Force field impact and spin-probe modeling in molecular dynamics simulations of spin-labeled T4 lysozyme

Journal of Molecular Modeling

Volumn 11, Issue 3, 2005, Pages 210-225

  Stoica, Ileana ^a  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

Electronic paramagnetic resonance (EPR); Force field; Molecular dynamics (MD); T4 lysozyme (T4L)

Indexed keywords

LYSOZYME;

ALGORITHM; ARTICLE; COMPUTER MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; DIAGNOSTIC ACCURACY; ELECTROMAGNETIC FIELD; ELECTRON SPIN RESONANCE; FOURIER ANALYSIS; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; ROTATION; SPIN LABELING; STRUCTURE ANALYSIS;

BACTERIOPHAGE T4; COMPUTER SIMULATION; ELECTRON SPIN RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOTION; MURAMIDASE; MUTATION, MISSENSE; ROTATION; SPIN LABELS; TORSION;

EID: 22144444896     PISSN: 09485023     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00894-005-0255-8     Document Type: Article

References (34)

1. Freed JH (2000) Annu Rev Phys Chem 51:655-689
2. Borbat PP, Freed JH (1999) Chem Phys Lett 313:145-154
3. Borbat PP, Costa-Filho AJ, Earle KA, Moscicki JK, Freed JH (2001) Science 291:266-269
4. Columbus L, Hubbell WL (2002) Trends Biochem Sci 27:288-295
5. Columbus L, Kalai T, Jeko J, Hideg L, Hubbell WL (2002) Biochemistry 40:3828-3846
6. Ge M, Freed JH (1999) Biophys J 76:264-280
7. Schwartz LJ, Stillman AE, Freed JH (1982) J Chem Phys 77:5410-5425
8. DJ Schneider JH Freed 1989 Calculating slow motional magnetic resonance spectra a users guide In: LJ Berliner J Reuben (Eds.) Biological magnetic resonance vol 8. Plenum Press NewYork 1-76
9. Fajer PG, Bennett RLH, Polnaszek CF, Fajer EA, Thomas DD (1990) J Magn Reson 88:111-125
10. Steinhoff HJ, Hubbell WL (1996) Biophys J 71:2201-2212
11. Robinson BH, Slutsky LJ, Auteri FP (1992) J Chem Phys 96:2609-2616
12. Usova N, Westlund PO, Fedchenia II (1995) J Chem Phys 103:96-103
13. Usova N, Perssoni L, Westlund PO (2000) Phys Chem Chem Phys 2:2785-2793
14. Hakansson P, Westlund PO, Lindahl E, Edholm O (2001) Phys Chem Chem Phys 3:5311-5319
15. LaConte LEW, Voelz V, Nelson W, Enz M, Thomas DD (2002) Biophys J 83:1854-1866
16. Levanon H, Mobius K (1997) Annu Rev Biophys Biomol Struct 26:495-540
17. Stoica I (2004) J Phys Chem B 108:1771-1782
18. Mchaourab HS, Lietzow MA, Hideg K, Hubbell WL (1999) Biochemistry 35:7692-7704
19. Stoica I (2004) J Biomol Struct Dyn 21:745-760
20. Mchaourab HS, Oh KJ, Fang CJ, Hubbell WL (1997) Biochemistry 36:307-316
21. Barnes J, Liang Z, Mchaourab H, Freed JH, Hubbell W (1999) Biophys J 76:3298-3306
22. Borbat PP, Mchaourab HS, Freed JH (2002) J Am Chem Soc 124:5304-5314
23. Spezia R, Aschi M, Di Nola A, Di Valentin M, Carbonera D, Amadei A (2003) Biophys J 84:2805-2813
24. MacKerell AD Jr, Wiorkiewicz-Kuczera J, Karplus M (1995) J Am Chem Soc 117:11946-11975
25. Elber R, Roitberg A, Simmerling C, Goldstein R, Li H, Verkhivker G, Keasar C, Zhang J, Ulitsky L (1995) Comp Phys Comm 91:159-189
26. Kaminski G, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) J Phys Chem B 105:6474-6487
27. Arora K, Schlick T (2003) Chem Phys Lett 378:1-8
28. Andersen HC (1983) J Comput Phys 52:24-34
29. Darden TA, York DM, Pedersen LG (1993) J Chem Phys 98:10089-10092 10.1063/1.464397
30. Kabsch W (1976) Acta Cryst A 32:922-923
31. Kabsch W (1978) Acta Cryst A 34:827-828
32. Smith LJ, Daura X, van Gunsteren WF (2002) Proteins Struct Funct Genet 48:487-496
33. Jolicoeur C, Friedman HL (1971) Ber Bunsenges Phys Chem 75:248-257
34. Koradi R, Billeter M, Wüthrich K (1996) J Mol Graph 14:51-55 10.1016/0263-7855(96)00009-4