451
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Valentin F, Squizzato S, Goujon M, McWilliam H, Paern J, Lopez R. Fast and efficient searching of biological data resources--using EB-eye. Brief Bioinform 2010; 11:375-84. [PMID: 20150321 DOI: 10.1093/bib/bbp065] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The EB-eye is a fast and efficient search engine that provides easy and uniform access to the biological data resources hosted at the EMBL-EBI. Currently, users can access information from more than 62 distinct datasets covering some 400 million entries. The data resources represented in the EB-eye include: nucleotide and protein sequences at both the genomic and proteomic levels, structures ranging from chemicals to macro-molecular complexes, gene-expression experiments, binary level molecular interactions as well as reaction maps and pathway models, functional classifications, biological ontologies, and comprehensive literature libraries covering the biomedical sciences and related intellectual property. The EB-eye can be accessed over the web or programmatically using a SOAP Web Services interface. This allows its search and retrieval capabilities to be exploited in workflows and analytical pipe-lines. The EB-eye is a novel alternative to existing biological search and retrieval engines. In this article we describe in detail how to exploit its powerful capabilities.
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452
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Jungo F, Estreicher A, Bairoch A, Bougueleret L, Xenarios I. Animal Toxins: How is Complexity Represented in Databases? Toxins (Basel) 2010; 2:262-82. [PMID: 22069583 PMCID: PMC3202812 DOI: 10.3390/toxins2020262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 02/10/2010] [Accepted: 02/11/2010] [Indexed: 11/16/2022] Open
Abstract
Peptide toxins synthesized by venomous animals have been extensively studied in the last decades. To be useful to the scientific community, this knowledge has been stored, annotated and made easy to retrieve by several databases. The aim of this article is to present what type of information users can access from each database. ArachnoServer and ConoServer focus on spider toxins and cone snail toxins, respectively. UniProtKB, a generalist protein knowledgebase, has an animal toxin-dedicated annotation program that includes toxins from all venomous animals. Finally, the ATDB metadatabase compiles data and annotations from other databases and provides toxin ontology.
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Affiliation(s)
- Florence Jungo
- Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel-Servet, 1211 Genève 4, Switzerland; (A.E.); (L.B.); (I.X.)
| | - Anne Estreicher
- Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel-Servet, 1211 Genève 4, Switzerland; (A.E.); (L.B.); (I.X.)
| | - Amos Bairoch
- Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Switzerland; (A.B.)
| | - Lydie Bougueleret
- Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel-Servet, 1211 Genève 4, Switzerland; (A.E.); (L.B.); (I.X.)
| | - Ioannis Xenarios
- Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel-Servet, 1211 Genève 4, Switzerland; (A.E.); (L.B.); (I.X.)
- Swiss Institute of Bioinformatics, Vital-IT Group, 1015 Lausanne, Switzerland
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453
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Owczarek S, Kiryushko D, Larsen MH, Kastrup JS, Gajhede M, Sandi C, Berezin V, Bock E, Soroka V. Neuroplastin-55 binds to and signals through the fibroblast growth factor receptor. FASEB J 2009; 24:1139-50. [PMID: 19952283 DOI: 10.1096/fj.09-140509] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neuroplastin (Np) is a glycoprotein belonging to the immunoglobulin superfamily of cell adhesion molecules (CAMs) and existing in two isoforms, Np55 and Np65, named according to their molecular weights. The extracellular part of Np65 contains three immunoglobulin (Ig)-like modules (Ig1, Ig2, and Ig3), whereas Np55 lacks the Ig1 module. Of these two isoforms, only Np65 is involved in homophilic interactions resulting in cell adhesion, whereas the role of Np55 is poorly understood. The present study reports for the first time the crystal structure of the ectodomain of Np55 at 1.95-A resolution and demonstrates that Np55 binds to and activates the fibroblast growth factor receptor 1 (FGFR1). Furthermore, we identify a sequence motif in the Ig2 module of Np55 interacting with FGFR1 and show that a synthetic peptide encompassing this motif, termed narpin, binds to and activates FGFR1. We show that both Np55 and the narpin peptide induce neurite outgrowth through FGFR1 activation and that Np55 increases synaptic calcium concentration in an FGFR1-dependent manner. Moreover, we demonstrate that narpin has an antidepressive-like effect in rats subjected to the forced swim test, suggesting that Np55-induced signaling may be involved in synaptic plasticity in vivo. Owczarek, S., Kiryushko, D., Larsen, M. H., Kastrup, J. S., Gajhede, M., Sandi, C., Berezin, V., Bock, E., Soroka, V. Neuroplastin-55 binds to and signals through the fibroblast growth factor receptor.
