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Sample records for deduced polypeptide structure

  1. Fibril structure of human islet amyloid polypeptide.

    PubMed

    Bedrood, Sahar; Li, Yiyu; Isas, J Mario; Hegde, Balachandra G; Baxa, Ulrich; Haworth, Ian S; Langen, Ralf

    2012-02-17

    Misfolding and amyloid fibril formation by human islet amyloid polypeptide (hIAPP) are thought to be important in the pathogenesis of type 2 diabetes, but the structures of the misfolded forms remain poorly understood. Here we developed an approach that combines site-directed spin labeling with continuous wave and pulsed EPR to investigate local secondary structure and to determine the relative orientation of the secondary structure elements with respect to each other. These data indicated that individual hIAPP molecules take up a hairpin fold within the fibril. This fold contains two β-strands that are much farther apart than expected from previous models. Atomistic structural models were obtained using computational refinement with EPR data as constraints. The resulting family of structures exhibited a left-handed helical twist, in agreement with the twisted morphology observed by electron microscopy. The fibril protofilaments contain stacked hIAPP monomers that form opposing β-sheets that twist around each other. The two β-strands of the monomer adopt out-of-plane positions and are staggered by about three peptide layers (∼15 Å). These results provide a mechanism for hIAPP fibril formation and could explain the remarkable stability of the fibrils. Thus, the structural model serves as a starting point for understanding and preventing hIAPP misfolding. PMID:22187437

  2. 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.

  3. Structure of Isometric Viruses Containing Nonidentical Polypeptide Chains

    PubMed Central

    Dunker, A. Keith

    1974-01-01

    The theory of Caspar and Klug (1962) for the structure of isometric viruses has been generalized to the case in which the identical repeating unit is composed of n nonidentical polypeptide chains. This modified theory accounts for the structure of picornaviruses, the lambda phage head, cowpea mosaic virus, and φX174, while at the same time conserving the principle of having identical subunits in identical environments. Furthermore, the modified theory suggests amending the triangulation number to T[n] for capsids with n nonidentical polypeptide chains as the repeating unit. Images PMID:4418754

  4. Islet Amyloid Polypeptide: Structure, Function, and Pathophysiology.

    PubMed

    Akter, Rehana; Cao, Ping; Noor, Harris; Ridgway, Zachary; Tu, Ling-Hsien; Wang, Hui; Wong, Amy G; Zhang, Xiaoxue; Abedini, Andisheh; Schmidt, Ann Marie; Raleigh, Daniel P

    2016-01-01

    The hormone islet amyloid polypeptide (IAPP, or amylin) plays a role in glucose homeostasis but aggregates to form islet amyloid in type-2 diabetes. Islet amyloid formation contributes to β-cell dysfunction and death in the disease and to the failure of islet transplants. Recent work suggests a role for IAPP aggregation in cardiovascular complications of type-2 diabetes and hints at a possible role in type-1 diabetes. The mechanisms of IAPP amyloid formation in vivo or in vitro are not understood and the mechanisms of IAPP induced β-cell death are not fully defined. Activation of the inflammasome, defects in autophagy, ER stress, generation of reactive oxygen species, membrane disruption, and receptor mediated mechanisms have all been proposed to play a role. Open questions in the field include the relative importance of the various mechanisms of β-cell death, the relevance of reductionist biophysical studies to the situation in vivo, the molecular mechanism of amyloid formation in vitro and in vivo, the factors which trigger amyloid formation in type-2 diabetes, the potential role of IAPP in type-1 diabetes, the development of clinically relevant inhibitors of islet amyloidosis toxicity, and the design of soluble, bioactive variants of IAPP for use as adjuncts to insulin therapy. PMID:26649319

  5. Islet Amyloid Polypeptide: Structure, Function, and Pathophysiology

    PubMed Central

    Akter, Rehana; Cao, Ping; Noor, Harris; Ridgway, Zachary; Tu, Ling-Hsien; Wang, Hui; Wong, Amy G.; Zhang, Xiaoxue; Abedini, Andisheh; Schmidt, Ann Marie; Raleigh, Daniel P.

    2016-01-01

    The hormone islet amyloid polypeptide (IAPP, or amylin) plays a role in glucose homeostasis but aggregates to form islet amyloid in type-2 diabetes. Islet amyloid formation contributes to β-cell dysfunction and death in the disease and to the failure of islet transplants. Recent work suggests a role for IAPP aggregation in cardiovascular complications of type-2 diabetes and hints at a possible role in type-1 diabetes. The mechanisms of IAPP amyloid formation in vivo or in vitro are not understood and the mechanisms of IAPP induced β-cell death are not fully defined. Activation of the inflammasome, defects in autophagy, ER stress, generation of reactive oxygen species, membrane disruption, and receptor mediated mechanisms have all been proposed to play a role. Open questions in the field include the relative importance of the various mechanisms of β-cell death, the relevance of reductionist biophysical studies to the situation in vivo, the molecular mechanism of amyloid formation in vitro and in vivo, the factors which trigger amyloid formation in type-2 diabetes, the potential role of IAPP in type-1 diabetes, the development of clinically relevant inhibitors of islet amyloidosis toxicity, and the design of soluble, bioactive variants of IAPP for use as adjuncts to insulin therapy. PMID:26649319

  6. Envelope polypeptides of Friend leukemia virus: purification and structural analysis.

    PubMed Central

    Schneider, J; Falk, H; Hunsmann, G

    1980-01-01

    Roughly 10% of surface glycoproteins in the envelope of mature Friend murine leukemia virus are coupled to membrane polypeptides by disulfide bridges. The remaining 90% of these glycoproteins are associated noncovalently. However, they could also be linked to membrane polypeptides by the treatment of purified Friend murine leukemia virus with 2,2'dithiobis(m-nitropyridine). These amphiphilic heterodimer polypeptides, gp84/86, were recovered almost quantitatively in the form of aggregates, termed rosettes, when prepared by solubilization of the viral membrane with Triton X-100 and subsequent velocity sedimentation. gp69/71 and p12(E)/15(E) were purified from these protein micelles after reduction of the disulfide bonds by gel chromatography. Electron micrographs of rosettes, as well as of purified p12(E)/15(E), showed structures different from native viral knobs. Isolated gp84/86 could be reassociated and then displayed more similarity to these viral surface projections. As shown by peptide mapping, the primary structures of the glycoproteins gp69/71 are highly related as are those of the membrane polypeptides p12(E) and p15(E). Furthermore, it was shown by two-dimensional polyacrylamide gel electrophoresis and re-electrophoresis of purified gp84/86 that the larger component, gp86, was composed of gp71 associated with p15(E) and p12(E), whereas the smaller component, gp84, was formed by gp69 bound only to p12(E). Images PMID:7411688

  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. 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

  9. Structure and Interactions in Polypeptide Cationic Lipid Complexes

    NASA Astrophysics Data System (ADS)

    Subramanian, G.; Hjelm, R. P.; Smith, G. S.; Safinya, C. R.

    1998-03-01

    Complexes of polypeptides and cationic lipids have elicited much interest recently because of their potential in developing novel biomolecular materials. We have investigated the solution structure of complexes made from the anionic polypeptide poly-L-glutamic acid (PGA), the cationic lipid DDAB, and the neutral lipid DLPC. X-ray scattering and SANS revealed the structure of the complexes to be multilamellar in nature with the PGA molecules sandwiched in between the lipid bilayers and that the PGA molecules are in the disordered state on the plane of the bilayers. Lipid dilution experiments at charge neutrality indicated that the "d" spacing of the complexes monotonically increases from 39Åupto 60Åat very high dilutions. While lipid chain stretching alone does not account for the increase in "d" spacing, we propose a "pinching" mechanism where the PGA and DDAB molecules are localized to form a tightly packed layer. Away from these "pinches" the system behaves as a pure DLPC membrane with an equilibrium spacing of 60ÅSupported by NSF-DMR-9624091, PRF-31352-AC7, and Los Alamos-STB/UC:96-108.

  10. 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.

  11. The NADH-binding subunit of the energy-transducing NADH-ubiquinone oxidoreductase of Paracoccus denitrificans: Gene cloning and deduced primary structure

    SciTech Connect

    Xu, Xuemin; Matsuno-Yagi, Akemi; Yagi, Takao )

    1991-07-02

    The NADH dehydrogenase complex isolated from Paracoccus denitrificans is composed of approximately 10 unlike polypeptides and contains noncovalently bound FMN, non-heme iron, and acid-labile sulfide. The NADH-binding subunit of this enzyme complex was identified by direct photoaffinity labeling with ({sup 32}P)NADH. primers were synthesized on the basis of the N-terminal amino acid sequency of this polypeptide, and these primers were used to synthesize an oligonucleotide probe by the polymerase chain reaction. This probe was utilized to isolate the gene encoding the NADH-binding subunit from a genomic library of P. denitrificans. The nucleotide sequence of the gene and the deduced amino acid sequence of the entire NADH-binding subunit were determined. The NADH-binding subunit has 431 amino acid residues and a calculated molecular weight of 47 191. The encoded protein contains a putative NAD(H)-binding and an iron-sulfur cluster-binding consensus sequence. The deduced amino acid sequence of the Paracoccus NADH-binding subunit shows remarkable similarity to the {alpha} subunit of the NAD-linked hydrogenase of Alcaligenes eutrophus H16. When partial DNA sequencing of the regions surrounding the gene encoding the NADH-binding subunit was carried out, sequences homologous to the 24-, 49-, and 75-kDa polypeptides of bovine complex 1 were detected, suggesting that the structural genes of the Paracoccus NADH dehydrogenase complex constitute a gene cluster.

  12. Shell structure of potassium isotopes deduced from their magnetic moments

    NASA Astrophysics Data System (ADS)

    Papuga, J.; Bissell, M. L.; Kreim, K.; Barbieri, C.; Blaum, K.; De Rydt, M.; Duguet, T.; Garcia Ruiz, R. F.; Heylen, H.; Kowalska, M.; Neugart, R.; Neyens, G.; Nörtershäuser, W.; Rajabali, M. M.; Sánchez, R.; Smirnova, N.; Somà, V.; Yordanov, D. T.

    2014-09-01

    Background: Ground-state spins and magnetic moments are sensitive to the nuclear wave function, thus they are powerful probes to study the nuclear structure of isotopes far from stability. Purpose: Extend our knowledge about the evolution of the 1/2+ and 3/2+ states for K isotopes beyond the N =28 shell gap. Method: High-resolution collinear laser spectroscopy on bunched atomic beams. Results: From measured hyperfine structure spectra of K isotopes, nuclear spins, and magnetic moments of the ground states were obtained for isotopes from N =19 up to N =32. In order to draw conclusions about the composition of the wave functions and the occupation of the levels, the experimental data were compared to shell-model calculations using SDPF-NR and SDPF-U effective interactions. In addition, a detailed discussion about the evolution of the gap between proton 1d3/2 and 2s1/2 in the shell model and ab initio framework is also presented. Conclusions: The dominant component of the wave function for the odd-A isotopes up to K45 is a π1d3/2-1 hole. For K47,49, the main component originates from a π2s1/2-1 hole configuration and it inverts back to the π1d3/2-1 in K51. For all even-A isotopes, the dominant configuration arises from a π1d3/2-1 hole coupled to a neutron in the ν1f7/2 or ν2p3/2 orbitals. Only for K48, a significant amount of mixing with π2s1/2-1⊗ν(pf) is observed leading to a Iπ=1- ground state. For K50, the ground-state spin-parity is 0- with leading configuration π1d3/2-1⊗ν2p3/2-1.

  13. 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. PMID:26201595

  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. PMID:25638009

  16. 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.

  17. Polypeptide/polysaccharides holographic micro-structuration for biophysics applications

    NASA Astrophysics Data System (ADS)

    Picart, Catherine; Grzymala, Romualda; Meyrueis, Patrick P.

    2004-09-01

    Protein and polysaccharide nano-patterning is of prime interest for biological applications but also for applications in the field of diffractive optics. In this work, we used a photo-nano-patterning process based on light interferences through a photo-sensitive material for patterning polysaccharides and polypeptides pure and mixed gels of gelatin, hyaluronan, and chitosan. Chromium ions were incorporated in the gels to render them photo-sensitive. Polyelectrolyte multilayer thin films of poly(L-lysine)/hyaluronan were also investigated either by incorporating chromium ions or by adsorbing a photo-sensitive hyaluronan. Depending on the weights ratios of the polymers, respectively gelatin/chitosan and gelatin/hyaluronan, the gel surfaces exhibit different fringe patterns, as can be visualized by atomic force microscopy. The diffracted intensity characterizing the holographic grating was also depending on gel type. Pure gelatin gels was taken as the reference material. The best results in terms of surface patterns and diffracted intensities were obtained for the gelatin/chitosan gels prepared at acidic pH and exposed at energies ranging from 100 to 400 mJ/cm2. Our results show that surface patterns of various depths and structures can be created by the photo-patterning technique on biological polymers. These results open new perspectives for the surface control of biological materials but also for making use of the optical properties of these biocompatible biopolymers.

  18. Complete cDNA and deduced amino acid sequence of the chaperonin containing T-complex polypeptide 1 (CCT) delta subunit from Aedes triseriatus mosquitoes.

    PubMed

    Blitvich, B J; Rayms-Keller, A; Blair, C D; Beaty, B J

    2001-01-01

    The chaperonin containing t-complex polypeptide 1 (CCT) assists in the ATP-dependent folding and assembly of newly translated actin and tubulin in the eukaryotic cytosol. CCT is composed of eight different subunits, each encoded by an independent gene. In this report, we used RT-PCR amplification and 5'- and 3'-rapid amplification of cDNA ends (RACE) to determine the complete cDNA sequence of the CCT delta subunit from Aedes triseriatus mosquitoes. The CCT delta cDNA is 1936 nucleotides in length and encodes a putative 533 amino acid protein with a calculated molecular mass of 57,179 daltons and pI of 7.15. Hydrophobic residues comprise 39.8% of the amino acid sequence and putative motifs for ATP-binding and ATPase-activity are present. The amino acid sequence displays strong sequence similarity to Drosophila melanogaster (92%), human (85%), puffer fish (84%) and mouse (84%) counterparts. CCT delta mRNA was detected in both biosynthetically active (embryonating) and dormant (diapausing) Ae. triseriatus embryos by RT-PCR analysis. PMID:11762197

  19. 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

  20. [Structural Features of Cysteine-Stabilized Polypeptides from Sea Anemones Venoms].

    PubMed

    Mikov, A N; Kozlov, S A

    2015-01-01

    Nowadays, venom-based drug discovery becomes popular again: pharmaceutical companies evaluate animal venom potential as a combinatory library of biologically-active compounds. Collaborations with research groups from academia are intensified, new toxins are being investigated, among which polypeptides are of paramount importance. Sea anemones produce the most diversified, from structural point of view, polypep- tide venom components among other animals. This particular review considers known polypeptide toxins from sea anemones, basically taking into account its classification by primary structural features. The most important functional characteristics are analyzed in each structural class. PMID:26762088

  1. Mapping of a gene coding for a major late structural polypeptide on the vaccinia virus genome.

    PubMed Central

    Wittek, R; Hänggi, M; Hiller, G

    1984-01-01

    Cell-free translation of total RNA isolated from vaccinia virus-infected cells late in infection results in a complex mixture of polypeptides. A monospecific antibody directed against one of the major structural proteins of the virus particle immunoprecipitated a single polypeptide with a molecular weight of 11,000 (11K) from this mixture. Immunoprecipitation was therefore used to identify the structural polypeptide among the in vitro translation products of RNA purified by hybridization selection to restriction fragments of the vaccinia virus genome. This allowed us to map the mRNA coding for the 11K polypeptide to the extreme left-hand end of the HindIII E fragment. Detailed transcriptional mapping of this region of the genome by nuclease S1 analysis revealed the presence of a late RNA transcribed from the rightward-reading strand. Its 5' end mapped at ca. 130 base pairs to the left of the HindIII site at the junction between the HindIII F and E fragments. The map position of this RNA coincided precisely with the map position of the late message coding for the 11K polypeptide. Images PMID:6319738

  2. Processes of ordered structure formation in polypeptide thin film solutions.

    SciTech Connect

    Botiz, I.; Schlaad, H.; Reiter, G.

