Sun, 27 Jul 2008 07:17:29 BST CiteULike: neils's crystallography http://www.citeulike.org/user/neils/tag/crystallography CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/neils/article/2966726 <i>Nature protocols, Vol. 3, No. 7. (June 2008), pp. 1171-1179.</i><br /><br />ARP/wARP is a software suite to build macromolecular models in X-ray crystallography electron density maps. Structural genomics initiatives and the study of complex macromolecular assemblies and membrane proteins all rely on advanced methods for 3D structure determination. ARP/wARP meets these needs by providing the tools to obtain a macromolecular model automatically, with a reproducible computational procedure. ARP/wARP 7.0 tackles several tasks: iterative protein model building including a high-level decision-making control module; fast construction of the secondary structure of a protein; building flexible loops in alternate conformations; fully automated placement of ligands, including a choice of the best-fitting ligand from a 'cocktail'; and finding ordered water molecules. All protocols are easy to handle by a nonexpert user through a graphical user interface or a command line. The time required is typically a few minutes although iterative model building may take a few hours. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Gerrit Langer Serge X Cohen Victor S Lamzin Anastassis Perrakis doi:10.1038/nprot.2008.91 Nature protocols, Vol. 3, No. 7. (June 2008), pp. 1171-1179. 2008-07-06T00:24:52-00:00 2008 Nature protocols 1750-2799 3 7 1171 1179 crystallography modelling protocol software x-ray http://www.citeulike.org/user/neils/article/2915779 <i>Acta Crystallographica Section D, Vol. 64, No. 7. (Jul 2008), pp. 810-814.</i> Federated repositories of X-ray diffraction images Steve Androulakis Jason Schmidberger Mark Bate Ross Degori Anthony Beitz Cyrus Keong Bob Cameron Sheena Mcgowan Corrine Porter Andrew Harrison Jane Hunter Jennifer Martin Bostjan Kobe Renwick Dobson Michael Parker James Whisstock Joan Gray Andrew Treloar David Groenewegen Neil Dickson Ashley Buckle doi:10.1107/S0907444908015540 Acta Crystallographica Section D, Vol. 64, No. 7. (Jul 2008), pp. 810-814. 2008-06-23T01:27:31-00:00 2008 Acta Crystallographica Section D 64 7 810 814 crystallography database images repository x-ray http://www.citeulike.org/user/neils/article/2884031 <i>Methods in molecular biology (Clifton, N.J.), Vol. 426 (2008), pp. 27-35.</i><br /><br />: Increasing the success in obtaining structures and maximizing the value of the structures determined are the two major goals of target selection in structural proteomics. This chapter presents an efficient and flexible target selection procedure supplemented with a Web-based resource that is suitable for small- to large-scale structural genomics projects that use crystallography as the major means of structure determination. Based on three criteria, biological significance, structural novelty, and "crystallizability," the approach first removes (filters) targets that do not meet minimal criteria and then ranks the remaining targets based on their "crystallizability" estimates. This novel procedure was designed to maximize selection efficiency, and its prevailing criteria categories make it suitable for a broad range of structural proteomics projects. A general target selection method for crystallographic proteomics. G Robin NP Cowieson G Guncar JK Forwood P Listwan DA Hume B Kobe JL Martin T Huber doi:10.1007/978-1-60327-058-8_2 Methods in molecular biology (Clifton, N.J.), Vol. 426 (2008), pp. 27-35. 2008-06-12T00:02:20-00:00 2008 Methods in molecular biology (Clifton, N.J.) 1064-3745 426 27 35 crystallography proteomics selection structure target http://www.citeulike.org/user/neils/article/2884027 <i>Methods in molecular biology (Clifton, N.J.), Vol. 426 (2008), pp. 577-587.