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Structural Genomics (structural + genomics)
Terms modified by Structural Genomics Selected AbstractsStructure of the conserved hypothetical protein MAL13P1.257 from Plasmodium falciparumACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 3 2006Margaret A. Holmes The structure of a conserved hypothetical protein, PlasmoDB sequence MAL13P1.257 from Plasmodium falciparum, Pfam sequence family PF05907, has been determined as part of the structural genomics effort of the Structural Genomics of Pathogenic Protozoa consortium. The structure was determined by multiple-wavelength anomalous dispersion at 2.17,Å resolution. The structure is almost entirely ,-sheet; it consists of 15 ,-strands and one short 310 -helix and represents a new protein fold. The packing of the two monomers in the asymmetric unit indicates that the biological unit may be a dimer. [source] Structural genomics: A pipeline for providing structures for the biologistPROTEIN SCIENCE, Issue 4 2002Mark R. Chance First page of article [source] Structural genomics of Caenorhabditis elegans: structure of the BAG domainACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2004J. Symersky Binding of the BAG domain to the eukaryotic chaperone heat-shock protein (Hsp70) promotes ATP-dependent release of the protein substrate from Hsp70. Although the murine and human BAG domains have been shown to form an antiparallel three-helix bundle, the Caenorhabditis elegans BAG domain is formed by two antiparallel helices, while the third helix is extended away and stabilized by crystal-packing interactions. A small ,-sheet between helices 2 and 3 interferes with formation of the intramolecular three-helix bundle. However, intermolecular three-helix bundles are observed throughout the crystal packing and suggest that stable functional dimers and tetramers can be formed in solution. The structure may represent a new folding type of the BAG domain. [source] Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 proteinACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2003Valérie Campanacci The aetiologic agent of the recent epidemics of Severe Acute Respiratory Syndrome (SARS) is a positive-stranded RNA virus (SARS-CoV) belonging to the Coronaviridae family and its genome differs substantially from those of other known coronaviruses. SARS-CoV is transmissible mainly by the respiratory route and to date there is no vaccine and no prophylactic or therapeutic treatments against this agent. A SARS-CoV whole-genome approach has been developed aimed at determining the crystal structure of all of its proteins or domains. These studies are expected to greatly facilitate drug design. The genomes of coronaviruses are between 27 and 31.5,kbp in length, the largest of the known RNA viruses, and encode 20,30 mature proteins. The functions of many of these polypeptides, including the Nsp9,Nsp10 replicase-cleavage products, are still unknown. Here, the cloning, Escherichia coli expression, purification and crystallization of the SARS-CoV Nsp9 protein, the first SARS-CoV protein to be crystallized, are reported. Nsp9 crystals diffract to 2.8,Å resolution and belong to space group P61/522, with unit-cell parameters a = b = 89.7, c = 136.7,Å. With two molecules in the asymmetric unit, the solvent content is 60% (VM = 3.1,Å3,Da,1). [source] Identifying native-like protein structures using physics-based potentialsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2002Brian N. Dominy Abstract As the field of structural genomics matures, new methods will be required that can accurately and rapidly distinguish reliable structure predictions from those that are more dubious. We present a method based on the CHARMM gas phase implicit hydrogen force field in conjunction with a generalized Born implicit solvation term that allows one to make such discrimination. We begin by analyzing pairs of threaded structures from the EMBL database, and find that it is possible to identify the misfolded structures with over 90% accuracy. Further, we find that misfolded states are generally favored by the solvation term due to the mispairing of favorable intramolecular ionic contacts. We also examine 29 sets of 29 misfolded globin sequences from Levitt's "Decoys ,R' Us" database generated using a sequence homology-based method. Again, we find that discrimination is possible with approximately 90% accuracy. Also, even in these less distorted structures, mispairing of ionic contacts results in a more favorable solvation energy for misfolded states. This is also found to be the case for collapsed, partially folded conformations of CspA and protein G taken from folding free energy calculations. We also find that the inclusion of the generalized Born solvation term, in postprocess energy evaluation, improves the correlation between structural similarity and energy in the globin database. This significantly improves the reliability of the hypothesis that more energetically favorable structures are