http://www.biomedcentral.com/bmcstructbiol/ The latest research articles published by BMC Structural Biology 2009-07-10T00:00:00Z This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ Background: It is increasingly recognized that protein functions often require intricate conformational dynamics, which involves a network of key amino acid residues that couple spatially separated functional sites. Tremendous efforts have been made to identify these key residues by experimental and computational means. Results: We have performed a large-scale evaluation of the predictions of dynamically important residues by a variety of computational protocols including three based on the perturbation and correlation analysis of a coarse-grained elastic model. This study is performed for two lists of test cases with >500 pairs of protein structures. The dynamically important residues predicted by the perturbation and correlation analysis are found to be strongly or moderately conserved in >67% of test cases. They form a sparse network of residues which are clustered both in 3D space and along protein sequence. Their overall conservation is attributed to their dynamic role rather than ligand binding or high network connectivity. Conclusion: By modeling how the protein structural fluctuations respond to residue-position-specific perturbations, our highly efficient perturbation and correlation analysis can be used to dissect the functional conformational changes in various proteins with a residue level of detail. The predictions of dynamically important residues serve as promising targets for mutational and functional studies. http://www.biomedcentral.com/1472-6807/9/45 Wenjun Zheng Mustafa Tekpinar BMC Structural Biology 2009, 9:45 2009-07-10T00:00:00Z doi:10.1186/1472-6807-9-45 BMC Structural Biology 1472-6807 9 45 2009-07-10T00:00:00Z PDF Background: Amyloidoses are a group of usually fatal diseases, probably caused by protein misfolding and subsequent aggregation into amyloid fibrillar deposits. The mechanisms involved in amyloid fibril formation are largely unknown and are the subject of current, intensive research. In an attempt to identify possible amyloidogenic regions in proteins for further experimental investigation, we have developed and present here a publicly available online tool that utilizes five different and independently published methods, to form a consensus prediction of amyloidogenic regions in proteins, using only protein primary structure data. Results: It appears that the consensus prediction tool is slightly more objective than individual prediction methods alone and suggests several previously not identified amino acid stretches as potential amyloidogenic determinants, which (although several of them may be overpredictions) require further experimental studies. The tool is available at: http://biophysics.biol.uoa.gr/AMYLPRED. Utilizing molecular graphics programs, like O and PyMOL, as well as the algorithm DSSP, it was found that nearly all experimentally verified amyloidogenic determinants (short peptide stretches favouring aggregation and subsequent amyloid formation), and several predicted, with the aid of the tool AMYLPRED, but not experimentally verified amyloidogenic determinants, are located on the surface of the relevant amyloidogenic proteins. This finding may be important in efforts directed towards inhibiting amyloid fibril formation. 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. http://www.biomedcentral.com/1472-6807/9/44 Kimon Frousios Vassiliki Iconomidou Carolina-Maria Karletidi Stavros Hamodrakas BMC Structural Biology 2009, 9:44 2009-07-09T00:00:00Z doi:10.1186/1472-6807-9-44 BMC Structural Biology 1472-6807 9 44 2009-07-09T00:00:00Z PDF Background: Notch signaling drives developmental processes in all metazoans. The receptor binding region of the human Notch ligand Jagged-1 is made of a DSL (Delta/Serrate/Lag-2) domain and two atypical epidermal growth factor (EGF) repeats encoded by two exons, exon 5 and 6, which are out of phase with respect to the EGF domain boundaries. Results: We determined the 1H-NMR solution structure of the polypeptide encoded by exon 6 of JAG1 and spanning the C-terminal region of EGF1 and the entire EGF2. We show that this single, evolutionary conserved exon defines an autonomous structural unit that, despite the minimal structural context, closely matches the structure of the same region in the entire receptor binding module. Conclusions: In eukaryotic genomes, exon and domain boundaries usually coincide. We report a case study where this assertion does not hold, and show that the autonomously folding, structural unit is delimited by exon boundaries, rather than by predicted domain boundaries. http://www.biomedcentral.com/1472-6807/9/43 Alessandro Pintar Corrado Guarnaccia Somdutta Dhir Sandor Pongor BMC Structural Biology 2009, 9:43 2009-07-08T00:00:00Z doi:10.1186/1472-6807-9-43 BMC Structural Biology 1472-6807 9 43 2009-07-08T00:00:00Z PDF Background: Purine nucleoside phosphorylase (PNP) is central to purine salvage mechanisms in Plasmodium parasites, the causative agents of malaria. Most human malaria results from infection either by Plasmodium falciparum (Pf), the deadliest form of the parasite, or by the widespread Plasmodium vivax (Pv). Whereas the PNP enzyme from Pf has previously been studied in detail, despite the prevalence of Pv little is known about many of the key metabolic enzymes from this parasite, including PvPNP. Results: The crystal structure of PvPNP is described and is seen to have many features in common with the previously