequence of the full-length functional protein and functional equivalents of the gene or the amino acid sequence. The invention also relates to methods for using the polypeptide in industrial processes. Also included in the invention are cells transformed with a polynucleotide according to the invention suitable for producing these proteins.

  6. Self-association and modification of a genetically engineered polypeptide

    NASA Astrophysics Data System (ADS)

    Top, Ayben

    A genetically synthesized polypeptide and polyethylene glycol (5 kDa or 10 kDa) functionalized forms of its alanine-rich helical domain were characterized. The polypeptide composed of an N-terminal histidine tag, and an alanine-rich domain, denoted as 17H6, has a sequence of: MGH10 SSGHIHM(AAAQEAAAAQAAAQAEAAQAAQ)6AGGYGGMG. 17H6 was originally designed as a scaffold to investigate multivalent interactions after glycosylation through reactive glutamic acid residues. We speculated that the protonation of the glutamic acid residues in these sequences would afford facile opportunities to manipulate their folding and assembly behavior considering the beta-sheet propensities of similar polypeptides at acidic pH. Thus, in the first part of this study, thermal unfolding, reversible self-association, and irreversible aggregation of 17H6 were investigated. Dynamic light scattering, and thermal unfolding measurements indicate that 17H6 spontaneously and reversibly self-associates at an acidic pH and ambient temperature. The resulting multimers have an average hydrodynamic radius of ˜ 10-20 nm and reversibly dissociate to monomers upon an increase to pH 7.4. Both free monomer and 17H6 chains within the multimers are beta-helical and folded at ambient and sub-ambient temperatures. Reversible unfolding of the monomer occurs upon heating of solutions at pH 7.4. At pH 2.3, heating first causes incomplete dissociation and unfolding of the constituent chains. Further incubation at an elevated temperature (80°C) induces additional structural and morphological changes and results in fibrils with a beta-sheet structure and a width of 5-10 nm (7 nm mean) as observed via transmission electron microscopy (TEM). In the second part, the histidine tag, which imparts solubility to the alanine-rich domain at acidic pH was cleaved. Propionaldehyde-functionalized poly(ethylene glycol) (PEG) molecules (5 kDa or 10 kDa) were attached to the N-terminus of the cleaved polypeptide, c17H6, as a

  7. Residue length and solvation model dependency of elastinlike polypeptides.

    PubMed

    Bilsel, Mustafa; Arkin, Handan

    2010-05-01

    We have performed exhaustive multicanonical Monte Carlo simulations of elastinlike polypeptides with a chain including amino acids (valine-proline-glycine-valine-glycine)n or in short (VPGVG)n, where n changes from 1 to 4, in order to investigate the thermodynamic and structural properties. To predict the characteristic secondary structure motifs of the molecules, Ramachandran plots were prepared and analyzed as well. In these studies, we utilized a realistic model where the interactions between all types of atoms were taken into account. Effects of solvation were also simulated by using an implicit-solvent model with two commonly used solvation parameter sets and compared with the vacuum case.

  8. Residue length and solvation model dependency of elastinlike polypeptides

    NASA Astrophysics Data System (ADS)

    Bilsel, Mustafa; Arkin, Handan

    2010-05-01

    We have performed exhaustive multicanonical Monte Carlo simulations of elastinlike polypeptides with a chain including amino acids (valine-proline-glycine-valine-glycine)n or in short (VPGVG)n , where n changes from 1 to 4, in order to investigate the thermodynamic and structural properties. To predict the characteristic secondary structure motifs of the molecules, Ramachandran plots were prepared and analyzed as well. In these studies, we utilized a realistic model where the interactions between all types of atoms were taken into account. Effects of solvation were also simulated by using an implicit-solvent model with two commonly used solvation parameter sets and compared with the vacuum case.

  9. Proteolytic processing of poliovirus polypeptides: antibodies to polypeptide P3-7c inhibit cleavage at glutamine-glycine pairs

    SciTech Connect

    Hanecak, R.; Semler, B.L.; Anderson, C.W.; Wimmer, E.

    1982-07-01

    Proteolytic processing of poliovirus polypeptides was examined by the addition of antibodies directed against the viral proteins P3-7c and P2-X to a cell-free translation extract prepared from infected HeLa cells. Antisera to P3-7c specifically inhibited in vitro processing at Gln-Gly pairs. Partial amino acid sequence analysis revealed a second Tyr-Gly pair that is utilized in protein processing. Neither Tyr-Gly cleavage is affected by antibody to P3-7C. Anti-P3-7c antibodies react not only with P3-7c but also with P3-6a and P3-2, two viral polypeptides NH/sub 2/-coterminal with P3-7c. Preimmune and anti-P2-X antibodies had no effect on the processing of poliovirus proteins in vitro. The authors conclude that the activity responsible for processing poliovirus polypeptides at Gln-Gly pairs resides in the primary structure of P3-7c and not in P2-X.

  10. Biodegradable Epoxy Networks Cured with Polypeptides

    NASA Astrophysics Data System (ADS)

    Nakamura, Shigeo; Kramer, Edward J.

    2006-03-01

    Epoxy resins are used widely for adhesives as well as coatings. However, once cured they are usually highly cross-linked and are not biodegradable. To obtain potentially biodegradable polypeptides that can cure with epoxy resins and achieve as good properties as the conventional phenol novolac hardeners, poly(succinimide-co-tyrosine) was synthesized by thermal polycondensation of L-aspartic acid and L-tyrosine with phosphoric acid under reduced pressure. The tyrosine/succinimide ratio in the polypeptide was always lower than the tyrosine/(aspartic acid) feed ratio and was influenced by the synthesis conditions. Poly(succinimide-tyrosine- phenylalanine) was also synthesized from L-aspartic acid, L- tyrosine and L-phenylalanine. The thermal and mechanical properties of epoxy resins cured with these polypeptides are comparable to those of similar resins cured with conventional hardeners. In addition, enzymatic degradability tests showed that Chymotrypsin or Subtilisin A could cleave cured films in an alkaline borate buffer.

  11. Maize mitochondria synthesize organ-specific polypeptides

    SciTech Connect

    Newton, K.J.; Walbot, V.

    1985-10-01

    The authors detected both quantitative and qualitative organ-specific differences in the total protein composition of mitochondria of maize. Labeling of isolated mitochondria from each organ demonstrated that a few protein differences are due to changes in the polypeptides synthesized by the organelle. The synthesis of developmental stage-specific mitochondrial polypeptides was found in the scutella of developing and germinating kernels. The approximately 13-kDa polypeptide synthesized by mitochondria from seedlings of the Texas (T) male-sterile cytoplasm was shown to be constitutively expressed in all organs of line B37T tested. Methomyl, an insecticide known to inhibit the growth of T sterile plants, was shown to be an effective inhibitor of protein synthesis in mitochondria from T plants.

  12. The design, synthesis, and characterization of novel alanine-rich polypeptides with varied functional group density

    NASA Astrophysics Data System (ADS)

    Farmer, Robin S.

    Protein engineering methods have proven valuable for the synthesis of protein-based polymers with controlled conformational properties and functional group placement for use in a variety of biological and materials applications. These strategies were employed to produce alanine-rich polypeptides with the general sequence [(AAAQ)y(AAAE)(AAAQ)y]x, which utilizes the high helical propensity of alanine and chemical functionality of glutamic acid. Modifications to the general sequence allow for variations in both the spacing between and the number of glutamic acid residues along the protein backbone. Three families of alanine-rich polypeptides with similar amino acid compositions were designed with glutamic acid residues displayed at nominal distances of 17A, 35A, and 65A. From these three families, four of these polypeptides were focused on for this work, 17-H-3, 17-H-6, 35-H-6 and 65-H-2. Understanding the conformational and thermal behavior of the polypeptides can give insight into how these molecules will behave after functionalization. The conformational behavior of the four polypeptides from the three alanine-rich families have been investigated via circular dichroic spectroscopy under multiple solution conditions; pH 2.3, 10 mM phosphate, pH 2.3, 10 mM phosphate, 150 mM NaCl, and pH 7.4 PBS. All the polypeptides adopt an alpha-helical conformation under all solution conditions and exhibit an alpha-helical to non-alpha-helical transition with increasing temperature. In pH 2.3, 10 mM phosphate buffer, the conformation differs between sequences at high temperature and high polypeptide concentration. Although the compositions of the three families are similar, changes in the amino acid sequences result in variations in hydrophobicity. The most hydrophobic sequence, 65-H-2 , undergoes the helix-to-coil transition but at high polypeptide concentrations and temperatures above 45°C, the polypeptide irreversibly adopts a beta-sheet structure. The less hydrophobic

  13. Construction and characterization of an experimental ISCOMS-based hepatitis B polypeptide vaccine

    PubMed Central

    Guan, Xiao-Ju; Guan, Xiao-Jun; Wu, Yu-Zhang; Jia, Zheng-Cai; Shi, Tong-Dong; Tang, Yan

    2002-01-01

    AIM: To characterize the biochemical and immunological properties of an experimental ISCOMS vaccine prepared from a novel therapeutic polypeptide based on T cell epitopes of HBsAg, and a heptatis B-ISCOMS was prepared and investigated. METHODS: An immunostimulating complexes (ISCOMS)-based vaccine containing a novel therapeutic hepatits B polypeptide was prepared by dialysis method, and its formation was visualized by electron microscopy and biochemically verified by SDS-polyacrylamide gel electrophoresis. Amount of the peptide within ISCOMS was determined by Bradford assay, and specific CTL response was detected by ELISPOT assay. RESULTS: Typical cage-like structures of submicroparticle with a diameter of about 40 nm were observed by electron microscopy. Results from Bradford assay showed that the level of peptide incorporation was about 0.33 g•L⁻¹. At the paralleled position close to the sixth band of the molecular weight marker (3480 kDa) a clear band was shown in SDS-PAGE analysis, indicating successful incorporation of polypeptide into ISCOMS. It is suggested that ISCOMS delivery system could efficiently improve the immunogenicity of polypeptide and elicit specific immune responses in vivo by the results of ELISPOT assay, which showed that IFN-γ producing cells (specific CTL responses) were increased (spots of ISCOMS-treated group: 47 ± 5, n = 3; control group: 5 ± 2, n = 3). CONCLUSION: ISCOMS-based hepatitis B polypeptide vaccine is successfully constructed and it induces a higher CTL response compared with short polypeptides vaccine in vivo. PMID:11925610

  14. Polypeptide composition of urea- and heat-resistant mutants of poliovirus types 1 and 2.

    PubMed

    Fennell, R; Phillips, B A

    1974-10-01

    Five urea-resistant and two heat-resistant mutants of poliovirus types 1 and 2 were isolated and their structural and nonstructural polypeptides compared to those of their wild-type, parental strains in an attempt to correlate mutant phenotypes with alterations in specific capsid polypeptides. Four of the seven mutants were found to contain polypeptides which differed in molecular weight from their respective parental viruses. However, resistance of virions to heat- or urea-inactivation could not be attributed to changes in particular capsid polypeptides because alterations were detected in all but one of the capsid components. For two of the urea-resistant mutants and one heat-resistant mutant, no differences were found in the molecular weights of the capsid and noncapsid polypeptides. These results, and the fact that at least 12 selective treatments were required to obtain stable mutants, indicate that: (i) such phenotypes probably can be expressed by mutations affecting one or more of the larger capsid polypeptides, and (ii) such phenotypes reflect multiple mutational steps.

  15. TOPOFOLD, the designed modular biomolecular folds: polypeptide-based molecular origami nanostructures following the footsteps of DNA.

    PubMed

    Kočar, Vid; Božič Abram, Sabina; Doles, Tibor; Bašić, Nino; Gradišar, Helena; Pisanski, Tomaž; Jerala, Roman

    2015-01-01

    Biopolymers, the essential components of life, are able to form many complex nanostructures, and proteins in particular are the material of choice for most cellular processes. Owing to numerous cooperative interactions, rational design of new protein folds remains extremely challenging. An alternative strategy is to design topofolds-nanostructures built from polypeptide arrays of interacting modules that define their topology. Over the course of the last several decades DNA has successfully been repurposed from its native role of information storage to a smart nanomaterial used for nanostructure self-assembly of almost any shape, which is largely because of its programmable nature. Unfortunately, polypeptides do not possess the straightforward complementarity as do nucleic acids. However, a modular approach can nevertheless be used to assemble polypeptide nanostructures, as was recently demonstrated on a single-chain polypeptide tetrahedron. This review focuses on the current state-of-the-art in the field of topological polypeptide folds. It starts with a brief overview of the field of structural DNA and RNA nanotechnology, from which it draws parallels and possible directions of development for the emerging field of polypeptide-based nanotechnology. The principles of topofold strategy and unique properties of such polypeptide nanostructures in comparison to native protein folds are discussed. Reasons for the apparent absence of such folds in nature are also examined. Physicochemical versatility of amino acid residues and cost-effective production makes polypeptides an attractive platform for designed functional bionanomaterials. © 2014 Wiley Periodicals, Inc.

  16. Molecular cloning, overexpression, purification, and sequence analysis of the giant panda (Ailuropoda melanoleuca) ferritin light polypeptide.

    PubMed

    Fu, L; Hou, Y L; Ding, X; Du, Y J; Zhu, H Q; Zhang, N; Hou, W R

    2016-08-30

    The complementary DNA (cDNA) of the giant panda (Ailuropoda melanoleuca) ferritin light polypeptide (FTL) gene was successfully cloned using reverse transcription-polymerase chain reaction technology. We constructed a recombinant expression vector containing FTL cDNA and overexpressed it in Escherichia coli using pET28a plasmids. The expressed protein was then purified by nickel chelate affinity chromatography. The cloned cDNA fragment was 580 bp long and contained an open reading frame of 525 bp. The deduced protein sequence was composed of 175 amino acids and had an estimated molecular weight of 19.90 kDa, with an isoelectric point of 5.53. Topology prediction revealed one N-glycosylation site, two casein kinase II phosphorylation sites, one N-myristoylation site, two protein kinase C phosphorylation sites, and one cell attachment sequence. Alignment indicated that the nucleotide and deduced amino acid sequences are highly conserved across several mammals, including Homo sapiens, Cavia porcellus, Equus caballus, and Felis catus, among others. The FTL gene was readily expressed in E. coli, which gave rise to the accumulation of a polypeptide of the expected size (25.50 kDa, including an N-terminal polyhistidine tag).

  17. Polypeptides and polyaminoacids in drug delivery.

    PubMed

    González-Aramundiz, José Vicente; Lozano, María Victoria; Sousa-Herves, Ana; Fernandez-Megia, Eduardo; Csaba, Noemi

    2012-02-01

    Advances achieved over the last few years in drug delivery have provided novel and versatile possibilities for the treatment of various diseases. Among the biomaterials applied in this field, it is worth highlighting the increasing importance of polyaminoacids and polypeptides. The appealing properties of these polymers are very promising for the design of novel compositions in a variety of drug delivery applications. This review provides an overview on the general characteristics of polyaminoacids and polypeptides and briefly discusses different synthetic pathways for their production. This is followed by a detailed description of different drug delivery applications of these polymers, emphasizing those examples that already reached advanced preclinical development or have entered clinical trials. Polyaminoacids and polypeptides are gaining much attention in drug delivery due to their exceptional properties. Their application as polymers for drug delivery purposes has been sped up by the significant achievements related to their synthesis. Certainly, cancer therapy has benefited the most from these advances, although other fields such as vaccine delivery and alternative administration routes are also being successfully explored. The design of new entities based on polyaminoacids and polypeptides and the improved insight gained in drug delivery guarantee exciting findings in the near future.

  18. Polypeptide Inhibitors of Mineral Scaling and Corrosion

    DTIC Science & Technology

    1990-06-30

    and the method of synthesis are subjects of patent applications. Corrosion inhibition has been demonstrated using polyaspartate , the simplest...observed that polyaspartate caused an upward shift in the open circuit potential (Ecorr), suggesting some anodic control of corrosion. However, Tafel...the presence of polypeptides are In progress. Examination of thermal polyaspartate effects on polarization resistance corrosion of 304 stainless

  19. The mining of toxin-like polypeptides from EST database by single residue distribution analysis.

    PubMed

    Kozlov, Sergey; Grishin, Eugene

    2011-01-31

    Novel high throughput sequencing technologies require permanent development of bioinformatics data processing methods. Among them, rapid and reliable identification of encoded proteins plays a pivotal role. To search for particular protein families, the amino acid sequence motifs suitable for selective screening of nucleotide sequence databases may be used. In this work, we suggest a novel method for simplified representation of protein amino acid sequences named Single Residue Distribution Analysis, which is applicable both for homology search and database screening. Using the procedure developed, a search for amino acid sequence motifs in sea anemone polypeptides was performed, and 14 different motifs with broad and low specificity were discriminated. The adequacy of motifs for mining toxin-like sequences was confirmed by their ability to identify 100% toxin-like anemone polypeptides in the reference polypeptide database. The employment of novel motifs for the search of polypeptide toxins in Anemonia viridis EST dataset allowed us to identify 89 putative toxin precursors. The translated and modified ESTs were scanned using a special algorithm. In addition to direct comparison with the motifs developed, the putative signal peptides were predicted and homology with known structures was examined. The suggested method may be used to retrieve structures of interest from the EST databases using simple amino acid sequence motifs as templates. The efficiency of the procedure for directed search of polypeptides is higher than that of most currently used methods. Analysis of 39939 ESTs of sea anemone Anemonia viridis resulted in identification of five protein precursors of earlier described toxins, discovery of 43 novel polypeptide toxins, and prediction of 39 putative polypeptide toxin sequences. In addition, two precursors of novel peptides presumably displaying neuronal function were disclosed.

  20. The mining of toxin-like polypeptides from EST database by single residue distribution analysis

    PubMed Central

    2011-01-01

    Background Novel high throughput sequencing technologies require permanent development of bioinformatics data processing methods. Among them, rapid and reliable identification of encoded proteins plays a pivotal role. To search for particular protein families, the amino acid sequence motifs suitable for selective screening of nucleotide sequence databases may be used. In this work, we suggest a novel method for simplified representation of protein amino acid sequences named Single Residue Distribution Analysis, which is applicable both for homology search and database screening. Results Using the procedure developed, a search for amino acid sequence motifs in sea anemone polypeptides was performed, and 14 different motifs with broad and low specificity were discriminated. The adequacy of motifs for mining toxin-like sequences was confirmed by their ability to identify 100% toxin-like anemone polypeptides in the reference polypeptide database. The employment of novel motifs for the search of polypeptide toxins in Anemonia viridis EST dataset allowed us to identify 89 putative toxin precursors. The translated and modified ESTs were scanned using a special algorithm. In addition to direct comparison with the motifs developed, the putative signal peptides were predicted and homology with known structures was examined. Conclusions The suggested method may be used to retrieve structures of interest from the EST databases using simple amino acid sequence motifs as templates. The efficiency of the procedure for directed search of polypeptides is higher than that of most currently used methods. Analysis of 39939 ESTs of sea anemone Anemonia viridis resulted in identification of five protein precursors of earlier described toxins, discovery of 43 novel polypeptide toxins, and prediction of 39 putative polypeptide toxin sequences. In addition, two precursors of novel peptides presumably displaying neuronal function were disclosed. PMID:21281459

  1. Deducing Reaction Mechanism: A Guide for Students, Researchers, and Instructors

    ERIC Educational Resources Information Center

    Meek, Simon J.; Pitman, Catherine L.; Miller, Alexander J. M.

    2016-01-01

    An introductory guide to deducing the mechanism of chemical reactions is presented. Following a typical workflow for probing reaction mechanism, the guide introduces a wide range of kinetic and mechanistic tools. In addition to serving as a broad introduction to mechanistic analysis for students and researchers, the guide has also been used by…

  2. Deducing Reaction Mechanism: A Guide for Students, Researchers, and Instructors

    ERIC Educational Resources Information Center

    Meek, Simon J.; Pitman, Catherine L.; Miller, Alexander J. M.

    2016-01-01

    An introductory guide to deducing the mechanism of chemical reactions is presented. Following a typical workflow for probing reaction mechanism, the guide introduces a wide range of kinetic and mechanistic tools. In addition to serving as a broad introduction to mechanistic analysis for students and researchers, the guide has also been used by…

  3. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    DOEpatents

    Liu, Ye; Harris, Paul; Tang, Lan; Wu, Wenping

    2013-11-19

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  4. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    DOEpatents

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2010-06-22

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  5. Polypeptide from a cellulolytic fungus having cellulolytic enhancing activity

    DOEpatents

    Brown, Kimberly [Elk Grove, CA; Harris, Paul [Carnation, WA; Zaretsky, Elizabeth [Reno, NV; Re, Edward [Davis, CA; Vlasenko, Elena [Davis, CA; McFarland, Keith [Davis, CA; Lopez de Leon, Alfredo [Davis, CA

    2008-04-22

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  6. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    Maiyuran, Suchindra; Kramer, Randall; Harris, Paul

    2013-10-29

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  7. Polypeptides having beta-glucosidase activity and polynucleotides encoding same

    DOEpatents

    Harris, Paul; Golightly, Elizabeth

    2007-07-17

    The present invention relates to isolated polypeptides having beta-glucosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  8. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    DOEpatents

    Liu, Ye; Tang, Lan; Harris, Paul; Wu, Wenping

    2012-10-02

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  9. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    DOEpatents

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2012-10-16

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  10. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    DOEpatents

    Morant, Marc D.; Harris, Paul

    2015-10-13

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  11. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    Maiyuran, Suchindra; Kramer, Randall; Harris, Paul

    2014-10-21

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  12. Polypeptides having beta-glucosidase activity and polynucleotides encoding same

    DOEpatents

    Morant, Marc

    2014-01-14

    The present invention relates to isolated polypeptides having beta-glucosidase activity, beta-xylosidase, or beta-glucosidase activity and isolated polynucleotides encoding polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  13. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    SciTech Connect

    Lopez de Leon, Alfredo; Ding, Hanshu; Brown, Kimberly

    2012-06-26

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  14. Polypeptides having endoglucanase activity and polynucleotides encoding same

    SciTech Connect

    Lopez de Leon, Alfredo; Rey, Michael

    2015-03-10

    The present invention relates to isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  15. Polypeptides having endoglucanase activity and polynucleotides encoding same

    DOEpatents

    Lopez de Leon, Alfredo; Rey, Michael

    2010-06-22

    The present invention relates to isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  16. Polypeptides having xylanase activity and polynucleotides encoding same

    DOEpatents

    Lopez de Leon, Alfredo; Rey, Michael

    2015-01-27

    The present invention relates to isolated polypeptides having xylanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  17. Polypeptides having endoglucanase activity and polynucleotides encoding same

    DOEpatents

    Lopez de Leon, Alfredo; Rey, Michael

    2012-09-18

    The present invention relates to isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  18. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    SciTech Connect

    Schnorr, Kirk; Kramer, Randall

    2016-04-05

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  19. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    Schnorr, Kirk; Kramer, Randall

    2016-08-09

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  20. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    DOEpatents

    Brown, Kimberly; Harris, Paul; Lopez De Leon, Alfredo; Merino, Sandra

    2007-05-22

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  1. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    SciTech Connect

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2016-08-09

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  2. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    SciTech Connect

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2014-09-30

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  3. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    Schnorr, Kirk; Kramer, Randall

    2017-08-08

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  4. Polypeptides having endoglucanase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2016-02-23

    The present invention relates to isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  5. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    DOEpatents

    Stringer, Mary Ann; McBrayer, Brett

    2016-11-29

    The present invention relates to isolated polypeptides having cellobiohydrolase activity, catalytic domains, and cellulose binding domains and polynucleotides encoding the polypeptides, catalytic domains, and cellulose binding domains. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides, catalytic domains, or cellulose binding domains.

  6. Polypeptides having endoglucanase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj; Shagasi, Tarana

    2015-06-30

    The present invention relates to isolated polypeptides having endoglucanase activity, catalytic domains, cellulose binding domains and polynucleotides encoding the polypeptides, catalytic domains or cellulose binding domains. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides, catalytic domains or cellulose binding domains.

  7. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    Tang, Lan; Liu, Ye; Duan, Junxin; Zhang, Yu; Jorgensen, Christian Isak; Kramer, Randall

    2013-04-16

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  8. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    Duan, Junxin; Tang, Lan; Liu, Ye; Wu, Wenping; Quinlan, Jason; Kramer, Randall

    2013-06-18

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  9. Polypeptides having endoglucanase activity and polynucleotides encoding same

    DOEpatents

    Lopez de Leon, Alfredo; Rey, Michael

    2013-06-18

    The present invention relates to isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  10. Polypeptides having xylanase activity and polynucleotides encoding same

    SciTech Connect

    Tang, Lan; Liu, Ye; Duan, Junxin; Hanshu, Ding

    2012-10-30

    The present invention relates to isolated polypeptides having xylanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  11. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    SciTech Connect

    Zhang, Yu; Duan, Junxin; Tang, Lan; Wu, Wenping

    2016-06-14

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  12. Polypeptides having xylanase activity and polynucleotides encoding same

    SciTech Connect

    Lopez de Leon, Alfredo; Rey, Michael

    2016-05-31

    The present invention relates to isolated polypeptides having xylanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  13. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    Zhang, Yu; Duan, Junxin; Tang, Lan; Wu, Wenping

    2016-11-22

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  14. Chimeric polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    Wogulis, Mark; Sweeney, Matthew; Heu, Tia

    2017-06-14

    The present invention relates to chimeric GH61 polypeptides having cellulolytic enhancing activity. The present invention also relates to polynucleotides encoding the chimeric GH61 polypeptides; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the chimeric GH61 polypeptides.

  15. Polypeptides having endoglucanase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj; Shagasi, Tarana

    2017-05-30

    The present invention relates to isolated polypeptides having endoglucanase activity, catalytic domains, cellulose binding domains and polynucleotides encoding the polypeptides, catalytic domains or cellulose binding domains. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides, catalytic domains or cellulose binding domains.

  16. Polypeptides having beta-xylosidase activity and polynucleotides encoding same

    DOEpatents

    Zhang, Yu; Liu, Ye; Duan, Junxin; Tang, Lan; McBrayer, Brett

    2017-07-04

    The present invention relates to isolated polypeptides having beta-xylosidase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  17. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    SciTech Connect

    Tang, Lan; Liu, Ye; Duan, Junxin; Zhang, Yu; Joergensen, Christian; Kramer, Randall

    2016-11-29

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  18. Polypeptides having xylanase activity and polynucleotides encoding the same

    DOEpatents

    Spodsberg, Nikolaj [Bagsvaed, DK

    2014-01-07

    The present invention relates to isolated polypeptides having xylanase activity and isolated polynucleotides encoding the polypeptides. The inventino also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  19. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding the same

    DOEpatents

    Tang, Lan; Liu, Ye; Duan, Junxin; Zhang, Yu; Jorgensen, Christian Isak; Kramer, Randall

    2013-12-24

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  20. Polypeptides having xylanase activity and polynucleotides encoding same

    DOEpatents

    Tang, Lan; Liu, Ye; Duan, Junxin; Ding, Hanshu

    2013-04-30

    The present invention relates to isolated polypeptides having xylanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  1. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    Dotson, William D.; Greenier, Jennifer; Ding, Hanshu

    2009-05-19

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated nucleic acids encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the nucleic acids as well as methods for producing and using the polypeptides.

  2. Polypeptides having endoglucanase activity and polynucleotides encoding same

    DOEpatents

    Harris, Paul; Lopez de Leon, Alfredo; Rey, Michael; Ding, Hanshu; Vlasenko, Elena

    2010-11-02

    The present invention relates to isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  3. Polynucleotides encoding polypeptides having beta-glucosidase activity

    DOEpatents

    Harris, Paul; Golightly, Elizabeth

    2010-03-02

    The present invention relates to isolated polypeptides having beta-glucosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  4. Polypeptides having beta-glucosidase activity and polynucleotides encoding same

    DOEpatents

    Harris, Paul; Golightly, Elizabeth

    2011-06-14

    The present invention relates to isolated polypeptides having beta-glucosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  5. Polypeptides having xylanase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2014-10-21

    The present invention relates to isolated polypeptides having xylanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  6. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding the same

    DOEpatents

    Duan, Junxin; Schnorr, Kirk Matthew; Wu, Wenping

    2013-11-19

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  7. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    SciTech Connect

    Duan, Junxin; Liu, Ye; Tang, Lan; Wu, Wenping; Quinlan, Jason; Kramer, Randall

    2012-03-27

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  8. Polypeptides having beta-glucosidase activity and polynucleotides encoding same

    SciTech Connect

    Morant, Marc D; Patkar, Shamkant; Ding, Hanshu

    2013-11-12

    The present invention relates to isolated polypeptides having beta-glucosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  9. Polypeptides having beta-glucosidase activity and polynucleotides encoding same

    SciTech Connect

    Morant, Marc Dominique

    2014-10-14

    The present invention relates to isolated polypeptides having beta-glucosidase activity, beta-xylosidase activity, or beta-glucosidase and beta-xylosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  10. Polypeptides having beta-glucosidase activity and polynucleotides encoding same

    SciTech Connect

    Harris, Paul; Golightly, Elizabeth

    2012-11-27

    The present invention relates to isolated polypeptides having beta-glucosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  11. Polypeptides having xylanase activity and polynucleotides encoding same

    DOEpatents

    Lopez de Leon, Alfredo; Rey, Michael

    2010-12-14

    The present invention relates to isolated polypeptides having xylanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  12. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    Dotson, William D.; Greenier, Jennifer; Ding, Hanshu

    2007-09-18

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated nucleic acids encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the nucleic acids as well as methods for producing and using the polypeptides.

  13. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    Lopez de Leon, Alfredo; Ding, Hanshu; Brown, Kimberly

    2011-10-25

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  14. Polypeptides having endoglucanase activity and polynucleotides encoding same

    DOEpatents

    Harris, Paul [Carnation, WA; Lopez de Leon, Alfredo [Davis, CA; Rey, Micheal [Davis, CA; Ding, Hanshu [Davis, CA; Vlasenko, Elena [Davis, CA

    2012-02-21

    The present invention relates to isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  15. Membrane Permeation Induced by Aggregates of Human Islet Amyloid Polypeptides

    PubMed Central

    Poojari, Chetan; Xiao, Dequan; Batista, Victor S.; Strodel, Birgit

    2013-01-01

    Several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases as well as nonneuropathic diseases such as type II diabetes and atrial amyloidosis are associated with aggregation of amyloid polypeptides into fibrillar structures, or plaques. In this study, we use molecular dynamics simulations to test the stability and orientation of membrane-embedded aggregates of the human islet amyloid polypeptide (hIAPP) implicated in type II diabetes. We find that in both monolayers and bilayers of dipalmitoylphosphatidylglycerol (DPPG) hIAPP trimers and tetramers remain inside the membranes and preserve their β-sheet secondary structure. Lipid bilayer-inserted hIAPP trimers and tetramers orient inside DPPG at 60° relative to the membrane/water interface and lead to water permeation and Na+ intrusion, consistent with ion-toxicity in islet β-cells. In particular, hIAPP trimers form a water-filled β-sandwich that induce water permeability comparable with channel-forming proteins, such as aquaporins and gramicidin-A. The predicted disruptive orientation is consistent with the amphiphilic properties of the hIAPP aggregates and could be probed by chiral sum frequency generation (SFG) spectroscopy, as predicted by the simulated SFG spectra. PMID:24268144

  16. POLYPEPTIDE AND POLYSACCHARIDE PROCESSING IN HYPERTHERMOPHILIC MICROORGANISMS

    SciTech Connect

    KELLY, ROBERT M.

    2008-12-22

    This project focused on the microbial physiology and biochemistry of heterotrophic hyperthermophiles with respect to mechanisms by which these organisms process polypeptides and polysaccharides under normal and stressed conditions. Emphasis is on two model organisms, for which completed genome sequences are available: Pyrococcus furiosus (growth Topt of 98°C), an archaeon, and Thermotoga maritima (growth Topt of 80°C), a bacterium. Both organisms are obligately anaerobic heterotrophs that reduce sulfur facultatively. Whole genome cDNA spotted microarrays were used to follow transcriptional response to a variety of environmental conditions in order to identify genes encoding proteins involved in the acquisition, synthesis, processing and utilization of polypeptides and polysaccharides. This project provided new insights into the physiological aspects of hyperthermophiles as these relate to microbial biochemistry and biological function in high temperature habitats. The capacity of these microorganisms to produce biohydrogen from renewable feedstocks makes them important for future efforts to develop biofuels.

