MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Biopolymers' source. Mon, 06 Feb 2012 13:31:34 +0100 http://www.medworm.com/index.php?rid=5656176&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22028 We report the cloning, successful overexpression and purification of recombinant Ost4p with a novel but simple method producing milligram quantities of pure protein. GB1 protein was found to be the most suitable tag for the large scale production of Ost4p. The cleavage of Ost4p conveniently leaves GB1 protein in solution eliminating further purification. The precipitated pure Ost4p is reconstituted in appropriate membrane mimetic. The recombinant protein is highly helical as indicated by the far‐UV CD spectrum. The well‐dispersed HSQC spectrum indicates that this minimembrane protein is well folded. The successful production of pure recombinant Ost4p with a novel yet simple method may have important ramification for the production of other membrane proteins. © 2012 Wiley Periodicals, ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5656176 Fri, 03 Feb 2012 18:24:50 +0100 5656176 http://www.medworm.com/index.php?rid=5656177&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22027 AbstractEM‐Fold was used to build models for nine proteins in the maps of GroEL (7.7 Å resolution) and ribosome (6.4 Å resolution) in the ab initio modeling category of the 2010 cryoEM modeling challenge. EM‐Fold assembles predicted secondary structure elements (SSEs) into regions of the density map that were identified to correspond to either α‐helices or β‐strands. The assembly uses a Monte Carlo algorithm where loop closure, density‐SSE length agreement, and strength of connecting density between SSEs are evaluated. Top scoring models are refined by translating, rotating and bending SSEs to yield better agreement with the density map. EM‐Fold produces models that contain backbone atoms within secondary structure elements only. The RMSD values of the models with respect t... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5656177 Fri, 03 Feb 2012 05:00:00 +0100 5656177 http://www.medworm.com/index.php?rid=5624465&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22026 AbstractThe challenge of stabilization of small molecules and proteins has received considerable interest. The biological activity of small molecules can be lost as a consequence of chemical modifications, while protein activity may be lost due to chemical or structural degradation, such as a change in macromolecular conformation or aggregation. In these cases stabilization is required to preserve therapeutic and bioactivity efficacy and safety. In addition to use in therapeutic applications, strategies to stabilize small molecules and proteins also have applications in industrial processes, diagnostics, and consumer products like food and cosmetics. Traditionally, therapeutic drug formulation efforts have focused on maintaining stability during product preparation and storage. However, wi... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5624465 Tue, 24 Jan 2012 18:46:32 +0100 5624465 http://www.medworm.com/index.php?rid=5603654&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22018 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=5603654 Wed, 18 Jan 2012 19:14:32 +0100 5603654 http://www.medworm.com/index.php?rid=5603653&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22014 AbstractProtein extracted from Moringa oleifera (MO) seeds has been advocated as a cheap and environmental friendly alternative to ionic flocculants for water purification. However, the nature and mechanism of its interaction with particles in water, as well as with dissolved surface‐active molecules, are not well understood. In this article, we report studies of the protein and its interaction with four surfactants using dynamic light scattering (DLS), zeta‐potential and turbidity measurements. Zeta‐potential measurements identified points of charge reversal and the turbidity and DLS measurements were used to characterize the microstructure and size of protein‐surfactant complexes. From the points of charge reversal, it was estimated that 7 anions are required to neutralize the po... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5603653 Wed, 18 Jan 2012 19:14:27 +0100 5603653 http://www.medworm.com/index.php?rid=5603652&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22025 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=5603652 Wed, 18 Jan 2012 19:14:24 +0100 5603652 http://www.medworm.com/index.php?rid=5592645&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22024 AbstractThe silk produced by silkworms are biopolymers and can be classified into two types – mulberry and non‐mulberry. Mulberry silk of silkworm Bombyx mori has been extensively explored and used for century old textiles and sutures. But for the last few decades it is being extensively exploited for biomedical applications. However, the transformation of non‐mulberry silk from being a textile commodity to biomaterials is relatively new. Within a very short period of time, the combination of load bearing capability and tensile strength of non‐mulberry silk has been equally envisioned for bone, cartilage, adipose and other tissue regeneration. Adding to its advantage is its diverse morphology, including macro to nano architectures with controllable degradation and biocompatibility ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5592645 Sun, 15 Jan 2012 07:33:25 +0100 5592645 http://www.medworm.com/index.php?rid=5592647&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22022 This study investigates the relationship between birefringence and mechanical properties in the dragline silk of the gold orb weaving spider Nephila edulis. Using a custom birefringence‐tensile testing device, we probed the orientation and water‐induced swelling of fibers spun at variety of drawing rates ranging from 0.003mms−1 to 400mms−1. Our results indicate that based upon drawing rate, silk fibers fall into 3 distinct regimes each with characteristic orientation and swelling properties. Further investigation using in‐situ tensile testing reveals interactions between a fiber's drawing speed, mechanical properties and orientation that support previous model predictions. We propose that simultaneous birefringence‐tensile testing provides a unique and readily accessible insigh... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5592647 Thu, 12 Jan 2012 05:00:00 +0100 5592647 http://www.medworm.com/index.php?rid=5592646&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22023 AbstractWe explore the properties of adsorption of flexible polyelectrolyte chains in confined spaces between the oppositely charged surfaces in three basic geometries. A method of approximate uniformly valid solutions for the Green function equation for the eigenfunctions of polymer density distributions is developed to rationalize the critical adsorption conditions. The same approach was implemented in our recent study for the “inverse” problem of polyelectrolyte adsorption onto a planar surface, and on the outer surface of rod‐like and spherical obstacles. For the three adsorption geometries investigated, the theory yields simple scaling relations for the minimal surface charge density that triggers the chain adsorption, as a function of the Debye screening length and surface curv... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5592646 Thu, 12 Jan 2012 05:00:00 +0100 5592646 http://www.medworm.com/index.php?rid=5532950&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22020 AbstractFour molecular fractions of gelatin produced by alkaline hydrolysis of collagen were investigated in the presence of co‐solute to record the mechanical properties of the glass transition in high‐solid preparations. Dynamic oscillatory and stress relaxation moduli in shear were recorded from 40°C to temperatures as low as ‐60°C. The small‐deformation behaviour of these linear polymers was separated by the method of reduced variables into a basic function of time alone and a basic function of temperature alone. The former allowed the reduction of isothermal runs into a master curve covering seventeen orders of magnitude in the time domain. The latter follows the passage from the rubbery plateau through the glass transition region to the glassy state seen in the variation of... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5532950 Fri, 23 Dec 2011 07:22:35 +0100 5532950 http://www.medworm.com/index.php?rid=5532951&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22017 We report here a variety of molecular dynamics simulations (mostly of 100 ns) using the GLYCAM06 force field and various water models, paying particular attention to comparisons to NMR measurements of residual dipolar couplings and electron‐mediated spin‐spin couplings. We focus on the glycosidic linkage conformation, the puckering phase angle of the fructose ring, and intramolecular hydrogen bonds between the two sugars. Our results show that sucrose is indeed a dynamic molecule, but the that crystal conformation is qualitatively the dominant one in dilute solution. A second conformational basin, populated in many force fields, is probably over‐stabilized in the calculations. © 2011 Wiley Periodicals, Inc. Biopolymers, 2011 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=5532951 Tue, 20 Dec 2011 05:00:00 +0100 5532951 http://www.medworm.com/index.php?rid=5512063&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21722 AbstractBiocompatible and biodegradable peptide hydrogels are drawing increasing attention as prospective materials for human soft tissue repair and replacement. To improve the rather unfavorable mechanical properties of our pure peptide hydrogels, in this work we examined the possibility of creating a double hydrogel network. This network was created by means of the coassembly of mutually attractive, but self‐repulsive oligopeptides within an already‐existing fibrous network formed by the charged, biocompatible polysaccharides chitosan, alginate, and chondroitin. Using dynamic oscillatory rheology experiments, it was found that the coassembly of the peptides within the existing polysaccharide network resulted in a less stiff material as compared to the pure peptide networks (the elast... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5512063 Sat, 17 Dec 2011 06:54:17 +0100 5512063 http://www.medworm.com/index.php?rid=5512062&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21721 We report here a comparative study of the molecular conformational energy landscape generated using the mutually orthogonal Latin squares (MOLS) method, molecular dynamics (MD), and Monte Carlo (MC) simulation. The MOLS method, as described earlier from our laboratory, uses an experimental design technique to rapidly and exhaustively sample the low energy conformations of a molecule. MD and MC simulations have been used to perform similar tasks. In the comparison reported here, the three methods were applied to a pair of neuropeptides, namely Met‐ and Leu‐enkephalin. A set of 1500 conformations of these enkephalins were generated using these methods with CHARMM22 force field, and the resulting samples were analyzed to determine the extent and nature of coverage of the conformational sp... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5512062 Sat, 17 Dec 2011 06:54:16 +0100 5512062 http://www.medworm.com/index.php?rid=5512060&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21710 We report NMR studies of transient hydrogen bonding in a polysaccharide (PS) dissolved in water without cosolvent at ambient temperature. The PS portion of the Escherichia coli O142 lipopolysaccharide is comprised of repeating pentasaccharide units of GalNAc (N‐acetyl galactosamine), GlcNAc (N‐acetyl glucosamine), and rhamnose in a 3:1:1 ratio, respectively. A 105‐ns molecular dynamics (MD) simulation on one pentasaccharide repeat unit predicts transient inter‐residue hydrogen bonds from the GalNAc NH groups in the PS. To investigate these predictions experimentally, the PS was uniformly 13C,15N enriched and the NH, carbonyl, C2, C4, and methyl resonances of the GalNAc and GlcNAc residues assigned using through‐bond triple‐resonance NMR experiments. Temperature dependence of am... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5512060 Sat, 17 Dec 2011 06:54:13 +0100 5512060 http://www.medworm.com/index.php?rid=5500904&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22016 In this study we investigated the blend electrospinning of poly(ε‐caprolactone) (PCL) and silk fibroin (SF) to improve the biodegradability and biocompatibility of PCL‐based nanofibrous scaffolds. Optimal conditions to fabricate PCL/SF (50/50) blend nanofiber were established for electrospinning using formic acid as a co‐solvent and three‐dimensional (3D) PCL/SF blend nanofibrous scaffolds were prepared by a modified electrospinning process using methanol coagulation bath. The physical properties of 2D PCL/SF blend nanofiber mats and 3D highly porous blend nanofibrous scaffolds were measured and compared. In order to evaluate cytocompatibility of the 3D blend scaffolds compared to 3D PCL nanofibrous scaffold, normal human dermal fibroblasts (NHDFs) were cultured. It is concluded t... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5500904 Wed, 14 Dec 2011 07:58:56 +0100 5500904 http://www.medworm.com/index.php?rid=5500906&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22014 AbstractProtein extracted from Moringa oleifera (MO) seeds has been advocated as a cheap and environmentally friendly alternative to ionic flocculants for water purification. However, the nature and mechanism of its interaction with particles in water, as well as with dissolved surface‐active molecules, is not well understood. In this article, we report studies of the protein and its interaction with four surfactants using dynamic light scattering (DLS), zeta potential and turbidity measurements. Zeta potential measurements identified points of charge reversal and the turbidity and DLS measurements were used to characterize the microstructure and size of protein‐surfactant complexes. From the points of charge reversal, it was estimated that 7 anions are required to neutralize the posit... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5500906 Wed, 14 Dec 2011 05:00:00 +0100 5500906 http://www.medworm.com/index.php?rid=5500905&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22015 This study presents the numerous challenges of designing biologically active stapled peptides and the conclusions have broad implications for optimizing a promising new class of compounds in drug discovery. © 2011 Wiley Periodicals, Inc. Biopolymers, 2011 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=5500905 Wed, 14 Dec 2011 05:00:00 +0100 5500905 http://www.medworm.com/index.php?rid=5492374&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22013 AbstractWe have examined the effect of like‐charged residues on the conformation of an oligoalanine sequence. This was facilitated by CD and NMR spectroscopic and differential scanning calorimetric (DSC) measurements, and molecular dynamics calculations, of the following three alanine‐based peptides: Ac‐K‐(A)5‐K‐NH2 (KAK5), Ac‐K‐(A)4‐K‐NH2 (KAK4), Ac‐K‐(A)3‐K‐NH2 (KAK3), where A and K denote alanine and lysine residues, respectively. Our earlier studies suggested that the presence of like‐charged residues at the end of a short polypeptide chain composed of nonpolar residues can induce a chain reversal. For all three peptides, canonical MD simulations with NMR‐derived restraints demonstrate the presence of ensembles of structures with a tendency to form a cha... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5492374 Sun, 11 Dec 2011 07:52:49 +0100 5492374 http://www.medworm.com/index.php?rid=5492375&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22011 AbstractLepidoperan silks provide a superb opportunity for comparative studies of spinning and fibre characteristics. Comparing the four species Bombyx mori (China), Actias selene (India), Antheraea yamamai (Japan), Gonometa postica (Africa), allows us to examine differences on the family, species and race levels. Measured rheological properties were consistent with phylogenetic relationships and in the context of resource allocation and gland morphology. We propose that the thorough domestication of the mulberry silkworm Bombyx mori for high silk yield has resulted in a compensatory optimisation for spinning efficiency. This is in stark contrast to the wild silkworms, where Saturnids appear to minimise their energetic input towards silk output and Gonometa postica seems to balance both. W... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5492375 Fri, 09 Dec 2011 05:00:00 +0100 5492375 http://www.medworm.com/index.php?rid=5464914&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21714 AbstractThe structure and properties of the 11 Camptothecin derivatives (CPTs) and their different mono‐, di‐, and triprotonated forms, depending on the number of proton accepting centers in the molecules are studied both theoretically and experimentally by quantum chemical approaches, electronic absorption, and CD spectroscopy. The study of the protonated forms of the CPTs and search of the electron‐withdrawing groups is crucial of the water‐solubility of the novel medications. Thus, the model interaction of the different protonated molecular species with the Topoisomerase I–DNA complex are elucidated and discussed with a view to understand the mode of binding of the CPTs depending on the type of the substituents and pH of the medium. © 2011 Wiley Periodicals, Inc. Biopolymers ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5464914 Fri, 02 Dec 2011 07:36:10 +0100 5464914 http://www.medworm.com/index.php?rid=5464913&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21709 This article focuses on the use of growth and storage conditions to control the length of amyloid fibrils formed from bovine insulin, with length distributions constructed from transmission electron microscopy (TEM) images. Growth temperature, pH, protein concentration, and storage conditions were examined and were seen to offer a range of conditions that favor different length distribution. The use of amyloid fibrils as nanowires is one area where control of fibril dimensions is desirable, for experimental setup and endpoint applications. The conductive properties of fibrils formed from bovine insulin are presented, with these insulin fibrils being shown to have high resistivity in their unmodified state, with current values in the nanoamp range. These low current values can be increased ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5464913 Fri, 02 Dec 2011 07:36:09 +0100 5464913 http://www.medworm.com/index.php?rid=5464912&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21706 In this study, the effects of this abundant modified nucleotide on the structure and stability of H69 were compared with those of uridine in double‐stranded (stem) regions. These results were compared with previous hairpin (stem plus single‐stranded loop) studies to understand the contributions of the loop sequences to H69 structure and stability. The role of a loop nucleotide substitution from an A in bacteria (position 1918 in Escherichia coli 23S rRNA) to a G in eukaryotes (position 3734 in H. sapiens 28S rRNA) was examined. Thermodynamic parameters for the duplex RNAs were obtained through UV melting studies, and differences in the modified and unmodified RNA structures were examined by circular dichroism spectroscopy. The overall folded structure of human H69 appears to be similar... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5464912 Fri, 02 Dec 2011 07:36:05 +0100 5464912 http://www.medworm.com/index.php?rid=5464911&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21701 This article provides intensive description on various extrusion based scaffold fabrication techniques and review their potential utility for TE applications. The extrusion‐based technique extrudes the molten polymer as a thin filament through a nozzle onto a platform layer‐by‐layer and thus building 3D scaffold. The technique allows full control over pore architecture and dimension in the x‐ and y‐ planes. However, the pore height in z‐direction is predetermined by the extruding nozzle diameter rather than the technique itself. This review attempts to assess the current state and future prospects of this technology. © 2011 Wiley Periodicals, Inc. Biopolymers 97: 83–93, 2012. (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=5464911 Fri, 02 Dec 2011 07:36:03 +0100 5464911 http://www.medworm.com/index.php?rid=5464910&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22008 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=5464910 Fri, 02 Dec 2011 07:36:02 +0100 5464910 http://www.medworm.com/index.php?rid=5447395&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22010 AbstractThe interaction of human linker histone H1(0) with short oligonucleotides was characterized. The capability of the histone to promote DNA strand exchange in this system has been demonstrated. The reaction is reversible at saturating amounts of H1 corresponding to complete binding of the oligonucleotide substrates with the histone. In our conditions the complete saturation of DNA with the histone occurs at a ratio of one protein molecule per about sixty nucleotides irrespectively of DNA strandedness. In contrast to the DNA strand exchange promoted by RecA‐like enzymes of homologous recombination the H1 promoted reaction exhibits low tolerance to interruptions of homology between oligonucleotide substrates comparable to those for the case of spontaneous strand exchange between free... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5447395 Sat, 26 Nov 2011 07:19:55 +0100 5447395 http://www.medworm.com/index.php?rid=5447396&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22009 AbstractThe binding free energies of the inhibitor‐heme model complexes are calculated using the density functional methods and the implicit solvation models in water, where the 16 structurally diverse compounds with a spectrum of IC50 values from 0.05 (clotrimazole) to 1000 (piroxicam) μM are chosen as inhibitors for Cytochrome P450 3A4 (CYP3A4). CYP3A4 is the most predominant constituent of the human hepatic CYP enzymes that play a role in metabolizing structurally diverse xenobiotics. The observed free energy change for each inhibitory binding, ΔG°inh, is obtained from its IC50 value. The total binding free energy (ΔG°b) of each inhibitor‐heme model complex is calculated by the sum of its relative free energy (ΔG°) in the gas phase and solvation free energy to the water‐hem... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5447396 Thu, 24 Nov 2011 05:00:00 +0100 5447396 http://www.medworm.com/index.php?rid=5396435&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22006 AbstractFibrous proteins in nature fulfill a wide variety of functions in different structures ranging from cellular scaffolds to very resilient structures like tendons and even extra‐corporal fibers such as silks in spider webs or silkworm cocoons. Despite their different origins and sequence varieties many of these fibrous proteins share a common building principle: they consist of a large repetitive core domain flanked by relatively small non‐repetitive terminal domains. Amongst protein fibers, spider dragline silk shows prominent mechanical properties that exceed those of man‐made fibers like Kevlar. Spider silk fibers assemble in a spinning process allowing the transformation from an aqueous solution into a solid fiber within milliseconds. Here, we highlight the role of the non�... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5396435 Fri, 11 Nov 2011 07:27:40 +0100 5396435 http://www.medworm.com/index.php?rid=5396437&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22004 We report 100 ns molecular dynamics simulations, at various temperatures, of sucrose in water (with concentrations of sucrose ranging from 0.02 to 4 M), and in a 7:3 water‐DMSO mixture. Convergence of the resulting conformational ensembles was checked using adaptive‐biased simulations along the glycosidic ϕ and ψ.torsion angles. NMR relaxation parameters, including longitudinal (R1) and transverse (R2) relaxation rates, nuclear Overhauser enhancements (NOE), and generalized order parameter (S2) were computed from the resulting time‐correlation functions. The amplitude and time scales of molecular motions change with temperature and concentration in ways that track closely with experimental results, and are consistent with a model in which sucrose conformational fluctuations are lim... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5396437 Sat, 05 Nov 2011 04:00:00 +0100 5396437 http://www.medworm.com/index.php?rid=5396436&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.22005 AbstractReported literature values of the tensile properties of natural silk cover a wide range. While much of this inconsistency is the result of variability that is intrinsic to silk, some is also a consequence of differences in the way that silk is prepared for tensile tests. Here we explore how measured mechanical properties of Bombyx mori cocoon silk are affected by two intrinsic factors (the location from which the silk is collected within the cocoon, and the color of the silk), and two extrinsic factors (the storage conditions prior to testing, and different styles of reeling the fiber). We find that extrinsic and therefore controllable factors can affect the properties more than the intrinsic ones studied. Our results suggest that enhanced inter‐laboratory collaborations, that le... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5396436 Sat, 05 Nov 2011 04:00:00 +0100 5396436 http://www.medworm.com/index.php?rid=5355065&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21705 AbstractThe X‐ray diffraction analysis of a stereocontrolled heterochiral designed model peptide Boc‐DPro‐Thr‐OMe (1) revealed the existence of an unusual folded molecular structure, stabilized via an effective unconventional CH…O type intramolecular hydrogen‐bond, encompassing a noncovalent 12‐membered ring‐motif. Together with an uncommon type a disposition of the urethane moiety, the tightly folded topology is compounded with a cis‐DPro imide‐bond. The overall conformation is suggested to be the reminiscent of specific type VI β‐turn structures, hitherto, characterized across the Aaa‐cis‐Pro peptide‐bonds in globular proteins and polypeptides. The 13C NMR spectrum of 1 in an apolar CDCl3 environment revealed the presence of approximately an equal populati... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5355065 Thu, 27 Oct 2011 23:27:58 +0100 5355065 http://www.medworm.com/index.php?rid=5355064&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21703 AbstractThe covalent linkage between the side‐chain and the backbone nitrogen atom of proline leads to the formation of the five‐membered pyrrolidine ring and hence restriction of the backbone torsional angle ϕ to values of −60 °± 30° for the L‐proline. Diproline segments constitute a chain fragment with considerably reduced conformational choices. In the current study, the conformational states for the diproline segment (LPro‐LPro) found in proteins has been investigated with an emphasis on the cis and trans states for the Pro‐Pro peptide bond. The occurrence of diproline segments in turns and other secondary structures has been studied and compared to that of Xaa‐Pro‐Yaa segments in proteins which gives us a better understanding on the restriction imposed on other res... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5355064 Thu, 27 Oct 2011 23:27:55 +0100 5355064 http://www.medworm.com/index.php?rid=5355063&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21700 AbstractAdrenomedullin (AM) is a regulatory peptide which plays many physiological roles including vasodilatation, bronchodilatation, hormone secretion regulation, growth, apoptosis, angiogenesis, and antimicrobial activities, among others. These regulatory activities make AM a relevant player in the pathophysiology of important diseases such as cardiovascular and renal conditions, cancer, and diabetes. Therefore, molecules that target the AM system have been proposed as having therapeutic potential. To guide the design and characterization of such molecules, we elucidated the three‐dimensional structure of AM in a membrane mimicking medium using NMR spectroscopy methods. Under the employed experimental conditions, the structure can be described as composed by a central α‐helical regi... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5355063 Thu, 27 Oct 2011 23:27:54 +0100 5355063 http://www.medworm.com/index.php?rid=5355062&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21691 AbstractMixing oppositely charged polyelectrolytes in aqueous solutions leads to the spontaneous formation of polyelectrolyte complexes. Here, we characterize the interaction between xanthan of two different chain lengths, a tri‐glucosamine and a chitosan polymer by isothermal titration calorimetry (ITC). Analysis of the experimental thermodynamic data assuming a single set of identical sites indicated both enthalpic and entropic contributions to the overall interaction in the interaction between xanthan and tri‐glucosamine. The relative contribution of entropy compared to enthalpy was found to be largest for the shortest chain length of xanthan. Using a chitosan polymer instead of tri‐glucosamine gave rise to two different stages in the interaction process. A model where the first s... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5355062 Thu, 27 Oct 2011 23:27:49 +0100 5355062 http://www.medworm.com/index.php?rid=5355061&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21726 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=5355061 Thu, 27 Oct 2011 23:27:47 +0100 5355061 http://www.medworm.com/index.php?rid=5355059&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21729 AbstractSpider dragline silk is a self‐assembling tunable protein composite fiber that rivals many engineering fibers in tensile strength, extensibility, and toughness, making it one of most versatile biocompatible materials and most inviting for synthetic mimicry. While experimental studies have shown that the peptide sequence and molecular structure of silk have a direct influence on the stiffness, toughness, and failure strength of silk, few molecular‐level analyses of the nanostructure of silk assemblies, in particular under variations of genetic sequences, have been reported. Here, atomistic‐level structures of wildtype as well as modified MaSp1 protein from the N. clavipes spider dragline silk sequences, obtained using an in silico approach based on replica exchange molecular d... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5355059 Thu, 27 Oct 2011 23:27:16 +0100 5355059 http://www.medworm.com/index.php?rid=5355060&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21730 AbstractExtensive studies on the structure of collagen have revealed that the hydroxylation of Pro residues in a variety of model peptides with the typical (X‐Y‐Gly)n repeats (X and Y: Pro and its analogues) represents one of the major factors influencing the stability of triple helices. While (2S,4R)‐hydroxyproline (Hyp) at the position Y stabilizes the triple helix, (2S,4S)‐hydroxyproline (hyp) at the X‐position destabilizes the helix as demonstrated that the triple helix of (hyp‐Pro‐Gly)15 is less stable than that of (Pro‐Pro‐Gly)15 and that a shorter peptide (hyp‐Pro‐Gly)10 does not form the helix. In order to clarify the role of the hydroxyl group of Pro residues to play in the stabilization mechanism of the collagen triple helix, we synthesized and crystallized ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5355060 Mon, 24 Oct 2011 04:00:00 +0100 5355060 http://www.medworm.com/index.php?rid=5343374&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21732 AbstractXIAP, an important regulator of apoptosis, has emerged as a target for the development of cancer therapeutics. The homodimeric Smac protein simultaneously binds to both the BIR2 and BIR3 domains of XIAP. Peptide‐based dimeric compounds that mimic the binding mode of Smac show promise as XIAP antagonists. Herein we characterize the first example of a Smac mimetic that incorporates a peptide sequence specific for BIR2. We show that the tetrapeptide motif Ala‐Glu‐Ala‐Val has a higher affinity for BIR2 than the BIR3‐specific sequence Ala‐Val‐Pro‐Phe, and we compare the binding characteristics of a heterodimeric peptide containing both tetrapeptide motifs to those of a homodimeric peptide featuring only AVPF. Despite the enhanced affinity of AEAV (relative to AVPF) for B... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5343374 Sun, 23 Oct 2011 22:26:45 +0100 5343374 http://www.medworm.com/index.php?rid=5343376&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21728 AbstractDNA electrostatic character is mostly determined by both water and counterions activities in the phosphate backbone which, together with base sequence, further confer its higher‐order structure. We overstretch individual double‐stranded DNA molecules in water‐ethanol solutions to investigate the modulation of its mechanical stability by hydration and polycations. We find that DNA denatures as ethanol concentration is increased and spermine concentration decreased. This is manifested by an increase in melting hysteresis between the stretch and release curves, with sharp transition at 10% ethanol and reentrant behavior at 60%, by a loss of cooperativity in the overstretching transition and by a dramatic decrease of both the persistence length and the flexural rigidity. Changes ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5343376 Sun, 23 Oct 2011 04:00:00 +0100 5343376 http://www.medworm.com/index.php?rid=5343375&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21731 AbstractAmyloid aggregates have been implicated in the pathogenesis of diseases such as type 2 diabetes, Alzheimer's, Parkinson's and prion disease. Recently determined microcrystal structures of several short peptide segments derived from fibril‐forming proteins revealed co‐existence of alternative aggregation modes (amyloid polymorphism) formed by the same segment. This polymorphism may help in understanding the influence of the side chain packing on the amyloid stability. Here we use Molecular Dynamics (MD) simulation to analyze the stability of five pairs of polar and nonpolar polymorphic oligomers. MD simulation shows polymorphs with steric zipper interface containing large polar and/or aromatic side chains (GNNQQNY, and NNQNTF) are more stable than steric zipper interfaces made o... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5343375 Sun, 23 Oct 2011 04:00:00 +0100 5343375 http://www.medworm.com/index.php?rid=5343377&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21724 AbstractThe two Flag/MaSp 2 silk proteins produced recombinantly were based on the basic consensus repeat of the dragline silk spidroin 2 protein (MaSp 2) from the Nephila clavipes orb weaving spider. However, the proline‐containing pentaptides juxtaposed to the polyalanine segments resembled those found in the flagelliform silk protein (Flag) composing the web spiral: (GPGGX1 GPGGX2)2 with X1/X2=A/A or Y/S. Fibers were formed from protein films in aqueous solutions or extruded from resolubilized protein dopes in organic conditions when the Flag motif was (GPGGX1 GPGGX2)2 with X1/X2 = Y/S or A/A, respectively. Post fiber processing involved similar drawing ratios (2‐2.5x) before or after water‐treatment. Structural (ssNMR and XRD) and morphological (SEM) changes in the fibers were co... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5343377 Thu, 20 Oct 2011 04:00:00 +0100 5343377 http://www.medworm.com/index.php?rid=5321230&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21725 AbstractFibrils of type I collagen in the skin are exposed to ultraviolet (UV) light and there have been claims that collagen photo‐degradation leads to wrinkles and may contribute to skin cancers. To understand the effects of UV radiation on collagen, type I collagen solutions were exposed to the UV‐C wavelength of 254 nm for defined lengths of time at 40C. Circular dichroism (CD) experiments show that irradiation of collagen leads to high loss of triple helical content with a new lower thermal stability peak and SDS‐gel electrophoresis indicates breakdown of collagen chains. To better define the effects of UV radiation on the collagen triple‐helix, the studies were extended to peptides which model the collagen sequence and conformation. CD studies showed irradiation for days led ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5321230 Sun, 16 Oct 2011 09:20:02 +0100 5321230 http://www.medworm.com/index.php?rid=5310471&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21723 AbstractA review of thermodynamic, materials science, and rheological liquid crystal models is presented and applied to a wide range of biological liquid crystals, including helicoidal plywoods, biopolymer solutions, and in‐vivo liquid crystals. The distinguishing characteristics of liquid crystals (self‐assembly, packing, defects, functionalities, processability) are discussed in relation to biological materials and the strong correspondence between different synthetic and biological materials is established. Biological polymer processing based on liquid crystalline precursors includes viscoelastic flow to form and shape fibers. Viscoelastic models for nematic and chiral nematics are reviewed and discussed in terms of key parameters that facilitate understanding and quantitative infor... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5310471 Thu, 13 Oct 2011 08:15:08 +0100 5310471 http://www.medworm.com/index.php?rid=5310472&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21722 AbstractBiocompatible and biodegradable peptide hydrogels are drawing increasing attention as prospective materials for human soft tissue repair and replacement. To improve the rather unfavorable mechanical properties of our pure peptide hydrogels, in this work we examined the possibility of creating a double hydrogel network. This network was created by means of the co‐assembly of mutually attractive but self‐repulsive oligopeptides within an already existing fibrous network formed by the charged, biocompatible polysaccharides chitosan, alginate, and chondroitin. Using dynamic oscillatory rheology experiments, it was found that the co‐assembly of the peptides within the existing polysaccharide network resulted in a less stiff material as compared to the pure peptide networks (the el... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5310472 Wed, 12 Oct 2011 04:00:00 +0100 5310472 http://www.medworm.com/index.php?rid=5268344&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21688 AbstractCatalytic mechanisms of carboxypeptidase A (CPA) are well known for their diversity and the relative inaccessibility for a decisive comprehension. Recent encouraging attempts through modern computational techniques promoted new challenges for the complementary experimental endeavors. In this work, we have applied the stopped‐flow technique and the method of reaction progress curve fitting to extract kinetic parameters for the CPA‐catalyzed hydrolyses of smaller (typical) peptide and ester substrates, known for their strong activating/inhibiting impact, thus to which the traditional method of “initial rates” is not applicable. Our approach that innately implies the overall constancy of the affecter (substrate plus “active” product) concentration, made it possible to rigo... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5268344 Fri, 30 Sep 2011 08:44:39 +0100 5268344 http://www.medworm.com/index.php?rid=5268343&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21687 AbstractNetworks made from chitosan and alginate have been utilized as prospective tissue engineering scaffolds due to material biocompatibility and degradability. Calcium (Ca2+) is often added to these networks as a modifier for mechanical strength enhancement. In this work, we examined changes in the bulk material properties of different concentrations of chitosan/alginate mixtures (2, 3, or 5% w/w) upon adding another modifier, chondroitin. We further examined how material properties depend on the order the modifiers, Ca2+ and chondroitin, were added. It was found that the addition of chondroitin significantly increased the mechanical strength of chitosan/alginate networks. Highest elastic moduli were obtained from samples made with mass fractions of 5% chitosan and alginate, modified b... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5268343 Fri, 30 Sep 2011 08:44:38 +0100 5268343 http://www.medworm.com/index.php?rid=5268342&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21683 We describe here the synthesis and properties of pH‐insensitive APols obtained by replacing isopropyles with taurine. Sulfonated APols (SAPols) can be used to trap MPs in the form of small complexes, to stabilize them, and to keep them water‐soluble even at low pH. [15N,1H]‐transverse relaxation‐optimized spectroscopy NMR spectra obtained at pH 6.8 of a bacterial outer MP folded in SAPols show that the protein is correctly folded. The spectra have a resolution similar to that achieved with A8‐35 and reveal water‐exposed amide and indole protons whose resonance peaks are absent at pH 8.0. © 2011 Wiley Periodicals, Inc. Biopolymers 95: 811–823, 2011. (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=5268342 Fri, 30 Sep 2011 08:44:34 +0100 5268342 http://www.medworm.com/index.php?rid=5256980&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21721 We report here a comparative study of the molecular conformational energy landscape generated using the MOLS method, molecular dynamics (MD) and Monte Carlo (MC) simulation. The MOLS method, as described earlier from our laboratory, uses an experimental design technique to rapidly and exhaustively sample the low energy conformations of a molecule. MD and MC simulation have been used to perform similar tasks. In the comparison reported here, the three methods were applied to a pair of neuropeptides, viz. Met‐ and Leu‐enkephalin. A set of 1500 conformations of these enkephalins were generated using these methods with CHARMM22 force field, and the resulting samples were analyzed to determine the extent and nature of coverage of the conformational space. The results indicate that the MOLS ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5256980 Mon, 26 Sep 2011 23:42:07 +0100 5256980 http://www.medworm.com/index.php?rid=5246002&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21720 AbstractCaddisflys (order Trichoptera) construct elaborate protective shelters and food harvesting nets with underwater adhesive silk. The silk fiber resembles a nanostructured tape composed of thousands of nanofibrils (∼120 nm) oriented with the major axis of the fiber, which in turn are composed of spherical subunits. Weaker lateral interactions between nanofibrils allow the fiber to conform to surface topography and increase contact area. Highly phosphorylated (pSX)4 motifs in H‐fibroin blocks of positively charged basic residues are conserved across all three suborders of Trichoptera. Electrostatic interactions between the oppositely charged motifs could drive liquid‐liquid phase separation of silk fiber precursors into a complex coacervates mesophase. Accessibility of phosphoser... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5246002 Fri, 23 Sep 2011 07:31:58 +0100 5246002 http://www.medworm.com/index.php?rid=5246003&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21719 AbstractThe antisense DNA sequence of mature mouse micro RNA, miR341, includes three repeats of the tetranucleotide (GACC). The –GAC– repeat is known to form a parallel duplex, in acidic environments. The thermal melting profile of miR341 DNA, at pH 4, 5, and 6 indicates the formation of a very stable structure, which loses its stability when pH is increased. Thus, the addition of a cytosine at the 3′ end of the (GAC) motif preserves the molecule's potential to fold into an unusual structure at low pH. The effect of modifying the nucleotide composition of the GACC sequence on the secondary structures formed by oligomers containing seven tandem repeats of the altered motifs was examined here. UV melting profiles were determined, as a function of pH, for 28‐mers of the two series (GA... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5246003 Thu, 22 Sep 2011 04:00:00 +0100 5246003 http://www.medworm.com/index.php?rid=5233054&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21718 AbstractWe prepared the water soluble model peptide, (E)8GGLGGQGAG(A)6GGAGQGGYGG, to throw light on the local structure of spidroin 1 (MaSpl) protein in spider dragline silk of Nephila clavipes before and after spinning. Solution 13C NMR showed that the conformation of the peptide in aqueous solution was essentially random coil. Solid‐state NMR was used to follow conformation‐dependent 13C chemical shifts in 13C selectively labeled versions of the peptide. The peptide lyophilized from an aqueous solution at neutral pH (hereafter referred to as “without acid treatment)”was used to mimic the state of the spidroin stored in the spider's silk gland while the peptide precipitated from the acidic solution (“with acid treatment”) was used to simulate the role of acid treatment in indu... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5233054 Mon, 19 Sep 2011 21:06:18 +0100 5233054 http://www.medworm.com/index.php?rid=5203832&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21716 AbstractThe structural consequences derived from the incorporation of either a methyl or a phenyl group at the α carbon of proline were recently investigated by quantum mechanical calculations (J Org Chem 2008, 73, 3418). In the present work, the effect produced by contraction of the pyrrolidine ring on such α‐substituted proline analogues has been explored using the same computational methods. Specifically, the intrinsic conformational preferences of the N‐acetyl‐N'‐methylamide derivatives of the lower proline homologue L‐azetidine‐2‐carboxylic acid (Aze), characterized by a four‐ instead of a five‐membered ring, and its α‐methyl (αMeAze) and α‐phenyl (αPhAze) derivatives have been determined using quantum mechanical calculations and compared to those observed ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5203832 Sun, 11 Sep 2011 03:15:55 +0100 5203832 http://www.medworm.com/index.php?rid=5203836&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21703 AbstractThe covalent linkage between the side‐chain and the backbone nitrogen atom of Proline leads to the formation of the five‐membered pyrrolidine ring and hence restriction of the backbone torsional angle ϕ to values of ‐60°?30° for the L‐Proline. Diproline segments constitute a chain fragment with considerably reduced conformational choices. In the current study, the conformational states for the diproline segment (LPro‐LPro) found in proteins has been investigated with an emphasis on the cis and trans states for the Pro‐Pro peptide bond. The occurrence of diproline segments in turns and other secondary structures has been studied and compared to that of Xaa‐Pro‐Yaa segments in proteins which gives us a better understanding on the restriction imposed on other residu... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5203836 Tue, 06 Sep 2011 04:00:00 +0100 5203836 http://www.medworm.com/index.php?rid=5203835&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21717 AbstractThe spinning process of spiders can modulate the mechanical properties of their silk fibers. It is therefore of primary importance to understand what are the key elements of the spider spinning process to develop efficient industrial spinning processes. We have exhaustively investigated the native conformation of major ampullate silk (MaS) proteins by comparing the content of the major ampullate gland of Nephila clavipes, solubilized MaS (SolMaS) fibers and the recombinant proteins rMaSpI and rMaSpII using 1H solution NMR spectroscopy. The results indicate that the protein secondary structure is basically identical for the recombinant protein rMaSpI, SolMaS proteins and the proteins in the dope, and corresponds to a disordered protein rich in 31‐helices. The data also show that g... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5203835 Tue, 06 Sep 2011 04:00:00 +0100 5203835 http://www.medworm.com/index.php?rid=5203834&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21714 AbstractThe structure and properties of the eleven Camptothecin derivatives (CPTs) and their different mono‐, di‐ and triprotonated forms, depending of the number of proton accepting centres in the molecules are studied both theoretically and experimentally by quantum chemical approaches, electronic absorption and CD spectroscopy. The study of the protonated forms of the CPTs and search of the electron‐withdrawing groups is crucial of the water‐solubility of the novel medications. Thus, the model interaction of the different protonated molecular species with the Topoisomerase I‐DNA complex are elucidated and discussed with a view to understand the mode of binding of the CPTs depending of the type of the substituents and pH of the medium. © 2011 Wiley Periodicals, Inc. Biopolymer... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5203834 Tue, 06 Sep 2011 04:00:00 +0100 5203834 http://www.medworm.com/index.php?rid=5203833&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21715 AbstractSpider silk is a fascinating material, combining remarkable mechanical properties with low density and biodegradability. Because of these properties and historical descriptions of medical applications, spider silk has been proposed to be the ideal biomaterial. However, overcoming the obstacles to produce spider silk in sufficient quantities and in a manner that meets regulatory demands has proven to be a difficult task. Also, there are relatively few studies of spider silk in biomedical applications available, and the methods and materials used vary a lot. Herein we summarize cell culture‐ and in vivo implantation studies of natural and synthetic spider silk, and also review the current status and future challenges in the quest for a large scale production of spider silk for medi... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5203833 Tue, 06 Sep 2011 04:00:00 +0100 5203833 http://www.medworm.com/index.php?rid=5190954&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21713 AbstractThe 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 compared it with the performance of HOBt and HOAt. In addition, the compatibility of these additives with the highly acid‐labile 2‐chlorotrityl chloride resin is examined. © 2011 Wiley Periodicals, Inc. Biopolymers, 2011. (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=5190954 Sun, 04 Sep 2011 01:52:27 +0100 5190954 http://www.medworm.com/index.php?rid=5190955&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21712 AbstractRaman spectroscopy has long been proved to be a useful tool to study the conformation of protein‐based materials such as silk. Thanks to recent developments, linearly polarized Raman spectromicroscopy has appeared very efficient to characterize the molecular structure of native single silk fibers and spinning dopes since it can provide information relative to the protein secondary structure, molecular orientation and amino acid composition. This review will describe recent advances in the study of the structure of silk by Raman spectromicroscopy. A particular emphasis is put on the spider dragline and silkworm cocoon threads, other fibers spun by orb‐weaving spiders, the spinning dope contained in their silk glands and the effect of mechanical deformation. Taken together, the r... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5190955 Tue, 30 Aug 2011 23:00:00 +0100 5190955 http://www.medworm.com/index.php?rid=5168686&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21672 AbstractEpstein‐Barr virus (EBV), a human γ‐herpesvirus, establishes lifelong infection by targeting the adaptive immune system of the host through memory B cells. Although normally benign, EBV contributes to lymphoid malignancies and lymphoproliferative syndromes in immunocompromised individuals. The viral oncoprotein latent membrane protein 1 (LMP‐1) is essential for B lymphocyte immortalization by EBV. The constitutive signaling activity of LMP‐1 is dependent on homo‐oligomerization of its six‐spanning hydrophobic transmembrane domain (TMD). However, the mechanism driving LMP‐1 intermolecular interaction is poorly understood. Here, we show that the fifth transmembrane helix (TM5) of LMP‐1 strongly self‐associates, forming a homotrimeric complex mediated by a polar res... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5168686 Sun, 28 Aug 2011 00:59:10 +0100 5168686 http://www.medworm.com/index.php?rid=5168685&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21645 AbstractProtein methylation, one of the most important post‐translational modifications, typically takes place on arginine or lysine residue. The reversible modification involves a series of basic cellular processes. Identification of methyl proteins with their sites will facilitate the understanding of the molecular mechanism of methylation. Besides the experimental methods, computational predictions of methylated sites are much more desirable for their convenience and fast speed. Here, we propose a method dedicated to predicting methylated sites of proteins. Feature selection was made on sequence conservation, physicochemical/biochemical properties, and structural disorder by applying maximum relevance minimum redundancy and incremental feature selection methods. The prediction models ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5168685 Sun, 28 Aug 2011 00:59:09 +0100 5168685 http://www.medworm.com/index.php?rid=5168684&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21642 AbstractSecondary amide cis peptide bonds are of even lower abundance than the cis tertiary amide bonds of prolines, yet they are of biochemical importance. Using 2D NMR exchange spectroscopy (EXSY) we investigated the formation of cis peptide bonds in several oligopeptides: Ac‐G‐G‐G‐NH2, Ac‐I‐G‐G‐NH2, Ac‐I‐G‐G‐N‐NH2 and its cyclic form: I‐G‐G‐N in dimethylsulfoxide (DMSO). From the NMR studies, using the amide protons as monitors, an occurrence of 0.13–0.23% of cis bonds was obtained at 296 K. The rate constants for the trans to cis conversion determined from 2D EXSY spectroscopy were 4–9 × 10−3 s−1. Multiple minor conformations were detected for most peptide bonds. From their thermodynamic and kinetic properties the cis isomers are distinguished f... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5168684 Sun, 28 Aug 2011 00:59:08 +0100 5168684 http://www.medworm.com/index.php?rid=5168683&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21644 AbstractFor systems involving highly and oppositely charged proteins, electrostatic forces dominate association and contribute to biomolecular complex stability. Using experimental or theoretical alanine‐scanning mutagenesis, it is possible to elucidate the contribution of individual ionizable amino acids to protein association. We evaluated our electrostatic free energy calculations by comparing calculated and experimental data for alanine mutants of five protein complexes. We calculated Poisson–Boltzmann electrostatic free energies based on a thermodynamic cycle, which incorporates association in a reference (Coulombic) and solvated (solution) state, as well as solvation effects. We observe that Coulombic and solvation free energy values correlate with experimental data in highly and... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5168683 Sun, 28 Aug 2011 00:59:08 +0100 5168683 http://www.medworm.com/index.php?rid=5168682&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21711 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=5168682 Sun, 28 Aug 2011 00:59:06 +0100 5168682 http://www.medworm.com/index.php?rid=5155294&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21710 We report NMR studies of transient hydrogen bonding in a polysaccharide dissolved in water without co‐solvent at ambient temperature. The polysaccharide portion of the Escherichia coli O142 lipopolysaccharide is comprised of repeating pentasaccharide units of GalNAc (N‐acetyl galactosamine), GlcNAc (N‐acetyl glucosamine) and rhamnose in a 3:1:1 ratio, respectively. A 105 ns MD (molecular dynamics) simulation on one pentasaccharide repeat unit predicts transient interresidue hydrogen bonds from the GalNAc NH groups in the polysaccharide. To investigate these predictions experimentally, the polysaccharide was uniformly 13C,15N enriched and the NH, carbonyl, C2, C4 and methyl resonances of the GalNAc and GlcNAc residues assigned using through‐bond triple‐resonance NMR experiments. T... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5155294 Thu, 25 Aug 2011 03:44:18 +0100 5155294 http://www.medworm.com/index.php?rid=5155300&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21704 AbstractProtein kinases (PK) control phosphorylation in eukaryotic cells, and thereby regulate metabolic pathways, cell cycle progression, apoptosis and transcription. Consequently there is significant interest in manipulating PK activity and treat diseases by using small‐molecule drugs. All PK catalytic domains undergo large conformational changes as a result of substrate binding and phosphorylation. The “closed” state of a PK cataltic domain is the only state able to phosphorylate the target substrate, which makes the two other observed states (the “open” and the “intermediate” states) interesting drug targets. We investigate if MD simulations starting from the closed state of the catalytic domain of protein kinase A (C‐PKA) can be used to produce realistic structures rep... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5155300 Thu, 18 Aug 2011 23:00:00 +0100 5155300 http://www.medworm.com/index.php?rid=5155299&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21705 AbstractThe X‐ray diffraction analysis of a stereocontrolled heterochiral designed model peptide Boc‐DPro‐Thr‐OMe (1) revealed the existence of an unusual folded molecular structure, stabilized via an effective unconventional C–H···O type intramolecular hydrogen‐bond, encompassing a non‐covalent 12‐membered ring‐motif. Together with an uncommon type a disposition of the urethane moiety, the tightly folded topology is compounded with a cis‐DPro imide‐bond. The overall conformation is suggested to be the reminiscent of specific type VI β‐turn structures, hitherto, characterized across the Aaa‐cis‐Pro peptide‐bonds in globular proteins and polypeptides. The 13C NMR spectrum of 1 in an apolar CDCl3 environment revealed the presence of approximately an equal po... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5155299 Thu, 18 Aug 2011 23:00:00 +0100 5155299 http://www.medworm.com/index.php?rid=5155298&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21706 In this study, the effects of this abundant modified nucleotide on the structure and stability of H69 were compared with those of uridine in double‐stranded (stem) regions. These results were compared with previous hairpin (stem plus single‐stranded loop) studies in order to understand the contributions of the loop sequences to H69 structure and stability. The role of a loop nucleotide substitution from an A in bacteria (position 1918 in E. coli 23S rRNA) to a G in eukaryotes (position 3734 in H. sapiens 28S rRNA) was examined. Thermodynamic parameters for the duplex RNAs were obtained through UV melting studies, and differences in the modified and unmodified RNA structures were examined by circular dichroism spectroscopy. The overall folded structure of human H69 appears to be similar... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5155298 Thu, 18 Aug 2011 23:00:00 +0100 5155298 http://www.medworm.com/index.php?rid=5155297&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21707 AbstractThe fibrillation of hen‐egg‐white lysozyme (HEWL) in the absence and presence of simple, unstructured D,L‐lysine‐co‐glycine (D,L‐Lys‐co‐gly) and D,L‐lysine‐co‐L‐phenylalanine (D,L‐Lys‐co‐Phe) copolypeptides was studied by using a variety of analytical techniques. The attenuating and decelerating effects on fibrillation are significantly dependent on the polypeptide concentration and the composition ratios in the polypeptide chain. Interestingly, D,L‐Lys‐co‐gly and D,L‐Lys‐co‐Phe copolypeptides with the same composition ratio have comparable attenuating effects on fibrillation. The copolypeptide with highest molar fraction of glycine residue exhibits the strongest suppression of HEWL fibrillation. The copolypeptide has the highest hydrophobi... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5155297 Thu, 18 Aug 2011 23:00:00 +0100 5155297 http://www.medworm.com/index.php?rid=5155296&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21708 AbstractEffect of polyethylene glycol (PEG) on protein solubility has been primarily ascribed to its large hydrodynamic size and thereby molecular crowding effect. However, PEG also shows characteristics of organic solvents. Here, we have examined the solubility of glycine and aliphatic and aromatic amino acids in PEG solutions. PEG400, PEG4000 and PEG20000 decreased the solubility of glycine, though to a much smaller magnitude than the level achieved by typical organic solvents, including ethanol and dimethyl sulfoxide. PEG4000 showed varying degree of interactions with amino acid side chains. The free energy of aliphatic side chains marginally increased by the addition of PEG4000, indicating their weak unfavorable interactions. However, it significantly decreased the free energy of the a... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5155296 Thu, 18 Aug 2011 23:00:00 +0100 5155296 http://www.medworm.com/index.php?rid=5155295&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21709 AbstractAmyloid fibrils have been recognised as having potential in a variety of bionanotechnological applications. However, realisation of these applications is constrained by a lack of control over morphology and alignment, both crucial for potential end uses. This paper focuses on the use of growth and storage conditions to control the length of amyloid fibrils formed from bovine insulin, with length distributions constructed from Transmission Electron Microscopy (TEM) images. Growth temperature, pH, protein concentration and storage conditions were examined and were seen to offer a range of conditions that favour different length distributions. The use of amyloid fibrils as nanowires is one area where control of fibril dimensions is desirable, for experimental setup and endpoint applic... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5155295 Thu, 18 Aug 2011 23:00:00 +0100 5155295 http://www.medworm.com/index.php?rid=5116863&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21702 AbstractIn this paper we review current knowledge about the silk produced by the larvae of bees, ants and hornets [Apoidea and Vespoidea: Hymenoptera]. Different species use the silk either alone or in composites for a variety of purposes including mechanical reinforcement, thermal regulation, or humidification. The characteristic molecular structure of this silk is α‐helical proteins assembled into tetrameric coiled coils. Gene sequences from seven species are available, and each species possesses a copy of each of four related silk genes that encode proteins predicted to form coiled coils. The proteins are ordered at multiple length scales within the labial gland of the final larval instar prior to spinning. The insects control the morphology of the silk during spinning to produce eit... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5116863 Thu, 11 Aug 2011 16:46:26 +0100 5116863 http://www.medworm.com/index.php?rid=5116865&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21700 AbstractAdrenomedullin (AM) is a regulatory peptide which plays many physiological roles including vasodilatation, bronchodilatation, hormone secretion regulation, growth, apoptosis, angiogenesis, and antimicrobial activities, among others. These regulatory activities make AM a relevant player in the pathophysiology of important diseases such as cardiovascular and renal conditions, cancer, and diabetes. Therefore, molecules that target the AM system have been proposed as having therapeutic potential. To guide the design and characterization of such molecules we elucidated the three‐dimensional structure of AM in a membrane mimicking medium using NMR spectroscopy methods. Under the employed experimental conditions, the structure can be described as composed by a central α‐helical regio... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5116865 Mon, 08 Aug 2011 23:00:00 +0100 5116865 http://www.medworm.com/index.php?rid=5116864&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21701 AbstractAdvances in scaffold design and fabrication technology have brought the tissue engineering field stepping into a new era. Conventional techniques used to develop scaffolds inherit limitations, such as lack of control over the pore morphology and architecture as well as reproducibility. Rapid prototyping (RP) technology, a layer‐by‐layer additive approach offers a unique opportunity to build complex 3D architectures overcoming those limitations that could ultimately be tailored to cater for patient‐specific applications. Using RP methods, researchers have been able to customize scaffolds to mimic the biomechanical properties (in terms of structural integrity, strength and micro‐environment) of the organ or tissue to be repaired/ replaced quite closely. This paper provides in... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5116864 Mon, 08 Aug 2011 23:00:00 +0100 5116864 http://www.medworm.com/index.php?rid=5061300&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21694 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=5061300 Mon, 25 Jul 2011 18:47:20 +0100 5061300 http://www.medworm.com/index.php?rid=5061297&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21698 This study examines whether amyloidogenic determinants (short peptides/amyloid forming favouring regions) exist in the sequence of NT‐proBNP, the N‐terminal part of proBNP, and if these determinants form amyloid‐like fibrils in vitro. We have predicted a possible amyloidogenic determinant in the sequence of the NT‐proBNP and we conclusively show, after its synthesis, that it forms amyloid‐like fibrils in‐vitro, utilizing transmission electron microscopy, X‐ray diffraction, ATR FT‐IR and polarizing microscopy. Thus, in this study, a possible biological role is attributed, for the first time, to a certain, specific, part of this important cardiac prohormone/natriuretic peptide, which acts as an important biomarker indicative of heart failure. Its possible direct involvement i... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5061297 Mon, 25 Jul 2011 18:46:49 +0100 5061297 http://www.medworm.com/index.php?rid=5061299&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21699 We describe an algorithm, PRONOX, for rapid computation of inter‐label distances based on calculation of spin label conformer distributions at any site of a protein. The program incorporates features of the label distribution established experimentally, including weighting of favorable conformers of the label. Distances calculated by PRONOX were compared with new DEER distances for amphiphysin and annexin B12, and with published data for FCHo2 (F‐BAR), endophilin, and α‐synuclein; a total of 44 inter‐label distances. The program reproduced these distances accurately (r2=0.94, slope=0.98). For 9 of the 11 distances for amphiphysin, PRONOX reproduced the experimental data to within 2.5 Å. The speed and accuracy of PRONOX suggests that the algorithm can be used for fitting to DEER d... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5061299 Sun, 24 Jul 2011 23:00:00 +0100 5061299 http://www.medworm.com/index.php?rid=5061298&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21697 AbstractAn 18‐residue sequence Boc‐Aib‐Val‐Ala‐Leu‐Aib‐Val‐Ala‐Leu‐Gly‐Pro‐Val‐Ala‐Leu‐Aib‐Val‐Ala‐Leu‐Aib‐OMe (UK18) was designed in order to examine the effect of introducing a Gly‐Pro segment into the middle of a potentially helical peptide. The crystal structures of two polymorphic forms yielded a view of the conformation of three independent molecules. Form 1 (space group P212121,a = 14.620Å; b = 26.506Å, c = 28.858Å, Z = 4) has one molecule in the asymmetric unit, with one co‐crystallized water molecule. Form 2 (space group P212121,a = 9.696Å; b = 19.641Å, c = 114.31Å, Z = 8) has two molecules in the asymmetric unit with four co‐crystallized water molecules. In Form 1 residues 1 to 18 adopt ϕ,ψ values which lie in the right‐hand... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5061298 Sun, 24 Jul 2011 23:00:00 +0100 5061298 http://www.medworm.com/index.php?rid=5057177&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21641 AbstractGlycosaminoglycans (GAGs) affect the efficiency of cellular uptake of a wide range of cell penetrating peptides (CPPs). GAGs have been proposed to cluster with CPPs at the cell surface before uptake but little is known about the formation or stability of CPP–GAG clusters. Here we apply a combination of heparin affinity chromatography, dynamic light scattering, and fluorescence spectroscopy to characterize the formation, stability, and size of the clusters formed between CPPs and heparin. Under conditions similar to those used in cell uptake experiments the CPP, penetratin (Antp), was observed to form significantly more stable clusters with heparin than the CPP TAT, despite TAT showing a comparable affinity for heparin. This difference in cluster stability may explain the origins ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5057177 Sun, 24 Jul 2011 03:53:41 +0100 5057177 http://www.medworm.com/index.php?rid=5057176&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21637 AbstractThe process of protein aggregation has attracted a great deal of research attention, as aggregates are first of all a nuisance to preparation of high quality protein and secondly used as novel materials. In the latter case, the process of protein aggregation needs to be controlled. Here, we show how arginine (Arg) regulates the process of heat‐induced protein aggregation. Dynamic light scattering and transmission electron microscopy revealed that heat‐induced aggregation of lysozyme at around the isoelectric point occurred in a two‐step process: formation of start aggregates, followed by further growth mediated by their sticking with diffusion‐limited cluster–cluster aggregation. In the presence of Arg, the diffusion‐limited regime changed to reaction‐limited cluster�... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5057176 Sun, 24 Jul 2011 03:53:40 +0100 5057176 http://www.medworm.com/index.php?rid=5057175&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21635 AbstractThe surface characteristics of scaffolds for bone tissue engineering must support cell adhesion, migration, proliferation, and osteogenic differentiation. In the study, poly(D,L‐lactide acid) (PDLLA) scaffolds were modified by combing ammonia (NH3) plasma pretreatment with Gly‐Arg‐Gly‐Asp‐Ser (GRGDS)‐peptides coupling technologies. The x‐ray photoelectron spectroscopy (XPS) survey spectra showed the peak of N1s at the surface of NH3 plasma pretreated PDLLA, which was further raised after GRGDS conjugation. Furthermore, N1s and C1s in the high‐resolution XPS spectra revealed the presence of CN (imine), CNH (amine), and CONH (amide) groups. The GRGDS conjugation increased amide groups and decreased amine groups in the plasma‐treated PDLLA.... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5057175 Sun, 24 Jul 2011 03:53:39 +0100 5057175 http://www.medworm.com/index.php?rid=5057174&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21629 This study provides a structural basis for the effect of the K85M mutation on the GSK3β‐FRATide complex. © 2011 Wiley Periodicals, Inc. Biopolymers 95: 669–;681, 2011. (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=5057174 Sun, 24 Jul 2011 03:53:39 +0100 5057174 http://www.medworm.com/index.php?rid=5057173&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21626 AbstractHelix (H)27 of 16S ribosomal (r)RNA from Escherichia coli was dubbed the “switch helix” when mutagenesis suggested that two alternative base pair registers may have distinct functional roles in the bacterial ribosome. Although more recent genetic analyses suggest that H27 conformational switching is not required for translation, previous solution studies demonstrated that the isolated E. coli H27 can dynamically convert between the 885 and 888 conformations. Here, we have solved the nuclear magnetic resonance solution structure of a locked 888 conformation. NOE and residual dipolar coupling restraints reveal an architecture that markedly differs from that of the 885 conformation found in crystal structures of the bacterial ribosome. In place of the loop E motif that characteriz... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5057173 Sun, 24 Jul 2011 03:53:38 +0100 5057173 http://www.medworm.com/index.php?rid=5048034&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21695 AbstractPer‐O‐methylated β‐cyclodextrin (CD) bearing an iodoacetamide group at the 6‐position was synthesized to functionalize protein surfaces. Bovine serum albumin (BSA) was quantitatively modified with the CD derivative by the SN2 reaction of iodoacetamide with a cysteine residue (Cys34) on the BSA surface. The resultant CD‐functionalized BSA (BSA‐CD) spontaneously dimerized upon addition of an anionic tetraarylporphyrin (TPPS) through the supramolecular 1:2 complexation between TPPS and CD on the protein surface. The BSA‐CD/TPPS complex further complexed with iron(III) protoporphyrin IX (hemin) in the hydrophobic pockets of albumin to form a hemin/BSA‐CD/TPPS ternary complex in which static fluorescence quenching occurred owing to intramolecular electron transfer from ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5048034 Thu, 21 Jul 2011 23:11:48 +0100 5048034 http://www.medworm.com/index.php?rid=5048035&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21696 AbstractHeparan sulfate is abundantly present in the extracellular matrix. As other glycosaminoglycans, it is synthesized in the Golgi apparatus and then exposed on the cell surface. The glucuronidase activity of human heparanase plays a major role in the structural remodeling of the extracellular matrix, which underlies cell migration, hence tumor invasion. Heparanase is therefore a major target for anti‐cancer treatment. Several inhibitors of its enzymatic activity have been synthesized. However, their design is limited by the absence of experimental structure of the protein.Homology modeling is proposed based on the structure of the endoxylanase from P. simplicissium co‐crystallized with a series of xylan oligosaccharide. The new heparanase model is consistent with the few experimen... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5048035 Wed, 20 Jul 2011 23:00:00 +0100 5048035 http://www.medworm.com/index.php?rid=5006148&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21691 AbstractMixing oppositely charged polyelectrolytes in aqueous solutions leads to the spontaneous formation of polyelectrolyte complexes. Here we characterize the interaction between xanthan of two different chain lengths, a tri‐glucosamine and a chitosan polymer by isothermal titration calorimetry (ITC). Analysis of the experimental thermodynamic data assuming a single set of identical sites indicated both enthalpic and entropic contributions to the overall interaction in the interaction between xanthan and tri‐glucosamine. The relative contribution of entropy compared to enthalpy was found to be largest for the shortest chain length of xanthan. Using a chitosan polymer instead of tri‐glucosamine gave rise to two different stages in the interaction process. A model where the first st... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5006148 Thu, 07 Jul 2011 20:13:24 +0100 5006148 http://www.medworm.com/index.php?rid=5006149&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21690 In this study, the interaction of serotonin and one of its derivatives, arachidonyl serotonin (AA‐5HT), with β‐LG was investigated using circular dichroism (CD) and fluorescence intensity measurements. These two ligands interact with β‐LG forming equimolar complexes. The binding constant for the serotonin/β‐LG interaction is between 105 and 106 M‐1, while for the AA‐5HT/β‐LG complex it is between 104 and 105 M‐1 as determined by measurements of either protein or ligand fluorescence. The observed binding affinities were higher in hydroethanolic media (25% EtOH). The interactions between serotonin/β‐LG and AA‐5HT/β‐LG may compete with self‐association (micellization) of both the ligand and the protein. According to far‐ and near‐UV CD results, these ligands ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=5006149 Mon, 04 Jul 2011 23:00:00 +0100 5006149 http://www.medworm.com/index.php?rid=4974493&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21682 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=4974493 Tue, 28 Jun 2011 17:38:59 +0100 4974493 http://www.medworm.com/index.php?rid=4974492&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21616 AbstractMolecular dynamics (MD) simulations were carried out to compare the free and bound structures of wild type U1A protein with several Phe56 mutant U1A proteins that bind the target stem loop 2 (SL2) RNA with a range of affinities. The simulations indicate the free U1A protein is more flexible than the U1A–RNA complex for both wild type and Phe56 mutant systems. A complete analysis of the hydrogen‐bonding (HB) and non‐bonded (VDW) interactions over the course of the MD simulations suggested that changes in the interactions in the free U1A protein caused by the Phe56Ala and Phe56Leu mutations may stabilize the helical character in loop 3, and contribute to the weak binding of these proteins to SL2 RNA. Compared with wild type, changes in HB and VDW interactions in Phe56 mutants o... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4974492 Tue, 28 Jun 2011 17:38:57 +0100 4974492 http://www.medworm.com/index.php?rid=4974491&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21611 AbstractA hexapeptide with amino acid sequence NNQNTF from the elk prion protein forms amyloid fibrils. Here we use molecular dynamic simulations of the oligomers and their single point glycine mutants to study their stability. In an effort to probe the structural stability and association thermodynamic in a realistic environment, all wildtype of NNQNTF polymorphic forms with different size and their corresponding double layer 5 strands single point glycine mutants were subjected to a total of 500 ns of explicit‐solvent molecular dynamics (MD) simulation. Our results show that the structural stability of the NNQNTF oligomers increases with increasing the number of β‐strands for double layers. Our results also demonstrated that hydrophobic interaction is the principle driving force to ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4974491 Tue, 28 Jun 2011 17:38:56 +0100 4974491 http://www.medworm.com/index.php?rid=4974490&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21685 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=4974490 Tue, 28 Jun 2011 17:38:56 +0100 4974490 http://www.medworm.com/index.php?rid=4959154&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21686 In this study, we examined whether a water jet system could be used to atomize crystalline cellulose, which comprises approximately 50% of plant biomass. The Star Burst System manufactured by Sugino Machine Limited (Sugino Machine; Toyama, Japan) is a unique atomization machine that uses a water jet to atomize materials and thereby places lower stress on the environment. After treatment with this system, the crystalline cellulose was converted into a gel‐like form. High‐angular annular dark‐field scanning transmission electron microscopy showed that the cellulose fibers had been converted from a solid crystalline into a matrix of cellulose nanofibers. In addition, our results show that this system can improve the saccharification efficiency of cellulases by more than three‐fold. He... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4959154 Thu, 23 Jun 2011 05:55:18 +0100 4959154 http://www.medworm.com/index.php?rid=4959156&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21688 AbstractCatalytic mechanisms of carboxypeptidase A are well‐known for their diversity and the relative inaccessibility for a decisive comprehension. Recent encouraging attempts through modern computational techniques promoted new challenges for the complementary experimental endeavors. In this work we have applied the stopped‐flow technique and the method of reaction progress curve fitting to extract kinetic parameters for the carboxypeptidase A‐catalyzed hydrolyses of smaller (typical) peptide and ester substrates, known for their strong activating/inhibiting impact, thus to which the traditional method of “initial rates” is not applicable. Our approach that innately implies the overall constancy of the affecter (substrate plus “active” product) concentration, made it possib... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4959156 Tue, 21 Jun 2011 23:00:00 +0100 4959156 http://www.medworm.com/index.php?rid=4959155&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21687 AbstractNetworks made from chitosan and alginate have been utilized as prospective tissue engineering scaffolds due to material biocompatibility and degradability. Calcium (Ca2+) is often added to these networks as a modifier for mechanical strength enhancement. In this work, we examined changes in the bulk material properties of different concentrations of chitosan/alginate mixtures (2%, 3% or 5% w/w) upon adding another modifier, chondroitin. We further examined how material properties depend on the order the modifiers, Ca2+ and chondroitin, were added. It was found that the addition of chondroitin significantly increased the mechanical strength of chitosan/alginate networks. Highest elastic moduli were obtained from samples made with mass fractions of 5% chitosan and alginate, modified ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4959155 Tue, 21 Jun 2011 23:00:00 +0100 4959155 http://www.medworm.com/index.php?rid=4891398&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21683 We describe here the synthesis and properties of pH‐insensitive APols obtained by replacing isopropyles with taurine. Sulfonated APols (SAPols) can be used to trap membrane proteins in the form of small complexes, to stabilize them, and to keep them water‐soluble even at low pH. [15N, 1H]‐TROSY NMR spectra obtained at pH 6.8 of a bacterial outer membrane protein folded in SAPols show that the protein is correctly folded. The spectra have a resolution similar to that achieved with A8‐35 and reveal water‐exposed amide and indole protons whose resonance peaks are absent at pH 8.0. © 2011 Wiley Periodicals, Inc. Biopolymers, 2011. (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=4891398 Fri, 03 Jun 2011 09:09:44 +0100 4891398 http://www.medworm.com/index.php?rid=4891399&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21684 AbstractWe measured the intrinsic viscosity of very small synthetic DNA molecules, of 20 to 395 base pairs, and incorporated them in a nearly complete picture for the whole span of molecular weights reported in the literature to date. A major transition is observed at M ∼ 2·106. It is found that in the range of ∼ 7·103 ≤ M ≤ 2·106 the intrinsic viscosity scales as [η] ∼ M1.05 suggesting that short DNA chains are not as rigid as generally thought. The corresponding scaling for the range of 2·106 ≤ M ≤ 8·1010 is [η] ∼ M0.69. A comparison of our results with existing equations, for much narrower data distributions, is made and the agreement is very satisfactory considering the huge range of data analyzed here. Experimental concerns, such as the effect of ionic strength,... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4891399 Wed, 01 Jun 2011 23:00:00 +0100 4891399 http://www.medworm.com/index.php?rid=4870489&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21638 AbstractUnstructured proteins, RNA or DNA components provide functionally important flexibility that is key to many macromolecular assemblies throughout cell biology. As objective, quantitative experimental measures of flexibility and disorder in solution are limited, small angle scattering (SAS), and in particular small angle X‐ray scattering (SAXS), provides a critical technology to assess macromolecular flexibility as well as shape and assembly. Here, we consider the Porod‐Debye law as a powerful tool for detecting biopolymer flexibility in SAS experiments. We show that the Porod‐Debye region fundamentally describes the nature of the scattering intensity decay by capturing the information needed for distinguishing between folded and flexible particles. Particularly for comparative... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4870489 Fri, 27 May 2011 22:08:11 +0100 4870489 http://www.medworm.com/index.php?rid=4870488&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21628 AbstractSmall‐angle X‐ray scattering (SAXS) is a powerful method for obtaining quantitative structural information on the size and shape of proteins, and it is increasingly used in kinetic studies of folding and association reactions. In this minireview, we discuss recent developments in using SAXS to obtain structural information on the unfolded ensemble and early folding intermediates of proteins using continuous‐flow mixing devices. Interfacing of these micromachined devices to SAXS beamlines has allowed access to the microsecond time regime. The experimental constraints in implementation of turbulence and laminar flow‐based mixers with SAXS detection and a comparison of the two approaches are presented. Current improvements and future prospects of microsecond time‐resolved SA... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4870488 Fri, 27 May 2011 22:08:11 +0100 4870488 http://www.medworm.com/index.php?rid=4870487&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21624 AbstractSmall‐angle X‐ray and neutron scattering with contrast variation have made important contributions in advancing our understanding of muscle regulatory protein structures in the context of the dynamic molecular processes governing muscle action. The contributions of the scattering investigations have depended upon the results of key crystallographic, NMR, and electron microscopy experiments that have provided detailed structural information that has aided in the interpretation of the scattering data. This review will cover the advances made using small‐angle scattering techniques, in combination with the results from these complementary techniques, in probing the structures of troponin and myosin binding protein C. A focus of the troponin work has been to understand the isofor... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4870487 Fri, 27 May 2011 22:08:09 +0100 4870487 http://www.medworm.com/index.php?rid=4870486&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21643 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=4870486 Fri, 27 May 2011 22:08:08 +0100 4870486 http://www.medworm.com/index.php?rid=4870485&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21673 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=4870485 Fri, 27 May 2011 22:08:08 +0100 4870485 http://www.medworm.com/index.php?rid=4860976&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21680 AbstractAmong heavy metals, whose toxicity cause a steadily increasing of environmental pollution, cadmium is of special concern due to its relatively high mobility in soils and potential toxicity at low concentrations. Given their ubiquitous role, zinc fingers domains have been proposed as mediators for the toxic and carcinogenic effects exerted by xenobiotic metals. To verify the structural effects of zinc replacement by cadmium in zinc fingers we have determined the high resolution structure of the single Cys2His2 zinc finger of the A. thaliana Superman protein (SUP37) complexed to the cadmium ion by means of UV‐Vis and NMR techniques. SUP37 is able to bind Cd(II) though with a dissociation constant higher than that measured for Zn(II). Cd‐SUP37 retains the ββα fold but experienc... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4860976 Wed, 25 May 2011 22:25:49 +0100 4860976 http://www.medworm.com/index.php?rid=4839422&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21677 AbstractThe effects of different surfactants on the conformational stability and structural similarity of salmon calcitonin (sCT) in aqueous solution and lyophilized forms were investigated by using microscopic Fourier transform infrared (FT‐IR) spectroscopy with second‐derivative spectral analysis. Six surfactants, HCO‐60, sodium dodecyl sulfate (SDS), Tween 80, PEG 400, Pluronic 68 and F127 were selected. The sCT aqueous solution with or without different surfactants was respectively incubated at 40oC for up to 35 hr. sCT films were casted on the CaF2 plates and IR spectra were collected as a function of incubation time. Second derivative analysis showed that the native sCT having a major α‐helical structure was gradually changed to the combination of α‐helix, random coil and... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4839422 Thu, 19 May 2011 19:23:08 +0100 4839422 http://www.medworm.com/index.php?rid=4839423&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21678 AbstractCollagen mimetic peptides (CMPs) provide critical insight into the assembly, stability and structure of the triple helical collagen protein. The majority of natural fibrous collagens are aab or abc heterotrimers, yet few examples of heterotrimeric CMPs have been reported. Previously CMP heterotrimers have only been accessible by total syntheses or by introducing complementary interstrand electrostatic or steric interactions. Here we describe an abc CMP heterotrimer in which each contributing CMP consists of only three amino acids: glycine, proline and 4‐hydroxyproline. Assembly of the heterotrimeric triple helix is directed by a combination of metal‐ion coordination to set the relative register of the CMPs, and minimization of valence frustration to direct heterotrimerization. ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4839423 Mon, 16 May 2011 23:00:00 +0100 4839423 http://www.medworm.com/index.php?rid=4811810&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21672 AbstractEpstein‐Barr virus (EBV), a human γ‐herpesvirus, establishes lifelong infection by targeting the adaptive immune system of the host through memory B cells. While normally benign, EBV contributes to lymphoid malignancies and lymphoproliferative syndromes in immunocompromised individuals. The viral oncoprotein Latent Membrane Protein 1 (LMP‐1) is essential for B lymphocyte immortalization by EBV. The constitutive signaling activity of LMP‐1 is dependent on homo‐oligomerization of its six‐spanning hydrophobic transmembrane domain (TMD). However, the mechanism driving LMP‐1 intermolecular interaction is poorly understood. Here we show that the fifth transmembrane helix (TM5) of LMP‐1 strongly self‐associates, forming a homotrimeric complex mediated by a polar residue... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4811810 Thu, 12 May 2011 04:34:19 +0100 4811810 http://www.medworm.com/index.php?rid=4787988&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21645 AbstractProtein methylation, one of the most important post‐translational modifications, typically takes place on arginine or lysine residue. The reversible modification involves a series of basic cellular processes. Identification of methyl proteins with their sites will facilitate the understanding of the molecular mechanism of methylation. Besides the experimental methods, computational predictions of methylated sites are much more desirable for their convenience and fast speed. Here, we proposed a method dedicated to predicting methylated sites of proteins. Feature selection was made on sequence conservation, physicochemical/biochemical properties and structural disorder by applying Maximum Relevance Minimum Redundancy and Incremental Feature Selection methods. The prediction models ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4787988 Fri, 06 May 2011 03:24:52 +0100 4787988 http://www.medworm.com/index.php?rid=4787989&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21646 AbstractProtein molecules are subjected to potentially denaturing fluid shear forces during processing and in circulation in the body. These complex molecules, involved in numerous biological functions and reactions, can be significantly impaired by molecular damage. There have been many studies on the effects of hydrodynamic shear forces on protein structure and function. These studies are reviewed and the implications to bioprocessing and pathophysiology of certain diseases are discussed. © 2011 Wiley Periodicals, Inc. Biopolymers, 2011. (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=4787989 Tue, 03 May 2011 23:00:00 +0100 4787989 http://www.medworm.com/index.php?rid=4774704&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21642 AbstractSecondary amide cis peptide bonds are of even lower abundance than the cis tertiary amide bonds of prolines, yet they are of biochemical importance. Using 2D NMR exchange spectroscopy we investigated the formation of cis peptide bonds in several oligopeptides: Ac‐G‐G‐G‐NH2, Ac‐I‐G‐G‐NH2, Ac‐I‐G‐G‐N‐NH2 and its cyclic form: I‐G‐G‐N in DMSO. From the NMR studies, using the amide protons as monitors, an occurrenc.e of 0.13% ‐ 0.23% of cis bonds was obtained at 296 K. The rate constants for the trans to cis conversion determined from 2D EXSY spectroscopy were 4‐9·10‐3 s‐1. Multiple minor conformations were detected for most peptide bonds. From their thermodynamic and kinetic properties the cis isomers are distinguished from minor trans isomers t... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4774704 Tue, 03 May 2011 03:37:56 +0100 4774704 http://www.medworm.com/index.php?rid=4774706&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21644 AbstractFor systems involving highly and oppositely charged proteins, electrostatic forces dominate association and contribute to biomolecular complex stability. Using experimental or theoretical alanine‐scanning mutagenesis, it is possible to elucidate the contribution of individual ionizable amino acids to protein association. We evaluated our electrostatic free energy calculations by comparing calculated and experimental data for alanine mutants of five protein complexes. We calculated Poisson‐Boltzmann electrostatic free energies based on a thermodynamic cycle, which incorporates association in a reference (Coulombic) and solvated (solution) state, as well as solvation effects. We observe that Coulombic and solvation free energy values correlate with experimental data in highly and... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4774706 Sun, 01 May 2011 23:00:00 +0100 4774706 http://www.medworm.com/index.php?rid=4774705&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21641 AbstractGlycosaminoglycans (GAGs) affect the efficiency of cellular uptake of a wide range of cell penetrating peptides (CPPs). GAGs have been proposed to cluster with CPPs at the cell surface before uptake but little is known about the formation or stability of CPP‐GAG clusters. Here we apply a combination of heparin affinity chromatography, dynamic light scattering, and fluorescence spectroscopy to characterize the formation, stability and size of the clusters formed between CPPs and heparin. Under conditions similar to those used in cell uptake experiments the CPP, penetratin (Antp), was observed to form significantly more stable clusters with heparin than the CPP TAT, despite TAT showing a comparable affinity for heparin. This difference in cluster stability may explain the origins o... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4774705 Sun, 01 May 2011 23:00:00 +0100 4774705 http://www.medworm.com/index.php?rid=4741626&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21639 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=4741626 Sat, 23 Apr 2011 04:02:35 +0100 4741626 http://www.medworm.com/index.php?rid=4741621&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21638 AbstractUnstructured proteins, RNA or DNA components provide functionally important flexibility that is key to many macromolecular assemblies throughout cell biology. As objective, quantitative experimental measures of flexibility and disorder in solution are limited, small angle scattering (SAS), and in particular small angle X‐ray scattering (SAXS), provides a critical technology to assess macromolecular flexibility as well as shape and assembly. Here, we consider the Porod‐Debye law as a powerful tool for detecting biopolymer flexibility in SAS experiments. We show that the Porod‐Debye region fundamentally describes the nature of the scattering intensity decay, which captures information needed for distinguishing between folded and flexible particles. Particularly for comparative ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4741621 Sat, 23 Apr 2011 04:02:07 +0100 4741621 http://www.medworm.com/index.php?rid=4741625&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21640 AbstractBioconjugates containing the GnRH‐III hormone decapeptide as a targeting moiety are able to deliver chemotherapeutic agents specifically to cancer cells expressing GnRH receptors, thereby increasing their local efficacy while limiting the peripheral toxicity. However, the number of GnRH receptors on cancer cells is limited and they desensitize under continuous hormone treatment. A possible approach to increase the receptor mediated tumor targeting and consequently the cytostatic effect of the bioconjugates would be the attachment of more than one chemotherapeutic agent to one GnRH‐III molecule.Here we report on the design, synthesis and biochemical characterization of multifunctional bioconjugates containing GnRH‐III as a targeting moiety and daunorubicin as a chemotherapeuti... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4741625 Tue, 19 Apr 2011 23:00:00 +0100 4741625 http://www.medworm.com/index.php?rid=4741624&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21635 AbstractThe surface characteristics of scaffolds for bone tissue engineering must support cell adhesion, migration, proliferation and osteogenic differentiation. In the study, Poly (D, L‐lactide acid) (PDLLA) scaffolds were modified by combing ammonia (NH3) plasma pre‐treatment with Gly‐Arg‐Gly‐Asp‐Ser (GRGDS)‐peptides coupling technologies. The X‐ray photoelectron spectroscopy (XPS) survey spectra showed the peak of N 1s at the surface of NH3 plasma pre‐treated PDLLA, which was further raised after GRGDS conjugation. Furthermore, N 1s and C 1s in the high‐resolution XPS spectra revealed the presence of ‐C=N (imine), ‐C‐NH‐ (amine) and ‐C=O‐NH‐ (amide) groups. The GRGDS conjugation increased amide groups and decreased amine groups in the plasma‐treated P... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4741624 Tue, 19 Apr 2011 23:00:00 +0100 4741624 http://www.medworm.com/index.php?rid=4741623&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21637 AbstractThe process of protein aggregation has attracted a great deal of research attention, as aggregates are first of all a nuisance to preparation of high quality protein and secondly used as novel materials. In the latter case, the process of protein aggregation needs to be controlled. Here we show how arginine (Arg) regulates the process of heat‐induced protein aggregation. Dynamic light scattering and transmission electron microscopy revealed that heat‐induced aggregation of lysozyme at around the isoelectric point occurred in a two‐step process: formation of start aggregates, followed by further growth mediated by their sticking with diffusion‐limited cluster‐cluster aggregation (DLCA). In the presence of Arg, the diffusion‐limited regime changed to reaction‐limited cl... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4741623 Tue, 19 Apr 2011 23:00:00 +0100 4741623 http://www.medworm.com/index.php?rid=4741622&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21636 AbstractElastin‐like polypeptides adopt complex supramolecular structures, showing either a hydrophobic or a hydrophilic surface, depending on their surrounding environment and the supporting substrate. The preferred organization is important in many situations ranging from biocompatibility to bio‐function.Here we compare the n‐repeat pentamer LeuGlyGlyValGly (n=7) with the analogue ValGlyGlyValGly (n=5), as water suspensions and as deposits on silicon substrates. These sequences contain the repeat XxxGlyGlyZzzGly (Xxx, Zzz = Val, Leu) motif belonging to the hydrophobic glycine‐rich domain of elastin and represent a simplified model from which to obtain information on molecular interactions functional to elastin itself. The compounds studied differ only by the presence of the ‐CH... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4741622 Tue, 19 Apr 2011 23:00:00 +0100 4741622 http://www.medworm.com/index.php?rid=4692384&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21634 AbstractThe G‐quadruplexes are four‐stranded nucleic acid structures with guanine‐rich sequences that play important biological roles in, for example, regulating telomerase association and activity. Recent evidence supports the hypothesis that the telomeric G‐quadruplex DNA represents a target of novel anticancer drug medication. In this work we present results of the molecular electrostatic potential (MEP), together with the HOMO and LUMO frontier orbitals, which are physical quantities of concern in the docking of compounds on the G‐quadruplex. The calculations are performed in the frame of density functional theory at the B88LYP/6‐31G* level of theory. Additional functionals that introduce dispersion effects were also taken into consideration. The MEP potential and electron ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4692384 Sat, 09 Apr 2011 03:11:04 +0100 4692384 http://www.medworm.com/index.php?rid=4675814&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21632 AbstractThe interaction between biopolymers and metal nanoparticles (AgNPs) is a key element in the development of biomimetic nanomaterials with applications in catalysis, delivery and recognition. Here we report a facile method for the functionalization of AgNPs by N‐substituted glycine oligomers, “peptoids”. Based on the established affinity between phenanthroline ligand and Ag(0), we synthesized a peptoid bearing 1,10‐phenanthroline at the N‐terminus (PHP). Treatment of AgNPs that were pre‐stabilized by citrate ions, with PHP, leads to the formation of aggregates as suggested by UV‐Vis spectroscopy. Transmission electron microscopy (TEM) revealed that the replacement of citrate ions by PHP yields spherical assemblies of AgNPs. These peptoids/AgNPs hybrids, as well as the a... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4675814 Tue, 05 Apr 2011 05:06:43 +0100 4675814 http://www.medworm.com/index.php?rid=4669182&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21631 AbstractIt is becoming increasingly clear that characterization of the protein ensemble – the collection of all conformations of which the protein is capable – will be a critical step in developing a full understanding of the linkage between structure, dynamics and function. X‐ray solution scattering in the small angle (SAXS) and wide‐angle (WAXS) regimes represents an important new window to exploring the behavior of ensembles. The characteristics of the ensemble express themselves in x‐ray solution scattering data in predictable ways. Here we present an overview of the effect that structural diversity intrinsic to protein ensembles has on scattering data. We then demonstrate the observation of these effects in scattering from four molecular systems; myoglobin; ubiquitin; alcoho... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4669182 Sat, 02 Apr 2011 12:34:05 +0100 4669182 http://www.medworm.com/index.php?rid=4669183&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21630 In this study SAXS has been used in a high‐throughput manner on a subset of 28 proteins where structural information is available from crystallographic and/or NMR techniques. These crystallographic and NMR structures were used to validate the accuracy of molecular envelopes reconstructed from SAXS data on a statistical level, to compare and highlight complementary structural information that SAXS provides, and to leverage biological information derived by crystallographers and spectroscopists from their structures. All of the ab initio molecular envelopes calculated from the SAXS data agree well with the available structural information. SAXS is a powerful albeit low‐resolution technique that can provide additional structural information in a high‐throughput and complementary manner ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4669183 Thu, 31 Mar 2011 23:00:00 +0100 4669183 http://www.medworm.com/index.php?rid=4641439&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21624 AbstractSmall‐angle X‐ray and neutron scattering with contrast variation have made important contributions in advancing our understanding muscle regulatory protein structures in the context of the dynamic molecular processes governing muscle action. The contributions of the scattering investigations have depended upon the results of key crystallographic, NMR and electron microscopy results that have provided detailed structural information that has aided in the interpretation of the scattering data. This review will cover the advances made using small‐angle scattering techniques, in combination with the results from these complementary techniques, in probing the structures of troponin and myosin binding protein C. A focus of the troponin work has been to understand the isoform differ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4641439 Mon, 28 Mar 2011 16:32:15 +0100 4641439 http://www.medworm.com/index.php?rid=4641443&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21629 This study provides a structural basis for the effect of the K85M mutation on the GSK3β‐FRATide complex. © 2011 Wiley Periodicals, Inc. Biopolymers, 2011. (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=4641443 Fri, 25 Mar 2011 00:00:00 +0100 4641443 http://www.medworm.com/index.php?rid=4641442&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21628 AbstractSmall‐angle x‐ray scattering (SAXS) is a powerful method for obtaining quantitative structural information on the size and shape of proteins, and it is increasingly used in kinetic studies of folding and association reactions. In this mini‐review, we discuss recent developments in using SAXS to obtain structural information on the unfolded ensemble and early folding intermediates of proteins using continuous‐flow mixing devices. Interfacing of these micromachined devices to SAXS beamlines has allowed access to the microsecond time regime. The experimental constraints in implementation of turbulence and laminar flow based mixers with SAXS detection and a comparison of the two approaches are presented. Current improvements and future prospects of microsecond time‐resolved S... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4641442 Fri, 25 Mar 2011 00:00:00 +0100 4641442 http://www.medworm.com/index.php?rid=4641441&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21626 AbstractHelix (H)27 of 16S ribosomal (r)RNA from Escherichia coli was dubbed the “switch helix” when mutagenesis suggested that two alternative base pair registers may have distinct functional roles in the bacterial ribosome. Although more recent genetic analyses suggest that H27 conformational switching is not required for translation, previous solution studies demonstrated that the isolated E. coli H27 can dynamically convert between the 885 and 888 conformations. Here, we have solved the NMR solution structure of a locked 888 conformation. NOE and residual dipolar coupling restraints reveal an architecture that markedly differs from that of the 885 conformation found in crystal structures of the bacterial ribosome. In place of the loop E motif that characterizes the 885 conformer an... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4641441 Fri, 25 Mar 2011 00:00:00 +0100 4641441 http://www.medworm.com/index.php?rid=4641440&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21625 AbstractThe single‐crystal structures of three collagen‐like host–guest peptides, (Pro‐Pro‐Gly)4‐Hyp‐Yaa‐Gly‐(Pro‐Pro‐Gly)4 [Yaa = Thr, Val, Ser; Hyp = (4R)‐4‐hydroxyproline] were analyzed at atomic resolution. These peptides adopted a 7/2‐helical structure similar to that of the (Pro‐Pro‐Gly)9 peptide. The stability of these triple helices showed a similar tendency to that observed in Ac‐(Gly‐Hyp‐Yaa)10‐NH2 (Yaa = Thr, Val, Ser) peptides. On the basis of their detailed structures, the differences in the triple‐helical stabilities of the peptides containing a Hyp‐Thr‐Gly, Hyp‐Val‐Gly, or Hyp‐Ser‐Gly sequence were explained in terms of van der Waals interactions and dipole–dipole interaction between the Hyp residue in the X position an... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4641440 Fri, 25 Mar 2011 00:00:00 +0100 4641440 http://www.medworm.com/index.php?rid=4569949&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21618 AbstractWater is an integral part of collagen's triple helical and higher order structure. Studies of model triple helical peptides have revealed the presence of repetitive intrachain, interchain, and intermolecular water bridges.1 In addition, an extended cylinder of hydration is thought to be responsible for collagen fiber assembly. Confocal Raman spectroscopy and dynamic vapor sorption (DVS) measurements of human Type I collagen and pigskin dermis were performed to probe relative humidity (RH) dependent differences in the nature and level of collagen hydration. Raman spectra were also acquired as a function of time for both Type I collagen and pigskin dermis samples upon exchange of a 100% RH H2O to deuterium oxide (D2O) environment. Alterations in Amide I and III modes were consistent ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4569949 Thu, 10 Mar 2011 00:00:00 +0100 4569949 http://www.medworm.com/index.php?rid=4569948&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21619 AbstractProtein synthesis on the ribosome involves a number of external protein factors that bind at its functional sites. One key factor is the elongation factor G (EF‐G) that facilitates the translocation of tRNAs between their binding sites, as well as advancement of the messenger RNA by one codon. The details of the EF‐G/ribosome diffusional encounter and EF‐G association pathway still remain unanswered. Here, we applied Brownian dynamics methodology to study bimolecular association in the bacterial EF‐G/70S ribosome system. We estimated the EF‐G association rate constants at 150mM and 300mM monovalent ionic strengths and obtained reasonable agreement with kinetic experiments. We have also elucidated the details of EF‐G/ribosome association paths and found that positioning ... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4569948 Thu, 10 Mar 2011 00:00:00 +0100 4569948 http://www.medworm.com/index.php?rid=4559213&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21616 AbstractMolecular dynamics (MD) simulations were carried out to compare the free and bound structures of wild type U1A protein with several Phe56 mutant U1A proteins that bind the target stem loop 2 (SL2) RNA with a range of affinities. The simulations indicate the free U1A protein is more flexible than the U1A‐RNA complex for both wild type and Phe56 mutant systems. A complete analysis of the hydrogen bonding (HB) and non‐bonded (VDW) interactions over the course of the MD simulations suggested that changes in the interactions in the free U1A protein caused by the Phe56Ala and Phe56Leu mutations may stabilize the helical character in loop 3, and contribute to the weak binding of these proteins to SL2 RNA. Compared to wild type, changes in HB and VDW interactions in Phe56 mutants of th... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4559213 Mon, 07 Mar 2011 00:00:00 +0100 4559213 http://www.medworm.com/index.php?rid=4559212&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21611 AbstractA hexapeptide with amino acid sequence NNQNTF from the elk prion protein forms amyloid fibrils. Here we use molecular dynamic simulations of various size of the oligomer of the wildtype polymorphic forms and their 5 stranded double layer single point glycine mutants to study their stability. In an effort to probe the structural stability and association thermodynamic in a realistic environment, all wildtype of NNQNTF polymorphic forms with different size and their corresponding double layer 5 strands single point glycine mutants were subjected to a total of 500 ns of explicit‐solvent molecular dynamics (MD) simulation. Our results show that the structural stability of the NNQNTF oligomers increases with increasing the number of β‐strands for double layers. Our results also dem... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4559212 Mon, 07 Mar 2011 00:00:00 +0100 4559212 http://www.medworm.com/index.php?rid=4559211&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21615 AbstractModern real‐time PCR systems make it easy to monitor fluorescence while temperature is varied for hundreds of samples in parallel, permitting high‐throughput studies. We employed such system to investigate melting transitions of ordered nucleic acid structures into disordered random coils. Fluorescent dye and quencher were attached to oligonucleotides such a way that changes of fluorescence intensity with temperature indicated progression of denaturation. When fluorescence melting data were compared with traditional ultraviolet optical experiments, commonly used dye/quencher combinations, like fluorescein and tetramethylrhodamine, showed substantial discrepancies. We have therefore screened 22 commercially available fluorophores and quenchers for their ability to reliably repor... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4559211 Mon, 07 Mar 2011 00:00:00 +0100 4559211 http://www.medworm.com/index.php?rid=4516593&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21592 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=4516593 Fri, 25 Feb 2011 00:15:27 +0100 4516593 http://www.medworm.com/index.php?rid=4516592&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21609 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=4516592 Fri, 25 Feb 2011 00:15:26 +0100 4516592 http://www.medworm.com/index.php?rid=4516590&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21608 AbstractWe have employed a combination of experiment and simulation to characterize the ensemble of structures sampled by human Peptide YY (hPYY), an important member of the neuropeptide Y family. Experimental structural characterization carried out with far UV circular dichroism spectroscopy and Fourier Transform Infrared measurements confirmed that the major feature of the secondary structure of hPYY is the α–helix, encompassing about half the peptide residues, with smaller contributions from turn and β–sheet like structures. The peptide undergoes thermal denaturation characterized by a melting temperature of 48 °C with an enthalpy change of ‐24.5 kcal/mol and entropy change of ‐76.2 cal/(mol K). In our computational studies, based on a 4 microsecond molecular dynamics traject... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4516590 Thu, 24 Feb 2011 00:00:00 +0100 4516590 http://www.medworm.com/index.php?rid=4488651&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21602 AbstractMolecular dynamics simulations have been carried out to characterize the structure and solubility of chitosan nanoparticle‐like structures as a function of the deacetylation level (0, 40, 60 and 100%) and the spatial distribution of the N‐acetyl groups in the particles. The polysaccharide chains of highly N‐deacetylated particles where the N‐acetyl groups are uniformly distributed present a high flexibility and preference for the relaxed 2‐fold helix and 5‐fold helix motifs. When these groups are confined to a given region of the particle, the chains adopt preferentially a 2‐fold helix with ϕ and ψ values close to crystalline chitin. Nanoparticles with up to 40% acetylation are moderately soluble, forming stable aggregates when the N‐acetyl groups are unevenly dis... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4488651 Wed, 16 Feb 2011 00:00:00 +0100 4488651 http://www.medworm.com/index.php?rid=4481875&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21604 AbstractSmall angle x‐ray scattering provides low resolution structural information about macromolecules in solution. When coupled with rapid mixing methods, SAXS reports time‐dependent conformational changes of RNA induced by the addition of Mg2+ to trigger folding. Thus time‐resolved SAXS provides unique information about the global or overall structures of transient intermediates populated during folding. Notably, SAXS provides information about the earliest folding events, which can evade detection by other methods. © 2011 Wiley Periodicals, Inc. Biopolymers, 2011. (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=4481875 Tue, 15 Feb 2011 00:00:00 +0100 4481875 http://www.medworm.com/index.php?rid=4481874&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21603 This study uses molecular dynamics (MD) simulations to determine the interaction between GSK3β and a peptide derived from GSKIP, a novel GSK3β interacting protein. Results show that GSKIPtide is inlaid in a binding pocket consisting of an α−helix and an extended loop near the carboxy‐terminal end. This binding pocket is hydrophobic, and is responsible for the protein‐protein interaction of two other GSK3β interacting proteins: FRAT and Axin. The GSKIPtide binding mode is closer to that of AxinGID (in the Axin‐GSK3‐interacting domain). The single‐point mutations of V267G and Y288F in GSK3β differentiate the binding modes between GSK3 and GSKIPtide, AxinGID, and FRATide. The V2677G mutation of GSK3β reduces the GSKIPtide binding affinity by 70% and abolishes the binding aff... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4481874 Tue, 15 Feb 2011 00:00:00 +0100 4481874 http://www.medworm.com/index.php?rid=4432585&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21598 AbstractThe folding of the nucleosome chain into a chromatin fiber is a central factor for controlling the DNA access of protein factors involved in transcription, DNA replication and repair. Force spectroscopy experiments with chromatin fibers are ideally suited to dissect the interactions that drive this process, and to probe the underlying fiber conformation. However, the interpretation of the experimental data is fraught with difficulties due to the complex interplay of the nucleosome geometry and the different energy terms involved. Here, we apply a Monte Carlo simulation approach to derive virtual chromatin fiber force spectroscopy curves. In the simulations the effect of the nucleosome geometry, repeat length, nucleosome‐nucleosome interaction potential and the unwrapping of the D... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4432585 Thu, 03 Feb 2011 00:00:00 +0100 4432585 http://www.medworm.com/index.php?rid=4432584&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21601 AbstractPlant Rho proteins (ROPs) are inactivated by specific GTPase activating proteins, called RopGAPs. Many of these comprise the exclusive combination of a classic, catalytic Arg‐containing RhoGAP domain and a Cdc42/Rac interactive binding (CRIB) motif which in animal and fungi has been identified in effectors for Cdc42 and Rac1, but never in any GAP protein. Both elements are required for an efficient RopGAP activity. Here, we analyzed the effect of the CRIB motif on the complex formation and the binding reaction with plant and human Rho proteins by using kinetic and equilibrium methods. We show that RopGAP2 from Arabidopsis thaliana dimerizes via its GAP domain and forms a 2:2 complex with ROP. The CRIB effector motif mediates high affinity and specificity in binding. The catalytic... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4432584 Thu, 03 Feb 2011 00:00:00 +0100 4432584 http://www.medworm.com/index.php?rid=4410977&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21576 In this study, a collagen‐mimic dendrimer modified with the longer collagen model peptides, (Pro‐Pro‐Gly)10, was synthesized and named PPG10‐den. Circular dichroism analysis shows that the efficiency of the triple helix formation in PPG10‐den was much improved over the original. The X‐ray diffraction analysis suggests that the higher order structure was similar to the collagen triple helix. The thermal stability of the triple helix in PPG10‐den was higher than in the PPG10 peptide itself and our previous collagen‐mimic polymers using (Pro‐Pro‐Gly)5. Interestingly, PPG10‐den also assembled at low temperatures. Self‐assembled structures with spherical and rod‐like shapes were observed by transmission electron microscopy. Furthermore, a hydrogel of PPG10‐den was su... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4410977 Fri, 28 Jan 2011 22:34:44 +0100 4410977 http://www.medworm.com/index.php?rid=4410976&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21595 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=4410976 Fri, 28 Jan 2011 22:34:42 +0100 4410976 http://www.medworm.com/index.php?rid=4410975&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21593 AbstractMolecular dynamics simulations were carried out to calculate the free energy change difference of two collagen‐like peptide models for Gly→Ser mutations causing two different osteogenesis imperfecta phenotypes. These simulations were performed to investigate the impact of local amino acid sequence environment adjacent to a mutation site on the stability of the collagen. The average free energy differences for a Gly→Ser mutant relative to a wild type are 3.4 kcal/mol and 8.2 kcal/mol for a non‐lethal site and a lethal site, respectively. The free energy change differences of mutant containing two Ser residues relative to the wild type at the nonlethal and lethal mutation sites are 4.6 and 9.8 kcal/mol, respectively. Although electrostatic interactions stabilize mutants conta... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4410975 Fri, 28 Jan 2011 00:00:00 +0100 4410975 http://www.medworm.com/index.php?rid=4410974&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21594 In this study, substitution of F5Phe or Cha for three Phe residues at positions 328, 338 and 341 in the tetramerization domain of the tumor suppressor protein p53 was performed. These residues are located at the interfaces of p53‐p53 interactions and are important in the stabilization of the tetrameric structure. The stability of the p53 tetrameric structure did not change significantly when F5Phe‐containing peptides at positions Phe328 or Phe338 were used. In contrast, the substitution of Cha for Phe341 in the hydrophobic core enhanced the stability of the tetrameric structure with a Tm value of ∼100 °C. Phe328 and Phe338 interact with each other through π‐interactions, whereas Phe341 is buried in the surrounding alkyl side‐chains of the hydrophobic core of the p53 tetrameriza... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4410974 Fri, 28 Jan 2011 00:00:00 +0100 4410974 http://www.medworm.com/index.php?rid=4410973&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21592 (Source: Biopolymers) Biopolymers journals http://www.medworm.com/rss/comments.php?id=4410973 Fri, 28 Jan 2011 00:00:00 +0100 4410973 http://www.medworm.com/index.php?rid=4398733&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21587 AbstractMechanical tension plays a large role in cell development ranging from morphology to gene expression. On the molecular level, the effects of tension can be seen in the dynamic arrangement of membrane proteins as well as the recruitment and activation of intracellular proteins. Forces applied to biopolymers during in vitro force measurements offer greater understanding of the effects of tension on molecules in live cells, and experimental techniques in test tubes and live cells can often overlap. Indeed, when forces exerted on cellular components can be calibrated ex vivo with force spectroscopy, a powerful tool is available for researchers in probing cellular mechanotransduction on the molecular scale. This review will discuss the techniques used in measuring both cellular traction... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4398733 Tue, 25 Jan 2011 00:00:00 +0100 4398733 http://www.medworm.com/index.php?rid=4376936&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21589 AbstractOne of the major challenges in genomics is to understand the function of gene products from their 3D structures. Computational methods are needed for the high‐throughput prediction of the function of proteins from their 3D structure. Methods that identify active sites are important for understanding and annotating the function of proteins. Traditional methods exploiting either sequence similarity or structural similarity can be unreliable and cannot be applied to proteins with novel folds or low homology with other proteins. Here, we present a machine learning application which combines computed electrostatic, evolutionary, and pocket geometric information for high‐performance prediction of catalytic residues. Input features consist of our structure‐based THEMATICS electrosta... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4376936 Thu, 20 Jan 2011 00:00:00 +0100 4376936 http://www.medworm.com/index.php?rid=4370160&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21586 AbstractLive‐cell fluorescence light microscopy has emerged as an important tool in the study of cellular biology. The development of fluorescent markers in parallel with super‐resolution imaging systems has pushed light microscopy into the realm of molecular visualization at the nanometer scale. Resolutions previously only attained with electron microscopes are now within the grasp of light microscopes. However, until recently, live‐cell imaging approaches have eluded super‐resolution microscopy, hampering it from reaching its full potential for revealing the dynamic interactions in biology occurring at the single molecule level. Here we examine recent advances in the super‐resolution imaging of living cells by reviewing recent breakthroughs in single molecule localization micro... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4370160 Wed, 19 Jan 2011 00:00:00 +0100 4370160 http://www.medworm.com/index.php?rid=4348961&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21585 AbstractLateral diffusion of proteins in the plane of a biological membrane is important for many vital processes, including energy conversion, signaling, chemotaxis, cell division, protein insertion and secretion. In bacteria, all these functions are located in a single membrane. Therefore, quantitative measurements of protein diffusion in bacterial membranes can provide insight into many important processes. Diffusion of membrane proteins in eukaryotes has been studied in detail using various experimental techniques, including fluorescence correlation spectroscopy (FCS), fluorescence recovery after photobleaching (FRAP), and particle tracking using single‐molecule fluorescence (SMF) microscopy. In case of bacteria, such experiments are intrinsically difficult due to the small size of t... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4348961 Fri, 14 Jan 2011 00:00:00 +0100 4348961 http://www.medworm.com/index.php?rid=4330192&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21584 This study investigated the activity of αB‐crystallin when covalently bound to a support surface; αB‐crystallin was immobilized onto a range of solid material surfaces and its characteristics and chaperone activity were assessed. Immobilization was achieved via a plasma‐deposited thin polymeric interlayer containing aldehyde surface groups and reductive amination, leading to the covalent binding of αB‐crystallin lysine residues to the surface aldehyde groups via Schiff base linkages. Immobilized αB‐crystallin was characterized by X‐ray photoelectron spectroscopy, atomic force microscopy and quartz crystal microgravimetry which showed that approximately 300ng.cm‐2 (dry mass) of oligomeric αB‐crystallin was bound to the surface. Immobilized αB‐crystallin exhibited a s... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4330192 Mon, 10 Jan 2011 00:00:00 +0100 4330192 http://www.medworm.com/index.php?rid=4317761&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21581 AbstractThe conformational preferences of the selenocysteine (Sec) dipeptides with selenol and selenolate groups (Ac‐Sec‐NHMe and Ac‐Sec−‐NHMe, respectively) and the apparent (i.e., macroscopic) pKa value of the Sec residue have been studied using the dispersion‐corrected density functionals M06‐2X and B2PLYP‐D with the implicit SMD solvation method in the gas phase and in water. In the gas phase, the backbone‐to‐backbone and/or side chain‐to‐backbone hydrogen bonds are found to contribute in stabilizing the most preferred conformations for the Sec and Sec− residues, as seen for the Cys and Cys− residues. However, the polyproline II‐like conformations prevail over the conformations with the backbone‐to‐backbone hydrogen bonds in water because of the weaken... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4317761 Thu, 06 Jan 2011 00:00:00 +0100 4317761 http://www.medworm.com/index.php?rid=4317760&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21582 AbstractApical membrane antigen 1 (AMA1) is essential for malaria parasite invasion of erythrocytes and is therefore an attractive target for drug development. Peptides that bind AMA1 have been identified from random peptide libraries expressed on the surface of phage. Of these, R1, which binds to a hydrophobic ligand binding site on AMA1, was a particularly potent inhibitor of parasite invasion of erythrocytes in vitro. The solution structure of R1 contains a turn‐like conformation between residues 5‐10. Here the importance of residues in this turn‐like structure for binding to AMA1 was examined by site‐directed mutagenesis and NMR spectroscopy. The peptide was expressed as a fusion protein following replacement of Met16 by Leu in order to accommodate cyanogen bromide cleavage. Th... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4317760 Thu, 06 Jan 2011 00:00:00 +0100 4317760 http://www.medworm.com/index.php?rid=4317759&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21583 We report on the investigation of the structure of DNA liquid crystal (LC) phases by means of polarization sensitive two‐photon microscopy (PSTPM). DNA was stained with fluorescent dyes, an intercalator propidium iodide or a groove binder Hoechst 3342 and the angular dependence of the intensity of two‐photon excited fluorescence (TPEF) emitted by the dye was collected. The local orientation of DNA molecules in cholesteric and columnar liquid crystal phases was established on the basis of the relative angle between the transition dipole of the dye and the long axis of DNA helix. Three dimensional images of the cholesteric phase were obtained making use of the intrinsic 3D resolving ability of two‐photon microscopy. We also discuss the influence of dyes on the parameters of DNA LC phas... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4317759 Thu, 06 Jan 2011 00:00:00 +0100 4317759 http://www.medworm.com/index.php?rid=4308860&cid=s_33994_60_f&fid=33994&url=http%3A%2F%2Fdx.doi.org%2F10.1002%252Fbip.21579 AbstractThe technologies associated with DNA sequencing are rapidly evolving. Indeed, single‐molecule DNA sequencing strategies are cheaper and faster than ever before. Despite this progress, every sequencing platform to date relies on reading the genome in small, abstract fragments, typically of less than a thousand bases in length. The overarching aim of the optical map is to complement the information derived from DNA sequencing by providing long‐range context upon which these short sequence reads can be built. This is typically done using an enzyme to target and modify at short DNA sequences of, say, 6‐bases in length throughout the genome. By accurately placing these short pieces of sequence on long genomic DNA fragments, up to several millions of bases in length, a scaffold for... Biopolymers journals http://www.medworm.com/rss/comments.php?id=4308860 Tue, 04 Jan 2011 00:00:00 +0100 4308860