also more similar to the native conformation. Additionally, we examine seven extensive collections of misfolded structures created by Park and Levitt using a four-state reduced model also contained in the "Decoys ,R' Us" database. Results from these large databases confirm those obtained in the EMBL and misfolded globin databases concerning predictive accuracy, the energetic advantage of misfolded proteins regarding the solvation component, and the improved correlation between energy and structural similarity due to implicit solvation. Z-scores computed for these databases are improved by including the generalized Born implicit solvation term, and are found to be comparable to trained and knowledge-based scoring functions. Finally, we briefly explore the dynamic behavior of a misfolded protein relative to properly folded conformations. We demonstrate that the misfolded conformation diverges quickly from its initial structure while the properly folded states remain stable. Proteins in this study are shown to be more stable than their misfolded counterparts and readily identified based on energetic as well as dynamic criteria. In summary, we demonstrate the utility of physics-based force fields in identifying native-like conformations in a variety of preconstructed structural databases. The details of this discrimination are shown to be dependent on the construction of the structural database. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 147,160, 2002 [source] High-resolution wide-angle X-ray scattering of protein solutions: effect of beam dose on protein integrityJOURNAL OF SYNCHROTRON RADIATION, Issue 5 2003Robert F. Fischetti Wide-angle X-ray scattering patterns from proteins in solution contain information relevant to the determination of protein fold. At relevant scattering angles, however, these data are weak, and the degree to which they might be used to categorize the fold of a protein is unknown. Preliminary work has been performed at the BioCAT insertion-device beamline at the Advanced Photon Source which demonstrates that one can collect X-ray scattering data from proteins in solution to spacings of at least 2.2,Å (q = 2.8,Å,1). These data are sensitive to protein conformational states, and are in good agreement with the scattering predicted by the program CRYSOL using the known three-dimensional atomic coordinates of the protein. An important issue in the exploitation of this technique as a tool for structural genomics is the extent to which the high intensity of X-rays available at third-generation synchrotron sources chemically or structurally damage proteins. Various data-collection protocols have been investigated demonstrating conditions under which structural degradation of even sensitive proteins can be minimized, making this technique a viable tool for protein fold categorization, the study of protein folding, unfolding, protein,ligand interactions and domain movement. [source] Introductory overview: X-ray absorption spectroscopy and structural genomicsJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2003Isabella Ascone A special issue of the journal is presented, dedicated to biological applications of X-ray absorption spectroscopy (BioXAS) and examining the role of this technique in post-genomic biology. The issue confirms that BioXAS has come of age and it can be expected to make a significant contribution in the structural genomics effort on metalloproteins, which are estimated to make up about 30% of proteins coded by genomes. [source] A structural genomics initiative on yeast proteinsJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2003Sophie Quevillon-Cheruel A canonical structural genomics programme is being conducted at the Paris-Sud campus area on baker's yeast proteins. Experimental strategies, first results and identified bottlenecks are presented. The actual or potential contributions to the structural genomics of several experimental structure-determination methods are discussed. [source] Synchrotron radiation circular-dichroism spectroscopy as a tool for investigating protein structuresJOURNAL OF SYNCHROTRON RADIATION, Issue 5 2000B. A. Wallace This paper reviews the use of synchrotron radiation circular dichroism (SRCD) spectroscopy for examining protein structures, discussing the differences between conventional circular dichroism and SRCD, as well as examples of what SRCD studies have revealed about protein structures to date. It further discusses the future potential of the technique, including roles in structural genomics, membrane protein structure elucidation, relationships to crystallographic studies, and protein folding and dynamics. [source] Evolutionary constraints on structural similarity in orthologs and paralogs,PROTEIN SCIENCE, Issue 6 2009Mark E. Peterson Abstract Although a quantitative relationship between sequence similarity and structural similarity has long been established, little is known about the impact of orthology on the relationship between protein sequence and structure. Among