- Email: [email protected]
Protein–nucleic acid interactions
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Folding and binding Protein–nucleic acid interactions Web alert Philip E Bourne*, Judith Murray-Rust† and Katrina L Gill‡ A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Structural Biology. Addresses *San Diego Supercomputing Centre, 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] ‡ School of Biochemistry and Genetics, The Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK; e-mail: [email protected] Current Opinion in Structural Biology 2002, 12:9–10
Folding and binding Protein interaction databases http://www.hgmp.mrc.ac.uk/GenomeWeb/prot-interaction.html This section of the GenomeWeb site simply provides a compilation of protein interaction database sites, one of which is described in more detail below. It is useful as a starting point for further exploration of this rapidly expanding area. GenomeWeb provides an authoritative collection of links to genome sites, such as centres, databases, courses and bibliography. As well as creating new links, the links on the site are verified regularly, so that it is always up to date. Database of interacting proteins (DIP) http://dip.doe-mbi.ucla.edu/ The DIP database catalogues experimentally determined interactions between proteins, combining information from a variety of sources to create a single, consistent set of protein–protein interactions. The site also includes several more specific databases, such as the database of ligand–receptor partners (DLRP). The DIP contains over 11 000 unique interactions among 5900 proteins from more than 80 organisms, with the vast majority being from yeast, H. pylori and human. It is cross-referenced to public sequence data banks and to literature citations, and has flexible search and display tools. European Science Foundation Programme on Integrated Approaches for Functional Genomics http://www.functionalgenomics.org.uk/sections/ programme/index.htm The European Science Foundation Programme on Integrated Approaches for Functional Genomics involves research councils and academics in 20 countries. It is active in eight main programme areas, including proteomics, structural genomics and data management. The programme arranges courses, workshops and conferences, and is designed to bring together a wide range of researchers. The extensive web site includes a resources page that provides background reviews on, for example, protein–protein interactions and bioinformatics.
Review on three-dimensional domain swapping http://www.prosci.uci.edu/Articles/Vol4/issue12/ 5301/5301.short.html The importance of domain swapping in protein oligomers was first recognised by the Eisenberg group at UCLA. Although this review is now a little dated, and many more examples are known, it still provides a clear background to how domain swapping can contribute both to the function of multisubunit proteins and to the evolution of multidomain proteins. Domain swapping in G-protein-coupled receptor dimers http://www.essex.ac.uk/bs/staff/reync/ds/dimer.html Domain swapping is a very efficient method of forming oligomers because the interactions within the monomer are reused in the dimer. This page by Christopher A Reynolds of the University of Essex and his collaborators presents some of the evidence for, and possible implications of, dimer formation and domain swapping in G-protein-coupled receptors. Folding@Home http://www.stanford.edu/group/pandegroup/Cosm/ Simulation of protein folding is computationally very demanding and has traditionally been the subject of large grant applications for supercomputer facilities. This group at Stanford has developed a new way to simulate protein folding, called distributed dynamics, which can do these simulations by using large numbers of small computers — anyone with spare time on a suitable PC can volunteer to do their small bit. Recent research papers using the method can be found at http://folding.stanford.edu/papers.html. 3D-Dock suite http://www.bmm.icnet.uk/docking/ The Sternberg laboratory at ICRF, London developed the program FTDock, which performs rigid-body docking of two biomolecules in order to predict their correct binding geometry. FTDock outputs multiple predictions that can be screened using biochemical information. Richard Jackson’s program MultiDock provides a way of refining the interface between two proteins at the atomic level given an initial docked complex, using multiple copies of the sidechains based on a rotamer library. This is one of several docking programs available on the World Wide Web; a listing of some others is given at http://www.bio.vu.nl/nvtb/Docking.html.
