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376 records returned

Conformations within soluble oligomers and insoluble aggregates revealed by resonance energy transferEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A fluorescently labeled 20-residue polyglutamic acid peptide E20 was used to study structural changes which occur in E20 as it co-aggregates with other unlabeled polyglutamic acid peptides. Resonance energy transfer was performed using an o-aminobenzamide donor at the N-terminus and 3-nitrotyrosine acceptor at the C-terminus of E20. Polyglutamic acid aggregates were not defined as amyloid, as they were non-fibrillar and did not bind Congo Red. Circular dichroism measurements indicate that polyglutamic acid aggregation involves a transition from [alpha]-helical monomers to aggregated [beta]-sheets. Soluble oligomers are als...
Source: Biopolymers - November 20, 2009 Category: Biochemistry Authors: Jyothi L. Digambaranath, Loan Dang, Monika Dembinska, Andrew Vasyluk, John M. Finke Source Type: journals

Interaction of [alpha]-gliadin with polyanions: Design considerations for sequestrants used in supportive treatment of celiac diseaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study provides insight into design considerations for polymer sequestrants used in the supportive treatment of celiac disease. © 2009 Wiley Periodicals, Inc. Biopolymers, 2009 (Source: Biopolymers)
Source: Biopolymers - November 18, 2009 Category: Biochemistry Authors: Li Liang, Maud Pinier, Jean-Christophe Leroux, Muriel Subirade Source Type: journals

Effect of pH on molecular constitution and distribution of hemoglobin in living erythrocyteEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The molecular constitution of in situ hemoglobin (Hb) and their distribution in living erythrocyte were investigated vs. pH using the technique of confocal Raman microscopy. Both Raman point spectra and line mapping measurements were performed on living erythrocytes in suspensions with pH values from 4.82 to 9.70. It was found that the hemoglobin inside a living erythrocyte would dissociate into monomer/dimer when the cells are in low and high pH environments. In contrast to the homogeneous distribution of the Hbs in the cells in neutral suspension, there are more Hbs distributing around the cell membrane or binding to the...
Source: Biopolymers - November 13, 2009 Category: Biochemistry Authors: Yue Wu, Yao-Xiong Huang, Li-Li Kang, Zheng-Jie Wu, Man Luo Source Type: journals

Energetic coupling between clustered lesions modulated by intervening triplet repeat bulge loops: Allosteric implications for DNA repair and triplet repeat expansionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Clusters of closely spaced oxidative DNA lesions present challenges to the cellular repair machinery. When located in opposing strands, base excision repair (BER) of such lesions can lead to double strand DNA breaks (DSB). Activation of BER and DSB repair pathways has been implicated in inducing enhanced expansion of triplet repeat sequences. We show here that energy coupling between distal lesions (8oxodG and/or abasic sites) in opposing DNA strands can be modulated by a triplet repeat bulge loop located between the lesion sites. We find this modulation to be dependent on the identity of the lesions (8oxodG versus abasic ...
Source: Biopolymers - November 5, 2009 Category: Biochemistry Authors: Jens Völker, G. Eric Plum, Horst H. Klump, Kenneth J. Breslauer Source Type: journals

Uncover the conserved property underlying sequence-distant and structure-similar proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
It is widely accepted that a protein's sequence determines its structure. The surprising finding that proteins of distant sequence can adopt similar 3D structures has raised interesting questions regarding underlying conserved properties that are essential for protein folding and stability. Uncovering the conserved properties may shed light on the folding mechanism of proteins and help with the development of computational tools for protein structure prediction. We compiled and analyzed a structure pair dataset of 66 high-resolution and low sequence identity (16-38%) soluble proteins. Structure deviation for each pair was ...
Source: Biopolymers - November 4, 2009 Category: Biochemistry Authors: Jun Gao, Zhijun Li Source Type: journals

Conformational preferences and prolyl Cis - trans isomerization of phosphorylated Ser/Thr-Pro motifsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The conformational study on Ac-pSer-Pro-NHMe and Ac-pThr-Pro-NHMe peptides has been carried out using hybrid density functional methods with the implicit solvation reaction field theory at the B3LYP/6-311++G(d,p)//B3LYP/6-31+G(d) level of theory in the gas phase and in solution (chloroform and water). For both pSer-Pro and pThr-Pro peptides in the gas phase and in chloroform, the most preferred conformation has the [alpha]-helical structure for the pSer/pThr residue, the down-puckered polyproline I structure for the Pro residue, and the cis prolyl peptide bond between the two residues, in which two hydrogen bonds between t...
Source: Biopolymers - November 3, 2009 Category: Biochemistry Authors: Byung Jin Byun, Young Kee Kang Source Type: journals