homologs, orthologs (derived by speciation) more frequently have similar functions than paralogs (derived by duplication). Here, we hypothesize that an orthologous pair will tend to exhibit greater structural similarity than a paralogous pair at the same level of sequence similarity. To test this hypothesis, we used 284,459 pairwise structure-based alignments of 12,634 unique domains from SCOP as well as orthology and paralogy assignments from OrthoMCL DB. We divided the comparisons by sequence identity and determined whether the sequence-structure relationship differed between the orthologs and paralogs. We found that at levels of sequence identity between 30 and 70%, orthologous domain pairs indeed tend to be significantly more structurally similar than paralogous pairs at the same level of sequence identity. An even larger difference is found when comparing ligand binding residues instead of whole domains. These differences between orthologs and paralogs are expected to be useful for selecting template structures in comparative modeling and target proteins in structural genomics. [source] Expectations from structural genomicsPROTEIN SCIENCE, Issue 1 2000Steven E. Brenner First page of article [source] Automated technologies and novel techniques to accelerate protein crystallography for structural genomicsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 4 2008Babu A. Manjasetty Dr. Abstract The sequence infrastructure that has arisen through large-scale genomic projects dedicated to protein analysis, has provided a wealth of information and brought together scientists and institutions from all over the world. As a consequence, the development of novel technologies and methodologies in proteomics research is helping to unravel the biochemical and physiological mechanisms of complex multivariate diseases at both a functional and molecular level. In the late sixties, when X-ray crystallography had just been established, the idea of determining protein structure on an almost universal basis was akin to an impossible dream or a miracle. Yet only forty years after, automated protein structure determination platforms have been established. The widespread use of robotics in protein crystallography has had a huge impact at every stage of the pipeline from protein cloning, over-expression, purification, crystallization, data collection, structure solution, refinement, validation and data management- all of which have become more or less automated with minimal human intervention necessary. Here, recent advances in protein crystal structure analysis in the context of structural genomics will be discussed. In addition, this review aims to give an overview of recent developments in high throughput instrumentation, and technologies and strategies to accelerate protein structure/function analysis. [source] An automatable screen for the rapid identification of proteins amenable to refoldingPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 6 2006Nathan P. Cowieson Dr. Abstract Insoluble expression of heterologous proteins in Escherichia coli is a major bottleneck of many structural genomics and high-throughput protein biochemistry projects. Many of these proteins may be amenable to refolding, but their identification is hampered by a lack of high-throughput methods. We have developed a matrix-assisted refolding approach in which correctly folded proteins are distinguished from misfolded proteins by their elution from affinity resin under non-denaturing conditions. Misfolded proteins remain adhered to the resin, presumably via hydrophobic interactions. The assay can be applied to insoluble proteins on an individual basis but is particularly well suited for high-throughput applications because it is rapid, automatable and has no rigorous sample preparation requirements. The efficacy of the screen is demonstrated on small-scale expression samples for 15,proteins. Refolding is then validated by large-scale expressions using SEC and circular dichroism. [source] A large-scale, high-efficiency and low-cost platform for structural genomics studiesACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2006Xiao-Dong Su A large-scale, high-efficiency and low-cost platform based on a Beckman Coulter Biomek FX and custom-made automation systems for structural genomics has been set up at Peking University, Beijing, People's Republic of China. This platform has the capacity to process up to 2000 genes per year for structural and functional analyses. Bacillus subtilis, a model organism for Gram-positive bacteria, and Streptococcus mutans, a major pathogen of dental caries, were selected as the main targets. To date, more than 470 B. subtilis and 1200 S.,mutans proteins and hundreds of proteins from other sources, including human liver proteins, have been selected as targets for this platform. The selected genes are mainly related to important metabolism pathways and/or have potential relevance for drug design. To date, 40 independent structures have been determined; of