Evolutionary basis for the coupled-domain motions in Thermus thermophilus leucyl-tRNA synthetase

Journal of Biological Chemistry

Volumn 284, Issue 15, 2009, Pages 10088-10099

  Weimer, Kristina Mary Ellen ^a   Shane, Brianne Leigh ^a   Brunetto, Michael ^a   Bhattacharyya, Sudeep ^a   Hati, Sanchita ^a  

^a UNIVERSITY OF WISCONSIN EAU CLAIRE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOACYL; COLLECTIVE MOTIONS; CONFORMATIONAL CHANGE; COORDINATED MOVEMENT; COUPLING ANALYSIS; COVALENT ATTACHMENT; DIFFERENT DOMAINS; DOMAIN MOTIONS; DOMAIN-DOMAIN COMMUNICATION; IN-CELL; LONG RANGE; LOW FREQUENCY; MECHANOCHEMICAL; MULTIDOMAIN PROTEINS; NORMAL MODES; PROTEIN SYNTHESIS; STRUCTURAL ELEMENTS; SUBSTRATE BINDING; SYNTHETASE; SYNTHETASES; THERMAL MOTION; THERMOPHILUS; THERMUS THERMOPHILUS; VAN DER WAALS CONTACTS;

AMINATION; AMINES; COORDINATION REACTIONS; NUCLEIC ACIDS; ORGANIC ACIDS; RNA; VAN DER WAALS FORCES;

AMINO ACIDS;

AMINO ACID; ISOLEUCINE TRANSFER RNA LIGASE; AMINO ACID TRANSFER RNA LIGASE; LEUCINE TRANSFER RNA LIGASE;

AMINO ACID ANALYSIS; ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CORRELATION FUNCTION; ENZYME LOCALIZATION; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; GENETIC CONSERVATION; MOLECULAR PROBE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; THERMUS THERMOPHILUS; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ENZYME SPECIFICITY; ENZYMOLOGY; MOLECULAR EVOLUTION; MOTION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; STATISTICAL MODEL; THERMODYNAMICS;

THERMUS THERMOPHILUS;

AMINO ACYL-TRNA SYNTHETASES; EVOLUTION, MOLECULAR; LEUCINE-TRNA LIGASE; MODELS, CHEMICAL; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; MOTION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY; THERMODYNAMICS; THERMUS THERMOPHILUS;

EID: 65649152953     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M807361200     Document Type: Article

References (71)