Importance of the spatial display of charged residues in heparin-peptide interactionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Many studies have examined consensus sequences required for protein-glycosaminoglycan interactions. Through the synthesis of helical heparin binding peptides, this study probes the relationship between spatial arrangement of positive charge and heparin binding affinity. Peptides with a linear distribution of positive charge along one face of the [alpha]-helix had the highest affinity for heparin. Moving the basic residues away from a single face resulted in drastic changes in heparin binding affinity of up to 3 orders of magnitude. These findings demonstrate that amino acid sequences, different from the known heparin bindi...
Source: Biopolymers - November 2, 2009 Category: Biochemistry Authors: Anthony Rullo, Mark Nitz Source Type: journals

Effects of hydrophobicity and anions on self-assembly of the peptide EMK16-IIEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Effects of hydrophobic and electrostatic interactions on the self-assembling process of the ionic-complementary peptide EMK16-II are investigated by AFM imaging, CD spectra, light scattering and chromatography. It is found that the hydrophobicity of the peptide promotes the aggregation in pure water even at a very low concentration, resulting in a much lower critical aggregation concentration (CAC) than that of another peptide, EAK16-II. The effect of anions in solution with different valences on electrostatic interactions is also important. Monovalent anions (Cl- and Ac-) with a proper concentration can facilitate the for...
Source: Biopolymers - November 2, 2009 Category: Biochemistry Authors: Dawei Zou, Zuoxiu Tie, Chunmei Lu, Meng Qin, Xiaomei Lu, Mu Wang, Wei Wang, P. Chen Source Type: journals

Research highlightsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No abstract. (Source: Biopolymers)
Source: Biopolymers - October 28, 2009 Category: Biochemistry Source Type: journals

Oligomerization of adenosin-5[prime]-O-ylmethylphosphonate, an isopolar AMP analogue: Evaluation of the route to short oligoadenylatesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In an attempt to prepare a library of short oligoadenylate analogues featuring both the enzyme-stable internucleotide linkage and the 5[prime]-O-methylphosphonate moiety and thus obtain a pool of potential RNase L agonists/antagonists, we studied the spontaneous polycondensation of the adenosin-5[prime]-O-ylmethylphosphonic acid (pcA), an isopolar AMP analogue, and its imidazolide derivatives employing N,N[prime]-dicyclohexylcarbodiimide (DCC) under non-aqueous conditions and uranyl ions under aqueous conditions, respectively. The RP LC-MS analyses of the reaction mixtures per se, and those obtained after the periodate tre...
Source: Biopolymers - October 20, 2009 Category: Biochemistry Authors: Martina Pressová, Milo[scaron] Bud[ecaron][scaron]ínský, Ivana Ko[scaron]iová, Vladimír Kopecký Jr., Josef Cva[ccaron]ka, Václav Ka[scaron]i[ccaron]ka, Ond[rcaron]ej [Scaron]imák, Zden[ecaron]k To[ccaron]ík, Ivan Rosenberg Source Type: journals

Thermal stability and conformational structure of salmon calcitonin in the solid and liquid statesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Salmon calcitonin (sCT) was selected as a model protein drug for investigating its intrinsic thermal stability and conformational structure in the solid and liquid states by using a Fourier transform infrared (FT-IR) microspectroscopy with or without utilizing thermal analyzer. The spectral correlation coefficient (r) analysis between two second-derivative IR spectra was applied to quantitatively estimate the structural similarity of sCT in the solid state before and after different treatments. The thermal FT-IR microspectroscopic data clearly evidenced that sCT in the solid state was not effected by temperature and had a ...
Source: Biopolymers - October 6, 2009 Category: Biochemistry Authors: Ting-Huei Lee, Wen-Ting Cheng, Shan-Yang Lin Source Type: journals

Analysis of a new crystal form of procarboxypeptidase B: further insights into the catalytic mechanismEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A new triclinic crystal structure form of porcine pancreatic procarboxypeptidase B (PCPB) was obtained at higher resolution than the previously known tetragonal crystal structure. This new crystal polymorph has allowed for a corrected, accurate assignment of residues along the polypeptide chain based on the currently available gene sequence information and crystallographic data. The present structure shows unbound PCPB in a distinct molecular packing as compared to the previous benzamidine complexed form. Its catalytically important Tyr248 residue is oriented and hydrogen-bonded to solvent water molecules, and locates the ...
Source: Biopolymers - October 2, 2009 Category: Biochemistry Authors: Daniel Fernández, Ester Boix, Irantzu Pallarès, Francesc X. Avilés, Josep Vendrell Source Type: journals