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Affiliation(s)
- Sylwia Owczarek
- Protein Laboratory, Department of Neuroscience and Pharmacology, Panum Institute, University of Copenhagen, Blegdamsvej 3C, Bldg. 24.2, 2200 Copenhagen, Denmark.
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454
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Strange RW, Antonyuk SV, Ellis MJ, Bessho Y, Kuramitsu S, Yokoyama S, Hasnain SS. The structure of an archaeal ribose-5-phosphate isomerase from Methanocaldococcus jannaschii (MJ1603). Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1214-7. [PMID: 20054114 PMCID: PMC2802866 DOI: 10.1107/s1744309109044923] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 10/27/2009] [Indexed: 11/10/2022]
Abstract
Ribose-5-phosphate isomerase is a ubiquitous intracellular enzyme of bacterial, plant and animal origin that is involved in the pentose phosphate cycle, an essential component of cellular carbohydrate metabolism. Specifically, the enzyme catalyses the reversible conversion of ribose 5-phosphate to ribulose 5-phosphate. The structure of ribose-5-phosphate isomerase from Methanocaldococcus jannaschii has been solved in space group P2(1) to 1.78 A resolution using molecular replacement with one homotetramer in the asymmetric unit and refined to an R factor of 14.8%. The active site in each subunit was occupied by two molecules of propylene glycol in different orientations, one of which corresponds to the location of the phosphate moiety and the other to the location of the furanose ring of the inhibitor.
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Affiliation(s)
- Richard W. Strange
- Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Mark J. Ellis
- STFC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, England
| | - Yoshitaka Bessho
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Seiki Kuramitsu
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shigeyuki Yokoyama
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - S. Samar Hasnain
- Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
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455
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May P, Kreuchwig A, Steinke T, Koch I. PTGL: a database for secondary structure-based protein topologies. Nucleic Acids Res 2009; 38:D326-30. [PMID: 19906706 PMCID: PMC2808981 DOI: 10.1093/nar/gkp980] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
With growing amount of experimental data, the number of known protein structures also increases continuously. Classification of protein structures helps to understand relationships between protein structure and function. The main classification methods based on secondary structures are SCOP, CATH and TOPS, which all classify under different aspects, and therefore can lead to different results. We developed a mathematically unique representation of protein structure topologies at a higher abstraction level providing new aspects of classification and enabling for a fast search through the data. Protein Topology Graph Library (PTGL; http://ptgl.zib.de) aims at providing a database on protein secondary structure topologies, including search facilities, the visualization as intuitive topology diagrams as well as in the 3D structure, and additional information. Secondary structure-based protein topologies are represented uniquely as undirected labeled graphs in four different ways allowing for exploration under different aspects. The linear notations, and the 2D and 3D diagrams of each notation facilitate a deeper understanding of protein topologies. Several search functions for topologies and sub-topologies, BLAST search possibility, and links to SCOP, CATH and PDBsum support individual and large-scale investigation of protein structures. Currently, PTGL comprises topologies of 54 859 protein structures. Main structural patterns for common structural motifs like TIM-barrel or Jelly Roll are pre-implemented, and can easily be searched.
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Affiliation(s)
- Patrick May
- Max Planck Institute for Molecular Plant Physiology, Bioinformatics, Am Muehlenberg 1, 14476 Potsdam-Golm, Germany.