reported structure of PfPNP. In particular, the composition and conformations of the active site regions are virtually identical. The crystal structure of a complex of PfPNP co-crystallised with inosine and arsenate is also described, and is found to contain a mixture of products and reactants - hypoxanthine, ribose and arsenate. The ribose C1' in this hybrid complex lies close to the expected point of symmetry along the PNP reaction coordinate, consistent with a conformation between the transition and product states. These two Plasmodium PNP structures confirm the similarity of structure and mechanism of these enzymes, which are also confirmed in enzyme kinetic assays using an array of substrates. These reveal an unusual form of substrate activation by 2' -deoxyinosine of PvPNP, but not PfPNP. Conclusions: The close similarity of the Pf and Pv PNP structures allows characteristic features to be identified that differentiate the Apicomplexa PNPs from the human host enzyme. This similarity also suggests there should be a high level of cross-reactivity for compounds designed to inhibit either of these molecular targets. However, despite these similarities, there are also small differences in the activities of the two Plasmodium enzymes. http://www.biomedcentral.com/1472-6807/9/42 Apirat Chaikuad R. Leo Brady BMC Structural Biology 2009, 9:42 2009-07-03T00:00:00Z doi:10.1186/1472-6807-9-42 BMC Structural Biology 1472-6807 9 42 2009-07-03T00:00:00Z PDF Background: Methods that can automatically assess the quality of computationally predicted protein structures are important, as they enable the selection of the most accurate structure from an ensemble of predictions. Assessment methods that determine the quality of a predicted structure by comparing it against the various structures predicted by different servers have been shown to outperform approaches that rely on the intrinsic characteristics of the structure itself. Results: We examined techniques to estimate the quality of a predicted protein structure based on prediction consensus. LGA is used toalign the structure in question to the structures for the same protein predicted by different servers. We examine both static (e.g. averaging) and dynamic (e.g. support vector machine) methods for aggregating these distances on two datasets. 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. http://www.biomedcentral.com/1472-6807/9/41 Kevin DeRonne George Karypis BMC Structural Biology 2009, 9:41 2009-06-30T00:00:00Z doi:10.1186/1472-6807-9-41 BMC Structural Biology 1472-6807 9 41 2009-06-30T00:00:00Z PDF Background: The Actinobacteria phylum represents one of the largest and most diverse groups of bacteria, encompassing many important and well-characterized organisms including Streptomyces, Bifidobacterium, Corynebacterium and Mycobacterium. Members of this phylum are remarkably diverse in terms of life cycle, morphology, physiology and ecology. Recent comparative genomic analysis of 19 actinobacterial species determined that only 5 genes of unknown function uniquely define this large phylum [1]. The cellular functions of these actinobacteria-specific proteins (ASP) are not known. Results: Here we report the first characterization of one of the 5 actinobacteria-specific proteins, ASP1 (Gene ID: SCO1997) from Streptomyces coelicolor. The X-ray crystal structure of ASP1 was determined at 2.2 A. The overall structure of ASP1 retains a similar fold to the large NP-1 family of nucleoside phosphorylase enzymes; however, the function is not related. Further comparative analysis revealed two regions expected to be important for protein function: a central, divalent metal ion binding pore, and a highly conserved elbow shaped helical region at the C-terminus. Sequence analyses revealed that ASP1 is paralogous to another actinobacteria-specific protein ASP2 (SCO1662 from S. coelicolor) and that both proteins likely carry out similar function. 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. http://www.biomedcentral.com/1472-6807/9/40 Beile Gao Seiji Sugiman-Marangos Murray Junop Radhey Gupta BMC Structural Biology 2009, 9:40 2009-06-10T00:00:00Z doi:10.1186/1472-6807-9-40 BMC Structural Biology 1472-6807 9 40 2009-06-10T00:00:00Z PDF Background: Previously, ways to adapt docking programs that were developed for modelling inhibitor-receptor interaction have been explored. Two main issues were discussed. First, when trying to model catalysis a reaction intermediate of the substrate is expected to provide more valid information than the ground state of the substrate. Second, the incorporation of protein flexibility is essential for reliable predictions. Results: Here we present a predictive and robust method to model substrate specificity and enantioselectivity of lipases and esterases that uses reaction intermediates and incorporates protein flexibility. Substrate-imprinted docking starts with covalent docking of reaction intermediates, followed by geometry optimisation of the resulting enzyme-substrate complex. After a second round of docking the same substrate into the geometry-optimised structures, productive poses are identified by geometric filter criteria and ranked by their docking scores. Substrate-imprinted docking was applied in order to model (i) enantioselectivity of Candida antarctica lipase B and a W104A mutant, (ii) enantioselectivity and substrate specificity of Candida rugosa lipase and Burkholderia cepacia lipase, and (iii) substrate specificity of an acetyl- and a butyrylcholine esterase toward the substrates acetyl- and butyrylcholine. Conclusion: 