    2010-06-17

    An experimental study is presented on the hierarchical assembly of {alpha}-helical block copolymers polystyrene-poly({gamma}-benzyl-L-glutamate) into anisotropic ordered structures. We transformed thin solid films into solutions through exposure to solvent vapor and studied the nucleation and growth of ordered three-dimensional structures in such solutions, with emphasis on the dependence of these processes on supersaturation with respect to the solubility limit. Interestingly, polymer solubility could be significantly influenced via variation of humidity in the surrounding gas phase. It is concluded that the interfacial tension between the ordered structures and the solution increased with humidity. The same effect was observed for other protic non-solvents in the surrounding gas phase and is attributed to a complexation of poly({gamma}-benzyl-L-glutamate) by protic non-solvent molecules (via hydrogen-bonding interactions). This change of polymer solubility was demonstrated to be reversible by addition or removal of small amounts of protic non-solvent in the surrounding gas phase. At a constant polymer concentration, ordered ellipsoidal structures could be dissolved by removing water or methanol present in the solution. Such structures formed once again when water or methanol was reintroduced via the vapor phase.

  3. Poly(L-lysine) and Clay Nanocomposite with Desired Matrix Secondary Structure: Effects of Polypeptide Molecular Weight

    SciTech Connect

    Hule,R.; Pochan, D.

    2007-01-01

    Nanocomposites (NC) were formed using cationic poly(L-lysine) (PLL), a semicrystalline polypeptide, that was reinforced by sodium montmorillonite (MMT) clay via solution intercalation technique. By varying solution conditions such as pH, temperature, and polypeptide concentration in the presence of clay platelets, the secondary structure of PLL was controllably altered into {alpha}-helical, {beta}-sheet, and random coil. The high molecular weight polypeptide shows a strong propensity to fold into the {beta}-sheet structure when cast as films, irrespective of the initial secondary structure in solution. Nanocomposite local morphology confirms intercalated MMT platelets with PLL over a wide range of compositions.

  4. From polypeptide sequences to structures using Monte Carlo simulations and an optimized potential

    NASA Astrophysics Data System (ADS)

    Derreumaux, Philippe

    1999-08-01

    The ab initio prediction of the structure of a polypeptide from its sequence necessarily requires the detection of the lowest energy forms which correspond to the native state of the polypeptide. A potential for modeling the energy hypersurface of polypeptides using a hybrid level of description is optimized for the structures of four training peptides which have been shown experimentally to adopt α, ββ, αβ, and ββα conformations in aqueous solution. This potential is then used in diffusion process-controlled Monte Carlo simulations to predict the native structures of this training set of peptides and a test set of 20 peptides which were not themselves used during the optimization of the potential. Starting from various fully extended conformations, all simulations lead to an ensemble of conformations compatible with experimental results. These conformations include simple motifs such as coil, α helix, β-turn, β-hairpin, βα, and coil-α conformations, but also more complex motifs such as turnlike, ββα, βββ, and α-helical hairpin conformations.

  5. 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.

  6. Deduced primary structure of two forms of vitellogenin in Japanese common goby (Acanthogobius flavimanus).

    PubMed

    Ohkubo, N; Andoh, T; Mochida, K; Adachi, S; Hara, A; Matsubara, T

    2004-05-15

    Complete nucleotide sequences of two forms of vitellogenin (Vg) cDNA in Japanese common goby were determined from a liver cDNA library of E(2)-treated male fish. These two Vg cDNAs contained complete open reading frames encoding 1664 and 1238 amino acid residues including signal peptides, respectively. From comparison of the deduced amino acid sequences of both Vgs and the partial amino acid sequences of the yolk proteins, the longer sequence was concluded to be cDNA of the Vg-530 and the shorter one was that of the Vg-320 of the Japanese common goby which were reported in our previous paper. The deduced sequence of Vg-530 without signal peptide was arranged by lipovitellin heavy-chain (LvH), phosvitin (Pv), lipovitellin light-chain (LvL), and beta'-component beta'-c) domains from the N-terminus, and showed a range of 40-45% sequence identity to those of other fish. Furthermore, the deduced sequence of Vg-320 showed no obvious Pv domain, has a shortened C-terminal coding region after the LvH domain, and showed a close similarity to the phosvitin-less Vg of zebrafish. Moreover, biochemical analysis of the yolk proteins verified that Vg-530 cleaves into the Lv-Pv complex (molecular mass: 470 kDa) and beta'-c (33 kDa), while Vg-320 showed no change when incorporated into oocytes. The present study demonstrated the existence of the two different forms of Vgs at both the cDNA and protein level, and showed molecular alteration of the two Vgs during vitellogenesis. Two Vg sequence data will aid in designing nucleotide probes for detecting Vg gene expressions as a biomarker of environmental estrogens. PMID:15094332

  7. 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

  8. 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

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

    DOE PAGESBeta

    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 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

  10. Bacteriocin AS-48, a microbial cyclic polypeptide structurally and functionally related to mammalian NK-lysin

    PubMed Central

    González, Carlos; Langdon, Grant M.; Bruix, Marta; Gálvez, Antonio; Valdivia, Eva; Maqueda, Mercedes; Rico, Manuel

    2000-01-01

    The solution structure of bacteriocin AS-48, a 70-residue cyclic polypeptide from Enterococcus faecalis, consists of a globular arrangement of five α-helices enclosing a compact hydrophobic core. The head-to-tail union lies in the middle of helix 5, a fact that is shown to have a pronounced effect on the stability of the three-dimensional structure. Positive charges in the side chains of residues in helix 4 and in the turn linking helix 4 to helix 5 form a cluster that most probably determine its antibacterial activity by promoting pore formation in cell membranes. A similar five-helix structural motif has been found in the antimicrobial NK-lysin, an effector polypeptide of T and natural killer (NK) cells. Bacteriocin AS-48 lacks the three disulfide bridges characteristic of the saposin fold present in NK-lysin, and has no sequence homology with it. Nevertheless, the similar molecular architecture and high positive charge strongly suggest a common mechanism of antibacterial action. PMID:11005847

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. Context dependence of the assembly, structure, and stability of polypeptide multilayer nanofilms.

    PubMed

    Zhang, Ling; Zhao, Wanhua; Rudra, Jai S; Haynie, Donald T

    2007-12-01

    Polyelectrolyte multilayer nanofilms and nanocomposites have shown considerable promise for the rational development of multifunctional materials with wide-ranging properties. Polypeptides are a distinctive and largely unexplored class of polyelectrolytes in this context. Methods now exist for the synthesis of peptides with control at the level of the amino acid sequence, and for the preparation of these polymers in massive quantities. Here, we analyze the roles of six designed 32mer peptides in the fabrication, structure, and stability of multilayer nanofilms prepared by layer-by-layer self-assembly. The data show that amino acid sequence and the specific combination of anionic and cationic peptides together have a marked impact on nanofilm growth behavior, secondary structure content, and density in experimental studies. The same factors determine physical properties of the corresponding interpolypeptide complexes in molecular dynamics simulations. PMID:19206669

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    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.

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

    PubMed

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

    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. PMID:26723626

  19. Antifungal polypeptides

    DOEpatents

    Altier, Daniel J.; Ellanskaya, Irina; Ellanskaya, legal representative, Natalia; Gilliam, Jacob T.; Hunter-Cevera, Jennie; Presnail, James K.; Schepers, Eric; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    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.

  20. A nanofiber assembly directed by the non-classical antiparallel β-structure from 4S-(OH) proline polypeptide.

    PubMed

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

    2016-04-01

    The antiparallel arrangement of two strands of the non-classical β-structure, formed exclusively via cis-4S-(OH) prolyl polypeptide as established by FRET, propagates into self-assembled nanofibers upon conjugation with C12/C14/C16 hydrocarbon chains. PMID:26961970

  1. 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.

  2. Coronal structures deduced from photospheric magnetic field and He I lambda 10830 observations

    NASA Technical Reports Server (NTRS)

    Harvey, Karen L.

    1995-01-01

    The National Solar Observatory synoptic program provides an extensive and unique data base of high-resolution full-disk observations of the line-of-sight photospheric magnetic fields and of the He I lambda 10830 equivalent width. These data have been taken nearly daily for more than 21 years since 1974 and provide the opportunity to investigate the behavior of the magnetic fields in the photosphere and those inferred for the corona spanning on the time scales of a day to that of a solar cycle. The intensity of structures observed in He I lambda 10830 are strongly modulated by overlying coronal radiation; areas with low coronal emission are generally brighter in He I lambda 10830, while areas with high coronal emission are darker. For this reason, He I lambda 10830 was selected in the mid-1970's as way to identify and monitor coronal holes, magnetic fields with an open configuration, and the sources of high-speed solar wind streams. The He I lambda 10830 spectroheliograms also show a wide variety of other structures from small-scale, short-lived dark points (less than 30 arc-sec, hours) to the large-scale, long-lived two 'ribbon' flare events that follow the filament eruptions (1000 arc-sec, days). Such structures provide clues about the connections and changes in the large-scale coronal magnetic fields that are rooted in concentrations of magnetic network and active regions in the photosphere. In this paper, what observations of the photospheric magnetic field and He I lambda 10830 can tell us about the short- and long-term evolution of the coronal magnetic fields will be discussed, focussing on the quiet Sun and coronal holes. These data and what we infer from them will be compared with direct observations of the coronal structure from the Yohkoh Soft X-ray Telescope.

  3. Active Structure Evolutions Deduced from Geomorphic and Geodetic Evidence, from Hsinchu to Taoyuan, Northwestern Taiwan

    NASA Astrophysics Data System (ADS)

    Chen, Y.; Wang, Y.; Hou, C.; Chen, W.

    2003-12-01

    As we know, Taiwan fault-and-thrust belt is built up by the arc-continent collision that is related to polarity flipping of subduction. The flipping boundary, delineated from Hsinchu to Hualien, divides the mountain belt into northern as well as southern part. Looking at the current tectonic configuration surrounding Taiwan, the northern one corresponds to the Ryukyu arc-trench system and has recently been influenced by back-arc rifting of Okinawa Trough (OT), which reactivated during Quaternary. As a consequence, the stress currently executing in northern Taiwan must be different from the southern Taiwan, manifesting to different neotectonic features. It is governed by the extensional stress transferred from OT. Basins, such as Taipei and Ilan, are the evidence to confirm this point. Along the western Taiwan located to the south of Taipei basin is the Taoyuan-Hsinchu area, where the landscape is still characterized by those previously produced under compression. In Taoyuan, two subparallel blind fault-related folds with axes trending NNE were developed due to the reactivation of preexisting normal fault system in continental margin. The entire system remained active until later than 30 ka. To the Hsinchu, the neotectonics is characterized by another two duplex systems (each one is composed of a thrust and its related anticline). The structural orientation is similar to of the Taoyuan. There are two main drainages, i,e.,Touchien and Fengshan rivers, flow across and separate Taoyuan and Hsinchu. Evident linear scarps and lineations have been developed aside oblique to the above-mentioned orientations of compression structures but roughly following the flowing direction. We interpret that they are generated by wrench fault systems tearing apart the original structures to accommodate the recently adjusted stress field. As recognized by the relevant geomorphic evidence, they are suggested as strike-slip faults with possibly normal dip-slip component. The newly

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

    PubMed

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

    2002-04-26

    beta-Defensins are mammalian antimicrobial peptides that share a unique disulfide-bonding motif of six conserved cysteines. An intragenic polymorphism of the DEFB1 gene that changes a highly conserved Cys to Ser in the peptide coding region has recently been described. The deduced peptide cannot form three disulfide bonds, as one of the cysteines is unpaired. We have determined the cysteine connectivities of a corresponding synthetic hBD-1(Ser35) peptide, investigated the structure by circular dichroism spectroscopy, and assayed the in vitro antimicrobial activity. Despite a different arrangement of the disulfides, hBD-1(Ser35) proved as active as hBD-1 against the microorganisms tested. This activity likely depends on the ability of hBD-1(Ser35) to adopt an amphipathic conformation in hydrophobic environment, similar to the wild type peptide, as suggested by CD spectroscopy. PMID:12054642

  5. 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.

  6. 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.

  7. 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.

  8. 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. PMID:16641489

  9. F region postsunset plasma structures at low latitudes deduced from the Swarm satellite constellation

    NASA Astrophysics Data System (ADS)

    Stolle, Claudia; Xiong, Chao; Kervalishvili, Guram; Lühr, Hermann; Rauberg, Jan; Michaelis, Ingo

    2016-04-01

    ESA's constellation mission Swarm was successfully launched on 22 November 2013. The three satellites are orbiting the Earth at 470 km and 520 km altitude. The spacecraft carry instruments to monitor the plasma density and magnetic eld magnitude and their variations with high quality. We will present results on low latitude F region post sunset plasma irregularities (EPIs). EPIs are characterised by severe plasma density gradients and distinct magnetic field variations and cause GPS signal detection degradations. Our results show rather small scale sizes of EPIs (>44 km) in the zonal direction as well as more fragmented irregularities in the southern hemisphere where the ambient magnetic field is lower than on the northern hemisphere. From the Swarm spacecraft constellation with a zonal separation of about 150 km, we conclude that larger zonal scale sizes of irregularities exist in the early evening hours (around 1900 LT) and that the irregularities break into smaller structures later in the evening. However, we also observe examples where only one satellite detects EPIs, while the others show undisturbed ionization. We will present also such an example, and compare these observations with detections of depletions on satellites from other missions. There exist a strong link to low-latitude space weather: the plasma irregularities give rise to severe disturbances of GPS navigational signals and these can also be monitored on board the Swarm satellites simultaneously with the plasma irregularities.

  10. 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.

  11. 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

    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.

  12. 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.

  13. Antifungal polypeptides

    DOEpatents

    Altier, Daniel J.; Dahlbacka, Glen; Ellanskaya, 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

    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.

  14. 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.

  15. Primary structure of human corticosteroid binding globulin, deduced from hepatic and pulmonary cDNAs, exhibits homology with serine protease inhibitors.

    PubMed Central

    Hammond, G L; Smith, C L; Goping, I S; Underhill, D A; Harley, M J; Reventos, J; Musto, N A; Gunsalus, G L; Bardin, C W

    1987-01-01

    We have isolated and sequenced cDNAs for corticosteroid binding globulin (CBG) prepared from human liver and lung mRNAs. Our results indicate that CBG mRNA is relatively abundant in the liver but is also present in the lung, testis, and kidney. The liver CBG cDNA contains an open reading frame for a 405-amino acid (Mr 45,149) polypeptide. This includes a predominantly hydrophobic, leader sequence of 22 residues that precedes the known NH2-terminal sequence of human CBG. We, therefore, predict that the mature protein is composed of 383 amino acids and is a polypeptide of Mr 42,646. A second, in-frame, 72-base-pair cistron of unknown significance exists between the TAA termination codon for CBG and a possible polyadenylylation signal (AATAAA) located 16 nucleotides before the polyadenylylation site. The deduced amino acid sequence of mature CBG contains two cysteine residues and consensus sequences for the attachment of six possible N-linked oligosaccharide chains. The sequences of the human lung and liver CBG cDNAs differ by only one nucleotide within the proposed leader sequence, and we attribute this to a point mutation. No sequence homology was found between CBG and other steroid binding proteins, but there is a remarkable similarity between the amino acid sequences of CBG and of alpha 1-antitrypsin, and this extends to other members of the serpin (serine protease inhibitor) superfamily. Images PMID:3299377

  16. Prediction of protein conformation on the basis of a search for compact structures: test on avian pancreatic polypeptide.

    PubMed Central

    Liwo, A.; Pincus, M. R.; Wawak, R. J.; Rackovsky, S.; Scheraga, H. A.

