Insight into the stability of cross-beta amyloid fibril from molecular dynamics simulation.

abstract：:Bleomycins A(2) and B(2) are the two active components in the antineoplastic drug Blenoxane. DNA is targeted by this drug in cancer cells and the mode of action of this drug involves DNA binding. Ambiguity exists as to the way in which bleomycin binds to DNA. Raman spectroscopy was used to examine both calf thymus DNA...

journal_title：Biopolymers

authors： Rajani C,Kincaid JR,Petering DH

更新日期：1999-01-01 00:00:00

abstract：:The solution conformations of a hybrid sequence peptide related to the bee venom peptide apamin have been determined using two-dimensional 1H-nmr. Apamin is an 18 amino acid peptide containing a C-terminal helix that is stabilized by two disulfide bonds. The deletion of one residue (K4) of the N-terminal "scaffold" re...

journal_title：Biopolymers

authors： Volkman BF,Wemmer DE

更新日期：1997-04-05 00:00:00

abstract：:alpha,beta-Dehydro amino acid residues are known to constrain the peptide backbone to the beta-bend conformation. A pentapeptide containing only one alpha,beta-dehydrophenylalanine (delta Phe) residue has been synthesized and crystallized, and its solid state conformation has been determined. The pentapeptide Boc-Leu-...

journal_title：Biopolymers

authors： Rajashankar KR,Ramakumar S,Mal TK,Jain RM,Chauhan VS

更新日期：1995-02-01 00:00:00

abstract：:The self-cleaving hepatitis delta virus (HDV) ribozyme is essential for the replication of HDV, a liver disease causing pathogen in humans. The catalytically critical nucleotide C75 of the ribozyme is buttressed by a trefoil turn pivoting around an extruded G76. In all available crystal structures, the conformation of...

journal_title：Biopolymers

authors： Sefcikova J,Krasovska MV,Spacková N,Sponer J,Walter NG

更新日期：2007-04-05 00:00:00

abstract：:H-Pro-Pro-Asp-NH2 is a highly active and selective catalyst for asymmetric aldol reactions. Here, the versatility of H-Pro-Pro-Asp-NH2 has been further improved by immobilization on a solid support and functionalization with a short polyethylene glycol linker at the C-terminus. The development, synthesis, and the cata...

journal_title：Biopolymers

authors： Revell JD,Gantenbein D,Krattiger P,Wennemers H

更新日期：2006-01-01 00:00:00

abstract：:Fourteen tryptic peptides and nine intermediates were identified as products of trypsin digestion of reduced and S-3-(trimethylated amino) propylated lysozyme. Kinetics of the appearance and disappearance of these products were observed by monitoring the peak areas on the chromatogram. In spite of the complicated reac...

journal_title：Biopolymers

authors： Noda Y,Fujiwara K,Yamamoto K,Fukuno T,Segawa S

更新日期：1994-02-01 00:00:00

abstract：:The results are presented for the deconvolution of IR spectra of disaccharides and polysaccharides with alpha and beta configurations of the 1 --> 4 glycosidic linkage (maltose, cellobiose, amylose, and cellulose), as well as of their corresponding monosaccharides (alpha- and beta-D-glucose) in the 1200-920 cm(-1) fre...

journal_title：Biopolymers

authors： Nikonenko NA,Buslov DK,Sushko NI,Zhbankov RG

更新日期：2000-01-01 00:00:00

abstract：:The chemical synthesis and x-ray crystal structure analysis of a model peptide incorporating a conformationally adaptable unsubstituted beta-Ala residue: Boc-beta-Ala-Acc6-OCH3 (C16H28N2O5, molecular weight = 328.41; 1) has been described. The peptide crystallized in the space group P2(1)2(1)2(1) a = 8.537 (3), b = 8....

journal_title：Biopolymers

authors： Thakur AK,Kishore R

更新日期：2000-05-01 00:00:00

abstract：:Combinatorial library composed of rigid rod-like peptides with a triple-helical scaffold was constructed. The component peptides were designed to have various combinations of basic and neutral (or hydrophobic) amino acid residues based on collagen-like (Gly-Pro-Yaa)-repeating sequences, inspired from the basic and amp...

