Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach

BMC Bioinformatics

Volumn 7, Issue SUPPL.5, 2006, Pages

  Lin, Hong Huang ^a   Han, L Y ^a   Zhang, H L ^a   Zheng, C J ^a   Xie, B ^a   Cao, Z W ^b   Chen, Y Z ^a,b  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

METABOLISM CONTROLS; METAL BINDING DOMAIN; METAL-BINDING PROTEIN; PHYSICOCHEMICAL PROPERTY; PREDICTION ACCURACY; SEQUENCE DIVERSITY; SEQUENCE SIMILARITY; STRUCTURAL STABILITIES; CALCIUM BINDING; COPPER BINDING; FUNCTIONAL CLASS; IMMUNE RESPONSE; INDEPENDENT SET; IRON BINDING; KERNEL FUNCTION; METAL HOMEOSTASIS; PREDICTION SYSTEMS; SWISS-PROT;

ENZYME ACTIVITY; FORECASTING; METALS; PROTEINS; STABILITY; SUPPORT VECTOR MACHINES; BIOINFORMATICS; COBALT; MAGNESIUM; MANGANESE; SODIUM;

COPPER;

CALCIUM; COBALT; COPPER; IRON; MAGNESIUM; MANGANESE; NICKEL; POTASSIUM; SODIUM; ZINC; CARRIER PROTEIN; METAL; PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; CALCIUM BINDING; COMPUTER PROGRAM; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; INTERNET; METAL BINDING; NONHUMAN; PHYSICAL CHEMISTRY; PREDICTION; PROTEIN DOMAIN; PROTEIN FUNCTION; SENSITIVITY AND SPECIFICITY; SEQUENCE HOMOLOGY; SUPPORT VECTOR MACHINE; UNINDEXED SEQUENCE; ALGORITHM; ANIMAL; CHEMISTRY; CLASSIFICATION; EVALUATION; HUMAN; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS; STRUCTURAL HOMOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; CARRIER PROTEINS; HUMANS; METALS; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 33947407691     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-S5-S13     Document Type: Article

References (73)

