Is alanine dipeptide a good model for representing the torsional preferences of protein backbones?

Journal of Chemical Theory and Computation

Volumn 4, Issue 9, 2008, Pages 1555-1564

  Feig, Michael ^a  

^a Michigan State University

Author keywords

[No Author keywords available]

Indexed keywords

EID: 57949107089     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct800153n     Document Type: Article

References (41)

1. Ramachandran, G. N.; Ramakrishnan, C.; Sasisekharan, V. Stereochemistry of Polypeptide Chain Configurations. J. Mol. Biol. 1963, 7, 95-99.
2. Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 1993, 26, 283-291.
3. Lovell, S. C.; Davis, I. W.; Arendall, W. B., III; de Bakker, P. I. W.; Word, J. M.; Prisant, M. G.; Richardson, J. S.; Richardson, D. C. Structure Validation by Cα Geometry: φ, ψ and Cβ Deviation. Proteins 2003, 50, 437-450.
4. Karplus, P. A. Experimentally observed conformation-dependent geometry and hidden strain in proteins. Protein Sci. 1996, 5, 1406-1420.
5. Kleywegt, G. J.; Jones, T. A. Phi/Psi-chology: Ramachandran revisited. Structure 1996, 4, 1395-1400.
6. Novmöller, S.; Zhou, T.; Ohlson, T. Conformations of amino acids in proteins. Acta Crystallogr., Sect. D 2002, 58, 768-776.
7. Chakrabarti, P.; Pal, D. The interrelationships of side-chain and main-chain conformations in proteins. Prog. Biophys. Mol. Biol. 2001, 76, 1-102.
8. Ho, B. K.; Brasseur, R. The Ramachandran plots of glycine and pre-proline. BMC Struct. Biol. 2005, 5, 14-24.
9. Anderson, R. J.; Weng, Z.; Campbell, R. K.; Jiang, X. Main-Chain Conformational Tendencies of Amino Acids. Proteins 2005, 60, 679-689.
10. Smith, P. E. The alanine dipeptide free energy surface in solution. J. Chem. Phys. 1999, 111, 5568-5579.
11. Drozdov, A. N.; Grossfield, A.; Pappu, R. V. Role of Solvent in Determining Conformational Preferences of Alanine Dipeptide in Water. J. Am. Chem. Soc. 2004, 126, 2574-2581.
12. Wang, Z. X.; Duan, Y. Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Phi.Psi) energy maps and eonformers in the gas phase, ether, and water. J. Comput. Chem. 2004, 25, 1699-1716.
13. Feig, M. Kinetics from Implicit Solvent Simulations of Biomolecules as a Function of Viscosity. J. Chem. Theory Comput. 2007, 3, 1734-1748.
14. Kwac, K.; Lee, K. K.; Han, J. B.; Oh, K. I.; Cho, M. Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: Comparisons with IR and vibrational circular dichroism spectra. J. Chem. Phys. 2008, 128, 105106.
15. Chekmarev, D. S.; Ishida, T.; Levy, R. M. Long-time conformational transitions of alanine dipeptide in aqueous solution: Continuous and discrete-state kinetic models. J. Phys. Chem. B 2004, 108 (50), 19487-19495.
16. Swope, W. C; Pitera, J. W.; Suits, F.; Pitman, M.; Eleftheriou, M.; Fitch, B. G.; Germain, R. S.; Rayshubski, A.; Ward, T. J. C; Zhestkov, Y.; Zhou, R. Describing protein folding kinetics by molecular dynamics simulations. 2. Example applications to alanine dipeptide and beta-hairpin peptide. J. