Metal-binding sites are designed to achieve optimal mechanical and signaling properties

Structure

Volumn 18, Issue 9, 2010, Pages 1140-1148

  Dutta, Anindita ^a   Bahar, Ivet ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

METAL ION;

ALLOSTERISM; ARTICLE; BINDING SITE; METAL BINDING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; SIGNAL TRANSDUCTION;

BINDING SITES; MARKOV CHAINS; METALLOPROTEINS; METALS; MODELS, MOLECULAR; PROTEIN CONFORMATION; SIGNAL TRANSDUCTION; SOLVENTS;

EID: 77956309711     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2010.06.013     Document Type: Article

References (36)

1. Auld D.S. Zinc coordination sphere in biochemical zinc sites. Biometals 2001, 14:271-313.
2. Babor M., Gerzon S., Raveh B., Sobolev V., Edelman M. Prediction of transition metal-binding sites from apo protein structures. Proteins 2008, 70:208-217.
3. Bahar I., Atilgan A.R., Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold. Des. 1997, 2:173-181.
4. Bahar I., Chennubhotla C., Tobi D. Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation. Curr. Opin. Struct. Biol. 2007, 17:633-640.
5. Bahar I., Lezon T.R., Bakan A., Shrivastava I.H. Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem. Rev. 2010, 110:1463-1497.
6. Bakan A., Bahar I. The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc. Natl. Acad. Sci. USA 2009, 106:14349-14354.
7. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 2000, 28:235-242.
8. Calhoun J.R., Liu W., Spiegel K., Dal Peraro M., Klein M.L., Valentine K.G., Wand A.J., DeGrado W.F. Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement. Structure 2008, 16:210-215.
9. Castagnetto J.M., Hennessy S.W., Roberts V.A., Getzoff E.D., Tainer J.A., Pique M.E. MDB: the Metalloprotein Database and Browser at The Scripps Research Institute. Nucleic Acids Res. 2002, 30:379-382.
10. Chennubhotla C., Bahar I. Signal propagation in proteins and relation to equilibrium fluctuations. PLoS Comput. Biol. 2007, 3:1716-1726.
11. Chennubhotla C., Yang Z., Bahar I. Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL. Mol. Biosyst. 2008, 4:287-292.
12. Cui Q., Bahar I. Normal mode analysis: theory and applications to biological and chemical systems 2006, Chapman & Hall/CRC, London, UK.
13. Ebert J.C., Altman R.B. Robust recognition of zinc binding sites in proteins. Protein Sci. 2008, 17:54-65.
14. Eisenmesser E.Z., Millet O., Labeikovsky W., Korzhnev D.M., Wolf-Watz M., Bosco D.A., Skalicky J.J., Kay L.E., Kern D. Intrinsic dynamics of an enzyme underlies catalysis. Nature 2005, 438:117-121.
15. Eyal E., Najmanovich R., McConkey B.J., Edelman M., Sobolev V. Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins. J. Comput. Chem. 2004, 25:712-724.
16. Geremia S., Di Costanzo L., Randaccio L., Engel D.E., Lombardi A., Nastri F., DeGrado W.F. Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography. J. Am. Chem. Soc. 2005, 127:17266-17276.
17. Golovin A., Dimitropoulos D., Oldfield T., Rachedi A., Henrick K. MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites. Proteins 2005, 58:190-199.
18. Gourley D.G., Schuttelkopf A.W., Anderson L.A., Price N.C., Boxer D.H., Hunter W.N. Oxyanion binding alters conformation and quaternary structure of the c-terminal domain of the transcriptional regulator mode. Implications for molybdate-dependent regulation, signaling, storage, and transport. J. Biol. Chem. 2001, 276:20641-20647.
19. Haliloglu T., Bahar I., Erman B. Gaussian Dynamics of Folded Proteins. Phys. Rev. Lett. 1997, 79:3090-3093.
20. Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 1998, 33:417-429.
21. Hinsen K., Petrescu A.-J., Dellerue S., Bellissent-Funel M.-C., Kneller G.R. Harmonicity in slow protein dynamics. Chem. Phys. 2000, 261:25-37.
22. Jain E., Bairoch A., Duvaud S., Phan I., Redaschi N., Suzek B.E., Martin M.J., McGarvey P., Gasteiger E. Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics 2009, 10:136.
23. Kendrik M.J., Plishka M.J., Robinson K.D. Metals in Biological Systems 1992, Prentice Hall Professional Technical Reference, New York.
24. Kundu S., Melton J.S., Sorensen D.C., Phillips G.N. Dynamics of proteins in crystals: comparison of experiment with simple models. Biophys. J. 2002, 83:723-732.
25. Lange O.F., Lakomek N.A., Fares C., Schroder G.F., Walter K.F., Becker S., Meiler J., Grubmuller H., Griesinger C., de Groot B.L. Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science 2008, 320:1471-1475.
26. Lin C.T., Lin K.L., Yang C.H., Chung I.F., Huang C.D., Yang Y.S. Protein metal binding residue prediction based on neural networks. Int. J. Neural Syst. 2005, 15:71-84.
27. Lin H.H., Han L.Y., Zhang H.L., Zheng C.J., Xie B., Cao Z.W., Chen Y.Z. Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach. BMC Bioinformatics 2006, 7(Suppl 5):S13.
28. McConkey B.J., Sobolev V., Edelman M. Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure. Bioinformatics 2002, 18:1365-1373.
29. Nicolay S., Sanejouand Y.H. Functional modes of proteins are among the most robust. Phys. Rev. Lett. 2006, 96:078104.
30. Passerini A., Punta M., Ceroni A., Rost B., Frasconi P. Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins 2006, 65:305-316.
31. Passerini A., Andreini C., Menchetti S., Rosato A., Frasconi P. Predicting zinc binding at the proteome level. BMC Bioinformatics 2007, 8:39.
32. Tainer J.A., Roberts V.A., Getzoff E.D. Protein metal-binding sites. Curr. Opin. Biotechnol. 1992, 3:378-387.
33. Tama F., Brooks C.L. Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annu. Rev. Biophys. Biomol. Struct. 2006, 35:115-133.
34. Tirion M.M. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 1996, 77:1905-1908.
35. Tobi D., Bahar I. Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc. Natl. Acad. Sci. USA 2005, 102:18908-18913.
36. Yang L.W., Bahar I. Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure 2005, 13:893-904.