Variations in clique and community patterns in protein structures during allosteric communication: Investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes

Biochemistry

Volumn 47, Issue 44, 2008, Pages 11398-11407

  Ghosh, Amit ^a   Vishveshwara, Saraswathi ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ABS RESINS; AMINES; AMINO ACIDS; DYNAMICS; MOLECULAR DYNAMICS; ORGANIC ACIDS; POPULATION STATISTICS; QUANTUM CHEMISTRY; RIGIDITY; TOPOLOGY;

ALLOSTERIC COMMUNICATIONS; ALLOSTERIC EFFECTS; AMINOACYL; BIOLOGICAL FUNCTIONS; CONFORMATIONAL CHANGES; CONFORMATIONAL ENSEMBLES; CONFORMATIONAL POPULATIONS; DO-MAINS; GENETIC CODES; GLOBAL TOPOLOGIES; INTERDOMAIN COMMUNICATIONS; LOCAL GEOMETRIES; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR INSIGHTS; NETWORK PARAMETERS; NONCOVALENT INTERACTIONS; PROTEIN STRUCTURES; RESIDUE LEVELS; SIDE CHAINS; STRUCTURAL DATUMS; STRUCTURAL RIGIDITIES; SYNTHETASE;

PROTEINS;

METHIONINE TRANSFER RNA LIGASE;

ALLOSTERISM; ARTICLE; CONFORMATIONAL TRANSITION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; RNA TRANSLATION;

ALLOSTERIC REGULATION; ALLOSTERIC SITE; ANTICODON; ESCHERICHIA COLI; METHIONINE-TRNA LIGASE; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; THERMODYNAMICS;

EID: 55249123363     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi8007559     Document Type: Article

References (51)

