Metalloproteins: Structure, conservation and prediction of metal binding sites

Structural Proteomics and its Impact on the Life Sciences

Volumn , Issue , 2008, Pages 181-205

  Edelman, Marvin ^a   Babor, Mariana ^a   Levy, Ronen ^a   Sobolev, Vladimir ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84967683932     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1142/9789812772053_0008     Document Type: Chapter

References (47)

1. Friedberg I, Jambon M, Godzik A. (2006) "New avenues in protein function prediction." Prot Sci 15: 1527-29.
2. Ibers JA, Holm RH. (1980) "Modeling coordination sites in metallobiomolecules." Science 209: 223-35.
3. Tainer JA, Roberts VA, Getzoff ED. (1992) "Protein metal-binding sites." Curr Opin Biotechnol 3: 378-87.
4. Williams RJ. (1985) 16th Sir Hans Krebs lecture. The symbiosis of metal and protein functions. Eur J Biochem 150: 231-48.
5. Bernstein FC, Koetzle TF, Williams GJB, et al. (1977) "Protein data bank - computer-based archival file for macromolecular structures." J Mol Biol 112: 535-42.
6. Yamashita MM, Wesson L, Eisenman G, Eisenberg D. (1990) "Where MetalIons Bind in Proteins." Proc Natl Acad Sci USA 87: 5648-52.
7. Gregory DS, Martin AC, Cheetham JC, Rees AR. (1993). "The prediction and characterization of metal binding sites in proteins." Prot Eng 6: 29-35.
8. Andreini C, Bertini I, Rosato A. (2004) "A hint to search for metalloproteins in gene banks." Bioinformatics 20: 1373-80.
9. Sodhi JS, Bryson K, McGuffin LJ, et al. (2004) "Predicting metal-binding site residues in low-resolution structural models." J Mol Biol 342: 307-20.
10. Lin CT, Lin KL, Yang CH, et al. (2005) "Protein metal binding residue prediction based on neural networks." Int JNeur Sys 15: 71-84.
11. Schymkowitz JW, Rousseau F, Martins IC, et al. (2005) "Prediction of water and metal binding sites and their affinities by using the Fold-X force field." Proc Natl Acad Sci USA 102: 10147-52.
12. Babor M, Gerzon S, Raveh B, et al. (2007) "Prediction of transition metal binding sites from apo protein structures." Proteins, in press.
13. Lin HH, Han LY, Zhang HL, et al. (2006) "Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach." BMC Bioinform 7(5); S13.
14. Babor M, Greenblatt HM, Edelman M, Sobolev V. (2005). "Flexibility of metal binding sites in proteins on a database scale." Proteins 59: 221-30.
15. Alberts IL, Nadassy K, Wodak SJ. (1998) "Analysis of zinc binding sites in protein crystal structures." Prot Sci 7: 1700-16.
16. Auld DS. (2001) "Zinc coordination sphere in biochemical zinc sites." Biometals 14: 271-313.
17. Dudev T, Lin YL, Dudev M, Lim C. (2003) "First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations." JAmer Chem Soc 125: 3168-80.
18. Tamames B, Sousa SF, Tamames J, et al. (2007) "Analysis of zinc-ligand bond lemgths in metalloproteins: trends and patterns." Proteins (in press).
19. Bock CW, Katz AK, Markham GD, Glusker JP. (1999) "Manganese as a replacement for magnesium and zinc: functional comparison of the divalent ions." J Amer Chem Soc 121: 7360-72.
20. Glusker JP. (1991) "Structural aspects of metal liganding to functional-groups in proteins." Adv Prot Chem 42: 1-76.
21. Katz AK, Glusker JP, Beebe SA, Bock CW. (1996) "Calcium ion coordination: a comparison with that of beryllium, magnesium, and zinc." J Amer Chem Soc 118:5752-63.
22. Chakrabarti P. (1990) "Interaction of metal-ions with carboxylic and carboxamide groups in protein structures." Prot Eng 4: 49-56.