    1993-01-01

    Based on the concept that hydrophobic interactions cause a polypeptide chain to adopt a compact structure, a method is proposed to predict the structure of a protein. The procedure is carried out in four stages: (1) use of a virtual-bond united-residue approximation with the side chains represented by spheres to search conformational space extensively using specially designed interactions to lead to a collapsed structure, (2) conversion of the lowest-energy virtual-bond united-residue chain to one with a real polypeptide backbone, with optimization of the hydrogen-bond network among the backbone groups, (3) perturbation of the latter structure by the electrostatically driven Monte Carlo (EDMC) procedure, and (4) conversion of the spherical representation of the side chains to real groups and perturbation of the whole molecule by the EDMC procedure using the empirical conformational energy program for peptides (ECEPP/2) energy function plus hydration. Application of this procedure to the 36-residue avian pancreatic polypeptide led to a structure that resembled the one determined by X-ray crystallography; it had an alpha-helix starting at residue 13, with the N-terminal portion of the chain in an extended conformation packed against the alpha-helix. Similar structures with slightly higher energies, but looser packing, were also obtained. PMID:8251944

  17. NMR solution structure and function of the C-terminal domain of eukaryotic class 1 polypeptide chain release factor.

    PubMed

    Mantsyzov, Alexey B; Ivanova, Elena V; Birdsall, Berry; Alkalaeva, Elena Z; Kryuchkova, Polina N; Kelly, Geoff; Frolova, Ludmila Y; Polshakov, Vladimir I

    2010-06-01

    Termination of translation in eukaryotes is triggered by two polypeptide chain release factors, eukaryotic class 1 polypeptide chain release factor (eRF1) and eukaryotic class 2 polypeptide chain release factor 3. eRF1 is a three-domain protein that interacts with eukaryotic class 2 polypeptide chain release factor 3 via its C-terminal domain (C-domain). The high-resolution NMR structure of the human C-domain (residues 277-437) has been determined in solution. The overall fold and the structure of the beta-strand core of the protein in solution are similar to those found in the crystal structure. The structure of the minidomain (residues 329-372), which was ill-defined in the crystal structure, has been determined in solution. The protein backbone dynamics, studied using (15)N-relaxation experiments, showed that the C-terminal tail 414-437 and the minidomain are the most flexible parts of the human C-domain. The minidomain exists in solution in two conformational states, slowly interconverting on the NMR timescale. Superposition of this NMR solution structure of the human C-domain onto the available crystal structure of full-length human eRF1 shows that the minidomain is close to the stop codon-recognizing N-terminal domain. Mutations in the tip of the minidomain were found to affect the stop codon specificity of the factor. The results provide new insights into the possible role of the C-domain in the process of translation termination. PMID:20553496

  18. Molecular Structure, Membrane Interactions, and Toxicity of the Islet Amyloid Polypeptide in Type 2 Diabetes Mellitus

    PubMed Central

    Caillon, Lucie; Hoffmann, Anais R. F.; Botz, Alexandra; Khemtemourian, Lucie

    2016-01-01

    Human islet amyloid polypeptide (hIAPP) is the major component of the amyloid deposits found in the pancreatic islets of patients with type 2 diabetes mellitus (T2DM). Mature hIAPP, a 37-aa peptide, is natively unfolded in its monomeric state but forms islet amyloid in T2DM. In common with other misfolded and aggregated proteins, amyloid formation involves aggregation of monomers of hIAPP into oligomers, fibrils, and ultimately mature amyloid deposits. hIAPP is coproduced and stored with insulin by the pancreatic islet β-cells and is released in response to the stimuli that lead to insulin secretion. Accumulating evidence suggests that hIAPP amyloid deposits that accompany T2DM are not just an insignificant phenomenon derived from the disease progression but that hIAPP aggregation induces processes that impair the functionality and the viability of β-cells. In this review, we particularly focus on hIAPP structure, hIAPP aggregation, and hIAPP-membrane interactions. We will also discuss recent findings on the mechanism of hIAPP-membrane damage and on hIAPP-induced cell death. Finally, the development of successful antiamyloidogenic agents that prevent hIAPP fibril formation will be examined. PMID:26636105

  19. Structure and expression of a pea nuclear gene encoding a chlorophyll a/b-binding polypeptide

    SciTech Connect

    Cashmore, A.R.

    1984-05-01

    A nuclear gene AB80 has been isolated from a phage lambda Charon 4 library of pea DNA. The sequence of the gene has been determined and it has been shown to contain an interrupted reading frame of 269 amino acids, corresponding to a precursor to a constituent polypeptide of the light-harvesting chlorophyll a/b-protein complex. Primer extension and S1 nuclease studies defined a cap site for AB80. The first methionine codon 3' from this site is 69 nucleotides away and is the initiating codon of the open reading frame. A TATA sequence occurs 31 nucleotides 5' from the cap site. A second TATA sequence is found 7 nucleotides on the 5' side of the initiating methionine codon and the sequences surrounding this TATA sequence are strikingly similar to those surrounding the first TATA sequence. The mature polypeptide encoded by AB80 differs by 5 amino acids from the polypeptide corresponding to a previously characterized cDNA sequence pAB96. This result is indicative of heterogeneity within the constituent polypeptides of the light-harvesting chlorophyll a/b-protein complex. The sequence Arg-Lys-Ser-Ala-Thr-Thr-Lys-Lys occurs at, or near, the NH/sub 2/-terminus of the mature polypeptide encoded by AB80. This basic peptide is of interest because of its apparent involvement in changes in excitation-energy distribution in chloroplast membranes. Some general similarities, but no extensive sequence homology, is found on comparing the transit sequence for the precursor to the chlorophyll a/b-binding polypeptide with the transit sequences previously determined for the precursors to the small subunit of ribulose-1,5-bisphosphate carboxylase. 40 references, 3 figures.

  20. Mapping of the structural gene of pseudorabies virus glycoprotein A and identification of two non-glycosylated precursor polypeptides.

    PubMed Central

    Mettenleiter, T C; Lukacs, N; Rziha, H J

    1985-01-01

    Cell-free translation of pseudorabies virus RNA isolated during the late phase of the infectious cycle yielded a variety of polypeptides. A monoclonal antibody directed against one of the major viral glycoproteins, gA, immunoprecipitated two polypeptides ranging in molecular weight from 78K to 83K. To localize the structural gene for gA, we used cloned BamHI fragments of the viral DNA to select specific mRNA species and immunoprecipitated their in vitro translation products with the anti-gA monoclonal antibody. This allowed us to map the genomic region encoding the mRNA for the gA within the short unique region of the viral genome on BamHI fragments 7 and 12. Additional polypeptides encoded by this region were characterized by their electrophoretic mobility. In three virus strains tested a similar, but strain-specific, pattern of the two gA precursors was found which was not dependent on the host cell or the state of infection after reaching the late phase. Images PMID:2981362

  1. 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.

  2. 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.

  3. Sequence-specific H NMR assignments and secondary structure in the sea anemone polypeptide Stichodactyla helianthus neurotoxin I

    SciTech Connect

    Fogh, R.H.; Mabbutt, B.C.; Kem, W.R.; Norton, R.S. )

    1989-02-21

    Sequence-specific assignments are reported for the 500-MHz H nuclear magnetic resonance (NMR) spectrum of the 48-residue polypeptide neurotoxin I from the sea anemone Stichodactyla helianthus (Sh I). Spin systems were first identified by using two-dimensional relayed or multiple quantum filtered correlation spectroscopy, double quantum spectroscopy, and spin lock experiments. Specific resonance assignments were then obtained from nuclear Overhauser enhancement (NOE) connectivities between protons from residues adjacent in the amino acid sequence. Of a total of 265 potentially observable resonances, 248 (i.e., 94%) were assigned, arising from 39 completely and 9 partially assigned amino acid spin systems. The secondary structure of Sh I was defined on the basis of the pattern of sequential NOE connectivities. NOEs between protons on separate strands of the polypeptide backbone, and backbone amide exchange rates. Sh I contains a four-stranded antiparallel {beta}-sheet encompassing residues 1-5, 16-24, 30-33, and 40-46, with a {beta}-bulge at residues 17 and 18 and a reverse turn, probably a type II {beta}-turn, involving residues 27-30. No evidence of {alpha}-helical structure was found.

  4. Modelling Al-4wt.%Cu as-cast structure using equiaxed morphological parameters deduced from in-situ synchrotron X-ray radiography

    NASA Astrophysics Data System (ADS)

    Ahmadein, M.; Wu, M.; Reinhart, G.; Nguyen-Thi, H.; Ludwig, A.

    2016-03-01

    The as-cast structure of laboratory scale Al-4wt.%Cu was numerically calculated using assumed morphological parameters. Two parameters are identified: The shape factor which correlates the growth velocity of dendrite envelope to that of the tip; and the sphericity of the equiaxed envelope or the circularity of the columnar trunk envelope which is required to calculate the averaged species diffusion flux across the envelope. In the present work, the real-time radiographs of equiaxed solidification experiment carried out on Al-4wt.%Cu at the European Synchrotron Radiation Facility are used to track the development of crystal envelope with time. The growth rate of the equivalent circular envelope was correlated to dendrite tip growth velocity to deduce the shape factor. The sphericity of dendrite envelope is estimated over the time. The average of the deduced morphological parameters is applied to the model to predict the as-cast structure. The results were compared to those obtained by using morphological parameters from literature. The predicted phase quantities, columnar-to- equiaxed transition, and macrosegregation exhibited significant dependence on those parameters. The predicted macrosegregation using the experimentally deduced parameters fits better to the measurements.

  5. 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. PMID:27311712

  6. 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.

  7. A common structural motif incorporating a cystine knot and a triple-stranded beta-sheet in toxic and inhibitory polypeptides.

    PubMed Central

    Pallaghy, P. K.; Nielsen, K. J.; Craik, D. J.; Norton, R. S.

    1994-01-01

    A common structural motif consisting of a cystine knot and a small triple-stranded beta-sheet has been defined from comparison of the 3-dimensional structures of the polypeptides omega-conotoxin GVIA (Conus geographus), kalata BI (Oldenlandia affinis DC), and CMTI-I (Curcurbita maxima). These 3 polypeptides have diverse biological activities and negligible amino acid sequence identity, but each contains 3 disulfide bonds that give rise to a cystine knot. This knot consists of a ring formed by the first 2 bonds (1-4 and 2-5) and the intervening polypeptide backbone, through which the third disulfide (3-6) passes. The other component of this motif is a triple-stranded, anti-parallel beta-sheet containing a minimum of 10 residues, XXC2, XC5X, XXC6X (where the numbers on the half-cysteine residues refer to their positions in the disulfide pattern). The presence in these polypeptides of both the cysteine knot and antiparallel beta-sheet suggests that both structural features are required for the stability of the motif. This structural motif is also present in other protease inhibitors and a spider toxin. It appears to be one of the smallest stable globular domains found in proteins and is commonly used in toxins and inhibitors that act by blocking the function of larger protein receptors such as ion channels or proteases. PMID:7849598

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

    SciTech Connect

    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.

  9. 3-D Structure of Arcade Type Flares Deduced from Soft X-Ray Observations of a Homologous Flare Series

    NASA Astrophysics Data System (ADS)

    Morita, S.; Uchida, Y.; Hirose, S.

    2002-01-01

    In the solar flare problems, no ultimate model that matches observations has been established. One of the reasons for this is due to the restrictions in the observational data lacking information about the third dimension. Thus, many researchers have tried to get information about the three dimensional (3-D) coronal structures by using various techniques or ideas; like movie analysis, calculations using vector or line-of-sight components of photospheric magnetic data, and etc.. In the near future, a mission named STEREO which will obtain information about the 3-D coronal structures from two satellites, is planned. In the present paper, we noted the homology in a homologous flare series of February 1992. We derived a 3-D coronal structures by making use of the images obtained from the three different sight-lines at some common phases in them with Yohkoh SXT. The result of this analysis has made it clear that the so-called ``cusped arcade'' at the maximum phase in the well-known 1992 February 21 flare is, contrary to the general views, an ``elongated arch'' seen with a shallow oblique angle. It is not the ``flare arcade'' seen axis-on as widely conceived. This elongated arch coincides roughly with a diagonal of the main body of the "soft X-ray arcade" that came up later. The magnetic structure causing the flare as a whole turned out in this analysis to be a structure with quadruple magnetic sources. The relative locations of these four characteristic sources stayed almost the same throughout the period of this homologous flare series, determining the fundamental shape of this homologous series. We also examined the corresponding features for other similar events, also using information from other satellites, and will report the results.

  10. Antimicrobial polypeptide multilayer nanocoatings.

    PubMed

    Rudra, Jai S; Dave, Komal; Haynie, Donald T

    2006-01-01

    A multilayer coating (or film) of nanometer-thick layers can be made by sequential adsorption of oppositely charged polyelectrolytes on a solid support. The method is known as layer-by-layer assembly (LBL). No special apparatus is required for LBL and nanofilms can be prepared under mild, physiological conditions. A multilayer nanofilm in which at least one of the constituent species is a polypeptide is a polypeptide multilayer nanofilm. The present work was aimed at assessing whether polypeptide multilayer nanofilms with specific antimicrobial properties could be prepared by incorporation of a known antimicrobial agent in the film structure, in this case the edible protein hen egg white lysozyme (HEWL). The chicken enzyme is widely employed as a human food preservative. An advantage of LBL in this context is that the nanofilm is fabricated directly on the surface of interest, eliminating the need to incorporate the antimicrobial in other packaging materials. Here, nanofilms were made of poly(L-glutamic acid) (PLGA), which is highly negatively charged in the mildly acidic pH range, and HEWL, which has a high net positive charge at acidic pH. We show that PLGA/HEWL nanofilms inhibit growth of the model microbe Microccocus luteus in the surrounding liquid medium. The amount of HEWL released from PLGA/HEWL films depends on the number of HEWL layers and therefore on the total quantity of HEWL in the films. This initial study provides a sketch of the scope for further development of LBL in the area of antimicrobial polypeptide multilayer films. Potential applications of such films include strategies for food preservation and coatings for implant devices. PMID:17176751

  11. 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.

  12. Observation of a Low-Temperature, Dynamically Driven, Structural Transition in a Polypeptide by Solid State NMR Spectroscopy

    PubMed Central

    Bajaj, Vikram S.; van der Wel, Patrick C.A.; Griffin, Robert G.

    2009-01-01

    At reduced temperatures, proteins and other biomolecules are generally found to exhibit dynamic as well as structural transitions. This includes a so-called protein glass transition that is universally observed in systems cooled between 200–230K, and which is generally attributed to interactions between hydrating solvent molecules and protein side chains. However, there is also experimental and theoretical evidence for a low-temperature transition in the intrinsic dynamics of the protein itself, absent any solvent. Here, we use low-temperature solid state NMR to examine site specific fluctuations in atomic structure and dynamics in the absence of solvents. In particular, we employ magic angle spinning NMR to examine a structural phase transition associated with dynamic processes in a solvent-free polypeptide, N-f-MLF-OH, lattice at temperatures as low as 90K. This transition is characterized by the appearance of an extra set of lines in 1D 15N spectra as well as additional cross peaks in 2D 13C-13C and 13C-15N spectra. Interestingly, the gradual, temperature-dependent appearance of the new spectral component is not accompanied by the line broadening typical of dynamic transitions. A direct comparison between the spectra of N-f-MLF-OH and the analog N-f-MLF-OMe, which does not display this transition, indicates a correlation of the structural transition to the temperature dependent motion of the aromatic phenylalanine side chain. Several quantitative solid state NMR experiments were employed to provide site-specific measurements of structural and motional features of the observed transition. PMID:19067520

  13. Deep crustal structure off Akita, eastern margin of the Japan Sea, deduced from ocean bottom seismographic measurements

    NASA Astrophysics Data System (ADS)

    Nishizawa, Azusa; Asada, Akira

    1999-06-01

    A seismic exploration was carried out to detect the heterogeneity of the seismic wavespeed structure associated with the plate convergence at the eastern margin of the Japan Sea. Two airgun-OBS (ocean bottom seismograph) profiles were shot off Akita, Japan, where a seismic gap seems to exist but the location of the plate boundary has not been confirmed. One of the profiles was 60 km long, trending NNE-SSW, named Line OBS-9, at the northeastern end of the Yamato Basin and the other was 170 km long, trending WNW-ESE, Line NT95-1, parallel to the direction of the supposed plate convergence. The crustal structure beneath Line OBS-9 consists of six layers. The uppermost layer is sediment. Three layers are identified beneath the top sedimentary layer and their P wavespeeds are estimated to be 3.3-3.4 km/s, 5.1-5.4 km/s and 5.8-6.3 km/s, which corresponds to the upper crust. Underneath these layers, a layer with P wavespeed ranges of 6.3-7.2 km/s comprises the middle and lower crust. The depth of Moho is inferred to be 19 km. These wavespeed values are comparable with those of the present Japanese island arc, while the thickness of the crust is one-half of that of the Japanese arc. The crustal model supports the scenario that the Yamato Basin is formed by extension of the island arc. The crustal model for Line NT95-1 shows a transition from the extended island arc structure beneath the Yamato Basin to a thicker crust similar to the Japanese arc. P wavespeed heterogeneity related to the plate boundary is not detected. However, a significant change in the structural model along the profile is found around the region where the largest change in the seafloor topography exists. In that region, the wavespeeds in the middle crust have lower values than those of the neighboring area and the Moho begins to deepen towards the Japanese island arc. From comparison with the relationship between P wavespeed structure and aftershock distribution of the 1993 Hokkaido

  14. 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

  15. Relationship between surface and subsurface structures of the northern Atlas foreland of Tunisia deduced from regional gravity analysis

    NASA Astrophysics Data System (ADS)

    Frifita, N.; Arfaoui, M. S.; Zargouni, F.

