Structure-based design of novel nonpeptide inhibitors of the Src SH2 domain:phosphotyrosine mimetics exploiting multifunctional group replacement chemistry.

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：: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：: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 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：: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：:Cyclotides are multifunctional plant cyclic peptides containing 28-37 amino acid residues and a pattern of three disulfide bridges, forming a motif known as the cyclic cystine knot. Due to their high biotechnological potential, the sequencing and characterization of cyclotide genes are crucial not only for cloning and...

journal_title：Biopolymers

authors： Cunha NB,Barbosa AE,de Almeida RG,Porto WF,Maximiano MR,Álvares LC,Munhoz CB,Eugênio CU,Viana AA,Franco OL,Dias SC

更新日期：2016-11-01 00:00:00

abstract：:Synthesis and CD and (13)C(alpha)-NMR studies in a near-neutral saline buffer are reported for a 65-residue peptide ((190)Tm(254)) comprising residues 190-254 of the alpha-tropomyosin chain. CD on a version disulfide cross-linked via the N-terminal cysteine side chains indicates that this dimer is highly helical and m...

journal_title：Biopolymers

authors： Emerson Holtzer M,Mints L,Hogue Angeletti R,d'Avignon DA,Holtzer A

更新日期：2001-10-05 00:00:00

abstract：:The x-ray conformations of 5-, 7-, 9-, and 12-residue loops in bovine pancreatic trypsin inhibitor (BPTI) were predicted by the use of multiple independent Monte Carlo simulating annealing (MCSA) runs starting from random conformations. Four buried water molecules interacted with a 12-residue loop that started at resi...

journal_title：Biopolymers

authors： Carlacci L

更新日期：2001-04-05 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 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：:A series of cyclic retro-inverso dipeptides--2-[(4-hydroxy)benzyl]-5-benzyl-4,6(1H,2H,3H,5H)-pyrimidinedi one (c[mPhe-gTyr]), 2-benzyl-5-[(4-hydroxy)benzyl]-4,6(1H,2H,3H,5H)-pyrimidinedione (c[mTyr-gPhe]), and 2-benzyl-5-amino-5-[(4-hydroxy)benzyl]-4,6(1H,2H,3H,5H)-pyrimidinedione (c[(alpha-amino)mTyr-gPhe])--were syn...

journal_title：Biopolymers

authors： Nunami K,Yamazaki T,Goodman M

更新日期：1991-11-01 00:00:00

abstract：:Porins from outer membrane of Gram-negative bacteria have a highly stable structure. Our previous studies on porin from Paracoccus denitrificans showed that the outer membrane protein porin is extremely stable toward heat, pH, and chemical denaturants. The major question we have addressed in this paper is whether the ...

journal_title：Biopolymers

authors： Sukumaran S,Hauser K,Maier E,Benz R,Mäntele W

更新日期：2006-07-01 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：: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 discovery of the prototype delta opioid antagonists TIPP (H-Tyr-Tic-Phe-Phe-OH) and TIP (H-Tyr-Tic-Phe-OH) in 1992 was followed by extensive structure-activity relationship studies, leading to the development of analogues that are of interest as pharmacological tools or as potential therapeutic agents. Stable TIPP...

journal_title：Biopolymers

authors： Schiller PW,Weltrowska G,Berezowska I,Nguyen TM,Wilkes BC,Lemieux C,Chung NN

更新日期：1999-01-01 00:00:00

abstract：:DNA sequences d-TGAGGAAAGAAGGT (a 14-mer) and d-CTCCTTTCTTCC (a 12-mer) are complementary in parallel orientation forming either Donohue (reverse Watson-Crick) base pairing at neutral pH or Hoogsteen base pairing at slightly acidic pH. The structure of the complex formed by dissolving the two strands in equimolar rati...

