Molecular dynamics (MD) simulations of VIP and PACAP27.

abstract：:The presence of low pKa N-hydroxylamines is beneficial in peptide chemistry as they reduce some base-mediated side reactions. Here we evaluated the applicability and buffering capacity of Ethyl 2-cyano-2-(hydroxyimino) acetate (Oxyma) in the prevention of aspartimide/piperidide formation and Pro-based overcoupling and...

journal_title：Biopolymers

authors： Subirós-Funosas R,El-Faham A,Albericio F

更新日期：2012-01-01 00:00:00

abstract：:Depsipeptide analogues of peptide sequences can help in elucidating the role of specific hydrogen bonds in determining the conformation in peptides. The repeating pentapeptide and hexapeptide sequences of elastin have been suggested to contain a type II beta-turn with a 4----1 hydrogen bond. Depsipeptide analogues of ...

journal_title：Biopolymers

authors： Arad O,Goodman M

更新日期：1990-10-01 00:00:00

abstract：:A theoretical method is proposed to identify structural domains in proteins of known structures. It is based on the distribution of the local axes of the polypeptide chain. In particular, a statistical analysis is applied to the contributions of the local axes to the absolute writhing number, a topological property of...

journal_title：Biopolymers

authors： Anselmi C,Bocchinfuso G,Scipioni A,De Santis P

更新日期：2001-02-01 00:00:00

abstract：:The DNA interaction of derivatives of ellipticine with heterocyclic ring systems with three, four, or five rings and a dimethylaminoethyl side chain was studied. Optical spectroscopy of drug complexes with calf thymus DNA, poly[(dA-dT).(dA-dT)], or poly[(dG-dC).(dG-dC)] showed a 10 nm bathochromic shift of the light a...

journal_title：Biopolymers

authors： Behravan G,Leijon M,Sehlstedt U,Nordén B,Vallberg H,Bergman J,Gräslund A

更新日期：1994-05-01 00:00:00

abstract：:Cellulose acetate (DS = 2.45) was extensively investigated by Circular Dichroism (CD) in acetonitrile and dioxane. We found great differences between the CD spectra of a 1 wt % acetonitrile solution and the corresponding dioxane solution of cellulose acetate (CA) indicating that the macromolecules exist in those solut...

journal_title：Biopolymers

authors： Meissner D,Einfeldt J,Schareina T

更新日期：1999-08-01 00:00:00

abstract：:The folding of membrane proteins was addressed using outer membrane protein porin from the soil bacterium Paracoccus denitrificans (P. den.). IR spectroscopy and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis were used to probe the effect of mutagenesis on the thermal stability of the pr...

journal_title：Biopolymers

authors： Sukumaran S,Zscherp C,Mäntele W

更新日期：2004-05-01 00:00:00

abstract：:Because of its involvement in HIV entry, the chemokine receptor CXCR4 is an attractive target for antiretroviral drugs. Despite the large number of CXCR4 inhibitors studied, the 3D pharmacophore for binding to CXCR4 remains elusive, mainly as a result of conformational flexibility inherent in the identified ligands. I...

journal_title：Biopolymers

authors： Våbenø J,Nikiforovich GV,Marshall GR

更新日期：2006-01-01 00:00:00

abstract：:The Lifson-Roig Model (LRM) and all its variants describe the α-helix to coil transition in terms of additive component-free energies within a free energy decomposition scheme, and these contributions are interpreted through sequence-context dependent nucleation and propagation parameters. Although this phenomenologic...

journal_title：Biopolymers

authors： Wood GG,Clinkenbeard DA,Jacobs DJ

更新日期：2011-04-01 00:00:00

abstract：:Interactions between biological macromolecules have characteristic values of affinity and specificity that are set according to the biological function that is served by the interaction in the organism. Here we examine the molecular mechanisms that are used to achieve the required values of affinity and specificity in...

journal_title：Biopolymers

authors： Szwajkajzer D,Carey J

更新日期：1997-01-01 00:00:00

abstract：:The ion atmosphere created by monovalent (Na(+) ) or divalent (Mg(2+) ) cations surrounding a B-form DNA duplex were examined using atomistic molecular dynamics (MD) simulations and the nonlinear Poisson-Boltzmann (PB) equation. The ion distributions predicted by the two methods were compared using plots of radial and...