Protein–nucleic acid interactions Protein–DNA complexes http://www.biochem.ucl.ac.uk/bsm/prot_dna/prot_dna_cover.html This web site presents a structural classification of DNA-binding motifs, grouped by their DNA recognition motif. Good structural data on the groups are shown by X-ray crystallography, with links to tables containing information on more than 50 protein families and the DNA sequences they bind. Protein–nucleic acid interaction server http://biochem.ucl.ac.uk/bsm/DNA/ This good site may be used as a tool to analyse the protein interface of any protein–nucleic acid complex. By simply submitting
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Web alert
the coordinates of your complex, it generates information on parameters such as the percentage of polar and nonpolar atoms in the interface, and secondary structure. Also available are comparable data for nonhomologous protein–DNA complexes and homologous families of DNA-binding proteins, and the sites they bind to. ProNIT database http://www.rtc.riken.go.jp/jouhou/pronit/pronit_more.html ProNIT is a thermodynamic database of protein–nucleic acid interactions. It contains data such as association and dissociation constants, and enthalpy and heat constants. It also includes sequence, structural and bibliographic information for over 40 different protein–nucleic acid complexes. The database has many useful links to sites such as the Protein Data Bank and the Protein Information Resource. A particularly good feature is the gallery of DNA-binding proteins, which displays over 600 DNA–protein and RNA–protein complexes. BamHI complexed with B-DNA http://www.clunet.edu/BioDev/omm/bamh1/molmast.htm BamHI is a type II restriction endonuclease that recognises short sequences of DNA. This web page provides information on the structure/function relationships of the enzyme, together
with excellent structural images. In addition, the site also contains information on other recombination, modification and repair proteins, as well as on DNA polymerases and ribonucleoproteins. DNA repair information pages http://www.ultranet.com/~jkimball/BiologyPages/ D/DNArepair.html This on-line biology textbook provides a good overview of the different types of DNA damage and repair mechanisms. The text is thoroughly cross-referenced, with plenty of interactive links and an easily accessible glossary. These pages are based on the print version of a biology textbook by John Kimball, yet take advantage of the medium of the Internet to update chapters and reflect current literature. ICRF molecular enzymology laboratory http://www.icnet.uk/labs/wigley/index.html This site describes the research carried out in Dale Wigley’s group on a variety of DNA-binding proteins, including topoisomerases, DNA ligases, helicases and primases. The pages include crystal structures of these DNA-binding proteins, with links to protein function and research information.
Folding and binding Protein–nucleic acid interactions Web alert Philip E Bourne*, Judith Murray-Rust† and Katrina L Gill‡ A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Structural Biology. Addresses *San Diego Supercomputing Centre, 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] ‡ School of Biochemistry and Genetics, The Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK; e-mail: [email protected] Current Opinion in Structural Biology 2002, 12:9–10
Folding and binding Protein interaction databases http://www.hgmp.mrc.ac.uk/GenomeWeb/prot-interaction.html This section of the GenomeWeb site simply provides a compilation of protein interaction database sites, one of which is described in more detail below. It is useful as a starting point for further exploration of this rapidly expanding area. GenomeWeb provides an authoritative collection of links to genome sites, such as centres, databases, courses and bibliography. As well as creating new links, the links on the site are verified regularly, so that it is always up to date. Database of interacting proteins (DIP) http://dip.doe-mbi.ucla.edu/ The DIP database catalogues experimentally determined interactions between proteins, combining information from a variety of sources to create a single, consistent set of protein–protein interactions. The site also includes several more specific databases, such as the database of ligand–receptor partners (DLRP). The DIP contains over 11 000 unique interactions among 5900 proteins from more than 80 organisms, with the vast majority being from yeast, H. pylori and human. It is cross-referenced to public sequence data banks and to literature citations, and has flexible search and display tools. European Science Foundation Programme on Integrated Approaches for Functional Genomics http://www.functionalgenomics.org.uk/sections/ programme/index.htm The European Science Foundation Programme on Integrated Approaches for Functional Genomics involves research councils and academics in 20 countries. It is active in eight main programme areas, including proteomics, structural genomics and data management. The programme arranges courses, workshops and conferences, and is designed to bring together a wide range of researchers. The extensive web site includes a resources page that provides background reviews on, for example, protein–protein interactions and bioinformatics.