</i><br /><br />: This chapter describes the methodology adopted in a project aimed at structural and functional characterization of proteins that potentially play an important role in mammalian macrophages. The methodology that underpins this project is applicable to both small research groups and larger structural genomics consortia. Gene products with putative roles in macrophage function are identified using gene expression information obtained via DNA microarray technology. Specific targets for structural and functional characterization are then selected based on a set of criteria aimed at maximizing insight into function. The target proteins are cloned using a modification of Gateway(R) cloning technology, expressed with hexa-histidine tags in E. coli, and purified to homogeneity using a combination of affinity and size exclusion chromatography. Purified proteins are finally subjected to crystallization trials and/or NMR-based screening to identify candidates for structure determination. Where crystallography and NMR approaches are unsuccessful, chemical cross-linking is employed to obtain structural information. This resulting structural information is used to guide cell biology experiments to further investigate the cellular and molecular function of the targets in macrophage biology. Jointly, the data sheds light on the molecular and cellular functions of macrophage proteins. Overview of the pipeline for structural and functional characterization of macrophage proteins at the University of Queensland. W Meng JK Forwood G Guncar G Robin NP Cowieson P Listwan D Mouradov G King IL Ross J Robinson M Puri JM Hill S Kellie T Huber DA Hume JL Martin B Kobe doi:10.1007/978-1-60327-058-8_38 Methods in molecular biology (Clifton, N.J.), Vol. 426 (2008), pp. 577-587. 2008-06-12T00:00:52-00:00 2008 Methods in molecular biology (Clifton, N.J.) 1064-3745 426 577 587 crystallography genomics macrophage methods structure uq http://www.citeulike.org/user/neils/article/2802894 <i>Nature, Vol. 453, No. 7193., pp. 363-367.</i> Crystal structure of squid rhodopsin Midori Murakami Tsutomu Kouyama doi:10.1038/nature06925 Nature, Vol. 453, No. 7193., pp. 363-367. 2008-05-15T23:29:37-00:00 Nature 0028-0836 453 7193 363 367 Nature Publishing Group crystallography rhodopsin squid structure http://www.citeulike.org/user/neils/article/2783970 <i>Nature, Vol. 389, No. 6649. (25 September 1997), pp. 406-412.</i><br /><br />Cytochrome cd1 nitrite reductase catalyses the conversion of nitrite to nitric oxide in the nitrogen cycle. The crystal structure of the oxidized enzyme shows that the d1 haem iron of the active site is ligated by His/Tyr side chains, and the c haem iron is ligated by a His/His ligand pair. Here we show that both haems undergo re-ligation during catalysis. Upon reduction, the tyrosine ligand of the d1 haem is released to allow substrate binding. Concomitantly, a refolding of the cytochrome c domain takes place, resulting in an unexpected change of the c haem iron coordination from His 17/His 69 to Met106/His69. This step is similar to the last steps in the folding of cytochrome c. The changes must affect the redox potential of the haems, and suggest a mechanism by which internal electron transfer is regulated. Structures of reaction intermediates show how nitric oxide is formed and expelled from the active-site iron, as well as how both haems return to their starting coordination. These results show how redox energy can be switched into conformational energy within a haem protein. Haem-ligand switching during catalysis in crystals of a nitrogen-cycle enzyme. PA Williams V Fülöp EF Garman NF Saunders SJ Ferguson J Hajdu doi:10.1038/38775 Nature, Vol. 389, No. 6649. (25 September 1997), pp. 406-412. 2008-05-11T09:17:32-00:00 1997 Nature 0028-0836 389 6649 406 412 crystallography haem mechanism nitrite protein reductase structure http://www.citeulike.org/user/neils/article/2783952 <i>PLoS ONE, Vol. 2, No. 10. (2007)</i><br /><br />BACKGROUND: Crystallization is a major bottleneck in the process of macromolecular structure determination by X-ray crystallography. Successful crystallization requires the formation of nuclei and their subsequent growth to crystals of suitable size. Crystal growth generally occurs spontaneously in a supersaturated solution as a result of homogenous nucleation. However, in a typical sparse matrix screening experiment, precipitant and protein concentration are not sampled extensively, and supersaturation conditions suitable for nucleation are often missed. METHODOLOGY/PRINCIPAL FINDINGS: We tested the effect of nine potential heterogenous nucleating agents on crystallization of ten test proteins in a sparse matrix screen. Several nucleating agents induced crystal formation under conditions where no crystallization occurred in the absence of the nucleating agent. Four nucleating agents: dried seaweed; horse hair; cellulose and hydroxyapatite, had a considerable overall positive effect on crystallization success. This effect was further enhanced when these nucleating agents were used in combination with each other. CONCLUSIONS/SIGNIFICANCE: Our