- Email: [email protected]
Catalysis and regulation: Proteins
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Catalysis and regulation Proteins Web alert David A Chalton*, Boojala Reddy† and Judith Murray-Rust‡ A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Structural Biology. Addresses *School of Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK; e-mail: [email protected] †San Diego Supercomputing Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA; e-mail: [email protected] ‡Crystallography Department, Birkbeck College, London WC1E 7HX, UK; e-mail: [email protected] Current Opinion in Structural Biology 2002, 12:693–694
Catalysis and regulation Biochemical reactions and enzyme catalysis http://www.biologie.uni-hamburg.de/b-online/e18/18.htm A resource from the University of Hamburg, Faculty of Biology, this is a chapter from an Internet hypertext botany book. The book describes biochemical reactions in detail, covering redox reactions, properties and energy contents of chemical bonds, mechanisms of enzyme catalysis, inhibition and regulation of enzyme activities, and allosteric enzymes. Some helpful basic thermodynamic terms are also given. LIGAND: Database of Chemical Compounds and Reactions in Biological Pathways http://www.genome.ad.jp/ligand/ LIGAND is a GenomeNet resource from the Bioinformatics Center, Institute of Chemical Research, Kyoto University. It is a composite database consisting of COMPOUND, a collection of chemical compounds that are related to various cellular processes; REACTION, a collection of reactions, mostly enzymatic reactions, involving those compounds; ENZYME, the enzyme nomenclature from IUBMB and IUPAC. KEGG regulatory and metabolic pathways http://www.genome.ad.jp/kegg/regulation.html http://www.genome.ad.jp/kegg/metabolism.html The Kyoto Encyclopaedia of Genes and Genomes (KEGG) is an effort to computerise current knowledge of molecular and cellular biology in terms of information pathways that consist of interacting molecules or genes and to provide links to the gene catalogues produced by genome sequencing projects. Graphical pathway maps, orthologue group tables and molecular catalogues are given for metabolic and regulatory pathways. Ligand binding databases http://sgedg.weizmann.ac.il/ferafael/ligdb.html These ligand binding databases were created by Rafael Najmanovich at the Weizmann Institute, Israel. The analysis was restricted to ligands listed as HETATM in the PDB and excludes nucleic acids, peptides and ligands that are covalently bound to
protein atoms, sulfates and phosphates. The three databases are maximal database, binding pocket database and ligand database. They are useful as a starting point for studies related to ligand binding that require the structural comparison of apo and holo forms of enzymes. LGICdb: The Ligand-Gated Ion Channel Database http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html Ligand-gated ion channels are polymeric transmembrane proteins involved in the fast response to numerous neurotransmitters. There are three different superfamilies: the cys-loop superfamily, ATP-gated channels and glutamate-activated cationic channels. This database contains annotated nucleic acid and protein sequence entries for ligand-gated ion channel subunits. It aims to provide only one entry for each gene. DIP: Database of Interacting Proteins http://dip.doe-mbi.ucla.edu/ DIPTM is a database for the study of cellular networks of protein interactions. It catalogues experimentally determined interactions between proteins and combines information from a variety of sources to create a single, consistent set of protein–protein interactions. The data stored within the DIP database were curated, both manually by expert curators and automatically using computational approaches that use knowledge about protein–protein interaction networks extracted from the most reliable core subset of the DIP data. BIND: Biomolecular Interaction Network Database http://www.bind.ca/ BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways. The BIND data model has virtually all components of molecular mechanisms, including interactions between any two molecules composed of proteins, nucleic acids and small molecules. Chemical reactions, photochemical activation and conformational changes are also described. Everything from small-molecule biochemistry to signal transduction is abstracted in such a way that graph theory methods may be applied for data mining. The database can be used to study networks of interactions, to map pathways across taxonomic branches and to generate information for kinetic simulations. MINT: a Molecular INTeractions