  17. Surface-grafted polypeptides on flat substrates

    NASA Astrophysics Data System (ADS)

    Wang, Yuli

    In this work, we improved the vapor deposition-polymerization (VDP) technique by re-designing a new vacuum chamber, and adding two heating plates to control the temperatures of the substrate and monomer evaporation. By optimizing the reaction parameters such as monomer amount, substrate temperature and reaction time, various polypeptides with sufficiently high molecular weight have been successfully grafted onto the solid substrates. The combination of VPD with photolithography has fabricated micro-patterned polypeptides, with geometry patternable in both lateral and vertical directions. Next, the conformations of the surface-grafted polypeptides were systematically examined. New ways have been found to switch their conformations between alpha-helix and beta-sheet, or between right-handed helix and left-handed helix. Two important ionic polypeptides, poly(L-glutamic acid) (PLGA) and poly(L-lysine) (PLL) were the focuses of this work. The conformational transitions of surface-grafted PLGA and PLL were successfully induced by pH, surfactants and ions. In addition, a surface-grafted PLGA-block-PLL copolypeptide was studied. Their unexpected pH-responsiveness was explained by the beta-sheet formation between the PLGA and PLL blocks. The orientation of the surface-grafted alpha-helical poly(gamma-benzyl L-glutamate) (PBLG) was greatly improved by a novel "solvent quenching" method, which involves treating the film sequentially with a good solvent and a poor solvent. The average tilt angle of the PBLG rods changed from 49° to 3° by applying this "quenching". Finally, a surface-grafted PLL film was used as the template to mimic the biosilicification. Silica was spontaneously synthesized from tetraethoxysilane inside the PLL film at room temperature and at neutral pH.

  18. Polypeptide multilayer nanofilm artificial red blood cells.

    PubMed

    Palath, Naveen; Bhad, Sujaykumar; Montazeri, Reza; Guidry, Christopher A; Haynie, Donald T

    2007-04-01

    Reliable encapsulation of hemoglobin (Hb) within polypeptide multilayer nanofilms has been achieved by a template-based approach, and protein functionality has been demonstrated postencapsulation. The method is general in scope and could be useful for many other encapsulants. Met-Hb was adsorbed onto 5 microm-diameter CaCO3 microparticles, and the Hb-coated particles were encapsulated within a multilayer nanofilm of poly(L-glutamic acid) (PLGA) and poly(L-lysine) (PLL) by layer-by-layer assembly. The CaCO3 templates were then dissolved within the PLGA/PLL nanofilms by addition of ethylenediaminetetraacetic acid. Encapsulation of Hb was proved by fluorescence microscopy, the pH-dependence of retention of Hb was determined by visible wavelength absorbance, and conversion of the encapsulated met-Hb to deoxy-Hb and oxy-Hb was demonstrated by spectroscopic analysis of the Soret absorption peak under various conditions. It thus has been shown that control of Hb oxygenation within polypeptide multilayer nanofilm artificial cells is possible, and that Hb thus encapsulated can bind, release, and subsequently rebind molecular oxygen. This work therefore represents an advance in the development of polypeptide multilayer film artificial red blood cells. (c) 2006 Wiley Periodicals, Inc.

  19. Heterogeneity of Glutamine Synthetase Polypeptides in Phaseolus vulgaris L. 1

    PubMed Central

    Lara, Miguel; Porta, Helena; Padilla, Jaime; Folch, Jorge; Sánchez, Federico

    1984-01-01

    Glutamine synthetases from roots, nodules, and leaves of Phaseolus vulgaris L. have been purified to homogeneity and their polypeptide composition determined. The leaf enzyme is composed of six polypeptides. The cytosolic fraction contains two 43,000 dalton polypeptides and the chloroplastic enzyme is formed by four 45,000 dalton polypeptides. Root glutamine synthetase consists only of the same two polypeptides of 43,000 dalton that are present in the leaf enzyme. The nodule enzyme is formed by two polypeptides of 43,000 dalton, one is common to the leaf and root enzyme but the other is specific for N2-fixing nodule tissue. The two glutamine synthetase forms of the nodule contain a different proportion of the 43,000 dalton polypeptides. Images Fig. 1 Fig. 2 Fig. 4 PMID:16663942

  20. Different polypeptide composition of two human rotavirus types.

    PubMed Central

    Espejo, R; Martínez, E; López, S; Muñoz, O

    1980-01-01

    Human rotaviruses, which are placed into two groups according to their ribonucleic acid patterns obtained by gel electrophoresis, were characterized both by polypeptide components from purified virions and by polypeptides translated from their denatured ribonucleic acids in rabbit reticulocyte lysates. Viruses assigned to different groups differed in the electrophoretic migration of the second largest of the polypeptides which compose the inner shell; polypeptides that had been synthetized in vitro from ribonucleic acid from each group showed this same difference, thus indicating that this is due to the genomic composition. This study suggests that there are differences in the third largest polypeptide of the inner shell and also in the three smaller polypeptides composing the outer shell. We also demonstrated that there are differences in genomic and polypeptide compositions between simian (SA11) and calf (Nebraska calf diarrhea virus) rotaviruses grown in tissue culture and human rotaviruses. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:6247284

  1. Redox-responsive, reversibly-crosslinked thiolated cationic helical polypeptides for efficient siRNA encapsulation and delivery.

    PubMed

    Zheng, Nan; Song, Ziyuan; Liu, Yang; Zhang, Rujing; Zhang, Ruoyan; Yao, Catherine; Uckun, Fatih M; Yin, Lichen; Cheng, Jianjun

    2015-05-10

    Cationic helical polypeptides, although highly efficient for inducing membrane penetration, cannot stably condense siRNA molecules via electrostatic interactions, which greatly limit the gene knockdown efficiency. By developing and crosslinking the thiolated polypeptide via formation of disulfide bonds post formation of the polypeptide/siRNA complexes, we were able to obtain stable complexes without compromising the helical secondary structure as well as the membrane activity of the polypeptide. As such, the stable polypeptide/siRNA complex was able to notably protect the siRNA cargo from nuclease digestion in the extracellular environment, while the functions of the polypeptide/siRNA complex for effective cellular internalization and endosomal escape are still largely preserved. Because the disulfide is susceptible to cleavage in response to intracellular redox triggers, siRNA release from the complex is expected upon redox triggering by glutathione (GSH) intracellularly and was actually observed upon redox triggers mediated by glutathione (GSH). With the collective contribution of the potent membrane activity and redox-responsive cargo release profiles, the crosslinked complexes enable efficient gene silencing without appreciable cytotoxicity, thus providing a potential strategy for polypeptide-based intracellular siRNA delivery. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Inhibition of the oxygen-evolving complex of photosystem II and depletion of extrinsic polypeptides by nickel.

    PubMed

    Boisvert, Steve; Joly, David; Leclerc, Sébastien; Govindachary, Sridharan; Harnois, Johanne; Carpentier, Robert

    2007-12-01

    The toxic effect of Ni(2+) on photosynthetic electron transport was studied in a photosystem II submembrane fraction. It was shown that Ni(2+) strongly inhibits oxygen evolution in the millimolar range of concentration. The inhibition was insensitive to NaCl but significantly decreased in the presence of CaCl(2). Maximal chlorophyll fluorescence, together with variable fluorescence, maximal quantum yield of photosystem II, and flash-induced fluorescence decays were all significantly declined by Ni(2+). Further, the extrinsic polypeptides of 16 and 24 kDa associated with the oxygen-evolving complex of photosystem II were depleted following Ni(2+) treatment. It was deduced that interaction of Ni(2+) with these polypeptides caused a conformational change that induced their release together with Ca(2+) from the oxygen-evolving complex of photosystem II with consequent inhibition of the electron transport activity.

  3. Competition between surface adsorption and folding of fibril-forming polypeptides

    NASA Astrophysics Data System (ADS)

    Ni, Ran; Kleijn, J. Mieke; Abeln, Sanne; Cohen Stuart, Martien A.; Bolhuis, Peter G.

    2015-02-01

    Self-assembly of polypeptides into fibrillar structures can be initiated by planar surfaces that interact favorably with certain residues. Using a coarse-grained model, we systematically studied the folding and adsorption behavior of a β -roll forming polypeptide. We find that there are two different folding pathways depending on the temperature: (i) at low temperature, the polypeptide folds in solution into a β -roll before adsorbing onto the attractive surface; (ii) at higher temperature, the polypeptide first adsorbs in a disordered state and folds while on the surface. The folding temperature increases with increasing attraction as the folded β -roll is stabilized by the surface. Surprisingly, further increasing the attraction lowers the folding temperature again, as strong attraction also stabilizes the adsorbed disordered state, which competes with folding of the polypeptide. Our results suggest that to enhance the folding, one should use a weakly attractive surface. They also explain the recent experimental observation of the nonmonotonic effect of charge on the fibril formation on an oppositely charged surface [C. Charbonneau et al., ACS Nano 8, 2328 (2014), 10.1021/nn405799t].

  4. General Constraints on Cross Sections Deduced from Surrogate Reactions

    SciTech Connect

    Younes, W

    2003-08-14

    Cross sections that cannot be measured in the laboratory, e.g. because the target lifetime is too short, can be inferred indirectly from a different reaction forming the same compound system, but with a more accessible beam/target combination (the ''surrogate-reaction'' technique). The reactions share the same compound system and a common decay mechanism, but they involve different formation processes. Therefore, an implicit constraint is imposed on the inferred cross section deduced from the measured surrogate-reaction data, through the common decay mechanism. In this paper, the mathematical consequences of this implicit constraint are investigated. General formulas are derived from upper and lower bounds on the inferred cross section, estimated from surrogate data in a procedure which does not require any modeling of the common decay process. As an example, the formulas developed here are applied to the case of the {sup 235}U(n,f) cross section, deduced from {sup 234}U(t,pf) surrogate data. The calculated bounds are not very tight in this particular case. However, by introducing a few qualitative assumptions about the physics of the fission process, meaningful bounds on the deduced cross section are obtained. Upper and lower limits for the cross-section ratio of the (n,f) reaction on the {sup 235}U isomer at E{sub x} = 77 eV relative to the (n,f) reaction on the ground state are also calculated. The generalization of this technique to other surrogate reactions is discussed.

  5. mim3 and nam3 omnipotent suppressor genes similarly affect the polypeptide composition of yeast mitoribosomes.

    PubMed

    Mieszczak, M; Zagórski, W

    1987-05-01

    Yeast informational suppressors of mit- mutations coded for by nuclear (nam3-1, nam3-2) or by mitochondrial DNA (mim3-1) affect the mitoribosome. Nuclear mutations result in the appearance of an additional polypeptide called SI in the small mitoribosomal subunit. An identical polypeptide, not detected in the wild type 37S subunit, is present in crude preparations of mitoribosomes isolated from a mim3-1 suppressor carrying strain. Traces of the SI polypeptide may be found in highly purified small subunits from the mim3-1 strain. Therefore, mutations affecting either mitochondrial rRNA (mim3-1) or mitochondrial r-proteins (nam3-1, nam3-2) could be followed by similar changes in overall mitoribosome structure. This may explain the functional similarity of nuclear and mitochondrially coded suppressors.

  6. Characterization of dopuin, a polypeptide with special residue distributions.

    PubMed

    Chen, Z W; Bergman, T; Ostenson, C G; Efendic, S; Mutt, V; Jörnvall, H

    1997-10-15

    A 62-residue polypeptide, dopuin, has been isolated from pig small intestine. It is distinguished by an N-terminal part with a high content of proline (7 in a 26-residue segment), a C-terminal part with a high proportion of histidine (3 in a 9-residue segment), and six half-cystine residues in three intrachain disulphide bridges (connecting positions 22-25, 23-54 and 35-44). The Cys and Pro distributions suggest a tight and special conformation. In contrast to PEC-60 and somatostatin, it has no established inhibitory effect on insulin secretion. At 10 nM concentration, a weak inhibitory tendency is less than half of that of the other two peptides. Like gastrointestinal trefoil peptides, dopuin has three disulphide bridges, Ala-Pro segments, and many charged residues, but they are differently distributed and dopuin belongs to a separate, apparently novel family. However, dopuin is similar to a peptide corresponding to an expressed-sequence-tag cDNA of human fetal liver and spleen, establishing the nature of the mature form of the product of this cDNA, and showing a general tissue, age, and species distribution of this peptide. A truncated form of vimentin, composed of its C-terminal 37 residues, vimentin-C37, was also purified and structurally characterized. These two peptides increase the complexity of known intestinal polypeptides and at least dopuin has properties compatible with specific biofunctions.

  7. Vibrational neutron spectroscopy of collagen and model polypeptides.

    PubMed Central

    Middendorf, H D; Hayward, R L; Parker, S F; Bradshaw, J; Miller, A

    1995-01-01

    A pulsed source neutron spectrometer has been used to measure vibrational spectra (20-4000 cm-1) of dry and hydrated type I collagen fibers, and of two model polypeptides, polyproline II and (prolyl-prolyl-glycine)10, at temperatures of 30 and 120 K. the collagen spectra provide the first high resolution neutron views of the proton-dominated modes of a protein over a wide energy range from the low frequency phonon region to the rich spectrum of localized high frequency modes. Several bands show a level of fine structure approaching that of optical data. The principal features of the spectra are assigned. A difference spectrum is obtained for protein associated water, which displays an acoustic peak similar to pure ice and a librational band shifted to lower frequency by the influence of the protein. Hydrogen-weighted densities of states are extracted for collagen and the model polypeptides, and compared with published calculations. Proton mean-square displacements are calculated from Debye-Waller factors measured in parallel quasi-elastic neutron-scattering experiments. Combined with the collagen density of states function, these yield an effective mass of 14.5 a.m.u. for the low frequency harmonic oscillators, indicating that the extended atom approximation, which simplifies analyses of low frequency protein dynamics, is appropriate. PMID:8527680

  8. Mechanically Controlled Electron Transfer in a Single-Polypeptide Transistor

    PubMed Central

    Sheu, Sheh-Yi; Yang, Dah-Yen

    2017-01-01

    Proteins are of interest in nano-bio electronic devices due to their versatile structures, exquisite functionality and specificity. However, quantum transport measurements produce conflicting results due to technical limitations whereby it is difficult to precisely determine molecular orientation, the nature of the moieties, the presence of the surroundings and the temperature; in such circumstances a better understanding of the protein electron transfer (ET) pathway and the mechanism remains a considerable challenge. Here, we report an approach to mechanically drive polypeptide flip-flop motion to achieve a logic gate with ON and OFF states during protein ET. We have calculated the transmission spectra of the peptide-based molecular junctions and observed the hallmarks of electrical current and conductance. The results indicate that peptide ET follows an NC asymmetric process and depends on the amino acid chirality and α-helical handedness. Electron transmission decreases as the number of water molecules increases, and the ET efficiency and its pathway depend on the type of water-bridged H-bonds. Our results provide a rational mechanism for peptide ET and new perspectives on polypeptides as potential candidates in logic nano devices. PMID:28051140

  9. Mechanically Controlled Electron Transfer in a Single-Polypeptide Transistor

    NASA Astrophysics Data System (ADS)

    Sheu, Sheh-Yi; Yang, Dah-Yen

    2017-01-01

    Proteins are of interest in nano-bio electronic devices due to their versatile structures, exquisite functionality and specificity. However, quantum transport measurements produce conflicting results due to technical limitations whereby it is difficult to precisely determine molecular orientation, the nature of the moieties, the presence of the surroundings and the temperature; in such circumstances a better understanding of the protein electron transfer (ET) pathway and the mechanism remains a considerable challenge. Here, we report an approach to mechanically drive polypeptide flip-flop motion to achieve a logic gate with ON and OFF states during protein ET. We have calculated the transmission spectra of the peptide-based molecular junctions and observed the hallmarks of electrical current and conductance. The results indicate that peptide ET follows an NC asymmetric process and depends on the amino acid chirality and α-helical handedness. Electron transmission decreases as the number of water molecules increases, and the ET efficiency and its pathway depend on the type of water-bridged H-bonds. Our results provide a rational mechanism for peptide ET and new perspectives on polypeptides as potential candidates in logic nano devices.

  10. The DEDUCE Guided Query Tool: Providing Simplified Access to Clinical Data for Research and Quality Improvement

    PubMed Central

    Horvath, Monica M.; Winfield, Stephanie; Evans, Steve; Slopek, Steve; Shang, Howard; Ferranti, Jeffrey

    2011-01-01

    In many healthcare organizations, comparative effectiveness research and quality improvement (QI) investigations are hampered by a lack of access to data created as a byproduct of patient care. Data collection often hinges upon either manual chart review or ad hoc requests to technical experts who support legacy clinical systems. In order to facilitate this needed capacity for data exploration at our institution (Duke University Health System), we have designed and deployed a robust Web application for cohort identification and data extraction—the Duke Enterprise Data Unified Content Explorer (DEDUCE). DEDUCE is envisioned as a simple, web-based environment that allows investigators access to administrative, financial, and clinical information generated during patient care. By using business intelligence tools to create a view into Duke Medicine's enterprise data warehouse, DEDUCE provides a guided query functionality using a wizard-like interface that lets users filter through millions of clinical records, explore aggregate reports, and, export extracts. Researchers and QI specialists can obtain detailed patient- and observation-level extracts without needing to understand structured query language or the underlying database model. Developers designing such tools must devote sufficient training and develop application safeguards to ensure that patient-centered clinical researchers understand when observation-level extracts should be used. This may mitigate the risk of data being misunderstood and consequently used in an improper fashion. PMID:21130181

  11. The DEDUCE Guided Query tool: providing simplified access to clinical data for research and quality improvement.

    PubMed

    Horvath, Monica M; Winfield, Stephanie; Evans, Steve; Slopek, Steve; Shang, Howard; Ferranti, Jeffrey

    2011-04-01

    In many healthcare organizations, comparative effectiveness research and quality improvement (QI) investigations are hampered by a lack of access to data created as a byproduct of patient care. Data collection often hinges upon either manual chart review or ad hoc requests to technical experts who support legacy clinical systems. In order to facilitate this needed capacity for data exploration at our institution (Duke University Health System), we have designed and deployed a robust Web application for cohort identification and data extraction--the Duke Enterprise Data Unified Content Explorer (DEDUCE). DEDUCE is envisioned as a simple, web-based environment that allows investigators access to administrative, financial, and clinical information generated during patient care. By using business intelligence tools to create a view into Duke Medicine's enterprise data warehouse, DEDUCE provides a Guided Query functionality using a wizard-like interface that lets users filter through millions of clinical records, explore aggregate reports, and, export extracts. Researchers and QI specialists can obtain detailed patient- and observation-level extracts without needing to understand structured query language or the underlying database model. Developers designing such tools must devote sufficient training and develop application safeguards to ensure that patient-centered clinical researchers understand when observation-level extracts should be used. This may mitigate the risk of data being misunderstood and consequently used in an improper fashion.

  12. Expansin polynucleotides, related polypeptides and methods of use

    DOEpatents

    Cosgrove, Daniel J.; Wu, Yajun

    2006-02-21

    The present invention relates to beta expansin polypeptides, nucleotide sequences encoding the same and regulatory elements and their use in altering cell wall structure in plants. Nucleic acid constructs comprising a beta expansin sequence operably linked to a promoter, or other regulatory sequence are disclosed as well as vectors, plant cells, plants, and transformed seeds containing such constructs are provided. Methods for the use of such constructs in repressing or inducing expression of a beta expansin sequences in a plant are also provided as well as methods for harvesting transgenic expansin proteins. In addition, methods are provided for inhibiting or improving cell wall structure in plants by repression or induction of expansin sequences in plants.

  13. Changes in vasoactive intestinal peptide, pituitary adenylate cyclase-activating polypeptide and neuropeptide Y-ergic structures of the enteric nervous system in the carcinoma of the human large intestine.

    PubMed

    Godlewski, Janusz; Łakomy, Ireneusz Mirosław

    2010-01-01

    This investigation was aimed at immunohistochemical analysis of potential changes in the enteric nervous system caused by cancer of the large intestine. In this purpose, neurons and nerve fibers of intestinal plexuses containing neuropeptides: vasoactive intestinal peptide (VIP), pituitary adenylate cyclase-activating polypeptide (PACAP) and neuropeptide Y (NPY), in pathologically changed part of the large intestine were microscpically observed and compared. Samples were taken from patients operated due to cancer of the sigmoid colon and rectum. The number of neurons and density of nerve fibres containing neuropeptides found in sections with cancer tissues were compared to those observed in sections from the uninvolved intestinal wall. Changes relating to reductions in the number of NPY-ergic neurons and density of nerve fibres in submucous and myenteric plexuses in the sections with cancer tissues (pathological sections) were statistically significant. A statistically similar presence of VIP-ergic and PACAP-ergic neurons in the submucosal and myenteric plexuses was observed in both the pathological and control sections. On the other hand, in the pathological sections, VIP-ergic nerve fibres in the myenteric plexuses and PACAP-ergic nerve fibres in the submucosal and myenteric plexuses were found to be less dense. Analysis revealed changes in pathologically affected part of the large intestine may caused disruption of proper intestinal function. Observed changes in the neural elements which are responsible for relaxation of the intestine may suggest dysfunction in the innervation of this part of the colon.

  14. ANTIGENICITY OF POLYPEPTIDES (POLY ALPHA AMINO ACIDS)

    PubMed Central

    Pinchuck, Paul; Maurer, Paul H.

    1965-01-01

    The response of mice to synthetic linear polypeptides of known composition but random sequence has been studied. Neither Swiss mice nor a number of inbred strains could respond to copolymers of only 2 amino acids (G60L40, G60A40, G90T10). Upon introduction of as little as 4 mole per cent of a third amino acid, good immune responses were obtained, regardless of the nature of the third amino acid. The level of the immune response to a series of glu-lys-ala polymers increased with increasing alanine content of the polymer. PMID:5849232

  15. Stimuli-Triggered Sol-Gel Transitions of Polypeptides Derived from α-Amino Acid N-Carboxyanhydride (NCA) Polymerizations.

    PubMed

    He, Xun; Fan, Jingwei; Wooley, Karen L

    2016-02-18

    The past decade has witnessed significantly increased interest in the development of smart polypeptide-based organo- and hydrogel systems with stimuli responsiveness, especially those that exhibit sol-gel phase-transition properties, with an anticipation of their utility in the construction of adaptive materials, sensor designs, and controlled release systems, among other applications. Such developments have been facilitated by dramatic progress in controlled polymerizations of α-amino acid N-carboxyanhydrides (NCAs), together with advanced orthogonal functionalization techniques, which have enabled economical and practical syntheses of well-defined polypeptides and peptide hybrid polymeric materials. One-dimensional stacking of polypeptides or peptide aggregations in the forms of certain ordered conformations, such as α helices and β sheets, in combination with further physical or chemical cross-linking, result in the construction of three-dimensional matrices of polypeptide gel systems. The macroscopic sol-gel transitions, resulting from the construction or deconstruction of gel networks and the conformational changes between secondary structures, can be triggered by external stimuli, including environmental factors, electromagnetic fields, and (bio)chemical species. Herein, the most recent advances in polypeptide gel systems are described, covering synthetic strategies, gelation mechanisms, and stimuli-triggered sol-gel transitions, with the aim of demonstrating the relationships between chemical compositions, supramolecular structures, and responsive properties of polypeptide-based organo- and hydrogels. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Characterization and Mutational Analysis of a Two-Polypeptide Bacteriocin Produced by Citrus Iyo-Derived Lactobacillus brevis 174A.

    PubMed

    Noda, Masafumi; Miyauchi, Rumi; Danshiitsoodol, Narandalai; Higashikawa, Fumiko; Kumagai, Takanori; Matoba, Yasuyuki; Sugiyama, Masanori

    2015-01-01

    In the present study, we isolated a lactic acid bacterium (LAB) from a citrus iyo fruit and identified it as Lactobacillus brevis. This plant-derived LAB strain, designated 174A, produces bacteriocin consisting of two polypeptides designated brevicin 174A-β and 174A-γ. Although each polypeptide itself displays antibacterial activity, the ability is enhanced 100 fold by mixing both polypeptides at a 1 : 1 ratio. Significantly, brevicin 174A inhibits even the growth of several pathogenic bacteria that are more resistant to a lantibiotic bacteriocin, nisin A, which is commonly utilized as a preservative added to foodstuffs. Structural analysis of the 174A bacteriocin using a program that predicts secondary structure suggests that both component polypeptides have a positively charged N-terminal region, as well as two cysteine residues in both the N- and C-terminals. Judging from a mutational analysis of the antibacterial polypeptides, these unique amino acid sequences of 174A-β might be important for the expression of the synergistic activity that occurs in the presence of the two polypeptides combined.

  17. Polypeptide having beta-glucosidase activity and uses thereof

    DOEpatents

    Schoonneveld-Bergmans, Margot Elisabeth Francoise; Heijne, Wilbert Herman Marie; De Jong, Rene Marcel; Damveld, Robbertus Antonius

    2016-09-13

    The invention relates to a polypeptide comprising the amino acid sequence set out in SEQ ID NO: 2 or an amino acid sequence encoded by the nucleotide sequence of SEQ ID NO: 1, or a variant polypeptide or variant polynucleotide thereof, wherein the variant polypeptide has at least 96% sequence identity with the sequence set out in SEQ ID NO: 2 or the variant polynucleotide encodes a polypeptide that has at least 96% sequence identity with the sequence set out in SEQ ID NO: 2. The invention features the full length coding sequence of the novel gene as well as the amino acid sequence of the full-length functional polypeptide and functional equivalents of the gene or the amino acid sequence. The invention also relates to methods for using the polypeptide in industrial processes. Also included in the invention are cells transformed with a polynucleotide according to the invention suitable for producing these proteins.

  18. Polypeptide having beta-glucosidase activity and uses thereof

    DOEpatents

    Schooneveld-Bergmans, Margot Elisabeth Francoise; Heijne, Wilbert Herman Marie; De Jong, Rene Marcel; Damveld, Robbertus Antonius

    2015-09-01

    The invention relates to a polypeptide comprising the amino acid sequence set out in SEQ ID NO: 2 or an amino acid sequence encoded by the nucleotide sequence of SEQ ID NO: 1, or a variant polypeptide or variant polynucleotide thereof, wherein the variant polypeptide has at least 70% sequence identity with the sequence set out in SEQ ID NO: 2 or the variant polynucleotide encodes a polypeptide that has at least 70% sequence identity with the sequence set out in SEQ ID NO: 2. The invention features the full length coding sequence of the novel gene as well as the amino acid sequence of the full-length functional polypeptide and functional equivalents of the gene or the amino acid sequence. The invention also relates to methods for using the polypeptide in industrial processes. Also included in the invention are cells transformed with a polynucleotide according to the invention suitable for producing these proteins.

  19. Polypeptide having acetyl xylan esterase activity and uses thereof

    DOEpatents

    Schoonneveld-Bergmans, Margot Elisabeth Francoise; Heijne, Wilbert Herman Marie; Los, Alrik Pieter

    2015-10-20

    The invention relates to a polypeptide comprising the amino acid sequence set out in SEQ ID NO: 2 or an amino acid sequence encoded by the nucleotide sequence of SEQ ID NO: 1, or a variant polypeptide or variant polynucleotide thereof, wherein the variant polypeptide has at least 82% sequence identity with the sequence set out in SEQ ID NO: 2 or the variant polynucleotide encodes a polypeptide that has at least 82% sequence identity with the sequence set out in SEQ ID NO: 2. The invention features the full length coding sequence of the novel gene as well as the amino acid sequence of the full-length functional polypeptide and functional equivalents of the gene or the amino acid sequence. The invention also relates to methods for using the polypeptide in industrial processes. Also included in the invention are cells transformed with a polynucleotide according to the invention suitable for producing these proteins.

  20. Polypeptide having carbohydrate degrading activity and uses thereof

    DOEpatents

    Schooneveld-Bergmans, Margot Elisabeth Francoise; Heijne, Wilbert Herman Marie; Vlasie, Monica Diana; Damveld, Robbertus Antonius

    2015-08-18

    The invention relates to a polypeptide comprising the amino acid sequence set out in SEQ ID NO: 2 or an amino acid sequence encoded by the nucleotide sequence of SEQ ID NO: 1, or a variant polypeptide or variant polynucleotide thereof, wherein the variant polypeptide has at least 73% sequence identity with the sequence set out in SEQ ID NO: 2 or the variant polynucleotide encodes a polypeptide that has at least 73% sequence identity with the sequence set out in SEQ ID NO: 2. The invention features the full length coding sequence of the novel gene as well as the amino acid sequence of the full-length functional polypeptide and functional equivalents of the gene or the amino acid sequence. The invention also relates to methods for using the polypeptide in industrial processes. Also included in the invention are cells transformed with a polynucleotide according to the invention suitable for producing these proteins.

  1. The Generation of Dehydroalanine Residues in Protonated Polypeptides: Ion/Ion Reactions for Introducing Selective Cleavages

    NASA Astrophysics Data System (ADS)

    Peng, Zhou; Bu, Jiexun; McLuckey, Scott A.

    2017-09-01

    We examine a gas-phase approach for converting a subset of amino acid residues in polypeptide cations to dehydroalanine (Dha). Subsequent activation of the modified polypeptide ions gives rise to specific cleavage N-terminal to the Dha residue. This process allows for the incorporation of selective cleavages in the structural characterization of polypeptide ions. An ion/ion reaction within the mass spectrometer between a multiply protonated polypeptide and the sulfate radical anion introduces a radical site into the multiply protonated polypeptide reactant. Subsequent collisional activation of the polypeptide radical cation gives rise to radical side chain loss from one of several particular amino acid side chains (e.g., leucine, asparagine, lysine, glutamine, and glutamic acid) to yield a Dha residue. The Dha residues facilitate preferential backbone cleavages to produce signature c- and z-ions, demonstrated with cations derived from melittin, mechano growth factor (MGF), and ubiquitin. The efficiencies for radical side chain loss and for subsequent generation of specific c- and z-ions have been examined as functions of precursor ion charge state and activation conditions using cations of ubiquitin as a model for a small protein. It is noted that these efficiencies are not strongly dependent on ion trap collisional activation conditions but are sensitive to precursor ion charge state. Moderate to low charge states show the greatest overall yields for the specific Dha cleavages, whereas small molecule losses (e.g., water/ammonia) dominate at the lowest charge states and proton catalyzed amide bond cleavages that give rise to b- and y-ions tend to dominate at high charge states. [Figure not available: see fulltext.

  2. The Generation of Dehydroalanine Residues in Protonated Polypeptides: Ion/Ion Reactions for Introducing Selective Cleavages

    NASA Astrophysics Data System (ADS)

    Peng, Zhou; Bu, Jiexun; McLuckey, Scott A.

    2017-05-01

    We examine a gas-phase approach for converting a subset of amino acid residues in polypeptide cations to dehydroalanine (Dha). Subsequent activation of the modified polypeptide ions gives rise to specific cleavage N-terminal to the Dha residue. This process allows for the incorporation of selective cleavages in the structural characterization of polypeptide ions. An ion/ion reaction within the mass spectrometer between a multiply protonated polypeptide and the sulfate radical anion introduces a radical site into the multiply protonated polypeptide reactant. Subsequent collisional activation of the polypeptide radical cation gives rise to radical side chain loss from one of several particular amino acid side chains (e.g., leucine, asparagine, lysine, glutamine, and glutamic acid) to yield a Dha residue. The Dha residues facilitate preferential backbone cleavages to produce signature c- and z-ions, demonstrated with cations derived from melittin, mechano growth factor (MGF), and ubiquitin. The efficiencies for radical side chain loss and for subsequent generation of specific c- and z-ions have been examined as functions of precursor ion charge state and activation conditions using cations of ubiquitin as a model for a small protein. It is noted that these efficiencies are not strongly dependent on ion trap collisional activation conditions but are sensitive to precursor ion charge state. Moderate to low charge states show the greatest overall yields for the specific Dha cleavages, whereas small molecule losses (e.g., water/ammonia) dominate at the lowest charge states and proton catalyzed amide bond cleavages that give rise to b- and y-ions tend to dominate at high charge states.

  3. The Generation of Dehydroalanine Residues in Protonated Polypeptides: Ion/Ion Reactions for Introducing Selective Cleavages.

    PubMed

    Peng, Zhou; Bu, Jiexun; McLuckey, Scott A

    2017-05-11

    We examine a gas-phase approach for converting a subset of amino acid residues in polypeptide cations to dehydroalanine (Dha). Subsequent activation of the modified polypeptide ions gives rise to specific cleavage N-terminal to the Dha residue. This process allows for the incorporation of selective cleavages in the structural characterization of polypeptide ions. An ion/ion reaction within the mass spectrometer between a multiply protonated polypeptide and the sulfate radical anion introduces a radical site into the multiply protonated polypeptide reactant. Subsequent collisional activation of the polypeptide radical cation gives rise to radical side chain loss from one of several particular amino acid side chains (e.g., leucine, asparagine, lysine, glutamine, and glutamic acid) to yield a Dha residue. The Dha residues facilitate preferential backbone cleavages to produce signature c- and z-ions, demonstrated with cations derived from melittin, mechano growth factor (MGF), and ubiquitin. The efficiencies for radical side chain loss and for subsequent generation of specific c- and z-ions have been examined as functions of precursor ion charge state and activation conditions using cations of ubiquitin as a model for a small protein. It is noted that these efficiencies are not strongly dependent on ion trap collisional activation conditions but are sensitive to precursor ion charge state. Moderate to low charge states show the greatest overall yields for the specific Dha cleavages, whereas small molecule losses (e.g., water/ammonia) dominate at the lowest charge states and proton catalyzed amide bond cleavages that give rise to b- and y-ions tend to dominate at high charge states. Graphical Abstract ᅟ.