On the mechanism of SDS-induced protein denaturationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
To understand the mechanism of ionic detergent-induced protein denaturation, this study examines the action of sodium dodecyl sulfate on ferrocytochrome c conformation under neutral and strongly alkaline conditions. Equilibrium and stopped-flow kinetic results consistently suggest that tertiary structure unfolding in the submicellar and chain expansion in the micellar range of SDS concentrations are the two major and discrete events in the perturbation of protein structure. The nature of interaction between the detergent and the protein is predominantly hydrophobic in the submicellar and exclusively hydrophobic at micellar...
Source: Biopolymers - October 1, 2009 Category: Biochemistry Authors: Abani K. Bhuyan Source Type: journals

Identifying protein stabilizing ligands using GroELEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Over the past five years, it has become increasingly apparent to researchers that the initial promise and excitement of using gene replacement therapies to ameliorate folding diseases are still far from being broadly or easily applicable. Because a large number of human diseases are protein folding diseases ([sim]30 to 50%), many researchers now realize that more directed approaches to target and reverse the fundamental misfolding reactions preceding disease are highly feasible and offer the potential of developing more targeted drug therapies. This is also true with a large number of so called "orphan protein folding dise...
Source: Biopolymers - October 1, 2009 Category: Biochemistry Authors: Subhashchandra Naik, Inamul Haque, Nick Degner, Boris Kornilayev, Gregory Bomhoff, Jacob Hodges, Ara-Azad Khorassani, Hiroo Katayama, Jill Morris, Jeffery Kelly, John Seed, Mark T. Fisher Source Type: journals

Probing nanostructures of bacterial extracellular polymeric substances (EPS) versus culture time by raman microspectroscopy and atomic force microscopyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The structure of a bacterial cell wall may alter during bacterial reproduction. Moreover, these cell wall variations, on a nanoscale resolution, have not yet fully been elucidated. In the present work, Raman spectroscopy and atomic force microscopy (AFM) technique are applied to evaluate the culture time-dependent cell wall structure variations of Pseudomonas putida KT2440 at a quorum and single cell level. The Raman spectra indicate that the appearance of DNA/RNA, protein, lipid, and carbohydrates occurs till six hours of cultivation time under our experimental conditions. AFM characterization reveals the changes of the c...
Source: Biopolymers - September 28, 2009 Category: Biochemistry Authors: Gerald D. McEwen, Yangzhe Wu, Anhong Zhou Source Type: journals

Exploration of human serum albumin binding sites by docking and molecular dynamics flexible ligand-protein interactionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study provides evidence that HSA binding sites I and II interact specifically with a variety of compounds through conformational adjustments of the protein structure, in conjunction with ligand conformational adaptation to these sites. These results serve to explain the high ligand promiscuity of HSA. © 2009 Wiley Periodicals, Inc. Biopolymers, 2009 (Source: Biopolymers)
Source: Biopolymers - September 25, 2009 Category: Biochemistry Authors: Omar Deeb, Martha Cecilia Rosales-Hernández, Carlos Gómez-Castro, Ramón Garduño-Juárez, José Correa-Basurto Source Type: journals

Structural transition from dimeric to tetrameric i-motif, caused by the presence of TAA at the 3[prime]-end of human telomeric C-rich sequenceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Widely dispersed in genomic DNA, the tandem C-rich repetitive stretches may fold below physiological pH, into i-motif structures, stabilized by C[bull]C+ pairing. Herein, structural status of a 9-mer stretch d(CCCTAACCC), [the truncated double repeat of human telomeric sequence], and its extended version, comprising of additional -TAA segment at the 3[prime]-end, representing the complete double repeat d(CCCTAACCCTAA), has been investigated. The pH dependent monophasic UV-melting, gel and CD data suggested that while the truncated version adopts a bimolecular i-motif structure, its complete double repeat (12-mer) sequence ...
Source: Biopolymers - September 24, 2009 Category: Biochemistry Authors: Mahima Kaushik, Manoj Prasad, Shikha Kaushik, Anju Singh, Shrikant Kukreti Source Type: journals

Students, postdoctoral researchers, and senior collaborators of Lelio MazzarellaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No abstract. (Source: Biopolymers)
Source: Biopolymers - September 23, 2009 Category: Biochemistry Source Type: journals

Publications of Lelio Mazzarella (1963-2008)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No abstract. (Source: Biopolymers)
Source: Biopolymers - September 23, 2009 Category: Biochemistry Source Type: journals

Prof. Lelio Mazzarella - Curriculum VitaeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No abstract. (Source: Biopolymers)
Source: Biopolymers - September 23, 2009 Category: Biochemistry Source Type: journals

IntroductionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
No abstract. (Source: Biopolymers)
Source: Biopolymers - September 23, 2009 Category: Biochemistry Authors: Giulietta Smulevich, Filomena Sica Source Type: journals