1. Monod, J., Wyman, J., and Changeux, J. P. (1965) On the nature of allosteric transitions: A plausible model. J. Mol. Biol. 12, 88-118.
2. Gunasekaran, K., Ma, B., and Nussinov, R. (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins: Struct., Funct., Bioinf. 57, 433-443.
3. Frauenfelder, H., McMahon, B. H., and Fenimore, P. W. (2003) Myoglobin: The hydrogen atom of biology and a paradigm of complexity. Proc. Natl. Acad. Sci. U.S.A. 100, 8615-8617.
4. Koshland, D. E., Nemethy, G., and Filmer, D. (1966) Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits. Biochemistry 5, 365-385.
5. Weber, G. (1972) Ligand binding and internal equilibiums in proteins. Biochemistry 11, 864-878.
6. Jardetzky, O. (1996) Protein dynamics and conformational transitions in allosteric proteins. Prog. Biophys. Mol. Biol. 65, 171-219.
7. Tsai, C.-J., del Sol, A., and Nussinov, R. (2008) Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play. J. Mol. Biol. 378, 1-11.
8. Przytycka, T., Aurora, R., and Rose, G. D. (1999) A protein taxonomy based on secondary structure. Nat. Struct. Mol. Biol. 6, 672-682.
9. Banavar, J. R., and Maritan, A. (2007) Physics of Proteins. Annu. Rev. Biophys. Biomol. Struct. 36, 261-280.
10. Bahar, I., Atilgan, A. R., and Erman, B. (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Folding Des. 2, 173-181.
11. Yang, L., Song, G., and Jernigan, R. L. (2007) How Well Can We Understand Large-Scale Protein Motions Using Normal Modes of Elastic Network Models? Biophys. J. 93, 920-929.
12. Brooks, B., and Karplus, M. (1983) Harmonic Dynamics of Proteins: Normal Modes and Fluctuations in Bovine Pancreatic Trypsin Inhibitor. Proc. Natl. Acad. Sci. U.S.A. 80, 6571-6575.
13. Chennubhotla, C., and Bahar, I. (2007) Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. PLoS Comput. Biol. 3, e172.
14. Jacobs, D. J., Rader, A. J., Kuhn, L. A., and Thorpe, M. F. (2001) Protein flexibility predictions using graph theory. Proteins: Struct., Funct., Genet. 44, 150-165.
15. Lockless, S. W., and Ranganathan, R. (1999) Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families. Science 286, 295-299.
16. Dima, R. I., and Thirumalai, D. (2006) Determination of network of residues that regulate allostery in protein families using sequence analysis. Protein Sci. 15, 258-268.
17. Ghosh, A., Brinda, K. V., and Vishveshwara, S. (2007) Dynamics of lysozyme structure network: Probing the process of unfolding. Biophys. J. 92, 2523-2535.
18. Ghosh, A., and Vishveshwara, S. (2007) A study of communication pathways in methionyl-tRNA synthetase by molecular dynamics simulations and structure network analysis. Proc. Natl. Acad. Sci. U.S.A. 104, 15711-15716.
19. Sathyapriya, R., and Vishveshwara, S. (2007) Structure networks of E. coli glutaminyl-tRNA synthetase: Effects of ligand binding. Proteins: Struct., Funct., Genet. 68, 541-550.
20. Gale, A. J., Shi, J. P., and Schimmel, P. (1996) Evidence that Specificity of Microhelix Charging by a Class I tRNA Synthetase Occurs in the Transition State of Catalysis. Biochemistry 35, 608-615.
21. Alexander, R. W., and Schimmel, P. (2001) Domain-domain communication in aminoacyl-tRNA synthetases. Prog. Nucleic Acid Res. Mol. Biol. 69, 317-349.
22. Alexander, R. W., and Schimmel, P. (1999) Evidence for breaking domain-domain functional communication in a synthetase-tRNA complex. Biochemistry 38, 16359-16365.
23. Burbaum, J. J., and Schimmel, P. (1991) Assembly of a class I tRNA synthetase from products of an artificially split gene. Biochemistry 30, 319-324.
24. Weygand-Durasevic, I., Rogers, M. J., and Soil, D. (1994) Connecting Anticodon Recognition with the Active Site of Escherichia coli Glutaminyl-tRNA Synthetase. J. Mol. Biol. 240, 111-118.
25. Sherman, J. M., Thomann, H. U., and Söll, D. (1996) Functional Connectivity Between tRNA Binding Domains in Glutaminyl-tRNA Synthetase. J. Mol. Biol. 256, 818-828.
26. Uter, N. T., and Perona, J. J. (2004) Long-range intramolecular signaling in a tRNA synthetase complex revealed by pre-steady-state kinetics. Proc. Natl. Acad. Sci. U.S.A. 101, 14396-14401.
27. Zhang, C. M., and Hou, Y. M. (2005) Domain-domain communication for tRNA aminoacylation: The importance of covalent connectivity. Biochemistry 44, 7240-7249.
28. Palla, G., Derenyi, I., Farkas, I., and Vicsek, T. (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature 435, 814-818.
29. Case, D. A., Darden, T. A., Cheatham, I. T. E., Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Merz, K. M., Pearlman, D. A., Crowley, M., Walker, R. C., Zhang, W., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Wong, K. F., Paesani, F., Wu, X., Brozell, S., Tsui, V., Gohlke, H., Yang, L., Tan, C., Mongan, J., Hornak, V., Cui, G., Beroza, P., Mathews, D. H., Schafmeister, C., Ross, W. S., and Kollman, P. A. (2006) AMBER 9, University of California, San Francisco.
30. Cheatham, T. E., III, Cieplak, P., and Kollman, P. A. (1999) A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn. 16, 845-862.
31. Mechulam, Y., Schmitt, E., Maveyraud, L., Zelwer, C., Nureki, O., Yokoyama, S., Konno, M., and Blanquet, S. (1999) Crystal structure of Escherichia coli methionyl-tRNA synthetase highlights species-specific features. J. Mol. Biol. 294, 1287-1297.
32. Serre, L., Verdon, G., Choinowski, T., Hervouet, N., Risler, J.-L., and Zelwer, C. (2001) How methionyl-tRNA synthetase creates its amino acid recognition pocket upon L-methionine binding. J. Mol. Biol. 306, 863-876.
33. Brunie, S., Zejwer, C., and Risler, J. L. (1990) Crystallographic study at 2.5 Å resolution of the interaction of methionyl-tRNA synthetase from Escherichia coli with ATP. J. Mol. Biol. 216, 411-424.
34. Crepin, T., Schmitt, E., Mechulam, Y., Sampson, P. B., Vaughan, M. D., Honek, J. F., and Blanquet, S. (2003) Use of analogues of methionine and methionyl adenylate to sample conformational changes during catalysis in Escherichia coli methionyl-tRNA synthetase. J. Mol. Biol. 332, 59-72.
35. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935.
36. Kannan, N., and Vishveshwara, S. (1999) Identification of side-chain clusters in protein structures by a graph spectral method. J. Mol. Biol. 292, 441-464.
37. Blinda, K. V., and Vishveshwara, S. (2005) A network representation of protein structures: Implications for protein stability. Biophys. J. 89, 4159-4170.
38. Adamcsek, B., Palla, G., Farkas, I. J., Derenyi, I., and Vicsek, T. (2006) CFinder: Locating cliques and overlapping modules in biological networks. Bioinformatics 22, 1021-1023.
39. Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: Visual molecular dynamics. J. Mol. Graphics 33, 33-38.
40. Budiman, M. E., Knaggs, M. H., Fetrow, J. S., and Alexander, R. W. (2007) Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase. Proteins: Struct., Funct., Bioinf. 68, 670-689.
41. 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.
42. Nakanishi, K., Ogiso, Y., Nakama, T., Fukai, S., and Nureki, O. (2005) Structural basis for anticodon recognition by methionyl-tRNA synthetase. Nat. Struct. Mol. Biol. 12, 931-932.
43. Schmitt, E., Meinnel, T., Blanquet, S., and Mechulam, Y. (1994) Methionyl-tRNA Synthetase Needs an Intact and Mobile 332KM-SKS336 Motif in Catalysis of Methionyl Adenylate Formation. J. Mol. Biol. 242, 566-577.
44. del Sol, A., Arauzo-Bravo, M., Amoros, D., and Nussinov, R. (2007) Modular architecture of protein structures and allosteric communications: Potential implications for signaling proteins and regulatory linkages. Genome Biol. 8, R92.
45. Liu, J., and Nussinov, R. (2008) Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design. Proc. Natl. Acad. Sci. U.S.A. 105, 901-906.
46. Popovych, N., Sun, S., Ebright, R. H., and Kalodimos, C. G. (2006) Dynamically driven protein allostery. Nat. Struct. Mol. Biol. 13, 831-838.
47. Kormos, B. L., Baranger, A. M., and Beveridge, D. L. (2006) Do collective atomic fluctuations account for cooperative effects? Molecular dynamics studies of the U1A-RNA complex. J. Am. Chem. Soc. 128, 8992-8993.
48. del Sol, A., Fujihashi, H., Amoros, D., and Nussinov, R. (2006) Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol. Syst. Biol. 2.
49. Fourmy, D., Mechulam, Y., Brunie, S., Blanquet, S., and Fayat, G. (1991) Identification of residues involved in the binding of methionine by Escherichia coli methionyl-tRNA synthetase. FEBS Lett. 292, 259-263.
50. Kim, H. Y., Ghosh, G., Schulman, L. H., Brunie, S., and Jakubowski, H. (1993) The Relationship Between Synthetic and Editing Functions of the Active Site of an Aminoacyl-tRNA Synthetase. Proc. Natl. Acad. Sci. U.S.A. 90, 11553-11557.
51. Schmitt, E., Panvert, M., Blanquet, S., and Mechulam, Y. (1995) Transition state stabilization by the 'high' motif of class I aminoacyl-tRNA synthetases: The case of Escherichia coli methionyl-tRNA synthetase. Nucleic Acids Res. 23, 4793-4798.