  4. Hierarchical Bionanotubes Formed By the Self Assembly of Microtubules With Cationic Membranes Or Polypeptides

    SciTech Connect

    Raviv, U.; Needleman, D.J.; Ewert, K.K.; Safinya, C.R.

    2009-06-05

    At present there is a surge in interest in biophysical research aimed at elucidating collective interactions between cellular proteins and associated biomolecules leading to supramolecular structures, with the ultimate goal of relating structure to function. The nerve cell cytoskeleton provides a rich example of highly ordered bundles and networks of interacting neurofilaments, microtubules and filamentous actin, where the nature of the interactions, structures and structure-function correlations remain poorly understood. We present synchrotron X-ray diffraction and electron microscopy data, in reconstituted protein systems from the bovine central nervous system, which reveal unexpected structures not predicted by current electrostatic theories. By mixing preassembled microtubules with charged membranes or polypeptides we found hierarchical bionanotubes made of microtubules coated by lipid bilayers or polypeptides, which in turn are coated with a third layer of tubulin oligomers forming rings or spirals.

  5. Facilitated Translocation of Polypeptides Through A Single Nanopore

    PubMed Central

    Bikwemu, Robert; Wolfe, Aaron J.; Xing, Xiangjun; Movileanu, Liviu

    2011-01-01

    The transport of polypeptides through nanopores is a key process in biology and medical biotechnology. Despite its critical importance, the underlying kinetics of polypeptide translocation through protein nanopores is not yet comprehensively understood. Here, we present a simple two-barrier, one-well kinetic model for the translocation of short positively charged polypeptides through a single transmembrane protein nanopore that is equiped with negatively charged rings, simply called traps. We demonstrate that the presence of these traps within the interior of the nanopore dramatically alters the free energy landscape for the partitioning of the polypeptide into the nanopore interior, as revealed by significant modifications in the activation free energies required for the transitions of the polypeptide from one state to other. Our kinetic model permits the calculation of the relative and absolute exit frequencies of the short cationic polypeptides through either opening of the nanopore. Moreover, this approach enabled quantitative assessment of the kinetics of translocation of the polypeptides through a protein nanopore, which is strongly dependent on several factors, including the nature of the translocating polypeptide, the position of the traps, the strength of the polypeptide-attractive trap interactions and the applied transmembrane voltage. PMID:21339604

  6. Photodynamic induction of a bacterial cell surface polypeptide.

    PubMed Central

    Hoober, J K

    1977-01-01

    The photodynamic action of several dyes on cells of a bacterium, tentatively identified as a species of Arthrobacter, resulted in remarkable stimulation of synthesis of a polypeptide 21,000 daltons in mass. This polypeptide resides on the cell surface and can be solubilized by sodium dodecyl sulfate without lysis of the cells. Chlorophyllin and rose bengal are effective in inducing synthesis of the polypeptide in proportion to their ability to sensitize the photooxidation of histidine. Etiolated cells of the alga Chlamydomonas reinhardtii y-1 excrete a substance into the medium that also sensitized the photoinduction of the polypeptide. Images PMID:885841

  7. Intracellularly Swollen Polypeptide Nanogel Assists Hepatoma Chemotherapy

    PubMed Central

    Shi, Bo; Huang, Kexin; Ding, Jianxun; Xu, Weiguo; Yang, Yu; Liu, Haiyan; Yan, Lesan; Chen, Xuesi

    2017-01-01

    Nowadays, chemotherapy is one of the principal modes of treatment for tumor patients. However, the traditional formulations of small molecule drugs show short circulation time, low tumor selectivity, and high toxicity to normal tissues. To address these problems, a facilely prepared, and pH and reduction dual-responsive polypeptide nanogel was prepared for selectively intracellular delivery of chemotherapy drug. As a model drug, doxorubicin (DOX) was loaded into the nanogel through a sequential dispersion and dialysis technique, resulting in a high drug loading efficiency (DLE) of 96.7 wt.%. The loading nanogel, defined as NG/DOX, exhibited a uniform spherical morphology with a mean hydrodynamic radius of 58.8 nm, pH and reduction dual-triggered DOX release, efficient cell uptake, and cell proliferation inhibition in vitro. Moreover, NG/DOX exhibited improved antitumor efficacy toward H22 hepatoma-bearing BALB/c mouse model compared with free DOX·HCl. Histopathological and immunohistochemical analyses were implemented to further confirm the tumor suppression activity of NG/DOX. Furthermore, the variations of body weight, histopathological morphology, bone marrow cell micronucleus rate, and white blood cell count verified that NG/DOX showed excellent safety in vivo. With these excellent properties in vitro and in vivo, the pH and reduction dual-responsive polypeptide nanogel exhibits great potential for on-demand intracellular delivery of antitumor drug, and holds good prospect for future clinical application. PMID:28255361

  8. Applications of elastin-like polypeptides in drug delivery

    PubMed Central

    MacEwan, Sarah R; Chilkoti, Ashutosh

    2014-01-01

    Elastin-like polypeptides (ELPs) are biopolymers inspired by human elastin. Their lower critical solution temperature phase transition behavior and biocompatibility make them useful materials for stimulus-responsive applications in biological environments. Due to their genetically encoded design and recombinant synthesis, the sequence and size of ELPs can be exactly defined. These design parameters control the structure and function of the ELP with a precision that is unmatched by synthetic polymers. Due to these attributes, ELPs have been used extensively for drug delivery in a variety of different embodiments—as soluble macromolecular carriers, self-assembled nanoparticles, cross-linked microparticles, or thermally coacervated depots. These ELP systems have been used to deliver biologic therapeutics, radionuclides, and small molecule drugs to a variety of anatomical sites for the treatment of diseases including cancer, type 2 diabetes, osteoarthritis, and neuroinflammation. PMID:24979207

  9. Domed Silica Microcylinders Coated with Oleophilic Polypeptides and Their Behavior in Lyotropic Cholesteric Liquid Crystals of the Same Polypeptide.

    PubMed

    Rosu, Cornelia; Jacobeen, Shane; Park, Katherine; Reichmanis, Elsa; Yunker, Peter; Russo, Paul S

    2016-12-13

    Liquid crystals can organize dispersed particles into useful and exotic structures. In the case of lyotropic cholesteric polypeptide liquid crystals, polypeptide-coated particles are appealing because the surface chemistry matches that of the polymeric mesogen, which permits a tighter focus on factors such as extended particle shape. The colloidal particles developed here consist of a magnetic and fluorescent cylindrically symmetric silica core with one rounded, almost hemispherical end. Functionalized with helical poly(γ-stearyl-l-glutamate) (PSLG), the particles were dispersed at different concentrations in cholesteric liquid crystals (ChLC) of the same polymer in tetrahydrofuran (THF). Defects introduced by the particles to the director field of the bulk PSLG/THF host led to a variety of phases. In fresh mixtures, the cholesteric mesophase of the PSLG matrix was distorted, as reflected in the absence of the characteristic fingerprint pattern. Over time, the fingerprint pattern returned, more quickly when the concentration of the PSLG-coated particles was low. At low particle concentration the particles were "guided" by the PSLG liquid crystal to organize into patterns similar to that of the re-formed bulk chiral nematic phase. When their concentration increased, the well-dispersed PSLG-coated particles seemed to map onto the distortions in the bulk host's local director field. The particles located near the glass vial-ChLC interfaces were stacked lengthwise into architectures with apparent two-dimensional hexagonal symmetry. The size of these "crystalline" structures increased with particle concentration. They displayed remarkable stability toward an external magnetic field; hydrophobic interactions between the PSLG polymers in the shell and those in the bulk LC matrix may be responsible. The results show that bio-inspired LCs can assemble suitable colloidal particles into soft crystalline structures.

  10. Primary structure analysis of an integral membrane glycoprotein of the nuclear pore

    PubMed Central

    1989-01-01

    The complete primary structure of an integral membrane glycoprotein of the nuclear pore was deduced from the cDNA sequence. The cDNA encodes a polypeptide of 204,205 D containing a 25-residue-long signal sequence, two hydrophobic segments that could function as transmembrane segments, and 13 potential N-linked oligosaccharide addition sites. Endoglycosidase H reduces the molecular mass by approximately 9 kD suggesting that not all of these 13 sites are used. We discuss possible models for the topology of this protein in the pore membrane as well as a possible role in the formation of pores and pore complexes. PMID:2738089

  11. cDNA encoding a polypeptide including a hev ein sequence

    DOEpatents

    Raikhel, Natasha V.; Broekaert, Willem F.; Chua, Nam-Hai; Kush, Anil

    2000-07-04

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74-79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

  12. Coordinating electrical activity of the heart: ankyrin polypeptides in human cardiac disease.

    PubMed

    Curran, Jerry; Mohler, Peter J

    2011-07-01

    Over the past ten years, ankyrin polypeptides have emerged as players in cardiac excitation-contraction coupling. Once thought to solely play a structural role, loss-of-function variants of genes encoding ankyrin polypeptides have highlighted how this protein mediates subcellular localization of various electrical components of the excitation-contraction coupling machinery. Evidence has revealed how disruption of this localization is the primary cause of various cardiomyopathies, ranging from long-QT syndrome 4, to sinus node disease, to more common forms of arrhythmias. The roles of ankyrin polypeptides in excitation-contraction coupling in the heart and the development of ankyrin-specific cardiomyopathies. How ankyrin polypeptides may be involved in structural and electrical remodeling of the heart, post-myocardial infarct. How ankyrin interactions with membrane-bound ion channels may regulate these channels' response to stimuli. New data, which offers the potential for unique therapies, for not only combating heart disease, but also for wider applications to various disease states. The ankyrin family of adapter proteins is emerging as an intimate player in cardiac excitation-contraction coupling. Until recently, these proteins have gone largely unappreciated for their importance in proper cardiac function. New insights into how these proteins function within the heart are offering potentially new avenues for therapies against cardiomyopathy.

  13. Coordinating Electrical Activity of the Heart: Ankyrin Polypeptides in Human Cardiac Disease

    PubMed Central

    Curran, Jerry; Mohler, Peter J

    2011-01-01

    Introduction Over the past ten years, ankyrin polypeptides have emerged as critical players in cardiac excitation-contraction coupling. Once thought to solely play only a structural role, loss-of-function variants in genes encoding ankyrin polypeptides have highlighted how this protein mediates the proper subcellular localization of the various electrical components of the excitation-contraction coupling machinery. A large body of evidence has revealed how the disruption of this localization is the primary cause of various cardiomyopathies, ranging from long QT syndrome 4, to sinus node disease, to more common forms of arrhythmias. Areas Covered This review details the varied roles that ankyrin polypeptides play in excitation-contraction coupling in the heart and the development of ankyrin-specific cardiomyopathies. It will further discuss how ankyrin polypeptides may be involved in structural and electrical remodeling of the heart, post-myocardial infarct. Attention is given to how ankyrin interactions with membrane bound ion channels may regulate these channels’ response to stimuli. Special attention is given to exciting new data, which may offer the potential for unique therapies, for not only combating heart disease, but which also holds promise for wider applications to various disease states. Expert Opinion The ankyrin family of adapter proteins is emerging as an intimate player in cardiac excitation-contraction coupling. Until recently, these proteins have gone largely unappreciated for their importance in proper cardiac function. New insights into how these proteins function within the heart are offering potentially new avenues for therapies against cardiomyopathy. PMID:21457127

  14. A role for helical intermediates in amyloid formation by natively unfolded polypeptides?

    NASA Astrophysics Data System (ADS)

    Abedini, Andisheh; Raleigh, Daniel P.

    2009-03-01

    Amyloid formation and aberrant protein aggregation have been implicated in more than 15 different human diseases and an even wider range of proteins form amyloid in vitro. From a structural perspective the proteins which form amyloid can be divided into two classes: those which adopt a compact globular fold and must presumably at least partially unfold to form amyloid and those which are unstructured in their monomeric state. Important examples of the latter include the Aβ peptide of Alzheimer's disease, atrial natriuretic factor, calcitonin, pro-calcitonin, islet amyloid polypeptide (IAPP, amylin), α-synuclein and the medin polypeptide. The kinetics of amyloid assembly are complex and typically involve a lag phase during which little or no fibril material is formed, followed by a rapid growth stage leading to the β-sheet-rich amyloid structure. Increasing evidence suggests that some natively unfolded polypeptides populate a helical intermediate during the lag phase. We propose a model in which early oligomerization is linked to helix formation and is promoted by helix-helix association. Recent work has highlighted the potential importance of polypeptide membrane interactions in amyloid formation and helical intermediates appear to play an important role here as well. Characterization of helical intermediates is experimentally challenging but new spectroscopic techniques are emerging which hold considerable promise and even have the potential to provide residue specific information.

  15. Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump-probe experiment.

    PubMed

    Pande, K; Schwander, P; Schmidt, M; Saldin, D K

    2014-07-17

    We propose a method for deducing time-resolved structural changes in uncrystallized biomolecules in solution. The method relies on measuring the angular correlations of the intensities, when averaged over a large number of diffraction patterns from randomly oriented biomolecules in solution in a liquid solvent. The experiment is somewhat like a pump-probe version of an experiment on small angle X-ray scattering, except that the data expected by the algorithm are not just the radial variation of the averaged intensities. The differences of these correlation functions as measured from a photoexcited and dark structure enable the direct calculation of the difference electron density with a knowledge of only the dark structure. We exploit a linear relation we derive between the difference in these correlation functions and the difference electron density, applicable for small structural changes.

  16. Deducing fast electron density changes in randomly orientated uncrystallized biomolecules in a pump–probe experiment

    PubMed Central

    Pande, K.; Schwander, P.; Schmidt, M.; Saldin, D. K.

    2014-01-01

    We propose a method for deducing time-resolved structural changes in uncrystallized biomolecules in solution. The method relies on measuring the angular correlations of the intensities, when averaged over a large number of diffraction patterns from randomly oriented biomolecules in solution in a liquid solvent. The experiment is somewhat like a pump–probe version of an experiment on small angle X-ray scattering, except that the data expected by the algorithm are not just the radial variation of the averaged intensities. The differences of these correlation functions as measured from a photoexcited and dark structure enable the direct calculation of the difference electron density with a knowledge of only the dark structure. We exploit a linear relation we derive between the difference in these correlation functions and the difference electron density, applicable for small structural changes. PMID:24914159

  17. Chain stiffness of elastin-like polypeptides

    PubMed Central

    Fluegel, Sabine; Fischer, Karl; McDaniel, Jonathan R.; Chilkoti, Ashutosh; Schmidt, Manfred

    2010-01-01

    The hydrodynamic radii of a series of genetically engineered monodisperse elastin like polypeptides (ELP) was determined by dynamic light scattering in aqueous solution as function of molar mass. Utilizing the known theoretical expression for the hydrodynamic radius of wormlike chains, the Kuhn statistical segment length was determined to be lk = 2.1 nm, assuming that the length of the peptide repeat unit was b = 0.365 nm, a value derived for a coiled conformation of ELP. The resulting chain stiffness is significantly larger than previously reported by force-distance curve analysis (lk < 0.4 nm). The possible occurrence of superstructures, such as hairpins or helices, would reduce the contour length of the ELP, further increasing lk. Accordingly, the value lk = 2.1 nm reported here represents a lower limit of the chain stiffness for ELP. PMID:20961120

  18. Fibrillar dimer formation of islet amyloid polypeptides

    SciTech Connect

    Chiu, Chi -cheng; de Pablo, Juan J.

    2015-05-08

    Amyloid deposits of human islet amyloid polypeptide (hIAPP), a 37-residue hormone co-produced with insulin, have been implicated in the development of type 2 diabetes. Residues 20 – 29 of hIAPP have been proposed to constitute the amyloidogenic core for the aggregation process, yet the segment is mostly unstructured in the mature fibril, according to solid-state NMR data. Here we use molecular simulations combined with bias-exchange metadynamics to characterize the conformational free energies of hIAPP fibrillar dimer and its derivative, pramlintide. We show that residues 20 – 29 are involved in an intermediate that exhibits transient β-sheets, consistent with recent experimental and simulation results. By comparing the aggregation of hIAPP and pramlintide, we illustrate the effects of proline residues on inhibition of the dimerization of IAPP. The mechanistic insights presented here could be useful for development of therapeutic inhibitors of hIAPP amyloid formation.

  19. Fibrillar dimer formation of islet amyloid polypeptides

    NASA Astrophysics Data System (ADS)

    Chiu, Chi-cheng; de Pablo, Juan J.

    2015-09-01

    Amyloid deposits of human islet amyloid polypeptide (hIAPP), a 37-residue hormone co-produced with insulin, have been implicated in the development of type 2 diabetes. Residues 20 - 29 of hIAPP have been proposed to constitute the amyloidogenic core for the aggregation process, yet the segment is mostly unstructured in the mature fibril, according to solid-state NMR data. Here we use molecular simulations combined with bias-exchange metadynamics to characterize the conformational free energies of hIAPP fibrillar dimer and its derivative, pramlintide. We show that residues 20 - 29 are involved in an intermediate that exhibits transient β-sheets, consistent with recent experimental and simulation results. By comparing the aggregation of hIAPP and pramlintide, we illustrate the effects of proline residues on inhibition of the dimerization of IAPP. The mechanistic insights presented here could be useful for development of therapeutic inhibitors of hIAPP amyloid formation.

  20. Fibrillar dimer formation of islet amyloid polypeptides

    SciTech Connect

    Chiu, Chi-cheng; de Pablo, Juan J.

    2015-05-08

    Amyloid deposits of human islet amyloid polypeptide (hIAPP), a 37-residue hormone co-produced with insulin, have been implicated in the development of type 2 diabetes. Residues 20 – 29 of hIAPP have been proposed to constitute the amyloidogenic core for the aggregation process, yet the segment is mostly unstructured in the mature fibril, according to solid-state NMR data. Here we use molecular simulations combined with bias-exchange metadynamics to characterize the conformational free energies of hIAPP fibrillar dimer and its derivative, pramlintide. We show that residues 20 – 29 are involved in an intermediate that exhibits transient β-sheets, consistent with recent experimental and simulation results. By comparing the aggregation of hIAPP and pramlintide, we illustrate the effects of proline residues on inhibition of the dimerization of IAPP. The mechanistic insights presented here could be useful for development of therapeutic inhibitors of hIAPP amyloid formation.

  1. Corneal Penetrating Elastin-Like Polypeptide Carriers

    PubMed Central

    George, Eric M.; Mahdi, Fakhri; Logue, Omar C.; Robinson, Grant G.

    2016-01-01

    Abstract Purpose: Elastin-like polypeptide (ELP) is a bioengineered protein widely applied as a drug carrier due to its biocompatibility and amenability to modification with cell-penetrating peptides (CPPs) and therapeutic agents. The purpose of this study was to determine whether topically applied ELP or CPP-fused ELPs penetrate the corneal barrier. Methods: In vitro binding and cytotoxicity to human corneal epithelial (HCE) cells were determined for ELP or CPP-ELPs. Corneal binding, clearance, and penetration were assessed in a rabbit model following topical application of the fluorescently labeled proteins by quantitative fluorescence imaging and histology. Results: ELP bound to HCE cells in vitro, and binding/uptake was enhanced 2- to 3-fold by the addition of CPPs. When applied topically to rabbit eyes, ELP accumulated in the cornea at levels 7.4-fold higher than did an equivalent dose of immunoglobulin G. Both ELP and a CPP-ELP penetrated the corneal epithelium and were detectable in the stroma. Addition of CPPs to ELP, however, did not significantly enhance corneal uptake or penetration in vivo relative to ELP alone. The polypeptides cleared from the cornea over a period of 20–30 min after application, after which cornea levels reached a steady state of 15–30 μg/mL for up to 3 h. Conclusions: The ELP drug carrier can penetrate the corneal epithelium and accumulate in the stroma. Given its amenability for fusion to multiple types of therapeutic agents, ELP has the potential to serve as a drug carrier for topical ocular applications. PMID:26672799

  2. Antipeptide antibodies that can distinguish specific subunit polypeptides of glutamine synthetase from bean (Phaseolus vulgaris L.)

    NASA Technical Reports Server (NTRS)

    Cai, X.; Henry, R. L.; Takemoto, L. J.; Guikema, J. A.; Wong, P. P.; Spooner, B. S. (Principal Investigator)

    1992-01-01

    The amino acid sequences of the beta and gamma subunit polypeptides of glutamine synthetase from bean (Phaseolus vulgaris L.) root nodules are very similar. However, there are small regions within the sequences that are significantly different between the two polypeptides. The sequences between amino acids 2 and 9 and between 264 and 274 are examples. Three peptides (gamma 2-9, gamma 264-274, and beta 264-274) corresponding to these sequences were synthesized. Antibodies against these peptides were raised in rabbits and purified with corresponding peptide-Sepharose affinity chromatography. Western blot analysis of polyacrylamide gel electrophoresis of bean nodule proteins demonstrated that the anti-beta 264-274 antibodies reacted specifically with the beta polypeptide and the anti-gamma 264-274 and anti-gamma 2-9 antibodies reacted specifically with the gamma polypeptide of the native and denatured glutamine synthetase. These results showed the feasibility of using synthetic peptides in developing antibodies that are capable of distinguishing proteins with similar primary structures.

  3. Antipeptide antibodies that can distinguish specific subunit polypeptides of glutamine synthetase from bean (Phaseolus vulgaris L.)

    NASA Technical Reports Server (NTRS)

    Cai, X.; Henry, R. L.; Takemoto, L. J.; Guikema, J. A.; Wong, P. P.; Spooner, B. S. (Principal Investigator)

    1992-01-01

    The amino acid sequences of the beta and gamma subunit polypeptides of glutamine synthetase from bean (Phaseolus vulgaris L.) root nodules are very similar. However, there are small regions within the sequences that are significantly different between the two polypeptides. The sequences between amino acids 2 and 9 and between 264 and 274 are examples. Three peptides (gamma 2-9, gamma 264-274, and beta 264-274) corresponding to these sequences were synthesized. Antibodies against these peptides were raised in rabbits and purified with corresponding peptide-Sepharose affinity chromatography. Western blot analysis of polyacrylamide gel electrophoresis of bean nodule proteins demonstrated that the anti-beta 264-274 antibodies reacted specifically with the beta polypeptide and the anti-gamma 264-274 and anti-gamma 2-9 antibodies reacted specifically with the gamma polypeptide of the native and denatured glutamine synthetase. These results showed the feasibility of using synthetic peptides in developing antibodies that are capable of distinguishing proteins with similar primary structures.

  4. The ribosome quality control pathway can access nascent polypeptides stalled at the Sec61 translocon.

    PubMed

    von der Malsburg, Karina; Shao, Sichen; Hegde, Ramanujan S

    2015-06-15

    Cytosolic ribosomes that stall during translation are split into subunits, and nascent polypeptides trapped in the 60S subunit are ubiquitinated by the ribosome quality control (RQC) pathway. Whether the RQC pathway can also target stalls during cotranslational translocation into the ER is not known. Here we report that listerin and NEMF, core RQC components, are bound to translocon-engaged 60S subunits on native ER membranes. RQC recruitment to the ER in cultured cells is stimulated by translation stalling. Biochemical analyses demonstrated that translocon-targeted nascent polypeptides that subsequently stall are polyubiquitinated in 60S complexes. Ubiquitination at the translocon requires cytosolic exposure of the polypeptide at the ribosome-Sec61 junction. This exposure can result from either failed insertion into the Sec61 channel or partial backsliding of translocating nascent chains. Only Sec61-engaged nascent chains early in their biogenesis were relatively refractory to ubiquitination. Modeling based on recent 60S-RQC and 80S-Sec61 structures suggests that the E3 ligase listerin accesses nascent polypeptides via a gap in the ribosome-translocon junction near the Sec61 lateral gate. Thus the RQC pathway can target stalled translocation intermediates for degradation from the Sec61 channel.

  5. The ribosome quality control pathway can access nascent polypeptides stalled at the Sec61 translocon

    PubMed Central

    von der Malsburg, Karina; Shao, Sichen; Hegde, Ramanujan S.

    2015-01-01

    Cytosolic ribosomes that stall during translation are split into subunits, and nascent polypeptides trapped in the 60S subunit are ubiquitinated by the ribosome quality control (RQC) pathway. Whether the RQC pathway can also target stalls during cotranslational translocation into the ER is not known. Here we report that listerin and NEMF, core RQC components, are bound to translocon-engaged 60S subunits on native ER membranes. RQC recruitment to the ER in cultured cells is stimulated by translation stalling. Biochemical analyses demonstrated that translocon-targeted nascent polypeptides that subsequently stall are polyubiquitinated in 60S complexes. Ubiquitination at the translocon requires cytosolic exposure of the polypeptide at the ribosome–Sec61 junction. This exposure can result from either failed insertion into the Sec61 channel or partial backsliding of translocating nascent chains. Only Sec61-engaged nascent chains early in their biogenesis were relatively refractory to ubiquitination. Modeling based on recent 60S–RQC and 80S–Sec61 structures suggests that the E3 ligase listerin accesses nascent polypeptides via a gap in the ribosome–translocon junction near the Sec61 lateral gate. Thus the RQC pathway can target stalled translocation intermediates for degradation from the Sec61 channel. PMID:25877867

  6. Biomimetic assembly of polypeptide-stabilized CaCO(3) nanoparticles.

    PubMed

    Zhang, Zhongping; Gao, Daming; Zhao, Hui; Xie, Chenggen; Guan, Guijian; Wang, Dapeng; Yu, Shu-Hong

    2006-05-04

    In this paper, we report a simple polypeptide-directed strategy for fabricating large spherical assembly of CaCO(3) nanoparticles. Stepwise growth and assembly of a large number of nanoparticles have been observed, from the formation of an amorphous liquidlike CaCO(3)-polypeptide precursor, to the crystallization and stabilization of polypeptide-capped nanoparticles, and eventually, the spherical assembly of nanoparticles. The "soft" poly(aspartate)-capping layer binding on a nanoparticle surface resulted in the unusual soft nature of nanoparticle assembly, providing a reservoir of primary nanoparticles with a moderate mobility, which is the basis of a new strategy for reconstructing nanoparticle assembly into complex nanoparticle architectures. Moreover, the findings of the secondary assembly of nanoparticle microspheres and the morphology transformation of nanoparticle assembly demonstrate a flexible and controllable pathway for manipulating the shapes and structures of nanoparticle assembly. In addition, the combination of the polypeptide with a double hydrophilic block copolymer (DHBC) allows it to possibly further control the shape and complexity of the nanoparticle assembly. A clear perspective is shown here that more complex nanoparticle materials could be created by using "soft" biological proteins or peptides as a mediating template at the organic-inorganic interface.

  7. Nucleic acids encoding antifungal polypeptides and uses thereof

    DOEpatents

    Altier, Daniel J.; Ellanskaya, I. A.; Gilliam, Jacob T.; Hunter-Cevera, Jennie; Presnail, James K; Schepers, Eric; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2010-11-02

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include an amino acid sequence, and variants and fragments thereof, for an antipathogenic polypeptide that was isolated from a fungal fermentation broth. Nucleic acid molecules that encode the antipathogenic polypeptides of the invention, and antipathogenic domains thereof, are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention are also disclosed.

  8. Isolated nucleic acids encoding antipathogenic polypeptides and uses thereof

    DOEpatents

    Altier, Daniel J.; Crane, Virginia C.; Ellanskaya, Irina; Ellanskaya, Natalia; Gilliam, Jacob T.; Hunter-Cevera, Jennie; Presnail, James K.; Schepers, Eric J.; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2010-04-20

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from fungal fermentation broths. Nucleic acids that encode the antipathogenic polypeptides are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention are also disclosed.

  9. Characteristics of middle and upper tropospheric clouds as deduced from rawinsonde data

    NASA Technical Reports Server (NTRS)

    Starr, D. D. O.; Cox, S. K.

    1982-01-01

    The static environment of middle and upper tropospheric clouds is characterized. Computed relative humidity with respect to ice is used to diagnose the presence of cloud layer. The deduced seasonal mean cloud cover estimates based on this technique are shown to be reasonable. The cases are stratified by season and pressure thickness, and the dry static stability, vertical wind speed shear, and Richardson number are computed for three layers for each case. Mean values for each parameter are presented for each stratification and layer. The relative frequency of occurrence of various structures is presented for each stratification. The observed values of each parameter and the observed structure of each parameter are quite variable. Structures corresponding to any of a number of different conceptual models may be found. Moist adiabatic conditions are not commonly observed and the stratification based on thickness yields substantially different results for each group.

  10. Effects of surface hydrophobicity on the conformational changes of polypeptides of different length

    NASA Astrophysics Data System (ADS)

    Mu, Yan

    2011-09-01

    We studied the effects of surface hydrophobicity on the conformational changes of different length polypeptides by calculating the free energy difference between peptide structures using the bias-potential Monte Carlo technique and the probability ratio method. It was found that the hydrophobic surface plays an important role in the stability of secondary structures of the polypeptides with hydrophobic side chains. For short GAAAAG peptides, the hydrophobic surface destabilizes the α helix but stabilizes the β hairpin in the entire temperature region considered in our study. Interestingly, when the surface hydrophobic strength ɛhpsf≥ɛhp, the most stable structure in the low temperature region changes from α helix to β hairpin, and the corresponding phase transition temperature increases slightly. For longer GAAAAAAAAAAG peptides, the effects of the relatively weak hydrophobic surface (ɛhpsf < ɛhp) on α-helical structures may be neglected, while the relatively strongly hydrophobic surface (ɛhpsf≥ɛhp) leads to the obvious partial helicity loss. In contrast, the stability of β structures can be enhanced significantly by the hydrophobic surface, especially by the strongly hydrophobic surface, at low and intermediate temperatures. At high temperatures, in addition to thermal fluctuations, the strongly hydrophobic surface (ɛhpsf>ɛhp) may further disturb the formation of both α-helical and β structures. Moreover, the phase transition temperature between α-helical structures and random coils significantly decreases due to the helicity loss when ɛhpsf>ɛhp. Our findings provide a basic and quantitative picture for understanding the effects of a hydrophobic surface on the conformational changes of the polypeptides with hydrophobic side chains. From an application viewpoint, the present study is helpful in developing alternative strategies of producing high-quality biological fibrillar materials and functional nanoscale devices by the self-assembly of

  11. Clinical endocrinology and metabolism. Glucose-dependent insulinotropic polypeptide/gastric inhibitory polypeptide.

    PubMed

    Meier, Juris J; Nauck, Michael A

    2004-12-01

    The 42 amino acid polypeptide glucose-dependent insulinotropic polypeptide/gastric inhibitory polypeptide (GIP) is released from intestinal K-cells in response to nutrient ingestion. Based on animal studies, the peptide was initially assumed to act as an endogenous inhibitor of gastric acid secretion. Later it was found that GIP is capable of augmenting glucose-stimulated insulin secretion, and subsequent studies provided evidence that, in humans, the peptide predominantly acts as an incretin hormone. A role for GIP in the regulation of lipid homeostasis and in the development of obesity has been inferred from different animal studies. While GIP strongly stimulates insulin release in healthy humans, the peptide has almost completely lost its insulinotropic effect in patients with type 2 diabetes. This is different from the actions of glucagon-like peptide 1, which stimulates insulin secretion even in the later stages of type 2 diabetes. This suggests that a diminished insulinotropic effect of GIP may contribute to the pathogenesis of type 2 diabetes. This review will summarize the actions of GIP in human physiology and discuss its role in the pathogenesis of type 2 diabetes, as well as the therapeutic options derived from these findings.