journal_title：Biopolymers

authors： Masuda R,Kudo M,Dazai Y,Mima T,Koide T

更新日期：2016-11-04 00:00:00

abstract：:Structural formation of segments plays pivotal roles in protein folding and stability, but how the segment influences the structural ensemble remains elusive. We engineered two hybrid proteins by replacing the central helical segment of immunoglobulin G binding domain of streptococcal protein G with an alpha-helix or ...

journal_title：Biopolymers

authors： Du HN,Zhang TY,Chang YG,Lin DH,Hu HY

更新日期：2005-09-01 00:00:00

abstract：:The secondary structure of a 38 kDa core protein from pig skin proteodermatan sulfate (PDS), was investigated in solution using CD and Fourier transform (FT) ir spectroscopy. Both techniques generally have provided complementary data on the secondary structures of proteins. CD spectral analysis has shown that the core...

journal_title：Biopolymers

authors： Renugopalakrishnan V,Damle SP,Horowitz PM,Moore S,Hutson TB,Gregory JD

更新日期：1989-11-01 00:00:00

abstract：:Two-dimensional nmr spectra [correlated spectroscopy (COSY), homonuclear Hartmann-Hahn (HOHAHA), nuclear Overhauser effect spectroscopy (NOESY)] have been observed for cross-linked lysozyme, a chemically modified lysozyme derivative with an extra ester cross-link between residues E35 and W108. Eight shifted cross-peak...

journal_title：Biopolymers

authors： Noda Y,Fukuda Y,Segawa S

更新日期：1997-02-01 00:00:00

abstract：:A method is presented for determining the concentrations of peptides and proteins having isodichroic points near 203 nm. The existence of an isodichroic point for a given substance indicates a local two-state (alpha-helix, random coil) population. The mean residue ellipticity at the isodichroic point, [theta lambda i]...

journal_title：Biopolymers

authors： Holtzer ME,Holtzer A

更新日期：1992-12-01 00:00:00

abstract：:The formation mechanism of an alanine-based peptide has been studied by all-atom molecular dynamics simulations with a recently developed all-atom point-charge force field and the Generalize Born continuum solvent model at an effective salt concentration of 0.2M. Thirty-two simulations were conducted. Each simulation ...

journal_title：Biopolymers

authors： Chowdhury S,Zhang W,Wu C,Xiong G,Duan Y

更新日期：2003-01-01 00:00:00

abstract：:In a seminal paper, Pakula and Sauer (Nature, 1990, 344, 363-364) demonstrated that the increase in side-chain hydrophobicity has a reverse relationship with protein stability. We have addressed this problem with several examples of mutants that span at different locations in protein structure based on secondary struc...

journal_title：Biopolymers

authors： Gromiha MM

更新日期：2009-07-01 00:00:00

abstract：:Translational GTPases (trGTPases) play key roles in facilitating protein synthesis on the ribosome. Despite the high degree of evolutionary conservation in the sequences of their GTP-binding domains, the rates of GTP hydrolysis and nucleotide exchange vary broadly between different trGTPases. EF-Tu, one of the best-ch...

journal_title：Biopolymers

authors： Maracci C,Rodnina MV

更新日期：2016-08-01 00:00:00

abstract：:Alpha-synuclein (alpha-Syn) has been identified as a component of intracellular fibrillar deposits in Parkinson's disease. Though the real pathogenesis is still unknown, many investigations have revealed that conformational alteration and fibril formation of alpha-Syn protein have an important role in causing the dise...

journal_title：Biopolymers

authors： Lin XJ,Zhang F,Xie YY,Bao WJ,He JH,Hu HY

更新日期：2006-10-15 00:00:00

abstract：:Optical melting curves of 22 DNA dumbbells with the 16-base pair duplex sequence 5'-G-C-A-T-C-A-T-C-G-A-T-G-A-T-G-C-3' linked on both ends by single-strand loops of A, or C, sequences (iota = 2, 3, 4, 6, 8, 10, 14). T sequences (iota = 2, 3, 4, 6, 8, 10), and G iota sequences (iota = 2, 4) were measured in phosphate b...

journal_title：Biopolymers

authors： Paner TM,Riccelli PV,Owczarzy R,Benight AS

更新日期：1996-12-01 00:00:00

abstract：:The characterization of elastic properties of biopolymers is crucial to understand many molecular reactions determined by conformational bending fluctuations of the polymer. Direct measurement of such elastic properties using single-molecule methods is usually hindered by the intrinsic tendency of such biopolymers to ...

