Determination of network of residues that regulate allostery in protein families using sequence analysis

Protein Science

Volumn 15, Issue 2, 2006, Pages 258-268

  Dima, Ruxandra I ^a   Thirumalai, D ^b  

^a University of Massachusetts Lowell   (United States)

^b Bldg 142   (United States)

Author keywords

Evolutionary relationships; Protein families; Proteomics; Structure

Indexed keywords

CELL ADHESION MOLECULE; G PROTEIN COUPLED RECEPTOR; LECTIN; MEMBRANE RECEPTOR; PDZ PROTEIN;

ALGORITHM; ALLOSTERISM; AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; CARBOXY TERMINAL SEQUENCE; DYNAMICS; ENDOTHELIUM; ENTROPY; INFLAMMATION; LEUKOCYTE; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS;

ALGORITHMS; ALLOSTERIC REGULATION; AMINO ACIDS; BINDING SITES; GTP-BINDING PROTEINS; HUMANS; LECTINS; LIGANDS; MODELS, MOLECULAR; MULTIGENE FAMILY; MUTATION; PROTEIN BINDING; PROTEIN CONFORMATION; RECEPTORS, CELL SURFACE; RECEPTORS, G-PROTEIN-COUPLED; SEQUENCE ANALYSIS, PROTEIN; SIGNAL TRANSDUCTION;

EID: 31344432159     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.051767306     Document Type: Article

References (37)

1. Altschuh, D., Lesk, A.M., Bloomer, A.C., and Klug, A. 1987. Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus. J. Mol. Biol. 193: 693-707.
2. Appel, R.D., Bairoch, A., and Hochstrasser, D.F. 1994. A new generation of information retrieval tools for biologists: The example of the ExPASy WWW server. Trends Biochem. Sci. 19: 258-260.
3. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffith-Jones, S., Howe, K.L., Marshall, M., and Sonnhammer, E.L. 2002. The Pfam protein families database. Nucleic Acids Res. 30: 276-280.
4. Blatt, M., Wiseman, S., and Domany, E. 1996. Superparamagnetic clustering of data. Phys. Rev. Lett. 76: 3251-3254.
5. Creighton, T.E. 1993. Proteins: Structures and molecular properties. W.H. Freeman and Company, New York.
6. Dima, R.I. and Thirumalai, D. 2004. Proteins associated with diseases show enhanced sequence correlation between charged residues. Bioinformatics 20: 2345-2354.
7. Domany, E. 1999. Superparamagnetic clustering of data-The definitive solution of an ill-poised problem. Physica A 263: 158-169.
8. Fodor, A. and Aldrich, R.W. 2004a. Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins 56: 211-221.
9. _. 2004b. On evolutionary conservation of thermodynamic coupling in proteins. J. Biol. Chem. 279: 19046-19050.
10. Getz, G., Levine, E., and Domany, E. 2000. Coupled two-way clustering analysis of gene microarray data. Proc. Natl. Acad. Sci. 97: 12079-12084.
11. Hatley, M.E., Lockless, S.W., Gibson, S.K., Gilman, A.G., and Ranganathan, R. 2003. Allosteric determinants in guanine nucleotide-binding proteins. Proc. Natl. Acad. Sci. 100: 14445-14450.
12. Higgins, D., Thompson, J., Gibson, T., Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
13. Horovitz, A., Fridmann, Y., Kafri, G., and Yifrach, O. 2001. Allostery in chaperonins. J. Struct. Biol. 135: 104-114.
14. Hulo, N., Sigrist, C.J.A., Saux, V.L., Langendijk-Genevaux, P., Bordoli, L., Gattiker, A., Castro, E.D., Bucher, P., and Bairoch, A. 2004. Recent improvements to the PROSITEdatabase. Nucleic Acids Res. 32: D134-D137.
15. Humphrey, W., Dalke, A., and Schulten, K. 1996. VMD-Visual Molecular Dynamics. J. Mol. Graph. 14: 33-38.
16. Kass, I. and Horovitz, A. 2002. Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations. Proteins 48: 611-617.
17. Kern, D. and Zuiderweg, E.R. 2003. The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 13: 748-757.
18. Lesk, A.M. and Chothia, C. 1980. How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins. J. Mol. Biol. 136: 225-270.
19. Lichtarge, O., Bourne, H.R., and Cohen, F.E. 1996. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257: 342-358.
20. Lockless, S.W. and Ranganathan, R. 1999. Evolutionary conserved pathways of energetic connectivity in protein families. Science 286: 295-299.
21. Monod, J., Wyman, J., and Changeux, J.P. 1965. On the nature of allosteric transitions: A plausible model. J. Mol. Biol. 12: 88-118.
22. Neher, E. 1994. How frequent are correlated changes in families of protein sequences? Proc. Natl. Acad. Sci. 91: 98-102.
23. Olmea, O., Rost, B., and Valencia, A. 1999. Effective use of sequence correlation and conservation in fold recognition. J. Mol. Biol. 295: 1221-1239.
24. Pazos, F., Helmer-Citterich, M., Ausiello, G., and Valencia, A. 1997. Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 271: 511-523.
25. Perutz, M.F., Wilkinson, A.J., Paoli, M., and Dobson, G.G. 1998. Stereochemistry of cooperative mechanisms in hemoglobin revisited. Annu. Rev. Biophys. Biomol. Struct. 27: 1-34.
26. Pollock, D.D. and Taylor, W.R. 1997. Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng. 10: 647-657.
27. Schreiber, G. and Fersht, A.R. 1995. Energetics of protein-protein interactions: Analysis of the barnase-barstar interface by single mutations and double mutant cycles. J. Mol. Biol. 248: 478-486.
28. Shulman, A.J., Larson, C., Mangelsdorf, D.J., and Ranganathan, R. 2004. Structural determinants of allosteric ligand activation in RXR heterodimers. Cell 116: 417-429.
29. Somers,W.S.,Tang, J., Shaw,G.D., andCamphausen,R.T. 2000. Insights into themolecular basis of leukocyte tethering and rolling revealed by structures of P- and E-Selectin bound to SLex and PSGL-1. Cell 103: 467-479.
30. Sowa, M.E., Hen, W., Slep, K.C., Kercher, M.A., Lichtarge, O., and Wensel, T.G. 2001. Prediction and confirmation of a site critical for effector regulation of RGS domain activity. Nat. Struct. Biol. 8: 234-237.
31. Steitz, T.A. 1999. DNA polymerases: Structural diversity and common mechanisms. J. Biol. Chem. 274: 17395-17398.
32. Suel, G.M., Lockless, S.W., Wall, M.A., and Ranganathan, R. 2003. Evolutionary conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10: 59-69.
33. Taylor, W.R. and Hatrick, K. 1994. Compensating changes in protein multiple sequence alignments. Protein Eng. 7: 341-348.
34. Valencia, A. and Pazos, F. 2002. Computational methods for prediction of protein interactions. Curr. Opin. Struct. Biol. 12: 368-373.
35. Wang, J.-S. and Swendsen, R.H. 1990. Cluster Monte Carlo algorithms. Physica A 167: 565-579.
36. Xu, Z. and Sigler, P.B. 1998. GroEL/GroES: Structure and function of a two-stroke folding machine. J. Struct. Biol. 124: 129-141.
37. Zheng, W.J., Brooks, B.R., Doniach, S., and Thirumalai, D. 2005. Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. Structure 13: 565-577.