  12. Structural gene and complete amino acid sequence of Vibrio alginolyticus collagenase.

    PubMed Central

    Takeuchi, H; Shibano, Y; Morihara, K; Fukushima, J; Inami, S; Keil, B; Gilles, A M; Kawamoto, S; Okuda, K

    1992-01-01

    The DNA encoding the collagenase of Vibrio alginolyticus was cloned, and its complete nucleotide sequence was determined. When the cloned gene was ligated to pUC18, the Escherichia coli expression vector, bacteria carrying the gene exhibited both collagenase antigen and collagenase activity. The open reading frame from the ATG initiation codon was 2442 bp in length for the collagenase structural gene. The amino acid sequence, deduced from the nucleotide sequence, revealed that the mature collagenase consists of 739 amino acids with an Mr of 81875. The amino acid sequences of 20 polypeptide fragments were completely identical with the deduced amino acid sequences of the collagenase gene. The amino acid composition predicted from the DNA sequence was similar to the chemically determined composition of purified collagenase reported previously. The analyses of both the DNA and amino acid sequences of the collagenase gene were rigorously performed, but we could not detect any significant sequence similarity to other collagenases. Images Fig. 2. PMID:1311172

  13. Kinematics of ICMEs Deduced From Remote Radio Observations

    NASA Astrophysics Data System (ADS)

    Reiner, M. J.; MacDowall, R. J.

    2009-12-01

    Low-frequency radio emissions, generated at the driven shock wave at the fundamental and harmonic of the plasma frequency, can directly reveal the kinematics of ICMEs as they propagate through the inner heliosphere. The reason is that the frequency of the radio emissions varies in a predictable way as a function of heliocentric distance. Hence, the observed frequency drift of these radio emissions is essentially a plot of the height above the Sun as a function of time. The derivative of the observed frequency-time curve at each point then gives the instantaneous speed of the propagating interplanetary shock. We have used these remote radio observations to determine the speed profiles for some 40 fast CMEs observed during solar cycle 23. The speed profiles for these fast ICMEs were found to imply an initial rapid deceleration at a constant rate, followed by a constant propagation speed to 1 AU (Reiner et al. ApJ 663, 1369, 2007), consistent with some earlier Doppler scintillation measurements (Woo et al., JGR 90, 154, 1985). Because of the large number of CME events for which this analysis was carried out, we were further able to study the correlations of the deceleration parameters of the ICME speed profiles. For most of those remote radio observations, there were no corresponding white-light observations beyond the 32 Rs (0.15 AU) limit of the LASCO coronagraph. After 2003, the all-sky camera SMEI permitted the first direct comparison between the remote radio and the white-light observations in interplanetary space (Reiner et al. JGR 110, A09S14, 2005). The STEREO spacecraft, launched in October of 2006, provide a new and unique opportunity to make direct comparisons between the radio and white-light observations of the ICME kinematics. The STEREO observations also allow the locations of the radio sources along the shock front to be directly deduced from two or three spacecraft triangulation measurement from STEREO and Wind (Reiner et al. Solar Physics 10.1007/s

  14. Polypeptide composition of bacterial cyclic diguanylic acid-dependent cellulose synthase and the occurrence of immunologically crossreacting proteins in higher plants.

    PubMed Central

    Mayer, R; Ross, P; Weinhouse, H; Amikam, D; Volman, G; Ohana, P; Calhoon, R D; Wong, H C; Emerick, A W; Benziman, M

    1991-01-01

    To comprehend the catalytic and regulatory mechanism of the cyclic diguanylic acid (c-di-GMP)-dependent cellulose synthase of Acetobacter xylinum and its relatedness to similar enzymes in other organisms, the structure of this enzyme was analyzed at the polypeptide level. The enzyme, purified 350-fold by enzyme-product entrapment, contains three major peptides (90, 67, and 54 kDa), which, based on direct photoaffinity and immunochemical labeling and amino acid sequence analysis, are constituents of the native cellulose synthase. Labeling of purified synthase with either [32P]c-di-GMP or [alpha-32P]UDP-glucose indicates that activator- and substrate-specific binding sites are most closely associated with the 67- and 54-kDa peptides, respectively, whereas marginal photolabeling is detected in the 90-kDa peptide. However, antibodies raised against a protein derived from the cellulose synthase structural gene (bcsB) specifically label all three peptides. Further, the N-terminal amino acid sequences determined for the 90- and 67-kDa peptides share a high degree of homology with the amino acid sequence deduced from the gene. We suggest that the structurally related 67- and 54-kDa peptides are fragments proteolytically derived from the 90-kDa peptide encoded by bcsB. The anti-cellulose synthase antibodies crossreact with a similar set of peptides derived from other cellulose-producing microorganisms and plants such as Agrobacterium tumefaciens, Rhizobium leguminosarum, mung bean, peas, barley, and cotton. The occurrence of such cellulose synthase-like structures in plant species suggests that a common enzymatic mechanism for cellulose biogenesis is employed throughout nature. Images PMID:1647035

  15. Cloning, expression and properties of porcine trachea UDP-galnac: polypeptide N-acetylgalactosaminyl transferase.

    PubMed

    Sangadala, Sreedhara; Swain, Ja Baris; McNear, Adrian; Mendicino, Joseph

    2004-11-01

    A UDP-GalNAc:polypeptide N-acetyl-galactosaminyl transferase which catalyses the transfer of GalNAc from UDP-GalNAc to serine and threonine residues in mucin polypeptide chains was purified to homogeneity from swine trachea epithelium (Mendicino J, Sangadala S: Mol Cell Biochem 185: 135-145, 1998). Peptides obtained by proteolysis of the purified enzyme were isolated, sequenced and used to prepare degenerate oligonucleotide primers. Amplified segments of a gene encoding GalNAc transferase were synthesised using the primers and a swine trachea epithelial cDNA library. Selected cDNA fragments were then used to screen the cDNA library, and a clone containing an open reading frame encoding 559 amino acids was isolated. The predicted amino acid sequence contains type II transmembrane region, three potential N-glycosylation sites as well as all of the isolated peptide sequences. The nucleotide sequence and predicted primary protein structure of the transferase were very similar to those of type T-1 GalNAc transferases. The isolated clone was transiently expressed in COS 7 cells and the recombinant enzyme, which contained an N-terminal hexa-histidine tag, was purified to homogeneity and its enzymatic properties were examined. The Vmax of the recombinant enzyme, 2.08 micromol/(min mg), was nearly the same as the native enzyme, 2.12 micromol/(min mg), when assayed with partially deglycosylated mucins as glycosyl acceptors. Both enzymes showed much higher activities when assayed with peptides prepared by limited acid hydrolysis of incompletely deglycosylated Cowper's gland, swine, and human respiratory mucins and tryptic peptides isolated from deglycosylated mucin polypeptide chains. However, as noted earlier (Mendicino J, Sangadala S: Mol Cell Biochem 185: 135-145, 1998), these enzymes showed very little activity with completely deglycosylated mucin polypeptide chains. When completely deglycosylated polypeptide chains were partially glycosylated by incubation with microsome

  16. pH responsiveness of fibrous assemblies of repeat-sequence amphipathic α-helix polypeptides

    PubMed Central

    Takei, Toshiaki; Tsumoto, Kouhei; Okonogi, Atsuhito; Kimura, Akiko; Kojima, Shuichi; Yazaki, Kazumori; Takei, Tsunetomo; Ueda, Takuya; Miura, Kin-ichiro

    2015-01-01

    We reported previously that our designed polypeptide α3 (21 residues), which has three repeats of a seven-amino-acid sequence (LETLAKA)3, forms not only an amphipathic α-helix structure but also long fibrous assemblies in aqueous solution. To address the relationship between the electrical states of the polypeptide and its α-helix and fibrous assembly formation, we characterized mutated polypeptides in which charged amino acid residues of α3 were replaced with Ser. We prepared the following polypeptides: 2Sα3 (LSTLAKA)3, in which all Glu residues were replaced with Ser residues; 6Sα3 (LETLASA)3, in which all Lys residues were replaced with Ser; and 2S6Sα3 (LSTLASA)3; in which all Glu and Lys residues were replaced with Ser. In 0.1M KCl, 2Sα3 formed an α-helix under basic conditions and 6Sα3 formed an α-helix under acid conditions. In 1M KCl, they both formed α-helices under a wide pH range. In addition, 2Sα3 and 6Sα3 formed fibrous assemblies under the same buffer conditions in which they formed α-helices. α-Helix and fibrous assembly formation by these polypeptides was reversible in a pH-dependent manner. In contrast, 2S6Sα3 formed an α-helix under basic conditions in 1M KCl. Taken together, these findings reveal that the charge states of the charged amino acid residues and the charge state of the Leu residue located at the terminus play an important role in α-helix formation. PMID:25694229

  17. pH responsiveness of fibrous assemblies of repeat-sequence amphipathic α-helix polypeptides.

    PubMed

    Takei, Toshiaki; Tsumoto, Kouhei; Okonogi, Atsuhito; Kimura, Akiko; Kojima, Shuichi; Yazaki, Kazumori; Takei, Tsunetomo; Ueda, Takuya; Miura, Kin-ichiro

    2015-05-01

    We reported previously that our designed polypeptide α3 (21 residues), which has three repeats of a seven-amino-acid sequence (LETLAKA)3, forms not only an amphipathic α-helix structure but also long fibrous assemblies in aqueous solution. To address the relationship between the electrical states of the polypeptide and its α-helix and fibrous assembly formation, we characterized mutated polypeptides in which charged amino acid residues of α3 were replaced with Ser. We prepared the following polypeptides: 2Sα3 (LSTLAKA)3, in which all Glu residues were replaced with Ser residues; 6Sα3 (LETLASA)3, in which all Lys residues were replaced with Ser; and 2S6Sα3 (LSTLASA)3; in which all Glu and Lys residues were replaced with Ser. In 0.1M KCl, 2Sα3 formed an α-helix under basic conditions and 6Sα3 formed an α-helix under acid conditions. In 1M KCl, they both formed α-helices under a wide pH range. In addition, 2Sα3 and 6Sα3 formed fibrous assemblies under the same buffer conditions in which they formed α-helices. α-Helix and fibrous assembly formation by these polypeptides was reversible in a pH-dependent manner. In contrast, 2S6Sα3 formed an α-helix under basic conditions in 1M KCl. Taken together, these findings reveal that the charge states of the charged amino acid residues and the charge state of the Leu residue located at the terminus play an important role in α-helix formation. © 2015 The Protein Society.

  18. Two N-myc polypeptides with distinct amino termini encoded by the second and third exons of the gene.

    PubMed Central

    Mäkelä, T P; Saksela, K; Alitalo, K

    1989-01-01

    The N-myc and c-myc genes encode closely related nuclear phosphoproteins. We found that the N-myc protein from human tumor cell lines appears as four closely migrating polypeptide bands (p58 to p64) in sodium dodecyl sulfate-polyacrylamide gels. This and the recent finding that the c-myc protein is synthesized from two translational initiation sites located in the first and second exons of the gene (S. R. Hann, M. W. King, D. L. Bentley, C. W. Anderson, and R. N. Eisenman, Cell 52:185-195, 1988) prompted us to study the molecular basis of the N-myc protein heterogeneity. Dephosphorylation by alkaline phosphatase reduced the four polypeptide bands to a doublet with an electrophoretic mobility corresponding to the two faster-migrating N-myc polypeptides (p58 and p60). When expressed transiently in COS cells, an N-myc deletion construct lacking the first exon produced polypeptides similar to the wild-type N-myc protein, indicating that the first exon of the N-myc gene is noncoding. Furthermore, mutants deleted of up to two thirds of C-terminal coding domains still retained the capacity to produce a doublet of polypeptides, suggesting distinct amino termini for the two N-myc polypeptides. The amino-terminal primary structure of the N-myc protein was studied by site-specific point mutagenesis of the 5' end of the long open reading frame and by N-terminal radiosequencing of the two polypeptides. Our results show that the N-myc polypeptides are initiated from two alternative in-phase AUG codons located 24 base pairs apart at the 5' end of the second exon. Both of these polypeptides are phosphorylated and localized to the nucleus even when expressed separately. Interestingly, DNA rearrangements activating the c-myc gene are often found in the 1.7-kilobase-pair region between the two c-myc translational initiation sites and correlate with the loss of the longer c-myc polypeptide. Thus the close spacing of the two N-myc initiation codons could explain the relative resistance

  19. Parametric sensitivity analysis of avian pancreatic polypeptide (APP).

    PubMed

    Zhang, H; Wong, C F; Thacher, T; Rabitz, H

    1995-10-01

    Computer simulations utilizing a classical force field have been widely used to study biomolecular properties. It is important to identify the key force field parameters or structural groups controlling the molecular properties. In the present paper the sensitivity analysis method is applied to study how various partial charges and solvation parameters affect the equilibrium structure and free energy of avian pancreatic polypeptide (APP). The general shape of APP is characterized by its three principal moments of inertia. A molecular dynamics simulation of APP was carried out with the OPLS/Amber force field and a continuum model of solvation energy. The analysis pinpoints the parameters which have the largest (or smallest) impact on the protein equilibrium structure (i.e., the moments of inertia) or free energy. A display of the protein with its atoms colored according to their sensitivities illustrates the patterns of the interactions responsible for the protein stability. The results suggest that the electrostatic interactions play a more dominant role in protein stability than the part of the solvation effect modeled by the atomic solvation parameters.

  20. Coarse-grained, foldable, physical model of the polypeptide chain

    PubMed Central

    Chakraborty, Promita; Zuckermann, Ronald N.

    2013-01-01

    Although nonflexible, scaled molecular models like Pauling–Corey’s and its descendants have made significant contributions in structural biology research and pedagogy, recent technical advances in 3D printing and electronics make it possible to go one step further in designing physical models of biomacromolecules: to make them conformationally dynamic. We report here the design, construction, and validation of a flexible, scaled, physical model of the polypeptide chain, which accurately reproduces the bond rotational degrees of freedom in the peptide backbone. The coarse-grained backbone model consists of repeating amide and α-carbon units, connected by mechanical bonds (corresponding to φ and ψ) that include realistic barriers to rotation that closely approximate those found at the molecular scale. Longer-range hydrogen-bonding interactions are also incorporated, allowing the chain to readily fold into stable secondary structures. The model is easily constructed with readily obtainable parts and promises to be a tremendous educational aid to the intuitive understanding of chain folding as the basis for macromolecular structure. Furthermore, this physical model can serve as the basis for linking tangible biomacromolecular models directly to the vast array of existing computational tools to provide an enhanced and interactive human–computer interface. PMID:23898168

  1. Laser enhanced hydrolysis of selected polypeptides

    NASA Astrophysics Data System (ADS)

    Ouzts, Mary Paige

    This project serves as a preliminary examination of selectively enhancing bond cleavage during chemical reactions in biological molecules by using continuous wave infrared lasers. To analyze protein content, polypeptides are broken into their constituent amino acids through hydrolysis. The cleaving of the peptide bond has traditionally been accomplished under harsh conditions, 110°C in 6 N hydrochloric acid for 24 hours. In this project hydrolysis was strongly enhanced by irradiating the dipeptides, threonyl-aspartate and alanyl-alanine, for 30 minutes with coherent infrared radiation from a tunable carbon dioxide laser. The dipeptide tyrosyl-tyrosine, the chemical N- methylacetimide, and the protein BSA were successfully hydrolyzed with the laser. The effect of reaction parameters such as laser power and HCl concentration were studied, as well as the effect of the primary parameter, the beam wavelength. The samples were analyzed using standard biological methods for determining the amino acid concentration, thin layer chromatography and ion exchange chromatography. These methods gave consistent results for the irradiated samples as well as for standard amino acids and polypeptide samples. The results from these methods were used to create the hydrolysis spectra. The catalytic action of the laser was strongly wavelength dependent. The hydrolysis spectra of the molecules were compared to the absorption spectra of the samples. Laser enhanced hydrolysis occurred when the laser wavelength coincided with a line in the dipeptide spectra. This weak line in each of the dipeptide spectra is consistent both in position and strength with a line in NMA, which has been identified as a fundamental mode associated with the peptide bond. From the experimental results, the enhanced process appears to occur in the vapor phase. The initially liquid sample was progressively evaporated, and fully hydrolyzed material was carried to a collection trap by the vapor. It can, in principle

  2. Nucleotide and deduced amino acid sequences of Torpedo californica acetylcholine receptor gamma subunit.

    PubMed Central

    Claudio, T; Ballivet, M; Patrick, J; Heinemann, S

    1983-01-01

    The nucleotide sequence has been determined of a cDNA clone that codes for the 60,000-dalton gamma subunit of Torpedo californica acetylcholine receptor. The length of the cDNA clone is 2,010 base pairs. The 5' and 3' untranslated regions have respective lengths of 31 and 461 base pairs. Data suggest that the putative polyadenylylation consensus sequence A-A-T-A-A-A may not be required for polyadenylylation of the mRNA corresponding to the cDNA clone described in this study. From the DNA sequence data, the amino acid sequence of the gamma subunit was deduced. The subunit is composed of 489 amino acids giving a molecular mass of 56,600 daltons. The deduced amino acid sequence data also indicate the presence of a 17-amino acid extension or signal peptide on this subunit. From these data, structural predictions for the gamma subunit are made such as potential membrane-spanning regions, possible asparagine-linked glycosylation sites, and the assignment of regions of the protein to the extracellular, internal, and cytoplasmic domains of the lipid bilayer. Images PMID:6573658

  3. A novel approach for large-scale polypeptide folding based on elastic networks using continuous optimization.

    PubMed

    Rakshit, Sourav; Ananthasuresh, G K

    2010-02-07

    We present a new computationally efficient method for large-scale polypeptide folding using coarse-grained elastic networks and gradient-based continuous optimization techniques. The folding is governed by minimization of energy based on Miyazawa-Jernigan contact potentials. Using this method we are able to substantially reduce the computation time on ordinary desktop computers for simulation of polypeptide folding starting from a fully unfolded state. We compare our results with available native state structures from Protein Data Bank (PDB) for a few de-novo proteins and two natural proteins, Ubiquitin and Lysozyme. Based on our simulations we are able to draw the energy landscape for a small de-novo protein, Chignolin. We also use two well known protein structure prediction software, MODELLER and GROMACS to compare our results. In the end, we show how a modification of normal elastic network model can lead to higher accuracy and lower time required for simulation.

  4. Selective posttranslational modification of phage-displayed polypeptides

    SciTech Connect

    Tsao, Meng-Lin; Tian, Feng; Schultz, Peter

    2013-11-19

    The invention relates to posttranslational modification of phage-displayed polypeptides. These displayed polypeptides comprise at least one unnatural amino acid, e.g., an aryl-azide amino acid such as p-azido-L-phenylalanine, or an alkynyl-amino acid such as para-propargyloxyphenylalanine, which are incorporated into the phage-displayed fusion polypeptide at a selected position by using an in vivo orthogonal translation system comprising a suitable orthogonal aminoacyl-tRNA synthetase and a suitable orthogonal tRNA species. These unnatural amino acids advantageously provide targets for posttranslational modifications such as azide-alkyne [3+2] cycloaddition reactions and Staudinger modifications.

  5. Selective posttranslational modification of phage-displayed polypeptides

    SciTech Connect

    Tsao, Meng-Lin; Tian, Feng; Schultz, Peter

    2013-02-05

    The invention relates to posttranslational modification of phage-displayed polypeptides. These displayed polypeptides comprise at least one unnatural amino acid, e.g., an aryl-azide amino acid such as p-azido-L-phenylalanine, or an alkynyl-amino acid such as para-propargyloxyphenylalanine, which are incorporated into the phage-displayed fusion polypeptide at a selected position by using an in vivo orthogonal translation system comprising a suitable orthogonal aminoacyl-tRNA synthetase and a suitable orthogonal tRNA species. These unnatural amino acids advantageously provide targets for posttranslational modifications such as azide-alkyne [3+2]cycloaddition reactions and Staudinger modifications.

  6. Isolation, sequencing and expression of Bartonella henselae omp43 and predicted membrane topology of the deduced protein.

    PubMed

    Burgess, A W; Paquet, J Y; Letesson, J J; Anderson, B E

    2000-08-01

    The infection of and interaction of human endothelial cells with Bartonella henselae is one of the most interesting aspects of Bartonella -associated disease. The gene encoding the 43 kDa B. henselae outer membrane protein (Omp43) that binds endothelial cells was cloned and sequenced. Sequence analysis revealed an open reading frame of 1206 nucleotides coding for a protein of 402 amino acids. Analysis of the deduced amino acid sequence shows 38% identity over the entire sequence to the Brucella spp. In addition to this Omp2b porin also shows a signal sequence and peptidase cleavage site. Cleavage of the signal peptide results in a mature 380 amino acid polypeptide with a predicted molecular weight of 42 kDa. Omp43 was expressed in Escherichia coli as a fusion protein. Purified recombinant Omp43 at concentrations of 11 and 2.75 microg/ml bound to intact human umbilical vein endothelial cells. Membrane topology analysis predicts that Omp43 exists as a 16 stranded beta barrel protein, similar to that predicted for the Omp2b Brucella abortus porin. Characterization and expression of the gene encoding Omp43 should provide a tool for further investigation of the role of adherence to endothelial cells in the pathogenesis of B. henselae. Copyright 2000 Academic Press.

  7. Chiral polyamines from reduction of polypeptides: asymmetric pyridoxamine-mediated transaminations.

    PubMed

    Zhou, Wenjun; Yerkes, Nancy; Chruma, Jason J; Liu, Lei; Breslow, Ronald

    2005-03-01

    BH3.THF can reduce polypeptides to polyamines with retention of chirality. The resulting polyamines are intriguing general platforms for asymmetric catalysis, given the diverse structures available and their relative ease of synthesis. We have constructed a number of chiral pyridoxamine catalysts based on reduced peptides. These compounds transaminate alpha-ketoacids with moderate to good enantioselectivity, while their peptidyl counterparts show almost no chiral induction.

  8. Fibrillar dimer formation of islet amyloid polypeptides

    DOE PAGES

    Chiu, Chi -cheng; de Pablo, Juan J.

    2015-05-08

    Amyloid deposits of human islet amyloid polypeptide (hIAPP), a 37-residue hormone co-produced with insulin, have been implicated in the development of type 2 diabetes. Residues 20 – 29 of hIAPP have been proposed to constitute the amyloidogenic core for the aggregation process, yet the segment is mostly unstructured in the mature fibril, according to solid-state NMR data. Here we use molecular simulations combined with bias-exchange metadynamics to characterize the conformational free energies of hIAPP fibrillar dimer and its derivative, pramlintide. We show that residues 20 – 29 are involved in an intermediate that exhibits transient β-sheets, consistent with recent experimentalmore » and simulation results. By comparing the aggregation of hIAPP and pramlintide, we illustrate the effects of proline residues on inhibition of the dimerization of IAPP. The mechanistic insights presented here could be useful for development of therapeutic inhibitors of hIAPP amyloid formation.« less

  9. Turnover of cytokeratin polypeptides in mouse hepatocytes

    SciTech Connect

    Denk, H.; Lackinger, E.; Zatloukal, K. ); Franke, W.W. )

    1987-11-01

    The turnover of cytokeratin polypeptides A (equivalent to No. 8 of the human cytokeratin catalog) and D (equivalent to human cytokeratin No. 18) of mouse hepatocytes was studied by pulse-labeling of mouse liver proteins after intraperitoneal injection of L-(guanido{sup 14}C)arginine and ({sup 14}C)sodium bicarbonate. With L-(guanido-{sup 14}C)arginine a rapid increase in the specific radioactivity of both cytokeratins was observed which reached a plateau between 12 and 24 h. With ({sup 14}C)sodium bicarbonate maximal specific radioactivity was obtained at 6 h followed by a rapid decrease to half maximum values within the subsequent 6 h and then a slower decrease. Half-lives were determined from the decrease of specific radioactivities after pulse-labeling by least-squares plots and found to be 84 h (for cytokeratin component A) and 104 h (component D) for arginine labeling . Values obtained after bicarbonate labeling were similar (95 h for A and 98 h for D). These results show that liver cytokeratins are relatively stable proteins and suggest that components A and D are synthesized and degraded at similar rates, probably in a coordinate way.

  10. Mechanisms of stability of electrospun polypeptide fibers

    NASA Astrophysics Data System (ADS)

    Gitnik, Alina; Khadka, Dhan; Cross, Michael; Le, Nicole; Haynie, Donald

    2013-03-01

    Electrospun nano- and microfibers made of biodegradable and absorbable polymers are of great interest in biomedical engineering for tissue engineering, wound healing and other purposes. We have investigated physical properties of fibers made of the synthetic organic polymer co-poly(L-glutamic acid4, L-tyrosine1) (PLEY). This water-soluble polypeptide has a net negative charge at neutral pH. Dehydrated fibers are crosslinked with a diimide reagent dissolved in ethanol, giving a maximum average number of crosslinks of 1 per polymer molecule. Fiber integrity has been assessed in an aqueous medium at pH 2, 7 and 12, before and after crosslinking. Non-crosslinked fibers dissolved rapidly at all pH values, on a timescale of seconds to minutes. Crosslinked fibers dissolved completely at pH 12, but not at pH 2 or pH 7, the rate depending on the concentration of crosslinking reagent and therefore the density of crosslinks. Dissolution at pH 12 is attributable to ionization of the tyrosine side chain, which has a nominal pKa of 10.4, an increase in electrostatic repulsion between side chains and the migration of counterions into the fiber. Fibers crosslinked in 50 mM EDC buckled on a timescale of minutes at pH 12 and dissolved shortly thereafter. Funding provided by the National Science Foundation

  11. Elastin-like Polypeptide Based Hydroxyapatite Bionanocomposites

    PubMed Central

    Wang, Eddie; Lee, Sang-Hyuk; Lee, Seung-Wuk

    2011-01-01

    In nature, organic matrix macromolecules play a critical role in enhancing the mechanical properties of biomineralized composites such as bone and teeth. Designing artificial matrix analogues is promising but challenging because relatively little is known about how natural matrix components function. Therefore, in lieu of using natural components, we created biomimetic matrices using genetically engineered elastin-like polypeptides (ELPs) then used them to construct mechanically robust ELP-hydroxyapatite (HAP) composites. ELPs were engineered with well-defined backbone charge distributions by periodic incorporation of negative, positive, or neutral side chains or with HAP-binding octaglutamic acid motifs at one or both protein termini. ELPs exhibited sequence-specific capacities to interact with ions, bind HAP, and disperse HAP nanoparticles. HAP-binding ELPs were incorporated into calcium phosphate cements resulting in materials with improved mechanical strength, injectability, and anti-washout properties. The results demonstrate that rational design of genetically engineered polymers is a powerful system for determining sequence-property relationships and for improving the properties of organic-inorganic composites. Our approach may be used to further develop novel, multifunctional bone cements and expanded to the design of other advanced composites. PMID:21218767

  12. Superoxide Dismutase as an Anaerobic Polypeptide 1

    PubMed Central

    Monk, Lorna S.; Fagerstedt, Kurt V.; Crawford, Robert M. M.

    1987-01-01

    The perennating organ, the rhizome, was chosen for examination of response to anoxia in the species Iris pseudacorus L., Iris germanica L. var Quechei, and Glyceria maxima (Hartm.) Holmberg. These monocots are known to differ in their tolerance of anoxia. Intact rhizomes were subjected to periods of prolonged anoxia of up to 28 days and superoxide dismutase (SOD) activity was determined in a 48 hour postanoxic recovery phase. Tests were performed to ensure the accuracy of the measured enzyme activities. In the most anoxia tolerant species, I. pseudacorus, SOD activity rose continuously during the period of imposed anoxia, and levels were maintained in the postanoxic recovery phases: 28 days brought about a 13-fold increase to 1576 U SOD per milligram protein. Small increases were found in the less anoxia tolerant I. germanica during anoxic/postanoxic phases, while a drop in activity was recorded in the least anoxia tolerant G. maxima. However, initial levels in G. maxima were more than twice as high as in the other two species. Experiments applying cycloheximide to anoxic rhizome slices of I. pseudacorus inhibited the increase in SOD activity. This indicates that SOD is, paradoxically, induced under anoxia and we suggest that in this species SOD is one of the enzymes identified as anaerobic polypeptides. The significance of the induction of an `oxygen-protecting' enzyme during complete oxygen deprivation is discussed with regard to a possible critical role during recovery from anoxic stress. PMID:16665795

  13. Gastric inhibitory polypeptide secretion after radical pancreatoduodenectomy.

    PubMed Central

    Miyata, M; Nakao, K; Tanaka, Y; Sakamoto, T; Hamaji, M; Taketani, H; Kawashima, Y

    1984-01-01

    To elucidate the role of gastric inhibitory polypeptide (GIP) in the alteration of insulin secretion following pancreatoduodenal resection, in which the main sources of GIP are removed, plasma levels of GIP were measured for 180 minutes after oral glucose administration, both before and after radical pancreatoduodenectomy in nine patients with periampullary cancer. Fasting plasma levels of GIP remained much the same before and after surgery, and were not different from those in normal controls. The levels of GIP after glucose ingestion were significantly greater in the preoperative patients than in normal controls throughout 180 minutes. After pancreatoduodenectomy, the postglucose levels significantly diminished but remained within normal limits. Changes in plasma levels of insulin early after glucose ingestion in these patients, however, were significantly less both before and after surgery than in normal controls, and were not concomitant with the initial increase in plasma GIP. On the other hand, plasma levels of insulin greatly increased immediately after glucose ingestion in accordance with a rapid elevation of plasma GIP in 11 gastrectomized patients in whom the duodenum and the pancreas were preserved intact and who served as the control group. Thus, the diminution in GIP secretion following pancreatoduodenectomy may relate to the lack of main sources of this gut hormone and not to factors involved in the reconstruction of the alimentary tract. We conclude that the impaired insulin secretion following oral glucose ingestion in patients before and after pancreatoduodenectomy does not relate to the secretion of GIP. PMID:6367676

  14. DEDUCE Clinical Text: An Ontology-based Module to Support Self-Service Clinical Notes Exploration and Cohort Development.

    PubMed

    Roth, Christopher; Rusincovitch, Shelley A; Horvath, Monica M; Brinson, Stephanie; Evans, Steve; Shang, Howard C; Ferranti, Jeffrey M

    2013-01-01

    Large amounts of information, as well as opportunities for informing research, education, and operations, are contained within clinical text such as radiology reports and pathology reports. However, this content is less accessible and harder to leverage than structured, discrete data. We report on an extension to the Duke Enterprise Data Unified Content Explorer (DEDUCE), a self-service query tool developed to provide clinicians and researchers with access to data within the Duke Medicine Enterprise Data Warehouse (EDW). The DEDUCE Clinical Text module supports ontology-based text searching, enhanced filtering capabilities based on document attributes, and integration of clinical text with structured data and cohort development. The module is implemented with open-source tools extensible to other institutions, including a Java-based search engine (Apache Solr) with complementary full-text indexing library (Lucene) employed with a negation engine (NegEx) modified by clinical users to include to local domain-specific negation phrases.

  15. Idealized models of protofilaments of human islet amyloid polypeptide

    PubMed Central

    Li, Yiyu; Hatmal, Ma'mon M.; Langen, Ralf; Haworth, Ian S.

    2012-01-01

    Fibrils formed by assembly of human islet amyloid polypeptide (hIAPP) are found in most patients with type II diabetes. Structurally, these fibrils are composed of multiple protofilaments and are characterized by extended beta sheets, variable helical twists, and different morphologies. We have previously derived models for the hIAPP protofilament using simulations constrained by data from EPR spectroscopy. In the current work, these models were used as a basis for generating idealized hIAPP protofilaments with symmetrical geometrical properties using a new algorithm, MFIBRIL. We show good agreement of the idealized protofilaments with experimental data for amino acid side chain orientations and geometrical features including the inter-beta sheet distance and the protofilament radius. These idealized protofilaments can be used in MFIBRIL to generate fibril models that may be experimentally testable at the molecular level. MFIBRIL can also be used for building structures of any repetitive molecular assembly starting with a single building block obtained from any source. PMID:23116372

  16. A major substrate for MPF: cDNA cloning and expression of polypeptide chain elongation factor 1 gamma from goldfish (Carassius auratus).

    PubMed

    Tokumoto, Mika; Nagahama, Yoshitaka; Tokumoto, Toshinobu

    2002-02-01

    One of the eukaryotic polypeptide chain elongation factors, EF-1 beta gamma delta complex, is involved in polypeptide chain elongation via the GDP/GTP exchange activity of EF-1 alpha. In the complex, EF-1 gamma has been reported to be a major substrate for maturation promoting factor (MPF). Here, we present the cloning, sequencing and expression analysis of goldfish, Carassius auratus, EF-1 gamma from the goldfish ovary. The cloned cDNA was 1490 bp in length and encoded 442 amino acids. The deduced amino acid sequence was highly homologous to EF-1 gamma from other species. Although, the phosphorylation site identified in Xenopus EF-1 gamma was not conserved in the goldfish homologue, phosphorylation analysis showed that the goldfish EF-1 gamma was phosphorylated by MPF. We concluded that EF-1 gamma is a substrate for MPF during oocyte maturation in goldfish.