Small-molecule reductants inhibit multicatalytic activity of AA-NADase from Agkistrodon acutus venom by reducing the disulfide-bonds and Cu(II) of enzymeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
AA-NADase from Agkistrodon acutus venom is a unique multicatalytic enzyme with both NADase and AT(D)Pase activities. Among all identified NADases, only AA-NADase contains Cu(II) and has disulfide-bond linkages between two peptide chains. The effects of the reduction of the disulfide-bonds and Cu(II) in AA-NADase by small-molecule reductants on its NADase and ADPase activities have been investigated by polyacrylamide gel electrophoresis, high performance liquid chromatography, electron paramagnetic resonance spectroscopy and isothermal titration calorimetry. The results show that AA-NADase has six disulfide-bonds and fiftee...
Source: Biopolymers - September 23, 2009 Category: Biochemistry Authors: Li-Yun Zhang, Xiao-Long Xu, Zhao-Feng Luo, Hao Wu, Deng-Ke Shen, Li-Li Peng, Yang-Zhong Liu Source Type: journals

Fluorescence spectroscopy of H-ras transfected murine fibroblasts: A comparison with monte carlo simulationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we measured the autofluorescence properties of H-ras transfected murine fibroblasts and the counterpart control cells. The pair of cells is genetically identical except of the transfected H-ras gene. We applied Monte Carlo simulations to evaluate the relative contributions of Rayleigh and Mie scattering effects towards fluorescence in an in-vitro model system of normal and H-ras transfected fibroblasts. The experimental results showed that fluorescence emission intensity was higher for normal cells than the malignant counterpart cells by about 30%. In normal cells, linearity in emission intensity was observe...
Source: Biopolymers - September 23, 2009 Category: Biochemistry Authors: Shlomo Mark, Ahmad Salman, Nili Grossman, Jacob Gopas, Ranjit Kumar Sahu, Shaul Mordechai Source Type: journals

Activation of lactoperoxidase by heme-linked protonation and heme-independent iodide bindingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Lactoperoxidase (LPO), a mammalian secretory heme peroxidase, catalyzes the oxidation of thiocyanate by hydrogen peroxide to produce hypothiocyanate, an antibacterial agent. Although LPO is known to be activated at acidic pH and in the presence of iodide, the structural basis of the activation is not well understood. We have examined the effects of pH and iodide concentration on the catalytic activity and the structure of LPO. Electrochemical and colorimetric assays have shown that the catalytic activity is maximized at pH 4.5. The heme Soret absorption band exhibits a small red-shift at pH 5.0 upon acidification, which is...
Source: Biopolymers - September 18, 2009 Category: Biochemistry Authors: Akira Toyama, Aya Tominaga, Tatsuo Inoue, Hideo Takeuchi Source Type: journals

Modulation of SHP-1 phosphatase activity by monovalent and bivalent SH2 phosphopeptide ligandsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com (Source: Biopolymers)
Source: Biopolymers - September 18, 2009 Category: Biochemistry Authors: Kathleen Teichmann, Toni Kühl, Ina Könnig, Karin Wieligmann, Martin Zacharias, Diana Imhof Source Type: journals

Structure and function of the molecular chaperone Hsp104 from yeastEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The molecular chaperone Hsp104 plays a central role in the clearance of aggregates after heat shock and the propagation of yeast prions. Hsp104's disaggregation activity and prion propagation have been linked to its ability to resolubilize or remodel protein aggregates. However, Hsp104 has also the capacity to catalyze protein aggregation of some substrates at specific conditions. Hence, it is a molecular chaperone with two opposing activities with respect to protein aggregation. In yeast models of Huntington's disease Hsp104 is required for the aggregation and toxicity of polyglutamine (polyQ), but the expression of Hsp10...
Source: Biopolymers - September 17, 2009 Category: Biochemistry Authors: Valerie Grimminger-Marquardt, Hilal A. Lashuel Source Type: journals

Hsp70 molecular chaperones and Parkinson's diseaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Because over-expression of Hsp70 molecular chaperones suppresses the toxicity of aberrantly folded proteins that occur in Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis, and various polyQ-diseases (Huntington's disease and ataxias), Hsp70 is garnering attention as a possible therapeutic agent for these various diseases. Here I review progress in this fascinating field of molecular chaperones and neurodegeneration and describe our current understanding of the mechanisms by which Hsp70 protects cells from the PD-related protein called alpha-synuclein ([alpha]-syn). © 2009 Wiley Periodicals...
Source: Biopolymers - September 17, 2009 Category: Biochemistry Authors: Stephan N. Witt Source Type: journals