results suggest that the addition of heterogeneous nucleating agents increases the chances of crystal formation when using sparse matrix screens. Improved success of sparse matrix protein crystallization screening with heterogeneous nucleating agents. AS Thakur G Robin G Guncar NF Saunders J Newman JL Martin B Kobe doi:10.1371/journal.pone.0001091 PLoS ONE, Vol. 2, No. 10. (2007) 2008-05-11T09:06:15-00:00 2007 PLoS ONE 1932-6203 2 10 crystallography nucleation protein screen http://www.citeulike.org/user/neils/article/2774439 <i>Biochemistry (9 May 2008)</i><br /><br />Abstract: The emergence of multi-drug-resistant strains of Plasmodium parasites has prompted the search for alternative therapeutic strategies for combating malaria. One possible strategy is to exploit existing drugs as lead compounds. FK506 is currently used in the clinic for preventing transplant rejection. It binds to a ±/² protein module of approximately 120 amino acids known as the FK506 binding domain (FKBD), which is found in various organisms, including human, yeast, and Plasmodium falciparum (PfFKBD). Antiparasitic effects of FK506 and its analogues devoid of immunosuppressive activities have been demonstrated. We report here the crystallographic structure at 2.35 Å resolution of PfFKBD complexed with FK506. Compared to the human FKBP12FK506 complex reported earlier, the structure reveals structural differences in the ²5²6 segment that lines the FK506 binding site. The presence in PfFKBD of Cys-106 and Ser-109 (substituting for His-87 and Ile-90, respectively, in human FKBP12), which are 45 Å from the nearest atom of the FK506 compound, suggests possible routes for the rational design of analogues of FK506 with specific antiparasitic activity. Upon ligand binding, several conformational changes occur in PfFKBD, including aromatic residues that shape the FK506 binding pocket as shown by NMR studies. A microarray analysis suggests that FK506 and cyclosporine A (CsA) might inhibit parasite development by interfering with the same signaling pathways. Crystal Structure of the FK506 Binding Domain of Plasmodium falciparum FKBP35 in Complex with FK506 Masayo Kotaka Hong Ye Reema Alag Guangan Hu Zbynek Bozdech Peter Preiser Ho Yoon Julien Lescar doi:10.1021/bi800004u Biochemistry (9 May 2008) 2008-05-09T05:52:09-00:00 2008 Biochemistry complex crystallography fkbp ligand plasmodium structure http://www.citeulike.org/user/neils/article/2643447 <i></i> Crystal structure of GH13 alpha-glucosidase GSJ from one of the deepest sea bacteria Tsuyoshi Shirai Vo Hung Katsuhito Morinaka Tohru Kobayashi Susumu Ito 2008-04-09T03:13:50-00:00 barophile crystallography glucosidase protein structure http://www.citeulike.org/user/neils/article/2643444 <i>Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.</i><br /><br />No abstract. Crystal structure of PAE0151 from <I>Pyrobaculum aerophilum</I>, a PIN-domain (VapC) protein from a toxin-antitoxin operon Richard Bunker Joanna Mckenzie Edward Baker Vickery Arcus doi:10.1002/prot.22048 Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. 2008-04-09T03:12:58-00:00 2008 Proteins: Structure, Function, and Bioinformatics 9999 9999 NA antitoxin archaea crystallography protein pyrobaculum structure toxin http://www.citeulike.org/user/neils/article/2600028 <i>Bioinformatics, Vol. 24, No. 7. (1 April 2008), pp. 901-907.</i><br /><br />The ability to rank proteins by their likely success in crystallization is useful in current Structural Biology efforts and in particular in high-throughput Structural Genomics initiatives. We present ParCrys, a Parzen Window approach to estimate a protein's propensity to produce diffraction-quality crystals. The Protein Data Bank (PDB) provided training data whilst the databases TargetDB and PepcDB were used to define feature selection data as well as test data independent of feature selection and training. ParCrys outperforms the OB-Score, SECRET and CRYSTALP on the data examined, with accuracy and Matthews correlation coefficient values of 79.1% and 0.582, respectively (74.0% and 0.227, respectively, on data with a real-world' ratio of positive:negative examples). ParCrys predictions and associated data are available from www.compbio.dundee.ac.uk/parcrys. Contact: geoff@compbio.dundee.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btn055 ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction Ian Overton Gianandrea Padovani Mark Girolami Geoffrey Barton doi:10.1093/bioinformatics/btn055 Bioinformatics, Vol. 24, No. 7. (1 April 2008), pp. 901-907. 