  17. Polypeptide and RNA composition of the reticuloendotheliosis viruses.

    PubMed

    Maldonado, R L; Bose, H R

    1975-01-01

    The RNA and polypeptide composition of chick syncytial virus (CSV) and duck infectious anemia virus (DIAV) was investigated and compared to that of reticuloendotheliosis virus (REV) strain T, the prototype of the newly recognized REV group of viruses. CSV and DIAV contain genomic RNA species which cosediment with those of REV in sucrose gradients. Five or six polypeptides, two of which are glycoproteins, were consistently found in CSV and DIAV preparations. The major nonglycosylated polypeptides and glycoproteins of CSV and DIAV comigrated with the corresponding polypeptides of REV strain T. Since the genomic RNA species and the glycoproteins of avian tumor viruses fail to comigrate, this suggests that the REV complex is a more homogeneous group.

  18. Biomedical applications of polypeptide multilayer nanofilms and microcapsules

    NASA Astrophysics Data System (ADS)

    Rudra, Jai Simha S.

    The past few years have witnessed considerable growth in synthetic polymer chemistry and physics, biomaterials science, and nano-scale engineering. Research on polypeptide multilayer films, coatings, and microcapsules is located at the intersection of these areas and are promising materials for applications in medicine, biotechnology, environmental science. Most envisioned applications of polypeptide multilayers have a biomedical bent. This dissertation on polypeptide multilayer film applications covers key points of polypeptides as materials, means of polymer production, film preparation, film characterization methods, and key points of current research in basic science. Both commercial and designed peptides have been used to fabricate films for in-vitro applications such as antimicrobial coatings and cell culture coatings and also microcapsules for drug delivery applications. Other areas of product development include artificial red blood cells, anisotropic coatings, enantioselective membranes, and artificial viruses.

  19. Folding and self-assembly of polypeptides: Dynamics and thermodynamics from molecular simulation

    NASA Astrophysics Data System (ADS)

    Fluitt, Aaron Michael

    Empowered by their exquisite three-dimensional structures, or "folds," proteins carry out biological tasks with high specificity, efficiency, and fidelity. The fold that optimizes biological function represents a stable configuration of the constituent polypeptide molecule(s) under physiological conditions. Proteins and polypeptides are not static, however: battered by thermal motion, they explore a distribution of folds that is determined by the sequence of amino acids, the presence and identity of other molecules, and the thermodynamic conditions. In this dissertation, we apply molecular simulation techniques to the study of two polypeptides that have unusually diffuse distributions of folds under physiological conditions: polyglutamine (polyQ) and islet amyloid polypeptide (IAPP). Neither polyQ nor IAPP adopts a predominant fold in dilute aqueous solution, but at sufficient concentrations, both are prone to self-assemble into stable, periodic, and highly regular aggregate structures known as amyloid. The appearance of amyloid deposits of polyQ in the brain, and of IAPP in the pancreas, are associated with Huntington's disease and type 2 diabetes, respectively. A molecular view of the mechanism(s) by which polyQ and IAPP fold and self-assemble will enhance our understanding of disease pathogenesis, and it has the potential to accelerate the development of therapeutics that target early-stage aggregates. Using molecular simulations with spatial and temporal resolution on the atomic scale, we present analyses of the structural distributions of polyQ and IAPP under various conditions, both in and out of equilibrium. In particular, we examine amyloid fibers of polyQ, the IAPP dimer in solution, and single IAPP fragments at a lipid bilayer. We also benchmark the molecular models, or "force fields," available for such studies, and we introduce a novel simulation algorithm.

  20. Recognition of subsets of the mammalian A/B-type core heterogeneous nuclear ribonucleoprotein polypeptides by novel autoantibodies.

    PubMed Central

    Dangli, A; Plomaritoglou, A; Boutou, E; Vassiliadou, N; Moutsopoulos, H M; Guialis, A

    1996-01-01

    The structurally related A/B-type core heterogeneous nuclear ribonucleoprotein (hnRNP) polypeptides of 34-39 kDa (A1, A2, B1 and B2) belong to a family of RNA-binding proteins that are major components of 40 S hnRNP complexes. By two-dimensional gel electrophoresis and peptide mapping analysis we compared each member of the A/B-type core proteins in the human and rat liver cells. This comparison revealed the unique presence in rat cells of major protein species, referred to as mBx polypeptides, that appeared as three charge isoforms at a position corresponding to the minor HeLa B1b protein spot. In addition, clear differences in the ratios of the A1 polypeptide to the A1b isoform were observed. The detection, in sera of patients with rheumatic autoimmune diseases, of two novel autoantibody specificities, one recognizing solely B2 protein and the second both the B2 and mBx polypeptides, helped to identify mBx proteins as new A/B-type hnRNP components, immunologically related to B2 protein. A common immunoreactive V8 protease peptide of approx. 17 kDa has been identified in B2 and mBx hnRNP polypeptides. mBx protein species are identified in cells of murine origin, and have a ubiquitous tissue distribution and developmental appearance. PMID:9003360

  1. Controlling assembly of helical polypeptides via PEGylation strategies†

    PubMed Central

    Top, Ayben; Zhong, Sheng; Yan, Congqi

    2013-01-01

    Recent studies in our laboratories have demonstrated that a helical polypeptide (17H6), equipped with a histidine tag and a helical alanine-rich, glutamic-acid-containing domain, exhibits pH-responsive assembly behavior useful in the production of polymorphological nanostructures. In this study, the histidine tag in these polypeptides was replaced by polyethylene glycol (PEG) with different molecular masses (5 kDa, or 10 kDa), and the self-association behavior of 17H6 and the PEGylated conjugates was characterized via dynamic light scattering (DLS), small angle neutron scattering (SANS), and cryogenic transmission electron microscopy (cryo-TEM). DLS experiments illustrated that the polypeptide and its PEG-conjugates undergo reversible assembly under acidic conditions, suggesting that the aggregation state of the polypeptide and the conjugates is controlled by the charged state of the glutamic acid residues. Nanoscale aggregates were detected at polypeptide/conjugate concentrations as low as 20 μM (∼0.3–0.5 mg ml−1) at physiological and ambient temperatures. Scattering and microscopy results showed that the size, the aggregation number, and the morphology of the aggregates can be tuned by the size and the nature of the hydrophilic tag. This tunable nature of the morphology of the aggregates, along with their low critical aggregation concentration, suggests that PEG-alanine-rich polypeptide conjugates may be useful as drug delivery vehicles in which the alanine-rich block serves as a drug attachment domain. PMID:24039625

  2. Empirical singular vectors of baroclinic flows deduced from experimental data

    NASA Astrophysics Data System (ADS)

    Harlander, Uwe; Hoff, Michael; Seelig, Torsten; Egbers, Christoph

    2013-04-01

    Instability is related to exponentially growing eigenmodes. Interestingly, when finite time intervals are considered, growth rates of certain initial perturbations can exceed the growth rates of the most unstable modes. Moreover, even when all modes are damped, such particular initial perturbations can grow dramatically during finite time intervals. The perturbations with the largest growth rates are called singular vectors or optimal perturbations. They not only play an important role in atmospheric ensemble predictions, but also for the theory of instability and turbulence. Starting point for the singular vector analysis is a linear dynamical system with a known system matrix. In atmospheric ensemble prediction, linearization is generally done around a nonlinear solution and then the system matrix is time-dependent. In contrast, in turbulence research linearization is done around a mean state. In that case the system matrix is time-independent. We consider the mathematically simpler latter case here. We decompose surface temperature data of a differentially heated rotating annulus experiment into principal oscillation patterns, that are the empirically estimated linear eigenmodes of the system. Using these modes we can estimate the modes of maximal growth, which are thus the empirically estimated singular vectors. In contrast to the traditional approach we deduce these modes from the data alone without using a linear model operator and thus without actually knowing the system matrix (Penland and Sardeshmukh, 1995). In our study we will address the following questions: What is the appropriate filter technique to remove noise from the data prior to the empirical singular vector analysis? Is there an objective mean to distinguish between noise and signal? How accurate are the empirical singular vectors? To answer the last question we compare the data based results with findings from a numerical model for which the system matrix is known. We want to test the idea

  3. Thermodynamic Approach to Enhanced Dispersion and Physical Properties in a Carbon Nanotube/Polypeptide Nanocomposite

    NASA Technical Reports Server (NTRS)

    Lovell, Conrad S.; Wise, Kristopher E.; Kim, Jae-Woo; Lillehei, Peter T.; Harrison, Joycelyn S.; Park, Cheol

    2009-01-01

    A high molecular weight synthetic polypeptide has been designed which exhibits favorable interactions with single wall carbon nanotubes (SWCNTs). The enthalpic and entropic penalties of mixing between these two molecules are reduced due to the polypeptide's aromatic sidechains and helical secondary structure, respectively. These enhanced interactions result in a well dispersed SWCNT/Poly (L-Leucine-ran-L-Phenylalanine) nanocomposite with enhanced mechanical and electrical properties using only shear mixing and sonication. At 0.5 wt% loading of SWCNT filler, the nanocomposite exhibits simultaneous increases in the Young's modulus, failure strain, and toughness of 8%, 120%, and 144%, respectively. At one kHz, the same nanotube loading level also enhances the dielectric constant from 2.95 to 22.81, while increasing the conductivity by four orders of magnitude.

  4. Self-assembling chimeric polypeptide-doxorubicin conjugate nanoparticles that abolish tumours after a single injection

    NASA Astrophysics Data System (ADS)

    Andrew Mackay, J.; Chen, Mingnan; McDaniel, Jonathan R.; Liu, Wenge; Simnick, Andrew J.; Chilkoti, Ashutosh

    2009-12-01

    New strategies to self-assemble biocompatible materials into nanoscale, drug-loaded packages with improved therapeutic efficacy are needed for nanomedicine. To address this need, we developed artificial recombinant chimeric polypeptides (CPs) that spontaneously self-assemble into sub-100-nm-sized, near-monodisperse nanoparticles on conjugation of diverse hydrophobic molecules, including chemotherapeutics. These CPs consist of a biodegradable polypeptide that is attached to a short Cys-rich segment. Covalent modification of the Cys residues with a structurally diverse set of hydrophobic small molecules, including chemotherapeutics, leads to spontaneous formation of nanoparticles over a range of CP compositions and molecular weights. When used to deliver chemotherapeutics to a murine cancer model, CP nanoparticles have a fourfold higher maximum tolerated dose than free drug, and induce nearly complete tumour regression after a single dose. This simple strategy can promote co-assembly of drugs, imaging agents and targeting moieties into multifunctional nanomedicines.

  5. A simple biochemical method in the search for bioactive polypeptides in a sea anemone (Anemonia sulcata).

    PubMed

    Sanchez, J; Bruhn, T; Aneiros, A; Wachter, E; Béress, L

    1996-01-01

    The sea anemone Anemonia sulcata is a well-known natural source of supply of biologically active polypeptides. So far, five toxins, ATX I, II, III, IV and AS V, several polyvalent protease inhibitors, an elastase inhibitor, two blood pressure-depressive polypeptides and very recently peptides that inhibit competitively the binding of 125I-dendrotoxin to rat brain membranes and block the voltage-sensitive K+ channels, have been isolated from it. The sea anemone toxins (especially toxin II of A. sulcata, ATX II) are very important tools in neurophysiological and pharmacological research, and their structure-function relationship has been investigated. Because of the great scientific value of the sea anemone toxins a simplification of their purification procedure was elaborated.

  6. Conserved motifs in prokaryotic and eukaryotic polypeptide release factors: tRNA-protein mimicry hypothesis.

    PubMed Central

    Ito, K; Ebihara, K; Uno, M; Nakamura, Y

    1996-01-01

    Translation termination requires two codon-specific polypeptide release factors in prokaryotes and one omnipotent factor in eukaryotes. Sequences of 17 different polypeptide release factors from prokaryotes and eukaryotes were compared. The prokaryotic release factors share residues split into seven motifs. Conservation of many discrete, perhaps critical, amino acids is observed in eukaryotic release factors, as well as in the C-terminal portion of elongation factor (EF) G. Given that the C-terminal domains of EF-G interacts with ribosomes by mimicry of a tRNA structure, the pattern of conservation of residues in release factors may reflect requirements for a tRNA-mimicry for binding to the A site of the ribosome. This mimicry would explain why release factors recognize stop codons and suggests that all prokaryotic and eukaryotic release factors evolved from the progenitor of EF-G. Images Fig. 2 Fig. 3 PMID:8643594

  7. Peptides and polypeptides as scaffolds for optoelectronics and biomaterials applications

    NASA Astrophysics Data System (ADS)

    Charati, Manoj B.

    Peptides and polypeptides are emerging as a new class of biomaterials due to their unique structural, physiochemical, mechanical, and biological properties. The development of peptide and protein-based biomaterials is driven by the convergence of convenient techniques for peptide/protein engineering and its importance in applications as smart biomaterials. The thesis is divided in two parts; the first part highlights the importance of incorporation of non-natural amino acids into peptides and proteins. In particular, incorporation on p-bromophenylalanine in short alpha-helical peptide templates to control the association of chromophores is discussed. In the second part, design of a multi-component, biocompatible polypeptide with superior elasticity is discussed. Part 1. Novel peptide templates to control association of chromophores. Tailor made peptide and protein materials have many versatile applications, as both conformation and functional group position can be controlled. Such control may have intriguing applications in the development of hybrid materials for electroactive applications. A critical need in fabricating devices from organic semiconducting materials is to achieve control over the conformation and distance between two conjugated chains. Controlling chromophore spacing and orientation with required precision over nanometer length scale poses a greater challenge. Here we propose a peptide based template to control the alignment of the methylstilbene and Oxa-PPV chromophores with desired orientations and spacing. The hybrid peptides were characterized via CD, exciton coupled CD, 1H NMR and photoluminescence experiments. It is observed that slight change in the orientation of molecules has pronounced effect on the photo-physical behavior of the molecules. Characterization of the hybrid peptides via circular dichroism (CD) confirmed the helical character of the designed peptides and indicated that inclusion of non-natural amino acids has significant

  8. Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains

    SciTech Connect

    Daidone, Isabella; Neuweiler, H; Doose, S; Sauer, M; Smith, Jeremy C

    2010-12-01

    Characterization of the length dependence of end-to-end loop-closure kinetics in unfolded polypeptide chains provides an understanding of early steps in protein folding. Here, loop-closure in poly-glycine-serine peptides is investigated by combining single-molecule fluorescence spectroscopy with molecular dynamics simulation. For chains containing more than 10 peptide bonds loop-closing rate constants on the 20-100 nanosecond time range exhibit a power-law length dependence. However, this scaling breaks down for shorter peptides, which exhibit slower kinetics arising from a perturbation induced by the dye reporter system used in the experimental setup. The loop-closure kinetics in the longer peptides is found to be determined by the formation of intra-peptide hydrogen bonds and transient beta-sheet structure, that accelerate the search for contacts among residues distant in sequence relative to the case of a polypeptide chain in which hydrogen bonds cannot form. Hydrogen-bond-driven polypeptide-chain collapse in unfolded peptides under physiological conditions found here is not only consistent with hierarchical models of protein folding, that highlights the importance of secondary structure formation early in the folding process, but is also shown to speed up the search for productive folding events.

  9. A Solid Phase Vibrational Circular Dichroism Study of Polypeptide-Surfactant Interaction.

    PubMed

    Novotná, Pavlína; Urbanová, Marie

    2015-12-01

    We studied the interaction of poly-l-lysine (PLL) and poly-l-arginine (PLAG) with sodium dodecyl sulfate (SDS) surfactant and the interaction of poly-l-glutamic acid (PLGA) and poly-l-aspartic acid (PLAA) with tetradecyltrimethylammonium bromide (TTAB) surfactant using vibrational circular dichroism (VCD) spectroscopy in the region of C-H stretching vibration and in the Amide I region both in solution and in mulls. A chirality transfer from polypeptides to achiral surfactants was observed in the C-H stretching region, where measurements in solution were impossible. This observation was enabled by a special sample treatment technique using lyophilization and the preparation of mulls. This technique demonstrated itself as an interesting and beneficial tool for VCD measurements. In addition, we observed that SDS changed the secondary structure of PLL to the β-sheet and of PLAG to the α-helix. TTAB disrupted the PLGA and PLAA structure. These results were obtained in the mull but were confirmed by the VCD spectra measured in solution and by electronic circular dichroism. The chirality transfer from the polypeptides to SDS was caused by polypeptides ordered into a specific conformation during the interaction, while in the TTBA system it was induced primarily by the chirality of the amino acid residues. © 2015 Wiley Periodicals, Inc.

  10. Characterization of defensin gene from abalone Haliotis discus hannai and its deduced protein

    NASA Astrophysics Data System (ADS)

    Hong, Xuguang; Sun, Xiuqin; Zheng, Minggang; Qu, Lingyun; Zan, Jindong; Zhang, Jinxing

    2008-11-01

    Defensin is one of preserved ancient host defensive materials formed in biological evolution. As a regulator and effector molecule, it is very important in animals’ acquired immune system. This paper reports the defensin gene from the mixed liver and kidney cDNA library of abalone Haliotis discus hannai Ino. Sequence analysis shows that the gene sequence of full-length cDNA encodes 42 mature peptides (including six Cys), molecular weight of 4 323 Da, and pI of 8.02. Amino acid sequence homology analysis shows that the peptides are highly similar (70% in common) to other insects defensin. Because of a typical insect-defensin structural character of mature peptide in the secondary structure, the polypeptide named Haliotis discus defensin (hd-def), a novel of antimicrobial peptides, belongs to insects defensin subfamily. The RT-PCR result of Haliotis discus defensin shows that the gene can be expressed only in the hepatopancreas by Gram-negative and positive bacteria stimulation, which is ascribed to inducible expression. Therefore, it is revealed that the Haliotis discus defensin gene expression was related to the antibacterial infection of Haliotis discus hannai Ino.

  11. Atrial natriuretic polypeptide-like material in rat lung

    SciTech Connect

    Chang, J.K.; Chang, D.; Xie, C.W.; Song, D.L.; Li, X.R.; Zhang, S.X.; Wang, T.L.; Tang, J.

    1986-03-05

    Atrial natriuretic polypeptide-like immunoreactive material (ANP-IR) was found in rat lung by radioimmunoassay, with the concentration ranging from 0.6-1.2 pmol/g of tissue in each lobe. PAP-immunohistochemical study demonstrated that specific staining of granules for ..cap alpha..-human ANP are mainly located in the muscular layer of the pulmonary vein. Fractionation of lung extract by gel filtration and reserve phase HPLC revealed the presence of multiple forms of ANP-IR, which possibly possessed molecular structure partially different from rat ANP, atriopeptin I and III. Intravenous injection of lung extract induced potent diuresis and natriuresis in rats. These responses could be abolished when the lung extract was preincubated with antiserum for ..cap alpha..-human ANP. Specific binding sites for /sup 125/I-labeled rat ANP were also found in lung membrane preparation by radioreceptor assay. Incubation of synthetic atriopeptin III (10/sup -9/ to 10/sup -6/M) with lung tissue induced 1-28 fold increase in lung cGMP content. The results suggest that ANP-IR and its receptors existing in rat lung may be involved in the regulation of pulmonary function and have a synergic effect with ANP of cardiac origin in the control of water-electrolytes balance.

  12. Volumetric properties of human islet amyloid polypeptide in liquid water.

    PubMed

    Brovchenko, I; Andrews, M N; Oleinikova, A

    2010-04-28

    The volumetric properties of human islet amyloid polypeptide (hIAPP) in water were studied in a wide temperature range by computer simulations. The intrinsic density rho(p) and the intrinsic thermal expansion coefficient alpha(p) of hIAPP were evaluated by taking into account the difference between the volumetric properties of hydration and bulk water. The density of hydration water rho(h) was found to decrease almost linearly with temperature upon heating and its thermal expansion coefficient was found to be notably higher than that of bulk water. The peptide surface exposed to water is more hydrophobic and its rho(h) is smaller in conformation with a larger number of intrapeptide hydrogen bonds. The two hIAPP peptides studied (with and without disulfide bridge) show negative alpha(p), which is close to zero at 250 K and decreases to approximately -1.5 x 10(-3) K(-1) upon heating to 450 K. The analysis of various structural properties of peptides shows a correlation between the intrinsic peptide volumes and the number of intrapeptide hydrogen bonds. The obtained negative values of alpha(p) can be attributed to the shrinkage of the inner voids of the peptides upon heating.

  13. Simple setup for gas-phase H/D exchange mass spectrometry coupled to electron transfer dissociation and ion mobility for analysis of polypeptide structure on a liquid chromatographic time scale.

    PubMed

    Mistarz, Ulrik H; Brown, Jeffery M; Haselmann, Kim F; Rand, Kasper D

    2014-12-02

    Gas-phase hydrogen/deuterium exchange (HDX) is a fast and sensitive, yet unharnessed analytical approach for providing information on the structural properties of biomolecules, in a complementary manner to mass analysis. Here, we describe a simple setup for ND3-mediated millisecond gas-phase HDX inside a mass spectrometer immediately after ESI (gas-phase HDX-MS) and show utility for studying the primary and higher-order structure of peptides and proteins. HDX was achieved by passing N2-gas through a container filled with aqueous deuterated ammonia reagent (ND3/D2O) and admitting the saturated gas immediately upstream or downstream of the primary skimmer cone. The approach was implemented on three commercially available mass spectrometers and required no or minor fully reversible reconfiguration of gas-inlets of the ion source. Results from gas-phase HDX-MS of peptides using the aqueous ND3/D2O as HDX reagent indicate that labeling is facilitated exclusively through gaseous ND3, yielding similar results to the infusion of purified ND3-gas, while circumventing the complications associated with the use of hazardous purified gases. Comparison of the solution-phase- and gas-phase deuterium uptake of Leu-Enkephalin and Glu-Fibrinopeptide B, confirmed that this gas-phase HDX-MS approach allows for labeling of sites (heteroatom-bound non-amide hydrogens located on side-chains, N-terminus and C-terminus) not accessed by classical solution-phase HDX-MS. The simple setup is compatible with liquid chromatography and a chip-based automated nanoESI interface, allowing for online gas-phase HDX-MS analysis of peptides and proteins separated on a liquid chromatographic time scale at increased throughput. Furthermore, online gas-phase HDX-MS could be performed in tandem with ion mobility separation or electron transfer dissociation, thus enabling multiple orthogonal analyses of the structural properties of peptides and proteins in a single automated LC-MS workflow.

  14. [Antiangiogenic Effect of Oyster Polypeptide (OPP).].

    PubMed

    Wang, Zhenhua; Liu, Jincheng; Su, Ai; Sun, Mi; Wang, Chunbo

    2009-08-20

    Drugs which block tumor angiogenesis will be likely effective towards inhibiting tumor growth for angiogenesis being a prerequisite for tumor growth and metastasis. Therefore, antiangiogenesis has become a promising strategy for the treatment of cancer. Investigation on both antiangiogenic effect and mechanism(s) of oyster polypeptide (OPP) were performed via experiments of chicken embryos model in vivo and human umbilical vein endothelial cells (HUVECs) in vitro. The methods employed in experiment were chorioallantoic membrane (CAM) angiogenesis in chicken embryos in vivo, MTT cell survival assay, flat plate scarification, transwell plates assay, matrigel-induced tube formation assay and transmission electron microscope et al. and the OPP's effects on angiogenesis was observed. Study showed that treatment with OPP resulted in significant inhibition of chorioallantoic membrane (CAM) angiogenesis in chicken embryos. MTT cell survival assay showed that treatment with OPP resulted in strong inhibition of HUVECs growth, with an IC50 of 400 mug/mL. Flat plate scarification suggested that OPP (200 mug/mL, 400 mug/mL and 800 mug/mL) distinctly inhibited HUVECs' migration (18.75%, 37.93%, 74.07% respectively, treatment for 12 h). Treatment with OPP of different concentrations (200 mug/mL, 400 mug/mL and 800 mug/mL) significantly reduced the density of the migration cells by 15.5%, 37.2% and 67.24% (P<0.05) respectively. Matrigel-induced tube formation assay showed that OPP resulted in striking inhibition of tube formation of 52.43%, 84.47% and 96.12% (P<0.01) at 200 mug/mL, 400 mug/mL and 800 mug/mL (treatment for 10 h) respectively. In addition, the apoptotic analysis by transmission electron microscope showed that OPP (400 mug/mL, treatment for 48 h) distinctly induced HUVECs' apoptosis. This study strikingly showed that OPP could inhibit angiogenesis through its effects on vascular endothelial cells directly and the inhibition of their proliferation, migration

  15. Mutational analysis of photosystem I polypeptides in the cyanobacterium Synechocystis sp. PCC 6803. Targeted inactivation of psaI reveals the function of psaI in the structural organization of psaL

    NASA Technical Reports Server (NTRS)

    Xu, Q.; Hoppe, D.; Chitnis, V. P.; Odom, W. R.; Guikema, J. A.; Chitnis, P. R.; Spooner, B. S. (Principal Investigator)

    1995-01-01

    We cloned, characterized, and inactivated the psaI gene encoding a 4-kDa hydrophobic subunit of photosystem I from the cyanobacterium Synechocystis sp. PCC 6803. The psaI gene is located 90 base pairs downstream from psaL, and is transcribed on 0.94- and 0.32-kilobase transcripts. To identify the function of PsaI, we generated a cyanobacterial strain in which psaI has been interrupted by a gene for chloramphenicol resistance. The wild-type and the mutant cells showed comparable rates of photoautotrophic growth at 25 degrees C. However, the mutant cells grew slower and contained less chlorophyll than the wild-type cells, when grown at 40 degrees C. The PsaI-less membranes from cells grown at either temperature showed a small decrease in NADP+ photoreduction rate when compared to the wild-type membranes. Inactivation of psaI led to an 80% decrease in the PsaL level in the photosynthetic membranes and to a complete loss of PsaL in the purified photosystem I preparations, but had little effect on the accumulation of other photosystem I subunits. Upon solubilization with nonionic detergents, photosystem I trimers could be obtained from the wild-type, but not from the PsaI-less membranes. The PsaI-less photosystem I monomers did not contain detectable levels of PsaL. Therefore, a structural interaction between PsaL and PsaI may stabilize the association of PsaL with the photosystem I core. PsaL in the wild-type and PsaI-less membranes showed equal resistance to removal by chaotropic agents. However, PsaL in the PsaI-less strain exhibited an increased susceptibility to proteolysis. From these data, we conclude that PsaI has a crucial role in aiding normal structural organization of PsaL within the photosystem I complex and the absence of PsaI alters PsaL organization, leading to a small, but physiologically significant, defect in photosystem I function.

  16. Mutational analysis of photosystem I polypeptides in the cyanobacterium Synechocystis sp. PCC 6803. Targeted inactivation of psaI reveals the function of psaI in the structural organization of psaL

    NASA Technical Reports Server (NTRS)

    Xu, Q.; Hoppe, D.; Chitnis, V. P.; Odom, W. R.; Guikema, J. A.; Chitnis, P. R.; Spooner, B. S. (Principal Investigator)

    1995-01-01

    We cloned, characterized, and inactivated the psaI gene encoding a 4-kDa hydrophobic subunit of photosystem I from the cyanobacterium Synechocystis sp. PCC 6803. The psaI gene is located 90 base pairs downstream from psaL, and is transcribed on 0.94- and 0.32-kilobase transcripts. To identify the function of PsaI, we generated a cyanobacterial strain in which psaI has been interrupted by a gene for chloramphenicol resistance. The wild-type and the mutant cells showed comparable rates of photoautotrophic growth at 25 degrees C. However, the mutant cells grew slower and contained less chlorophyll than the wild-type cells, when grown at 40 degrees C. The PsaI-less membranes from cells grown at either temperature showed a small decrease in NADP+ photoreduction rate when compared to the wild-type membranes. Inactivation of psaI led to an 80% decrease in the PsaL level in the photosynthetic membranes and to a complete loss of PsaL in the purified photosystem I preparations, but had little effect on the accumulation of other photosystem I subunits. Upon solubilization with nonionic detergents, photosystem I trimers could be obtained from the wild-type, but not from the PsaI-less membranes. The PsaI-less photosystem I monomers did not contain detectable levels of PsaL. Therefore, a structural interaction between PsaL and PsaI may stabilize the association of PsaL with the photosystem I core. PsaL in the wild-type and PsaI-less membranes showed equal resistance to removal by chaotropic agents. However, PsaL in the PsaI-less strain exhibited an increased susceptibility to proteolysis. From these data, we conclude that PsaI has a crucial role in aiding normal structural organization of PsaL within the photosystem I complex and the absence of PsaI alters PsaL organization, leading to a small, but physiologically significant, defect in photosystem I function.

  17. A major protein precursor of zebra mussel (Dreissena polymorpha) byssus: deduced sequence and significance.

    PubMed

    Anderson, K E; Waite, J H

    1998-04-01

    The zebra mussel is a nonindigenous invader of North American lakes and rivers and one of the few freshwater bivalve molluscs having a byssus--a sclerotized organ used by the mussel for opportunistic attachment to hard surfaces. We have sequenced a foot-specific cDNA whose composite protein sequence was deduced from a series of overlapping but occasionally nonidentical cDNA fragments. The overall deduced sequence matches tryptic peptides from a major byssal precursor protein--Dreissena polymorpha foot protein 1 (Dpfp1). The calculated mass of Dpfp1 is 49 kDa; but this is known to be extensively hydroxylated and O-glycosylated during maturation. Purified native Dpfp1 analyzed using matrix-assisted laser-desorption ionization mass spectrometry with time-of-flight indicates that the protein occurs as at least two size variants with masses of 48.6 and 54.5 kDa. In all probability, the sequence variants reported in this study are related to the larger mass variant. Dpfp1 has a block copolymer-like structure defined by two consensus motifs that are sharply segregated into domains. The N-terminal side of Dpfp1 has 22 tandem repeats of a heptapeptide consensus (P-[V/E]-Y-P-[T/S/delta]-[K/Q]-X); the C-terminal side has 16 repeats of a tridecapeptide motif (K-P-G-P-Y-D-Y-D-G-P-Y-D-K). Both consensus repeats are unique, with some limited homology to other proteins functioning in tension: marine mussel adhesives, plant extensins, titin, and trematode eggshell precursors.

  18. Multiple site-selective insertions of non-canonical amino acids into sequence-repetitive polypeptides

    PubMed Central

    Wu, I-Lin; Patterson, Melissa A.; Carpenter Desai, Holly E.; Mehl, Ryan A.; Giorgi, Gianluca

    2013-01-01

    A simple and efficient method is described for introduction of non-canonical amino acids at multiple, structurally defined sites within recombinant polypeptide sequences. E. coli MRA30, a bacterial host strain with attenuated activity for release factor 1 (RF1), is assessed for its ability to support the incorporation of a diverse range of non-canonical amino acids in response to multiple encoded amber (TAG) codons within genetic templates derived from superfolder GFP and an elastin-mimetic protein polymer. Suppression efficiency and isolated protein yield were observed to depend on the identity of the orthogonal aminoacyl-tRNA synthetase/tRNACUA pair and the non-canonical amino acid substrate. This approach afforded elastin-mimetic protein polymers containing non-canonical amino acid derivatives at up to twenty-two positions within the repeat sequence with high levels of substitution. The identity and position of the variant residues was confirmed by mass spectrometric analysis of the full-length polypeptides and proteolytic cleavage fragments resulting from thermolysin digestion. The accumulated data suggest that this multi-site suppression approach permits the preparation of protein-based materials in which novel chemical functionality can be introduced at precisely defined positions within the polypeptide sequence. PMID:23625817

  19. PEG–Polypeptide Block Copolymers as pH-Responsive Endosome-Solubilizing Drug Nanocarriers

    PubMed Central

    2015-01-01

    Herein we report the potential of click chemistry-modified polypeptide-based block copolymers for the facile fabrication of pH-sensitive nanoscale drug delivery systems. PEG–polypeptide copolymers with pendant amine chains were synthesized by combining N-carboxyanhydride-based ring-opening polymerization with post-functionalization using azide–alkyne cycloaddition. The synthesized block copolymers contain a polypeptide block with amine-functional side groups and were found to self-assemble into stable polymersomes and disassemble in a pH-responsive manner under a range of biologically relevant conditions. The self-assembly of these block copolymers yields nanometer-scale vesicular structures that are able to encapsulate hydrophilic cytotoxic agents like doxorubicin at physiological pH but that fall apart spontaneously at endosomal pH levels after cellular uptake. When drug-encapsulated copolymer assemblies were delivered systemically, significant levels of tumor accumulation were achieved, with efficacy against the triple-negative breast cancer cell line, MDA-MB-468, and suppression of tumor growth in an in vivo mouse model. PMID:24813025

  20. Polycarbophil-cysteine conjugates as platforms for oral polypeptide delivery systems.

    PubMed

    Bernkop-Schnürch, A; Thaler, S C

    2000-07-01

    The purpose of the present study was to evaluate the potential of polycarbophil-cysteine conjugates as carrier systems for orally administered peptide and protein drugs. Mediated by a carbodiimide, cysteine was covalently attached to polycarbophil. The properties of resulting conjugates, displaying 35-50 microM thiol groups per gram of polymer, to bind polypeptides and to inhibit pancreatic proteases was evaluated in vitro. Results demonstrated that only some polypeptides are immobilized to the polycarbophil-cysteine conjugate. Due to the covalent attachment of cysteine to polycarbophil, the inhibitory effect of the polymer toward carboxypeptidase A (EC 3.4. 17.1) and carboxypeptidase B (EC 3.4.17.2) could be significantly (p < 0.05) improved. As the zinc binding affinity of polycarbophil could be improved by the covalent attachment of cysteine, the raised inhibitory effect seems to be based on the complexation of this divalent cation from the enzyme structure. Whereas the covalent attachment of cysteine on polycarbophil had no influence on the enzymatic activity of trypsin (EC 3.4.21.4) and elastase (EC 3.4.21. 36), the inhibitory effect of the polymer-cysteine conjugate toward chymotrypsin (EC 3.4.21.1) was significantly (p < 0.05) higher than that of the unmodified polymer. Because of these inhibitory features, polycarbophil-cysteine conjugates seem to be a promising tool in protecting orally administered therapeutic polypeptides, which are not bound to the polymer, from presystemic metabolism in the intestine.