Heating-induced conformational change of a novel [beta]-(1[rarr]3)-D-glucan from Pleurotus geestanusEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recently, we isolated and purified a neutral polysaccharide (PGN) from edible fungus pleurotus geesteraus. Its structure was characterized by a range of physical chemical methods, including high performance anion exchange chromatography, uronic acid and protein analyses, size exclusion chromatography with ultraviolet, refractive index and light scattering detectors, and nuclear magnetic resonance. Our results revealed that PGN is a novel [beta]-(1[rarr]3)-D-glucan with glucose attached to every other sugar residues at position 6 in the backbone. It has a degree of branching of 1/2. Such structure is different from typical ...
Source: Biopolymers - September 17, 2009 Category: Biochemistry Authors: Mei Zhang Source Type: journals

Interplay between protein homeostasis networks in protein aggregation and proteotoxicityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The misfolding and aggregation of disease proteins is characteristic of numerous neurodegenerative diseases. Particular neuronal populations are more vulnerable to proteotoxicity while others are more apt to tolerate the misfolding and aggregation of disease proteins. Thus, the cellular environment must play a significant role in determining whether disease proteins are converted into toxic or benign forms. The endomembrane network of eukaryotes divides the cell into different subcellular compartments that possess distinct sets of molecular chaperones and protein interaction networks. Chaperones act as agonists and antagon...
Source: Biopolymers - September 17, 2009 Category: Biochemistry Authors: Peter M. Douglas, Douglas M. Cyr Source Type: journals

The effect of deuterium oxide on the stability of the collagen model peptides H-(Pro-Pro-Gly)10-OH, H-(Gly-Pro-4(R)Hyp)9-OH, and type I collagenEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The collagen triple helix has a larger accessible surface area per molecular mass than globular proteins, and therefore potentially more water interaction sites. The effect of deuterium oxide on the stability of collagen model peptides and type I collagen molecules was analyzed by circular dichroism and differential scanning calorimetry. The transition temperatures (Tm) of the protonated peptide (Pro-Pro-Gly)10 were 25.4 °C, and 28.7 °C in H2O and D2O, respectively. The increase of the Tm of (Pro-Pro-Gly)10 measured calorimetrically at 1.0 °C/min in a low pH solution from the protonated to the deuterated solvent was 5.1...
Source: Biopolymers - September 17, 2009 Category: Biochemistry Authors: Kazunori Mizuno, Hans Peter Bächinger Source Type: journals

NMR studies of an immunomodulatory benzodiazepine binding to its molecular target on the mitochondrial F1F0-ATPaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Bz-423 is an inhibitor of the mitochondrial F1F0-ATPase, with therapeutic properties in murine models of immune diseases. Here we study the binding of a water-soluble Bz-423 analog (5-(3-(aminomethyl)phenyl)-7-chloro-1-methyl-3-(naphthalen-2-ylmethyl)-1H-benzo[e][1,4]diazepin-2(3H)-one); (1) to its target subunit on the enzyme, the oligomycin sensitivity conferring protein (OSCP), by NMR spectroscopy using chemical shift perturbation and cross-relaxation experiments. Titration experiments with constructs representing residues 1-120 or 1-145 of the OSCP reveals that (a) 1 binds to a region of the protein, at the minimum, co...
Source: Biopolymers - September 17, 2009 Category: Biochemistry Authors: Andrew C. Stelzer, Richard W. Frazee, Chad Van Huis, Joanne Cleary, Anthony W. Opipari Jr, Gary D. Glick, Hashim M. Al-Hashimi Source Type: journals

Modulation of SHP-1 phosphatase activity by mono- and bivalent SH2 phosphopeptide ligandsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A sequence derived from epithelial receptor tyrosine kinase Ros (pY2267) represents a high affinity binding partner for protein tyrosine phosphatase SHP-1 and was recently used as lead structure to analyse recognition requirements for the enzyme's N-SH2 domain. Here, we focused on a set of peptides comprising C-terminally extended linear and conformationally constrained side chain-bridged cyclic N-SH2 ligands based on the consensus sequence LxpYhxh(h/b)(h/b) (x = any amino acid, h = hydrophobic and b = basic residue). Furthermore, the bivalent peptides described were designed to modulate activity of SHP-1 through binding t...
Source: Biopolymers - September 17, 2009 Category: Biochemistry Authors: Kathleen Teichmann, Toni Kühl, Ina Könnig, Karin Wieligmann, Martin Zacharias, Diana Imhof Source Type: journals

Direct real-time imaging of protein adsorption onto hydrophilic and hydrophobic surfacesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Atomic force microscopy has been used to follow in real-time the adsorption from solution of two of the gliadin group of wheat seed storage proteins onto hydrophilic (mica) and hydrophobic (graphite) surfaces. The liquid cell of the microscope was used initially to acquire images of the substrate under a small quantity of pure solvent (1% acetic acid). Continuous imaging as an injection of gliadin solution entered the liquid cell enabled the adsorption process to be followed in-situ from zero time. For [omega]-gliadin a monolayer was formed on the mica substrate over a period of [sim]2000 s, with the protein molecules orie...
Source: Biopolymers - September 2, 2009 Category: Biochemistry Authors: Simon J. Haward, Peter R. Shewry, Mervyn J. Miles, Terence J. McMaster Source Type: journals

