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 'BMC Structural Biology - Latest articles' source. Thu, 09 Feb 2012 16:56:38 +0100 http://www.medworm.com/index.php?rid=5643860&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F12%2F1 Conclusion: Using a combination of different types of data, we build and validate a relevant model of the tridimensional structure of a biologically important protein-DNA complex. Then, based on published observations, we propose more elaborated multimeric models that may be biologically important to understand molecular mechanisms. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5643860 Mon, 30 Jan 2012 05:00:00 +0100 5643860 http://www.medworm.com/index.php?rid=5533461&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F50 Conclusions: Considering the significant increase of biotechnology applications of halophiles, the understanding of halophilicity can provide the theoretical basis for the engineering of proteins of great interest because stable at concentrations of salts that cause the denaturation or aggregation of the majority of macromolecules. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5533461 Thu, 22 Dec 2011 05:00:00 +0100 5533461 http://www.medworm.com/index.php?rid=5533462&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F49 Conclusions: For the first time the interaction of full-length Vpr and CypA has been characterized and quantified. A non-proline-containing 16-residue region of C-terminal Vpr which binds specifically to CypA with similar high affinity as full-length Vpr has been identified. The fact that this is the first non-proline containing binding motif of any protein found to bind to CypA, changes the view on how CypA is able to interact with other proteins. It is interesting to note that several previously reported key functions of HIV-1 Vpr are associated with the identified N- and C-terminal binding domains of the protein to CypA. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5533462 Tue, 20 Dec 2011 05:00:00 +0100 5533462 http://www.medworm.com/index.php?rid=5512427&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F48 Conclusions: The availability of crystal structures of TrmI from mesophilic, thermophilic or hyperthermophilic organisms allows a detailed analysis of the architecture of this protein family. Our structural comparisons provide insight into the different molecular strategies used to achieve the tetrameric organization in order to maintain the enzyme activity under extreme conditions. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5512427 Wed, 14 Dec 2011 05:00:00 +0100 5512427 http://www.medworm.com/index.php?rid=5501130&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F47 Conclusions: The docking results showed that the addition of the cholesteryl and guanosine esters to the 'DNA gyrase binding' region of gatifloxacin and moxifloxacin enhanced the binding affinity of these parent molecules with the mutant DNA gyrase receptors. Viewing the positive correlation for the docking and in vitro results with the parent compounds, these lead structures could be further evaluated for their in vitro and in vivo activity against MDR-TB. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5501130 Mon, 12 Dec 2011 05:00:00 +0100 5501130 http://www.medworm.com/index.php?rid=5447664&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F46 Conclusions: We conclude that the NMR restraint redundancy is connected to the instability of the SH3 nph domain. This restraint redundancy generalizes the contact order parameter, which is calculated from the contact map of a folded protein and was shown in the literature to be correlated to the protein folding rate. The relationship between the NMR restraint redundancy and the protein folding is also reminiscent of the previous use of the Gaussian Network Model to predict protein folding parameters. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5447664 Thu, 24 Nov 2011 05:00:00 +0100 5447664 http://www.medworm.com/index.php?rid=5375445&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F45 Conclusions: We believe these benchmarks are important for the development of better interaction potentials and TF-DNA docking algorithms, which bears important implications to structure-based prediction of transcription factor binding sites and drug design. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5375445 Tue, 01 Nov 2011 04:00:00 +0100 5375445 http://www.medworm.com/index.php?rid=5343528&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F43 Conclusions: Based on the present findings, we conclude that the changes made to the amino acids in ETF:QO are likely to influence the FAD-binding stability. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5343528 Fri, 21 Oct 2011 04:00:00 +0100 5343528 http://www.medworm.com/index.php?rid=5343527&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F44 Conclusions: We obtained a convergent protein hydration landscape that indicated how the shape and stability of the Sso7d hydration shell could modulate the function of the protein. The DNA binding domain overlaps with the protein region involved in chaperon activity and this domain is hydrated only in a very small central region. This localized hydration seems to favor intermolecular approaches from a large variety of ligands. Conversely, high water density was found in surface regions of the protein where the ATP binding site is located, suggesting that surface water molecules play a role in protecting the protein from unspecific interactions. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5343527 Fri, 21 Oct 2011 04:00:00 +0100 5343527 http://www.medworm.com/index.php?rid=5343529&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F42 Conclusions: These findings suggest that embedded water molecules may play a significant role in cavity flexibility, and therefore, overall protein flexibility. Thus, our results point to the important role enzyme flexibility plays in adaptation to cold environments. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5343529 Thu, 20 Oct 2011 04:00:00 +0100 5343529 http://www.medworm.com/index.php?rid=5330680&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F40 Conclusions: Our results suggest that the central domains, previously appointed as important features for substrate binding, are also relevant keeping the J-domains in their specific relative positions. The clamp-like architecture observed seems also to be favorable to the interactions of Hsp40 with Hsp70. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5330680 Wed, 19 Oct 2011 04:00:00 +0100 5330680 http://www.medworm.com/index.php?rid=5330679&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F41 Conclusions: The hydration sites around unpaired RNA bases were found. They do not replicate the atom positions of complementary bases in the Watson-Crick pairs. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5330679 Wed, 19 Oct 2011 04:00:00 +0100 5330679 http://www.medworm.com/index.php?rid=5321533&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F39 Conclusion: The C. immitis RpiB contains the same fold and similar features as other members of this class of enzymes such as a highly reactive active site cysteine residue, but utilizes a divergent phosphate recognition strategy and may recognize a different substrate altogether. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5321533 Thu, 13 Oct 2011 04:00:00 +0100 5321533 http://www.medworm.com/index.php?rid=5281492&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F37 Conclusions: The PARP-1 BRCT domain has the conserved BRCT fold that is known to be an important protein:protein interaction module in DNA repair and cell signalling pathways. Data indicating no significant protein:protein interactions between PARP-1 and XRCC1 likely results from the absence of poly(ADP-ribose) in one or both binding partners, and further implicates a poly(ADP-ribose)-dependent mechanism for localization of XRCC1 to sites of DNA damage. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5281492 Mon, 03 Oct 2011 04:00:00 +0100 5281492 http://www.medworm.com/index.php?rid=5268665&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F36 Conclusions: Dimerization dramatically increases the 'ice-active' surface area of the protein by doubling its width, increasing its length, and presenting identical ice-forming surfaces on both sides of the protein. We suggest that this allows sufficient anchored clathrate waters to align on the INP surface to nucleate freezing. As PbINP is highly similar to all known bacterial INPs, we predict its fold and mechanism of action will apply to these other INPs. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5268665 Tue, 27 Sep 2011 04:00:00 +0100 5268665 http://www.medworm.com/index.php?rid=5257296&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F35 Conclusion: Molecular modelling and subsequent analysis of putative interactions involving these class-specific residues suggest a structural basis for the molecular mechanism behind high velocity of plant myosin XI. We propose a model of a more flexible switch I region that contributes to faster ADP release leading to high velocity movement of the algal myosin XI. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5257296 Mon, 26 Sep 2011 04:00:00 +0100 5257296 http://www.medworm.com/index.php?rid=5233506&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F34 Conclusions: Probabilistic analysis of atomic central distances in globular proteins is capable of capturing distinct orientational preferences of amino acids as resulting from dierent sizes, charges and hydrophobic characters of their side chains. When idealized spatial preferences can be inferred from the sole amino acid composition of a protein, residues located in hydrophobically unfavorable environments can be easily detected. Such residues turn out to be often directly involved in binding ligands or interfacing with other proteins. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5233506 Sun, 18 Sep 2011 04:00:00 +0100 5233506 http://www.medworm.com/index.php?rid=5155681&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F33 Conclusions: The data accumulated here suggest that EhpR confers resistance by binding D-alanyl-griseoluteic acid and acting as a chaperone involved in exporting the antibiotic rather than by altering it chemically. It is tempting to speculate that EhpR acts in concert with EhpJ, a transport protein of the major facilitator superfamily that is also encoded in the phenazine biosynthesis operon of E. agglomerans. The low affinity of EhpR for griseoluteic acid may be required for its physiological function. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5155681 Tue, 16 Aug 2011 23:00:00 +0100 5155681 http://www.medworm.com/index.php?rid=5026853&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F32 Conclusions: The molecular docking protocol, as applied to a combinatorial library of peptides, models the peptide-HLA-DP2 protein interaction effectively, generating reliable predictions in a quantitative assessment. The method is structure-based and does not require extensive experimental sequence-based data. Thus, it is universal and can be applied to model any peptide - protein interaction. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5026853 Wed, 13 Jul 2011 23:00:00 +0100 5026853 http://www.medworm.com/index.php?rid=5017849&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F31 Conclusions: The dynamic study of HIV-1 protease elucidates functional importance of common drug-resistance mutations, and suggests a unifying mechanism for drug-resistance residues based on their dynamical properties. The results support the robustness of the elastic network model as a potential predictive tool for drug resistance. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=5017849 Thu, 07 Jul 2011 23:00:00 +0100 5017849 http://www.medworm.com/index.php?rid=4959279&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F29 Conclusions: We classified entire regions of proteins into the two categories, SDs and ID regions and thereby obtained various kinds of complete genome-wide statistics. The results of the present study are important basic information for understanding protein structural architectures and have been made publicly available at http://spock.genes.nig.ac.jp/~genome/DICHOT. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4959279 Tue, 21 Jun 2011 23:00:00 +0100 4959279 http://www.medworm.com/index.php?rid=4959278&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F30 Conclusions: This work helps to define the structural basis of substrate specificity of matriptase and the interactions between the inhibitor and protease. The complex structure also provides a structural template for designing new SFTI-1 derivatives with better potency and selectivity against matriptase and other proteases. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4959278 Tue, 21 Jun 2011 23:00:00 +0100 4959278 http://www.medworm.com/index.php?rid=4932312&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F28 Conclusions: The two models obtained for the FtsB/FtsL/FtsQ complex were stable and thus compatible with the in vivo periplasmic complex structure. Although the hexameric model 2:2:2 has features that indicate that this is the most plausible structure, the ternary complex 1:1:1 cannot be discarded. Both models could be further stabilized by the binding of the other proteins of the divisome. The bioinformatics modelling of this kind of protein complex, whose function is mainly structural, provide useful information. Experimental results should confirm or reject these models and provide new data for future bioinformatics studies to refine the models. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4932312 Mon, 13 Jun 2011 23:00:00 +0100 4932312 http://www.medworm.com/index.php?rid=4870714&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F27 Conclusion: Thus, this hypothetical protein was assigned to the AhpD-like protein family with peroxidase-related activity. The functional relationship of specific oligomeric structures of AhpD-like structural family is discussed. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4870714 Wed, 25 May 2011 23:00:00 +0100 4870714 http://www.medworm.com/index.php?rid=4983304&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F26 Conclusions: We succeeded in reducing the variation in the TMD limits to only 2 residues and in gaining structural information. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4983304 Mon, 23 May 2011 23:00:00 +0100 4983304 http://www.medworm.com/index.php?rid=4861249&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F26 Conclusions: We succeeded in reducing the variation in the TMD limits to only 2 residues and in gaining structural information. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4861249 Mon, 23 May 2011 23:00:00 +0100 4861249 http://www.medworm.com/index.php?rid=4827624&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F25 Conclusions: Data published so far emphasize unique biological properties of the DraD invasin as fimbrial subunit: a chaperone independent folding, an usher independent surface localization and the possibility to exist in two forms: as unbound subunits and as loosely bound at fimbrial tip.Presented calorimetric and FT-IR stability data combined with structural correlations has underlined that the DraD invasin is also characterized by unique physicochemical and structural attributes in the context of its belonging to the family of fimbrial subunits. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4827624 Sun, 15 May 2011 23:00:00 +0100 4827624 http://www.medworm.com/index.php?rid=4819683&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F24 Conclusions: NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4819683 Wed, 11 May 2011 23:00:00 +0100 4819683 http://www.medworm.com/index.php?rid=4811967&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F22 Conclusion: The structure of the F-spondin FS domain completes the structural studies of the multiple-domain ECM molecule. The homology of its core structure to a common Ca2+- and lipid-binding C2 domain suggests that the F-spondin FS domain may be responsible for part of the membrane targeting of F-spondin in its regulation of axon development. The structural properties of the FS domain revealed in this study pave the way for further exploration into the functions of F-spondin. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4811967 Mon, 09 May 2011 23:00:00 +0100 4811967 http://www.medworm.com/index.php?rid=4811966&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F23 Conclusions: The reported structures of MSH from Haloferax volcanii allow a detailed analysis and comparison with previously solved structures of isoforms A and G. These structural comparisons provide insight into evolutionary relationships among these isoforms, and also indicate that despite the size and sequence variation, and the truncated C-terminal domain of the H isoform, the catalytic mechanism is conserved. Sequence analysis in light of the structure indicates that additional members of isoform H likely exist in the databases but have been misannotated. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4811966 Mon, 09 May 2011 23:00:00 +0100 4811966 http://www.medworm.com/index.php?rid=4801619&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F21 Conclusion: Structural similarities between BcDHPS and orthologues from other Gram-negative species are evident as expected on the basis of a high level of sequence identity. The presence of 7,8-dihydropteroate in the binding site provides details about ligand recognition by the enzyme and the different states of the enzyme allow us to visualize distinct conformational states of loops adjacent to the active site. Improved drugs to combat infections by Burkholderia sp. and related Gram-negative bacteria are sought and our study now provides templates to assist that process and allow us to discuss new ways of inhibiting DHPS. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4801619 Sun, 08 May 2011 23:00:00 +0100 4801619 http://www.medworm.com/index.php?rid=4788151&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F20 Conclusions: We expect that this high-quality, generic surface patch library will add a new perspective to the description of protein structures and improve our ability to predict them. In particular, we expect that it will help improve the prediction of surface features that are apparently neglected by current techniques.The surface patch libraries are publicly available at http://www.cs.bgu.ac.il/~keasar/patchLibrary. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4788151 Tue, 03 May 2011 23:00:00 +0100 4788151 http://www.medworm.com/index.php?rid=4741773&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F19 Conclusions: The overall basic active site displays pronounced hydrophobic character on one side and these properties complement those of the substrate. A complex network of hydrogen bonds involving well-ordered water molecules serves to position key residues participating in the recognition of substrate and subsequent catalysis. We propose a proton shuttle mechanism, reliant on a catalytic triad consisting of Ser89, Asp216 and His243. The reaction is initiated by proton abstraction from the substrate by an activated Ser89. The propensity to form a conjugated system provides the driving force for pyruvate elimination. During the elimination, a methylene group is converted to a methyl and we judge it likely that His243 provides a proton, previously acquired from Ser89 for that reduction. A ... BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4741773 Thu, 21 Apr 2011 23:00:00 +0100 4741773 http://www.medworm.com/index.php?rid=4732656&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F18 Conclusions: The HSA-iophenoxic acid structure indicates that high-affinity binding to drug site 1 is likely to be due to extensive desolvation of the compound, coupled with the ability of the binding pocket to provide a full set of salt-bridging or hydrogen bonding partners for its polar groups. Consistent with this interpretation, the structure also suggests that the lower-affinity binding of iopanoic acid arises because replacement of the 3-hydroxyl by an amino group eliminates hydrogen bonding to Arg 257. This finding underscores the importance of polar interactions in high-affinity binding to albumin. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4732656 Sun, 17 Apr 2011 23:00:00 +0100 4732656 http://www.medworm.com/index.php?rid=4708668&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F17 Conclusions: Our results suggest that G alpha 16 can signal through TPR1/Ras and PLC beta simultaneously and independently. The beta 3 region of G alpha 16 is essential for interaction with TPR1 and the subsequent activation of Ras, but has relatively minor influence on the PLC beta interaction. G alpha 16 may utilize different structural domains to bind TPR1 and PLC beta. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4708668 Tue, 12 Apr 2011 23:00:00 +0100 4708668 http://www.medworm.com/index.php?rid=4641702&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F15 Conclusions: Our structural studies indicate the biosensing mechanism of a fluorescein-labelled beta-lactamase. Such findings confirm our previous proposal based on molecular modelling and provide useful information for the rational design of beta-lactamase-based biosensor to detect the wide spectrum of beta-lactam antibiotics. The observation of increased omega-loop flexibility upon conjugation of fluorophore may have the potential to serve as a screening tool for novel beta-lactamase inhibitors that target the omega-loop and not the active site. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4641702 Sun, 27 Mar 2011 23:00:00 +0100 4641702 http://www.medworm.com/index.php?rid=4641701&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F16 Conclusion: Altogether, our manual in silico curation suggested that TlyA is involved in ribosomal biogenesis and that there is a functional annotation error regarding this protein family in several microbial and plant genomes, including the M. tuberculosis genome. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4641701 Sun, 27 Mar 2011 23:00:00 +0100 4641701 http://www.medworm.com/index.php?rid=4630850&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F14 Conclusion: DNA-bound protamine in sperm nuclei contains large amounts of defined secondary structure stabilized by intramolecular hydrogen bonding. Both salmine and squid protamine contain similar amounts of beta-turns, but differ in the proportions of alpha-helix and non-hydrogen bonded conformations. In spite of the large differences in the proportions of secondary structure motifs between salmon and squid protamines, they appear to be equally efficient in promoting tight hexagonal packing of the DNA molecules in sperm nuclei. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4630850 Thu, 24 Mar 2011 00:00:00 +0100 4630850 http://www.medworm.com/index.php?rid=4544423&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F13 Conclusions: Our analysis revealed that heme binding pockets show special features and that most of the heme proteins undergo small conformational changes after heme binding, suggesting the apo structures can be used for structure-based heme protein prediction and as scaffolds for future heme protein design. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4544423 Thu, 03 Mar 2011 00:00:00 +0100 4544423 http://www.medworm.com/index.php?rid=4477007&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F12 Conclusions: Our data present the first low resolution 3D structure of hNek6 protein in solution. SAXS, comparative modeling and SEC-MALS analysis revealed that hNek6 is a monomeric kinase of slightly elongated shape and a short unfolded N-terminal domain. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4477007 Mon, 14 Feb 2011 00:00:00 +0100 4477007 http://www.medworm.com/index.php?rid=4459247&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F11 Conclusions: These results demonstrate that some PH domains possess enough specificity to discriminate between myo-inositol pentakisphosphate isomers allowing for these molecules to differentially regulate interactions with phosphoinositides. Furthermore, this work contributes to the growing body of evidence supporting myo-inositol phosphates as regulators of important PH domain-phosphoinositide interactions. Finally, in addition to expanding our knowledge of cellular signaling, these results provide a basis for developing tools to probe biological pathways. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4459247 Thu, 10 Feb 2011 00:00:00 +0100 4459247 http://www.medworm.com/index.php?rid=4432704&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F10 Conclusions: Here, we provide fold-specific guidelines to control thermostability in endoglucanases that will aid in making production of biofuels from plant biomass more efficient. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4432704 Thu, 03 Feb 2011 00:00:00 +0100 4432704 http://www.medworm.com/index.php?rid=4423590&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F7 Conclusions: The DeStripe denoising effect on AFM images is illustrated in the present work. It allows extracting extended information from the topographic measurements and implicitly enhances the molecular features in the image. All the presented images were processed by DeStripe with the raw image as the only input without any requirement for other prior information. A web service, http://biodev.cea.fr/destripe, is available for running DeStripe. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4423590 Tue, 01 Feb 2011 00:00:00 +0100 4423590 http://www.medworm.com/index.php?rid=4423589&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F8 Conclusions: :Bulk electric moments of proteins considered here provide insights into target recognition by RNA-binding proteins, as well as ability to recognize one type of RBP from others. These results help in understanding the mechanism of protein-RNA recognition, and identifying RNA-binding proteins. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4423589 Tue, 01 Feb 2011 00:00:00 +0100 4423589 http://www.medworm.com/index.php?rid=4423588&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F9 Conclusion: The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4423588 Tue, 01 Feb 2011 00:00:00 +0100 4423588 http://www.medworm.com/index.php?rid=4398876&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F5 Conclusions: The contour map near R1 indicates that substitution of a bulkier and polar group to the ortho position of the benzene ring enhances the inhibitory effect. This explains why compounds with a nitro group have good inhibitory potency. Molecular fragment analyses shed light on some essential structural and topological features of third generation MDR modulators. Fragments analysis showed that the presence of tertiary nitrogen, a central phenyl ring and an aromatic dimethoxy group contributed to the inhibitory effect. Based on contour map information and fragment information, five new molecules with variable R1 substituents were designed. The activity of these designed molecules was predicted by the Topomer CoMFA and HQSAR models. The novel compounds showed higher potency than exis... BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4398876 Wed, 26 Jan 2011 00:00:00 +0100 4398876 http://www.medworm.com/index.php?rid=4398875&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F6 Conclusions: The GUI considerably extends the analysis and validation possibilities of the PROPKA approach. The PROPKA GUI can conveniently be used to investigate ionizable groups, and their interactions, of residues with significantly perturbed pKa values or residues that contribute to the stabilization energy the most. Charge-dependent properties can be studied either for a single protein or simultaneously with other homologous structures, which makes it a helpful tool, for instance, in protein design studies or structure-based function predictions. The GUI is implemented as a Tcl/Tk plug-in for VMD, and can be obtained online at http://propka.ki.ku.dk/~luca/wiki/index.php/GUI_Web. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4398875 Wed, 26 Jan 2011 00:00:00 +0100 4398875 http://www.medworm.com/index.php?rid=4398877&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F4 Conclusions: These models provide the first structural insights into the architecture of VirB4 proteins. In particular, our results highlight the modular arrangement and the functional relevance of the dimeric, membrane form of TraB. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4398877 Tue, 25 Jan 2011 00:00:00 +0100 4398877 http://www.medworm.com/index.php?rid=4393630&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F3 Conclusions: Despite sharing similar pharmacological profiles toward both IKCa and Kv1.2 channels, MTX adopted totally diverging modes in the two association processes. All the molecular information unveiled here could not only offer a better understanding about the structural differences between the IKCa and Kv1.2 channels, but also provide novel structural clews that will help in the designing of more selective molecular probes to discriminate between these two channels. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4393630 Tue, 25 Jan 2011 00:00:00 +0100 4393630 http://www.medworm.com/index.php?rid=4330273&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F2 Conclusions: Although the focus of the PSI was structural coverage, many of the structures solved by the MCSG can also be associated with functional classes and biological roles of possible biomedical value. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4330273 Mon, 10 Jan 2011 00:00:00 +0100 4330273 http://www.medworm.com/index.php?rid=4313513&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F11%2F1 Conclusions: Based on our results, we propose that the local and global level versatility of B-DNA structure may be a significant factor modulating the formation of nucleosomes in the vicinity of high-plasticity genes, and in varying the probability of binding by regulatory proteins. Hence, these factors should be incorporated in the prediction algorithms and there may not be a unique 'template' for predicting putative nucleosome sequences. In addition, the multimodal distribution of dinucleotide parameters for some steps and the presence of a large number of kinks in the nucleosomal DNA structure indicate that the linear elastic model, used by several algorithms to predict the energetic cost of nucleosome formation, may lead to incorrect results. (Source: BMC Structural Biology - Latest a... BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4313513 Wed, 05 Jan 2011 00:00:00 +0100 4313513 http://www.medworm.com/index.php?rid=4200069&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F42 Conclusions: The results show differences in the organization of the intra-protein energy-networks responsible for the stabilization of the protein conformations recognizing and binding DNA. These, in turn, are reflected into different modulation of the ZF's internal dynamics. The results also show a correlation between energetic and dynamic properties of the different proteins and their specificity/selectivity for DNA sequences. Finally, a dynamic and energetic model for the recognition of DNA by Zinc Fingers is proposed. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4200069 Wed, 24 Nov 2010 00:00:00 +0100 4200069 http://www.medworm.com/index.php?rid=4167121&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F40 Conclusions: Our results show that, using the LP approach, we were able to train our potentials using a dataset of transient complexes only the newly developed potentials outperform three other known potentials in this test. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4167121 Mon, 15 Nov 2010 00:00:00 +0100 4167121 http://www.medworm.com/index.php?rid=4117082&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F39 Conclusions: Our results present a new conceptual method for the evaluation of dynamic conformational ensembles resulting from NMR structure determination. The designed CoNSEnsX approach gives a complete evaluation of these ensembles and is freely available as a web service at http://consensx.chem.elte.hu. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4117082 Thu, 28 Oct 2010 23:00:00 +0100 4117082 http://www.medworm.com/index.php?rid=4104808&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F38 Conclusion: For the structural analysis of very high-resolution data we have used a new 'two-chain-isotropic-refinement' strategy. This refinement provides an alternative and easy to interpret strategy to reflect the conformational variability within crystal structures of biological macromolecules. The presented fluorescent form of H-Ras p21 will be advantageous for fluorescence studies on H-Ras p21 in which the use of fluorescent nucleotides is not feasible. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4104808 Sun, 24 Oct 2010 23:00:00 +0100 4104808 http://www.medworm.com/index.php?rid=4096021&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F37 Conclusions: DockAnalyse makes the interpretation of the docking solutions through graphical and visual representations easier by guiding the user to find the representative solutions. We have applied our new approach to analyze several protein interactions and model the dynamic protein interaction behavior of a protein complex. DockAnalyse might also be used to describe interaction regions between proteins and, therefore, guide future flexible dockings. The application (implemented in the R package) is accessible. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4096021 Thu, 21 Oct 2010 23:00:00 +0100 4096021 http://www.medworm.com/index.php?rid=4076676&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F35 Conclusion: A flexible linker and a proper binding site of the polyamide-type recognition agents play an important role in improving the DNA cleavage selectivity of copper nucleases. Current investigations provide an insight into the DNA cleavage specificities of chemical nucleases assisted by an appropriate nucleic acid recognition agent. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4076676 Sat, 16 Oct 2010 23:00:00 +0100 4076676 http://www.medworm.com/index.php?rid=4072995&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F34 Conclusions: Functionally relevant structural sites of CYPs were predicted. Regions involved in substrate binding were analyzed in all sequences among the CYPED. For all CYPs that require a reductase, two reductase interaction sites were identified and classified according to their length. The newly gained insights promise an improvement of engineered enzyme properties for potential biotechnological application. The annotated sequences are accessible on the current version of the CYPED. The prediction tool can be applied to any CYP sequence via the web interface at http://www.cyped.uni-stuttgart.de/cgi-bin/strpred/dosecpred.pl. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4072995 Thu, 14 Oct 2010 23:00:00 +0100 4072995 http://www.medworm.com/index.php?rid=4044364&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F33 Conclusion: The hydrophobic core and the beta-helix backbone conformation are important for maintaining the quinolone resistance property of Qnr proteins. QnrC may share structural similarity with MfpA. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4044364 Thu, 07 Oct 2010 23:00:00 +0100 4044364 http://www.medworm.com/index.php?rid=4035774&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F32 Conclusions: This is the first study to investigate complex multivariate associations between affinity profiles and the geometric properties of protein binding sites. We found that, except for few specific cases, the shapes of the binding pockets have relatively low weights in the determination of the affinity profiles of proteins. Since the MAF profile is closely related to the target specificity of ligand binding sites we can conclude that the shape of the binding site is not a pivotal factor in selecting drug targets. Nonetheless, based on strong specific associations between certain MAF profiles and specific geometric descriptors we identified, the shapes of the binding sites do have a crucial role in virtual drug design for certain drug categories, including morphine derivatives, benz... BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4035774 Mon, 04 Oct 2010 23:00:00 +0100 4035774 http://www.medworm.com/index.php?rid=4030356&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F31 Conclusions: Only N-terminal peptides of Vpr containing Pro-35, which appears to be vital for manifold functions of Vpr, bind to CypA in a biosensor assay. This indicates that Pro-35 is essential for a specific CypA-Vpr binding interaction, in contrast to the general prolyl cis/trans isomerisation observed for all proline residues of Vpr, which only involve transient enzyme-substrate interactions. Previously suggested models depicting CypA as a chaperone that plays a role in HIV-1 virulence are now supported by our data. In detail the SPR data of this interaction were compatible with a two-state binding interaction model that involves a conformational change during binding. This is in accord with the structural changes observed by NMR suggesting CypA catalyzes the prolyl cis/trans intercon... BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4030356 Sun, 03 Oct 2010 23:00:00 +0100 4030356 http://www.medworm.com/index.php?rid=4017624&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F30 Conclusion: A combination of experimental approaches including gene shuffling, enzyme assays and reverse mutation allied to molecular modeling has shed light upon the unexpected inhibitory properties of certain cystatin mutants against Cathepsin B. We conclude that mutations disrupting the hydrophobic core of phytocystatins increase the flexibility of the N-terminus, leading to an increase in inhibitory activity. Such mutations need not affect the inhibitory site directly but may be observed distant from it and manifest their effects via an uncoupling of its three components as a result of increased protein flexibility. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4017624 Wed, 29 Sep 2010 23:00:00 +0100 4017624 http://www.medworm.com/index.php?rid=4011559&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F29 Conclusions: The results contradict the earlier perception of isotropic nature of amino acid propensities in themiddle region of beta-strands. These position-specific propensities should be of immense help in understandingthe factors responsible for beta-strand design and efficient prediction of beta-strand structure in unknown proteins. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=4011559 Mon, 27 Sep 2010 23:00:00 +0100 4011559 http://www.medworm.com/index.php?rid=3942248&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F28 Conclusions: These calculations present evidence that Glu 498 is the only proton-active group in the vicinity of the trinuclear centre. This strongly suggests that this residue may be responsible for channelling the protons needed for the reduction. These results are compared with other data available for these enzymes, highlighting similarities and differences within laccases and multicopper oxidases. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3942248 Mon, 06 Sep 2010 23:00:00 +0100 3942248 http://www.medworm.com/index.php?rid=3857686&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F27 Conclusions: In this article, we provide details of a novel method for the identification of conformational changes in the different ligand bound states of the protein, evaluation of ligand-induced free energy changes and the biological relevance of our results in the context of LuxS structure-function. The methodology outlined here is highly generalized to illuminate the linkage between structure and function in any protein of known structure. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3857686 Wed, 11 Aug 2010 23:00:00 +0100 3857686 http://www.medworm.com/index.php?rid=3830931&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F25 Conclusions: We found that the inability of the two-residue shorter ALG-2 isoform to bind Alix is not due to the absence of bulky side chain of F122 but due to deformation of a main-chain wall facing pockets 1 and 2. Moreover, a residue at the position of F122 contributes to target specificity and a smaller side chain is preferable for Alix binding but not favored to bind annexin A11. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3830931 Thu, 05 Aug 2010 23:00:00 +0100 3830931 http://www.medworm.com/index.php?rid=3822422&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F24 Conclusions: The analysis demonstrated that protein structures have the "plasticity" to tolerate short indels. This study can provide valuable guides in modeling protein AS isoform structures and homologous proteins with indels through placing the indels at the right locations since the accuracy of sequence alignments dictate model qualities in homology modeling. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3822422 Tue, 03 Aug 2010 23:00:00 +0100 3822422 http://www.medworm.com/index.php?rid=3757278&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F21 Conclusions: From primary to quaternary structure, these results presented here suggest that a symmetric dimerization interface is conserved across bacterial class II chaperones. In light of previous data which have described the structure and function of asymmetric dimerization, our results raise the possibility that class II chaperones may transition between asymmetric and symmetric dimers in response to changes in either biochemical modifications (e.g. proteolytic cleavage) or other biological cues. Such transitions may contribute to the broad range of protein-protein interactions and functions attributed to class II chaperones. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3757278 Wed, 14 Jul 2010 23:00:00 +0100 3757278 http://www.medworm.com/index.php?rid=3749668&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F20 Conclusions: Finally, we applied the proposed method predicting the internal motion to a set of 20 proteins that undergo large conformational change upon protein-protein interaction. Results show significant overlaps between the predicted high internal motion regions and the observed conformational change regions. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3749668 Mon, 12 Jul 2010 23:00:00 +0100 3749668 http://www.medworm.com/index.php?rid=3726394&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F19 Conclusions: Force generation by minus-end Ncd involves docking of the C-terminus, which forms a structure resembling the kinesin-1 neck linker. The mechanism by which the plus- and minus-end motors produce force to move to opposite ends of the microtubule appears to involve the same conformational changes, but distinct structural linkers. Unstable ADP binding may destabilize the motor-ADP state, triggering Ncd stalk rotation and C-terminus docking, producing a working stroke of the motor. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3726394 Sun, 04 Jul 2010 23:00:00 +0100 3726394 http://www.medworm.com/index.php?rid=3670887&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F18 Conclusions: Our study demonstrates that the application of entropic measures to molecules representing graphsis useful to characterize such structures meaningfully. For instance, we have found that if one extends themeasures for determining the structural information content of unlabeled graphs to labeled graphs, theuniqueness of the resulting indices is higher. Because measures to structurally characterize labeled graphs areclearly underrepresented so far, the further development of such methods might be valuable and fruitful forsolving problems within biological network analysis. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3670887 Wed, 16 Jun 2010 23:00:00 +0100 3670887 http://www.medworm.com/index.php?rid=3665483&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F17 Conclusions: Thus, using computational approach the present analysis has provided better insights into the preexisting low resolution structures of virus assemblies, the findings of which can be made use of in designing effective antivirals against these deadly human pathogens. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3665483 Tue, 15 Jun 2010 23:00:00 +0100 3665483 http://www.medworm.com/index.php?rid=3655284&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F16 Conclusion: The results define the structure of the S28 family of proteases, provide the structural basis of PRCP and DPP7 substrate specificity and enable the rational design of selective PRCP modulators. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3655284 Thu, 10 Jun 2010 23:00:00 +0100 3655284 http://www.medworm.com/index.php?rid=3644324&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F15 Conclusion: Our SAXS and analytical ultracentrifugation experiments indicated that RACK1 is predominantly a monomer in solution. RACK1 and Ki-1/57(122-413) interact strongly under the tested conditions. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3644324 Mon, 07 Jun 2010 23:00:00 +0100 3644324 http://www.medworm.com/index.php?rid=3607037&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F13 Conclusions: Although multiple-domain constructs of ZHX1 selected by bioinformatics studies could be expressed solubly, only single homeodomains yielded crystals. The crystal structure of ZHX1 HD4 showed additional hydrophobic interactions relative to many known homeodomains via extensive contacts formed by the novel C-terminal helix V with, in particular, helix I. Additionally, the replacement of some charged covariant residues (which are commonly observed to form salt bridges in non-homeotherms such as the Drosophila 'engrailed' homeodomain), by apolar residues further increases hydrophobic contacts within ZHX1 HD4, and potentially stability, relative to engrailed homeodomain. ZHX1 HD4 helix V points away from the normally observed DNA major groove binding site on homeodomains and thus ... BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3607037 Thu, 27 May 2010 23:00:00 +0100 3607037 http://www.medworm.com/index.php?rid=3595068&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F11 Conclusions: The ENM approach to small molecule activation of proteins may offer a first pass predictive methodology where affinity is encoded in residues remote from the active site, and aid in the design of specific protein agonists that enhance the allosteric coupling and antagonist that repress it. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3595068 Mon, 24 May 2010 23:00:00 +0100 3595068 http://www.medworm.com/index.php?rid=3573093&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F10 Conclusion: Given the high level of structural similarity between OxyR from N. meningitidis and E. coli, we conclude that the redox response mechanism is likely to be similar in both species, involving the reversible formation of a disulphide between C199-C208. Modelling suggests that disulphide formation would directly affect the interface between regulatory domains in an OxyR tetramer which in turn may lead to an alteration in the spacing/ orientation of the DNA-binding domains and hence the interaction of OxyR with its DNA binding sites. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3573093 Sun, 16 May 2010 23:00:00 +0100 3573093 http://www.medworm.com/index.php?rid=3424173&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F9 Conclusions: Our results show that structurally conserved pockets are a common feature of protein families. The structural conservation of protein pockets, combined with other characteristics, can be exploited in drug discovery procedures, in particular, for the selection of the most appropriate target protein and pocket for the design of drugs against entire protein families or subfamilies (e.g. for the development of broad-spectrum antimicrobials) or against a specic protein (e.g. in attempting to reduce side effects). (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3424173 Tue, 30 Mar 2010 23:00:00 +0100 3424173 http://www.medworm.com/index.php?rid=3306187&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F7 Conclusions: MD simulations predicted that the acidic linker peptide (a1) between the A1 and A2 domains is largely flexible and appears to mask the exposure of putative fIXa enzyme binding loop (Tyr555-Asp569) region in the A2 domain. The simulation of fVIIIa, generated from the zymogen structure, predicted that the linker peptide (a1) undergoes significant conformational reorganization upon activation by relocating completely to the A1-domain. The conformational transition led to the exposure of the Tyr555-Asp569 loop and the surrounding region in the A2 domain. While the proposed linker peptide conformation is predictive in nature and warrants further experimental validation, the observed conformational differences between the zymogen and activated forms may explain and support the large... BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3306187 Thu, 25 Feb 2010 00:00:00 +0100 3306187 http://www.medworm.com/index.php?rid=3293994&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F6 Conclusion: The identified terminal segment, strongly conserved in both RNA and protein sequences, is especially significant as it is surface exposed and structural chemistry reveals the probable role of this stretch in tetrameric stabilization. It could also participate in other biological processes associated with conserved surface residues. A RNA double hairpin secondary structure found in this segment in a majority of the H5N1 strains also supports this observation. In this paper we propose this conserved region as a probable site for designing inhibitors for broad-spectrum pandemic control of flu viruses with similar NA structure. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3293994 Mon, 22 Feb 2010 00:00:00 +0100 3293994 http://www.medworm.com/index.php?rid=3266449&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F5 Conclusions: Accuracy of protein modeling, as demonstrated for the problem of loop modeling, could be improved by the combinations of different modeling techniques. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3266449 Thu, 11 Feb 2010 00:00:00 +0100 3266449 http://www.medworm.com/index.php?rid=3235293&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F4 Conclusions: The use of microenvironments instead of backbone geometric criteria enables flexible exploration of protein function space, and detection of recurring motifs that are discontinuous in sequence and diverse in structure. Clustering microenvironments may thus help to functionally characterize novel proteins and better understand the protein structure-function relationship. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3235293 Tue, 02 Feb 2010 00:00:00 +0100 3235293 http://www.medworm.com/index.php?rid=3222769&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F3 Conclusion: Mutational analysis of PCNA suggests that positively charged residues in the center of the clamp create a binding surface that makes contact with DNA. Disruption of this positive surface, which had not previously been implicated in clamp loading function, reduces RFC ATPase activity in the presence of DNA, most likely by reducing the affinity of RFC and PCNA for DNA. The interaction of DNA is not, however, restricted to one orientation, as indicated by analysis of the PCNA-DNA co-crystals. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3222769 Sat, 30 Jan 2010 00:00:00 +0100 3222769 http://www.medworm.com/index.php?rid=3211775&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F2 Conclusions: The CC structure of sGCbeta1 revealed a tetrameric arrangement comprised of a dimer of CC dimers. Each monomer is comprised of a long alpha-helix, a turn near residue P399, and a short second alpha-helix. The CC structure also offers insights as to how sGC homodimers are not as stable as (functionally) active heterodimers via a possible role for inter-helix salt-bridge formation. The structure also yielded insights into the residues involved in dimerization. In addition, the CC region is also known to harbor a number of congenital and man-made mutations in both membrane and soluble guanylyl cyclases and those function-affecting mutations have been mapped onto the CC structure. This mutant analysis indicated an importance for not only certain dimerization residue positions, but... BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3211775 Wed, 27 Jan 2010 00:00:00 +0100 3211775 http://www.medworm.com/index.php?rid=3163273&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F10%2F1 Conclusion: Peptaibol biosynthesis incorporates a single R domain, which appears to catalyze the four-electron reduction reaction of a peptidyl carrier protein (PCP)-bound peptide to its corresponding primary alcohol. Analysis of R domains present in the non-redundant (nr) database of the NCBI showed that the R domain always resides in the last NRPS module and is involved in either a two or four-electron reduction reaction. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3163273 Tue, 12 Jan 2010 00:00:00 +0100 3163273 http://www.medworm.com/index.php?rid=3099980&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F75 Conclusions: Combined structural, genomic and proteomic analyses have allowed the identification and in silico characterization of a new putative immunity protein from S. pyogenes, possibly the first structure of an immunity protein protective against potential class IIb two-peptide bacteriocins. We have named the two pairs of putative bacteriocins found in S. pyogenes pyogenecin 1, 2, 3 and 4. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3099980 Thu, 17 Dec 2009 00:00:00 +0100 3099980 http://www.medworm.com/index.php?rid=3096111&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F74 Conclusions: These structural differences are discussed in the context of the different types of L-domains regulating distinct cellular pathways in virus budding. EIAV p9 mediates virus release by recruiting the ALG2-interacting protein X (ALIX) via the YPDL-motif to the site of virus budding, the counterpart of the YPXnL-motif found in p6. However, p6 contains an additional PTAP L-domain that promotes HIV-1 release by binding to the tumor susceptibility gene 101 (Tsg101). The notion that structures found in p9 differ form that of p6 further support the idea that different mechanisms regulate binding of ALIX to primary versus secondary L-domains types. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3096111 Thu, 17 Dec 2009 00:00:00 +0100 3096111 http://www.medworm.com/index.php?rid=3084433&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F73 Conclusions: TIM-Finder can serve as a competitive tool for proteome-wide TIM-barrel protein identification. The TIM-Finder web server is freely accessible at http://202.112.170.199/TIM-Finder/. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3084433 Mon, 14 Dec 2009 00:00:00 +0100 3084433 http://www.medworm.com/index.php?rid=3082045&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F72 Conclusion: Protein crystal structures are a potentially rich source of functional information. When loops are missing in these structures, we may be losing important information about binding sites and active sites. We have shown that limited loop modeling (e.g. loops less than 17 residues) combined with pattern matching algorithms can recover functions and propose putative conformations associated with these functions. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=3082045 Fri, 11 Dec 2009 00:00:00 +0100 3082045 http://www.medworm.com/index.php?rid=2995303&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F71 Conclusions: We have introduced a method to split knowledge-based potentials and to solve the problem of defining a reference state. The new scores have detected near-native structures as accurately as state-of-art methods and have been successful to identify wrongly modeled regions of many near-native conformations. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2995303 Mon, 16 Nov 2009 00:00:00 +0100 2995303 http://www.medworm.com/index.php?rid=2984390&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F70 Conclusions: This report provides the first explanation of the mutant phenotypes caused by non-synonymous substitutions in the Dishevelled and Axin DIX domain by correlating their presumed functional significance with molecular structure. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2984390 Thu, 12 Nov 2009 00:00:00 +0100 2984390 http://www.medworm.com/index.php?rid=2934211&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F69 Conclusions: By using the software, named HaptiMol ISAS (available from www.haptimol.co.uk), one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water accessibility of the biomolecular surface that cannot be so easily attained using conventional molecular graphics software. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2934211 Tue, 27 Oct 2009 00:00:00 +0100 2934211 http://www.medworm.com/index.php?rid=2930480&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F68 Conclusions: The partially-supervised clustering revealed biologically meaningful sub-families even for highly heterogeneous domains and the predicted functional residues provide insights into the basis of the different substrate specificities. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2930480 Mon, 26 Oct 2009 00:00:00 +0100 2930480 http://www.medworm.com/index.php?rid=2923000&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F67 Conclusion: The quaternary structure of Nce103 resembles the typical plant type beta-CAs of known structure, with an N-terminal arm indispensable for the enzymatic activity. Comparative structure analysis enables us to draw a possible tunnel for the substrate to access the active site which is located at the bottom of a funnel-shaped substrate pocket. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2923000 Fri, 23 Oct 2009 23:00:00 +0100 2923000 http://www.medworm.com/index.php?rid=2875217&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F65 Conclusions: We suggest that cold lability of E. coli Trpases is primarily affected by PLP release. The enhanced loss of activity of the three mutants is presumably due to the reduced size of the side chain of the amino acids. This prevents the tight assembly of the active tetramer, making it more susceptible to the cold driven changes in hydrophobic interactions which facilitate PLP release. The hydrophobic interactions along the non catalytic interface overshadow the effect of point mutations and may account for the differences in the dissociation of E. coli Trpase to dimers and P. vulgaris Trpase to monomers. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2875217 Wed, 07 Oct 2009 23:00:00 +0100 2875217 http://www.medworm.com/index.php?rid=2868554&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F64 Conclusions: Molecular models have been generated for a large number of G_3 X_n1 G_3 X_n2 G_3 X_n3 G_3 sequences. For a given sequence not all topologies are possible with the available repertoire of fragments due to steric hindrance and low superimposability. Since all molecular models are generated by fragments coming from observed quadruplex structures, molecular models are in principle reliable and may be used for interpretation of experimental data. Some examples of applications are given. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2868554 Tue, 06 Oct 2009 23:00:00 +0100 2868554 http://www.medworm.com/index.php?rid=2842052&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F63 Conclusions: The novel data reported here provide information about the biochemically and structurally important determinants of biotin binding. This information may facilitate the discovery of novel tools for biotechnology. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2842052 Mon, 28 Sep 2009 23:00:00 +0100 2842052 http://www.medworm.com/index.php?rid=2838637&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F62 Conclusions: Our results (i) contribute to better understanding of the origin of the novel A/H1N1 influenza virus, (ii) provide a tool for monitoring its molecular evolution (iii) predicts hotspots associated with enhanced infectivity in humans and (iv) identify therapeutic and diagnostic targets for prevention and treatment of A/H1N1 infection. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2838637 Sun, 27 Sep 2009 23:00:00 +0100 2838637 http://www.medworm.com/index.php?rid=2819062&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F61 Conclusions: By examining left-handed -turns containing L-amino acids, new interaction motifs for incorporating D-amino acids into right-handed alpha-helices are identified. These will provide a basis for de novo design of novel heterochiral protein folds. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2819062 Mon, 21 Sep 2009 23:00:00 +0100 2819062 http://www.medworm.com/index.php?rid=2809426&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F59 Conclusions: Our studies further clarify the structural features that are relevant for Sam-Sam interactions involving Ship2 and give additional hints that could be used for the identification of new molecules able to selectively inhibit Sam-Sam associations. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2809426 Thu, 17 Sep 2009 23:00:00 +0100 2809426 http://www.medworm.com/index.php?rid=2740873&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F57 Conclusions: Our data reveal the first low resolution, structural information for human STC1. Theoretical predictions and circular dichroism spectroscopy both suggested that STC1 has a high content of alpha-helices and SAXS experiments revealed that STC1 is a dimer of slightly elongated shape in solution. The dimerization was confirmed by mass spectrometry as was the highly conserved disulfide pattern, which is similar to that found in fish STC1. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2740873 Wed, 26 Aug 2009 23:00:00 +0100 2740873 http://www.medworm.com/index.php?rid=2733603&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F56 Conclusions: The 66.3 kDa protein closely resembles conjugated bile acid hydrolase (CBAH) and penicillin V acylase (PVA) suggesting a hydrolytic activity on non-peptide amide bonds. The similarity to these bacterial proteins also implies an autocatalytic maturation of the lysosomal 66.3 kDa protein. Upon cleavage between S248 and C249, a deep pocket becomes solvent accessible, which harbors the putative active site of the 66.3 kDa protein. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2733603 Mon, 24 Aug 2009 23:00:00 +0100 2733603 http://www.medworm.com/index.php?rid=2724223&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F55 Conclusions: The extent to which individual proteins adapt to halophilic conditions varies, presumably due to their diverse characteristics and roles within the cell. The number of ion pairs observed in the HvPCNA monomer-monomer interface was unexpectedly low. This may reflect the fact that the trimer is intrinsically stable over a wide range of salt concentrations and therefore additional modifications for trimer maintenance in high salt conditions are not required. Halophilic proteins frequently bind anions and cations and in HvPCNA cation binding may compensate for the remarkable reduction in positive charge in the pore region, to facilitate functional interactions with DNA. In this way, HvPCNA may harness its environment as opposed to simply surviving in extreme halophilic conditions.... BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2724223 Fri, 21 Aug 2009 23:00:00 +0100 2724223 http://www.medworm.com/index.php?rid=2723003&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F54 Conclusions: Overall, similarities between FND and DnaD-like domains as well as previously reported observations on Ftn6 suggest that FND may function as a DNA-interacting module thereby providing an as yet missing link between DNA replication and cell division in cyanobacteria. Consistently, we also showed that Ftn6 is involved in tolerance to DNA damages generated by UV rays. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2723003 Thu, 20 Aug 2009 23:00:00 +0100 2723003 http://www.medworm.com/index.php?rid=2719265&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F53 Conclusions: The chloride ion in AlrBax is functioning effectively as a carbamylated lysine making it an integral and unique part of this structure. Despite differences in space group and crystal form, the two AlrBax structures are very similar, supporting the case that reductive methylation is a valid rescue strategy for proteins recalcitrant to crystallization, and does not, in this case, result in artifacts in the tertiary structure. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2719265 Wed, 19 Aug 2009 23:00:00 +0100 2719265 http://www.medworm.com/index.php?rid=2666959&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F52 Conclusions: The developed tool is very useful for the research on protein binding site analysis and prediction. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2666959 Sun, 02 Aug 2009 23:00:00 +0100 2666959 http://www.medworm.com/index.php?rid=2660304&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F50 Background: Current protocols yield crystals for (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2660304 Thu, 30 Jul 2009 23:00:00 +0100 2660304 http://www.medworm.com/index.php?rid=2660303&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F51 Conclusions: The performance of the neural networks was evaluated on a commonly used set of sequences known as the CB513 set. An overall Pearson's correlation coefficient of 0.72 was obtained, which is comparable to the performance of the currently best public available method, Real-SPINE. Both methods associate a reliability score with the individual predictions. However, our implementation of reliability scores in the form of a Z-score is shown to be the more informative measure for discriminating good predictions from bad ones in the entire range from completely buried to fully exposed amino acids. This is evident when comparing the Pearson's correlation coefficient for the upper 20 % of predictions sorted according to reliability. For this subset, values of 0.79 and 0.74 are obtained u... BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2660303 Thu, 30 Jul 2009 23:00:00 +0100 2660303 http://www.medworm.com/index.php?rid=2657046&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F49 Conclusions: The greater extent of hydrogen bonding and neighbor atom density in the unreactive nucleotide pairs is consistent with reduced flexibility at a majority of the unreactive sites. The reactive photocrosslinking sites are clustered in the 30S subunit and this indicates nonuniform patterns of hydrogen bonding and packing density in the 16S rRNA tertiary structure. Because this analysis addresses inter-nucleotide distances and geometry between nucleotides distant in the primary sequence, the results indicate regional and global flexibility of the rRNA. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2657046 Wed, 29 Jul 2009 23:00:00 +0100 2657046 http://www.medworm.com/index.php?rid=2629459&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F47 Conclusion: Our results showed that the above mechanisms lead to the disruption of the electrostatic interactions between the A-loop and the alpha C-helix in the activating mutants, which presumably contribute to the flipping of the activation segment to an active form. Conversely, in the B-RAFD594V mutant that has impaired kinase activity, and in B-RAFWT these interactions were strong and stabilized the kinase inactive form. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2629459 Tue, 21 Jul 2009 23:00:00 +0100 2629459 http://www.medworm.com/index.php?rid=2597744&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F46 Conclusions: We have provided new insight into the structure and function of the Asp-box motif and of Asp-box beta-propellers, and expect that the classification and analysis presented here will prove helpful in interpreting future data on Asp-box proteins in general and on Asp-box beta-propellers in particular. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2597744 Sun, 12 Jul 2009 23:00:00 +0100 2597744 http://www.medworm.com/index.php?rid=2587749&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F44 Conclusion: The most significant result of this work is the observation that virtually all, experimentally determined amyloidogenic determinants, to date, and the majority of predicted, but not yet experimentally verified short amyloidogenic stretches, lie 'exposed' on the surface of the relevant amyloidogenic proteins, and also several of them have the ability to act as conformational 'switches'. Experiments, focused on these fragments, should be performed to test this idea. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2587749 Wed, 08 Jul 2009 23:00:00 +0100 2587749 http://www.medworm.com/index.php?rid=2560182&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F41 Conclusions: We find that a constrained regression approach showsconsistently good performance. Although it is not always the absolute best performing scheme, it is always performs on par with the best schemes across multiple datasets. The work presented here provides the basis for the construction of a regression model trained on data from existing structureprediction servers. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2560182 Mon, 29 Jun 2009 23:00:00 +0100 2560182 http://www.medworm.com/index.php?rid=2504215&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F40 Conclusions: Our structural data in combination with sequence analysis supports the idea that two of the 5 actinobacteria-specific proteins, ASP1 and ASP2, mediate similar function. This function is predicted to be novel since the structures of these proteins do not match any known protein with or without known function. Our results suggest that this function could involve divalent metal ion binding/transport. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2504215 Tue, 09 Jun 2009 23:00:00 +0100 2504215 http://www.medworm.com/index.php?rid=2456081&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F39 Conclusions: The experimentally observed differences in selectivity and specificity of the enzymes were reproduced with an accuracy of 81%. The method was robust toward small differences in initial structures (different crystallisation conditions or a co-crystallised ligand), although large displacements of catalytic residues often resulted in substrate poses that did not pass the geometric filter criteria. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2456081 Wed, 03 Jun 2009 04:00:00 +0100 2456081 http://www.medworm.com/index.php?rid=2439874&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F37 Conclusions: The analysis led to predictions regarding the functional classification and identification of possible catalytic residues of a number of hot dog fold-containing hypothetical proteins whose structures were determined in high throughput structural genomics projects. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2439874 Thu, 28 May 2009 04:00:00 +0100 2439874 http://www.medworm.com/index.php?rid=2439873&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F38 Conclusion: Conformational transitions between the experimentally observed closed and open conformation of the lid were observed by multiple molecular dynamics simulations of B. cepacia lipase. Transitions in both directions occurred without applying restraints or external forces. The opening and closing was driven by the solvent and independent of a bound substrate molecule. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2439873 Thu, 28 May 2009 04:00:00 +0100 2439873 http://www.medworm.com/index.php?rid=2427042&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F36 Conclusions: Our results suggest a mechanism for autoinhibition of RGSL family of GEFs, in which the RGSL domain and a unique sequence motif upstream of the DH domain, act cooperatively to reduce the ability of the DH domain to bind the nucleotide free RhoA. The activation mechanism is likely to involve two independent steps, i.e. displacement of the RGSL domain and conformational change involving the autoinhibitory sequence motif containing several negatively charged residues. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2427042 Thu, 21 May 2009 04:00:00 +0100 2427042 http://www.medworm.com/index.php?rid=2422790&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F33 Conclusions: Structure similarity searches using domain boundaries based on conserved sequence information can provide an additional method for investigators to identify interesting similarities between proteins with known structures. Because of the improvement in performance of structure similarity searches using sequence domain boundaries, we are in the process of implementing their inclusion into the VAST search and MMDB resources in the NCBI Entrez system. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2422790 Tue, 19 May 2009 04:00:00 +0100 2422790 http://www.medworm.com/index.php?rid=2413378&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F31 Conclusion: The present work suggested a characterization method for the intermolecular weak interaction. It is potentially useful for elucidating the toxigenicity of perfluorochemicals when combined with biomolecular function effect, transmembrane transport, toxicological testing and the other experiments. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2413378 Thu, 14 May 2009 04:00:00 +0100 2413378 http://www.medworm.com/index.php?rid=2413379&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F30 Conclusion: Most residue-nucleotide contacts can be predicted with high accuracy using only sequence and evolutionary information. Major and minor groove contacts, however, depend profoundly on the local structure. Overall, this study takes us a step closer to the ultimate goal of predicting mutual recognition sites in protein and DNA sequences. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2413379 Wed, 13 May 2009 04:00:00 +0100 2413379 http://www.medworm.com/index.php?rid=2413380&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F29 Conclusion: Our study provides an effective technique to compare the shape of flexible proteins. The experimental results demonstrate the insensitivity of LD descriptor to the protein shape deformation. The demos and supplemental materials are available on https://engineering.purdue.edu/PRECISE/LDD. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2413380 Tue, 12 May 2009 04:00:00 +0100 2413380 http://www.medworm.com/index.php?rid=2396832&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F28 Conclusions: Reducing server correlation and optimally combining independent latent servers show a significant improvement over the traditional consensus methods. This approach can hopefully provide a powerful tool for protein structure refinement and prediction use. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2396832 Wed, 06 May 2009 04:00:00 +0100 2396832 http://www.medworm.com/index.php?rid=2374623&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F25 Conclusions: HOA based normalization of solvent accessibility from native structures is proposed and it shows improvement in sequence-based predictability, as well as enrichment in interface residues on surface. There may still be some difference between the highest possible ASA and highest observed ASA due to an insufficiently covered space of ASA distribution in the PDB, which limit the overall improvement in prediction to a relatively modest degree. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2374623 Mon, 27 Apr 2009 04:00:00 +0100 2374623 http://www.medworm.com/index.php?rid=2363804&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F24 Conclusions: The results illustrate that the free DNA molecule, even in the crystalline state, samples a large amount of conformational space, encompassing both the A and the B-forms, in the absence of any large ligands. A-form as well as some non-A, non-B, distorted geometries are observed for a small number of dinucleotide steps in DNA structures bound to the proteins belonging to a few specific families. However, for most of the bound DNA structures, across a wide variety of protein families, the average step parameters for various dinucleotide sequences as well as backbone torsion angles are observed to be quite close to the free 'B-like' DNA oligomer values, highlighting the flexibility and biological significance of this structural form. (Source: BMC Structural Biology - Latest artic... BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2363804 Fri, 24 Apr 2009 04:00:00 +0100 2363804 http://www.medworm.com/index.php?rid=2340240&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F22 Conclusions: Our analysis, despite the complexity of its possible general applicability, opens up that the consideration of water may have an impact on the improvement of the contact predictions obtained by correlated mutations approaches. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2340240 Wed, 15 Apr 2009 04:00:00 +0100 2340240 http://www.medworm.com/index.php?rid=2340241&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F21 Conclusions: The presented results may help to better understand the interaction of influenza virus with its receptor(s) and to identify new therapeutic targets for drug development. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2340241 Tue, 07 Apr 2009 04:00:00 +0100 2340241 http://www.medworm.com/index.php?rid=2340242&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F20 Conclusions: Atoms with zero per-atom ASA have a significantly larger chemical shift dispersion and often have a different chemical shift distribution compared to those that are solvent accessible. With higher per-atom ASA, the chemical shift values also tend towards random coil values. The per-atom ASA, although not the determinant of the chemical shift, thus provides a way to directly correlate chemical shift information to the atomic coordinates. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2340242 Thu, 02 Apr 2009 04:00:00 +0100 2340242 http://www.medworm.com/index.php?rid=2340243&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F19 Conclusions: By programming to the graphics processor unit, ProteinShader is able to produce high quality images and illustrative rendering effects in real-time. The main feature that distinguishes ProteinShader from other free molecular visualization tools is its use of texture mapping techniques that allow two-dimensional images to be mapped onto the curved three-dimensional surfaces of ribbons and tubes with minimum distortion of the images. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2340243 Mon, 30 Mar 2009 04:00:00 +0100 2340243 http://www.medworm.com/index.php?rid=2295785&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F18 Conclusions: We show that the estimation errors for the CTF detection methodology proposed in \cite{Sorzano2007a} does not show a significant deterioration of the CTF correction capabilities of subsequent algorithms. All together, the methodology described in this paper constitutes a powerful tool for the quantitative analysis of CTF models that can be applied to other models different from the one analyzed here. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2295785 Thu, 26 Mar 2009 04:00:00 +0100 2295785 http://www.medworm.com/index.php?rid=2295787&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F17 Conclusions: Detailed structural description of the S. aureus PrsA-PPIase lays the foundation for structure-based design of enzyme inhibitors. The structure resembles hPin1-type parvulins both structurally and regarding substrate preference. Even though a wealth of structural data is available on parvulins, the catalytic mechanism has yet to be resolved. The structure of S. aureus PrsA-PPIase and our findings on the role of the conserved active site histidines help in designing further experiments to solve the detailed catalytic mechanism. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2295787 Tue, 24 Mar 2009 04:00:00 +0100 2295787 http://www.medworm.com/index.php?rid=2283581&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F15 Conclusions: The method has been incorporated into the Norine database, available at http://bioinfo.lifl.fr/norine. Less than one second is needed to search for a pattern in the entire database. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2283581 Wed, 18 Mar 2009 04:00:00 +0100 2283581 http://www.medworm.com/index.php?rid=2283579&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F16 Conclusions: This set of strategies and automation technologies was used successfully to yield a primary crystal MK2 structure bound to an ATP-competitive inhibitor. The crystal form was an excellent candidate for soaking methods to solve subsequent liganded structures. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2283579 Wed, 18 Mar 2009 04:00:00 +0100 2283579 http://www.medworm.com/index.php?rid=2268176&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F14 Conclusions: The structural details underlying hUPP1's active site and additional surfaces beyond these catalytic residues, which coordinate binding of BAU and other acyclouridine analogues, suggest avenues for future design of more potent inhibitors of this enzyme. Notably, the loop forming the back wall of the substrate binding pocket is conformationally different and substantially less flexible in hUPP1 than in previously studied microbial homologues. These distinctions can be utilized to discover novel inhibitory compounds specifically optimized for efficacy against the human enzyme as a step toward the development of more effective chemotherapeutic regimens that can selectively protect normal tissues with inherently lower UPP activity. (Source: BMC Structural Biology - Latest articles... BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2268176 Mon, 16 Mar 2009 04:00:00 +0100 2268176 http://www.medworm.com/index.php?rid=2239770&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F11 Conclusions: It is proposed that the two glycine residues function as hinges and that the glycine brace influences guanine nucleotide binding or release by interacting with these hinges. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2239770 Thu, 05 Mar 2009 05:00:00 +0100 2239770 http://www.medworm.com/index.php?rid=2215970&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F8 Conclusion: The structure network approach employed in this study for the analysis of dimeric interfaces in LuxS has brought out certain structural details at the side-chain interaction level, which were elusive from the conventional structure comparison methods. The results from this study provide a better understanding of the relation between the luxS gene and its functional role in the prokaryotes. This study also makes it possible to explore the potential direction towards the design of inhibitors of LuxS and thus towards a wide range of antimicrobials. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2215970 Wed, 25 Feb 2009 05:00:00 +0100 2215970 http://www.medworm.com/index.php?rid=2215969&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F9%2F9 Conclusions: The structures of the C. parvum GAPDH ternary complex and other GAPDH complexes demonstrate the plasticity of the substrate binding site. We propose that the active site of GAPDH can accommodate the substrate in multiple conformations at multiple locations during the initial encounter. However, the C-3 phosphate group clearly prefers the 'new Pi' site for initial binding in the active site. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=2215969 Wed, 25 Feb 2009 05:00:00 +0100 2215969 http://www.medworm.com/index.php?rid=1984467&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F8%2F51 Conclusions: PDBalert will accelerate the information flow from the PDB database to all those who can profit from the newly released protein structures for predicting the 3D structure or function of their proteins of interest. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=1984467 Tue, 25 Nov 2008 05:00:00 +0100 1984467 http://www.medworm.com/index.php?rid=1974526&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F8%2F50 Conclusions: Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of how two structurally similar proteins utilize different mechanisms to form a ligand-bound state. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=1974526 Wed, 19 Nov 2008 05:00:00 +0100 1974526 http://www.medworm.com/index.php?rid=1933742&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F8%2F47 Conclusion: LRRML is an information source for investigators involved in both theoretical and applied research on LRR proteins. It is available at http://zeus.krist.geo.uni-muenchen.de/~lrrml. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=1933742 Wed, 05 Nov 2008 05:00:00 +0100 1933742 http://www.medworm.com/index.php?rid=1815074&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F8%2F39 Conclusion: pi-turns have been characterized, first using hydrogen bond and the distance between Calpha atoms of the terminal residues, and then using backbone torsion angles. While the Schellman motif has a structural role in helix termination, many of the pi-HB turns, being located on surface cavities, have functional role and there is also sequence conservation. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=1815074 Mon, 22 Sep 2008 04:00:00 +0100 1815074 http://www.medworm.com/index.php?rid=1749942&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F8%2F36 Conclusion: Our tests have shown that theoretically predicted contacts can be very beneficial for protein structure prediction. Depending on the protein modeling method, a contact data set applied should be prepared with differently balanced coverage and accuracy of predicted contacts. Namely, high coverage of contact data is important for the model ranking and high accuracy for the folding simulations. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=1749942 Mon, 11 Aug 2008 04:00:00 +0100 1749942 http://www.medworm.com/index.php?rid=1652095&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F8%2F33 Conclusions: : The presence of an inorganic phosphate in the crystallographic structure opposite the known AMP binding site relative to the thiamine moiety suggests that a second AMP molecule could be accommodated in the C. albicans structure. Together with the crystallographic structures of the enzyme/substrate complexes this suggests the existence of a secondary, less specific, nucleotide binding site in the Candida albicans thiamine pyrophosphokinase which could transiently serve during the release or the binding of ATP. The structures also highlight a conserved Glutamine residue (Q138) which could interact with the ATP alpha-phosphate and act as gatekeeper. Finally, the TPK/Thiamine-PNP complex is consistent with a one step mechanism of pyrophosphorylation. (Source: BMC Structural Biol... BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=1652095 Thu, 24 Jul 2008 04:00:00 +0100 1652095 http://www.medworm.com/index.php?rid=1530612&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F8%2F30 Conclusion: The graphical tools and outputs described here significantly extend the validation and analysis possibilities of NOE assignments given by ARIA as well as the analysis of the quality of the final structure ensemble. These tools are included in the latest version of ARIA, which is available at http://aria.pasteur.fr. The Web site also contains an installation guide, a user manual and example calculations. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=1530612 Thu, 05 Jun 2008 04:00:00 +0100 1530612 http://www.medworm.com/index.php?rid=1487663&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F8%2F29 Conclusions: This study clearly established the preservation of the enzyme structure in a SDS/MPD mixture. It is hypothesized that high concentrations of MPD would change the properties of SDS and lower or avoid interactions between the denaturant and the protein. These structural data therefore support the hypothesis that MPD avoids disruption of the enzyme structure by SDS and can protect proteins from SDS denaturation. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=1487663 Tue, 03 Jun 2008 04:00:00 +0100 1487663 http://www.medworm.com/index.php?rid=1472128&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F8%2F26 Conclusion: The CHIP:UbcH5a structure emphasizes the importance of specificity determinants located on the long loops and central helix of the CHIP U-box, and on the N-terminal helix and loops L4 and L7 of its cognate E2 enzymes. The S-P-A motif and other specificity determinants define the set of cognate E2 enzymes for CHIP, which likely includes several Class III E2 enzymes. CHIP's interactions with UbcH5, Ube2e2 and Ubc13-Uev1a are consistent with the notion that Ubc13-Uev1a may work sequentially with other E2 enzymes to carry out K63-linked polyubiquitination of CHIP substrates. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=1472128 Fri, 16 May 2008 04:00:00 +0100 1472128 http://www.medworm.com/index.php?rid=1422564&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F8%2F24 Conclusions: This novel approach can be applied without any manual intervention to improve the quality of comparative predictions where multiple template/alignment combinations are available for modeling, producing conformational models of higher quality than the starting initial predictions. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=1422564 Mon, 05 May 2008 04:00:00 +0100 1422564 http://www.medworm.com/index.php?rid=1416092&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F8%2F23 Conclusions: A set of residues and/or structural elements that are potentially involved in allosteric communication in G-alpha is presented. This information can be used as a guide to structural, spectroscopic, mutational, and theoretical studies on the allosteric network in G-alpha proteins, which will provide a better understanding of G protein-mediated signal transduction. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=1416092 Fri, 02 May 2008 04:00:00 +0100 1416092 http://www.medworm.com/index.php?rid=1376498&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F8%2F22 Conclusions: Combining NMR experiments on the complex with docking results allowed us to build a three dimensional structural model. This model serves as the starting point for further structural studies aimed at improving the affinity of pamoic acid for binding to DNA polymerase beta. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=1376498 Wed, 16 Apr 2008 04:00:00 +0100 1376498 http://www.medworm.com/index.php?rid=1332345&cid=s_34050_67_f&fid=34050&url=http%3A%2F%2Fwww.biomedcentral.com%2F1472-6807%2F8%2F20 Conclusions: The near identity of backbone structures of this pair of proteins entails that the significant differences in their thermal stabilities are encoded exclusively by the identity of the amino acid side-chains. Furthermore, the degree of sequence divergence is strongly correlated with structure; with a high degree of conservation in the core progressing to increased diversity in the boundary and surface regions. Different factors that may possibly contribute to thermal stability appear to be differentially encoded in each of these regions of the protein. The tteRBP/ecRBP pair therefore offers an opportunity to dissect contributions to thermal stability by side-chains alone in the absence of large structural differences. (Source: BMC Structural Biology - Latest articles) BMC Structural Biology - Latest articles journals http://www.medworm.com/rss/comments.php?id=1332345 Fri, 28 Mar 2008 04:00:00 +0100 1332345