Probing the allosteric mechanism in pyrrolysyl-tRNA synthetase using energy-weighted network formalism

Biochemistry

Volumn 50, Issue 28, 2011, Pages 6225-6236

  Bhattacharyya, Moitrayee ^a   Vishveshwara, Saraswathi ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ALLOSTERIC COMMUNICATION; ALLOSTERIC MECHANISMS; ALLOSTERIC REGULATION; ALLOSTERY; ANTICODONS; ATOMIC LEVELS; BETWEENNESS; DESULFITOBACTERIUM; DIMERIC PROTEINS; FUNCTIONAL ASPECTS; GLOBAL LEVELS; MOLECULAR DYNAMICS SIMULATIONS; PYRROLYSINE; SHORTEST PATH; SOCIAL NETWORKS; STRUCTURE NETWORK; SYNTHETASES; WEIGHTED GRAPH;

CONFORMATIONS; LIGANDS; MOLECULAR DYNAMICS; PROTEINS;

COMPLEXATION;

AMINO ACID TRANSFER RNA LIGASE; LIGAND; PYRROLYSYL TRANSER RNA SYNTHETASE; SYNTHETASE; TRANSFER RNA; UNCLASSIFIED DRUG;

ALLOSTERISM; AMINO ACID SEQUENCE; ARTICLE; DESULFITOBACTERIUM; DESULFITOBACTERIUM HAFNIENSE; ENERGY; ENZYME CONFORMATION; ENZYME STRUCTURE; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE;

ALLOSTERIC REGULATION; AMINO ACYL-TRNA SYNTHETASES; BACTERIAL PROTEINS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; DESULFITOBACTERIUM; ENERGY METABOLISM; LIGANDS; LYSINE; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN MULTIMERIZATION;

DESULFITOBACTERIUM HAFNIENSE;

EID: 79960284776     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi200306u     Document Type: Article

References (41)