Viral structural transition mechanisms revealed by multiscale molecular dynamics/order parameter extrapolation simulationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, MD/OPX is optimized and implemented to simulate viral capsid structural transitions. Specifically, 200ns MD/OPX simulation of the swollen state of cowpea chlorotic mottle virus (CCMV) capsid reveals that it undergoes significant energy-driven shrinkage in vacuum, which is a symmetry-breaking process involving local initiation and front propagation. © 2009 Wiley Periodicals, Inc. Biopolymers, 2009 (Source: Biopolymers)
Source: Biopolymers - September 1, 2009 Category: Biochemistry Authors: Yinglong Miao, Peter J. Ortoleva Source Type: journals

Revisiting the neighbor exclusion model and its applicationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present methods to quantitatively analyze the variation of these two quantities, allowing one to determine important parameters of the interaction such as the intrinsic binding constant and the exclusion number of the ligand. © 2009 Wiley Periodicals, Inc. Biopolymers, 2009 (Source: Biopolymers)
Source: Biopolymers - August 31, 2009 Category: Biochemistry Authors: M. S. Rocha Source Type: journals

Conformational stability of the full-atom hexameric model of the ClpB chaperone from Escherichia coliEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Escherichia coli heat shock protein ClpB, a member of the Hsp100 family, plays a crucial role in cellular thermotolerance. In co-operation with the Hsp70 chaperone system, it is able to solubilize proteins aggregated by heat shock conditions and refold them into the native state in an ATP-dependent way. It was established that the mechanism of ClpB action depends on the formation of a ring-shaped hexameric structure and the translocation of a protein substrate through an axial channel. The structural aspects of this process are not fully known. By means of homology modeling and protein-protein docking we obtained a mod...
Source: Biopolymers - August 27, 2009 Category: Biochemistry Authors: Szymon Zi[eogon]tkiewicz, Magdalena J. [Sacute]lusarz, Rafa[lstrok] [Sacute]lusarz, Krzysztof Liberek, Sylwia Rodziewicz-Motowid[lstrok]o Source Type: journals

Hsp90 and co-chaperones twist the functions of diverse client proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Hsp90 molecular chaperones are required for the stability and activity of a diverse range of client proteins that have critical roles in signal transduction, cellular trafficking, chromatin remodeling, cell growth, differentiation and reproduction. Mammalian cells contain three types of Hsp90s: cytosolic Hsp90, mitochondrial Trap-1, and Grp94 of the endoplasmic reticulum. Each of the Hsp90s, as well as the bacterial homolog, HtpG, hydrolyze ATP and undergo similar conformational changes. Unlike the other forms of Hsp90, cytosolic Hsp90 function is dependent on a battery of co-chaperone proteins that regulate the ATPase act...
Source: Biopolymers - August 20, 2009 Category: Biochemistry Authors: Abbey Zuehlke, Jill L. Johnson Source Type: journals

Understanding the mode of action of ThDP in benzoylformate decarboxylaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The mechanism of all elementary steps involved in the catalytic cycle of benzoylformate decarboxylase (BFD, E.C. 4.1.1.7) to generate the acyloin linkage is investigated by extensive molecular dynamics simulations. Models involving different charge states of amino acids and/or mutants of critical residues were constructed in order to understand the involvement of the catalytically active residues and the reactivity differences between different substrates in this reaction. Our calculations confirm that H70, S26 and H281 are catalytically active amino acids. H281 functions as a base to accept Hdonor in the first nucleophili...
Source: Biopolymers - August 17, 2009 Category: Biochemistry Authors: Gocmen Topal Kevser, Atilgan Canan, Demir Ayhan S., Av[idot]yente Viktorya Source Type: journals

ILPR repeats adopt diverse G-quadruplex conformations that determine insulin bindingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Insulin Linked Polymorphic Region (ILPR) is a VNTR region located upstream of the Insulin (INS) gene consisting of the repeat 5[prime]-ACAGGGGTGTGGGG (repeat a) and several less abundant sequence repeats (b-n). Here, we have investigated the structural polymorphism of G-quadruplexes formed from the most common repeat sequences (a-c) and their effect on Insulin protein binding. We first established that the ILPR repeats 'b' and 'c' can form quadruplex structures. Insulin has previously been shown to bind a G-quadruplex formed by a dimer of the repeat 'a'. Our findings show that Insulin binds preferentially to the repeat...
Source: Biopolymers - August 16, 2009 Category: Biochemistry Authors: Joseph D. Schonhoft, Arijit Das, Firehiwot Achamyeleh, Sheema Samdani, Abby Sewell, Hanbin Mao, Soumitra Basu Source Type: journals