journal_title：Biopolymers

authors： Robbins TJ,Ziebarth JD,Wang Y

更新日期：2014-08-01 00:00:00

abstract：:Bovine carbonmonoxy hemoglobin investigated with light scattering studies is found to dissociate from its native tetramer structure into dimers and monomers. The values of the hydrated tetramer radius, RT = 32.1 A, and the fractional dissociation vs pH, have been obtained at different ionic strengths from the autocorr...

journal_title：Biopolymers

authors： Lunelli L,Zuliani P,Baldini G

更新日期：1994-06-01 00:00:00

abstract：:The oxidation of methionine to methionine sulfoxide both in vivo and in vitro can lead to the loss of biological activity in a variety of proteins. This loss of activity can be reversed by an enzyme called methionine sulfoxide reductase. The gene for this enzyme has been cloned and sequenced from a variety of prokaryo...

journal_title：Biopolymers

authors： Brot N,Weissbach H

更新日期：2000-01-01 00:00:00

abstract：:Synthetic model membrane-interactive peptides--both of natural and designed sequence--have become convenient and systematic tools for determination of how the membrane-spanning segments within integral membrane proteins confer protein structure and biology. Conformational studies on these peptides demonstrate that the...

journal_title：Biopolymers

authors： Deber CM,Li SC

更新日期：1995-01-01 00:00:00

abstract：:A novel nucleic acid model using peptide ribonucleic acid (PRNA), which contains 5'-amino-5'-deoxypyrimidine ribonucleoside as a recognition site for nucleic acids, has been designed, synthesized and applied to the external reversible control of recognition behavior of the complementary polynucleotide through the orie...

journal_title：Biopolymers

authors： Wada T,Sato H,Inoue Y

更新日期：2004-01-01 00:00:00

abstract：:For the controlled synthesis of even the simplest dipeptide, the N(alpha)-amino group of one of the amino acids and the C-terminal carboxyl group of the other should both be blocked with suitable protecting groups. Formation of the desired amide bond can now occur upon activation of the free carboxyl group. After coup...

journal_title：Biopolymers

authors： Albericio F

更新日期：2000-01-01 00:00:00

abstract：:The various motifs of RNA molecules are closely related to their structural and functional properties. To better understand the nature and distributions of such structural motifs (i.e., paired and unpaired bases in stems, junctions, hairpin loops, bulges, and internal loops) and uncover characteristic features, we ana...

journal_title：Biopolymers

authors： Zorn J,Gan HH,Shiffeldrim N,Schlick T

更新日期：2004-02-15 00:00:00

abstract：:Neurokinins and their receptors are a complex system consisting of at least three endogenous agents--substance P (SP), neurokinin A (NKA), and neurokinin B (NKB)--and their corresponding receptor types, respectively, NK-1, NK-2, and NK-3. Investigations on receptors have been made using sensitive and fairly selective ...

journal_title：Biopolymers

authors： Regoli D,Dion S,Rhaleb NE,Rouissi N,Tousignant C,Jukic D,D'Orleans-Juste P,Drapeau G

更新日期：1989-01-01 00:00:00

abstract：:Hydrophobicity has proven to be an extremely useful parameter in small molecule drug discovery programmes given that it can be used as a predictive tool to enable rational design. For larger molecules, including peptoids, where folding is possible, the situation is more complicated and the average hydrophobicity (as d...

journal_title：Biopolymers

authors： Bolt HL,Williams CEJ,Brooks RV,Zuckermann RN,Cobb SL,Bromley EHC

更新日期：2017-07-01 00:00:00

abstract：:The photophysics of Trp-containing peptides is extremely affected by the position of the indole ring with respect to substituents. In this work an unusual temperature fluorescence quenching behavior is presented. The N-tryptophan terminal peptides (N-Trp) show an increase of the static emission intensity as rising the...

journal_title：Biopolymers

authors： Brancaleon L,Crippa PR,Diemmi D

更新日期：1995-12-01 00:00:00

abstract：:RADA-16-I is a self-assembling peptide which forms biocompatible fibrils and hydrogels. We used molecular dynamics simulations, atomic-force microscopy, NMR spectroscopy, and thioflavin T binding assay to examine size, structure, and morphology of RADA-16-I aggregates. We used the native form of RADA-16-I (H-(ArgAlaAs...

journal_title：Biopolymers

authors： Bagrov D,Gazizova Y,Podgorsky V,Udovichenko I,Danilkovich A,Prusakov K,Klinov D

更新日期：2016-01-01 00:00:00

abstract：:A suite of FORTRAN programs, PREF, is described for calculating preference functions from the data base of known protein structures and for comparing smoothed profiles of sequence-dependent preferences in proteins of unknown structure. Amino acid preferences for a secondary structure are considered as functions of a s...