1. Wintz H, Fox T, Wu YY, Feng V, Chen W, Chang HS, Zhu T, Vulpe C: Expression profiles of Arabidopsis thaliana in mineral deficiencies reveal novel transporters involved in metal homeostasis. J Biol Chem 2003, 278(48):47644-47653.
2. Cox EH, McLendon GL: Zinc-dependent protein folding. Curr Opin Chem Biol 2000, 4(2):162-165.
3. Michel SL, Berg JM: Building a metal binding domain, one half at a time. Chem Biol 2002, 9(6):667-668.
4. de la Calle Guntinas MB, Bordin G, Rodriguez AR: Identification, characterization and determination of metal-binding proteins by liquid chromatography. A review. Anal Bioanal Chem 2002, 374(3):369-378.
5. Yang W, Lee HW, Hellinga H, Yang JJ: Structural analysis, identification, and design of calcium-binding sites in proteins. Proteins 2002, 47(3):344-356.
6. Jensen MR, Petersen G, Lauritzen C, Pedersen J, Led JJ: Metal binding sites in proteins: Identification and characterization by paramagnetic NMR relaxation. Biochemistry 2005, 44(33):11014-11023.
7. Wu H, Yang Y, Jiang SJ, Chen LL, Gao HX, Fu QS, Li F, Ma BG, Zhang HY: DCCP and DICP: Construction and analyses of databases for copper- and iron-chelating proteins. Genomics Proteomics Bioinformatics 2005, 3(1):52-57.
8. Hantke K: Iron and metal regulation in bacteria. Curr Opin Microbiol 2001, 4(2):172-177.
9. Bouton CM, Pevsner J: Effects of lead on gene expression. Neurotoxicology 2000, 21(6):1045-1055.
10. Feng M, Patel D, Dervan JJ, Ceska T, Suck D, Haq I, Sayers JR: Roles of divalent metal ions in flap endonuclease-substrate interactions. Nat Struct Mol Biol 2004, 11(5):450-456.
11. Carafoli E: CAlcium signaling: a tale for all seasons. Proc Natl Acad Sci U S A 2002, 99(3):1115-1122.
12. Harris ED: Cellular copper transport and metabolism. Annu Rev Nutr 2000, 20:291-310.
13. O'Halloran TV, Culotta VC: Metallochaperones, an intracellular shuttle service for metal ions. J Biol Chem 2000, 275(33):25057-25060.
14. Vallee BL, Auld DS: Active-site zinc ligands and activated H2O of zinc enzymes. Proc Natl Acad Sci U S A 1990, 87(1):220-224.
15. Cobbett C, Goldsbrough P: PhytoRhelatins and metallothioneins: roles in heavy metal detoxification and homeostasis. Annu Rev Plant Biol 2002, 53:159-182.
16. Papoyan A, Kochian LV: Identification of Thlaspi caerulescens genes that may be involved in heavy metal hyperaccumulation and tolerance. Characterization of a novel heavy metal transporting ATPase. Plant Physiol 2004, 136(3):3814-3823.
17. Zhou T, Hamer DH, Hendrickson WA, Sattentau QJ, Kwong PD: Interfacial metal and antibody recognition. Proc Natl Acad Sci U S A 2005, 102(41):14575-14580.
18. Lieu PT, Heiskala M, Peterson PA, Yang Y: The roles of iron in health and disease. Mol Aspects Med 2001, 22(1-2):1-87.
19. Barondeau DP, Getzoff ED: Structural insights into proteinmetal ion partnerships. Curr Opin Struct Biol 2004, 14(6):765-774.
20. Sandier A, Amiel C, Sebille B, Rouchaud JC, Fedoroff M, Soltes L: Chromatographic method involving inductively coupled plasma atomic emission spectrometric detection for the study of metal-protein complexes. J Chromatogr A 1997, 776(1):93-100.
21. Reed GH, Poyner RR: Mn2+ as a probe of divalent metal ion binding and function in enzymes and other proteins. Met Ions Biol Syst 2000, 37:183-207.
22. Binet MR, Ma R, McLeod CW, Poole RK: Detection and characterization of zinc- and cadmium-binding proteins in Escherichia coli by gel electrophoresis and laser ablation-inductively coupled plasma-mass spectrometry. Anal Biochem 2003, 318(1):30-38.
23. Herald VL, Heazlewood JL, Day DA, Millar AH: Proteomic identification of divalent metal cation binding proteins in plant mitochondria. FEBS Lett 2003, 537(1-3):96-100.
24. Schnepf R, Haehnel W, Wieghardt K, Hildebrandt P: Spectroscopic identification of different types of copper centers generated in synthetic four-helix bundle proteins. J Am Chem Soc 2004, 126(44):14389-14399.
25. Gregory DS, Martin AC, Cheetham JC, Rees AR: The prediction and characterization of metal binding sites in proteins. Protein Eng 1993, 6(1):29-35.