Diverse modes of 5[prime]-[4-(aminoiminomethyl)phenyl]-[2,2[prime]-Bifuran]-5-carboximidamide (DB832) interaction with multi-stranded DNA structuresEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The modes of binding of 5[prime]-[4-(aminoiminomethyl)phenyl]-[2,2[prime]-Bifuran]-5-carboximidamide (DB832) to multi-stranded DNAs: human telomere quadruplex, monomolecular R-triplex, pyr/pur/pyr triplex consisting of 12 T*(T·A) triplets and to DNA double helical hairpin were studied. The optical adsorption of the ligand was used for monitoring the binding and for determination of the association constants and the numbers of binding sites. CD spectra of DB832 complexes with the oligonucleotides and the data on the energy transfer from DNA bases to the bound DB832 assisted in elucidating the binding modes. The affinity of...
Source: Biopolymers - July 29, 2009 Category: Biochemistry Authors: Dmitry N. Kaluzhny, Olga F. Borisova, Anna K. Shchyolkina Source Type: journals

Biomimetic potential of some methacrylate-based copolymers: A comparative studyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Preparation of new biocompatible materials for bone recovery has consistently gained interest in the last few decades. Special attention was given to polymers that contain negatively charged groups, such as phosphate, carboxyl and sulfonic groups towards calcification.The present paperwork demonstrates that other functional groups present also potential application in bone pathology. New copolymers of 2-hydroxyethyl methacrylate with diallyldimethylammonium chloride (DADMAC), glycidyl methacrylate (GlyMA), methacrylic acid (MAA), 2-methacryloyloxymethyl acetoacetate (MOEAA), 2-methacryloyloxyethyltriethylammonium chloride ...
Source: Biopolymers - July 28, 2009 Category: Biochemistry Authors: Teodora Zecheru, Robert Filmon, Edina Rusen, Bogdan M[abreve]rculescu, Amar Zerroukhi, Corneliu Cincu, Daniel Chappard Source Type: journals

Sequence-dependent folding and unfolding of ligand-bound purine riboswitchesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Riboswitch regulation of gene expression requires ligand-mediated RNA folding. From the fluorescence lifetime distribution of bound 2-aminopurine ligand, we resolve three RNA conformers (Co, Ci, Cc) of the liganded G- and A-sensing riboswitches from Bacillus subtilis. The ligand binding affinities, and sensitivity to Mg2+, together with results from mutagenesis, suggest that Co and Ci are partially unfolded species compromised in key loop-loop interactions present in the fully folded Cc. These data verify that the ligand-bound riboswitches may dynamically fold and unfold in solution, and reveal differences in the distribut...
Source: Biopolymers - July 14, 2009 Category: Biochemistry Authors: Oksana Prychyna, Michael S. Dahabieh, Jay Chao, Melanie A. O'Neill Source Type: journals

Spectroscopic and molecular modeling studies on the binding of the flavonoid luteolin and human serum albuminEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Luteolin (lut) is a polyphenolic compound, found in a variety of fruits, vegetables, and seeds, which has a variety of pharmacological properties. in the present contribution binding of lut to human serum albumin (hsa), the most abundant carrier protein in the blood, was investigated with the aim of describing the binding mode and parameters of the interaction. the application of circular dichroism, uv-vis absorption, fluorescence, raman and surface-enhanced raman scattering spectroscopy combined with molecular modelling afforded a clear picture of the association mode of lut to hsa.Specific interactions with protein amino...
Source: Biopolymers - July 13, 2009 Category: Biochemistry Authors: Zuzana Jurasekova, Giancarlo Marconi, Santiago Sanchez-Cortes, Armida Torreggiani Source Type: journals

Comparison of the internalization of targeted dendrimers and dendrimer-entrapped gold nanoparticles into cancer cellsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study underlines the fact that metal or inorganic NPs entrapped within dendrimers interact with cells in a similar way to that of dendrimers lacking host NPs. © 2009 Wiley Periodicals, Inc. Biopolymers, 2009 (Source: Biopolymers)
Source: Biopolymers - July 13, 2009 Category: Biochemistry Authors: Xiangyang Shi, Su He Wang, Inhan Lee, Mingwu Shen, James R. Baker Jr Source Type: journals