journal_title：Biopolymers

authors： Juretić D,Lee B,Trinajstić N,Williams RW

更新日期：1993-02-01 00:00:00

abstract：:A natural rubber was identified and characterized for the first time in the latex of the perennial Mediterranean shrub Euphorbia characias. Four different methods, i.e., acetone, acetic acid, trichloroacetic acid, and Triton® X-100, followed by successive treatments with cyclohexane/ethanol, were employed to extract t...

journal_title：Biopolymers

authors： Spanò D,Pintus F,Mascia C,Scorciapino MA,Casu M,Floris G,Medda R

更新日期：2012-08-01 00:00:00

abstract：:Interactions between the diketopiperazine cyclo-alanylglycine and four fluorinated alcohols in water-fluoroalcohol mixtures were examined by (1)H[(19)F] intermolecular nuclear Overhauser effects (NOE) experiments. The alcohols studied were trifluoroethanol, hexafluoroacetone trihydrate, 1,1,1,3,3,3-hexafluoroisopropan...

journal_title：Biopolymers

authors： Strickler MA,Gerig JT

更新日期：2002-08-15 00:00:00

abstract：:Myosins are a large family of molecular motors that use the common P-loop, Switch 1 and Switch 2 nucleotide binding motifs to recognize ATP, to create a catalytic site than can efficiently hydrolyze ATP and to communicate the state of the nucleotide pocket to other allosteric binding sites on myosin. The energy of ATP...

journal_title：Biopolymers

authors： Geeves MA

更新日期：2016-08-01 00:00:00

abstract：:Fe(III)-Mimochrome VI (MC6) is a recently reported artificial heme-peptide conjugate system with a high peroxidase-like activity. By design, its structure features a five-coordinated Fe(III)-deuteroporphyrin active site, embedded in a compact α-helix-heme-α-helix "sandwich" motif. Up to now, no detailed MC6 structural...

journal_title：Biopolymers

authors： Perrella F,Raucci U,Chiariello MG,Chino M,Maglio O,Lombardi A,Rega N

更新日期：2018-08-01 00:00:00

abstract：:Previous studies have demonstrated that His 12 plays a major role in the pH-dependent stability of the helix formed by the isolated C-peptide (residues 1-13 of ribonuclease A). Here, amino acid replacement experiments show that His 12+ stabilizes the C-peptide helix chiefly by interacting with Phe 8. The Phe 8 ... His...

journal_title：Biopolymers

authors： Shoemaker KR,Fairman R,Schultz DA,Robertson AD,York EJ,Stewart JM,Baldwin RL

更新日期：1990-01-01 00:00:00

abstract：:To validate the existing hypothesis put forward by Navarro et al., we performed single crystal X-ray diffraction structural analysis of a designed model peptide incorporating an unsubstituted achiral γ-aminobutyric acid: Boc-Pro-γ-Abu-OH (1) lacking C-terminal amide group. The analysis established existence of an over...

journal_title：Biopolymers

authors： Kumar N,Venugopalan P,Kishore R

更新日期：2010-11-01 00:00:00

abstract：:Serine palmitoyltransferase (SPT) catalyses the first step in the de novo biosynthesis of sphingolipids (SLs). It uses a decarboxylative Claisen-like condensation reaction to couple L-serine with palmitoyl-CoA to generate a long-chain base product, 3-ketodihydrosphingosine. SLs are produced by mammals, plants, yeast, ...

journal_title：Biopolymers

authors： Raman MC,Johnson KA,Clarke DJ,Naismith JH,Campopiano DJ

更新日期：2010-09-01 00:00:00

abstract：:The comprehensive structural analysis reported herein of eight N-glycopeptides, in three different solvents, is based on quantitative CD experiments, homonuclear nuclear Overhauser effect measurements, and molecular dynamics (MD) calculations. Although several orientations of the two amide planes attached to the carbo...

journal_title：Biopolymers

authors： Perczel A,Kollát E,Hollósi M,Fasman GD

更新日期：1993-04-01 00:00:00

abstract：:Amphipathic peptides composed of alternating polar and nonpolar residues have a strong tendency to self-assemble into one-dimensional, amyloid-like fibril structures. Fibrils derived from peptides of general (XZXZ)(n) sequence in which X is hydrophobic and Z is hydrophilic adopt a putative β-sheet bilayer. The bilayer...

journal_title：Biopolymers

authors： Bowerman CJ,Nilsson BL

更新日期：2012-01-01 00:00:00