23. Harding MM. (2001) "Geometry ofmetal-ligand interactions in proteins." Acta Cryst Sec D 57: 401-11.
24. Chakrabarti P. (1990) "Geometry of interaction of metal-ions with histidine residues in protein structures." Prot Eng 4: 57-63.
25. Ouzounis C, Pérez-Irratxeta C, Sander C, Valencia A. (1998) "Are binding residues conserved?" Pac Symp Biocomput 3: 401-12.
26. Janin J, Wodak SJ. (1983) "Structural domains in proteins and their role in the dynamics of protein function." Progr Biophys Mol Biol 42: 21-78.
27. Feinberg H, Greenblatt HM, Shoham G. (1993) "Structural studies of the activesite metal in metalloenzymes." J Chem Inf Comp Sci 33: 501-16.
28. Bruns CM, Anderson DS, Vaughan KG, et al. (2001) "Crystallographic and biochemical analyses of the metal-free Haemophilus influenzae Fe3+ -binding protein." Biochemistry 40: 15631-37.
29. Chakrabarti P. (1989) "Geometry of interaction of metal-ions with sulfur containing ligands in protein structures." Biochemistry 28: 6081-85.
30. Sobolev V, Sorokine A, Prilusky J, et al. (1999). "Automated analysis of interatomic contacts in proteins." Bioinformatics 15: 327-32.
31. Maret W. (2005) "Zinc coordination environments in proteins determine zinc functions." J Trace Elem Med Biol 19: 7-12.
32. Murzin AG, Brener SE, Hubbard T, Chothia C. (1995) "SCOP: a structural classification of protein database for the investigation of sequences and structures." J Mol Biol 247: 536-40.
33. Guerois R, Nielsen JE, Serrano L. (2002) "Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations." J Mol Biol 320: 369-87.
34. Andreini C, Banci L, Bertini I, Rosato A. (2006) "Counting the zinc-proteins encoded in the human genome." JProteome Res 5: 196-201.
35. Dunbrack RL, Cohen FE. (1997) "Bayesian statistical analysis of protein side chain rotamer preferences." Prot Sci 6: 1661-81.
36. Bondi A. (1964) "Van der Waals volumes and radii." JPhys Chem 68: 441-51.
37. Breiman L, Friedman J, Stone CJ, Olshen RA. (1998) "Classification and Regression Trees." CRC Press, Boca Raton.
38. Chapelle O, Haffner P, Vapnik VN. (1999) "Support vector machines for histogram-based image classification." IEEE Trans Neural Net 10: 1055-64.
39. Scholkopf B, Smola AJ, Williamson RC, Barlett PL. (2000) "New support vector algorithms." Neural Comput 12: 1207-45.
40. Sander C, Schneider R. (1991) "Database of homology-derived protein structures and the structural meaning of sequence alignment." Proteins 9: 56-68.
41. Mirny L, Shakhnovich E. (2001) "Evolutionary conservation of the folding nucleus." J Mol Biol 308: 123-29.
42. Sobolev V, Eyal E, Gerzon S, et al. (2005) "SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment." Nucl Acids Res 33: W39-43.
43. Wang G, Dunbrack RL. (2003) "PISCES: a protein sequence culling server." Bioinformatics 19: 1589-91.
44. Marti-Renom MA, Stuart A, Fiser A, et al. (2000) "Comparative protein structure modeling of genes and genomes." Ann Rev Biophys Biomol Struct 29: 291-325.
45. Schwede T, Kopp J, Guex N, Peitsch MC. (2003) "SWISS-MODEL: an automated protein homology-modeling server." Nucl Ac Res 31: 3381-85.
46. Eyal E, Najmanovich R, McConkey BJ, et al. (2004) "Importance of solvent accessibility and contact surfaces in modeling side-chain conformation in proteins." J Comp Chem 25: 712-24.
47. Canutescu AA, Dunbrack RL. (2005) "MollDE: a homology modeling framework you can click with." Bioinformatics 21: 2914-16.