journal_title：Biopolymers

authors： Alemany A,Ritort F

更新日期：2014-12-01 00:00:00

abstract：:The 32-residue leucine zipper subsequence, called here Jun-lz, associates in benign media to form a parallel two-stranded coiled coil. Studies are reported of its thermal unfolding/folding transition by circular dichroism (CD) on samples of natural isotopic abundance and by both equilibrium and spin inversion transfer...

journal_title：Biopolymers

authors： d'Avignon DA,Bretthorst GL,Holtzer ME,Schwarz KA,Angeletti RH,Mints L,Holtzer A

更新日期：2006-10-15 00:00:00

abstract：:Physiological properties of soluble antigen-antibody (Ag-Ab) complexes depend in part on the size of the complexes. In previous work, the size distribution and structure of model Ag-Ab complexes were determined by electron microscopy. In this study, we used constrained regularization analysis of quasi-elastic light sc...

journal_title：Biopolymers

authors： Murphy RM,Yarmush ML,Colton CK

更新日期：1991-10-01 00:00:00

abstract：:Over the past decade a large number of studies have focused attention on the role of nucleosomes as negative and positive regulators of specific nuclear functions. Due to the lack of an analytical method to determine the higher order conformation of the nucleosomal arrays that encompass specific genetic loci (e.g., pr...

journal_title：Biopolymers

authors： Georgel PT,Hansen JC

更新日期：2003-04-01 00:00:00

abstract：:This work theoretically investigates the mechanical properties of a novel silk-derived biopolymer as polymerized in silico from sericin and elastin-like monomers. Molecular Dynamics simulations and Steered Molecular Dynamics were the principal computational methods used, the latter of which applies an external force o...

journal_title：Biopolymers

authors： Golas EI,Czaplewski C

更新日期：2014-09-01 00:00:00

abstract：:Although the structural analysis of membrane proteins is advancing, an understanding of the basic principles that underlie their folding and assembly remains limited because of the high insolubility intrinsic to these molecules and concomitant challenges in obtaining crystals. Fortunately, from an experimental standpo...

journal_title：Biopolymers

authors： Rath A,Johnson RM,Deber CM

更新日期：2007-01-01 00:00:00

abstract：:It was shown earlier, from database analysis, model building studies, and molecular dynamics simulations that formation of cross-strand bifurcated or Extra Watson-Crick hydrogen (EWC) bonds between successive base pairs may lead to extra rigidity to DNA double helices of certain sequences. The strengths of these hydro...

journal_title：Biopolymers

authors： Bandyopadhyay D,Bhattacharyya D

更新日期：2006-10-15 00:00:00

abstract：:Guanine-rich sequences are able to form quadruplexes consisting of G-quartet structural units. Quadruplexes play an important role in the regulation of gene expression and have therapeutic and biotechnological potential. The HIV-1 integrase inhibitor, (GGGT)4 , and its variants demonstrate unusually high thermal stabi...

journal_title：Biopolymers

authors： Lomidze L,Kelley S,Gogichaishvili S,Metreveli N,Musier-Forsyth K,Kankia B

更新日期：2016-11-01 00:00:00

abstract：:The degradation of elastin, the insoluble biopolymer of tropoelastin, can lead to the production of small peptides. These elastin-derived peptides (EDPs) are playing a key role in cellular behavior within the extracellular matrix, showing a great variety of biological effects such as chemotaxis, stimulation of cell pr...

journal_title：Biopolymers

authors： Moroy G,Alix AJ,Héry-Huynh S

更新日期：2005-07-01 00:00:00

abstract：:The discovery of extreme halophile microorganisms in the Dead Sea, which are specifically dependent on a multimolar salt environment to survive, stimulated major developments in biology and physical chemistry. The minireview focuses on the molecular level. After a brief introduction to the history of halophile studies...

journal_title：Biopolymers

authors： Zaccai G

更新日期：2013-04-01 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

abstract：:The creation of peptide libraries by site-selective modification of a few peptide substrates would increase the efficiency of discovery processes, but still is a real synthetic challenge. The site-selective modification of small peptides at serine or threonine residues, by using a short scission-addition procedure, al...

journal_title：Biopolymers

authors： Romero-Estudillo I,Saavedra C,Boto A,Álvarez E

更新日期：2015-09-01 00:00:00