these 11 are in the category of novel structures by the criterion of having less than 30% sequence identity to known structures. More than 13 structures were determined by SAD/MAD phasing. The macromolecular crystallography beamline at the Beijing Synchrotron Radiation Facility and modern phasing programs have been crucial components of the operation of the platform. The idea and practice of the genomic approach have been successfully adopted in a moderately funded structural biology program and it is believed this adaptation will greatly improve the production of protein structures. The goal is to be able to solve a protein structure of moderate difficulty at a cost about US $10,000. [source] The SUPERFAMILY database in structural genomicsACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2002Julian Gough The SUPERFAMILY hidden Markov model library representing all proteins of known structure predicts the domain architecture of protein sequences and classifies them at the SCOP superfamily level. This analysis has been carried out on all completely sequenced genomes. The ways in which the database can be useful to crystallographers is discussed, in particular with a view to high-throughput structure determination. The application of the SUPERFAMILY database to different target-selection strategies is suggested: novel folds, novel domain combinations and targeted attacks on genomes. Use of the database for more general inquiry in the context of structural studies is also explained. The database provides evolutionary relationships between target proteins and other proteins of known structure through the SCOP database, genome assignments and multiple sequence alignments. [source] Generating isomorphous heavy-atom derivatives by a quick-soak method.ACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2002Part II: phasing of new structures A quick-soak method has been applied to generate de novo heavy-atom phasing to solve two new protein structures, a type II transforming growth factor , receptor (TBRII) and a natural killer cell receptor,ligand complex, NKG2D,ULBP3. In the case of TBRII, a crystal derivatized for only 10,min in saturated HgCl2 provided adequate phasing for structure determination. Comparison between HgCl2 derivatives generated by 10,min soaking and by 12,h soaking revealed similar phasing statistics. The shorter soak, however, resulted in a derivative more isomorphous to the native than the longer soak as judged by changes in the unit-cell parameter a upon derivatization as well as by the quality of a combined SIRAS electron-density map. In the case of the NKG2D,ULBP3 structure, all overnight soaks in heavy-atom solutions resulted in crystal lattice disorder and only the quick soaks preserved diffraction. Despite fragile lattice packing, the quick-soaked K2PtCl4 derivative was isomorphous with the native crystal and the electron-density map calculated from combined SIR and MAD phases is better than that calculated from MAD phases alone. Combined with mass-spectrometry-assisted solution heavy-atom derivative screening and the use of synchrotron radiation, the quick-soak derivatization has the potential to transform the time-consuming conventional heavy-atom search into a real-time `on-the-fly' derivatization process that will benefit high-throughput structural genomics. [source] Protein crystallization for genomics: towards high-throughput optimization techniquesACTA CRYSTALLOGRAPHICA SECTION D, Issue 6-2 2002Naomi E. Chayen Protein crystallization has gained a new strategic and commercial relevance in the next phase of the genome projects, in which X-ray crystallography will play a major role. Considerable advances have been made in the automation of protein preparation and also in the X-ray analysis and bioinformatics stages once diffraction-quality crystals are available. These advances have not yet been matched by equally good methods for the crystallization process itself. In the area of crystallization, the main effort and resources are currently being invested into the automation of screening procedures to identify potential crystallization conditions. However, in spite of the ability to generate numerous trials, so far only a small percentage of the proteins produced have led to structure determinations. This is because screening in itself is not usually enough; it has to be complemented by an equally important procedure in crystal production, namely crystal optimization. In the rush towards structural genomics, optimization techniques have been somewhat neglected, mainly because it was hoped that large-scale screening alone would produce the desired results. In addition, optimization has relied on particular individual methods that are often difficult to automate and to adapt to high throughput. This article addresses a major gap in the field of structural genomics by describing practical ways of automating individual optimization methods in order to adapt them to high-throughput techniques. [source] | ||||||||||||||||||||||