  1. Polypept(o)ides: Hybrid Systems Based on Polypeptides and Polypeptoids.

    PubMed

    Klinker, Kristina; Barz, Matthias

    2015-11-01

    Polypept(o)ides combine the multifunctionality and intrinsic stimuli-responsiveness of synthetic polypeptides with the "stealth"-like properties of the polypeptoid polysarcosine (poly(N-methyl glycine)). This class of block copolymers can be synthesized by sequential ring opening polymerization of α-amino acid N-carboxy-anhydrides (NCAs) and correspondingly of the N-substituted glycine N-carboxyanhydride (NNCA). The resulting block copolymers are characterized by Poisson-like molecular weight distributions, full end group integrity, and dispersities below 1.2. While polysarcosine may be able to tackle the currently arising issues regarding the gold standard PEG, including storage diseases in vivo and immune responses, the polypeptidic block provides the functionalities for a specific task. Additionally, polypeptides are able to form secondary structure motives, e.g., α-helix or β-sheets, which can be used to direct self-assembly in solution. In this feature article, we review the relatively new field of polypept(o)ides with respect to synthesis, characterization, and first data on the application of block copolypept(o)ides in nanomedicine. The summarized data already indicates the great potential of polypept(o)ides. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Double-hydrophobic elastin-like polypeptides with added functional motifs: Self-assembly and cytocompatibility.

    PubMed

    Le, Duc H T; Tsutsui, Yoko; Sugawara-Narutaki, Ayae; Yukawa, Hiroshi; Baba, Yoshinobu; Ohtsuki, Chikara

    2017-09-01

    We have recently developed a novel double-hydrophobic elastin-like triblock polypeptide called GPG, designed after the uneven distribution of two different hydrophobic domains found in elastin, an extracellular matrix protein providing elasticity and resilience to tissues. Upon temperature trigger, GPG undergoes a sequential self-assembling process to form flexible beaded nanofibers with high homogeneity and excellent dispersibility in water. Given that GPG might be a potential elastin-mimetic material, we sought to explore the biological activities of this block polypeptide. Besides GPG, several functionalized derivatives were also constructed by fusing functional motifs such as KAAK or KAAKGRGDS at the C-terminal of GPG. Although the added motifs affected the kinetics of fiber formation and β-sheet contents, all three GPGs assembled into beaded nanofibers at the physiological temperature. The resulting GPG nanofibers preserved their beaded structures in cell culture medium; therefore, they were coated on polystyrene substrates to study their cytocompatibility toward mouse embryonic fibroblasts, NIH-3T3. Among the three polypeptides, GPG having the cell-binding motif GRGDS derived from fibronectin showed excellent cell adhesion and cell proliferation properties compared to other conventional materials, suggesting its promising applications as extracellular matrices for mammalian cells. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 2475-2484, 2017. © 2017 Wiley Periodicals, Inc.

  3. Poly(ADP-ribosyl)ation of a herpes simplex virus immediate early polypeptide

    SciTech Connect

    Preston, C.M.; Notarianni, E.L.

    1983-12-01

    In vitro poly(ADP-ribosyl)ation of the herpes simplex virus type 1 (HSV-1) immediate early polypeptide Vmw175 is reported. The phenomenon was most clearly observed by use of the temperature-sensitive mutant tsK, which overproduces Vmw175 at the nonpermissive temperature (NPT) and has a mutation in the coding sequences for this polypeptide. Nuclei prepared from cells which were infected with tsK at NPT and subsequently downshifted to the permissive temperature incorporated (/sup 32/P)NAD into Vmw175. This reaction did not occur when nuclei were prepared from cells constantly maintained at NPT, showing that only functional Vmw175 can be radiolabeled with (/sup 32/P)NAD. The identity of the acceptor protein was confirmed by demonstrating the expected electrophoretic mobility differences between the HSV-1 and HSV-2 counterparts of Vmw175. The use of suitable inhibitors demonstrated that the reaction represented mono- or poly(ADP-ribosyl)ation, and further analysis showed the presence of long poly(ADP-ribose) chains attached to Vmw175. Poly(ADP-ribosyl)ation may be important as a cause or result of the regulation of viral transcription by Vmw175. Radiolabeling of another virus-specified polypeptide (approximate molecular weight 38,000), thought to be a structural component of the input virus, is also reported.

  4. Sugar-nucleotide-binding and autoglycosylating polypeptide(s) from nasturtium fruit: biochemical capacities and potential functions.

    PubMed

    Faik, A; Desveaux, D; MacLachlan, G

    2000-05-01

    Polypeptide assemblies cross-linked by S-S bonds (molecular mass>200 kDa) and single polypeptides folded with internal S-S cross-links (<41 kDa) have been detected by SDS/PAGE in particulate membranes and soluble extracts of developing cotyledons of nasturtium (Tropaeolum majus L.). When first prepared from fruit homogenates, these polypeptides were found to bind reversibly to UDP-Gal (labelled with [(14)C]Gal or [(3)H]uridine), and to co-precipitate specifically with added xyloglucan from solutions made with 67% ethanol. Initially, the bound UDP-[(14)C]Gal could be replaced (bumped) by adding excess UDP, or exchanged (chased) with UDP-Gal, -Glc, -Man or -Xyl. However, this capacity for turnover was lost during incubation in reaction media, or during SDS/PAGE under reducing conditions, even as the glycone moiety was conserved by autoglycosylation to form a stable 41 kDa polypeptide. Polyclonal antibodies raised to a similar product purified from Arabidopsis bound to all the labelled nasturtium polypeptides in immunoblotting tests. The antibodies also inhibited the binding of nasturtium polypeptides to UDP-Gal, the uptake of UDP-[(14)C]Gal into intact nasturtium membrane vesicles and the incorporation of [(14)C]Gal into nascent xyloglucan within these vesicles. This is the first direct evidence that these polypeptides facilitate the channelling of UDP-activated sugars from the cytoplasm through Golgi vesicle membranes to lumenal sites, where they can be used as substrates for glycosyltransferases to synthesize products such as xyloglucan.

  5. Density functional theory study of the conformational space of an infinitely long polypeptide chain

    NASA Astrophysics Data System (ADS)

    Ireta, Joel; Scheffler, Matthias

    2009-08-01

    The backbone conformational space of infinitely long polyalanine is investigated with density-functional theory and mapping the potential energy surface in terms of (L, θ) cylindrical coordinates. A comparison of the obtained (L, θ) Ramachandran-like plot with results from an extended set of protein structures shows excellent conformity, with the exception of the polyproline II region. It is demonstrated the usefulness of infinitely long polypeptide models for investigating the influence of hydrogen bonding and its cooperative effect on the backbone conformations. The results imply that hydrogen bonding together with long-range electrostatics is the main actuator for most of the structures assumed by protein residues.

  6. Methods of increasing secretion of polypeptides having biological activity

    SciTech Connect

    Merino, Sandra

    2015-04-14

    The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.

  7. Human jagged polypeptide, encoding nucleic acids and methods of use

    DOEpatents

    Li, Linheng; Hood, Leroy

    2000-01-01

    The present invention provides an isolated polypeptide exhibiting substantially the same amino acid sequence as JAGGED, or an active fragment thereof, provided that the polypeptide does not have the amino acid sequence of SEQ ID NO:5 or SEQ ID NO:6. The invention further provides an isolated nucleic acid molecule containing a nucleotide sequence encoding substantially the same amino acid sequence as JAGGED, or an active fragment thereof, provided that the nucleotide sequence does not encode the amino acid sequence of SEQ ID NO:5 or SEQ ID NO:6. Also provided herein is a method of inhibiting differentiation of hematopoietic progenitor cells by contacting the progenitor cells with an isolated JAGGED polypeptide, or active fragment thereof. The invention additionally provides a method of diagnosing Alagille Syndrome in an individual. The method consists of detecting an Alagille Syndrome disease-associated mutation linked to a JAGGED locus.

  8. Methods of increasing secretion of polypeptides having biological activity

    DOEpatents

    Merino, Sandra

    2013-10-01

    The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.

  9. Methods of increasing secretion of polypeptides having biological activity

    DOEpatents

    Merino, Sandra

    2014-10-28

    The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.

  10. Methods of increasing secretion of polypeptides having biological activity

    DOEpatents

    Merino, Sandra

    2014-05-27

    The present invention relates to methods for producing a secreted polypeptide having biological activity, comprising: (a) transforming a fungal host cell with a fusion protein construct encoding a fusion protein, which comprises: (i) a first polynucleotide encoding a signal peptide; (ii) a second polynucleotide encoding at least a catalytic domain of an endoglucanase or a portion thereof; and (iii) a third polynucleotide encoding at least a catalytic domain of a polypeptide having biological activity; wherein the signal peptide and at least the catalytic domain of the endoglucanase increases secretion of the polypeptide having biological activity compared to the absence of at least the catalytic domain of the endoglucanase; (b) cultivating the transformed fungal host cell under conditions suitable for production of the fusion protein; and (c) recovering the fusion protein, a component thereof, or a combination thereof, having biological activity, from the cultivation medium.

  11. Polypeptide formation on polar mineral surfaces: possibility of complete chirality

    NASA Astrophysics Data System (ADS)

    Schrader, Malcolm E.

    2017-01-01

    In the present work, it is shown that thermodynamically feasible polymerization of cyanomethanol, which can be formed from formaldehyde and hydrogen cyanide, can lead to synthesis of polypeptides as well as to the previously reported synthesis of RNA. If the polymerization takes place on a one-dimensional feature of a mineral, such as for example a crack on its surface, the concept of quasi-chirality is introduced to describe the adsorbed polypeptide. This, in principle, would lead to formation of proteins that are completely homochiral in their alpha carbon groups. The concept of quasi-chirality can also be introduced in the condensation of glycine under similar conditions to form a polypeptide. This again leads to proteins completely chiral in their alpha carbon groups.

  12. Separation, antitumor activities, and encapsulation of polypeptide from Chlorella pyrenoidosa.

    PubMed

    Wang, Xiaoqin; Zhang, Xuewu

    2013-01-01

    Chlorella pyrenoidosa is a unicellular green algae and has been a popular foodstuff worldwide. However, no reports on the antitumor peptides from such a microalgae are available in the literature. In this study, using low-temperature high-pressure extraction, enzymatic hydrolysis, ion exchange, and gel filtration chromatography, we separated a polypeptide that exhibited inhibitory activity on human liver cancer HepG2 cells, and named the polypeptide CPAP (C. pyrenoidosa antitumor polypeptide). Furthermore, the micro- and nanoencapsulation of CPAP were investigated by using two methods: complex coacervation and ionotropic gelation. The in vitro release tests revealed that CPAP was well preserved against gastric enzymatic degradation after micro/nanoencapsulation and the slowly controlled release in the intestine could be potentially achieved. These results suggest that CPAP may be a useful ingredient in food, nutraceutical, and pharmaceutical applications. © 2013 American Institute of Chemical Engineers.

  13. cDNA cloning, primary structure and gene expression for H-protein, a component of the glycine-cleavage system (glycine decarboxylase) of pea (Pisum sativum) leaf mitochondria.

    PubMed Central

    Macherel, D; Lebrun, M; Gagnon, J; Neuburger, M; Douce, R

    1990-01-01

    We have isolated and characterized cDNA clones encoding the H-protein of the glycine-cleavage system of pea (Pisum sativum) leaf mitochondria. The deduced primary structure revealed that the 131-amino-acid polypeptide is cytoplasmically synthesized with a 34-amino-acid mitochondrial targeting peptide. The lipoate-binding site was assigned to be lysine-63, as deduced from a sequence comparison with several lipoate-bearing proteins. The expression of the gene encoding H-protein was shown to occur specifically in the leaf tissue, with light exerting an additional effect by increasing the mRNA levels severalfold. Two polyadenylation sites were found in the mRNA, and a single-copy gene encoding the H-protein was detected in pea genome. Images Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. PMID:2363710

  14. Structure of a mitochondrial ribosome with minimal RNA

    PubMed Central

    Sharma, Manjuli R.; Booth, Timothy M.; Simpson, Larry; Maslov, Dmitri A.; Agrawal, Rajendra K.

    2009-01-01

    The Leishmania tarentolae mitochondrial ribosome (Lmr) is a minimal ribosomal RNA (rRNA)-containing ribosome. We have obtained a cryo-EM map of the Lmr. The map reveals several features that have not been seen in previously-determined structures of eubacterial or eukaryotic (cytoplasmic or organellar) ribosomes to our knowledge. Comparisons of the Lmr map with X-ray crystallographic and cryo-EM maps of the eubacterial ribosomes and a cryo-EM map of the mammalian mitochondrial ribosome show that (i) the overall structure of the Lmr is considerably more porous, (ii) the topology of the intersubunit space is significantly different, with fewer intersubunit bridges, but more tunnels, and (iii) several of the functionally-important rRNA regions, including the α-sarcin-ricin loop, have different relative positions within the structure. Furthermore, the major portions of the mRNA channel, the tRNA passage, and the nascent polypeptide exit tunnel contain Lmr-specific proteins, suggesting that the mechanisms for mRNA recruitment, tRNA interaction, and exiting of the nascent polypeptide in Lmr must differ markedly from the mechanisms deduced for ribosomes in other organisms. Our study identifies certain structural features that are characteristic solely of mitochondrial ribosomes and other features that are characteristic of both mitochondrial and chloroplast ribosomes (i.e., organellar ribosomes). PMID:19497863

  15. Effects of chain length of an amphipathic polypeptide carrying the repeated amino acid sequence (LETLAKA)(n) on α-helix and fibrous assembly formation.

    PubMed

    Takei, Toshiaki; Hasegawa, Kazuya; Imada, Katsumi; Namba, Keiichi; Tsumoto, Kouhei; Kuriki, Yukino; Yoshino, Masakuni; Yazaki, Kazumori; Kojima, Shuichi; Takei, Tsunetomo; Ueda, Takuya; Miura, Kin-ichiro

    2013-04-23

    Polypeptide α3 (21 residues), with three repeats of a seven-amino-acid sequence (LETLAKA)(3), forms an amphipathic α-helix and a long fibrous assembly. Here, we investigated the ability of α3-series polypeptides (with 14-42 residues) of various chain lengths to form α-helices and fibrous assemblies. Polypeptide α2 (14 residues), with two same-sequence repeats, did not form an α-helix, but polypeptide α2L (15 residues; α2 with one additional leucine residue on its carboxyl terminal) did form an α-helix and fibrous assembly. Fibrous assembly formation was associated with polypeptides at least as long as polypeptide α2L and with five leucine residues, indicating that the C-terminal leucine has a critical element for stabilization of α-helix and fibril formation. In contrast, polypeptides α5 (35 residues) and α6 (42 residues) aggregated easily, although they formed α-helices. A 15-35-residue chain was required for fibrous assembly formation. Electron microscopy and X-ray fiber diffraction showed that the thinnest fibrous assemblies of polypeptides were about 20 Å and had periodicities coincident with the length of the α-helix in a longitudinal direction. These results indicated that the α-helix structures were orientated along the fibrous axis and assembled into a bundle. Furthermore, the width and length of fibrous assemblies changed with changes in the pH value, resulting in variations in the charged states of the residues. Our results suggest that the formation of fibrous assemblies of amphipathic α-helices is due to the assembly of bundles via the hydrophobic faces of the helices and extension with hydrophobic noncovalent bonds containing a leucine.

  16. Elastin-like polypeptides: biomedical applications of tunable biopolymers.

    PubMed

    MacEwan, Sarah R; Chilkoti, Ashutosh

    2010-01-01

    Artificial repetitive polypeptides have grown in popularity as a bioinspired alternative to synthetic polymers. The genetically encoded synthesis, monodispersity, potential lack of toxicity, and biocompatibility are attractive features of these biopolymers for biological applications. Elastin-like polypeptides (ELPs) are one such class of biopolymers that are of particular interest because of their "smart"-stimuli responsive-properties. Herein, we discuss the genetically encoded design and recombinant synthesis of ELPs that enable precise control of their physicochemical properties and which have led to a wide range of biomedical applications of these biopolymers in the last decade. (c) 2010 Wiley Periodicals, Inc.

  17. Reovirus-specific polypeptides: analysis using discontinuous gel electrophoresis.

    PubMed Central

    Cross, R K; Fields, B N

    1976-01-01

    The electrophoretic analysis of reovirus-specific polypeptides in infected cells using a discontinuous gel system has allowed the resolution of additional viral-specific polypeptides, including one large-sized gamma3 and two (or possibly three) medium-sized (mu3, mu4, mu5(?)) species. The proteins designated mu0, sigma1, and sigma2 based on electrophoretic mobility in gel systems containing phosphate-urea correspond to mu4, sigma2, and sigma1, respectively, when analyzed in systems containing Tris-glycine. It is likely that protein modifications (phosphorylation and glycosylation) are responsible for at least some of these differences. Images PMID:950684

  18. Atomic Layer Deposition of L-Alanine Polypeptide

    SciTech Connect

    Fu, Yaqin; Li, Binsong; Jiang, Ying-Bing; Dunphy, Darren R.; Tsai, Andy; Tam, Siu-Yue; Fan, Hongyou Y.; Zhang, Hongxia; Rogers, David; Rempe, Susan; Atanassov, Plamen; Cecchi, Joseph L.; Brinker, C. Jeffrey

    2014-10-30

    L-Alanine polypeptide thin films were synthesized via atomic layer deposition (ALD). Rather, instead of using an amino acid monomer as the precursor, an L-alanine amino acid derivatized with a protecting group was used to prevent self-polymerization, increase the vapor pressure, and allow linear cycle-by-cycle growth emblematic of ALD. Moreover, the successful deposition of a conformal polypeptide film has been confirmed by FTIR, TEM, and Mass Spectrometry, and the ALD process has been extended to polyvaline.

  19. Modulation of concentration fluctuations in phase-separated lipid membranes by polypeptide insertion.

    PubMed Central

    Fahsel, S; Pospiech, E-M; Zein, M; Hazlet, T L; Gratton, E; Winter, Roland

    2002-01-01

    The lateral membrane organization and phase behavior of the binary lipid mixture DMPC (1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine) - DSPC (1,2-distearoyl-sn-glycero-3-phosphatidylcholine) without and with incorporated gramicidin D (GD) as a model biomembrane polypeptide was studied by small-angle neutron scattering, Fourier-transform infrared spectroscopy, and by two-photon excitation fluorescence microscopy on giant unilamellar vesicles. The small-angle neutron scattering method allows the detection of concentration fluctuations in the range from 1 to 200 nm. Fluorescence microscopy was used for direct visualization of the lateral lipid organization and domain shapes on a micrometer length scale including information of the lipid phase state. In the fluid-gel coexistence region of the pure binary lipid system, large-scale concentration fluctuations appear. Infrared spectral parameters were used to determine the peptide conformation adopted in the different lipid phases. The data show that the structure of the temperature-dependent lipid phases is significantly altered by the insertion of 2 to 5 mol% GD. At temperatures corresponding to the gel-fluid phase coexistence region the concentration fluctuations drastically decrease, and we observe domains in the giant unilamellar vesicles, which mainly disappear by the incorporation of 2 to 5 mol% GD. Further, the lipid matrix has the ability to modulate the conformation of the inserted polypeptide. The balance between double-helical and helical dimer structures of GD depends on the phospholipid chain length and phase state. A large hydrophobic mismatch, such as in gel phase one-component DSPC bilayers, leads to an increase in population of double-helical structures. Using an effective molecular sorting mechanism, a large hydrophobic mismatch can be avoided in the DMPC-DSPC lipid mixture, which leads to significant changes in the heterogeneous lipid structure and in polypeptide conformation. PMID:12080124

  20. Advance of the perihelion of Mercury deduced from QFT

    NASA Astrophysics Data System (ADS)

    Chen, Shao-Guang

    I deduce the new gravitational formula from the variance in mass of QFT and GR (H05-0029-08, E15-0039 -08, E14-0032-08, D31-0054-10) in the partial differential: f (QFT) = f (GR) = delta∂ (m v)/delta∂ t = f _{P} + f _{C} , f _{P} = m delta∂ v / delta∂ t = - ( G m M /r (2) ) r / r, f _{C} = v delta∂ m / delta∂ t = - ( G m M / r (2) ) v / c (1), f (QFT) is the quasi-Casimir pressure of net virtual neutrinos nuν _{0} flux (after counteract contrary direction nuν _{0}). f (GR) is equivalent to Einstein’s equation, Eq. (1) is a new version of GR and can be solved exactly. Its core content is that the gravity produced by particles collide cannot linear addition, i.e., the nonlinearity of Einstein equation had been replaced by the nonlinearity caused by the variable mass in Eq.(1). Einstein equation can be inferred from Eq.(1) thereby from QFT, but QFT cannot be inferred from Eq.(1) or GR. f (QFT) is essential but f (GR) is phenomenological. Eq.(1) is obtained just by to absorb the essence of corpuscule collided gravitation origin ism proposed by Fatio in 1690 and 1920 Majorana’s experiment concept about gravitational shield effect again fuse with QFT. In my paper ‘QFT’S advance of the perihelion of Mercury, China Science &Technology Overview 125 88-90 (2011)’ QFT gravitational potential U = - G M /r is just the distribution density of net nuν _{0} flux, from SR we again get that: f (QFT) = f _{P} + f _{C}, f _{P} = - m ( delta∂ U / delta∂ r) r / r, f _{C} = - m ( delta∂U / delta∂ r) v / c (2), f _{ P} correspond the change rate of three-dimensional momentum p, f _{C} correspond the change rate of fourth dimensional momentum i m c which show directly as a dissipative force of mass change. According to Eq.(2) the circular motion is instability and elliptic motion is in the auto-stability state. In the fluctuation vacuum a particle with mass M neighbor another particle with mass m, the renormalization mass M and m will be less than that when

  1. A polypeptide of 59 kDa is associated with bundles of cytoplasmic filaments in Neurospora crassa.

    PubMed Central

    Rosa, A L; Alvarez, M E; Lawson, D; Maccioni, H J

    1990-01-01

    Complex arrangements of filamentous structures have been isolated from vegetative cells of the fungus Neurospora crassa. They were enriched by differential centrifugation and purified by permeation chromatography. The filamentous structures are made up of units of 8-10 nm diameter and were isolated in bundles of up to six to nine units. The main constituent of these structures is a polypeptide with an apparent molecular mass of 59 kDa (P59Nc), which represents 4-5% of the total N. crassa proteins. The filamentous structures are cold-stable and are not affected by high-ionic-strength solutions or by the presence of 10 mM-EDTA or 1% (w/v) Triton X-100; they were disassembled by raising the pH of the solution or by using Tris-based buffers. The disassembled form assembled into structures sedimentable at 105,000 g after dialysis against the isolation buffer. The sedimentable structures were organized in the form of regular aggregates of 42-45 nm polypeptides and reacted weakly with anti-IFA, a monoclonal antibody which recognizes an epitope common to many of the higher-eukaryote intermediate-filament polypeptides. Immunofluorescence examination of wall-digested hyphae of N. crassa using affinity-purified antibodies prepared against P59Nc showed immunostaining of abundant filamentous and dot-shaped structures distributed in the cytoplasm. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7. PMID:2141976

  2. Morphological variation of stimuli-responsive polypeptide at air-water interface

    NASA Astrophysics Data System (ADS)

    Shin, Sungchul; Ahn, Sungmin; Cheng, Jie; Chang, Hyejin; Jung, Dae-Hong; Hyun, Jinho

    2016-12-01

    The morphological variation of stimuli-responsive polypeptide molecules at the air-water interface as a function of temperature and compression was described. The surface pressure-area (π-A) isotherms of an elastin-like polypeptide (ELP) monolayer were obtained under variable external conditions, and Langmuir-Blodgett (LB) monolayers were deposited onto a mica substrate for characterization. As the compression of the ELP monolayer increased, the surface pressure increased gradually, indicating that the ELP monolayer could be prepared with high stability at the air-water interface. The temperature in the subphase of the ELP monolayer was critical in the preparation of LB monolayers. The change in temperature induced a shift in the π-A isotherms as well as a change in ELP secondary structures. Surprisingly, the compression of the ELP monolayer influenced the ELP secondary structure due to the reduction in the phase transition temperature with decreasing temperature. The change in the ELP secondary structure formed at the air-water interface was investigated by surface-enhanced Raman scattering. Moreover, the morphology of the ELP monolayer was subsequently imaged using atomic force microscopy. The temperature responsive behavior resulted in changes in surface morphology from relatively flat structures to rugged labyrinth structures, which suggested conformational changes in the ELP monolayers.

  3. Structure of chymopapain M the late-eluted chymopapain deduced by comparative modelling techniques and active-centre characteristics determined by pH-dependent kinetics of catalysis and reactions with time-dependent inhibitors: the Cys-25/His-159 ion-pair is insufficient for catalytic competence in both chymopapain M and papain.

    PubMed

    Thomas, M P; Topham, C M; Kowlessur, D; Mellor, G W; Thomas, E W; Whitford, D; Brocklehurst, K

    1994-06-15

    Chymopapain M, the monothiol cysteine proteinase component of the chymopapain band eluted after chymopapains A and B in cation-exchange chromatography, was isolated from the dried latex of Carica papaya and characterized by kinetic and chromatographic analysis. This late-eluted chymopapain is probably a component of the cysteine proteinase fraction of papaya latex discovered by Schack [(1967) Compt. Rend. Trav. Lab. Carlsberg 36, 67-83], named papaya peptidase B by Lynn [(1979) Biochim. Biophys. Acta 569, 193-201] and partially characterized by Polgár [(1981) Biochim. Biophys. Acta 658, 262-269] and is the enzyme with unusual specificity characteristics (papaya proteinase IV) that Buttle, Kembhavi, Sharp, Shute, Rich and Barrett [Biochem. J. (1989) 261, 469-476] claimed to be a previously undetected cysteine proteinase eluted from a cation-exchange column near to the early-eluted chymopapains. A study of the time-dependent chromatographic consequences of thiol-dependent proteolysis of the components of papaya latex is reported. Chymopapain M was isolated by (i) affinity chromatography followed by separation from papain using cation-exchange f.p.l.c. on a Mono S HR5/5 column and (ii) cation-exchange chromatography followed by an unusual variant of covalent chromatography by thiol-disulphide interchange. The existence in chymopapain M of a nucleophilic interactive Cys/His catalytic-site system analogous to those in papain (EC 3.4.22.2) and other cysteine proteinases was deduced from the characteristics shape of the pH-second-order rate constant (k) profiles for its reactions with 2,2'-dipyridyl disulphide and ethyl 2-pyridyl disulphide. Analysis of the pH-k data for the reactions of chymopapain M with the 2-pyridyl disulphides and with 4,4'-dipyridyl disulphide permits the assignment of molecular pKa values of 3.4 and 8.7 to the formation and subsequent dehydronation of the Cys-S-/His-Im+H state of the catalytic site and reveals three other kinetically influential

  4. Biosynthesis and characterization of a non-repetitive polypeptide derived from silk fibroin heavy chain.

    PubMed

    Yang, Gaoqiang; Wu, Mingyang; Yi, Honggen; Wang, Jiannan

    2016-02-01

    Silk fibroin heavy chain is the major protein component of Bombyx mori silk fibroin and is composed of 12 repetitive and 11 non-repetitive regions, with the non-repetitive domain consisting of a hydrophilic polypeptide chain. In order to determine the biomedical function of the non-repetitive domain or potentially use it to modify hydrophobic biomaterials, high-purity isolation is necessary. Previously, we cloned and extended a gene motif (f(1)) encoding the non-repetitive domain. Here, this motif and its multimers are inserted into a glutathione S-transferase (GST)-tagged fusion-protein expression vector. Motif f(1) and multimers f(4) and f(8) were expressed in Escherichia coli BL21 cells following isopropyl β-D-1-thiogalactopyranoside induction, purified by GST-affinity chromatography, and single bands of purified fusion proteins GST-F(1), GST-F(4), and GST-F(8), were visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Target polypeptides F(1), F(4), and F(8), were cleaved clearly from the GST-fusion tag following thrombin digestion. Mass spectrometry results indicate that the molecular weights associated with fusion proteins GST-F(1), GST-F(4), and GST-F(8) are 31.5, 43.8, and 59.0kDa, respectively, and with the cleaved polypeptides F(1), F(4), and F(8) are 4.8, 16.8, and 32.8kDa, respectively. The F(1), F(4), and F(8) polypeptide chains are negatively charged with isoelectric points (pI) of 3.3, 3.2, and 3.0, respectively. The molecular weight and pI values of the polypeptide chains are consistent with the predicted values and the amino acid compositions similar to predicted sequences. FTIR and CD results show the molecular conformation of F(1) was mainly random coil, and more stable α-helix structure formed in longer molecular chain.

  5. Properties of the lithosphere and asthenosphere deduced from geoid observations

    NASA Technical Reports Server (NTRS)

    Turcotte, D. L.

    1985-01-01

    Data from the GEOS-3 and SEASAT Satellites provided a very accurate geoid map over the oceans. Broad bathymetric features in the oceans such as oceanic swells and plateaus are fully compensated. It is shown that the geoid anomalies due to the density structures of the lithosphere are proportional to the first moment of the density distribution. The deepening of the ocean basins is attributed to thermal isostasy. The thickness of the oceanic lithosphere increases with age due to the loss of heat to the sea floor. Bathymetry and the geoid provide constraints on the extent of this heat loss. Offsets in the geoid across major fracture zones can also be used to constrain this problem. Geoid bathymetry correlations show that the Hawaiian and Bermuda swells and the Cape Verde Rise are probably due to lithospheric thinning.

  6. A pH- and ionic strength-responsive polypeptide hydrogel: synthesis, characterization, and preliminary protein release studies.

    PubMed

    Markland, P; Zhang, Y; Amidon, G L; Yang, V C

    1999-12-15

    A novel polypeptide hydrogel has been synthesized by crosslinking poly(L-glutamic acid) (PLG) with poly(ethylene glycol) (PEG). The PLG-PEG hydrogel was shown to be highly hydrophilic, and the extent of swelling varied with pH, increasing at higher ionization of the PLG. Aside from electrostatic effects, such as ion-ion repulsion and internal ion osmotic pressure, circular dichroism studies showed that swelling response to pH also is affected by secondary structural attributes associated with the polypeptide backbone. Modification of the polypeptide by changing its hydrophobicity and degree of ionization was an effective method for altering the overall extent of pH-responsive swelling. Rapid de-swelling (contraction) was observed when the PLG-PEG hydrogel was transferred from high to low pH buffer solution, and this swelling/de-swelling behavior was reversible over repeated cycles. Drug release from swollen hydrogels was examined using the model protein lysozyme. Rapid de-swelling of the hydrogel was found to be an effective means of facilitating lysozyme release. The crosslinking of synthetic polypeptides with PEG appears to be a highly versatile approach to the preparation of pH-responsive biodegradable hydrogels.

  7. The vasorelaxant effect of pituitary adenylate cyclase activating polypeptide and vasoactive intestinal polypeptide in isolated rat basilar arteries is partially mediated by activation of nitrergic neurons.

