Combined experimental and theoretical study of long-range interactions modulating dimerization and activity of yeast geranylgeranyl diphosphate synthase

Journal of the American Chemical Society

Volumn 131, Issue 11, 2009, Pages 4051-4062

  Lo, Chia Hsiang ^a   Chang, Ying Hsuan ^a   Wright, Jon D ^c   Chen, Shih Hsun ^d   Kan, Daphne ^b   Lim, Carmay ^c   Liang, Po Huang ^a,b  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^b INSTITUTE OF BIOLOGICAL CHEMISTRY   (Taiwan)

^c INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

^d NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; AMINO ACIDS; CENTRIFUGATION; CHLOROPHYLL; ENZYMES; MODULATION; MOLECULAR DYNAMICS; ORGANIC ACIDS; PORPHYRINS; YEAST;

3D STRUCTURE; AMINO ACID RESIDUES; DIMER INTERFACE; ENERGY DECOMPOSITION ANALYSIS; FARNESYL DIPHOSPHATE; GERANYLGERANYL DIPHOSPHATE; ISOPENTENYL DIPHOSPHATE; LONG RANGE INTERACTIONS; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR MECHANISM; N-TERMINAL HELIX; PROTEIN STRUCTURES; SACCHAROMYCES CEREVISIAE; SITE DIRECTED MUTAGENESIS; SYNTHASE; THEORETICAL STUDY; ULTRACENTRIFUGATION;

DIMERIZATION;

AMINO ACID; CAROTENOID; CHLOROPHYLL; FARNESYL DIPHOSPHATE; FARNESYL TRANS TRANSFERASE; ISOPENTENYL DIPHOSPHATE;

AMINO TERMINAL SEQUENCE; ARTICLE; DIMERIZATION; ENZYME ACTIVITY; ENZYME STRUCTURE; MOLECULAR DYNAMICS; NONHUMAN; SACCHAROMYCES CEREVISIAE; SITE DIRECTED MUTAGENESIS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENZYMOLOGY; GENETICS; KINETICS; METABOLISM; MUTAGENESIS; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; THERMODYNAMICS;

COMPUTER SIMULATION; FARNESYLTRANSTRANSFERASE; KINETICS; MODELS, MOLECULAR; MUTAGENESIS; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; SACCHAROMYCES CEREVISIAE; THERMODYNAMICS;

EID: 67849092756     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja808699c     Document Type: Article

References (38)