Review on three-dimensional domain swapping http://www.prosci.uci.edu/Articles/Vol4/issue12/ 5301/5301.short.html The importance of domain swapping in protein oligomers was first recognised by the Eisenberg group at UCLA. Although this review is now a little dated, and many more examples are known, it still provides a clear background to how domain swapping can contribute both to the function of multisubunit proteins and to the evolution of multidomain proteins. Domain swapping in G-protein-coupled receptor dimers http://www.essex.ac.uk/bs/staff/reync/ds/dimer.html Domain swapping is a very efficient method of forming oligomers because the interactions within the monomer are reused in the dimer. This page by Christopher A Reynolds of the University of Essex and his collaborators presents some of the evidence for, and possible implications of, dimer formation and domain swapping in G-protein-coupled receptors. Folding@Home http://www.stanford.edu/group/pandegroup/Cosm/ Simulation of protein folding is computationally very demanding and has traditionally been the subject of large grant applications for supercomputer facilities. This group at Stanford has developed a new way to simulate protein folding, called distributed dynamics, which can do these simulations by using large numbers of small computers — anyone with spare time on a suitable PC can volunteer to do their small bit. Recent research papers using the method can be found at http://folding.stanford.edu/papers.html. 3D-Dock suite http://www.bmm.icnet.uk/docking/ The Sternberg laboratory at ICRF, London developed the program FTDock, which performs rigid-body docking of two biomolecules in order to predict their correct binding geometry. FTDock outputs multiple predictions that can be screened using biochemical information. Richard Jackson’s program MultiDock provides a way of refining the interface between two proteins at the atomic level given an initial docked complex, using multiple copies of the sidechains based on a rotamer library. This is one of several docking programs available on the World Wide Web; a listing of some others is given at http://www.bio.vu.nl/nvtb/Docking.html.
Protein–nucleic acid interactions Protein–DNA complexes http://www.biochem.ucl.ac.uk/bsm/prot_dna/prot_dna_cover.html This web site presents a structural classification of DNA-binding motifs, grouped by their DNA recognition motif. Good structural data on the groups are shown by X-ray crystallography, with links to tables containing information on more than 50 protein families and the DNA sequences they bind. Protein–nucleic acid interaction server http://biochem.ucl.ac.uk/bsm/DNA/ This good site may be used as a tool to analyse the protein interface of any protein–nucleic acid complex. By simply submitting
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Web alert
the coordinates of your complex, it generates information on parameters such as the percentage of polar and nonpolar atoms in the interface, and secondary structure. Also available are comparable data for nonhomologous protein–DNA complexes and homologous families of DNA-binding proteins, and the sites they bind to. ProNIT database http://www.rtc.riken.go.jp/jouhou/pronit/pronit_more.html ProNIT is a thermodynamic database of protein–nucleic acid interactions. It contains data such as association and dissociation constants, and enthalpy and heat constants. It also includes sequence, structural and bibliographic information for over 40 different protein–nucleic acid complexes. The database has many useful links to sites such as the Protein Data Bank and the Protein Information Resource. A particularly good feature is the gallery of DNA-binding proteins, which displays over 600 DNA–protein and RNA–protein complexes. BamHI complexed with B-DNA http://www.clunet.edu/BioDev/omm/bamh1/molmast.htm BamHI is a type II restriction endonuclease that recognises short sequences of DNA. This web page provides information on the structure/function relationships of the enzyme, together
with excellent structural images. In addition, the site also contains information on other recombination, modification and repair proteins, as well as on DNA polymerases and ribonucleoproteins. DNA repair information pages http://www.ultranet.com/~jkimball/BiologyPages/ D/DNArepair.html This on-line biology textbook provides a good overview of the different types of DNA damage and repair mechanisms. The text is thoroughly cross-referenced, with plenty of interactive links and an easily accessible glossary. These pages are based on the print version of a biology textbook by John Kimball, yet take advantage of the medium of the Internet to update chapters and reflect current literature. ICRF molecular enzymology laboratory http://www.icnet.uk/labs/wigley/index.html This site describes the research carried out in Dale Wigley’s group on a variety of DNA-binding proteins, including topoisomerases, DNA ligases, helicases and primases. The pages include crystal structures of these DNA-binding proteins, with links to protein function and research information.