database http://cbm.bio.uniroma2.it/mint/ MINT is a database designed to store information about functional interactions between biological molecules (proteins, RNA, DNA). Beyond cataloguing the formation of binary complexes, MINT was conceived to store details concerning the enzymatic modification of one of the interacting partners. Presently, MINT focuses on experimentally verified protein–protein interactions. Both direct and indirect relationships are considered. MINT consists of entries extracted from the scientific literature by expert curators assisted by ‘MINT Assistant’, software that targets abstracts containing interaction information and presents them to the curator in a user-friendly format. The interaction
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data can be easily extracted and viewed graphically by ‘MINT Viewer’. SENTRA: a Database of Signal Transduction Proteins for Prokaryotes http://www-wit.mcs.anl.gov/sentra/ SENTRA is a database of sensory signal transduction proteins, developed at the Argonne National Laboratory. The database has been updated to include classes of signal transduction systems modulated by either phosphorylation or methylation reactions, such as PAS proteins and serine/threonine kinases, as well as the classical two-component histidine kinases and methylaccepting proteins. Currently, SENTRA contains signal transduction proteins from 43 completely sequenced prokaryotic genomes, as well as sequences from 264 organisms from SWISS-PROT and TrEMBL.
Proteins BioCarta: pathways of life http://www.biocarta.com/genes/index.asp This link is the starting point for exploring the BioCarta pathways. These are very clear graphical depictions of molecular relationships, from the acetylation and deacetylation of RelA in the nucleus through to the Wnt signalling pathway. Clicking on any of the components involved in a pathway will bring up a list of links to a large number of relevant databases. Despite involving 120 000 genes from multiple species at the time of writing (October 2002) and with over 200 pathways to explore, it remains a clear and broad-ranging site. Home page of Timothy Springer http://sprsgi.med.harvard.edu/~webpage/index.html This page contains a set of links to various tools, web sites and laboratory protocols for adhesion receptor research. It also has a structure gallery, which contains not only visual renderings of relevant domains but also links to references and database entries for specific domains. It has an impressive list of links that manages to collate pointers to huge bodies of diverse information, which, from this page, will just be a ‘click’ away.
AAA server home page http://aaa-proteins.uni-graz.at/AAA/Default.html This web page provides a useful starting point for researchers interested in AAA proteins (ATPases associated with various cellular activities). It has phylogenetic trees, as well as lists of references and researchers in the field. It also has a limited database of information on specific AAA proteins, as well as a list of hyperlinks to more general pages of interest to many researchers. ABCISSE database http://www.pasteur.fr/recherche/unites/pmtg/abc/database.iphtml The ABCISSE (ABC systems: Information on Sequence, Structure and Evolution) database is the result of a phylogenetic and functional classification of ATP-binding cassette (ABC) systems. The database can be searched by a quick search facility, by species, by list of substrates and by gene name. Hosted by the Pasteur Institute, the database provides comprehensive results, including links to other database entries. Kazuhiko Kinosita’s single-molecule movies page http://www.k2.ims.ac.jp/Movies.html This page contains a number of movies of experiments involving labelled single-molecule manipulation. The movies are very broad ranging and cover such subjects as membrane protrusion driven by actin polymerisation, torsional rigidity of actin filaments, stepping rotation of F1-ATPase at low ATP concentrations, tying a knot in an actin filament and DNA molecule, and Ca2+ wave and membrane reorientation upon egg fertilisation. Lecture Series on Medical Cell Biology http://www.cytochemistry.net/cell-biology/medical/main.htm This set of lectures includes some very clear diagrams and animations, probably aimed at late undergraduate/early postgraduate level or for a general introduction to the field. Prepared by Gwen Childs at the University of Arkansas for Medical Sciences, the presentations on the page are comprehensive and very well designed. They include subjects such as receptor-mediated endocytosis, the actin cytoskeleton, membranes, membrane proteins and mitochondria.