1. Ling, J., Reynolds, N., and Ibba, M. (2009) Aminoacyl-tRNA Synthesis and Translational Quality Control Annu. Rev. Microbiol. 63, 61-78
2. Krzycki, J. A. (2005) The direct genetic encoding of pyrrolysine Curr. Opin. Microbiol. 8, 706-712 (Pubitemid 41643039)
3. Kobayashi, T., Yanagisawa, T., Sakamoto, K., and Yokoyama, S. (2009) Recognition of Non-α-amino Substrates by Pyrrolysyl-tRNA Synthetase J. Mol. Biol. 385, 1352-1360
4. Yanagisawa, T., Ishii, R., Fukunaga, R., Kobayashi, T., Sakamoto, K., and Yokoyama, S. (2008) Crystallographic Studies on Multiple Conformational States of Active-site Loops in Pyrrolysyl-tRNA Synthetase J. Mol. Biol. 378, 634-652
5. Herring, S., Ambrogelly, A., Polycarpo, C. R., and Söll, D. (2007) Recognition of pyrrolysine tRNA by the Desulfitobacterium hafniense pyrrolysyl-tRNA synthetase Nucleic Acids Res. 35, 1270-1278 (Pubitemid 46522978)
6. Nozawa, K., O'Donoghue, P., Gundllapalli, S., Araiso, Y., Ishitani, R., Umehara, T., Söll, D., and Nureki, O. (2009) Pyrrolysyl-tRNA synthetase-tRNAPyl structure reveals the molecular basis of orthogonality Nature 457, 1163-1167
7. Monod, J., Wyman, J., and Changeux, J. P. (1965) On the nature of allosteric transitions: A plausible model J. Mol. Biol. 12, 88-118
8. Koshland, D. E., Némethy, G., and Filmer, D. (1966) Comparison of experimental binding data and theoretical models in proteins containing subunits Biochemistry 5, 365-385
9. Gunasekaran, K., Ma, B., and Nussinov, R. (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins: Struct., Funct., Bioinf. 57, 433-443 (Pubitemid 39390799)
10. del Sol, A., Tsai, C. J., Ma, B., and Nussinov, R. (2009) The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways Structure 17, 1042-1050
11. 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
12. Gandhi, P. S., Chen, Z., Mathews, F. S., and Di Cera, E. (2008) Structural identification of the pathway of long-range communication in an allosteric enzyme Proc. Natl. Acad. Sci. U.S.A. 105, 1832-1837 (Pubitemid 351439425)
13. Peterson, E. S. and Friedman, J. M. (1998) A Possible Allosteric Communication Pathway Identified through a Resonance Raman Study of Four ?37 Mutants of Human Hemoglobin A Biochemistry 37, 4346-4357 (Pubitemid 28217153)
14. Chen, J., Dima, R. I., and Thirumalai, D. (2007) Allosteric Communication in Dihydrofolate Reductase: Signaling Network and Pathways for Closed to Occluded Transition and Back J. Mol. Biol. 374, 250-266 (Pubitemid 47600224)
15. Lockless, S. W. and Ranganathan, R. (1999) Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families Science 286, 295-299 (Pubitemid 29484693)
16. 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 (Pubitemid 350035365)
17. Bhattacharyya, M., Ghosh, A., Hansia, P., and Vishveshwara, S. (2010) Allostery and conformational free energy changes in human tryptophanyl-tRNA synthetase from essential dynamics and structure networks Proteins: Struct., Funct., Bioinf. 78, 506-517
18. 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, 0019
19. Sethi, A., Eargle, J., Black, A. A., and Luthey-Schulten, Z. (2009) Dynamical networks in tRNA:protein complexes Proc. Natl. Acad. Sci. U.S.A. 106, 6620-6625
20. Chennubhotla, C. and Bahar, I. (2007) Signal Propagation in Proteins and Relation to Equilibrium Fluctuations PLoS Comput. Biol. 3, e172
21. Hill, T. L. and Levitzki, A. (1980) Subunit Neighbor Interactions in Enzyme Kinetics: Half-Of-The-Sites Reactivity in a Dimer Proc. Natl. Acad. Sci. U.S.A. 77, 5741-5745 (Pubitemid 11206394)
22. Shi, J., Dertouzos, J., Gafni, A., Steel, D., and Palfey, B. A. (2006) Single-molecule kinetics reveals signatures of half-sites reactivity in dihydroorotate dehydrogenase A catalysis Proc. Natl. Acad. Sci. U.S.A. 103, 5775-5780
23. Kavran, J. M., Gundllapalli, S., O'Donoghue, P., Englert, M., Söll, D., and Steitz, T. A. (2007) Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation Proc. Natl. Acad. Sci. U.S.A. 104, 11268-11273 (Pubitemid 47175130)
24. Case, D. A., Darden, T. A., Cheatham, T. E., III, 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) AMBER9, University of California, San Fransisco.
25. 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 (Pubitemid 29157655)
26. Vijayabaskar, M. S. and Vishveshwara, S. (2010) Interaction Energy Based Protein Structure Networks Biophys. J. 99, 3704-3715
27. Kong, Y. and Karplus, M. (2009) Signaling pathways of PDZ2 domain: A molecular dynamics interaction correlation analysis Proteins: Struct., Funct., Bioinf. 74, 145-154
28. Kong, Y. and Karplus, M. (2007) The Signaling Pathway of Rhodopsin Structure 15, 611-623 (Pubitemid 46702686)
29. Newman, M. E. J. (2001) Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality Phys. Rev. E 64, 016132
30. Sukhwal, A., Bhattacharyya, M., and Vishveshwara, S. (2011) Network approach for capturing ligand induced subtle global changes in protein structures Acta Crystallogr. D67, 429-439
31. Palla, G., Derényi, I., Farkas, I., and Vicsek, T. (2005) Uncovering the overlapping community structure of complex networks in nature and society Nature 435, 814-818 (Pubitemid 40839731)
32. Adamcsek, B., Palla, G., Farkas, I., Derényi, I., and Vicsek, T. (2006) CFinder: Locating cliques and overlapping modules in biological networks Bioinformatics 22, 1021-1023
33. Bhattacharyya, M. and Vishveshwara, S. (2010) Elucidation of the conformational free energy landscape in H. pylori LuxS and its implications to catalysis BMC Struct. Biol. 10, 27
34. Milgram, S. (1967) The Small World Problem Psychol. Today 2, 60-67
35. Huang, C. Y., Rhee, S. G., and Chock, P. B. (1982) Subunit Cooperation and Enzymatic Catalysis Annu. Rev. Biochem. 51, 935-971
36. Bloom, C. R., Kaarsholm, N. C., Ha, J., and Dunn, M. F. (1997) Half-Site Reactivity, Negative Cooperativity, and Positive Cooperativity: Quantitative Considerations of a Plausible Model Biochemistry 36, 12759-12765 (Pubitemid 27465385)
37. Brzovic, P. S., Choi, W. E., Borchardt, D., Kaarsholm, N. C., and Dunn, M. F. (1994) Structural Asymmetry and Half-Site Reactivity in the T to R Allosteric Transition of the Insulin Hexamer Biochemistry 33, 13057-13069 (Pubitemid 24364753)
38. Fersht, A. R. (1975) Demonstration of two active sites on a monomeric aminoacyl-tRNA synthetase. Possible roles of negative cooperativity and half-of-the-sites reactivity in oligomeric enzymes Biochemistry 14, 5-12
39. Trezeguet, V., Merle, M., Gandar, J. C., and Labouesse, B. (1986) Kinetic evidence for half-of-the-sites reactivity in tRNATrp aminoacylation by tryptophanyl-tRNA synthetase from beef pancreas Biochemistry 25, 7125-7136 (Pubitemid 17201619)
40. Ambrogelly, A., Kamtekar, S., Stathopoulos, C., Kennedy, D., and Söll, D. (2005) Asymmetric behavior of archaeal prolyl-tRNA synthetase FEBS Lett. 579, 6017-6022 (Pubitemid 41546239)
41. Ghosh, A. and Vishveshwara, S. (2008) Variations in Clique and Community Patterns in Protein Structures during Allosteric Communication: Investigation of Dynamically Equilibrated Structures of Methionyl tRNA Synthetase Complexes Biochemistry 47, 11398-11407