2008-03-26T23:39:04-00:00 2008 Bioinformatics 24 7 901 907 bioinformatics crystallography prediction propensity protein structural-genomics http://www.citeulike.org/user/neils/article/2476640 <i>Nature (05 March 2008)</i> X-ray structure of a prokaryotic pentameric ligand-gated ion channel Ricarda Hilf Raimund Dutzler doi:10.1038/nature06717 Nature (05 March 2008) 2008-03-06T04:09:10-00:00 2008 Nature 0028-0836 Nature Publishing Group crystallography ion-channel ligand-gated prokaryotic structure http://www.citeulike.org/user/neils/article/2054452 <i>J Mol Biol, Vol. 361, No. 2. (Aug 2006), pp. 312-326.</i><br /><br />The p21-activated kinases (PAKs) are serine/threonine kinases that are involved in a wide variety of cellular functions including cytoskeletal motility, apoptosis, and cell cycle regulation. PAKs are inactivated by blockage of the active site of the kinase domain by an N-terminal regulatory domain. GTP-bound forms of Cdc42 and Rac bind to the regulatory domain and displace it, thereby allowing phosphorylation of the kinase domain and maximal activation. A key step in the activation process is the phosphorylation of the activation loop of one PAK kinase domain by another, but little is known about the underlying recognition events that make this phosphorylation specific. We show that the phosphorylated kinase domain of PAK2 dimerizes in solution and that this association is prevented by addition of a substrate peptide. We have identified a crystallographic dimer in a previously determined crystal structure of activated PAK1 in which two kinase domains are arranged face to face and interact through a surface on the large lobe of the kinase domain that is exposed upon release of the auto-inhibitory domain. The crystallographic dimer is suggestive of an engagement that mediates trans-autophosphorylation. Mutations at the predicted dimerization interface block dimerization and reduce the rate of autophosphorylation, supporting the role of this interface in PAK activation. A dimeric kinase assembly underlying autophosphorylation in the p21 activated kinases. Michelle Pirruccello Holger Sondermann Jeffrey Pelton Patricia Pellicena André Hoelz Jonathan Chernoff David Wemmer John Kuriyan J Mol Biol, Vol. 361, No. 2. (Aug 2006), pp. 312-326. 2007-12-04T03:22:10-00:00 2006 J Mol Biol 361 2 312 326 activation amino-acid article-predikin binding catalysis catalytic conformation crystallography data dimerization domain enzyme folding homology human kinase kinetics models molecular mutation p21-activated phosphopeptides phosphorylation protein protein-serine-threonine sequence sites structure tertiary x-ray http://www.citeulike.org/user/neils/article/2054445 <i>Structure, Vol. 11, No. 11. (Nov 2003), pp. 1453-1459.</i><br /><br />A great challenge in the proteomics and structural genomics era is to predict protein structure and function, including identification of those proteins that are partially or wholly unstructured. Disordered regions in proteins often contain short linear peptide motifs (e.g., SH3 ligands and targeting signals) that are important for protein function. We present here DisEMBL, a computational tool for prediction of disordered/unstructured regions within a protein sequence. As no clear definition of disorder exists, we have developed parameters based on several alternative definitions and introduced a new one based on the concept of "hot loops," i.e., coils with high temperature factors. Avoiding potentially disordered segments in protein expression constructs can increase expression, foldability, and stability of the expressed protein. DisEMBL is thus useful for target selection and the design of constructs as needed for many biochemical studies, particularly structural biology and structural genomics projects. The tool is freely available via a web interface (http://dis.embl.de) and can be downloaded for use in large-scale studies. Protein disorder prediction: implications for structural proteomics. Rune Linding Lars Jensen Francesca Diella Peer Bork Toby Gibson Robert Russell Structure, Vol. 11, No. 11. (Nov 2003), pp. 1453-1459. 2007-12-04T03:22:10-00:00 2003 Structure 11 11 1453 1459 article-nar article-predikin circular computer conformation crystallography dichroism domain homology ligand magnetic models network neural protein proteome ray resonance sensitivity specificity spectroscopy src statistics temperature theoretical topic ultraviolet x-ray