    PubMed

    Seebeck, Jörg; Löwe, Marcus; Kruse, Marie Luise; Schmidt, Wolfgang E; Mehdorn, H Maximilian; Ziegler, Albrecht; Hempelmann, Ralf G

    2002-07-15

    The structurally related neuropeptides pituitary adenylate cyclase activating polypeptide (PACAP) and vasoactive intestinal polypeptide (VIP) are recognised by two G protein-coupled receptors, termed VPAC(1)-R and VPAC(2)-R, with equal affinity. PACAP and VIP have previously been shown to relax cerebral arteries in an endothelium-independent manner. The aim of the present study was to test if intramural neurons are involved in the mediation of PACAP/VIP-induced vasodilatory responses. Therefore, the vascular tone of isolated rat basilar arteries was measured by means of a myograph. The vasorelaxing effect of PACAP was assessed in arteries precontracted by serotonin in the absence or presence of different test compounds known to selectively inhibit certain signaling proteins. The vasorelaxant effect of PACAP could be significantly reduced by the inhibitor of neuronal N-type calcium channels omega-conotoxin GVIA (omega-CgTx), as well as by 3-bromo-7-nitroindazole (3Br-7-Ni), an inhibitor of the neuronal nitric oxide-synthase (nNOS). The localization of N-type calcium channels and VPAC-Rs within the rat basilar artery was investigated by confocal laser scanning microscopy using omega-CgTx- and VIP-analogs labelled with fluorescent dyes. These findings suggest that activation of intramural neurons may represent an important effector mechanism for mediation of the vasorelaxant PACAP-response.

  8. Methods of using viral replicase polynucleotides and polypeptides

    DOEpatents

    Gordon-Kamm, William J.; Lowe, Keith S.; Bailey, Matthew A.; Gregory, Carolyn A.; Hoerster, George J.; Larkins, Brian A.; Dilkes, Brian R.; Burnett, Ronald; Woo, Young Min

    2007-12-18

    The invention provides novel methods of using viral replicase polypeptides and polynucleotides. Included are methods for increasing transformation frequencies, increasing crop yield, providing a positive growth advantage, modulating cell division, transiently modulating cell division, and for providing a means of positive selection.

  9. Porin polypeptide contributes to surface charge of gonococci.

    PubMed Central

    Swanson, J; Dorward, D; Lubke, L; Kao, D

    1997-01-01

    Each strain of Neisseria gonorrhoeae elaborates a single porin polypeptide, with the porins expressed by different strains comprising two general classes, Por1A and Por1B. In the outer membrane, each porin molecule folds into 16 membrane-spanning beta-strands joined by top- and bottom-loop domains. Por1A and Por1B have similar membrane-spanning regions, but the eight surface-exposed top loops (I to VIII) differ in length and sequence. To determine whether porins, and especially their top loop domains, contribute to bacterial cell surface charge, strain MS11 gonococci that were identical except for expressing a recombinant Por1A, Por1B, or mosaic Por1A-1B polypeptide were compared by whole-cell electrophoresis. These porin variants displayed different electrophoretic mobilities that correlated with the net numbers of charged amino acids within surface-exposed loops of their respective porin polypeptides. The susceptibilities of porin variants to polyanionic sulfated polymers correlated roughly with gonococcal surface charge; those porin variants with diminished surface negativity showed increased sensitivity to the polyanionic sulfated compounds. These observations indicate that porin polypeptides in situ contribute to the surface charge of gonococci, and they suggest that the bacterium's interactions with large sulfated compounds are thereby affected. PMID:9171398

  10. New evidence for the antiquity of man in North America deduced from aspartic acid racemization.

    PubMed

    Bada, J L; Schroeder, R A; Carter, G F

    1974-05-17

    Ages of several Californzia Paleo-Indlian skeletons have been deduced from the extent of aspartic acid racemization. These dates suggest that man was present in North America at least 50,000 years before the present.

  11. The effects of the side chains of hydrophobic aliphatic amino acid residues in an amphipathic polypeptide on the formation of alpha helix and its association.

    PubMed

    Takei, Toshiaki; Okonogi, Atsuhito; Tateno, Kumiko; Kimura, Akiko; Kojima, Shuichi; Yazaki, Kazumori; Miura, Kin-ichiro

    2006-02-01

    The polypeptide alpha3, which was synthesized by us to produce an amphipathic helix structure, contains the regular three times repeated sequence (LETLAKA)(3), and alpha3 forms a fibrous assembly. To clarify how the side chains of amino acid residues affect the formation of alpha helix, Leu residues, which are located in the hydrophobic surface of an amphipathic helix, were replaced by other hydrophobic aliphatic amino acid residues systematically, and the characters of the resulting polypeptides were studied. According to the circular dichroism (CD) spectra, the Ile-substituted polypeptides formed alpha helix like alpha3. However, their helix formation ability was weaker than that of alpha3 under some conditions. The Val-substituted polypeptides formed alpha helix only under restricted condition. The Ala-substituted polypeptides did not form alpha helix under any condition. Thus, it is clear that the order of the alpha helix formation ability is as follows: Leu >or= Ile > Val > Ala. The formation of alpha helix was confirmed by Fourier Transform Infrared (FTIR) spectra. Through electron microscopic observation, it was clarified that the formation of the alpha helix structure correlates with the formation of a fibrous assembly. The amphipathic alpha helix structure would be stabilized by the formation of the fibrous assembly.

  12. Chronic overproduction of islet amyloid polypeptide/amylin in transgenic mice: lysosomal localization of human islet amyloid polypeptide and lack of marked hyperglycaemia or hyperinsulinaemia.

    PubMed

    Höppener, J W; Verbeek, J S; de Koning, E J; Oosterwijk, C; van Hulst, K L; Visser-Vernooy, H J; Hofhuis, F M; van Gaalen, S; Berends, M J; Hackeng, W H

    1993-12-01

    Type 2 (non-insulin-dependent) diabetes mellitus is characterised by hyperglycaemia, peripheral insulin resistance, impaired insulin secretion and pancreatic islet amyloid formation. The major constituent of islet amyloid is islet amyloid polypeptide (amylin). Islet amyloid polypeptide is synthesized by islet beta cells and co-secreted with insulin. The ability of islet amyloid polypeptide to form amyloid fibrils is related to its species-specific amino acid sequence. Islet amyloid associated with diabetes is only found in man, monkeys, cats and racoons. Pharmacological doses of islet amyloid polypeptide have been shown to inhibit insulin secretion as well as insulin action on peripheral tissues (insulin resistance). To examine the role of islet amyloid polypeptide in the pathogenesis of Type 2 diabetes, we have generated transgenic mice with the gene encoding either human islet amyloid polypeptide (which can form amyloid) or rat islet amyloid polypeptide, under control of an insulin promoter. Transgenic islet amyloid polypeptide mRNA was detected in the pancreas in all transgenic mice. Plasma islet amyloid polypeptide levels were significantly elevated (up to 15-fold) in three out of five transgenic lines, but elevated glucose levels, hyperinsulinaemia and obesity were not observed. This suggests that insulin resistance is not induced by chronic hypersecretion of islet amyloid polypeptide. Islet amyloid polypeptide immunoreactivity was localized to beta-cell secretory granules in all mice. Islet amyloid polypeptide immunoreactivity in beta-cell lysosomes was seen only in mice with the human islet amyloid polypeptide gene, as in human beta cells, and might represent an initial step in intracellular formation of amyloid fibrils.(ABSTRACT TRUNCATED AT 250 WORDS)

  13. Catalytic and reactive polypeptides and methods for their preparation and use

    DOEpatents

    Schultz, Peter

    1993-01-01

    Catalytic and reactive polypeptides include a binding site specific for a reactant or reactive intermediate involved in a chemical reaction of interest. The polypeptides further include at least one active functionality proximate the bi.

  14. Interfacial energy of polypeptide complex coacervates measured via capillary adhesion.

    PubMed

    Priftis, Dimitrios; Farina, Robert; Tirrell, Matthew

    2012-06-12

    A systematic study of the interfacial energy (γ) of polypeptide complex coacervates in aqueous solution was performed using a surface forces apparatus (SFA). Poly(L-lysine hydrochloride) (PLys) and poly(L-glutamic acid sodium salt) (PGA) were investigated as a model pair of oppositely charged weak polyelectrolytes. These two synthetic polypeptides of natural amino acids have identical backbones and differ only in their charged side groups. All experiments were conducted using equal chain lengths of PLys and PGA in order to isolate and highlight effects of the interactions of the charged groups during complexation. Complex coacervates resulted from mixing very dilute aqueous salt solutions of PLys and PGA. Two phases in equilibrium evolved under the conditions used: a dense polymer-rich coacervate phase and a dilute polymer-deficient aqueous phase. Capillary adhesion, associated with a coacervate meniscus bridge between two mica surfaces, was measured upon the separation of the two surfaces. This adhesion enabled the determination of the γ at the aqueous/coacervate phase interface. Important experimental factors affecting these measurements were varied and are discussed, including the compression force (1.3-35.9 mN/m) and separation speed (2.4-33.2 nm/s). Physical parameters of the system, such as the salt concentration (100-600 mM) and polypeptide chain length (N = 30, 200, and 400) were also studied. The γ of these polypeptide coacervates was separately found to decrease with both increasing salt concentration and decreasing polypeptide chain length. In most of the above cases, γ measurements were found to be very low, <1 mJ/m(2). Biocompatible complex coacervates with low γ have a strong potential for applications in surface coatings, adhesives, and the encapsulation of a wide range of materials.

  15. On the strength of the hydrogen-carbon interaction as deduced from physisorption.

    PubMed

    Nguyen, T X; Bae, J-S; Wang, Y; Bhatia, S K

    2009-04-21

    We deduce a new value for the potential well depth for the C-H2 interaction on the basis of experimental validations of isotherms of H2 and D2 predicted using independently characterized microstructural parameters. We use two carbons, one an activated carbon fiber whose structure has been recently characterized by us (Nguyen, T. X.; cohaut, N.; Bae, J.-S.; Bhatia, S. K. Langmuir 2008, 24, 7912) using hybrid reverse Monte Carlo simulation (HRMC) and the other the commercial Takeda 3A carbon molecular sieve whose pore size distribution is determined here from the 273 K CO2 adsorption isotherm. The conventional grand canonical Monte Carlo simulation technique incorporating a semiclassical Feynman and Hibbs (FH) potential approximation (FHGCMC) as well as path integral Monte Carlo calculations is employed to determine theoretical adsorption isotherms. It is found that curvature enhances the well depth for the LJ C-H2 interaction by a factor of 1.134 over that for a flat graphite surface, consistent with our recent study (Nguyen, T. X.; cohaut, N.; Bae, J.-S.; Bhatia, S. K. Langmuir 2008, 24, 7912). A value of the C-C well depth of 37.26 K, used for estimating the C-H2 well depth in conjunction with the Berthelot rules, with the Steele C-C well depth used for interaction with heavier gases (Ar, CO2 and CH4), leads to excellent agreement with experimental isotherms in all cases.

  16. Epitopes of human testis-specific lactate dehydrogenase deduced from a cDNA sequence

    SciTech Connect

    Millan, J.L.; Driscoll, C.E.; LeVan, K.M.; Goldberg, E.

    1987-08-01

    The sequence and structure of human testis-specific L-lactate dehydrogenase (LDHC/sub 4/, LDHX; (L)-lactate:NAD/sup +/ oxidoreductase, EC 1.1.1.27) has been derived from analysis of a complementary DNA (cDNA) clone comprising the complete protein coding region of the enzyme. From the deduced amino acid sequence, human LDHC/sub 4/ is as different from rodent LDHC/sub 4/ (73% homology) as it is from human LDHA/sub 4/ (76% homology) and porcine LDHB/sub 4/ (68% homology). Subunit homologies are consistent with the conclusion that the LDHC gene arose by at least two independent duplication events. Furthermore, the lower degree of homology between mouse and human LDHC/sub 4/ and the appearance of this isozyme late in evolution suggests a higher rate of mutation in the mammalian LDHC genes than in the LDHA and -B genes. Comparison of exposed amino acid residues of discrete anti-genic determinants of mouse and human LDHC/sub 4/ reveals significant differences. Knowledge of the human LDHC/sub 4/ sequence will help design human-specific peptides useful in the development of a contraceptive vaccine.

  17. The abundance and organization of polypeptides associated with antigens of the Rh blood group system.

    PubMed

    Gardner, B; Anstee, D J; Mawby, W J; Tanner, M J; von dem Borne, A E

    1991-06-01

    Twelve murine monoclonal antibodies, which react with human red cells of common Rh phenotype but give weak or negative reactions with Rh null erythrocytes, were used in quantitative binding assays and competitive binding assays to investigate the abundance and organization of polypeptides involved in the expression of antigens of the Rh blood group system. Antibodies of the R6A-type (R6A, BRIC-69, BRIC-207) and the 2D10-type (MB-2D10, LA18.18, LA23.40) recognize related structures and 100,000-200,000 molecules of each antibody bind maximally to erythrocytes of common Rh phenotype. Antibodies of the BRIC-125 type (BRICs 32, 122, 125, 126, 168, 211) recognize structures that are unrelated to those recognized by R6A-type and 2D10-type antibodies and between 10,000 and 50,000 antibody molecules bind maximally to erythrocytes of the common Rh phenotype. The binding of antibodies of the R6A-type and the 2D10-type, but not of antibodies of the BRIC-125-type could be partially inhibited by human anti-D antibodies (polyclonal and monoclonal) and a murine anti-e-like antibody. These results are consistent with evidence (Moore & Green 1987; Avent et al., 1988b) that the Rh blood group antigens are associated with a complex that comprises two groups of related polypeptides of M(r) 30,000 and M(r) 35,000-100,000, respectively, and suggest that there are 1-2 x 10(5) copies of this complex per erythrocyte. The polypeptide recognized by antibodies of the BRIC-125 type is likely to be associated with this complex.

  18. Virion polypeptide heterogeneity among virulent and avirulent strains of eastern equine encephalitis (EEE) virus.

    PubMed

    Walder, R; Rosato, R R; Eddy, G A

    1981-01-01

    Comparative analysis of structural virion polypeptides of 24 selected EEE virus strains, representing North and South American types, was performed by one-dimensional discontinuous sodium dodecyl sulfate (SDS)-polyacrylamide-gel electrophoresis (PAGE). The structural proteins of different EEE virus isolates, resolved by this method, exhibited mol.wts. values in the range of 57-60 X 10(3) for (E-1), 51-54 X 10(3) for (E-2) and 35-38 X 10(3) daltons for the core (NP) nucleocapsid. The exception was the South American human lethal virus, TRVL-89287 strain, which was shown to possess only a single envelope glycoprotein. The high molecular weight envelope (E-1) glycoprotein species was absent or co-migrated adjacent to the smaller envelope (E-2) glycoprotein. Results indicated similarities in the core (NP) proteins, however greater variability in the envelope (E-/ and/or E-2) glycoproteins. Based on these variations seven distinct profiles could be observed among the EEE virus strain studied. The classification based on the patterns of structural polypeptides obtained by SDS-PAGE of these strains does not correlate well with any other previously reported in vitro characteristics (antigenic subtypes, HTP elution profiles) nor with the in vivo virulence markers.

  19. Polypeptides having beta-glucosidase activity and polynucleotides encoding the same

    DOEpatents

    Brown, Kimberly; Harris, Paul

    2013-12-17

    The present invention relates to isolated polypeptides having beta-glucosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  20. Recombinant host cells and nucleic acid constructs encoding polypeptides having cellulolytic enhancing activity

    DOEpatents

    Schnorr, Kirk; Kramer, Randall

    2017-03-28

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  1. Polypeptides having beta-glucosidase activity and beta-xylosidase activity and polynucleotides encoding same

    SciTech Connect

    Morant, Marc Dominique

    2014-05-06

    The present invention relates to isolated polypeptides having beta-glucosidase activity, beta-xylosidase activity, or beta-glucosidase and beta-xylosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  2. Polypeptides having beta-glucosidase activity and beta-xylosidase activity and polynucleotides encoding same

    SciTech Connect

    Morant, Marc Dominique

    2014-04-29

    The present invention relates to isolated polypeptides having beta-glucosidase activity, beta-xylosidase activity, or beta-glucosidase and beta-xylosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  3. Polypeptides having beta-glucosidase and beta-xylosidase activity and polynucleotides encoding same

    SciTech Connect

    Morant, Marc Dominique

    2014-05-06

    The present invention relates to isolated polypeptides having beta-glucosidase activity, beta-xylosidase activity, or beta-glucosidase and beta-xylosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  4. Evaporation-induced assembly of biomimetic polypeptides

    SciTech Connect

    Keyes, Joseph; Junkin, Michael; Cappello, Joseph; Wu Xiaoyi; Wong, Pak Kin

    2008-07-14

    We report an evaporation assisted plasma lithography (EAPL) process for guided self-assembly of a biomimetic silk-elastinlike protein (SELP). We demonstrate the formation of SELP structures from millimeter to submicrometer range on plasma-treatment surface templates during an evaporation-induced self-assembly process. The self-assembly processes at different humidities and droplet volumes were investigated. The process occurs efficiently in a window of optimized operating conditions found to be at 70% relative humidity and 8 {mu}l volume of SELP solution. The EAPL approach provides a useful technique for the realization of functional devices and systems using these biomimetic materials.

  5. Comparison of intestinal brush-border 95-Kdalton polypeptide and alpha- actinins

    PubMed Central

    1980-01-01

    To explore the suggestion that alpha-actinin cross-links actin filaments to the microvillar membrane (Mooseker and Tilney, 1975, J. Cell Biol. 67:725--743; Mooseker, 1976, J. Cell Biol. 71-417--433), we have assessed the possible relatedness of alpha-actinin and the brush- border 95-kdalton protein by four independent criteria: antigenicity, mobility on SDS gels, extractability in nonionic detergents, and peptide maps. We have found that anti-chicken gizzard alpha-actinin stains the junctional complex region of intact cells (Craig and Pardo, 1979, J. Cell Biol. 80:203--210) but does not stain isolated brush borders even though these structures contain a 95-kdalton polypeptide. Lack of staining is not caused by failure of the antibody to penetrate, as antiactin stains both the terminal web and the microvilli of isolated brush borders. By the antibody SDS gel overlay technique, we have established that anti-gizzard alpha-actinin recognizes homologous molecules in chicken skeletal and cardiac muscles, as well as in intestinal epithelial cells, but fails to recognize the brush-border 95- kdalton polypeptide. Conversely, anti-95-kdalton polypeptide does not recognize gizzard alpha-actinin. On high-resolution SDS polyacrylamide gel electrophoresis, alpha-actinin and brush-border 95-kdalton protein exhibit distinct mobilities. The two proteins also differ in their ability to be extracted in nonionic mobilities. The two proteins also differ in their ability to be extracted in nonionic detergent: epithelial cell immunoreactive alpha-actinin is soluble in NP-40, whereas 95-kdalton protein is insoluble. Finally, two-dimensional peptide mapping of iodinated tryptic peptides, as well as one- dimensional fingerprinting of partial tryptic, chymotryptic, papain, and S. aureus V8 protease digests, have revealed less than 5% homology between gizzard alpha-actinin and brush-border 95-kdalton polypeptide. The data suggest that there is no major structural homology between gizzard

  6. Angioplastic necrolytic migratory erythema. Unique association of necrolytic migratory erythema, extensive angioplasia, and high molecular weight glucagon-like polypeptide

    SciTech Connect

    Franchimont, C.; Pierard, G.E.; Luyckx, A.S.; Gerard, J.; Lapiere, C.M.

    1982-12-01

    A diabetic patient developed necrolytic migratory erythema with extensive angioplasia and high molecular weight glucagon-like polypeptide. There was no associated neoplasm such as glucagonoma. Lesions in the skin were studied by standard optical microscopy and by radioautography after incorporation of tritiated thymidine. Alterations in the skin begin as focal necrosis in the epidermis and in epithelial structures of adnexa, followed by marked angioplasia and a superficial and deep perivascular dermatitis.

  7. Subcellular Localization and Topology of the p7 Polypeptide of Hepatitis C Virus

    PubMed Central

    Carrère-Kremer, Séverine; Montpellier-Pala, Claire; Cocquerel, Laurence; Wychowski, Czeslaw; Penin, François; Dubuisson, Jean

    2002-01-01

    Although biological and biochemical data have been accumulated on most hepatitis C virus proteins, the structure and function of the 63-amino-acid p7 polypeptide of this virus have never been investigated. In this work, sequence analyses predicted that p7 contains two transmembrane passages connected by a short hydrophilic segment. The C-terminal transmembrane domain of p7 was predicted to function as a signal sequence, which was confirmed experimentally by analyzing the translocation of a reporter glycoprotein fused at its C terminus. The p7 polypeptide was tagged either with the ectodomain of CD4 or with a Myc epitope to study its membrane integration, its subcellular localization, and its topology. Alkaline extraction studies confirmed that p7 is an integral membrane polypeptide. The CD4-p7 chimera was detected by immunofluorescence on the surface of nonpermeabilized cells, indicating that it is exported to the plasma membrane. However, pulse-chase analyses showed that only approximately 20% of endoglycosidase H-resistant CD4-p7 was detected after long chase times, suggesting that a large proportion of p7 stays in an early compartment of the secretory pathway. Finally, by inserting a Myc epitope in several positions of p7 and analyzing the accessibility of this epitope on the plasma membrane of HepG2 cells, we showed that p7 has a double membrane-spanning topology, with both its N and C termini oriented toward the extracellular environment. Altogether, these data indicate that p7 is a polytopic membrane protein that could have a functional role in several compartments of the secretory pathway. PMID:11907211

  8. Injectable, Biomolecule-Responsive Polypeptide Hydrogels for Cell Encapsulation and Facile Cell Recovery through Triggered Degradation.

    PubMed

    Xu, Qinghua; He, Chaoliang; Zhang, Zhen; Ren, Kaixuan; Chen, Xuesi

    2016-11-16

    Injectable hydrogels have been widely investigated in biomedical applications, and increasing demand has been proposed to achieve dynamic regulation of physiological properties of hydrogels. Herein, a new type of injectable and biomolecule-responsive hydrogel based on poly(l-glutamic acid) (PLG) grafted with disulfide bond-modified phloretic acid (denoted as PLG-g-CPA) was developed. The hydrogels formed in situ via enzymatic cross-linking under physiological conditions in the presence of horseradish peroxidase and hydrogen peroxide. The physiochemical properties of the hydrogels, including gelation time and the rheological property, were measured. Particularly, the triggered degradation of the hydrogel in response to a reductive biomolecule, glutathione (GSH), was investigated in detail. The mechanical strength and inner porous structure of the hydrogel were influenced by the addition of GSH. The polypeptide hydrogel was used as a three-dimensional (3D) platform for cell encapsulation, which could release the cells through triggered disruption of the hydrogel in response to the addition of GSH. The cells released from the hydrogel were found to maintain high viability. Moreover, after subcutaneous injection into rats, the PLG-g-CPA hydrogels with disulfide-containing cross-links exhibited a markedly faster degradation behavior in vivo compared to that of the PLG hydrogels without disulfide cross-links, implying an interesting accelerated degradation process of the disulfide-containing polypeptide hydrogels in the physiological environment in vivo. Overall, the injectable and biomolecule-responsive polypeptide hydrogels may serve as a potential platform for 3D cell culture and easy cell collection.

  9. Tensile mechanics of alanine-based helical polypeptide: force spectroscopy versus computer simulations.

    PubMed

    Afrin, Rehana; Takahashi, Ichiro; Shiga, Kazuki; Ikai, Atsushi

    2009-02-01

    In nature, an alpha-helix is commonly used to build thermodynamically stable and mechanically rigid protein conformations. In view of growing interest in the mechanical rigidity of proteins, we measured the tensile profile of an alanine-based alpha-helical polypeptide on an atomic-force microscope to investigate the basic mechanics of helix extension with minimal interference from side-chain interactions. The peptide was extended to its maximum contour length with much less force than in reported cases of poly-L-Glu or poly-L-Lys, indicating that chain stiffness strongly depended on the physicochemical properties of side chains, such as their bulkiness. The low tensile-force extension originated presumably in locally unfolded parts because of spontaneous structural fluctuations. In 50% trifluoroethanol, the well-known helix-promoting agent, the rigidity of the sample polypeptide was markedly increased. Computer simulations of the peptide-stretching process showed that a majority of constituent residues underwent a transition from an alpha-helical to an extended conformation by overcoming an energy barrier around psi approximately 0 degrees on the Ramachandran plot. The observed lability of an isolated helix signified the biological importance of the lateral bundling of helices to maintain a rigid protein structure.

  10. Toughening of Thermoresponsive Arrested Networks of Elastin-Like Polypeptides To Engineer Cytocompatible Tissue Scaffolds.

    PubMed

    Glassman, Matthew J; Avery, Reginald K; Khademhosseini, Ali; Olsen, Bradley D

    2016-02-08

    Formulation of tissue engineering or regenerative scaffolds from simple bioactive polymers with tunable structure and mechanics is crucial for the regeneration of complex tissues, and hydrogels from recombinant proteins, such as elastin-like polypeptides (ELPs), are promising platforms to support these applications. The arrested phase separation of ELPs has been shown to yield remarkably stiff, biocontinuous, nanostructured networks, but these gels are limited in applications by their relatively brittle nature. Here, a gel-forming ELP is chain-extended by telechelic oxidative coupling, forming extensible, tough hydrogels. Small angle scattering indicates that the chain-extended polypeptides form a fractal network of nanoscale aggregates over a broad concentration range, accessing moduli ranging from 5 kPa to over 1 MPa over a concentration range of 5-30 wt %. These networks exhibited excellent erosion resistance and allowed for the diffusion and release of encapsulated particles consistent with a bicontinuous, porous structure with a broad distribution of pore sizes. Biofunctionalized, toughened networks were found to maintain the viability of human mesenchymal stem cells (hMSCs) in 2D, demonstrating signs of osteogenesis even in cell media without osteogenic molecules. Furthermore, chondrocytes could be readily mixed into these gels via thermoresponsive assembly and remained viable in extended culture. These studies demonstrate the ability to engineer ELP-based arrested physical networks on the molecular level to form reinforced, cytocompatible hydrogel matrices, supporting the promise of these new materials as candidates for the engineering and regeneration of stiff tissues.

  11. Principles Governing the Self Assembly of Polypeptide Nanoparticles

    NASA Astrophysics Data System (ADS)

    Wahome, Newton

    Self assembling systems on the nanometer scale afford the advantage of being able to control submicron level events. In this study, we focus on the self-assembling polypeptide nanoparticles (SAPN). The SAPN scaffold is made up of oligomerizing domains that align along the principle rotational axes of icosahedral symmetry. By aligning them along these axes, a particle with spherical geometry can be achieved. This particle can be utilized as a vaccine, as a drug delivery vehicle, or as a biomedical imaging device. This research will try to answer why the SAPN self-assembles into distinct molecular weight ranges while mostly maintaining a spherical morphology. The first means will be theoretical and computational, where we will utilize a mathematical formalism to find out how the packing of SAPN's monomeric units can occur within symmetric space. Then molecular dynamics will be run within this symmetric space to test the per amino acid residue susceptibility of SAPN towards becoming polymorphic in nature. Means for examining the aggregation propensity of SAPN will be also be tested. Specifically, the relationship of different sequences of SAPN with pH will be elucidated. Co-assembly of SAPN to reduce the surface density of an aggregation prone epitope will be tested. Also, aggregation reduction consisting of the exchange of an anionic denaturant with a positively charged suppressor in order to mitigate a priori peptide association and misfolding, will also be attempted. SAPN has been shown to be an immunogenic platform for the presentation of pathogen derived antigens. We will attempt to show the efficacy of presenting an antigen from HIV-1 which is structurally restrained to best match the native conformation on the virus. Immunological studies will be performed to test the effect of this approach, as well testing the antigenicity of the nanoparticle in the absence of adjuvant. Finally, the antigen presenting nanoparticles will undergo formulation testing, to measure

  12. Two-dimensional sup 1 H nuclear magnetic resonance study of AaH IT, an anti-insect toxin from the scorpion Androctonus australis Hector. Sequential resonance assignments and folding of the polypeptide chain

    SciTech Connect

    Darbon, H. ); Weber, C.; Braun, W. )

    1991-02-19

    Sequence-specific nuclear magnetic resonance assignments for the polypeptide backbone and for most of the amino acid side-chain protons, as well as the general folding of AaH IT, are described. AaH IT is a neurotoxin purified from the venom of the scorpion Androctonus australis Hector and is specifically active on the insect nervous system. The secondary structure and the hydrogen-bonding patterns in the regular secondary structure elements are deduced from nuclear Overhauser effects and the sequence locations of the slowly exchanging amide protons. The backbone folding is determined by distance geometry calculations with the DISMAN program. The regular secondary structure includes two and a half turns of {alpha}-helix running from residues 21 to 30 and a three-stranded antiparallel {beta}-sheet including peptides 3-5, 34-38, and 41-46. Two tight turns are present, one connecting the end of the {alpha}-helix to an external strand of the {beta}-sheet, i.e., turn 31-34, and another connecting this same strand to the central one, i.e., turn 38-41. The differences in the specificity of these related proteins, which are able to discriminate between mammalian and insect voltage-dependent sodium channels of excitable tissues, are most probably brought about by the position of the C-terminal peptide with regard to a hydrophobic surface common to all scorpion toxins examined thus far. Thus, the interaction of a given scorpion toxin with its receptor might well be governed by the presence of this solvent-exposed hydrophobic surface, whereas adjacent areas modulate the specificity of the interaction.

  13. Compositions and methods for making selenocysteine containing polypeptides

    DOEpatents

    Soll, Dieter; Aldag, Caroline; Hohn, Michael

    2016-10-11

    Non-naturally occurring tRNA.sup.Sec and methods of using them for recombinant expression of proteins engineered to include one or more selenocysteine residues are disclosed. The non-naturally occurring tRNA.sup.Sec can be used for recombinant manufacture of selenocysteine containing polypeptides encoded by mRNA without the requirement of an SECIS element. In some embodiments, selenocysteine containing polypeptides are manufactured by co-expressing a non-naturally occurring tRNA.sup.Sec a recombinant expression system, such as E. coli, with SerRS, EF-Tu, SelA, or PSTK and SepSecS, and an mRNA with at least one codon that recognizes the anticodon of the non-naturally occurring tRNA.sup.Sec.

  14. Imparting large macroscopic changes with small changes in polypeptide composition

    NASA Astrophysics Data System (ADS)

    Sing, Michelle; McKinley, Gareth; Olsen, Bradley

    Block copolymers composed of polypeptides provide an excellent platform for exploring the underlying physics surrounding macroscopic associative network behavior. Previous work in our group has elucidated a difference in the mechanical properties of two nearly identical elastin-like polypeptide (ELP) endblocks. In poly(ELP)s, this substitution is known to result in tighter beta turns. These beta turns exhibit slower responses to changes in temperature within the material. Under shear, the modulus for the alanine-containing ELP triblock is almost three times higher than the glycine-containing ELP. Additionally, preliminary tensile tests show higher stress and strain at break for the alanine ELP triblock. We are able to explain the reasons for this behavior using a variety of spectroscopic and analytical techniques. Small angle neutron and x-ray scattering indicate differences in ordering between the alanine and glycine containing ELP materials both in shear and in stagnant flow.

  15. Interplay between Folding and Assembly of Fibril-Forming Polypeptides

    NASA Astrophysics Data System (ADS)

    Ni, Ran; Abeln, Sanne; Schor, Marieke; Cohen Stuart, Martien A.; Bolhuis, Peter G.

    2013-08-01

    Polypeptides can self-assemble into hierarchically organized fibrils consisting of a stack of individually folded polypeptides driven together by hydrophobic interaction. Using a coarse-grained model, we systematically studied this self-assembly as a function of temperature and hydrophobicity of the residues on the outside of the building block. We find the self-assembly can occur via two different pathways—a random aggregation-folding route and a templated-folding process—thus indicating a strong coupling between folding and assembly. The simulation results can explain experimental evidence that assembly through stacking of folded building blocks is rarely observed, at the experimental concentrations. The model thus provides a generic picture of hierarchical fibril formation.

  16. Side-chain and backbone ordering in a polypeptide.

    PubMed

    Wei, Yanjie; Nadler, Walter; Hansmann, Ulrich H E

    2006-10-28

    We report results from multicanonical simulations of polyglutamic acid chains of length of ten residues. For this simple polypeptide we observe a decoupling of backbone and side-chain ordering in the folding process. While the details of the two transitions vary between the peptide in gas phase and in an implicit solvent, our results indicate that, independent of the specific surroundings, upon continuously lowering the temperature side-chain ordering occurs only after the backbone topology is completely formed.