Catalysis and regulation Proteins Web alert David A Chalton*, Boojala Reddy† and Judith Murray-Rust‡ A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Structural Biology. Addresses *School of Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK; e-mail: [email protected] †San Diego Supercomputing Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA; e-mail: [email protected] ‡Crystallography Department, Birkbeck College, London WC1E 7HX, UK; e-mail: [email protected] Current Opinion in Structural Biology 2002, 12:693–694
Catalysis and regulation Biochemical reactions and enzyme catalysis http://www.biologie.uni-hamburg.de/b-online/e18/18.htm A resource from the University of Hamburg, Faculty of Biology, this is a chapter from an Internet hypertext botany book. The book describes biochemical reactions in detail, covering redox reactions, properties and energy contents of chemical bonds, mechanisms of enzyme catalysis, inhibition and regulation of enzyme activities, and allosteric enzymes. Some helpful basic thermodynamic terms are also given. LIGAND: Database of Chemical Compounds and Reactions in Biological Pathways http://www.genome.ad.jp/ligand/ LIGAND is a GenomeNet resource from the Bioinformatics Center, Institute of Chemical Research, Kyoto University. It is a composite database consisting of COMPOUND, a collection of chemical compounds that are related to various cellular processes; REACTION, a collection of reactions, mostly enzymatic reactions, involving those compounds; ENZYME, the enzyme nomenclature from IUBMB and IUPAC. KEGG regulatory and metabolic pathways http://www.genome.ad.jp/kegg/regulation.html http://www.genome.ad.jp/kegg/metabolism.html The Kyoto Encyclopaedia of Genes and Genomes (KEGG) is an effort to computerise current knowledge of molecular and cellular biology in terms of information pathways that consist of interacting molecules or genes and to provide links to the gene catalogues produced by genome sequencing projects. Graphical pathway maps, orthologue group tables and molecular catalogues are given for metabolic and regulatory pathways. Ligand binding databases http://sgedg.weizmann.ac.il/ferafael/ligdb.html These ligand binding databases were created by Rafael Najmanovich at the Weizmann Institute, Israel. The analysis was restricted to ligands listed as HETATM in the PDB and excludes nucleic acids, peptides and ligands that are covalently bound to
protein atoms, sulfates and phosphates. The three databases are maximal database, binding pocket database and ligand database. They are useful as a starting point for studies related to ligand binding that require the structural comparison of apo and holo forms of enzymes. LGICdb: The Ligand-Gated Ion Channel Database http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html Ligand-gated ion channels are polymeric transmembrane proteins involved in the fast response to numerous neurotransmitters. There are three different superfamilies: the cys-loop superfamily, ATP-gated channels and glutamate-activated cationic channels. This database contains annotated nucleic acid and protein sequence entries for ligand-gated ion channel subunits. It aims to provide only one entry for each gene. DIP: Database of Interacting Proteins http://dip.doe-mbi.ucla.edu/ DIPTM is a database for the study of cellular networks of protein interactions. It catalogues experimentally determined interactions between proteins and combines information from a variety of sources to create a single, consistent set of protein–protein interactions. The data stored within the DIP database were curated, both manually by expert curators and automatically using computational approaches that use knowledge about protein–protein interaction networks extracted from the most reliable core subset of the DIP data. BIND: Biomolecular Interaction Network Database http://www.bind.ca/ BIND is a database designed to store full descriptions of interactions, molecular complexes and pathways. The BIND data model has virtually all components of molecular mechanisms, including interactions between any two molecules composed of proteins, nucleic acids and small molecules. Chemical reactions, photochemical activation and conformational changes are also described. Everything from small-molecule biochemistry to signal transduction is abstracted in such a way that graph theory methods may be applied for data mining. The database can be used to study networks of interactions, to map pathways across taxonomic branches and to generate information for kinetic simulations. MINT: a Molecular INTeractions database