Predicting calcium-binding sites in proteins - A graph theory and geometry approach

Proteins: Structure, Function and Genetics

Volumn 64, Issue 1, 2006, Pages 34-42

  Deng, Hai ^a   Chen, Guantao ^a   Yang, Wei ^a   Yang, Jenny J ^a  

^a GEORGIA STATE UNIVERSITY   (United States)

Author keywords

Calcium binding proteins; Function prediction; Graph theory; Metal binding geometry; Oxygen cluster

Indexed keywords

OXYGEN;

ACCURACY; ALGORITHM; ARTICLE; BINDING SITE; CALCIUM BINDING; GENOMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; SENSITIVITY AND SPECIFICITY; THEORETICAL MODEL;

ALGORITHMS; BINDING SITES; CALCIUM; CALCIUM-BINDING PROTEINS; MODELS, MOLECULAR; MODELS, THEORETICAL; SOLVENTS;

EID: 33744803962     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20973     Document Type: Article

References (58)

1. Kawasaki H, Nakayama S, Kretsinger RH. Classification and evolution of EF-hand proteins. Biometals 1998;11:277-295.
2. Inesi G. Mechanism of calcium transport. Annu Rev Physiol 1985;47:573-601.
3. 2+ binding. Biometals 1998;11:297-318.
4. Ikura M. Calcium binding and conformational response in EF-hand proteins. Trends Biochem Sci 1996;21:14-17.
5. 2+-binding sites in proteins. Proc Natl Acad Sci USA 1994;91:817-821.
6. McPhalen CA, Strynadka NC, James MN. Calcium-binding sites in proteins: a structural perspective. Adv Protein Chem 1991;42:77-144.
7. Pidcock E, Moore GR. Structural characteristics of protein binding sites for calcium and lanthanide ions. J Biol Inorg Chem 2001;6:479-489.
8. Yang W, Lee HW, Hellinga H, Yang JJ. Structural analysis, identification, and design of calcium-binding sites in proteins. Proteins 2002;47:344-356.
9. Yang W, Jones LM, Isley L, Ye Y, Lee HW, Wilkins A, Liu ZR, Hellinga HW, Malchow R, Ghazi M, Yang JJ. Rational design of a calcium-binding protein. J Am Chem Soc 2003;125:6165-6171.
10. Yang W, Wilkins AL, Ye Y, Liu ZR, Li SY, Urbauer JL, Hellinga HW, Kearney A, van der Merwe PA, Yang JJ. Design of a calcium-binding protein with desired structure in a cell adhesion molecule. J Am Chem Soc 2005;127:2085-2093.
11. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
12. Kunishima N, Shimada Y, Tsuji Y, Sato T, Yamamoto M, Kumasaka T, Nakanishi S, Jingami H, Morikawa K. Structural basis of glutamate recognition by a dimeric metabotropic glutamate receptor. Nature 2000;407:971-977.
13. Francesconi A, Duvoisin RM. Divalent cations modulate the activity of metabotropic glutamate receptors. J Neurosci Res 2004;75:472-479.
14. 3+. Proc Natl Acad Sci USA 2002;99:2660-2665.
15. Laskowski RA, Watson JD, Thornton JM. From protein structure to biochemical function? J Struct Funct Genomics 2003;4:167-177.
16. Laskowski RA, Watson JD, Thornton JM. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 2005;33(Web Server issue):W89-W93.
17. Watson JD, Laskowski RA, Thornton JM. Predicting protein function from sequence and structural data. Curr Opin Struct Biol 2005;15:275-284.
18. Brocchieri L, Kledal TN, Karlin S, Mocarski ES. Predicting coding potential from genome sequence: application to betaherpesviruses infecting rats and mice. J Virol 2005;79:7570-7596.
19. Zhu ZY, Karlin S. Clusters of charged residues in protein three-dimensional structures. Proc Natl Acad Sci USA 1996;93:8350-8355.
20. Bolon DN, Mayo SL. Enzyme-like proteins by computational design. Proc Natl Acad Sci USA 2001;98:14274-14279.
21. Yang JJ, Yang W. Calcium binding proteins. In: King RB, editor. The encyclopedia of inorganic chemistry, 2nd ed., vol. II, Chichester, England: Wiley 2005; pp. 630-666.
22. Wei L, Huang ES, Altman RB. Are predicted structures good enough to preserve functional sites? Struct Fold Des 1999;7:643-650.
23. Sodhi JS, Bryson K, McGuffin LJ, Ward JJ, Wernisch L, Jones DT. Predicting metal-binding site residues in low-resolution structural models. J Mol Biol 2004;342:307-320.
24. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J Mol Biol 1982;161:269-288.
25. Bagley SC, Altman RB. Characterizing the microenvironment surrounding protein sites. Protein Sci 1995;4:622-635.
26. Liang MP, Banatao DR, Klein TE, Brutlag DL, Altman RB. WebFEATURE: an interactive Web tool for identifying and visualizing functional sites on macromolecular structures. Nucleic Acids Res 2003;31;3324-3327.
27. Liang MP, Brutlag DL, Altman RB. Automated construction of structural motifs for predicting functional sites on protein structures. Pac Symp Biocomput 2003:204-215.
28. Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992;89:2195-2199.
29. Rychlewski L, Fischer D, Elofsson A. LiveBench-6: large-scale automated evaluation of protein structure prediction servers. Proteins 2003;53(Suppl 6):542-547.
30. Yamashita MM, Wesson L, Eisenman G, Eisenberg D. Where metal ions bind in proteins. Proc Natl Acad Sci USA 1990;87:5648-5652.
31. Samudrala R, Moult J. A graph-theoretic algorithm for comparative modeling of protein structure. J Mol Biol 1998;279:287-302.
32. Canutescu AA, Shelenkov AA, Dunbrack RL Jr. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003;12:2001-2014.
33. Babu YS, Bugg CE, Cook WJ. Structure of calmodulin refined at 2.2 A resolution. J Mol Biol 1988;204:191-204.
34. Ravishankar R, Ravindran M, Suguna K, Surolia A, Vijayan M. The specificity of peanut agglutinin for Thomsen-Friedenreich antigen is mediated by water-bridges. Curr Sci 1997;72:855-861.
35. Flocco MM, Mowbray SL. The 1.9 A X-ray structure of a closed unliganded form of the periplasmic glucose/galactose receptor from Salmonella typhimurium. J Biol Chem 1994;269:8931-8936.
36. Done SH, Brannigan JA, Moody PC, Hubbard RE. Ligand-induced conformational change in penicillin acylase. J Mol Biol 1998;284:463-475.
37. Bewley MC, Boustead CM, Walker JH, Waller DA, Huber R. Structure of chicken annexin V at 2.25-A resolution. Biochemistry 1993;32:3923-3929.
38. Divne C, Stahlberg J, Reinikainen T, Ruohonen L, Pettersson G, Knowles JK, Teeri TT, Jones TA. The three-dimensional crystal structure of the catalytic core of cellobiohydrolase I from Trichoderma reesei. Science 1994;265:524-528.
39. Weis WI, Drickamer K, Hendrickson WA. Structure of a C-type mannose-binding protein complexed with an oligosaccharide. Nature 1992;360:127-134.
40. Monzingo AF, Matthews BW. Binding of N-carboxymethyl dipeptide inhibitors to thermolysin determined by X-ray crystallography: a novel class of transition-state analogues for zinc peptidases. Biochemistry 1984;23:5724-5729.
41. Hausrath AC, Matthews BW. Redetermination and refinement of the complex of benzylsuccinic acid with thermolysin and its relation to the complex with carboxypeptidase A. J Biol Chem 1994;269:18839-18842.
42. Holland DR, Tronrud DE, Pley HW, Flaherty KM, Stark W, Jansonius JN, McKay DB, Matthews BW. Structural comparison suggests that thermolysin and related neutral proteases undergo hinge-bending motion during catalysis. Biochemistry 1992;31:11310-11316.
43. Stark W, Pauptit RA, Wilson KS, Jansonius JN. The structure of neutral protease from Bacillus cereus at 0.2-nm resolution. Eur J Biochem 1992;207:781-791.
44. Emsley J, White HE, O'Hara BP, Oliva G, Srinivasan N, Tickle IJ, Blundell TL, Pepys MB, Wood SP. Structure of pentameric human serum amyloid P component. Nature 1994;367:338-345.
45. Teplyakov A, Polyakov K, Obmolova G, Strokopytov B, Kuranova I, Osterman A, Grishin N, Smulevitch S, Zagnitko O, Galperina O, et al. Crystal structure of carboxypeptidase T from Thermoactinomyces vulgaris. Eur J Biochem 1992;208:281-288.
46. Hohenester E, Maurer P, Hohenadl C, Timpl R, Jansonius JN, Engel J. Structure of a novel extracellular Ca(2+)-binding module in BM-40. Nat Struct Biol 1996;3:67-73.
47. Stein PE, Leslie AG, Finch JT, Carrell RW. Crystal structure of uncleaved ovalbumin at 1.95 A resolution. J Mol Biol 1991;221:941-959.
48. 2+, and the inhibitor pdTp, refined at 1.65 A. Proteins 1989;5:183-201.
49. Bott R, Ultsch M, Kossiakoff A, Graycar T, Katz B, Power S. The three-dimensional structure of Bacillus amyloliquefaciens subtilisin at 1.8 A and an analysis of the structural consequences of peroxide inactivation. J Biol Chem 1988;263:7895-7906.
50. Essen LO, Perisic O, Katan M, Wu Y, Roberts MF, Williams RL. Structural mapping of the catalytic mechanism for a mammalian phosphoinositide-specific phospholipase C. Biochemistry 1997;36:1704-1718.
51. Xie X, Harrison DH, Schlichting I, Sweet RM, Kalabokis VN, Szent-Gyorgyi AG, Cohen C. Structure of the regulatory domain of scallop myosin at 2.8 A resolution. Nature 1994;368:306-312.
52. Singh TP, Sharma S, Karthikeyan S, Betzel C, Bhatia KL. Crystal structure of a complex formed between proteolytically-generated lactoferrin fragment and proteinase K. Proteins 1998;33:30-38.
53. Hoover DM, Ludwig ML. A flavodoxin that is required for enzyme activation: the structure of oxidized flavodoxin from Escherichia coli at 1.8 A resolution. Protein Sci 1997;6:2525-2537.
54. Glusker JP. Structural aspects of metal liganding to functional groups in proteins. Adv Protein Chem 1991;42:1-76.
55. Linse S, Forsen S. Determinants that govern high-affinity calcium binding. Adv Second Messenger Phosphoprotein Res 1995;30:89-151.
56. Prod'hom B, Karplus M. The nature of the ion binding interactions in EF-hand peptide analogs: free energy simulation of Asp to Asn mutations. Protein Eng 1993;6:585-592.
57. Marsden BJ, Shaw GS, Sykes BD. Calcium binding proteins. Elucidating the contributions to calcium affinity from an analysis of species variants and peptide fragments. Biochem Cell Biol 1990;68:587-601.
58. Khalili M, Saunders JA, Liwo A, Oldziej S, Scheraga HA. A united residue force-field for calcium-protein interactions. Protein Sci 2004;13:2725-2735.