    2016-08-01

    Gravity data were analyzed in the northern Atlas of Tunisia in order to identify the deep structures of the region and their relationship to the geological outcrop. The analysis based on the Bouguer gravity maps related to upward continuation at 1, 2, 4, 6, 10 and 12 km. The lineaments obtained by the horizontal gradient method were interpreted as deep faults with two global directions NE–SW and NW–SE related to major tectonic corridors. These lineaments were confirmed by the automatic estimation of depth solutions using the Euler deconvolution technique. By separation between the gravity anomaly bodies in different levels, it shows that almost all of the lineaments are oriented in NE–SW and NW–SE directions. The NW–SE-trending lineaments are related to deep faults and the NE–SW-oriented lineaments define the global direction of the surface, and they are related to shallow structures. 2.5D gravity modeling was used to improve the results obtained by the Maxima and the Euler deconvolution techniques. The 2.5D model points out the variation of depths of the NE–SW-trending major faults. In this study, we demonstrate the relationship between the NE–SW and the NW–SE directions. These two major sets of faults have been determined by the statistical study of the lineaments. This study confirms some faults already recognized or supposed by the classical geological studies, and it also detects a new deep fault masked in the surface, and gives information about major fault depths and the relation between different structures.

  16. Crust and mantle lithospheric structure of the Iberian Peninsula deduced from potential field modeling and thermal analysis

    NASA Astrophysics Data System (ADS)

    Torne, Montserrat; Fernàndez, Manel; Vergés, Jaume; Ayala, Conxi; Salas, Maria Carolina; Jimenez-Munt, Ivone; Buffett, Grant George; Díaz, Jordi

    2015-11-01

    We investigate the lithospheric structure of the Iberian Peninsula and lateral crustal density variations using a three-step approach. First the crustal and mantle lithosphere thicknesses are calculated from joint geoid and elevation modeling 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. Finally we invert the residual gravity anomalies to highlight lateral average crustal density variations and discuss them in terms of crustal structures. Our results show that for the majority of the study area the crustal thickness does correlate with the regional topography pattern. The highest topography - above 1500 m - shows thicknesses above 44 km with local values up to 48 km. Crustal thicknesses in the range of 36-40 km are obtained in the uplifted Alpine areas while a thinner crust is observed in sedimentary basins and in the Iberian Massif (30 to 35 km) with the exception of SW Iberia region where the crust thins from 30 to 28 km. Thick lithosphere - above 140 km - is found along the Pyrenees, the Cantabrian Mountains, the Iberian Chain and in the Betics while the thinnest lithosphere is found in SW Iberia (90 km). 3D inversion of residual anomalies show that for the majority of the area the average density of the crust is in the range of 2810 ± 10 kg m- 3. The denser crust is found in the NW and SW regions of the Iberian Massif (+ 30 kg m- 3 on average) and locally in the Pyrenees (above + 70 kg m- 3), NW of the Iberian Chain (+ 15 kg m- 3 on average) and in the southern Internal Betics (+ 70 kg m-3). The least dense crust is found in the central and western Betic Chain (- 30 kg m- 3 on average) and in sedimentary basin depocenters.

  17. Primary structure of the human melanoma-associated antigen p97 (melanotransferrin) deduced from the mRNA sequence.

    PubMed Central

    Rose, T M; Plowman, G D; Teplow, D B; Dreyer, W J; Hellström, K E; Brown, J P

    1986-01-01

    p97 is a cell-surface glycoprotein that is present in most human melanomas but only in trace amounts in normal adult tissues. To determine the structure of this tumor-associated antigen and to identify its functional domains, we have purified and cloned p97 mRNA and determined its nucleotide sequence. The mRNA encodes a 738-residue precursor, which contains the previously determined N-terminal amino acid sequence of p97. After removal of a 19-residue signal peptide, the mature p97 molecule comprises extracellular domains of 342 and 352 residues and a C-terminal 25-residue stretch of predominantly uncharged and hydrophobic amino acids, which we believe acts as a membrane anchor. Each extracellular domain contains 14 cysteine residues, which form seven intradomain disulfide bridges, and one or two potential N-glycosylation sites. Protease digestion studies show that the three major antigenic determinants of p97 are present on the N-terminal domain. The domains are strikingly homologous to each other (46% amino acid sequence homology) and to the corresponding domains of human serum transferrin (39% homology). Conservation of disulfide bridges and of amino acids thought to compose the iron binding pockets suggests that p97 is also related to transferrin in tertiary structure and function. We propose that p97 be renamed melanotransferrin to denote its original identification in melanoma cells and its evolutionary relationship to serotransferrin and lactotransferrin, the other members of the transferrin superfamily. Images PMID:2419904

  18. Structural features that specify tyrosine kinase activity deduced from homology modeling of the epidermal growth factor receptor.

    PubMed Central

    Knighton, D R; Cadena, D L; Zheng, J; Ten Eyck, L F; Taylor, S S; Sowadski, J M; Gill, G N

    1993-01-01

    To identify structural features that distinguish protein-tyrosine kinases from protein-serine kinases, a molecular model of the kinase domain of epidermal growth factor receptor was constructed by substituting its amino acid sequence for the amino acid sequence of the catalytic subunit of cAMP-dependent protein kinase in a 2.7-A refined crystallographic model. General folding was conserved as was the configuration of invariant residues at the active site. Two sequence motifs that distinguish the two families correspond to loops that converge at the active site of the enzyme. A conserved arginine in the catalytic loop is proposed to interact with the gamma phosphate of ATP. The second loop provides a binding surface that positions the tyrosine of the substrate. A positively charged surface provides additional sites for substrate recognition. Images Fig. 2 Fig. 3 Fig. 4 PMID:8389462

  19. Targeted polypeptide degradation

    DOEpatents

    Church, George M.; Janse, Daniel M.

    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.

  20. Neutral hydrogen shell structure near Comet P/Halley deduced from Vega-1 and Giotto energetic particle data

    NASA Astrophysics Data System (ADS)

    Verigin, M. I.; McKenna-Lawlor, S.; Richter, A. K.; Szego, K.; Veselovskii, I. S.

    An existing model based on Vega-1 (Tunde-M) and Giotto (EPONA) energetic particle data, representing neutral gas shells expanding about Comet Halley, has been updated by incorporating additional information concerning energetic particles recorded by Tunde-M, and neutral gas measurements recorded aboard the Vega-1 and Vega-2 spacecraft, in the original data set. The modified model reproduces reasonably well the positions of the maxima in the intensity profiles of energetic cometary ions observed along the Vega and Giotto trajectories, and it is estimated that the velocity of gas in the envisioned neutral shells is about 7.3 km/s, i.e., close to the velocity (about 8 km/s) of the slow hydrogen component of cometary neutrals. Detailed arguments are presented to support the suggestion that, at distances of 2-10 x exp 6 km from the comet nucleus, the energetic particles recorded in the quasi-periodic structures identified by the Tunde-M and EPONA instruments were protons.

  1. The structure of the upper crust in the Alps-Apennines boundary region deduced from refraction seismic data

    NASA Astrophysics Data System (ADS)

    Biella, G. C.; Gelati, R.; Maistrello, M.; Mancuso, M.; Massiotta, P.; Scarascia, S.

    1987-10-01

    Analysis of data gathered during the 1983 European Geotraverse southern segment (EGT-S '83) experiments in the region extending from the Emilia-Liguria Apennines to the western Alpine Arc together with data from seismic profiles in the northwestern Apennines accumulated within the framework of the Alps-Apennines Orogene Study Group indicate new details on the structure of the upper crust east and west of the Alps-Apennines boundary. The main results of this analysis centre on two areas. In the Piedmont Tertiary Basin we could determine the depocenter configurations of the 6-7 km thick terrigenous sequence and differentiate the tectonic units in the Piedmont (Alpine) and the Ligurian (Apennine) domains within the basement. In the other area, the Insubric domain underneath the Ligurian nappes of the northern Apennines, we found indications of tectonic doubling within the terrigenous-carbonate sequence in which thrusting attenuates towards the underlying basement, detected at a depth of 12-15 km. In addition, we found that, on a line from the Emilia Apennines to the Monferrato Hills, displacement of the Ligurian nappes over the Insubric domain diminishes to nearly one-third its original extent.

  2. Structure and Expression of Class II Defective Herpes Simplex Virus Genomes Encoding Infected Cell Polypeptide Number 8

    PubMed Central

    Locker, Hilla; Frenkel, Niza; Halliburton, Ian

    1982-01-01

    Defective genomes present in serially passaged virus stocks derived from the tsLB2 mutant of herpes simplex virus type 1 were found to consist of repeat units in which sequences from the UL region, within map coordinates 0.356 and 0.429 of standard herpes simplex virus DNA, were covalently linked to sequences from the end of the S component. The major defective genome species consisted of repeat units which were 4.9 × 106 in molecular weight and contained a specific deletion within the UL segment. These tsLB2 defective genomes were stable through more than 35 sequential virus passages. The ratios of defective virus genomes to helper virus genomes present in different passages fluctuated in synchrony with the capacity of the passages to interfere with standard virus replication. Cells infected with passages enriched for defective genomes overproduced the infected cell polypeptide number 8, which had previously been mapped within the UL sequences present in the tsLB2 defective genomes. In contrast, the synthesis of most other infected cell polypeptides was delayed and reduced. The abundant synthesis of infected cell polypeptide number 8 followed the β regulatory pattern, as evident from kinetic studies and from experiments in which cycloheximide, canavanine, and phosphonoacetate were used. However, in contrast to many β (early) and γ (late) viral polypeptides, the synthesis of infected cell polypeptide number 8 was only minimally reduced when cells infected with serially passaged tsLB2 were incubated at 39°C. The tsLB2 mutation had previously been mapped within the domains of the gene encoding infected cell polypeptide number 4, the function of which was shown to be required for β and γ viral gene expression. It is thus possible that the tsLB2 mutation affects the synthesis of only a subset of the β and γ viral polypeptides. An additional polypeptide, 74.5 × 103 in molecular weight, was abundantly produced in cells infected with a number of tsLB2 passages

  3. Bioactive glasses-incorporated, core-shell-structured polypeptide/polysaccharide nanofibrous hydrogels.

    PubMed

    Chen, Jian; Chen, Xiaoyi; Yang, Xianyan; Han, Chunmao; Gao, Changyou; Gou, Zhongru

    2013-01-30

    Although the synthetic hydrogel materials capable of accelerating wound healing are being developed at a rapid pace, achieving inorganic-organic hybrid at nanoscale dimension in nanofibrous hydrogels is still a great challenge because of its notorious brittleness and microstructural stability in wet state. Here, we developed a new nanofibrous gelatin/bioactive glass (NF-GEL/BG) composite hydrogel by phase separation method and followed by arming the nanofibers network with counterionic chitosan-hyaluronic acid pairs for improving microstructural and thermal integrity. We achieve this feature by carrying an optimal balance of charges that allows the inorganic ion release in aqueous solution without minimal structure collapse. Therefore, such NF-GEL-based, polysaccharide-crosslinked bioactive hydrogel could afford a close biomimicry to the fibrous nanostructure and constituents of the hierarchically organized natural soft tissues to facilitate chronic, nonhealing wound treatment. PMID:23218343

  4. The integration of gravity, magnetic and seismic data in delineating the sedimentary basins of northern Sinai and deducing their structural controls

    NASA Astrophysics Data System (ADS)

    Selim, El Sayed Ibrahim

    2016-01-01

    The Sinai Peninsula is a part of the Sinai sub-plate that located between the southeast Nubian-Arabian shield and the southeastern Mediterranean northward. The main objectives of this investigation are to deduce the main sedimentary basin and its subdivisions, identify the subsurface structural framework that affects the study area and determine the thickness of sedimentary cover of the basement surface. The total intensity magnetic map, Bouguer gravity map and seismic data were used to achieve the study aims. Structural interpretation of the gravity and magnetic data were done by applying advanced processing techniques. These techniques include; Reduce to the pole (RTP), Power spectrum, Tile derivative and Analytical Signal techniques were applied on gravity and magnetic data. Two dimensional gravity and magnetic modeling and interpretation of seismic sections were done to determine the thickness of sedimentary cover of the study area. The integration of our interpretation suggests that, the northern Sinai area consists of elongated troughs that contain many high structural trends. Four major structural trends have been identified, that, reflecting the influence of district regional tectonic movements. These trends are: (1) NE-SW trend; (2) NNW-SSE trend; (3) ENE-WSW trend and (4) WNW-ESE trend. There are also many minor trends, E-W, NW-SE and N-S structural trends. The main sedimentary basin of North Sinai is divided into four sub-basins; (1) Northern Maghara; (2) Northeastern Sinai; (3) Northwestern Sinai and (4) Central Sinai basin. The sedimentary cover ranges between 2 km and 7 km in the northern part of the study area.

  5. Combined effects of solvation and aggregation propensity on the final supramolecular structures adopted by hydrophobic, glycine-rich, elastin-like polypeptides.

    PubMed

    Salvi, Anna M; Moscarelli, Pasquale; Bochicchio, Brigida; Lanza, Giuseppe; Castle, James E

    2013-05-01

    Previous work on elastin-like polypeptides (ELPs) made of hydrophobic amino acids of the type XxxGlyGlyZzzGly (Xxx, Zzz = Val, Leu) has consistently shown that differing dominant supramolecular structures were formed when the suspending media were varied: helical, amyloid-like fibers when suspended in water and globules evolving into "string of bead" structures, poly(ValGlyGlyValGly), or cigar-like bundles, poly(ValGlyGlyLeuGly), when suspended in methyl alcohol. Comparative experiments with poly(LeuGlyGlyValGly) have further indicated that the interface energy plays a significant role and that solvation effects act in concomitance with the intrinsic aggregation propensity of the repeat sequence. Continuing our investigation on ELPs using surface (X-ray photoelectron spectroscopy, atomic force microscopy) and bulk (circular dichroism, Fourier transform infrared spectroscopy) techniques for their characterization, here we have compared the effect of suspending solvents (H(2)O, dimethylsulfoxide, ethylene glycol, and MeOH) on poly(ValGlyGlyValGly), the polypeptide most inclined to form long and well-refined helical fibers in water, searching for the signature of intermolecular interactions occurring between the polypeptide chains in the given suspension. The influence of sequence specificities has been studied by comparing poly(ValGlyGlyValGly) and poly(LeuGlyGlyValGly) with a similar degree of polymerization. Deposits on substrates of the polypeptides were characterized taking into account the differing evaporation rate of solvents, and tests on their stability in ultra high vacuum were performed. Finally, combining experimental and computational studies, we have revaluated the three-dimensional modeling previously proposed for the supramolecular assembly in water of poly(ValGlyGlyValGly). The results were discussed and rationalized also in the light of published data. PMID:23426573

  6. Amino-terminal amino acid sequence of the major structural polypeptides of avian retroviruses: sequence homology between reticuloendotheliosis virus p30 and p30s of mammalian retroviruses.

    PubMed Central

    Hunter, E; Bhown, A S; Bennett, J C

    1978-01-01

    The major structural polypeptides, p30 of reticuloendotheliosis virus (REV) (strain T) and p27 of avian sarcoma virus B77, have been compared with regard to amino acid composition. NH2-terminal amino acid sequence, and immunological crossreactions. The amino acid composition of the two polypeptides is distinct, and a comparison of the first 30 NH2-terminal amino acids of REV p30 with that for the first 25 of B77 p27 yields only three homologous residues. In competition radioimmunoassays the polypeptides show no crossreactivity. A comparison of the amino acid composition and NH2-terminal amino acid sequence of REV p30 with those reported for several mammalian retrovirus p30s shows remarkable similarities. Both REV and mammalian p30s contain a large number of polar residues in their amino acid composition and show approximately 40% homology in the first 30 NH2-terminal amino acids. No crossreactivity could be observed, however, in competition radioimmunoassays between Rauscher murine leukemia virus p30 and that of REV. The observations reported here suggest a close evolutionary relationship between REV and the mammalian retroviruses. Images PMID:208072

  7. 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

  8. Molecular and biophysical analysis of herbicide-resistant mutants of Chlamydomonas reinhardtii: structure-function relationship of the photosystem II D1 polypeptide.