1. Alexander, R. W., and Schimmel, P. (2001) Prog. Nucleic Acid Res. Mol. Biol. 69, 317-349
2. Zhang, C. M., and Hou, Y. M. (2005) Biochemistry 44, 7240-7249
3. Ibba, M., and Söll, D. (2000) Annu. Rev. Biochem. 69, 617-650
4. Jakubowski, H., and Goldman, E. (1992) Microbiol. Rev. 56, 412-429
5. Mascarenhas, A., Martinis, S. A., An, S., Rosen, A. E., and Musier-Forsyth, K. (2009) in Protein Engineering (RajBhandary, U. L., and Koehrer, C. eds) pp. 153-200, Springer-Verlag New York Inc., New York
6. Uter, N. T., and Perona, J. J. (2004) Proc. Natl. Acad. Sci. U. S. A. 101, 14396-14401
7. Budiman, M. E., Knaggs, M. H., Fetrow, J. S., and Alexander, R. W. (2007) Proteins 68, 670-689
8. Estabrook, R. A., Luo, J., Purdy, M. M., Sharma, V., Weakliem, P., Bruice, T. C., and Reich, N. O. (2005) Proc. Natl. Acad. Sci. U. S. A. 102, 994-999
9. Tukalo, M., Yaremchuk, A., Fukunaga, R., Yokoyama, S., and Cusack, S. (2005) Nat. Struct. Mol. Biol. 12, 923-930
10. Mascarenhas, A. P., and Martinis, S. A. (2008) Biochemistry 47, 4808-4816
11. Cusack, S., Yaremchuk, A., and Tukalo, M. (2000) EMBO J. 19, 2351-2361
12. Vu, M. T., and Martinis, S. A. (2007) Biochemistry 46, 5170-5176
13. Harte, W. E., Jr., Swaminathan, S., Mansuri, M. M., Martin, J. C., Rosenberg, I. E., and Beveridge, D. L. (1990) Proc. Natl. Acad. Sci. U. S. A. 87, 8864-8868
14. Benkovic, S. J., and Hammes-Schiffer, S. (2003) Science 301, 1196-1202
15. Bu, Z., Biehl, R., Monkenbusch, M., Richter, D., and Callaway, D. J. (2005) Proc. Natl. Acad. Sci. U. S. A. 102, 17646-17651
16. Benkovic, S. J., and Hammes-Schiffer, S. (2006) Science 312, 208-209
17. Hawkins, R. J., and McLeish, T. C. (2006) Biophys. J. 91, 2055-2062
18. Yu, H., Ma, L., Yang, Y., and Cui, Q. (2007) PLOS Comput. Biol. 3, 214-230
19. Brooks, B., and Karplus, M. (1983) Proc. Natl. Acad. Sci. U. S. A. 80, 6571-6575
20. Marques, O., and Sanejouand, Y. H. (1995) Proteins 23, 557-560
21. Bahar, I., Atilgan, A. R., and Erman, B. (1997) Fold. Des. 2, 173-181
22. Tama, F., and Sanejouand, Y. H. (2001) Protein Eng. 14, 1-6
23. Yildirim, Y., and Doruker, P. (2004) J. Biomol. Struct. Dyn. 22, 267-280
24. Bahar, I., and Rader, A. J. (2005) Curr. Opin. Struct. Biol. 15, 586-592
25. Ma, J. (2005) Structure 13, 373-380
26. Tama, F., and Brooks, C. L., III (2005) J. Mol. Biol. 345, 299-314
27. Eyal, E., Yang, L. W., and Bahar, I. (2006) Bioinformatics 22, 2619-2627
28. Kong, Y., Ma, J., Karplus, M., and Lipscomb, W. N. (2006) J. Mol. Biol. 356, 237-247
29. Lockless, S. W., and Ranganathan, R. (1999) Science 286, 295-299
30. Suel, G. M., Lockless, S. W., Wall, M. A., and Ranganathan, R. (2003) Nat. Struct. Biol. 10, 59-69
31. Humphrey, W., Dalke, A., and Schulten, K. (1996) J. Mol. Graph. 14, 33-38
32. Go, N., Noguti, T., and Nishikawa, T. (1983) Proc. Natl. Acad. Sci. U. S. A. 80, 3696-3700
33. Harrison, R. W. (1984) Biopolymers 23, 2943-2949
34. Kitao, A., and Go, N. (1999) Curr. Opin. Struct. Biol. 9, 164-169
35. Brooks, B., and Karplus, M. (1985) Proc. Natl. Acad. Sci. U. S. A. 82, 4995-4999
36. Frank, J., and Agrawal, R. K. (2000) Nature 406, 318-322
37. Atilgan, A. R., Durell, S. R., Jernigan, R. L., Demirel, M. C., Keskin, O., and Bahar, I. (2001) Biophys. J. 80, 505-515
38. Bruschweiler, R. (1995) J. Chem. Phys. 102, 3396-3403
39. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Nucleic Acids Res. 25, 3389-3402
40. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) Nucleic Acids Res. 22, 4673-4680
41. Silvian, L. F., Wang, J., and Steitz, T. A. (1999) Science 285, 1074-1077
42. Rock, F. L., Mao, W., Yaremchuk, A., Tukalo, M., Crepin, T., Zhou, H., Zhang, Y. K., Hernandez, V., Akama, T., Baker, S. J., Plattner, J. J., Shapiro, L., Martinis, S. A., Benkovic, S. J., Cusack, S., and Alley, M. R. (2007) Science 316, 1759-1761
43. Fukunaga, R., and Yokoyama, S. (2005) Nat. Struct. Mol. Biol. 12, 915-922
44. Li, T., Guo, N., Xia, X., Wang, E. D., and Wang, Y. L. (1999) Biochemistry 38, 13063-13069
45. Chen, J. F., Li, T., Wang, E. D., and Wang, Y. L. (2001) Biochemistry 40, 1144-1149
46. Du, X., and Wang, E. D. (2002) Biochemistry 41, 10623-10628
47. Williams, A. M., and Martinis, S. A. (2006) Proc. Natl. Acad. Sci. U. S. A. 103, 3586-3591
48. Boniecki, M. T., Vu, M. T., Betha, A. K., and Martinis, S. A. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 19223-19228
49. Hati, S., Ziervogel, B., Sternjohn, J., Wong, F. C., Nagan, M. C., Rosen, A. E., Siliciano, P. G., Chihade, J. W., and Musier-Forsyth, K. (2006) J. Biol. Chem. 281, 27862-27872
50. Lue, S. W., and Kelley, S. O. (2007) Biochemistry 46, 4466-4472
51. Nawaz, M. H., Pang, Y. L., and Martinis, S. A. (2007) J. Mol. Biol. 367, 384-394
52. Rho, S. B., Lincecum, T. L., Jr., and Martinis, S. A. (2002) EMBO J. 21, 6874-6881
53. Tousignant, A., and Pelletier, J. N. (2004) Chem. Biol. 11, 1037-1042
54. Hammes-Schiffer, S. (2002) Biochemistry 41, 13335-13343
55. Hammes-Schiffer, S., and Benkovic, S. J. (2006) Annu. Rev. Biochem. 75, 519-541
56. Ma, J., and Karplus, M. (1997) J. Mol. Biol. 274, 114-131
57. Hansson, T., Oostenbrink, C., and van Gunsteren, W. (2002) Curr. Opin. Struct. Biol. 12, 190-196
58. Karplus, M. (2002) Acc. Chem. Res. 35, 321-323
59. Truhlar, D. G., Gao, J., Alhambra, C., Garcia-Viloca, M., Corchado, J., Sanchez, M. L., and Villa, J. (2002) Acc. Chem. Res. 35, 341-349
60. Garcia-Viloca, M., Gao, J., Karplus, M., and Truhlar, D. G. (2004) Science 303, 186-195
61. Truhlar, D. G., Gao, J., Garcia-Viloca, M., Alhambra, C., Corchado, J., Sanchez, M. L., and Poulsen, T. D. (2004) Int. J. Quantum Chem. 100, 1136-1152
62. Bhattacharyya, S., Ma, S., Stankovich, M. T., Truhlar, D. G., and Gao, J. (2005) Biochemistry 44, 16549-16562
63. Bhattacharyya, S., Stankovich, M. T., Truhlar, D. G., and Gao, J. (2007) J. Phys. Chem. A 111, 5729-5742
64. Soares, T. A., Lins, R. D., Straatsma, T. P., and Briggs, J. M. (2002) Biopolymers 65, 313-323
65. Mustata, G. I., Soares, T. A., and Briggs, J. M. (2003) Biopolymers 70, 186-200
66. Barreca, M. L., Lee, K. W., Chimirri, A., and Briggs, J. M. (2003) Biophys. J. 84, 1450-1463
67. Mursinna, R. S., Lee, K. W., Briggs, J. M., and Martinis, S. A. (2004) Biochemistry 43, 155-165
68. Brigo, A., Lee, K. W., Fogolari, F., Mustata, G. I., and Briggs, J. M. (2005) Proteins 59, 723-741
69. Bartlett, G. J., and Taylor, W. R. (2008) Proteins 71, 950-959
70. Nascimento, A. S., Krauchenco, S., Golubev, A. M., Gustchina, A., Wlodawer, A., and Polikarpov, I. (2008) J. Mol. Biol. 382, 763-778
71. Zheng, W., Brooks, B. R., and Thirumalai, D. (2006) Proc. Natl. Acad. Sci. U. S. A. 103, 7664-7669