Automatic annotation of BIND molecular interactions from three-dimensional structures.

abstract：:A water-insoluble polysaccharide (TM8) was isolated from sclerotium of Pleurotus tuber-regium by extraction with 0.5M NaOH aqueous solutions at 120 degrees C. Its chemical structure was confirmed by infrared, high performance liquid chromatography, gas chromatography, and (13)C NMR in dimethylsulfoxide (DMSO) to be co...

journal_title：Biopolymers

authors： Zhang L,Zhang M,Dong J,Guo J,Song Y,Cheung PC

更新日期：2001-11-01 00:00:00

abstract：:The pharmacological therapy for gastrointestinal (GI) diseases, such as inflammatory bowel diseases, continues to present challenges in targeting efficacy. The need for maximal local drug exposure at the inflamed regions of the GI tract has led research to focus on a disease-targeted drug delivery approach. Smart nano...

journal_title：Biopolymers

authors： Bertoni S,Machness A,Tiboni M,Bártolo R,Santos HA

更新日期：2020-01-01 00:00:00

abstract：:Fourier transform IR (FTIR) spectroscopy has been successfully applied in recent years to examine the functional and structural properties of the membrane protein rhodopsin, a prototype G protein coupled receptor. Unlike UV-visible spectroscopy, FTIR spectroscopy is structurally sensitive. It may give us both global i...

journal_title：Biopolymers

authors： Vogel R,Siebert F

更新日期：2003-01-01 00:00:00

abstract：:While end capping in alpha-helices is well understood, the concept of capping a beta-hairpin is a relatively recent development; to date, favorable Coulombic interactions are the only example of sidechains at the termini influencing the overall stability of a beta-hairpin. While cross-strand hydrophobic residues gener...

journal_title：Biopolymers

authors： Eidenschink L,Crabbe E,Andersen NH

更新日期：2009-07-01 00:00:00

abstract：:The Electrostatically Driven Monte Carlo (EDMC) method was applied in a study of a decamer of glycine whose conformational behavior is described by the Empirical Conformational Energy Program for Peptides (ECEPP/2) potential energy model. When free neutral end groups were used, it was found that conformations that wer...

journal_title：Biopolymers

authors： Ripoll DR,Vásquez MJ,Scheraga HA

更新日期：1991-02-15 00:00:00

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：:Calculations of the normal mode spectrum of a netropsin-DNA complex, an isolated DNA helix of the same sequence, and a free netropsin molecule were carried out and compared with observations. We find that the frequency of modes of the complex that are primarily vibrations localized to the helix are relatively unchange...

journal_title：Biopolymers

authors： Chen YZ,Prohofsky EW

更新日期：1995-06-01 00:00:00

abstract：:Substance P, one of the mammalian tachykinins, is known to interact strongly with lipid bilayers and this interaction may play a role in the receptor-peptide recognition process. The conformation of substance P bound to vesicles consisting of perdeuterated phosphatidylcholine has been investigated by means of two-dime...

journal_title：Biopolymers

authors： Augé S,Bersch B,Tropis M,Milon A

更新日期：2000-10-15 00:00:00

abstract：:Although several models have been proposed for the interaction of collagen with gelatinase-A (matrix metalloproteinases-2 (MMP-2)), the extensive role of each domain of gelatinase A in hydrolyzing the collagens with and without interruptions is still elusive. Molecular docking, molecular dynamics (MD) simulation, norm...

journal_title：Biopolymers

authors： Azhagiya Singam ER,Rajapandian V,Subramanian V

更新日期：2014-07-01 00:00:00

abstract：:Study of model beta-hairpin peptides allows for better understanding of the factors involved in the formation of beta-sheet secondary structure in proteins. It is known that turn sequence, sidechain-sidechain interactions, interstrand hydrogen bonding, and beta-sheet propensity of residues are all important for beta-h...

journal_title：Biopolymers

authors： Riemen AJ,Waters ML

更新日期：2008-01-01 00:00:00

abstract：:A large number of potent and selective therapeutic agents, useful for the treatment of several diseases, have been isolated from natural sources. For example, the most active thrombin inhibitors are those secreted by the salivary glands of leeches. One peculiar feature of these agents is the lack of any significant in...

journal_title：Biopolymers

authors： Lombardi A,De Simone G,Galdiero S,Staiano N,Nastri F,Pavone V

更新日期：1999-01-01 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：:While our understanding of the folding and structure of water-soluble proteins has progressed to the point where they can be artificially designed and produced from first principles, there has been only limited work toward the de novo design of membrane proteins. Such studies have been hindered in large part due to th...

journal_title：Biopolymers

authors： Tulumello DV,Johnson RM,Isupov I,Deber CM

更新日期：2012-01-01 00:00:00

abstract：:The enhanced nucleophilicity and redox sensitivity of the thiol group renders cysteine residues susceptible to numerous electrophilic and oxidative post-translational modifications to form disulfides, sulfenic acids, nitrosothiols, and lipid-modified species. Outside of these well-characterized modifications of cystei...

journal_title：Biopolymers

authors： Shannon DA,Weerapana E

更新日期：2014-02-01 00:00:00

abstract：:The existence of an "RNA world" as an early step in the history of life increases the interest for the characterization of these biomolecules. The hairpin ribozyme studied here is a self-cleaving/ligating motif found in the minus strand of the satellite RNA associated with Tobacco ringspot virus. Surface-enhanced Rama...

journal_title：Biopolymers

authors： Percot A,Lecomte S,Vergne J,Maurel MC

更新日期：2009-05-01 00:00:00

abstract：:The spectroscopic properties of syringomycin E, an antibiotic lipodepsinonapeptide associated with pathological states in plants, have been investigated by uv absorbance and CD spectroscopies, and by the synthesis of relevant model compounds. Initial studies [E. Vaillo, A. Ballio, P. L. Luisi, and R. M. Thomas (1990) ...