http://cbm.bio.uniroma2.it/mint/ MINT is a database designed to store information about functional interactions between biological molecules (proteins, RNA, DNA). Beyond cataloguing the formation of binary complexes, MINT was conceived to store details concerning the enzymatic modification of one of the interacting partners. Presently, MINT focuses on experimentally verified protein–protein interactions. Both direct and indirect relationships are considered. MINT consists of entries extracted from the scientific literature by expert curators assisted by ‘MINT Assistant’, software that targets abstracts containing interaction information and presents them to the curator in a user-friendly format. The interaction
694
Web alert
data can be easily extracted and viewed graphically by ‘MINT Viewer’. SENTRA: a Database of Signal Transduction Proteins for Prokaryotes http://www-wit.mcs.anl.gov/sentra/ SENTRA is a database of sensory signal transduction proteins, developed at the Argonne National Laboratory. The database has been updated to include classes of signal transduction systems modulated by either phosphorylation or methylation reactions, such as PAS proteins and serine/threonine kinases, as well as the classical two-component histidine kinases and methylaccepting proteins. Currently, SENTRA contains signal transduction proteins from 43 completely sequenced prokaryotic genomes, as well as sequences from 264 organisms from SWISS-PROT and TrEMBL.
Proteins BioCarta: pathways of life http://www.biocarta.com/genes/index.asp This link is the starting point for exploring the BioCarta pathways. These are very clear graphical depictions of molecular relationships, from the acetylation and deacetylation of RelA in the nucleus through to the Wnt signalling pathway. Clicking on any of the components involved in a pathway will bring up a list of links to a large number of relevant databases. Despite involving 120 000 genes from multiple species at the time of writing (October 2002) and with over 200 pathways to explore, it remains a clear and broad-ranging site. Home page of Timothy Springer http://sprsgi.med.harvard.edu/~webpage/index.html This page contains a set of links to various tools, web sites and laboratory protocols for adhesion receptor research. It also has a structure gallery, which contains not only visual renderings of relevant domains but also links to references and database entries for specific domains. It has an impressive list of links that manages to collate pointers to huge bodies of diverse information, which, from this page, will just be a ‘click’ away.
AAA server home page http://aaa-proteins.uni-graz.at/AAA/Default.html This web page provides a useful starting point for researchers interested in AAA proteins (ATPases associated with various cellular activities). It has phylogenetic trees, as well as lists of references and researchers in the field. It also has a limited database of information on specific AAA proteins, as well as a list of hyperlinks to more general pages of interest to many researchers. ABCISSE database http://www.pasteur.fr/recherche/unites/pmtg/abc/database.iphtml The ABCISSE (ABC systems: Information on Sequence, Structure and Evolution) database is the result of a phylogenetic and functional classification of ATP-binding cassette (ABC) systems. The database can be searched by a quick search facility, by species, by list of substrates and by gene name. Hosted by the Pasteur Institute, the database provides comprehensive results, including links to other database entries. Kazuhiko Kinosita’s single-molecule movies page http://www.k2.ims.ac.jp/Movies.html This page contains a number of movies of experiments involving labelled single-molecule manipulation. The movies are very broad ranging and cover such subjects as membrane protrusion driven by actin polymerisation, torsional rigidity of actin filaments, stepping rotation of F1-ATPase at low ATP concentrations, tying a knot in an actin filament and DNA molecule, and Ca2+ wave and membrane reorientation upon egg fertilisation. Lecture Series on Medical Cell Biology http://www.cytochemistry.net/cell-biology/medical/main.htm This set of lectures includes some very clear diagrams and animations, probably aimed at late undergraduate/early postgraduate level or for a general introduction to the field. Prepared by Gwen Childs at the University of Arkansas for Medical Sciences, the presentations on the page are comprehensive and very well designed. They include subjects such as receptor-mediated endocytosis, the actin cytoskeleton, membranes, membrane proteins and mitochondria.