26. Andreini C, Banci L, Bertini I, Rosato A: Counting the zinc-proteins encoded in the human genome. J Proteome Res 2006, 5(1):196-201.
27. 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(1):307-320.
28. Nayal M, Di Cera E: Predicting Ca(2+)-binding sites in proteins. Proc Natl Acad Sci U S A 1994, 91(2):817-821.
29. Schymkowitz JW, Rousseau F, Martins IC, Ferkinghoff-Borg J, Stricher F, Serrano L: Prediction of water and metal binding sites and their affinities by using the Fold-X force field. Proc Natl Acad Sci U S A 2005, 102(29):10147-10152.
30. Khalili M, Saunders JA, Liwo A, Oldziej S, Scheraga HA: A united residue force-field for calcium-protein interactions. Protein Sci 2004, 13(10):2725-2735.
31. EAtema TJ, Huynen MA, de Vos WM, van der Oost J: TRASH: a novel metal-binding domain predicted to be involved in heavy-metal sensing, trafficking and resistance. Trends Biochem Sci 2003, 28(4):170-173.
32. Rigden DJ, Galperin MY: The DxDxMG motif for calcium binding: multiple structural contexts and implications for evolution. J Mol Biol 2004, 343(4):971-984.
33. Lin CT, Lin KL, Yang CH, Chung IF, Huang CD, Yang YS: Protein metal binding residue prediction based on neural networks. Int J Neural Syst 2005, 15(1-2):71-84.
34. Birch PJ, Dekker LV, James IF, Southan A, Cronk D: Strategies to identify ion channel modulators: Current and novel approaches to target neuropathic pain. Drug Discov Today 2004, 9(9):410-418.
35. Cai YD, Lin SL: Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence. Biochim Biophys Acta 2003, 1648(1-2):127-133.
36. Lin HH, Han LY, Zhang HL, Zheng CJ, Xie B, Chen YZ: Prediction of the functional class of lipid-binding proteins from sequence derived properties irrespective of sequence similarity. J Lipid Res 2006, 47(4):824-831.
37. Lin HH, Han LY, Cai CZ, Ji ZL, Chen YZ: Prediction of transporter family from protein sequence by support vector machine approach. Proteins 2006, 62(1):218-231.
38. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL: The Pfam protein families database. Nucleic Acids Res 2002, 30(1):276-280.
39. Frausto da Silva JJR, Williams RJP: The biological chemistry of the elements: The inorganic chemistry of life. New York: Oxford University Press; 1991.
40. Fierro-Monti I, Mathews MB: Oroteins binding to duplexed RNA: one motif, multiple functions. Trends Biochem Sci 2000, 25(5):241-246.
41. Perez-Canadillas JM, Varani G: Recent advances in RNA-protein recognition. Curr Opin Struct Biol 2001, 11(1):53-58.
42. Bairoch A, Apweiler R: The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 2000, 28(1):45-48.
43. Veropoulos K, Campbell C, Cristianini N: Controlling the sensitivity of Support Vector machines. In Proceedings of the International Joint Conference on Artificial Intelligence (UCAI99) Edited by: Dean T. Sweden: Morgan Kaufmann; 1999:55-60.
44. Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M Jr, Haussler D: Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A 2000, 97(1):262-267.
45. Han LY, Cai CZ, Ji ZL, Cao ZW, Cui J, Chen YZ: Predicting functional family of novel enzymes irrespective of sequence similarity: A statistical learning approach. Nucleic Acids Res 2004, 32(21):6437-6444.
46. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PAI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402.
47. Skirgaila R, Grazulis S, Bozic D, Huber R, Siksnys V: Structure-based redesign of the catalytic/metal binding site of Cfr10I restriction endonuclease reveals importance of spatial rather than sequence conservation of active centre residues. J Mol Biol 1998, 279(2):473-481.
48. Thickman KR, Davis A, Berg JM: Site selection in tandem arrays of metal-binding domains. Inorg Chem 2004, 43(25):7897-7901.
49. Ledwidge R, Patel B, Dong A, Fiedler D, Falkowski M, Zelikova J, Summers AO, Pai EF, Miller SM: NmerA, the metal binding domain of mercuric ion reductase, removes Hg2+ from proteins, delivers it to the catalytic core, and protects cells under glutathione-depleted conditions. Biochemistry 2005, 44(34):11402-11416.