journal_title：Biopolymers

authors： Vaillo E,Ballio A,Luisi PL,Thomas RM

更新日期：1992-10-01 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：:Structural data produced by a 2-ns molecular dynamics (MD) simulation on Geobacillus alanine racemase (AlaR; PDB: 1SFT) was used to study hydration around the two AlaR active sites. AlaR is a crucial enzyme for bacterial cell wall biosynthesis. It has been shown previously that the potency of an inhibitor can be incre...

journal_title：Biopolymers

authors： Huang HC,Jupiter D,Qiu M,Briggs JM,Vanburen V

更新日期：2008-03-01 00:00:00

abstract：:An electron paramagnetic resonance (EPR) study was performed for potato and wheat starch containing Cu2+ ions as a paramagnetic probe. Distribution of water in the starch granules as well as the interactions between the copper and starch matrix of different crystalline structures were determined. EPR spectra of the na...

journal_title：Biopolymers

authors： Łabanowska M,Bidzińska E,Dyrek K,Szymońska J

更新日期：2006-08-15 00:00:00

abstract：:Using a variety of spectroscopic techniques, a number of molecular functionalities have been studied in relation to the adsorption process of proteins to air-water interfaces. While ellipsometry and drop tensiometry are used to derive information on adsorbed amount and exerted surface pressure, external reflection cir...

journal_title：Biopolymers

authors： de Jongh HH,Kosters HA,Kudryashova E,Meinders MB,Trofimova D,Wierenga PA

更新日期：2004-05-01 00:00:00

abstract：:In the first two papers of this series, the tools necessary to evaluate substrate ring deformations were developed, and then the modeling of short amylose fragments (maltotriose and maltopentaose) inside the catalytic site of barley alpha-amylase was performed. In this third paper, this docking has been extended to th...

journal_title：Biopolymers

authors： André G,Buléon A,Haser R,Tran V

更新日期：1999-12-01 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：:A Monte Carlo method has been developed for generating the conformations of short single-stranded DNAs from arbitrary starting states. The chain conformers are constructed from energetically favorable arrangements of the constituent mononucleotides. Minimum energy states of individual dinucleotide monophosphate molecu...

journal_title：Biopolymers

authors： Erie DA,Breslauer KJ,Olson WK

更新日期：1993-01-01 00:00:00

abstract：:The use of alpha,alpha-disubstituted amino acids represents a valuable strategy to exercise conformational control in peptides. Incorporation of the nonstereogenic alpha-aminoisobutyryl-glycyl (Aib-Gly) dipeptidyl sequence into i+1 and i+2 positions of an acyclic peptide sequence, originally designed and investigated ...

journal_title：Biopolymers

authors： Masterson LR,Etienne MA,Porcelli F,Barany G,Hammer RP,Veglia G

更新日期：2007-01-01 00:00:00

abstract：:The 13C off-resonance rotating frame spin-lattice relaxation technique is applicable to the study of protein rotational diffusion behavior in a variety of experimental situations. The original formalism of James and co-workers (1978) (J. Amer. Chem. Soc. 100, 3590-3594) was constrained by the assumption of random isot...

journal_title：Biopolymers

authors： Morgan CF,Schleich T,Caines GH,Michael D

更新日期：1990-02-15 00:00:00

abstract：:Despite detailed knowledge of the overall structural changes and stoichiometries of surfactant binding, little is known about which protein regions constitute the preferred sites of attack for initial unfolding. Here we have exposed three proteins to limited proteolysis at anionic (SDS) and cationic (DTAC) surfactant ...

journal_title：Biopolymers

authors： Hansen JH,Petersen SV,Andersen KK,Enghild JJ,Damhus T,Otzen D

更新日期：2009-03-01 00:00:00

abstract：:Peptide-bond modification via N-hydroxylation has been explored as a strategy for metal coordination to induce conformational rigidity and orient side chains for specific molecular recognition. N-Hydroxyamides were prepared by reacting N-benzyloxyamino acid esters or amides with Fmoc-AA-Cl/AgCN (Fmoc: 9-fluorenylmetho...

journal_title：Biopolymers

authors： Ye Y,Liu M,Kao JL,Marshall GR

更新日期：2003-01-01 00:00:00

abstract：:The second derivative FTIR study of heat-induced and pressure-assisted cold-induced changes in the secondary structure of bovine alpha-lactalbumin was carried out for native holoprotein and calcium ion depleted apoprotein. The secondary structure and compactness of alpha-lactalbumin were examined in a temperature rang...

journal_title：Biopolymers

authors： Dzwolak W,Kato M,Shimizu A,Taniguchi Y

更新日期：2001-01-01 00:00:00

abstract：:MD simulations have been carried out to understand the dynamical behavior of the DNA substrate of the Thermus aquaticus DNA methyltransferase (M.TaqI) in the methylation process at N6 of adenine. As starting structures, an x-ray structure of M.TaqI in complex with DNA and cofactor analogue (PDB code: 1G 38) and free d...

journal_title：Biopolymers

authors： Wibowo FR,Rauch C,Trieb M,Liedl KR

更新日期：2005-10-15 00:00:00

abstract：:We have utilized a de novo designed two-stranded α-helical coiled-coil template to display conserved α-helical epitopes from the stem region of hemagglutinin (HA) glycoproteins of influenza A. The immunogens have all the surface-exposed residues of the native α-helix in the native HA protein of interest displayed on t...

journal_title：Biopolymers

authors： Jiang Z,Gera L,Mant CT,Hirsch B,Yan Z,Shortt JA,Pollock DD,Qian Z,Holmes KV,Hodges RS

更新日期：2016-03-01 00:00:00