  17. An engineered coiled-coil polypeptide assembled onto quantum dots for targeted cell imaging

    NASA Astrophysics Data System (ADS)

    Yao, Ming-Hao; Yang, Jie; Song, Ji-Tao; Zhang, Lin; Fang, Bi-Yun; Zhao, Dong-Hui; Xia, Rui-Xue; Jin, Rui-Mei; Zhao, Yuan-Di; Liu, Bo

    2015-12-01

    Quantum dot (QD)-polypeptide probes have been developed through the specific metal-affinity interaction between polypeptides appended with N-terminal polyhistidine sequences and CdSe/ZnS core-shell QDs. The size and charge of a QD-polypeptide can be tuned by using different coiled-coil polypeptides. Compared to glutathione-capped QDs (QD-GSH), QD-polypeptide probes showed an approximately two- to three-fold luminescence increase, and the luminescence increase was not obviously related to the charge of the polypeptide. QD-polypeptide probes with different charge have a great effect on nonspecific cellular uptake. QD-polypeptide probes with negative charge exhibited lower nonspecific cellular uptake in comparison to the QD-GSH, while positively charged QD-polypeptide probes presented higher cellular uptake than the QD-GSH. A targeted QD-ARGD probe can obviously increase targeted cellular uptake in α v β 3 overexpressing HeLa cells compared to QD-A. In addition, QD-polypeptide probes showed lower in vitro cytotoxicity compared to the original QDs. These results demonstrate that these QD-polypeptide probes with high specific cellular uptake, high fluorescence intensity and low background noise are expected to have great potential applications in targeted cell imaging.

  18. Birth, life and death of nascent polypeptide chains

    PubMed Central

    Jha, Sujata; Komar, Anton A

    2011-01-01

    The journey of nascent polypeptides from synthesis at the peptidyl transferase center of the ribosome (“birth”) to full function (“maturity”) involves multiple interactions, constraints, modifications and folding events. Each step of this journey impacts the ultimate expression level and functional capacity of the translated protein. It has become clear that the kinetics of protein translation is predominantly modulated by synonymous codon usage along the mRNA, and that this provides an active mechanism for coordinating the synthesis, maturation and folding of nascent polypeptides. Multiple quality control systems ensure that proteins achieve their native, functional form. Unproductive co-translational folding intermediates that arise during protein synthesis may undergo enhanced interaction with components of these systems, such as chaperones, and/or be subjects of co-translational degradation (“death”). This review provides an overview of our current understanding of the complex co-translational events that accompany the synthesis, maturation, folding and degradation of nascent polypeptide chains. PMID:21538896

  19. Generation of polypeptide-templated gold nanoparticles using ionizing radiation.

    PubMed

    Walker, Candace Rae; Pushpavanam, Karthik; Nair, Divya Geetha; Potta, Thrimoorthy; Sutiyoso, Caesario; Kodibagkar, Vikram D; Sapareto, Stephen; Chang, John; Rege, Kaushal

    2013-08-13

    Ionizing radiation, including γ rays and X-rays, are high-energy electromagnetic radiation with diverse applications in nuclear energy, astrophysics, and medicine. In this work, we describe the use of ionizing radiation and cysteine-containing elastin-like polypeptides (C(n)ELPs, where n = 2 or 12 cysteines in the polypeptide sequence) for the generation of gold nanoparticles. In the presence of C(n)ELPs, ionizing radiation doses higher than 175 Gy resulted in the formation of maroon-colored gold nanoparticle dispersions, with maximal absorbance at 520 nm, from colorless metal salts. Visible color changes were not observed in any of the control systems, indicating that ionizing radiation, gold salt solution, and C(n)ELPs were all required for nanoparticle formation. The hydrodynamic diameters of nanoparticles, determined using dynamic light scattering, were in the range of 80-150 nm, while TEM imaging indicated the formation of gold cores 10-20 nm in diameter. Interestingly, C2ELPs formed 1-2 nm diameter gold nanoparticles in the absence of radiation. Our results describe a facile method of nanoparticle formation in which nanoparticle size can be tailored based on radiation dose and C(n)ELP type. Further improvements in these polypeptide-based systems can lead to colorimetric detection of ionizing radiation in a variety of applications.

  20. Chirality-mediated polypeptide micelles for regulated drug delivery.

    PubMed

    Ding, Jianxun; Li, Chen; Zhang, Ying; Xu, Weiguo; Wang, Jincheng; Chen, Xuesi

    2015-01-01

    Two kinds of triblock poly(ethylene glycol)-polyleucine (PEG-PLeu) copolymers were synthesized through the ring-opening polymerization of L-Leu N-carboxyanhydride (NCA), or equivalent D-Leu NCA and L-Leu NCA with amino-terminated PEG as a macroinitiator. The amphiphilic copolymers spontaneously self-assembled into spherical micellar aggregations in an aqueous environment. The micelle with a racemic polypeptide core exhibited smaller critical micelle concentration and diameter compared to those with a levorotatory polypeptide core. A model anthracycline antineoplastic agent, i.e., doxorubicin (DOX), was loaded into micelles through nanoprecipitation, and the PEG-P(D,L-Leu) micelle exhibited higher drug-loading efficacy than that with a P(L-Leu) core-this difference was attributed to the flexible and compact P(L-Leu) core. Sustained in vitro DOX release from micelles with both levorotatory and racemic polypeptide cores was observed, and the DOX-loaded PEG-P(D,L-Leu) micelle exhibited a slower release rate. More interestingly, DOX-loaded micelles exhibited chirality-mediated antitumor efficacy in vitro and in vivo, which are all better than that of free DOX. Furthermore, both enhanced tumor inhibition and excellent security in vivo were confirmed by histopathological or in situ cell apoptosis analyses. Therefore, DOX-loaded PEG-PLeu micelles appear to be an interesting nanoscale polymeric formulation for promising malignancy chemotherapy.

  1. Separation and nanoencapsulation of antitumor polypeptide from Spirulina platensis.

    PubMed

    Zhang, Bochao; Zhang, Xuewu

    2013-01-01

    Spirulina platensis is a multicellular edible blue-green alga with abundant proteins (∼ 60%). No report is available on the antitumor polypeptides from the whole proteins of S. platensis. In this study, for the first time, an antitumor polypeptide Y2 from trypsin digest of S. platensis proteins was obtained by using freeze-thawing plus ultrasonication extraction, hydrolysis with four enzymes (trypsin, alcalase, papain, and pepsin), and gel filtration chromatography. The results showed that the degree of hydrolysis can be ordered as: trypsin (38.5%) > alcalase (31.2%) > papain (27.8%) > pepsin (7.1%). For MCF-7 and HepG2 cells, at 250 µg/mL, the maximum inhibitory rate of Y2 was 97%, while standard drug 5-FU was 55 and 97%, respectively. Furthermore, the nanoencapsulation of Y2 with chitosan (CS) was also investigated. After nanoencapsulation, the maximum encapsulation efficiency and polypeptides contents are 49 and 15%, respectively; and the antitumor activity is basically not lost. These data demonstrated the potential of nanopolypeptides (Y2-CS) in food and pharmaceutical applications.

  2. Effects of Cationic Polypeptides on Thrombasthenic and Afibrinogenemic Blood Platelets

    PubMed Central

    White, James G.

    1972-01-01

    Cationic polypeptides are known to cause the conversion of fibrinogen to fibrin gel and the immediate aggregation of blood platelets. In the present study, the effects of the cationic polypeptides, polybrene and polylysine, on normal, afibrinogenemic and thrombasthenic platelets were examined by nephelometry and electron microscopy. Normal and afibrinogenemic platelets aggregated rapidly and irreversibly after exposure to either agent. Thus, fibrinogen was not an essential factor for the interaction, though it may facilitate the rate of clumping produced by polybrene or polylysine. Thrombasthenic platelets did not aggregate rapidly or irreversibly in the presence of either agent. Shape change and slight degrees of clumping were induced by the cationic substances, a response essentially identical to the reaction of thrombasthenic platelets to collagen. The failure of cationic polypeptides to cause immediate aggregation of thrombasthenic platelets was not due to a failure of the agents to interact with the abnormal cells. Electron microscopy revealed that normal, afibrinogenemic and thrombasthenic platelets all adsorbed polybrene and polylysine, and transferred the agents to intracellular organelles. ImagesFig 3Fig 4Fig 1Fig 2 PMID:5054252

  3. Polypeptide synthesis induced in Nicotiana clevelandii protoplasts by infection with raspberry ringspot nepovirus.

    PubMed

    Acosta, O; Mayo, M A

    1993-01-01

    Infection of Nicotiana clevelandii protoplasts by raspberry ringspot nepovirus resulted in the accumulation of about 24 polypeptides that differed in M(r) and pI from polypeptides accumulating in mock-inoculated protoplasts. Similar polypeptides accumulated in protoplasts infected with the S and E strains of RRV but different infection-specific polypeptides were detected in protoplasts infected with tobacco ringspot nepovirus. The M(r) of RRV-specific polypeptides ranged from 210,000 to 18,000 and most are presumed to be derived from others by proteolytic cleavage. No evidence was found for marked changes in polypeptide abundance with time after inoculation or for any virus-specific polypeptide becoming disproportionately abundant in the medium during culture.

  4. Three-Dimensional Polypeptide Architectures Through Tandem Catalysis and Click Chemistry

    NASA Astrophysics Data System (ADS)

    Rhodes, Allison Jane

    Rapid renal clearance, liver accumulation, proteolytic degradation and non-specificity are challenges small molecule drugs, peptides, proteins and nucleic acid therapeutics encounter en route to their intended destination within the body. Nanocarriers (i.e. dendritric polymers, vesicles, and micelles) of approximately 100 nm in diameter, shuttle small molecule drugs to their desired location through passive (EPR effect) and active (ligand-mediated) targeting, maximizing therapeutic efficiency. Polypeptide-based polymers are water-soluble, biocompatible, non-toxic and are therefore excellent candidates for nanocarriers. Dendritic polymers, including dendrimers, cylindrical brushes, and star polymers, are the newest class of nanomedicine drug delivery vehicles. The synthesis and characterization of dendritic polymers is challenging, with tedious and costly procedures. Dendritic polymers possess peripheral pendent functional groups that can potentially be used in ligand-mediated drug delivery vehicles and bioimaging applications. More specifically, cylindrical brushes are dendritic polymers where a single linear polymer (primary chain) has polymer chains (secondary chains) grafted to it. Recently, research groups have shown that cylindrical brush polymers are capable of nanoparticle and supramolecular structure self-assembly. The facile preparation of high-density brush copolypeptides by the "grafting from" approach will be discussed. This approach utilizes a novel, tandem catalytic methodology where alloc-alpha-aminoamide groups are installed within the side-chains of the alpha-amino-N-carboxyanhydride (NCA) monomer serving as masked initiators. These groups are inert during cobalt initiated NCA polymerization, and give alloc-alpha-aminoamide substituted polypeptide main-chains. The alloc-alpha-aminoamide groups are activated in situ using nickel to generate initiators for growth of side-chain brush segments. This method proves to be efficient, yielding well

  5. Fabricating and Characterizing Physical Properties of Electrospun Polypeptide-based Nanofibers

    NASA Astrophysics Data System (ADS)

    Khadka, Dhan Bahadur

    This dissertation has aimed to fabricate polypeptide based biomaterial and characterize physical properties. Electrospinning is used as a tool for the sample fabrication. Project focused on determining the feasibility of electrospinning of certain synthetic polypeptides and certain elastin-like peptides from aqueous feedstocks and to characterize physical properties of polymer aqueous solution, cast film and spun fibers and fiber mats. The research involves peptide design, polymer electrospinning, fibers crosslinking, determining the extent of crosslinking, fibers protease degradation study, fibers stability and self-organization analysis, structure and composition determination by various spectroscopy and microscopy techniques and characterization of mechanical properties of individual suspended fibers. Fiber mats of a synthetic cationic polypeptide poly(L-ornithine) (PLO) and an anionic co-polypeptide of L-glutamic acid and L-tyrosine (PLEY) of defined composition have been produced by electrospinning. Fibers were obtained from polymer aqueous solution at concentrations of 20-45% (w/v) in PLO and at concentrations of 20-60% (w/v) in PLEY. Applied voltage and spinneret-collector distance were also found to influence polymer spinnability and fibers morphology. Oriented fibers were obtained by parallel electrodes geometry. Fiber diameter and morphology was analyzed by scanning electron microscopy (SEM) and atomic force microscopy (AFM). PLO fibers exposed on glutaraldehyde (GTA) vapor rendered fiber mats water-insoluble. A common chemical reagent, carbodiimide was used to crosslink PLEY fibers. Fiber solubility in aqueous solution varied as a function of crosslinking time and crosslinker concentration. Crosslink density has been quantified by a visible-wavelength dye-based method. Degradation of crosslinked fibers by different proteases has been demonstrated. Investigation of crosslinked PLEY fibers has provided insight into the mechanisms of stability at different

  6. A novel computational framework for deducing muscle synergies from experimental joint moments

    PubMed Central

    Gopalakrishnan, Anantharaman; Modenese, Luca; Phillips, Andrew T. M.

    2014-01-01

    Prior experimental studies have hypothesized the existence of a “muscle synergy” based control scheme for producing limb movements and locomotion in vertebrates. Such synergies have been suggested to consist of fixed muscle grouping schemes with the co-activation of all muscles in a synergy resulting in limb movement. Quantitative representations of these groupings (termed muscle weightings) and their control signals (termed synergy controls) have traditionally been derived by the factorization of experimentally measured EMG. This study presents a novel approach for deducing these weightings and controls from inverse dynamic joint moments that are computed from an alternative set of experimental measurements—movement kinematics and kinetics. This technique was applied to joint moments for healthy human walking at 0.7 and 1.7 m/s, and two sets of “simulated” synergies were computed based on two different criteria (1) synergies were required to minimize errors between experimental and simulated joint moments in a musculoskeletal model (pure-synergy solution) (2) along with minimizing joint moment errors, synergies also minimized muscle activation levels (optimal-synergy solution). On comparing the two solutions, it was observed that the introduction of optimality requirements (optimal-synergy) to a control strategy solely aimed at reproducing the joint moments (pure-synergy) did not necessitate major changes in the muscle grouping within synergies or the temporal profiles of synergy control signals. Synergies from both the simulated solutions exhibited many similarities to EMG derived synergies from a previously published study, thus implying that the analysis of the two different types of experimental data reveals similar, underlying synergy structures. PMID:25520645

  7. Deducing logical relationships between spatially registered cortical parcellations under conditions of uncertainty.

    PubMed

    Bezgin, Gleb; Wanke, Egon; Krumnack, Antje; Kötter, Rolf

    2008-10-01

    We propose a new technique, called Spatial Objective Relational Transformation (SORT), as an automated approach for derivation of logical relationships between cortical areas in different brain maps registered in the same Euclidean space. Recently, there have been large amounts of voxel-based three-dimensional structural and functional imaging data that provide us with coordinate-based information about the location of differently defined areas in the brain, whereas coordinate-independent, parcellation-based mapping is still commonly used in the majority of animal tracing and mapping studies. Because of the impact of voxel-based imaging methods and the need to attribute their features to coordinate-independent brain entities, this mapping becomes increasingly important. Our motivation here is not to make vague statements where more precise spatial statements would be better, but to find criteria for the identity (or other logical relationships) between areas that were delineated by different methods, in different individuals, or mapped to three-dimensional space using different deformation algorithms. The relevance of this problem becomes immediately obvious as one superimposes and compares different datasets in multimodal databases (e.g. CARET, http://brainmap.wustl.edu/caret), where voxel-based data are registered to surface nodes exploited by the procedure presented here. We describe the SORT algorithm and its implementation in the Java 2 programming language (http://java.sun.com/, which we make available for download. We give an example of practical use of our approach, and validate the SORT approach against a database of the coordinate-independent statements and inferences that have been deduced using alternative techniques.

  8. Macromolecular Instabilities and Dynamical Coding in Brain Enzymes, Polypeptide Ligands, Polypeptide and Cholinergic Receptors, and Sodium and Cholinergic Channel Proteins

    DTIC Science & Technology

    1988-03-01

    digital computers using dynamical equations (including those of the reduced Hodgkin - Huxley variety) as well as data-analytic tools which ha-e been and are...behavior of an enzyme, a receptor, a neuron , the heart, the EEG, and even hydrostatic pressure in the kidney is a sign of loss of regulatory potential ...hydrophobic minima. Certain polypeptide families am examirud in this context and the actions of a group of equally potent corticotrophic releasing facrs

  9. Linker polypeptides of the phycobilisome from the cyanobacterium Mastigocladus laminosus. I. Isolation and characterization of phycobiliprotein-linker-polypeptide complexes.

    PubMed

    Füglistaller, P; Suter, F; Zuber, H

    1986-07-01

    Phycobilisomes from the cyanobacterium Mastigocladus laminosus cultured in white and red light were isolated and compared with respect to the phycoerythrocyanin (PEC) and linker polypeptide contents. It was verified that the production of PEC is induced by low light intensities. A PEC complex, (alpha PEC beta PEC)6LR34.5,PEC, and a phycocyanin (PC) complex, (alpha PC beta PC)6LR34.5,PC, were isolated from phycobilisomes by Cellex-D anion exchange chromatography and sucrose density gradient centrifugation. The absorption and fluorescence emission maxima of the PEC complex are at 575 and 620 nm and those of the PC complex are at 631 and 647 nm, respectively. The extinction coefficients of the two complexes were determined. From different experiments it was concluded that PEC is present as a hexameric complex, (alpha PEC beta PEC)6LR34.5,PEC, in the phycobilisome. The two linker polypeptides LR34.5,PEC and LR34.5,PC were isolated from their phycobiliprotein complexes by gel filtration on Bio-Gel P-100 in 50% formic acid. A 5-kDa terminal segment of both linker polypeptides was found to influence the hexamer formation of the phycobiliproteins. The same segments have been described to be responsible for the hexamer-hexamer linkage (Yu, M.-H. & Glazer, A.N. (1982) J. Biol. Chem. 257, 3429-3433). A 8.9-kDa linker polypeptide, LR(C)8.9, was isolated from a PEC fraction of the Cellex-D column by Bio-Gel P-100 gel filtration in 50% formic acid. Localisation of this protein within the phycobilisome was attempted. Its most probable function is to terminate the phycobilisomal rods at the end distal to the allophycocyanin core.

  10. Bionanotechnology application of polypeptides in a hair color product: self-assembly enables expression, processing, and functionality.

    PubMed

    Rouvière, Pierre E; Li, Jing; Brill, Donald J; Reiss, Lisa D; Schwartz, Timothy R; Butterick, Lisa A; Fahnestock, Stephen R; Gruber, Tanja

    2013-02-01

    Bionanotechnology aims to impart new properties to materials from unique functionalities present in biomolecules. However, the promise of bionanotechnology has not materialized beyond the biomedical field due in large part to issues of scalability, purity, and cost of manufacturing. In this work we demonstrate an approach to co-engineer production and system functionality into a single polypeptide. We designed a system to anchor particles onto hair via a multifunctional polypeptide composed of two domains, one with affinity to hair and the other capable of strong interactions with the particle surface. These strong interactions, exemplified by resistance to anionic surfactants, stem from the ability to self-assemble into higher order structures, which were observed by atomic force microscopy. At the same time, the controlled solubility properties of the particle binding domain permit the scalable production in Escherichia coli via inclusion bodies and cost effective purification. We believe this is a significant advance toward the development of bionanotechnology for industrial applications.

  11. Temperature-dependent morphology of hybrid nanoflowers from elastin-like polypeptides

    SciTech Connect

    Ghosh, Koushik; Balog, Eva Rose M.; Sista, Prakash; Williams, Darrick J.; Martinez, Jennifer S. E-mail: rcrocha@lanl.gov; Rocha, Reginaldo C. E-mail: rcrocha@lanl.gov; Kelly, Daniel

    2014-02-01

    We report a method for creating hybrid organic-inorganic “nanoflowers” using calcium or copper ions as the inorganic component and a recombinantly expressed elastin-like polypeptide (ELP) as the organic component. Polypeptides provide binding sites for the dynamic coordination with metal ions, and then such noncovalent complexes become nucleation sites for primary crystals of metal phosphates. We have shown that the interaction between the stimuli-responsive ELP and Ca{sup 2+} or Cu{sup 2+}, in the presence of phosphate, leads to the growth of micrometer-sized particles featuring nanoscale patterns shaped like flower petals. The morphology of these flower-like composite structures is dependent upon the temperature of growth and has been characterized by scanning electron microscopy. The composition of nanoflowers has also been analyzed by energy-dispersive X-ray spectroscopy, X-ray photoelectron spectroscopy, and X-ray diffraction. The temperature-dependent morphologies of these hybrid nanostructures, which arise from the controllable phase transition of ELPs, hold potential for morphological control of biomaterials in emerging applications such as tissue engineering and biocatalysis.

  12. Elastin-like polypeptides as a promising family of genetically-engineered protein based polymers.

    PubMed

    Kowalczyk, Tomasz; Hnatuszko-Konka, Katarzyna; Gerszberg, Aneta; Kononowicz, Andrzej K

    2014-08-01

    Elastin-like polypeptides (ELP) are artificial, genetically encodable biopolymers, belonging to elastomeric proteins, which are widespread in a wide range of living organisms. They are composed of a repeating pentapeptide sequence Val-Pro-Gly-Xaa-Gly, where the guest residue (Xaa) can be any naturally occurring amino acid except proline. These polymers undergo reversible phase transition that can be triggered by various environmental stimuli, such as temperature, pH or ionic strength. This behavior depends greatly on the molecular weight, concentration of ELP in the solution and composition of the amino acids constituting ELPs. At a temperature below the inverse transition temperature (Tt), ELPs are soluble, but insoluble when the temperature exceeds Tt. Furthermore, this feature is retained even when ELP is fused to the protein of interest. These unique properties make ELP very useful for a wide variety of biomedical applications (e.g. protein purification, drug delivery etc.) and it can be expected that smart biopolymers will play a significant role in the development of most new materials and technologies. Here we present the structure and properties of thermally responsive elastin-like polypeptides with a particular emphasis on biomedical and biotechnological application.

  13. Biomimetic Synthesis of Gelatin Polypeptide-Assisted Noble-Metal Nanoparticles and Their Interaction Study

    NASA Astrophysics Data System (ADS)

    Liu, Ying; Liu, Xiaoheng; Wang, Xin

    2011-12-01

    Herein, the generation of gold, silver, and silver-gold (Ag-Au) bimetallic nanoparticles was carried out in collagen (gelatin) solution. It first showed that the major ingredient in gelatin polypeptide, glutamic acid, acted as reducing agent to biomimetically synthesize noble metal nanoparticles at 80°C. The size of nanoparticles can be controlled not only by the mass ratio of gelatin to gold ion but also by pH of gelatin solution. Interaction between noble-metal nanoparticles and polypeptide has been investigated by TEM, UV-visible, fluorescence spectroscopy, and HNMR. This study testified that the degradation of gelatin protein could not alter the morphology of nanoparticles, but it made nanoparticles aggregated clusters array (opposing three-dimensional α-helix folding structure) into isolated nanoparticles stabilized by gelatin residues. This is a promising merit of gelatin to apply in the synthesis of nanoparticles. Therefore, gelatin protein is an excellent template for biomimetic synthesis of noble metal/bimetallic nanoparticle growth to form nanometer-sized device.

  14. Temperature-dependent morphology of hybrid nanoflowers from elastin-like polypeptides

    NASA Astrophysics Data System (ADS)

    Ghosh, Koushik; Balog, Eva Rose M.; Sista, Prakash; Williams, Darrick J.; Kelly, Daniel; Martinez, Jennifer S.; Rocha, Reginaldo C.

    2014-02-01

    We report a method for creating hybrid organic-inorganic "nanoflowers" using calcium or copper ions as the inorganic component and a recombinantly expressed elastin-like polypeptide (ELP) as the organic component. Polypeptides provide binding sites for the dynamic coordination with metal ions, and then such noncovalent complexes become nucleation sites for primary crystals of metal phosphates. We have shown that the interaction between the stimuli-responsive ELP and Ca2+ or Cu2+, in the presence of phosphate, leads to the growth of micrometer-sized particles featuring nanoscale patterns shaped like flower petals. The morphology of these flower-like composite structures is dependent upon the temperature of growth and has been characterized by scanning electron microscopy. The composition of nanoflowers has also been analyzed by energy-dispersive X-ray spectroscopy, X-ray photoelectron spectroscopy, and X-ray diffraction. The temperature-dependent morphologies of these hybrid nanostructures, which arise from the controllable phase transition of ELPs, hold potential for morphological control of biomaterials in emerging applications such as tissue engineering and biocatalysis.

  15. Purification of recombinant protein by cold-coacervation of fusion constructs incorporating resilin-inspired polypeptides.

    PubMed

    Lyons, Russell E; Elvin, Christopher M; Taylor, Karin; Lekieffre, Nicolas; Ramshaw, John A M

    2012-12-01

    Polypeptides containing between 4 and 32 repeats of a resilin-inspired sequence AQTPSSYGAP, derived from the mosquito Anopheles gambiae, have been used as tags on recombinant fusion proteins. These repeating polypeptides were inspired by the repeating structures that are found in resilins and sequence-related proteins from various insects. Unexpectedly, an aqueous solution of a recombinant resilin protein displays an upper critical solution temperature (cold-coacervation) when held on ice, leading to a separation into a protein rich phase, typically exceeding 200 mg/mL, and a protein-poor phase. We show that purification of recombinant proteins by cold-coacervation can be performed when engineered as a fusion partner to a resilin-inspired repeat sequence. In this study, we demonstrate the process by the recombinant expression and purification of enhanced Green fluorescent protein (EGFP) in E. coli. This facile purification system can produce high purity, concentrated protein solutions without the need for affinity chromatography or other time-consuming or expensive purification steps, and that it can be used with other bulk purification steps such as low concentration ammonium sulfate precipitation. Protein purification by cold-coacervation also minimizes the exposure of the target protein to enhanced proteolysis at higher temperature.

  16. Escherichia coli ClpB is a non-processive polypeptide translocase.

    PubMed

    Li, Tao; Weaver, Clarissa L; Lin, Jiabei; Duran, Elizabeth C; Miller, Justin M; Lucius, Aaron L

    2015-08-15

    Escherichia coli caseinolytic protease (Clp)B is a hexameric AAA+ [expanded superfamily of AAA (ATPase associated with various cellular activities)] enzyme that has the unique ability to catalyse protein disaggregation. Such enzymes are essential for proteome maintenance. Based on structural comparisons to homologous enzymes involved in ATP-dependent proteolysis and clever protein engineering strategies, it has been reported that ClpB translocates polypeptide through its axial channel. Using single-turnover fluorescence and anisotropy experiments we show that ClpB is a non-processive polypeptide translocase that catalyses disaggregation by taking one or two translocation steps followed by rapid dissociation. Using single-turnover FRET experiments we show that ClpB containing the IGL loop from ClpA does not translocate substrate through its axial channel and into ClpP for proteolytic degradation. Rather, ClpB containing the IGL loop dysregulates ClpP leading to non-specific proteolysis reminiscent of ADEP (acyldepsipeptide) dysregulation. Our results support a molecular mechanism where ClpB catalyses protein disaggregation by tugging and releasing exposed tails or loops.

  17. Architecture effects on multivalent interactions by polypeptide-based multivalent ligands

    NASA Astrophysics Data System (ADS)

    Liu, Shuang

    protein materials, including structural as well as functional proteins. Therefore, polypeptide-based multivalent scaffolds are used to display ligands to assess the contribution of different architectural parameters to the multivalent binding events. In this work, a family of alanine-rich alpha-helical glycopolypeptides was designed and synthesized by a combination of protein engineering and chemical coupling, to display two types of saccharide ligands for two different multivalent binding systems. The valencies, chain length and spacing between adjacent ligands of these multivalent ligands were designed in order to study architecture effects on multivalent interactions. The polypeptides and their glycoconjugates were characterized via various methods, including SDS-PAGE, NMR, HPLC, amino acid analysis (AAA), MALDI, circular dichroism (CD) and GPC. In the first multivalent binding system, cholera toxin B pentamer (CT B5) was chosen to be the protein receptor due to its well-characterized structure, lack of significant steric interference of binding to multiple binding sites, and requirement of only simple monosaccharide as ligands. Galactopyranoside was incorporated into polypeptide scaffolds through amine-carboxylic acid coupling to the side chains of glutamic acid residues. The inhibition and binding to CT B5 of these glycopolypeptide ligands were evaluated by direct enzyme-linked assay (DELA). As a complement method, weak affinity chromatography (WAC) was also used to evaluate glycopolypeptides binding to a CT B5 immobilized column. The architecture effects on CT B 5 inhibition are discussed. In the second system, cell surface receptor L-selectin was targeted by polypeptide-based multivalent ligands containing disulfated galactopyranoside ligands, due to its important roles in various immunological activities. The effects of glycopolypeptide architectural variables L-selectin shedding were evaluated via ELISA-based assays. These polypeptide-based multivalent ligands

  18. Antibodies to high molecular weight polypeptides of desmosomes: specific localization of a class of junctional proteins in cells and tissue.

    PubMed

    Franke, W W; Schmid, E; Grund, C; Müller, H; Engelbrecht, I; Moll, R; Stadler, J; Jarasch, E D

    1981-01-01

    Desmosome-enriched fractions were isolated from bovine muzzle epidermis either as desmosome-tonofilament complexes using a procedure involving treatment at pH9 or in the form of desmosomal residue fractions using a modification of the citric acid buffer (pH 2.3) method of Skerrow and Matoltsy [1]. Major polypeptides of high molecular weights (mol. wt.) were separated by gel electrophoresis, individual polypeptide bands were excised, and protein was eluted and used for immunization. Guinea pig antibodies raised against two prominent polypeptides of high mol. wt. (250,000 and 215,000) showed, on nitrocellulose paper blots of desmosome-tonofilament polypeptides separated by gel electrophoresis, extensive cross-reaction between a group or large polypeptides characteristic of desmosome-containing fractions, most notably polypeptides of 250 K, 215 K, 200 k, 175 K, and 164 K. These antibodies allowed, when used in immunofluorescence microscopy, the specific localization of desmosomal junctions (i) in sections through epithelia-containing tissue (e.g., epidermis, mucosae of tongue and esophagus, cornea, mammary gland, small intestine, liver, thymus, urothelium of bladder) and myocardium; (ii) on dissociated cells from these tissues; (iii) on various epithelial cells grown in culture; an (iv) in tumor-like proliferations of cultured epithelial cells injected into nude mice. Individual desmosomes could be visualized and resolved at the light microscopic level. No reaction was found in cells devoid of desmosomes and on other classes of intercellular junctions. Electron microscopic localization using immunoperoxidase techniques indicated that these proteins are located in, or close to, the desmosomal plague structure. It is proposed to use such antibodies against desmosomal proteins as markers specific to this so far only morphologically define class of junctions. Use of these markers will (i) improve identification and classification of intercellular junctions; (ii

  19. Islet amyloid polypeptide and high hydrostatic pressure: towards an understanding of the fibrillization process

    NASA Astrophysics Data System (ADS)

    Lopes, D. H. J.; Smirnovas, V.; Winter, R.

    2008-07-01

    Type II Diabetes Mellitus is a disease which is characterized by peripheral insulin resistance coupled with a progressive loss of insulin secretion that is associated with a decrease in pancreatic islet β-cell mass and the deposition of amyloid in the extracellular matrix of β-cells, which lead to islet cell death. The principal component of the islet amyloid is a pancreatic hormone called islet amyloid polypeptide (IAPP). High-pressure coupled with FT-IR, CD, ThT fluorescence spectroscopic and AFM studies were carried out to reveal information on the aggregation pathway as well as the aggregate structure of IAPP. Our data indicate that IAPP pre-formed fibrils exhibit a strong polymorphism with heterogeneous structures very sensitive to high hydrostatic pressure, indicating a high percentage of ionic and hydrophobic interactions being responsible for the stability the IAPP fibrils.

  20. Protective effect of polypeptide from Chlamys farreri on hairless mice damaged by ultraviolet A.

    PubMed

    Wang, Chun-Bo; Yao, Ru-Yong; Liu, Zhan-Tao; Zhong, Wei-Zhen; Liu, Xiao-Ping; Wang, Yue-Jun

    2002-09-01

    To study the protective effect of the polypeptide isolated from Chlamys farreri (PCF) on hairless mice skin damaged by ultraviolet A. Enzymes and malondialdehyde (MDA) were determined by biochemical methods; the expressions of Bcl-2 protein and NOS protein were examined by immunohistochemical technique. The ultra-structure of the skin was observed through electronic microscope. PCF could enhance the activities of glutathione peroxidase (GSH-px), superoxide dismutase (SOD), and total anti-oxidative capacity (T-AOC). Also PCF could reduce the amount of MDA, increase the expression of Bcl-2 protein, and inhibit the expression of NOS protein. The ultra-structure of epidermis and fibroblasts remained normal in 20 % PCF groups; there were vacuoles in smooth endoplasm reticulum in epidermis of mice and the number of rough endoplasm reticulum in fibroblasts was decreased in model group. PCF had the protective effects on hairless mice skin damaged by ultraviolet A via its anti-oxidative mechanisms.