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. http://www.biomedcentral.com/1472-6807/9/39 Benjamin Juhl Peter Trodler Sadhna Tyagi Jurgen Pleiss BMC Structural Biology 2009, 9:39 2009-06-03T00:00:00Z doi:10.1186/1472-6807-9-39 BMC Structural Biology 1472-6807 9 39 2009-06-03T00:00:00Z XML Background: The characteristic of most lipases is the interfacial activation at a lipid interface or in non-polar solvents. Interfacial activation is linked to a large conformational change of a lid, from a closed to an open conformation which makes the active site accessible for substrates. While for many lipases crystal structures of the closed and open conformation have been determined, the pathway of the conformational transition and possible bottlenecks are unknown. Therefore, molecular dynamics simulations of a closed homology model and an open crystal structure of Burkholderia cepacia lipase in water and toluene were performed to investigate the influence of solvents on structure, dynamics, and the conformational transition of the lid. Results: The conformational transition of B. cepacia lipase was dependent on the solvent. In simulations of closed B. cepacia lipase in water no conformational transition was observed, while in three independent simulations of the closed lipase in toluene the lid gradually opened during the first 10–15 ns. The pathway of conformational transition was accessible and a barrier was identified, where a helix prevented the lid from opening to the completely open conformation. The open structure in toluene was stabilized by the formation of hydrogen bonds.In simulations of open lipase in water, the lid closed slowly during 30 ns nearly reaching its position in the closed crystal structure, while a further lid opening compared to the crystal structure was observed in toluene. While the helical structure of the lid was intact during opening in toluene, it partially unfolded upon closing in water. The closing of the lid in water was also observed, when with eight intermediate structures between the closed and the open conformation as derived from the simulations in toluene were taken as starting structures. A hydrophobic β-hairpin was moving away from the lid in all simulations in water, which was not observed in simulations in toluene. The conformational transition of the lid was not correlated to the motions of the β-hairpin structure. 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 were driven by the solvent and independent of a bound substrate molecule. http://www.biomedcentral.com/1472-6807/9/38 Peter Trodler Rolf Schmid Jurgen Pleiss BMC Structural Biology 2009, 9:38 2009-05-28T00:00:00Z doi:10.1186/1472-6807-9-38 BMC Structural Biology 1472-6807 9 38 2009-05-28T00:00:00Z XML Background: The hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago. The fold appears to have a strong association with fatty acid biosynthesis, its regulation and metabolism, as the proteins with this fold are predominantly coenzyme A-binding enzymes with a variety of substrates located at their active sites. Results: We have analyzed the structural features and sequences of proteins having the hot dog fold. This study reveals that though the basic architecture of the fold is well conserved in these proteins, significant differences exist in their sequence, nature of substrate and oligomerization. Segments with certain conserved sequence motifs seem to play crucial structural and functional roles in various classes of these proteins. Conclusion: 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. http://www.biomedcentral.com/1472-6807/9/37 Lakshmi Pidugu Koustav Maity Karthikeyan Ramaswamy Namita Surolia Kaza Suguna BMC Structural Biology 2009, 9:37 2009-05-28T00:00:00Z doi:10.1186/1472-6807-9-37 BMC Structural Biology 1472-6807 9 37 2009-05-28T00:00:00Z XML Background: The Dbl-family of guanine nucleotide exchange factors (GEFs) activate the cytosolic GTPases of the Rho family by enhancing the rate of exchange of GTP for GDP on the cognate GTPase. This catalytic activity resides in the DH (Dbl-homology) domain, but typically GEFs are multidomain proteins containing other modules. It is believed that GEFs are autoinhibited in the cytosol due to supramodular architecture, and become activated in diverse signaling pathways through conformational change and exposure of the DH domain, as the protein is translocated to the membrane. A small family of RhoA-specific GEFs, containing the RGSL (regulators of G-protein signaling-like) domain, act as effectors of select GPCRs via Gα12/13, although the molecular mechanism by which this pathway operates is not known. These GEFs include p115, LARG and PDZRhoGEF (PRG). Results: Here we show that the autoinhibition of PRG is caused largely by an interaction of a short negatively charged sequence motif, immediately upstream of the DH-domain and including residues Asp706, Glu708, Glu710 and Asp712, with a patch on the catalytic surface of the DH-domain including Arg867 and Arg868. In the absence of both PDZ and RGSL domains, the DH-PH tandem with additional 21 residues upstream, is 50% autoinhibited. However, within the full-length protein, the PDZ and/or RGSL domains significantly restore autoinhibition. Conclusion: 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. http://www.biomedcentral.com/1472-6807/9/36 Meiying Zheng Tomasz Cierpicki Ko Momotani Mykhaylo Artamonov Urszula Derewenda John Bushweller Avril Somlyo Zygmunt Derewenda BMC Structural Biology 2009, 9:36 2009-05-21T00:00:00Z doi:10.1186/1472-6807-9-36 BMC Structural Biology 1472-6807 9 36 2009-05-21T00:00:00Z XML