CysView: protein classification based on cysteine pairing patterns

CysView is a web-based application tool that identifies and classifies proteins according to their disulfide connectivity patterns. It accepts a dataset of annotated protein sequences in various formats and returns a graphical representation of cysteine pairing patterns. CysView displays cysteine patterns for those records in the data with disulfide annotations. It allows the viewing of records grouped by connectivity patterns. CysView's utility as an analysis tool was demonstrated by the rapid and correct classification of scorpion toxin entries from GenPept on the basis of their disulfide pairing patterns. It has proved useful for rapid detection of irrelevant and partial records, or those with incomplete annotations. CysView can be used to support distant homology between proteins. CysView is publicly available at http://research.i2r.a-star.edu.sg/CysView/.

[1]  R. Sowdhamini,et al.  Conformations of disulfide bridges in proteins. , 2009, International journal of peptide and protein research.

[2]  J. Pratt,et al.  What can toxins tell us for drug discovery? , 1998, Toxicon : official journal of the International Society on Toxinology.

[3]  H. Scheraga,et al.  Disulfide bonds and protein folding. , 2000, Biochemistry.

[4]  Piero Fariselli,et al.  Prediction of the disulfide‐bonding state of cysteines in proteins at 88% accuracy , 2002, Protein science : a publication of the Protein Society.

[5]  G. Lambeau,et al.  What can venom phospholipases A(2) tell us about the functional diversity of mammalian secreted phospholipases A(2)? , 2000, Biochimie.

[6]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[7]  Koreaki Ito,et al.  Respiratory chain strongly oxidizes the CXXC motif of DsbB in the Escherichia coli disulfide bond formation pathway , 1999, The EMBO journal.

[8]  J. Thornton.  Disulphide bridges in globular proteins. , 1981, Journal of molecular biology.

[9]  H. Scheraga,et al.  Oxidative folding of proteins. , 2000, Accounts of chemical research.

[10]  Paolo Frasconi,et al.  Disulfide connectivity prediction using recursive neural networks and evolutionary information , 2004, Bioinform..

[11]  P. Hains,et al.  Modeling of acanthoxin A1, a PLA2 enzyme from the venom of the common death adder (Acanthophis antarcticus) , 1999, Proteins.

[12]  M. Delepierre,et al.  Scorpion toxins specific for Na+-channels. , 1999, European journal of biochemistry.

[13]  J. Richardson,et al.  The anatomy and taxonomy of protein structure. , 1981, Advances in protein chemistry.

[14]  K. Rajarathnam,et al.  13C NMR chemical shifts can predict disulfide bond formation , 2000, Journal of biomolecular NMR.

[15]  David L. Wheeler,et al.  GenBank: update , 2004, Nucleic Acids Res..

[16]  Herman W T van Vlijmen,et al.  A novel database of disulfide patterns and its application to the discovery of distantly related homologs. , 2004, Journal of molecular biology.

[17]  Craig J. Benham,et al.  Disulfide bonding patterns and protein topologies , 1993, Protein science : a publication of the Protein Society.

[18]  M. Sternberg,et al.  Analysis and classification of disulphide connectivity in proteins. The entropic effect of cross-linkage. , 1994, Journal of molecular biology.

[19]  B D Sykes,et al.  Disulfide bridges in interleukin-8 probed using non-natural disulfide analogues: dissociation of roles in structure from function. , 1999, Biochemistry.

[20]  P. Lyu,et al.  Relationship between protein structures and disulfide‐bonding patterns , 2003, Proteins.

[21]  Hideaki Sugawara,et al.  DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams , 2000, Nucleic Acids Res..

[22]  P Tufféry,et al.  Predicting the disulfide bonding state of cysteines using protein descriptors , 2002, Proteins.

[23]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[24]  Ramanathan Sowdhamini,et al.  SDBASE: a consortium of native and modelled disulphide bonds in proteins , 2004, Nucleic Acids Res..

[25]  Piero Fariselli,et al.  Prediction of disulfide connectivity in proteins , 2001, Bioinform..

[26]  D. Craik,et al.  The cystine knot motif in toxins and implications for drug design. , 2001, Toxicon : official journal of the International Society on Toxinology.

[27]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[28]  S. Petersen,et al.  Amino acid neighbours and detailed conformational analysis of cysteines in proteins. , 1999, Protein engineering.

[29]  Vladimir Brusic,et al.  Bioinformatics for Venom and Toxin Sciences , 2003, Briefings Bioinform..

[30]  Jon Beckwith,et al.  Protein disulfide bond formation in prokaryotes. , 2003, Annual review of biochemistry.

[31]  Alan L Harvey,et al.  Toxins 'R' Us: more pharmacological tools from nature's superstore. , 2002, Trends in pharmacological sciences.

[32]  P. Hogg,et al.  Disulfide bonds as switches for protein function. , 2003, Trends in biochemical sciences.

[33]  M. Martí-Renom,et al.  Classification of protein disulphide-bridge topologies , 2001, J. Comput. Aided Mol. Des..

[34]  M. Sternberg,et al.  The disulphide beta-cross: from cystine geometry and clustering to classification of small disulphide-rich protein folds. , 1996, Journal of molecular biology.

[35]  Seng Hong Seah,et al.  SCORPION, a molecular database of scorpion toxins. , 2002, Toxicon : official journal of the International Society on Toxinology.

[36]  B. Matthews,et al.  Substantial increase of protein stability by multiple disulphide bonds , 1989, Nature.

[37]  M. Martí-Renom,et al.  Protein similarities beyond disulphide bridge topology. , 1998, Journal of molecular biology.