1. De Clercq, E. Nat. Rev. Drue Discovery 2002, 1, 13-25.
2. Fan, K.; Wei, P.; Feng, Q.; Chen, S.; Huang, C.; Ma, L.; Lai, B.; Pei, J.; Liu, Y.; Chen, J.; Lai, L. J. Biol. Chem. 2004, 279, 1637-1642.
3. Drake, P. L.; Cole, J. L.; Waxman, L.; Hall, D. L.; Sardana, M. K.; Kuo, L. C. J. Biol. Chem. 1996, 271, 7445-7449.
4. Margosiak, S. A.; Vanderpool, D. L.; Sisson, W.; Pinko, C.; Kan, C. C. Biochemistry 1996, 35, 5300-5307.
5. Chien, C. H.; Huang, L. H.; Chou, C. Y.; Chen, Y. S.; Han, Y. S.; Chang, G. G.; Liang, P. H.; Chen, X. J. Biol. Chem. 2004, 279, 52338-52345.
6. Sacchettini, J. C.; Poulter, C. D. Science 1997, 277, 1788-1789.
7. Ogura, K.; Koyama, T. Chem. Rev. 1998, 98, 1263-1276.
8. Liang, P. H.; Ko, T. P.; Wang, A. H. Eur. J. Biochem. 2002, 269, 3339-3354.
9. Rudiger, W.; Benz, J.; Guthoff, C. Eur. J. Biochem. 1980, 109, 193-200.
10. Jiang, Y.; Proteau, P.; Poulter, D.; Ferro-Novick, S. J. Biol. Chem. 1995, 270, 21793-21799.
11. Olszewski, N.; Sun, T.; Gubler, F. Plant Cell 2002, 14, S61-S80.
12. Dogbo, O.; Laferriere, A.; D'Harlingue, A.; Camara, B. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 7054-7058.
13. Kuzuguchi, T.; Morita, Y.; Sagami, I.; Sagami, H.; Ogura, K. J. Biol. Chem. 1999, 274, 5888-5894.
14. Guo, R. T.; Cao, R.; Liang, P. H.; Ko, T. P.; Chang, T. H.; Hudock. M. P.; Jeng, W. Y.; Chen, C.; Zhang, Y.; Song, Y.; Kuo, C. J.; in, F.; Oldfield, E.; Wang, A. H. Proc. Natl. Acad. Sci. U.S.A. 2007,104. 10022-10027.
15. Goffinet, M.; Thoulouzan, M.; Pradines, A.; Lajoie-Mazenc, I.; Weinbaum, C.; Faye, J. C.; Seronie-Vivien, S. BMC Cancer 2006, 6, 60.
16. Guo, R. T.; Kuo, C. J.; Chou, C. C.; Ko, T. P.; Shr, H. L.; Liang, P. H.; Wang, A. H. J. Biol. Chem. 2004, 279, 4903-4912.
17. Hosfield, D. J.; Zhang, Y.; Dougan, D. R.; Broun, A.; Tari, L. W.; Swanson, R. V.; Finn, J. J. Biol. Chem. 2004, 279, 8526-8529.
18. Sun, H. Y.; Ko, T. P.; Kuo, C. J.; Guo, R. T.; Chou, C. C.; Liang,P. H.; Wang, A. H. J. Bacteriol. 2005, 187, 8137-8148.
19. Gabelli, S. B.; McLellan, J. S.; Montalvetti, A.; Oldfield, E.; Docampo, R.; Amzel, L. M. Proteins 2006, 62, 80-88.
20. Chang, T. H.; Guo, R. T.; Ko, T. P.; Wang, A. H. J.; Liang, P. H. J. Biol. Chem. 2006, 281, 14991-15000.
21. Kavanagh, K. L.; Dunford, J. E.; Bunkoczi, G.; Russell, R. G. G.; Oppermann, U. J. Biol. Chem. 2006, 281, 22004-22012.
22. Kloer, D. P.; Welsch, P.; Beyer, P.; Schulz, G. E. Biochemistry 2006, 45, 15197-15204.
23. Chang, H. C.; Chang, G. G. J. Biol. Chem. 2004, 278, 23996-24002.
24. Pan, J. J.; Chiou, S. T.; Liang, P. H. Biochemistry 2000, 39, 10936-10942.
25. Eftink, M. R. Methods Enzymol. 1995, 259, 478-512.
26. Fiser, A.; Do, R. K. G.; Sali, A. Protein Sci. 2000, 9, 1753-1773.
27. Fiser, A.; Sali, A. Bioinformatics 2003, 18, 2500-2501.
28. Brooks, B. R.; Bruccoleria, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
29. MacKerell, J. A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616.
30. Vriend, G. J. Mol. Graph. 1990, 8, 52-56.
31. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
32. Feller, S. E.; Pastor, R. W.; Rojnuckarin, A.; Bogusz, S.; Brooks, B. R. J. Phys. Chem. 1996, 100, 17011-17020.
33. Sharp, K. A.; Nicholls, A.; Fine, R. F.; Honig, B. Science 1991, 252, 106-109.
34. Jayaram, B.; McConnell, K. J.; Surjit, B. D.; Beveridge, D. L. J. Comp. Phys. 1999, 151, 333-357.
35. Nina, M.; Beglov, D.; Roux, B. J. Phys. Chem. B. 1997, 101, 5239-5248.
36. Hendsch, Z. S.; Tidor, B. Protein Sci. 1999, 8, 1381-1392.
37. Lafont, V.; Schaefer, M.; Stote, R. H.; Altschuh, D.; Dejaegere, A. Proteins: Struct., Funct., Bioinfo. 2007, 67, 418-434.
38. DeLano, W. L.; DeLano Scientific LLC: Palo Alto, CA, 2008.