    PubMed Central

    Erickson, J M; Pfister, K; Rahire, M; Togasaki, R K; Mets, L; Rochaix, J D

    1989-01-01

    Plants and green algae can develop resistance to herbicides that block photosynthesis by competing with quinones in binding to the chloroplast photosystem II (PSII) D1 polypeptide. Because numerous herbicide-resistant mutants of Chlamydomonas reinhardtii with different patterns of resistance to such herbicides are readily isolated, this system provides a powerful tool for examining the interactions of herbicides and endogenous quinones with the photosynthetic membrane, and for studying the structure-function relationship of the D1 protein with respect to PSII electron transfer. Here we report the results of DNA sequence analysis of the D1 gene from four mutants not previously characterized at the molecular level, the correlation of changes in specific amino acid residues of the D1 protein with levels of resistance to the herbicides atrizine, diuron, and bromacil, and the kinetics of fluorescence decay for each mutant, which show that changes at two different amino acid residues dramatically slow PSII electron transfer. Our analyses, which identify a region of 57 amino acids of the D1 polypeptide involved in herbicide binding and which define a D1 binding niche for the second quinone acceptor, QB of PSII, provide a strong basis of support for structural and functional models of the PSII reaction center. PMID:2535507

  9. Agouti polypeptide compositions

    DOEpatents

    Woychik, Richard P.; Bultman, Scott J.; Michaud, Edward J.

    2001-10-30

    Disclosed are methods and compositions comprising novel agouti polypeptides and the polynucleotides which encode them. Also disclosed are DNA segments encoding these proteins derived from human and murine cell lines, and the use of these polynucleotides and polypeptides in a variety of diagnostic and therapeutic applications. Methods, compositions, kits, and devices are also provided for identifying compounds which are inhibitors of agouti activity, and for altering fatty acid synthetase activity and intracellular calcium levels in transformed cells.

  10. cDNA sequence and deduced primary structure of an alpha-amylase inhibitor from a bruchid-resistant wild common bean.

    PubMed

    Suzuki, K; Ishimoto, M; Kitamura, K

    1994-06-12

    alpha-Amylase inhibitor-2 (alpha AI-2), a seed storage protein present in a bruchid-resistant wild common bean (Phaseolus vulgaris), inhibits the growth of bruchid pests. The authors isolated and determined the sequence of an 852 nucleotide cDNA, designated as alpha ai2, and found it to contain a 720 base open reading frame (ORF). This ORF encodes a 240 amino-acid alpha AI-2 polypeptide 75.8% identical with alpha-amylase inhibitor-1 (alpha AI-1) and 50.6-55.6% with arcelin-1, phytohemagglutinin (PHA)-L and PHA-E of common bean. The high degree of sequence homology suggests that there is an evolutionary relationship among these genes. PMID:8003534

  11. 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

  12. Structural Studies of Avian Myeloblastosis Virus: Comparison of Polypeptides in Virion and Core Component by Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis

    PubMed Central

    Stromberg, Kurt; Hurley, Nancy E.; Davis, Nancy L.; Rueckert, Roland R.; Fleissner, Erwin

    1974-01-01

    Two different systems of dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in separate laboratories detected analogous patterns of dye bands in virions of avian myeloblastosis virus (AMV). At least 11 of the dye bands co-migrated with the major polypeptides reported in Rous sarcoma virus. Particles with the morphology of the AMV core component, obtained after exposure of AMV to the nonionic surfactant Sterox SL, contained major polypeptides p12, p27, p60, p64, p91, and p98. The polypeptide p12 has been previously shown to be the major constituent of the inner ribonucleoprotein (RNP) of the AMV core, and has been designated p12(N). Two RNP polypeptides, p64 and p91, co-electrophoresed with purified AMV DNA polymerase and have now been designated p64(P) and p91(P). The polypeptide p27 has been identified as a probable constituent of the core shell, and has accordingly now been designated p27(C). In comparison to virions of AMV, the AMV core component contained a greatly reduced amount of polypeptide p15 and appeared to lack a major polypeptide, p19. Consequently, these polypeptides may be associated either with the exterior of the core shell or the interior of the viral envelope. Glycopeptides were not detected in AMV cores, in agreement with earlier reports that they reside in external projections from the viral envelope. Images PMID:4129794

  13. 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!

  14. Peppytides: Interactive Models of Polypeptide Chains

    ScienceCinema

    Zuckermann, Ron; Chakraborty, Promita; Derisi, Joe

    2014-10-28

    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!

  15. 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. PMID:27607147

  16. Helical antimicrobial polypeptides with radial amphiphilicity

    PubMed Central

    Xiong, Menghua; Lee, Michelle W.; Mansbach, Rachael A.; Song, Ziyuan; Bao, Yan; Peek, Richard M.; Yao, Catherine; Chen, Lin-Feng; Ferguson, Andrew L.; Wong, Gerard C. L.; Cheng, Jianjun

    2015-01-01

    α-Helical antimicrobial peptides (AMPs) generally have facially amphiphilic structures that may lead to undesired peptide interactions with blood proteins and self-aggregation due to exposed hydrophobic surfaces. Here we report the design of a class of cationic, helical homo-polypeptide antimicrobials with a hydrophobic internal helical core and a charged exterior shell, possessing unprecedented radial amphiphilicity. The radially amphiphilic structure enables the polypeptide to bind effectively to the negatively charged bacterial surface and exhibit high antimicrobial activity against both gram-positive and gram-negative bacteria. Moreover, the shielding of the hydrophobic core by the charged exterior shell decreases nonspecific interactions with eukaryotic cells, as evidenced by low hemolytic activity, and protects the polypeptide backbone from proteolytic degradation. The radially amphiphilic polypeptides can also be used as effective adjuvants, allowing improved permeation of commercial antibiotics in bacteria and enhanced antimicrobial activity by one to two orders of magnitude. Designing AMPs bearing this unprecedented, unique radially amphiphilic structure represents an alternative direction of AMP development; radially amphiphilic polypeptides may become a general platform for developing AMPs to treat drug-resistant bacteria. PMID:26460016

  17. 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.

  18. 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.

  19. 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

    2015-01-01

    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. PMID:25751078

  20. A Bio-Inspired Two-Layer Sensing Structure of Polypeptide and Multiple-Walled Carbon Nanotube to Sense Small Molecular Gases

    PubMed Central

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

    2015-01-01

    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. PMID:25751078

  1. The Na(+)-translocating ATPase of Acetobacterium woodii is a F1F0-type enzyme as deduced from the primary structure of its beta, gamma and epsilon subunits.

    PubMed

    Forster, A; Daniel, R; Müller, V

    1995-05-10

    A 4.5 kbp EcoRI fragment hybridizing to a fragment of uncD (coding for subunit beta of F1F0-ATPases) was cloned from chromosomal DNA of Acetobacterium woodii. The nucleotide sequence was determined and revealed five open reading frames (ORF), four of which were identified to code for subunits of the Na(+)-ATPase. The deduced amino acid sequences of these ORF's are homologous to subunit alpha (partial coding sequence, C-terminal end), gamma, beta and epsilon of F1F0-ATPases from various organisms; furthermore, the organization of the genes in the order uncA (alpha), uncG (gamma), uncD (beta), uncC (epsilon) is identical to the structure of unc operon as present in most bacteria. Downstream of uncC is an ORF whose deduced amino acid sequence has 53% sequence homology to AlgD from Pseudomonas aeruginosa. The structure and organization of the unc genes are the final proof that the Na(+)-ATPase from A. woodii is a member of the family of F1F0-ATPases. PMID:7748890

  2. Virus-coded origin of a 32,000-dalton protein from avian retrovirus cores: structural relatedness of p32 and the beta polypeptide of the avian retrovirus DNA polymerase.

    PubMed Central

    Schiff, R D; Grandgenett, D P

    1978-01-01

    A 32,000-dalton protein (p32) located in avian retrovirus cores was immunoprecipitated from [35S]methionine-labeled avian myeloblastosis virus (AMV) propagated in cultured chicken embryo fibroblast cells by an antiserum preparation (sarc III) derived from tumor-bearing hamsters injected with cloned and passaged cells from an avian sarcoma virus-induced primary hamster tumor. Since sarc III serum apparently contained antibodies only to virus-coded proteins and not to chicken cellular proteins, the immunoprecipitation of p32 from AMV by sarc III serum strongly suggested that p32 is virus coded. The origin of p32 was more definitively established by demonstrating the existence of a structural relationship between p32 and the AMV DNA polymerase. AMV p32 cross-reacted with the beta polypeptide of AMV alphabeta DNA polymerase in radioimmunoprecipitation and radioimmunoprecipitation inhibition assays, indicating that p32 and beta share common antigenic determinants. This relationship was clarified by sodium do-decyl sulfate-polyacrylamide gel electrophoretic analysis of the peptides generated by limited proteolysis of 125I-labeled AMV DNA polymerase polypeptides and of 125I-labeled AMV p32 by chymotrypsin or Staphylococcus aureus V-8 protease. The peptides which appeared during proteolytic digestion of p32 were a subset of those produced by digestion of the beta polypeptide; however, p32 had no discernible peptides in common with the alpha polypeptide. Further, all of the peptides produced by limited proteolysis of beta were present in the digests of either p32 or alpha. Our findings suggest that p32 is apparently derived by cleavage of the beta polypeptide of AMV DNA polymerase, presumably at a site near or identical to that at which alpha is generated from beta by proteolytic cleavage. Images PMID:81316

  3. The three-dimensional NMR-solution structure of the polypeptide fragment 195-286 of the LFB1/HNF1 transcription factor from rat liver comprises a nonclassical homeodomain.

    PubMed Central

    Leiting, B; De Francesco, R; Tomei, L; Cortese, R; Otting, G; Wüthrich, K

    1993-01-01

    The three-dimensional backbone fold of a polypeptide fragment from the rat LFB1/HNF1 transcription factor was determined by nuclear magnetic resonance (NMR) spectroscopy in solution. This fragment contains an amino acid sequence that is approximately 22% homologous to the well known homeodomains, but which contains 81 amino acid residues as compared with 60 residues in 'typical' homeodomains. For the present studies we used a recombinant 99 amino acid polypeptide containing this sequence in positions 10-90, which was uniformly labelled with 15N and also doubly labelled with 15N and 13C. The NMR structure of this polypeptide contains three alpha-helices comprising the residues 18-29, 36-50 and 71-84, a loop formed by residues 30-35, and a long stretch of non-regular secondary structure linking the second and third helices. The relative location and orientation of the helices is very similar to that in the Antennapedia (Antp) homeodomain structure, despite the fact that helix II is elongated by about one turn. This confirms a recently advanced hypothesis based on sequence comparisons that this polypeptide segment of LFB1/HNF1 might represent a homeodomain-like structural element. The helix-turn-helix motif, which has been shown to comprise the DNA recognition helix in the Antp homeodomain, can readily be recognized in the LFB1/HNF1 homeodomain, in spite of an extensive modification of the primary structure. The two residues of the tight turn in the Antp homeodomain are replaced by a 23 residue linker region between the two helices in LFB1/HNF1, which bulges out from the rest of the molecule and thus enables the formation of a non-classical helix--turn--helix motif. Images PMID:8491172

  4. 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.

  5. 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

  6. Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte-Carlo simulations

    PubMed Central

    Czapla, Luke; Swigon, David; Olson, Wilma K.

    2009-01-01

    The histone-like heat unstable HU protein plays a key role in the organization and regulation of the Escherichia coli genome. The non-specific nature of HU binding to DNA complicates analysis of the mechanism by which the protein contributes to the looping of DNA. Conventional models of the looping of HU-bound duplexes attribute the changes in biophysical properties of DNA brought about by the random binding of protein to changes in the effective parameters of an ideal helical wormlike chain. Here we introduce a novel Monte-Carlo approach to study the effects of non-specific HU binding on the configurational properties of DNA directly. We randomly decorate segments of an ideal double-helical DNA with HU molecules that induce the bends and other structural distortions of the double helix found in currently available X-ray structures. We find that the presence of HU at levels approximating those found in the cell reduces the persistence length by roughly threefold compared to that of naked DNA. The binding of protein has particularly striking effects on the cyclization properties of short duplexes, altering the dependence of ring closure on chain length in a way that cannot be mimicked by a simple wormlike model and accumulating at higher than expected levels on successfully closed chains. Moreover, the uptake of protein on small minicircles depends upon chain length, taking advantage of the HU-induced deformations of DNA structure to facilitate ligation. Circular duplexes with bound HU show a much greater propensity than protein-free DNA to exist as negatively supercoiled topoisomers, suggesting a potential role of HU in organizing the bacterial nucleoid. The local bending and undertwisting of DNA by HU, in combination with the number of bound proteins, provide a structural rationale for the condensation of DNA and the observed expression levels of reporter genes in vivo. PMID:18586040

  7. 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

  8. 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. PMID:27095198

  9. Relationship of the crustal structure and its deformation from arc to back-arc basin in the eastern Japan Sea deduced from the seismic survey

    NASA Astrophysics Data System (ADS)

    Sato, Takeshi; No, Tetsuo; Miura, Seiichi; Kodaira, Shuichi; Sato, Hiroshi

    2015-04-01

    The Japan Sea is a back-arc basin in the northwestern Pacific. Based on geophysical, geological, and petrological results, it is suggested that the opening of the Japan Sea was initiated by crustal rifting and the separation of Japan Island arcs from the Asian continent in the Early Oligocene, followed by the ocean floor spreading in the Late Oligocene (e.g., Tamaki et al., 1992). After 3.5 Ma, the crustal shortening by a strong compression occurred in the eastern margin (e.g., Sato, 1994). In the eastern margin, because of the extension associated with the opening of the Japan Sea and this shortening, the deformation such as active faults and folds formed have developed and large earthquakes with magnitudes-7 class repeatedly occurred (e.g., Okamura et al., 2007). The Japan Sea has a unique setting in terms of the connection between the back-arc basin opening and the crustal deformation. However, we have little information concerning with a crustal structure formed by the back-arc opening in the margin and the deformation. To obtain the information, we have been carrying out active-source seismic surveys using ocean bottom seismographs (OBSs) and multi-channel streamer system (MCS) to cover the eastern margin of the Japan Sea. The obtained results show a difference in crustal structures between the northern and the southern parts of the eastern Japan Sea. In the northern part from the arc to the back-arc basin, the crust is divided into three types; the rifted island arc crust, the thicker oceanic crust and the oceanic crust, based on the comparison of the P-wave velocity distribution and the crustal thickness of a typical oceanic crust (White et al., 1992) and of the northeastern Japan Island arc crust (Iwasaki et al., 2001). On the other hand, the southern part from the arc to the back-arc basin has two crustal types, which are the rifted island arc crust and the thicker oceanic crust. In the northern part, the deformation is distributed in a structural boundary

  10. 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.

  11. 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.

  12. Chirality-selected phase behaviour in ionic polypeptide complexes

    DOE PAGESBeta

    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.; et al

    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

  13. 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

  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. Hypothesis/review: the structural basis of sweetness perception of sweet-tasting plant proteins can be deduced from sequence analysis.

    PubMed

    Wintjens, René; Viet, Tran Melody Vu Ngoc; Mbosso, Emmanuel; Huet, Joëlle

    2011-10-01

    Human perception of sweetness, behind the felt pleasure, is thought to play a role as an indicator of energy density of foods. For humans, only a small number of plant proteins taste sweet. As non-caloric sweeteners, these plant proteins have attracted attention as candidates for the control of obesity, oral health and diabetic management. Significant advances have been made in the characterization of the sweet-tasting plant proteins, as well as their binding interactions with the appropriate receptors. The elucidation of sweet-taste receptor gene sequences represents an important step towards the understanding of sweet taste perception. However, many questions on the molecular basis of sweet-taste elicitation by plant proteins remain unanswered. In particular, why homologues of these proteins do not elicit similar responses? This question is discussed in this report, on the basis of available sequences and structures of sweet-tasting proteins, as well as of sweetness-sensing receptors. A simple procedure based on sequence comparisons between sweet-tasting protein and its homologous counterparts was proposed to identify critical residues for sweetness elicitation. The open question on the physiological function of sweet-tasting plant proteins is also considered. In particular, this review leads us to suggest that sweet-tasting proteins may interact with taste receptor in a serendipity manner. PMID:21889040

  16. Deformation history during chain building deduced by outcrop structural analysis: The case of the Sicilian fold-and-thrust belt (Central Mediterranean)

    NASA Astrophysics Data System (ADS)

    Napoli, G.; Nigro, F.; Favara, R.; Renda, P.; Salvaggio, G.