The four cysteines ring motif in proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Disulfide bonds play fundamental roles in proteins. This paper is devoted to highly rare motifs containing disulfide bonds. A search for four cysteines, forming a 16-atom membered ring (4CR) embodying 2 disulfide bonds, was carried out against all entries in the Protein Data Bank. Searching the crystallographic subset, only few protein molecules, all dimeric, were found to embody this peculiar structural feature, which establishes a covalent link between two different polypeptide chains. In contrast, in a peptide studied in solution by NMR, the 4 cysteines moiety includes only residues from one chain. A comparative analysi...
Source: Biopolymers - July 13, 2009 Category: Biochemistry Authors: Adriana Zagari Source Type: journals

Refinement of the long-range order parameter in predicting folding rates of two-state proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Long-range order (LRO) is one of the most successful descriptors in relating the three-dimensional structures of proteins with their folding rates. LRO highlights the importance of long-range contacts (residues that are far in sequence and closer in the 3-D structure) in determining the folding rates of proteins across all structural classes of proteins. In the present work, we have updated the data set of two-state folding proteins to examine the robustness of LRO parameter and to assess whether any refinements are required in defining the computation of LRO. LRO shows a better correlation (r = - 0.85) for the increased d...
Source: Biopolymers - July 13, 2009 Category: Biochemistry Authors: B. Harihar, S. Selvaraj Source Type: journals

Human tropoelastin sequence: Dynamics of polypeptide coded by exon 6 in solutionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Calorimetric studies were performed on exon 6 in powdered form and in solution (water and 2,2,2-trifluoroethanol (TFE), a structure-inducing solvent or cosolvent). Dynamic Dielectric Spectroscopy (DDS) analyses were realized in water and 20% TFE. The major role of solvent-peptide organization is evidenced with these techniques. Calorimetric measurements reveal the structural water organization around the polypeptide as well as the presence of hydrophobic interactions in TFE solution. Dielectric measurements showed for exon 6/water a decrease of relaxations times of bulk solvent implying a faster dynamics with a slight incr...
Source: Biopolymers - July 13, 2009 Category: Biochemistry Authors: D. Tintar, V. Samouillan, J. Dandurand, C. Lacabanne, A. Pepe, B. Bochicchio, Antonio M. Tamburro Source Type: journals

The effect of the side chain length of Asp and Glu on coordination structure of Cu2+ in a de novo designed proteinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Metal ions in proteins are important not only for the formation of the proper structures but also for various biological activities. For biological functions such as hydrolysis and oxidation, metal ions often adopt unusual coordination structures. We constructed a stable scaffold for metal binding to create distorted metal coordination structures. A stable four stranded [alpha]-helical coiled-coil structure was used as the scaffold, and the metal binding site was in the cavity created at the center of the structure. Two His residues and one Asp or Glu residue were used to coordinate the metal ions, AM2D and AM2E, respectiv...
Source: Biopolymers - July 13, 2009 Category: Biochemistry Authors: Daigo Shiga, Daisuke Nakane, Tomohiko Inomata, Hideki Masuda, Masayuki Oda, Masanori Noda, Susumu Uchiyama, Kiichi Fukui, Yu Takano, Haruki Nakamura, Toshihisa Mizuno, Toshiki Tanaka Source Type: journals

A statistical thermodynamic approach for predicting the sequence-dependent nucleosome positioning along genomesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nucleosomes are the fundamental repeating unit of chromatin and constitute the structural building blocks of the eukaryotic genome. The distribution of nucleosomes along the genome is a significant aspect of chromatin structure and influences gene regulation through modulation of DNA accessibility. For this reason, an increasing interest is arising in models capable of predicting the nucleosome positioning along genomes. Toward this goal, we propose a theoretical model for predicting nucleosome thermodynamic stability in terms of DNA sequence. The model, based on a statistical mechanical approach allows the calculation of ...
Source: Biopolymers - July 12, 2009 Category: Biochemistry Authors: Anita Scipioni, Stefano Morosetti, Pasquale De Santis Source Type: journals

Bioencapsulation of apomyoglobin in nanoporous organosilica sol-gel glasses: Influence of the siloxane network on the conformation and stability of a model proteinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nanoporous sol-gel glasses were used as host materials for the encapsulation of apomyoglobin, a model protein employed to probe in a rational manner the important factors that influence the protein conformation and stability in silica-based materials. The transparent glasses were prepared from tetramethoxysilane (TMOS) and modified with a series of mono-, di- and tri-substituted alkoxysilanes, RnSi(OCH3)4-n (R= methyl-, n = 1; 2; 3) of different molar content (5; 10; 15%) to obtain the decrease of the siloxane linkage (-Si-O-Si-). The conformation and thermal stability of apomyoglobin characterized by circular dichroism sp...
Source: Biopolymers - July 7, 2009 Category: Biochemistry Authors: Bouzid Menaa, Yuya Miyagawa, Masahide Takahashi, Mar Herrero, Vicente Rives, Farid Menaa, Daryl K. Eggers Source Type: journals