Smoluchowski dynamics of the vnd/NK-2 homeodomain from Drosophila melanogaster: First-order mode-coupling approximation

Biopolymers

Volumn 49, Issue 3, 1999, Pages 235-254

  Penna, Giovanni La ^a   Mormino, Michele ^a   Pioli, Franco ^a   Perico, Angelo ^a   Fioravanti, Roberto ^a   Gruschus, James M ^b   Ferretti, James A ^b  

^a CNR   (Italy)

^b NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

Author keywords

Homeodomain containing protein; Molecular dynamics simulations; nmr relaxation; Protein dynamics; Smoluchowski diffusion

Indexed keywords

HOMEODOMAIN PROTEIN; POLYMER;

ARTICLE; CALCULATION; CHEMICAL BOND; DIFFUSION; DROSOPHILA MELANOGASTER; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN ANALYSIS; PROTEIN STRUCTURE; SIMULATION;

ANIMALS; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; HOMEODOMAIN PROTEINS; INSECT PROTEINS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; THERMODYNAMICS; TRANSCRIPTION FACTORS;

DROSOPHILA MELANOGASTER; MELANOGASTER;

EID: 0033052210     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0282(199903)49:3<235::AID-BIP5>3.0.CO;2-7     Document Type: Article

References (43)

1. Young, R. D.; Frauenfelder, H.; Johnson, J. B.; Lamb, D. C.; Nienhaus, G. U.; Philipp, R.; Scholl, R. Chem Phys 1991, 158, 315-327.
2. Brooks, C. L., III; Karplus, M.; Petitt, B. M. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics; John Wiley & Sons: New York, USA, 1988.
3. McCammon, J. A.; Harvey, S. C. Dynamics of Proteins and Nucleic Acids; Cambridge University Press: Cambridge, UK, 1987.
4. Zwanzig, R. J Chem Phys 1974, 60, 2717-2720.
5. Perico, A. Accounts Chem Res 1989, 22, 336-342.
6. Perico, A.; Pratolongo, R.; Freed, K. F.; Pastor, R. W.; Szabo, A. J Chem Phys 1993, 98, 564-573.
7. Perico, A.; Pratolongo, R.; Freed, K. F.; Szabo, A. J Chem Phys 1994, 101, 2554-2561.
8. Chang, X. Y.; Freed, K. F. J Chem Phys 1993, 99, 8016-8030.
9. Tang, W. H.; Chang, X. Y.; Freed, K. F. J Chem Phys 1995, 103, 9492-9501.
10. Perico, A.; Pratolongo, R. Macromolecules 1997, 30, 5958-5969.
11. Bixon, M.; Zwanzig, R. J Chem Phys 1978, 68, 1896-1902.
12. Perico, A.; Guenza, M. J Chem Phys 1985, 83, 3103-3109.
13. Hu, Y.; Fleming, G. R.; Freed, K. F.; Perico, A. Chem Phys 1991, 158, 395-408.
14. Hu, Y.; Kostov, K.; Perico, A.; Smithline, S.; Freed, K. F. J Chem Phys 1995, 103, 9091-9100.
15. Perico, A.; Guenza, M.; Mormino, M.; Fioravanti, R. Biopolymers 1994, 35, 47-54.
16. Gehring, W. J.; Affolter, M.; Burglin, T. Ann Rev Biochem 1994, 63, 487-526.
17. Kim, Y.; Nirenberg, M. Proc Natl Acad Sci 1989, 86, 7716-7720.
18. Nirenberg, M.; Nakayama, N.; Kim, Y. S.; Mellerick, D.; Wang, L.-H.; Weber, K.; Lad, R. Ann NY Acad Sci 1995, 758, 224-242.
19. Gruschus, J. M.; Tsao, D. H. H.; Wang, L.-H.; Nirenberg, M.; Ferretti, J. A. Biochemistry 1997, 36, 5372-5380.
20. Lipari, G.; Szabo, A. J Am Chem Soc 1982, 104, 4546-4559, 4559-4570.
21. Clore, G. M.; Gronenborn, A. M.; Szabo, A.; Tjandra, N. J Am Chem Soc 1998, 120, 4889-4890.
22. Clore, G. M.; Gronenborn, A. M. NMR of Proteins; MacMillan Press: London, UK, 1993.
23. Risken, H. The Fokker-Planck Equation; Springer, New York, USA, 1989.
24. Perico, A.; Piaggio, P.; Cuniberti, C. J Chem Phys 1975, 62, 4911-4918.
25. Edward, J. T. J Chem Educ 1970, 47, 261-269.
26. Parak, F. In The Enzyme Catalysis Process Nato-Asi Series; Cooper, A.; Houben, J. L.; Chien, L. C., Eds.; Plenum Press: New York, USA, 1989; pp 197-221.
27. Tsao, D. H. H.; Gruschus, J. M.; Wang, L.-H.; Nirenberg, M.; Ferretti, J. A. Biochemistry 1994, 33, 15053-15060.
28. Tjandra, N.; Kuboniwa, H.; Bax, A. Eur J Biochem 1995, 230, 1014-1024.
29. Barbato, G.; Ikura, M.; Kay, L. E.; Pastor, R. W.; Bax, A. Biochemistry 1992, 31, 5269-5278.
30. Delaglio, F.; Grzesiek, S.; Vuister, G. W.; Zhu, G.; Pfeifer, J.; Bax, A. J Biomol NMR 1995, 6, 277-293.
31. Garrett, D. S.; Powers, R.; Gronenborn, A. M.; Clore, J. M. J Magn Res 1991, 94, 214-220.
32. Tsao, H. H. D.; Gruschus, J. M.; Wang, L.-H.; Nirenberg, M.; Ferretti, J. A. J Mol Biol 1995, 251, 297-307.
33. Discover 95.0/3.00, Biosym/MSI, San Diego, CA, 1995.
34. Dauber-Osguthorpe, P.; Roberts, V. A.; Osguthorpe, D. J.; Wolff, J.; Genest, M.; Hagler, A. T. Proteins Struct Funct Genet 1988, 4, 31-47.
35. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J Chem Phys 1983, 79, 926-935.
36. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J Comp Phys 1977, 23, 327-341.
37. Favro, D. L. Phys Rev 1960, 119, 53-62.
38. Bernal, J. M. G.; de la Torre, J. G. Biopolymers 1980, 19, 751-766.
39. Perico, A.; Moe, N. E.; Ediger, M. D. J Chem Phys 1998, 108, 1245-1252.
40. Xiang, B.; Weiler, S.; Nirenberg, M.; Ferretti, J. A. Proc Natl Acad Sci 1998, 95, 7412-7416.
41. Abragam, A. Principles of Nuclear Magnetism; Clarendon Press: Oxford, UK, 1986.
42. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J Chem Phys 1995, 103, 8577-8593.
43. Procacci, P.; Darden, T.; Marchi, M. J Phys Chem 1996, 100, 10464-10468.