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456
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Velankar S, Best C, Beuth B, Boutselakis CH, Cobley N, Sousa Da Silva AW, Dimitropoulos D, Golovin A, Hirshberg M, John M, Krissinel EB, Newman R, Oldfield T, Pajon A, Penkett CJ, Pineda-Castillo J, Sahni G, Sen S, Slowley R, Suarez-Uruena A, Swaminathan J, van Ginkel G, Vranken WF, Henrick K, Kleywegt GJ. PDBe: Protein Data Bank in Europe. Nucleic Acids Res 2009; 38:D308-17. [PMID: 19858099 PMCID: PMC2808887 DOI: 10.1093/nar/gkp916] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Protein Data Bank in Europe (PDBe) (http://www.ebi.ac.uk/pdbe/) is actively working with its Worldwide Protein Data Bank partners to enhance the quality and consistency of the international archive of bio-macromolecular structure data, the Protein Data Bank (PDB). PDBe also works closely with its collaborators at the European Bioinformatics Institute and the scientific community around the world to enhance its databases and services by adding curated and actively maintained derived data to the existing structural data in the PDB. We have developed a new database infrastructure based on the remediated PDB archive data and a specially designed database for storing information on interactions between proteins and bound molecules. The group has developed new services that allow users to carry out simple textual queries or more complex 3D structure-based queries. The newly designed 'PDBeView Atlas pages' provide an overview of an individual PDB entry in a user-friendly layout and serve as a starting point to further explore the information available in the PDBe database. PDBe's active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis.
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Affiliation(s)
- S Velankar
- Protein Databank in Europe, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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457
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Abstract
Methylation of DNA, protein, and even RNA species are integral processes in epigenesis. Enzymes that catalyze these reactions using the donor S-adenosylmethionine fall into several structurally distinct classes. The members in each class share sequence similarity that can be used to identify additional methyltransferases. Here, we characterize these classes and in silico approaches to infer protein function. Computational methods such as hidden Markov model profiling and the Multiple Motif Scanning program can be used to analyze known methyltransferases and relay information into the prediction of new ones. In some cases, the substrate of methylation can be inferred from hidden Markov model sequence similarity networks. Functional identification of these candidate species is much more difficult; we discuss one biochemical approach.
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Affiliation(s)
- Tanya Petrossian
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095-1570
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458
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Wang R, Natarajan K, Margulies DH. Structural basis of the CD8 alpha beta/MHC class I interaction: focused recognition orients CD8 beta to a T cell proximal position. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2009; 183:2554-64. [PMID: 19625641 PMCID: PMC2782705 DOI: 10.4049/jimmunol.0901276] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In the immune system, B cells, dendritic cells, NK cells, and T lymphocytes all respond to signals received via ligand binding to receptors and coreceptors. Although the specificity of T cell recognition is determined by the interaction of T cell receptors with MHC/peptide complexes, the development of T cells in the thymus and their sensitivity to Ag are also dependent on coreceptor molecules CD8 (for MHC class I (MHCI)) and CD4 (for MHCII). The CD8alphabeta heterodimer is a potent coreceptor for T cell activation, but efforts to understand its function fully have been hampered by ignorance of the structural details of its interactions with MHCI. In this study we describe the structure of CD8alphabeta in complex with the murine MHCI molecule H-2D(d) at 2.6 A resolution. The focus of the CD8alphabeta interaction is the acidic loop (residues 222-228) of the alpha3 domain of H-2D(d). The beta subunit occupies a T cell membrane proximal position, defining the relative positions of the CD8alpha and CD8beta subunits. Unlike the CD8alphaalpha homodimer, CD8alphabeta does not contact the MHCI alpha(2)- or beta(2)-microglobulin domains. Movements of the CD8alpha CDR2 and CD8beta CDR1 and CDR2 loops as well as the flexibility of the H-2D(d) CD loop facilitate the monovalent interaction. The structure resolves inconclusive data on the topology of the CD8alphabeta/MHCI interaction, indicates that CD8beta is crucial in orienting the CD8alphabeta heterodimer, provides a framework for understanding the mechanistic role of CD8alphabeta in lymphoid cell signaling, and offers a tangible context for design of structurally altered coreceptors for tumor and viral immunotherapy.