journal_title：Biopolymers

authors： Bhaumik SR,Chary KV,Govil G,Liu K,Miles HT

更新日期：1997-06-01 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：: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：:Vibrational spectroscopy coupled with thermogravimetry (TG) and differential scanning calorimetry (DSC) was used to characterize racemic propanoic acid, 2-methyl-5,6,7,8-tetrahydro-6-(methylamino)-1,2-naphthalenediyl ester hydrochloride (CHF-1035), which is a new DA2 dopaminergic receptor/alpha2 agonist and beta block...

journal_title：Biopolymers

authors： Taddei P,Torreggiani A,Fini G

更新日期：2002-01-01 00:00:00

abstract：:We report on an unrestrained molecular dynamics simulation of the flavin mononucleotide (FMN)-RNA aptamer. The simulated average structure maintains both cross-strand and intermolecular FMN-RNA nuclear Overhauser effects from the nmr experiments and has all qualitative features of the nmr structure including the G10-U...

journal_title：Biopolymers

authors： Schneider C,Sühnel J

更新日期：1999-09-01 00:00:00

abstract：:Shorter analogues of a continuous epitope of hepatitis A virus, VP3(110-121) peptide, failed to react with convalescent sera, indicating the importance of the entire peptide in the epitope structure. To better understand the influence of the structural properties of this 12-mer peptide epitope on its biological activi...

journal_title：Biopolymers

authors： Sospedra P,Muñoz M,García M,Alsina MA,Mestres C,Haro I

更新日期：2000-12-01 00:00:00

abstract：:Understanding the high temperature behavior of collagen and collagenous tissue is important for surgical procedures and biomaterials processing for the food, pharmaceutical, and cosmetics industries. One primary event for proteins is thermal denaturation that involves unfolding the polypeptide chains while maintaining...

journal_title：Biopolymers

authors： Fields M,Spencer N,Dudhia J,McMillan PF

更新日期：2017-06-01 00:00:00

abstract：:Flow linear dichroism measurements extended into the vacuum uv region yield inclinations for the base normal from the helix axis of 21 degrees for dA and 40 degrees for dT in the X-form of poly(dAdT).poly(dAdT). These inclination angles are similar to the B form of the synthetic polymer, but the axes around which the ...

journal_title：Biopolymers

authors： Riazance-Lawrence JH,Kang H,Chou PJ,Johnson WC Jr,Vorlícková M

更新日期：1994-11-01 00:00:00

abstract：:Computer simulations can provide in principle quantitative correlation between the structures of DNA polymerases and the replication fidelity. This paper describes our progress in this direction. Using several theoretical approaches, including the free energy perturbation (FEP), linear response approximation (LRA), an...

journal_title：Biopolymers

authors： Florián J,Goodman MF,Warshel A

更新日期：2003-03-01 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：: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：:Cyclotides are disulfide-rich miniproteins with a circular backbone and a knotted arrangement ofdisulfide bonds. Because these plant-derived peptides are resistant to degradation and exhibit a diverse range of bioactivity they have become important agronomic and industrial objectives. They belong to a group of compoun...

journal_title：Biopolymers

authors： Dörnenburg H

更新日期：2010-01-01 00:00:00

abstract：:Functional RNAs such as ribosomal RNA and structured domains of mRNA are targets for small molecule ligands that can act as modulators of the RNA biological activity. Natural ligands for RNA display a bewildering structural and chemical complexity that has yet to be matched by synthetic RNA binders. Comparison of natu...

journal_title：Biopolymers

authors： Hermann T

更新日期：2003-09-01 00:00:00

abstract：:Human saliva contains hundreds of small proline-rich peptides originated by the proteolytic cleavage of the salivary basic Proline-Rich Proteins. Nevertheless only for few of them a specific biological activity has been assigned to date. Among them, the 1932 Da peptide (p1932) has been patented as an anti-HIV agent. I...

journal_title：Biopolymers

authors： Righino B,Pirolli D,Radicioni G,Marzano V,Longhi R,Arcovito A,Sanna MT,De Rosa MC,Paoluzi S,Cesareni G,Messana I,Castagnola M,Vitali A

更新日期：2016-09-01 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