Evaluating the performance of the FF99SB force field based on NMR scalar coupling data

Biophysical Journal

Volumn 97, Issue 3, 2009, Pages 853-856

  Wickstrom, Lauren ^a   Okur, Asim ^a,b   Simmerling, Carlos ^a  

^a STONY BROOK UNIVERSITY   (United States)

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

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOMOLECULAR ELECTRONICS; FORCE FIELD; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; NUCLEAR MAGNETIC RESONANCE; SIMULATION;

EID: 68949086461     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.04.063     Document Type: Article

References (28)

1. Cornell, W. D., P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, et al. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197.
2. Okur, A., B. Strockbine, V. Hornak, and C. Simmerling. 2003. Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins. J. Comput. Chem. 24:21-31.
3. Hornak, V., R. Abel, A. Okur, B. Strockbine, A. Roitberg, et al. 2006. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 65:712-725.
4. Showalter, S. A., and R. Bruschweiler. 2007. Quantitative molecular ensemble interpretation of NMR dipolar couplings without restraints. J. Am. Chem. Soc. 129:4158-4159.
5. Koller, A. N., H. Schwalbe, and H. Gohlke. 2008. Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality. Biophys. J. 95:L4-L6.
6. Fawzi, N. L., A. H. Phillips, J. Z. Ruscio, M. Doucleff, D. E. Wemmer, et al. 2008. Structure and dynamics of the AB(21-30) peptide from the interplay of NMR experiments and molecular simulations. J. Am. Chem. Soc. 130:6145-6158.
7. Wickstrom, L., A. Okur, K. Song, V. Hornak, D. P. Raleigh, et al. 2006. The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure. J. Mol. Biol. 360:1094-1107.
8. Showalter, S. A., E. Johnson, M. Rance, and R. Bruschweiler. 2007. Toward quantitative interpretation of methyl side-chain dynamics from NMR by molecular dynamics simulations. J. Am. Chem. Soc. 129:14146-14147.
9. Shi, Z. S., K. Chen, Z. G. Liu, and N. R. Kallenbach. 2006. Conformation of the backbone in unfolded proteins. Chem. Rev. 106:1877-1897.
10. Zagrovic, B., J. Lipfert, E. J. Sorin, I. S. Millettt, W. F. van Gunsteren, et al. 2005. Unusual compactness of a polyproline type II structure. Proc. Natl. Acad. Sci. USA. 102:11698-11703.
11. Makowska, J., S. Rodziewicz-Motowidlo, K. Baginska, J. A. Vila, A. Liwo, et al. 2006. Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins. Proc. Natl. Acad. Sci. USA. 103:1744-1749.
12. Mezei, M., P. J. Fleming, R. Srinivasan, and G. D. Rose. 2004. Polyproline II helix is the preferred conformation for unfolded polyalanine in water. Proteins. 55:502-507.
13. Graf, J., P. H. Nguyen, G. Stock, and H. Schwalbe. 2007. Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study. J. Am. Chem. Soc. 129:1179-1189.
14. Best, R. B., N. V. Buchete, and G. Hummer. 2008. Are current molecular dynamics force fields too helical? Biophys. J. 95:L7-L9.
15. Case, D. A., T. E. Cheatham, T. Darden, H. Gohlke, R. Luo, et al. 2005. The Amber biomolecular simulation programs. J. Comput. Chem. 26:1668-1688.
16. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, et al. 1983. CHARMM - a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
17. van Gunsteren, W. F., S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, et al. 1996. Biomolecular Simulation: The GROMOS96 Manual and User Guide. Vdf Hochschulverlag, ETH Zurich, Switzerland.
18. Jorgensen, W. L., D. S. Maxwell, and J. Tirado-Rives. 1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118:11225-11236.
19. Best, R. B., N. V. Buchete, and G. Hummer. 2008. Are current molecular dynamics force fields too helical? Erratum in Biophys. J. 95:4494.
20. Hansmann, U. H. E. 1997. Parallel tempering algorithm for conformational studies of biological molecules. Chem. Phys. Lett. 281:140-150.
21. Sugita, Y., and Y. Okamoto. 1999. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314:141-151.
22. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
23. Horn, H. W., W. C. Swope, J. W. Pitera, J. D. Madura, T. J. Dick, et al. 2004. Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. J. Chem. Phys. 120:9665-9678.
24. Wong, V., and D. A. Case. 2008. Evaluating rotational diffusion from protein MD simulations. J. Phys. Chem. B. 112:6013-6024.
25. Shirts, M. R., and V. S. Pande. 2005. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. J. Chem. Phys. 122:134508.
26. Case, D. A., C. Scheurer, and R. Bruschweiler. 2000. Static and dynamic effects on vicinal scalar J couplings in proteins and peptides: a MD/DFT analysis. J. Am. Chem. Soc. 122:10390-10397.
27. Bruschweiler, R., and D. A. Case. 1994. Adding harmonic motion to the Karplus relation for spin-spin coupling. J. Am. Chem. Soc. 116:11199-11200.
28. Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure-pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.