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Affiliation(s)
- Rui Wang
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892,Address correspondence and reprint requests to Dr. Kannan Natarajan, or Dr. David H. Margulies, Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg. 10, Room 11N311; 10 Center Drive, Bethesda, MD 20892-1892. and
| | - David H. Margulies
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892,Address correspondence and reprint requests to Dr. Kannan Natarajan, or Dr. David H. Margulies, Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg. 10, Room 11N311; 10 Center Drive, Bethesda, MD 20892-1892. and
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459
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Bialek W, Krzywda S, Jaskolski M, Szczepaniak A. Atomic-resolution structure of reduced cyanobacterial cytochromec6with an unusual sequence insertion. FEBS J 2009; 276:4426-36. [DOI: 10.1111/j.1742-4658.2009.07150.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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460
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Sequence and structural analysis of the Asp-box motif and Asp-box beta-propellers; a widespread propeller-type characteristic of the Vps10 domain family and several glycoside hydrolase families. BMC STRUCTURAL BIOLOGY 2009; 9:46. [PMID: 19594936 PMCID: PMC2716378 DOI: 10.1186/1472-6807-9-46] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 07/13/2009] [Indexed: 11/25/2022]
Abstract
Background The Asp-box is a short sequence and structure motif that folds as a well-defined β-hairpin. It is present in different folds, but occurs most prominently as repeats in β-propellers. Asp-box β-propellers are known to be characteristically irregular and to occur in many medically important proteins, most of which are glycosidase enzymes, but they are otherwise not well characterized and are only rarely treated as a distinct β-propeller family. We have analyzed the sequence, structure, function and occurrence of the Asp-box and s-Asp-box -a related shorter variant, and provide a comprehensive classification and computational analysis of the Asp-box β-propeller family. Results We find that all conserved residues of the Asp-box support its structure, whereas the residues in variable positions are generally used for other purposes. The Asp-box clearly has a structural role in β-propellers and is highly unlikely to be involved in ligand binding. Sequence analysis of the Asp-box β-propeller family reveals it to be very widespread especially in bacteria and suggests a wide functional range. Disregarding the Asp-boxes, sequence conservation of the propeller blades is very low, but a distinct pattern of residues with specific properties have been identified. Interestingly, Asp-boxes are occasionally found very close to other propeller-associated repeats in extensive mixed-motif stretches, which strongly suggests the existence of a novel class of hybrid β-propellers. Structural analysis reveals that the top and bottom faces of Asp-box β-propellers have striking and consistently different loop properties; the bottom is structurally conserved whereas the top shows great structural variation. Interestingly, only the top face is used for functional purposes in known structures. A structural analysis of the 10-bladed β-propeller fold, which has so far only been observed in the Asp-box family, reveals that the inner strands of the blades are unusually far apart, which explains the surprisingly large diameter of the central tunnel of sortilin. Conclusion We have provided new insight into the structure and function of the Asp-box motif and of Asp-box β-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 β-propellers in particular.
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461
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Abstract
Detection of structural motif of residues in protein structures allows identification of structural or functional similarity between proteins. In the field of protein engineering, structural motif identification is essential to select protein scaffolds on which a motif of residues can be transferred to design a new protein with a given function. We describe here the RASMOT-3D PRO webserver (http://biodev.extra.cea.fr/rasmot3d/) that performs a systematic search in 3D structures of protein for a set of residues exhibiting a particular topology. Comparison is based on Cα and Cβ atoms in two steps: inter-atomic distances and RMSD. RASMOT-3D PRO takes in input a PDB file containing the 3D coordinates of the searched motif and provides an interactive list of identified protein structures exhibiting residues of similar topology as the motif searched. Each solution can be graphically examined on the website. The topological search can be conducted in structures described in PDB files uploaded by the user or in those deposited in the PDB. This characteristic as well as the possibility to reject scaffolds sterically incompatible with the target, makes RASMOT-3D PRO a unique webtool in the field of protein engineering.
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Affiliation(s)
- Gaëlle Debret
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), iBiTec-S, DSV, CEA, CE-Saclay, 91191 Gif Sur Yvette Cedex, France
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462
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Lee S, Brown A, Pitt WR, Higueruelo AP, Gong S, Bickerton GR, Schreyer A, Tanramluk D, Baylay A, Blundell TL. Structural interactomics: informatics approaches to aid the interpretation of genetic variation and the development of novel therapeutics. MOLECULAR BIOSYSTEMS 2009; 5:1456-72. [DOI: 10.1039/b906402h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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