50. Evans RMG Hollenberg SM: Zinc fingers: gilt by association. Cell 1988, 52(1):1-3.
51. Grabarek Z: Structural basis for diversity of the EF-hand calcium-binding proteins. J Mol Biol 2006, 359(3):509-525.
52. Sweeney WV, Rabinowitz JC: ProtAins containing 4Fe-4S clusters: an overview. Annu Rev Biochem 1980, 49:139-161.
53. Laity JH, Lee BMN Wright PE: Zinc finger proteins: new insights into structural and functional diversity. Curr Opin Struct Biol 2001, 11(1):39-46.
54. Barrera FN, Poveda JA, Gonzalez-Ros JM, Neira JL: Binding of the C-terminal sterile alpha motif (SAM) domain of human p73 to lipid membranes. J Biol Chem 2003, 278(47):46878-46885.
55. Chang S, ran Ma T, Miranda RD, Balestra ME, Mahley RW, Huang Y: Lipid- and receptor-binding regions of apolipoprotein E4 fragments act in concert to cause mitochondrial dysfunction and neurotoxicity. Proc Natl Acad Sci U S A 2005, 102(51):18694-18699.
56. Chen MH, Ben-Efraim I, Mitrousis G, Walker-Kopp N, Sims PJ, Cingolani G: Phospholipid scramblase 1 contains a nonclassical nuclear localization signal with unique binding site in importin alpha. J Biol Chem 2005, 280(11):10599-10606.
57. Vishwanathan SVN, Smola AJ: Fast Kernels for String and Tree Matching. In Proceedings of Neural Information Processing Systems 2002 2002.
58. Ratsch G, Sonnenburg S, Scholkopf B: RASE: recognition of alternatively spliced exons in C.elegans. Bioinformatics 2005, 21(Suppl 1):i369-i377.
59. Kuang R, Ie E, Wang K, Wang K, Siddiqi M, Freund Y, Leslie C: Profile-based string kernels for remote homology detection and motif extraction. J Bioinform Comput Biol 2005, 3(3):527-550.
60. Leslie C, Kuang R, Eskin E: Inexact matching string kernels for protein classification. In Kernel Methods in Computational Biology Cambridge: MIT Press; 2003:95-112.
61. Han LY, Cai CZ, Lo SL, Chung MC, Chen YZ: Prediction of RNA-binding proteins from primary sequence by a support vector machine approach. Rna 2004, 10(3):355-368.
62. Ding CH, Dubchak I: Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics 2001, 17(4):349-358.
63. Hunt JA, Ahmed M, Fierke CA: Metal binding specificity in carbonic anhydrase is influenced by conserved hydrophobic core residues. Biochemistry 1999, 38(28):9054-9062.
64. Rapisarda VA, Chehin RN, De Las Rivas J, Rodriguez-Montelongo L, Farias RN, Massa EM: Evidence for Cu(I)-thiolate ligation and prediction of a putative copper-binding site in the Escherichia coli NADH dehydrogenase-2. Arch Biochem Biophys 2002, 405(1):87-94.
65. Abbott JJ, Pei J, Ford JL, Qi Y, Grishin VN, Pitcher LA, Phillips MA, Grishin NV: Structure prediction and active site analysis of the metal binding determinants in gamma -glutamylcysteine synthetase. J Biol Chem 2001, 276(45):42099-42107.
66. Maglio O, Nastri F, Calhoun JR, Lahr S, Wade H, Pavone V, DeGrado WF, Lombardi A: Artificial Si-iron proteins: solution characterization of four helix bundles containing two distinct types of inter-helical loops. J Biol Inorg Chem 2005, 10(5):539-549.
67. SVMProt Server [http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi]
68. Cai CZ, Han LY, Ji ZL, Chen X, Chen YZ: SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res 2003, 31(13):3692-3697.
69. Cai CZ, Han LY, Ji ZL, Chen YZ: Enzyme family classification by support vector machines. Proteins 2004, 55(1):66-76.
70. Bock JR, Gough DA: Predicting protein - protein interactions from primary structure. Bioinformatics 2001, 17(5):455-460.
71. Cai YD, Liu XJ, Xu XB, Chou KC: Support Vector Machines for predicting HIV protease cleavage sites in protein. J Comput Chem 2002, 23(2):267-274.
72. Cai YD, Liu XJ, Xu XB, Chou KC: Prediction of protein structural classes by support vector machines. Comput Chem 2002, 26(3):293-296.
73. Burges CJC: A tutorial on support vector machine for pattern recognition. Data Min Knowl Disc 1998, 2:121-167.