CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

Cavities on a proteins surface as well as specific amino acid positioning within it create the physicochemical properties needed for a protein to perform its function. CASTp () is an online tool that locates and measures pockets and voids on 3D protein structures. This new version of CASTp includes annotated functional information of specific residues on the protein structure. The annotations are derived from the Protein Data Bank (PDB), Swiss-Prot, as well as Online Mendelian Inheritance in Man (OMIM), the latter contains information on the variant single nucleotide polymorphisms (SNPs) that are known to cause disease. These annotated residues are mapped to surface pockets, interior voids or other regions of the PDB structures. We use a semi-global pair-wise sequence alignment method to obtain sequence mapping between entries in Swiss-Prot, OMIM and entries in PDB. The updated CASTp web server can be used to study surface features, functional regions and specific roles of key residues of proteins.

[1]  J. Thompson,et al.  Liver fatty acid binding protein: species variation and the accommodation of different ligands. , 1999, Biochimica et biophysica acta.

[2]  H. Edelsbrunner,et al.  Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design , 1998, Protein science : a publication of the Protein Society.

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

[4]  J Liang,et al.  Chemical complementation identifies a proton acceptor for redox-active tyrosine D in photosystem II. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[5]  D C Richardson,et al.  Kinemages--simple macromolecular graphics for interactive teaching and publication. , 1994, Trends in biochemical sciences.

[6]  Herbert Edelsbrunner,et al.  On the Definition and the Construction of Pockets in Macromolecules , 1998, Discret. Appl. Math..

[7]  D. Bernlohr,et al.  Surface properties of adipocyte lipid‐binding protein: Response to lipid binding, and comparison with homologous proteins , 1998, Proteins.

[8]  J. Ory,et al.  Studies of the ligand binding reaction of adipocyte lipid binding protein using the fluorescent probe 1, 8-anilinonaphthalene-8-sulfonate. , 1999, Biophysical journal.

[9]  M. Swindells,et al.  Protein clefts in molecular recognition and function. , 1996, Protein science : a publication of the Protein Society.

[10]  M. Paetzel,et al.  Common protein architecture and binding sites in proteases utilizing a Ser/Lys dyad mechanism , 2008, Protein science : a publication of the Protein Society.

[11]  R A Sayle,et al.  RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.

[12]  J. Naylor,et al.  Mendelian inheritance in man: A catalog of human genes and genetic disorders , 1996 .

[13]  S. Kasif,et al.  Structural location of disease-associated single-nucleotide polymorphisms. , 2003, Journal of molecular biology.

[14]  M. Ludwig,et al.  Crystal structure of the quorum-sensing protein LuxS reveals a catalytic metal site , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Simon Kasif,et al.  topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association , 2004, Nucleic Acids Res..

[16]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[17]  V. McKusick.  Mendelian inheritance in man , 1971 .

[18]  G B Quinn,et al.  Development of Internet-based multimedia applications. , 1999, Trends in biochemical sciences.

[19]  Ron D. Appel,et al.  ExPASy: the proteomics server for in-depth protein knowledge and analysis , 2003, Nucleic Acids Res..

[20]  Jie Liang,et al.  CASTp: Computed Atlas of Surface Topography of proteins , 2003, Nucleic Acids Res..

[21]  Renyu Liu,et al.  The Role of Electrostatic Interactions in Human Serum Albumin Binding and Stabilization by Halothane* , 2002, The Journal of Biological Chemistry.

[22]  Lesa J Beamer,et al.  Crystal structure of PMM/PGM: an enzyme in the biosynthetic pathway of P. aeruginosa virulence factors. , 2002, Structure.

[23]  T. Poulos,et al.  Crystal Structures of Zinc-free and -bound Heme Domain of Human Inducible Nitric-oxide Synthase , 1999, The Journal of Biological Chemistry.

[24]  L. Banaszak,et al.  Lipid-protein interactions in lipovitellin. , 2002, Biochemistry.