    2015-11-01

    The Sicilian fold-and-thrust belt is located in the central Mediterranean area, and it represents the south-eastern arcuate segment of the Apennine-Maghrebide orogen. The tectonic evolution of the Sicilian belt is documented after outcrop analysis of small-scale structural features carried out throughout the region. Results are consistent with the following four main deformation stages having affected the study area, from the oldest to the youngest: (i) multilayer weakening; (ii) folding-and-thrusting, (iii) extension, and (iv) renewed thrusting. The first deformation stage included three different substages (layer-parallel shortening, bed-parallel simple shear and fold nucleation), the second one by both thrusting and fold amplification and tightening. The third deformation stage involved re-activation of the pre-existing mechanical discontinuities and formation of low-to-high angle normal faults. Out-of-sequence thrusting postdated the aforementioned extensional stage, and formed the latest orogenic deformation stage that affected the Sicilian belt.

  17. Phylogeny of immunoglobulin heavy chain isotypes: structure of the constant region of Ambystoma mexicanum upsilon chain deduced from cDNA sequence.

    PubMed

    Fellah, J S; Kerfourn, F; Wiles, M V; Schwager, J; Charlemagne, J

    1993-01-01

    An RNA polymerase chain reaction strategy was used to amplify and clone a cDNA segment encoding for the complete constant part of the axolotl IgY heavy (C upsilon) chain. C upsilon is 433 amino acids long and organized into four domains (C upsilon 1-C upsilon 4); each has the typical internal disulfide bond and invariant tryptophane residues. Axolotl C upsilon is most closely related to Xenopus C upsilon (40% identical amino acid residues) and C upsilon 1 shares 46.4% amino acid residues among these species. The presence of additional cysteines in C upsilon 1 and C upsilon 2 domains is consistent with an additional intradomain S-S bond similar to that suggested for Xenopus C upsilon and C chi, and for the avian C upsilon and the human C epsilon. C upsilon 4 ends with the Gly-Lys dipeptide characteristic of secreted mammalian C gamma 3, human C epsilon 4, and avian and anuran C upsilon 4, and contains the consensus [G/GT(AA)] nucleotide splice signal sequence for joining C upsilon 4 to the transmembrane region. These results are consistent with the hypothesis of an ancestral structural relationship between amphibian, avian upsilon chains, and mammalian epsilon chains. However, these molecules have different biological properties: axolotl IgY is secretory Ig, anuran and avian IgY behave like mammalian IgG, and mammalian IgE is implicated in anaphylactic reactions. PMID:8344718

  18. Domain structures and molecular evolution of class I and class II major histocompatibility gene complex (MHC) products deduced from amino acid and nucleotide sequence homologies

    NASA Astrophysics Data System (ADS)

    Ohnishi, Koji

    1984-12-01

    Domain structures of class I and class II MHC products were analyzed from a viewpoint of amino acid and nucleotide sequence homologies. Alignment statistics revealed that class I (transplantation) antigen H chains consist of four mutually homologous domains, and that class II (HLA-DR) antigen β and α chains are both composed of three mutually homologous ones. The N-terminal three and two domains of class I and class II (both β and α) gene products, respectively, all of which being ˜90 residues long, were concluded to be homologous to β2-microglobulin (β2M). The membraneembedded C-terminal shorter domains of these MHC products were also found to be homologous to one another and to the third domain of class I H chains. Class I H chains were found to be more closely related to class II α chains than to class II β chains. Based on these findings, an exon duplication history from a common ancestral gene encoding a β2M-like primodial protein of one-domain-length up to the contemporary MHC products was proposed.

  19. Sequence comparison of new prokaryotic and mitochondrial members of the polypeptide chain release factor family predicts a five-domain model for release factor structure.

    PubMed Central

    Pel, H J; Rep, M; Grivell, L A

    1992-01-01

    We have recently reported the cloning and sequencing of the gene for the mitochondrial release factor mRF-1. mRF-1 displays high sequence similarity to the bacterial release factors RF-1 and RF-2. A database search for proteins resembling these three factors revealed high similarities to two amino acid sequences deduced from unassigned genomic reading frames in Escherichia coli and Bacillus subtilis. The amino acid sequence derived from the Bacillus reading frame is 47% identical to E.coli and Salmonella typhimurium RF-2, strongly suggesting that it represents B.subtilis RF-2. Our comparison suggests that the expression of the B.subtilis gene is, like that of the E.coli and S. typhimurium RF-2 genes, autoregulated by a stop codon dependent +1 frameshift. A comparison of prokaryotic and mitochondrial release factor sequences, including the putative B.subtilis RF-2, leads us to propose a five-domain model for release factor structure. Possible functions of the various domains are discussed. PMID:1408743

  20. Polypeptide-Coated Silica Particles Dispersed in Lyotropic Liquid Crystals of the Same Polypeptide.

    PubMed

    Rosu, Cornelia; Balamurugan, Sreelatha; Cueto, Rafael; Roy, Amitava; Russo, Paul S

    2016-07-28

    When a particle is introduced into a liquid crystal (LC), it distorts the LC director field, leading to new arrangements of the particles. This phenomenon is ordinarily studied using >100 nm particles and ∼2 nm mesogens. Usually the particle surface and mesogens are chemically distinct, which adds an enthalpic effect, even though the more interesting interactions are entropic. To raise the structures to the visible regime, while minimizing chemical differences between the particle surface and mesogen, silica particles coated with an α-helical polypeptide have been prepared and dispersed in lyotropic polypeptide LCs. The polypeptide is poly(γ-stearyl-α,l-glutamate) or PSLG. To make the particles easy to manipulate and easy to find, the silica core included superparamagnetic magnetite (Fe3O4) and covalently attached dye. Two methods were used to place polypeptides on these magnetic, fluorescent particles: a multistep grafting-to approach in which whole polypeptides were attached and a one-pot grafting-from approach in which the polymerization of the monomers was initiated from the particle surface. These approaches resulted in sparse and dense surface coverages, respectively. The influence of surface curvature and polypeptide molecular weight on the design of sparsely covered particles was investigated using the grafting-to approach. The aggregated grafting-from particles when freshly dispersed in a PSLG/solvent matrix disrupted the orientation of the characteristic cholesteric LC (ChLC) phase directors. In time, the hybrid particles were expelled from some domains, enabling the return of the familiar helical twist of the cholesteric mesophase. The sparsely coated grafting-to hybrid particles when inserted in the PSLG/solvent matrix assembled into stable islet-like formations that could not be disrupted even by an external magnetic field. The bulk particles aligned in chains that were easily manipulated by a magnetic field. These results indicate that

  1. 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

  2. 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

  3. The slow folding reaction of barstar: the core tryptophan region attains tight packing before substantial secondary and tertiary structure formation and final compaction of the polypeptide chain.

    PubMed

    Sridevi, K; Juneja, J; Bhuyan, A K; Krishnamoorthy, G; Udgaonkar, J B

    2000-09-15

    The slow folding of a single tryptophan-containing mutant of barstar has been studied in the presence of 2 M urea at 10 degrees C, using steady state and time-resolved fluorescence methods and far and near-UV CD measurements. The protein folds in two major phases: a fast phase, which is lost in the dead time of measurement during which the polypeptide collapses to a compact form, is followed by a slow observable phase. During the fast phase, the rotational correlation time of Trp53 increases from 2.2 ns to 7.2 ns, and its mean fluorescence lifetime increases from 2.3 ns to 3.4 ns. The fractional changes in steady-state fluorescence, far-UV CD, and near-UV CD signals, which are associated with the fast phase are, respectively, 36 %, 46 %, and 16 %. The product of the fast phase can bind the hydrophobic dye ANS. These observations together suggest that the folding intermediate accumulated at the end of the fast phase has: (a) about 20 % of the native-state secondary structure, (b) marginally formed or disordered tertiary structure, (c) a water-intruded and mobile protein interior; and (d) solvent-accessible patches of hydrophobic groups. Measurements of the anisotropy decay of Trp53 suggest that it undergoes two types of rotational motion in the intermediate: (i) fast (tau(r) approximately 1 ns) local motion of its indole side-chain, and (ii) a slower (tau(r) approximately 7.2 ns) motion corresponding to global tumbling of the entire protein molecule. The ability of the Trp53 side-chain to undergo fast local motion in the intermediate, but not in the fully folded protein where it is completely buried in the hydrophobic core, suggests that the core of the intermediate is still poorly packed. The global tumbling time of the fully folded protein is faster at 5.6 ns, suggesting that the volume of the intermediate is 25 % more than that of the fully folded protein. The rate of folding of this intermediate to the native state, measured by steady-state fluorescence, far

  4. Methods for producing secreted polypeptides

    DOEpatents

    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.

  5. Poly(ethylene glycol)-polypeptide Copolymer Micelles for Therapeutic Agent Delivery.

    PubMed

    Cheng, Yilong

    2016-01-01

    Poly(ethylene glycol)-polypeptide (PEG-polypeptide) based polymeric micelles as therapeutic agent carriers have received considerable interest due to their advanced achievements in clinical trials. Polypeptides not only show well-defined secondary structure (alfa-helix and beta-sheet) and good biocompatibility, but can also be functionalized with various groups by direct N-carboxyanhydrides (NCAs) polymerization or further modification. Additionally, the ionizable side chains enable them to deliver diverse therapeutic agents, such as negative nucleic acid and positive doxorubicin. In this review, we firstly summarized the synthetic methods of amphiphilic copolymers PEG-polypeptide, and emphatically discussed recent progress on their applications as nanocarriers for therapeutic agents from following aspects: PEG-nonionic polypeptide copolymer micelles, PEG-anionic polypeptide micelles, and PEGcationic polypeptide micelles. PMID:26696015

  6. 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.

  7. 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. PMID:24354281

  8. 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

  9. 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

  10. The flaA locus of Bacillus subtilis is part of a large operon coding for flagellar structures, motility functions, and an ATPase-like polypeptide.

    PubMed Central

    Albertini, A M; Caramori, T; Crabb, W D; Scoffone, F; Galizzi, A

    1991-01-01

    We cloned and sequenced 8.3 kb of Bacillus subtilis DNA corresponding to the flaA locus involved in flagellar biosynthesis, motility, and chemotaxis. The DNA sequence revealed the presence of 10 complete and 2 incomplete open reading frames. Comparison of the deduced amino acid sequences to data banks showed similarities of nine of the deduced products to a number of proteins of Escherichia coli and Salmonella typhimurium for which a role in flagellar functioning has been directly demonstrated. In particular, the sequence data suggest that the flaA operon codes for the M-ring protein, components of the motor switch, and the distal part of the basal-body rod. The gene order is remarkably similar to that described for region III of the enterobacterial flagellar regulon. One of the open reading frames was translated into a protein with 48% amino acid identity to S. typhimurium FliI and 29% identity to the beta subunit of E. coli ATP synthase. PMID:1828465

  11. Dynamical Transition in polypeptides

    NASA Astrophysics Data System (ADS)

    He, Yunfen; Markelz, Andrea

    2008-03-01

    Two of the possible causes for the so called dynamical transition (the rapid increase in flexibility for biomolecules at ˜ 200 K) are: thermally activated side chain diffusive motions with hydration dependent activation energies; or a glass transition in the biological water directly adjacent to the biomolecule. If the transition is strictly due to side chain activation, it should not depend on protein structure. Previously we demonstrated that the dynamical transition remains after tertiary structure was removed using THz time domain dielectric spectroscopy (0.2 -2.0 THz, 0.5-5ps). Here measurements on polyalanine as a function of chain length show that the dynamical transition does not occur for peptide length shorter than 5. However, the transition is observed for 5 mer and higher. Structural and simulation studies indicate that the 5 mer transiently occupies structured forms [1,2]. These results suggest that A) the dynamical transition is not due to thermally activated side chain motion and B) secondary structure is necessary for the dynamical transition. Secondary structure possibly induces sufficient ordering in the adjacent water to result in a fragile to strong glass transition resulting in increased protein flexibility [3]. [1] KAH Wildman et al. Solid State Nucl. Magn. Reson. 24 (2003) 94-109. [2] Yuguang Mu,et al. Proteins 58, (2005) 45-52. [3] S.H. Chen et al. PNAS (2006) 9012--9016.

  12. Structure and mapping of the human thymopoietin (TMPO) gene and relationship of human TMPO {beta} to rat lamin-associated polypeptide 2

    SciTech Connect

    Harris, C.A.; Andryuk, P.J.; Cline, S.W.; Seikierka, J.J.; Goldstein, G.

    1995-07-20

    Thymopoietins (TMPOs, previously abbreviated TPs) {alpha}(75kDa), {beta}(51 kDa), and {gamma}(39 kDa) are related nuclear proteins expressed in many or all tissues. TMPO {alpha} is present diffusely throughout the nucleus, while TMPOs {beta} and {gamma} are localized to the nuclear membrane. Here we report the cloning and analysis of a single TMPO gene encoding TMPOs {alpha}, {beta}, and {gamma}, which are produced by alternative mRNA splicing, as previously inferred from cDNA sequences. The eight exons of the TMPO gene are spread over {approximately}35 kb. Exon 4, which is spliced into TMPS {alpha} mRNA, contains sequences that encode a putative basic nuclear localization motif. Exon 8, which is spliced into TMPO {beta} and {gamma} mRNAs, encodes a hydrophobic putative membrane-spanning domain that is thought to target TMPOs {beta} and {gamma} to the nuclear membrane. TMPO {Beta} appears to be the human homologue of the recently described rat protein LAP2 (lamina-associated polypeptide 2), which is thought to play an important role in the regulation of nuclear architecture by binding lamin B1 and chromosomes in a manner regulated by phosphorylation during mitosis. The human TMPO gene maps to chromosome band 12q22. 28 refs., 6 figs., 1 tab.

  13. 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. PMID:25647481

  14. Structural and functional identification of the pituitary adenylate cyclase-activating polypeptide receptor VPAC2 from the frog Rana tigrina rugulosa.

    PubMed

    Hoo, R L; Alexandre, D; Chan, S M; Anouar, Y; Pang, R T; Vaudry, H; Chow, B K

    2001-10-01

    Recently, a frog pituitary adenylate cyclase-activating polypeptide (PACAP)/vasoactive intestinal peptide (VIP) receptor (fPVR) has been characterized, and interestingly, this receptor exhibits characteristics of both mammalian PACAP type II receptors VPAC(1)R and VPAC(2)R. In order to investigate the receptors responsible for mediating the actions of VIP and PACAP in amphibians, in this report, a frog VPAC(2) receptor (fVPAC(2)R) cDNA was isolated. fVPAC(2)R shares 47.7, 46.9 and 62.5% amino acid sequence identity with fPVR, human VPAC(1)R and human VPAC(2)R respectively. Functionally, fVPAC(2)R, when expressed in CHO cells, was responsive to both frog peptides including VIP, PACAP38 and PACAP27 where the EC(50) values of these peptides in intracellular cAMP production were 0.15, 0.18 and 0.16 microM respectively. The pharmacological profiles of human peptides (VIP, PACAP38 and peptide histidine methionine) to stimulate frog and human VPAC(2)Rs were compared, and it was found that these peptides could only activate the frog receptor at micromolar concentrations. fVPAC(2)R was found to be widely distributed in various peripheral tissues as well as several regions of the brain. The presence of the receptor transcripts suggests the functional roles of the receptor in mediating the actions of PACAP and/or VIP in these tissues. As VIP and particularly PACAP27 are highly conserved peptides in vertebrate evolution, comparative studies of these peptides and their receptors in non-mammalian vertebrates should provide clues to better understand the physiology of these important peptides in human and other vertebrates. PMID:11564605

  15. Calculation of the isotope cluster for polypeptides by probability grouping.

    PubMed

    Olson, Matthew T; Yergey, Alfred L

    2009-02-01

    This paper presents a novel theoretical basis for accurately calculating the isotope cluster of polypeptides. In contrast to previous approaches to this problem, which consider exhaustive or near exhaustive combinations of isotopic species, the program, Neutron Cluster, groups probabilities to yield highly accurate information without elucidating any fine structure within a nominal mass unit. This is a fundamental difference from any previously described algorithm for calculating the isotope cluster. As a result of this difference, the accurate isotope clusters for high molecular weight polypeptides can be calculated rapidly without any pruning. When applied to isotope enriched polypeptides, the algorithm introduces "grouping error", which is described, quantified, and avoided by using probability partitioning. PMID:19026561

  16. Calculation of the Isotope Cluster for Polypeptides by Probability Grouping

    PubMed Central

    Olson, Matthew T.; Yergey, Alfred L.

    2014-01-01

    This paper presents a novel theoretical basis for accurately calculating the isotope cluster of polypeptides. In contrast to previous approaches to this problem, which consider exhaustive or near exhaustive combinations of isotopic species, the program, Neutron Cluster, groups probabilities to yield highly accurate information without elucidating any fine structure within a nominal mass unit. This is a fundamental difference from any previously described algorithm for calculating the isotope cluster. As a result of this difference, the accurate isotope clusters for high molecular weight polypeptides can be calculated rapidly without any pruning. When applied to isotope enriched polypeptides, the algorithm introduces “grouping error”, which is described, quantified, and avoided by using probability partitioning. PMID:19026561

  17. Evaluation of Conformation and Association Behavior of Multivalent Alanine-Rich Polypeptides

    PubMed Central

    Farmer, Robin S.; Top, Ayben; Argust, Lindsey M.; Liu, Shuang; Kiick, Kristi L.

    2008-01-01

    Purpose Helical alanine-rich polypeptides with functional groups displayed along the backbone can display desired molecules such as saccharides or therapeutic molecules at a prescribed spacing. Because these polypeptides have promise for application as biomaterials, the conformation and association of these molecules have been investigated under biologically relevant conditions. Methods Three polypeptide sequences, 17-H-3, 17-H-6, and 35-H-6, have been produced through recombinant techniques. Circular dichroic (CD) spectroscopy was used to monitor the secondary structure of the polypeptides in PBS (phosphate buffered saline, pH 7.4). The aggregation behavior in PBS was monitored via analytical ultracentrifugation and non-denaturing polyacrylamide gel electrophoresis. Results The three polypeptides adopt a highly helical structure at low and ambient temperatures, and when heated, undergo a helix-to-coil transition, typical of other alanine-rich peptide sequences. The melting temperatures and van’t Hoff enthalpies, extracted from the CD data, suggest similar stability of the sequences. Although alanine-rich sequences can be prone to aggregation, there is no indication of aggregation for the three polypeptides at a range of concentrations relevant for possible biological applications. Conclusions The helical polypeptides are monomeric under biologically relevant conditions enabling application of these polypeptides as useful scaffolds for ligand or drug display. PMID:17674161

  18. Polypeptide having swollenin activity and uses thereof

    SciTech Connect

    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.

  19. Polypeptide having cellobiohydrolase activity and uses thereof

    SciTech Connect

    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.

  20. Precipitation processes as deduced by combining Doppler radar and disdrometer

    NASA Astrophysics Data System (ADS)

    Thomson, Alan Douglas

    Precipitation processes are investigated in stratiform and convective weather systems by combining Doppler radar and disdrometer measurements. Vertical scans are designed to measure the standard radar data fields and the power spectrum of the vertical Doppler velocities with high spatial and temporal resolution. A new method, based on iterative application of a disdrometer-determined Z-R relation, is developed to estimate vertical winds from the vertical scan data. Using this method, radar-based raindrop size spectra calculated near the surface in light stratiform rain compare well with simultaneous measurements from a collocated disdrometer. A full raindrop size spectrum profile is deduced for a specific steady state case. It is found that the spectrum does not vary with height, suggesting that the spectral shape is mainly controlled by the ice particles occurring above the 0oC level. Vertical scan data are also combined with volume scan data obtained by the Atmospheric Environment Service King City radar to examine the precipitation structure of a hail producing region within a severe squall line. The vertical scan shows a large variation in precipitation structure and also reveals important storm features which, in this case, are not detected by the conventional volume scans, such as a weak echo vault, a downdraught outflow, and streaks of very high downward velocity corresponding to separate hail trajectories. The power spectra were used to identify and locate hailstones, to deduce the growth of descending hailstones, and to qualitatively examine properties of raindrop size spectra. A conceptual model of hail formation is proposed by comparing the deduced storm structure and precipitation processes with the analyses of two somewhat similar storms documented in the literature.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  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.

    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.

  8. 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. PMID:27152720

  9. 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

  10. Structure and dynamics in solution of the stop codon decoding N-terminal domain of the human polypeptide chain release factor eRF1.

    PubMed

    Polshakov, Vladimir I; Eliseev, Boris D; Birdsall, Berry; Frolova, Ludmila Yu

    2012-06-01

    The high-resolution NMR structure of the N-domain of human eRF1, responsible for stop codon recognition, has been determined in solution. The overall fold of the protein is the same as that found in the crystal structure. However, the structures of several loops, including those participating in stop codon decoding, are different. Analysis of the NMR relaxation data reveals that most of the regions with the highest structural discrepancy between the solution and solid states undergo internal motions on the ps-ns and ms time scales. The NMR data show that the N-domain of human eRF1 exists in two conformational states. The distribution of the residues having the largest chemical shift differences between the two forms indicates that helices α2 and α3, with the NIKS loop between them, can switch their orientation relative to the β-core of the protein. Such structural plasticity may be essential for stop codon recognition by human eRF1. PMID:22517631

  11. Structure and dynamics in solution of the stop codon decoding N-terminal domain of the human polypeptide chain release factor eRF1

    PubMed Central

    Polshakov, Vladimir I; Eliseev, Boris D; Birdsall, Berry; Frolova, Ludmila Yu

    2012-01-01

    The high-resolution NMR structure of the N-domain of human eRF1, responsible for stop codon recognition, has been determined in solution. The overall fold of the protein is the same as that found in the crystal structure. However, the structures of several loops, including those participating in stop codon decoding, are different. Analysis of the NMR relaxation data reveals that most of the regions with the highest structural discrepancy between the solution and solid states undergo internal motions on the ps–ns and ms time scales. The NMR data show that the N-domain of human eRF1 exists in two conformational states. The distribution of the residues having the largest chemical shift differences between the two forms indicates that helices α2 and α3, with the NIKS loop between them, can switch their orientation relative to the β-core of the protein. Such structural plasticity may be essential for stop codon recognition by human eRF1. PMID:22517631

  12. Chirality-selected phase behavior in ionic polypeptide complexes

    NASA Astrophysics Data System (ADS)

    Tirrell, Matthew

    2015-03-01

    We demonstrate that chirality determines the phase state of polyelectrolyte complexes formed from mixing dilute solutions of oppositely charged polypeptides. In these systems, the physical state of the resultant complex is determined by the combination of electrostatic and hydrogen bonding interactions. The formation of fluid complexes occurs 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 on mixing. Analogous behavior occurs in micellar cores formed from polypeptide block copolymers with polyethylene oxide, where microphase separation into discrete, self-assembled 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 systems based on polyelectrolyte complexation. Its role in these systems gives insight into polyelectrolyte complex phase behavior more broadly. This work was supported by the U.S. Department of Energy Office of Science Program in Basic Energy Sciences, Materials Sciences and Engineering Division.

  13. 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.

  14. New polypeptide components purified from mamba venom.

    PubMed

    Tytgat, J; Vandenberghe, I; Ulens, C; Van Beeumen, J

    2001-03-01

    New polypeptide components have been isolated from Dendroaspis angusticeps venom using chromatography. Two polypeptides containing 59 and 57 amino acids, called 'DaE1' and 'DaE2' respectively, have been purified to homogeneity and fully sequenced. Spectrometric analysis yielded masses of 6631.5 and 6389.0 Da, respectively. The polypeptides share 98 and 95% identity, respectively, with trypsin inhibitor E (DpE) of Dendroaspis polylepis polylepis. 'DaE' polypeptides inhibit Kv1.1 channels with an IC(50) value in the range of 300 nM. They can be considered as new dendrotoxins, albeit with fairly low affinity as compared to alpha-DTX. 'DaE' polypeptides do not affect Kir2.1 channels. PMID:11240130

  15. Supramolecular Polymerization from Polypeptide-Grafted Comb Polymers

    SciTech Connect

    Wang, Jing; Lu, Hua; Kamat, Ranjan K; Pingali, Sai Venkatesh; Urban, Volker S; Cheng, Jianjun; Lin, Yao

    2011-01-01

    The helical and tubular structures self-assembled from proteins have inspired scientists to design synthetic building blocks that can be 'polymerized' into supramolecular polymers through coordinated noncovalent interactions. However, cooperative supramolecular polymerization from large, synthetic macromolecules remains a challenge because of the difficulty of controlling the structure and interactions of macromolecular monomers. Herein we report the synthesis of polypeptide-grafted comb polymers and the use of their tunable secondary interactions in solution to achieve controlled supramolecular polymerization. The resulting tubular supramolecular structures, with external diameters of hundreds of nanometers and lengths of tens of micrometers, are stable and resemble to some extent biological superstructures assembled from proteins. This study shows that highly specific intermolecular interactions between macromolecular monomers can enable the cooperative growth of supramolecular polymers. The general applicability of this strategy was demonstrated by carrying out supramolecular polymerization from gold nanoparticles grafted with the same polypeptides on the surface.

  16. 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.

  17. 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.

  18. 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.

  19. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2015-03-10

    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.

  20. 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.

  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 endoglucanase activity and polynucleotides encoding same

    DOEpatents

    Spodsberg, Nikolaj

    2015-07-14

    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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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)

  12. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    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.

  13. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    SciTech Connect

    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.

  14. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    SciTech Connect

    Liu, Ye; Tang, Lan

    2015-07-14

    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.

  15. Polypeptides having endoglucanase activity and polynucleotides encoding same

    SciTech Connect

    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.

  16. 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.

  17. 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.

  18. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    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.

  19. Pancreatic Polypeptide Inhibits Somatostatin Secretion

    PubMed Central

    Kim, Wook; Fiori, Jennifer L.; Shin, Yu-Kyong; Okun, Eitan; Kim, Jung Seok; Rapp, Peter R.; Egan, Josephine M.

    2014-01-01

    Pancreatic polypeptide (PP) is a major agonist for neuropeptide Y4 receptors (NPY4R). While NPY4R has been identified in various tissues, the cells on which it is expressed and its function in those cells has not been clearly delineated. Here we report that NPY4R is present in all somatostatin-containing cells of tissues that we tested, including pancreatic islets, duodenum, hippocampus, and hypothalamus. Its agonism by PP decreases somatostatin secretion from human islets. Mouse embryonic hippocampal (mHippo E18) cells expressed NPY4Rs and their activation by PP consistently decreased somatostatin secretion. Furthermore, central injection of PP in mice induced c-Fos immunoreactivity in somatostatin-containing cells in the hippocampus compared with PBS-injected mice. In sum, our results identify PP as a pivotal modulator of somatostatin secretion. PMID:25019573

  20. Papain-Catalyzed Chemoenzymatic Synthesis of Telechelic Polypeptides Using Bis(Leucine Ethyl Ester) Initiator.

    PubMed

    Tsuchiya, Kousuke; Numata, Keiji

    2016-07-01

    In order to construct unique polypeptide architectures, a novel telechelic-type initiator with two leucine ethyl ester units is designed for chemoenzymatic polymerization. Glycine or alanine ethyl ester is chemoenzymatically polymerized using papain in the presence of the initiator, and the propagation occurs at each leucine ethyl ester unit to produce the telechelic polypeptide. The formation of the telechelic polypeptides is confirmed by (1) H NMR and MALDI-TOF mass spectroscopies. It is revealed by AFM observation that long nanofibrils are formed from the telechelic polyalanine, whereas a conventional linear polyalanine with a similar degree of polymerization shows granule-like structures. The telechelic polyglycine and polyalanine show the crystalline structures of Polyglycine II and antiparallel β-sheet, respectively. It is demonstrated that this method to synthesize telechelic-type polypeptides potentially opens up a pathway to construct novel hierarchical structures by self-assembly. PMID:26947148

  1. Sequence analysis and protein import studies of an outer chloroplast envelope polypeptide.

    PubMed Central

    Salomon, M; Fischer, K; Flügge, U I; Soll, J

    1990-01-01

    A chloroplast outer envelope membrane protein was cloned and sequenced and from the sequence it was possible to deduce a polypeptide of 6.7 kDa. It has only one membrane-spanning region; the C terminus extends into the cytosol, whereas the N terminus is exposed to the space between the two envelope membranes. The protein was synthesized in an in vitro transcription-translation system to study its routing into isolated chloroplasts. The import studies revealed that the 6.7-kDa protein followed a different and heretofore undescribed translocation pathway in the respect that (i) it does not have a cleavable transit sequence, (ii) it does not require ATP hydrolysis for import, and (iii) protease-sensitive components that are responsible for recognition of precursor proteins destined for the inside of the chloroplasts are not involved in routing the 6.7-kDa polypeptide to the outer chloroplast envelope. Images PMID:2377616

  2. Restriction/modification polypeptides, polynucleotides, and methods

    SciTech Connect

    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.

  3. Mechanistic Contributions of Biological Cofactors in Islet Amyloid Polypeptide Amyloidogenesis

    PubMed Central

    Nguyen, Phuong Trang; Andraka, Nagore; De Carufel, Carole Anne; Bourgault, Steve

    2015-01-01

    Type II diabetes mellitus is associated with the deposition of fibrillar aggregates in pancreatic islets. The major protein component of islet amyloids is the glucomodulatory hormone islet amyloid polypeptide (IAPP). Islet amyloid fibrils are virtually always associated with several biomolecules, including apolipoprotein E, metals, glycosaminoglycans, and various lipids. IAPP amyloidogenesis has been originally perceived as a self-assembly homogeneous process in which the inherent aggregation propensity of the peptide and its local concentration constitute the major driving forces to fibrillization. However, over the last two decades, numerous studies have shown a prominent role of amyloid cofactors in IAPP fibrillogenesis associated with the etiology of type II diabetes. It is increasingly evident that the biochemical microenvironment in which IAPP amyloid formation occurs and the interactions of the polypeptide with various biomolecules not only modulate the rate and extent of aggregation, but could also remodel the amyloidogenesis process as well as the structure, toxicity, and stability of the resulting fibrils. PMID:26576436

  4. Computational approaches to the design and analysis of stability of polypeptide multilayer thin films

    NASA Astrophysics Data System (ADS)

    Zheng, Bin

    The focus of this research is the development of computational approaches to understanding the physical basis of layer-by-layer assembly (LBL), a key methodology of nanomanufacturing. The results provided detailed information on structure which cannot be obtained directly by experiments. The model systems chosen for study are polypeptide chains. Reasons for this are that polypeptides are no less polyelectrolytes than the more usual polyions, and one can control the primary structure of a polypeptide on a residue-by-residue basis using modern synthetic methods. Moreover, as peptides constitute one of the four major classes of biological macromolecules, research in this direction is expected to advance development of bionanotechnology. Polypeptide thin films are a type of new material, and there is great potential for applications in biocompatible implants, drug delivery, and other areas. A key consideration in polypeptide design for LBL is charge properties as a function of pH. This work presents a computational approach to identify structural motifs in amino acid sequence data and to minimize the immune response to polypeptides based on the structural motifs and demonstrate by experiments. This work also presents innovative molecular dynamics (MD) work on LBL. All-atom models have been used to investigate polypeptide LBL at the sub-molecular level. The peptide structures studied---homopolymers of lysine and of glutamic acid, and designed cysteine-containing peptides---correspond to ones for which experimental data have been obtained in the Haynie research laboratory. Simulations were carried out to study structural and dynamical properties of peptide models having some combination of parallel and anti-parallel beta sheets, as such structures are known to be formed by the indicated peptides in LBL films. The MD work suggests that hydrophobic interactions too play an important role in polypeptide LBL. Moreover, hydrogen bonding appears to be a consequence of

  5. 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.

  6. Urinary polypeptides related to collagen synthesis

    PubMed Central

    Krane, Stephen M.; Muñoz, Alberto J.; Harris, Edward D.

    1970-01-01

    Of the total urinary hydroxyproline in normal subjects and those with skeletal disorders, between 4 and 20% was nondialyzable. In some patients with Paget's disease of bone, hyperparathyroidism with osteitis fibrosa, hyperphosphatasia, and extensive fibrous dysplasia the total urinary hydroxyproline was sufficiently high to permit purification of this polypeptide hydroxyproline by gel filtration and ion exchange chromatography. The partially purified polypeptides had molecular weights between 4500 and 10,000 and amino acid compositions and physical properties resembling those of gelatin. The polypeptide fractions also contained neutral sugar and glucosamine. These fragments had been shown to be susceptible to cleavage by purified bacterial collagenase suggesting the presence of the sequence-Pro-X-Gly-Pro-Y-. After administration of proline-14C to patients with Paget's disease hydroxyproline-14C was excreted in the urine. The hydroxyproline-14C specific activity reached a peak in 2-4 hr and declined rapidly. The specific activity of the polypeptide (retentate) portion was severalfold greater than that of the raw urine and diffusate. When the labeled urines were subjected to gel filtration the hydroxyproline-14C fractions of highest molecular weight which were eluted first from the columns had the highest specific activities. Exposure of the hydroxyproline-14C-containing polypeptides to bacterial collagenase rendered them dialyzable. Four patients with hyperparathyroidism and osteitis fibrosa were studied before and after removal of a parathyroid adenoma, a period of transition from a predominance of bone collagen resorption to one of relatively increased bone collagen synthesis. The total urinary hydroxyproline fell rapidly after operation whereas the ratio of the polypeptide fraction to the total rose three- to fourfold. The results of these studies suggest that the urinary polypeptides represent fragments of collagen related to collagen synthesis. Changes in the

  7. Carbohydrate degrading polypeptide and uses thereof

    SciTech Connect

    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.

  8. Metal ion-dependent, reversible, protein filament formation by designed beta-roll polypeptides

    PubMed Central

    Scotter, Andrew J; Guo, Meng; Tomczak, Melanie M; Daley, Margaret E; Campbell, Robert L; Oko, Richard J; Bateman, David A; Chakrabartty, Avijit; Sykes, Brian D; Davies, Peter L

    2007-01-01

    Background A right-handed, calcium-dependent β-roll structure found in secreted proteases and repeat-in-toxin proteins was used as a template for the design of minimal, soluble, monomeric polypeptides that would fold in the presence of Ca2+. Two polypeptides were synthesised to contain two and four metal-binding sites, respectively, and exploit stacked tryptophan pairs to stabilise the fold and report on the conformational state of the polypeptide. Results Initial analysis of the two polypeptides in the presence of calcium suggested the polypeptides were disordered. The addition of lanthanum to these peptides caused aggregation. Upon further study by right angle light scattering and electron microscopy, the aggregates were identified as ordered protein filaments that required lanthanum to polymerize. These filaments could be disassembled by the addition of a chelating agent. A simple head-to-tail model is proposed for filament formation that explains the metal ion-dependency. The model is supported by the capping of one of the polypeptides with biotin, which disrupts filament formation and provides the ability to control the average length of the filaments. Conclusion Metal ion-dependent, reversible protein filament formation is demonstrated for two designed polypeptides. The polypeptides form filaments that are approximately 3 nm in diameter and several hundred nm in length. They are not amyloid-like in nature as demonstrated by their behaviour in the presence of congo red and thioflavin T. A capping strategy allows for the control of filament length and for potential applications including the "decoration" of a protein filament with various functional moieties. PMID:17908326

  9. Two small virus-specific polypeptides are produced during infection with Sindbis virus.

    PubMed Central

    Welch, W J; Sefton, B M

    1979-01-01

    We have identified and characterized two small virus-specific polypeptides which are produced during infection of cells with Sindbis virus, but which are not incorporated into the mature virion. The larger of these is a glycoprotein with an approximate molecular weight of 9,800 and is found predominantly in the medium of infected cells. Three independent lines of evidence demonstrate conclusively that this 9,800-dalton glycoprotein is produced during the proteolytic conversion of the precursor polypeptide, PE2, to the virion glycoprotein E2. This small glycoprotein is therefore analogous to the virion glycoprotein E3 of the very closely related alphavirus, Semliki Forest virus. The 9,800-dalton glycoprotein of Sindbis virus, unlike the E3 glycoprotein of Semliki Forest virus, is not, however, present in the viral particle. The other virus-specific polypeptide is 4,200 daltons in size, does not appear to be a glycoprotein, and is neither incorporated into the mature virus nor released into the culture medium. The gene for this small polypeptide is present in the viral 26S mRNA (the mRNA which encodes all the viral structural polypeptides) and appears to be located in the portion of the mRNA which encodes the two viral glycoproteins. The possibility that this 4,200-dalton polypeptide functions as a signal peptide during the synthesis of the viral membrane glycoproteins is discussed. Images PMID:448798

  10. 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

  11. Two polypeptide chains in yeast transcription factor tau interact with DNA

    SciTech Connect

    Gabrielsen, O.S.; Marzouki, N.; Ruet, A.; Sentenac, A.; Fromageot, P.

    1989-05-05

    Yeast transcription factor tau interacts with the A and B blocks of the intragenic promoter of tRNA genes. The structure of tau was investigated by identifying the polypeptide chains specifically complexed to the tRNA3Glu gene. Highly purified factor, obtained by an improved purification procedure, contained several polypeptide chains, four of which (Mr = 145,000, 135,000, 100,000 and 65,000) comigrated with tau-DNA complex by polyacrylamide gel electrophoresis. Antibodies raised against the 145- and 100-kDa components altered the migration of tau-DNA complexes in band shift assays and inhibited tRNA synthesis in a reconstituted transcription system. These components are immunologically unrelated proteins. By UV cross-linking to /sup 32/P-body-labeled tDNA followed by extensive DNase treatment, two polypeptides of the same size (145 and 100 kDa) were found to be radioactively labeled. Factor tau, therefore, appears to be a multisubunit DNA-binding protein with two distinct polypeptides contributing to DNA recognition. Limited proteolysis of tau generated a protease-resistant tau B (tau B) domain that binds solely to the B block. tau B-tDNA complexes were recognized by anti-145 IgG and contained a 120-kDa polypeptide that could originate from the 145-kDa component by proteolysis. These results strongly suggest that the 145-kDa polypeptide belongs to tau B and is responsible for B block binding.

  12. Stepwise assembling of polypeptide chain energy distributions.

    PubMed

    Jacchieri, S G

    2001-03-01

    The principles and application of conformational analysis software that makes use of a new algorithm are described. It is known that the existence of a local energy minimum in the energy landscape is in general related to the clustering of polypeptide chain conformations near that energy value or, in other words, to a high density of states. A criterion based on this principle is part of an algorithm employed to select subsets of polypeptide chain conformations in broad energy ranges. Chain fragments belonging to these subsets are then combined to build larger polypeptide chains and the corresponding energy distributions. The functionality of the various operations employed in the process is described and the FORTRAN 77 source code that defines the algorithm is listed. The methodology is illustrated with a calculation involving three chain fragments belonging to the cellular prion protein (PrP(C)). PMID:11219430

  13. 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.

  14. Anharmonic Theoretical Vibrational Spectroscopy of Polypeptides.

    PubMed

    Panek, Paweł T; Jacob, Christoph R

    2016-08-18

    Because of the size of polypeptides and proteins, the quantum-chemical prediction of their vibrational spectra presents an exceptionally challenging task. Here, we address one of these challenges, namely, the inclusion of anharmonicities. By performing the expansion of the potential energy surface in localized-mode coordinates instead of the normal-mode coordinates, it becomes possible to calculate anharmonic vibrational spectra of polypeptides efficiently and reliably. We apply this approach to calculate the infrared, Raman, and Raman optical activity spectra of helical alanine polypeptides consisting of up to 20 amino acids. We find that while anharmonicities do not alter the band shapes, simple scaling procedures cannot account for the different shifts found for the individual bands. This closes an important gap in theoretical vibrational spectroscopy by making it possible to quantify the anharmonic contributions and opens the door to a first-principles calculation of multidimensional vibrational spectra. PMID:27472016

  15. Conformational Instability of the Cholera Toxin A1 Polypeptide

    PubMed Central

    Pande, Abhay H.; Scaglione, Patricia; Taylor, Michael; Nemec, Kathleen N.; Tuthill, Summer; Moe, David; Holmes, Randall K.; Tatulian, Suren A.; Teter, Ken

    2007-01-01

    Summary Cholera toxin (CT) moves from the cell surface to the endoplasmic reticulum (ER) by vesicular transport. In the ER, the catalytic CTA1 subunit dissociates from the holotoxin and enters the cytosol by exploiting the quality control system of ER-associated degradation (ERAD). It is hypothesized that CTA1 triggers its ERAD-mediated translocation into the cytosol by masquerading as a misfolded protein, but the process by which CTA1 activates the ERAD system remains unknown. Here, we directly assess the thermal stability of the isolated CTA1 polypeptide by biophysical and biochemical methods and correlate its temperature-dependent conformational state with susceptibility to degradation by the 20S proteasome. Measurements with circular dichroism and fluorescence spectroscopy demonstrated that CTA1 is a thermally unstable protein with a disordered tertiary structure and a disturbed secondary structure at 37°C. A protease sensitivity assay likewise detected the temperature-induced loss of native CTA1 structure. This protease-sensitive conformation was not apparent when CTA1 remained covalently associated with the CTA2 subunit. Thermal instability in the dissociated CTA1 polypeptide could thus allow it to appear as a misfolded protein for ERAD-mediated export to the cytosol. In vitro, the disturbed conformation of CTA1 at 37°C rendered it susceptible to ubiquitin-independent degradation by the core 20S proteasome. In vivo, CTA1 was also susceptible to degradation by a ubiquitin-independent proteasomal mechanism. ADP-ribosylation factor 6, a cytosolic eukaryotic protein that enhances the enzymatic activity of CTA1, stabilized the heat-labile conformation of CTA1 and protected it from in vitro degradation by the 20S proteasome. Thermal instability in the reduced CTA1 polypeptide has not been reported before, yet both the translocation and degradation of CTA1 may depend upon this physical property. PMID:17976649

  16. 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

  17. [Interaction of sea amemone Heteractis crispa Kunitz type polypeptides with pain vanilloid receptor TRPV1: in silico investigation].

    PubMed

    Zelepuga, E A; Tabakmakher, V M; Chausova, V E; monastyrnaia, M M; Isaeva, M P; Kozlovskaia, É P

    2012-01-01

    Using methods of molecular biology we defined the structures of the 31 sea anemone Heteractis crispa genes encoding polypeptides which are structurally homologous to the Kunitz proteinase inhibitor family. Identified amino acid sequences have point residue substitutions, high degree of homology with sequences of known H. crispa Kunitz family members, and represent a combinatorial library of polypeptides. We generated their three-dimensional structures by homologous modeling methods. Analysis of their molecular electrostatic potential enabled us to divide given polypeptides into three clusters. One of them includes polypeptides APHC1, APHC2 and APHC3, which were earlier shown to possess a unique property of inhibiting of the pain vanilloid receptor TRPV1 in vitro and providing the analgesic effects in vivo in addition to their trypsin inhibitory activity. Molecular docking made possible establishing the spatial structure of the complexes, the nature of the polypeptides binding with TRPV1, as well as functionally important structural elements involved in the complex formation. Structural models have enabled us to propose a hypothesis contributing to understanding the APHC1-3 impact mechanism for the pain signals transduction by TRPV1: apparently, there is an increase of the receptor relaxation time resulted in binding of its two chains with the polypeptide molecule, which disrupt the functioning of the TRPV1 and leads to partial inhibition of signal transduction in electrophysiological experiments. PMID:22792722

  18. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

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

    2012-04-03

    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

    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.

  20. 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.

  1. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    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.

  2. Polypeptide from a cellulolytic fungus having cellulolytic enhancing activity

    DOEpatents

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

    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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

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

    DOEpatents

    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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  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 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.

  20. 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.

  1. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    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.

  2. Polypeptides having xylanase activity and polynucleotides encoding same

    DOEpatents

    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.

  3. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    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.

  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

    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.

  5. 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.

  6. Polypeptides having endoglucanase activity and polynucleotides encoding same

    DOEpatents

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

    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.

  7. 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.

  8. 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.

  9. 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

    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 xylanase activity and polynucleotides encoding same

    DOEpatents

    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 xylanase activity and polynucleotides encoding same

    SciTech Connect

    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.

  12. Polypeptides having endoglucanase activity and polynucleotides encoding same

    SciTech Connect

    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.

  13. 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.

  14. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    SciTech Connect

    Spodsberg, Nikolaj

    2015-11-17

    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.

  15. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    SciTech Connect

    Liu, Ye; Tang, Lan

    2015-11-20

    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.

  16. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    SciTech Connect

    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.

  17. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

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

    2014-09-16

    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.

  18. 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.

  19. 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.

  20. 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.

  1. Polypeptides having xylanase activity and polynucleotides encoding same

    SciTech Connect

    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.

  2. 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.

  3. 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.

  4. 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

  5. Role of Side-Chain Molecular Features in Tuning Lower Critical Solution Temperatures (LCSTs) of Oligoethylene Glycol Modified Polypeptides.

    PubMed

    Gharakhanian, Eric G; Deming, Timothy J

    2016-07-01

    A series of thermoresponsive polypeptides has been synthesized using a methodology that allowed facile adjustment of side-chain functional groups. The lower critical solution temperature (LCST) properties of these polymers in water were then evaluated relative to systematic molecular modifications in their side-chains. It was found that in addition to the number of ethylene glycol repeats in the side-chains, terminal and linker groups also have substantial and predictable effects on cloud point temperatures (Tcp). In particular, we found that the structure of these polypeptides allowed for inclusion of polar hydroxyl groups, which significantly increased their hydrophilicity and decreased the need to use long oligoethylene glycol repeats to obtain LCSTs. The thioether linkages in these polypeptides were found to provide an additional structural feature for reversible switching of both polypeptide conformation and thermoresponsive properties. PMID:27102972

  6. Synthesis and properties of chitosan/polypeptide bioconjugate composite

    NASA Astrophysics Data System (ADS)

    Wang, Jing; Liu, Changsheng; Wei, Jie; Chi, Ping; Lu, Xin; Yin, Min

    2007-03-01

    Adhesive polypeptide containing the key component of mussel adhesive protein was synthesized by ring-opening polymerization, and a hybrid material of the adhesive polypeptide and chitosan was prepared through the solution method. Some strong hydrogen bond interaction existed, but without the chemical bond between chitosan and polypeptide molecular in the composites, which was demonstrated by IR and XRD. Tensile strength and elongation-at-break of the composite increased with the increase of the polypeptide content. However, the mechanical properties decreased when the content of polypeptide was more than 2% in the composite; all in all, the mechanical properties of the composite were better than the pure chitosan. Furthermore, the introduction of polypeptide was beneficial in improving the hydrophilicity and cell affinity of the composite. The results indicated that the novel chitosan/polypeptide composite has excellent biocompatibility, which could be a scaffold material for cell culture in tissue engineering.

  7. 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.

  8. 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].

  9. Hemoglobin variants as models for investigation of dissociation of intact polypeptide chains by ESI tandem mass spectrometry

    SciTech Connect

    Light, K.J.; Loo, J.A.; Edmonds, C.G.; Smith, R.D.

    1991-06-01

    Electrospray ionization mass spectroscopy (ESI-MS) is rapidly becoming a practical biochemical tool for peptide and protein sequence analysis. The utility of ESI-MS is through use of Collisionally Activated Dissociation (ESI-CAD-MS). Human hemoglobin (Hb, {approximately}62 kDa) consists of four polypeptide chains and a prosthetic heme group. There are over 400 Hb variants, characterized by amino acid substitutions in either the alpha or beta polypeptide chains. We investigated ESI-CAD-MS as a tool for rapidly analyzing amino acid substitutions, using eight Hb beta chain variants. The approximate location of the modification can be deduced from comparison of the CAD mass spectra and observance of the mass shifts of the fragment ion containing the substitution. Fragmentation occurs preferentially at the amino terminus of proline residues. For most substitutions, differences in CAD mass spectra were not seen. 2 figs.

  10. Design of polypeptide-functionalized polystyrene microspheres.

    PubMed

    Bousquet, A; Perrier-Cornet, R; Ibarboure, E; Papon, E; Labrugère, C; Héroguez, V; Rodríguez-Hernández, J

    2008-07-01

    In this contribution, the principle of spontaneous surface segregation has been applied for the preparation of polypeptide-functionalized polystyrene microspheres. For that purpose, an amphiphilic diblock copolymer was introduced in the mixture styrene/divinylbenzene and polymerized using AIBN as initiator. During the polymerization, cross-linked particles were obtained in which the diblock copolymer was encapsulated. The amphiphilic diblock copolymers used throughout this study contain a hydrophilic polypeptide segment, either poly(L-lysine) or poly(L-glutamic acid) and a hydrophobic polystyrene block. After 4 h of polymerization, rather monodisperse particles with sizes of approximately 3-4 microm were obtained. Upon annealing in hot water, the hydrophilic polypeptides migrate to the interface, hence, either positively charged or neutral particles were obtained when poly(L-lysine) is revealed at the surface and exposed to acidic or basic pH, respectively. On the opposite, negatively charged particles were achieved in basic pH water by using poly(L-glutamic acid) as additive. The surface chemical composition was modified by changing the environment of the particles. Thus, exposure in toluene provoked a surface rearrangement, and due to its affinity, the polystyrene block reorients toward the interface. PMID:18517246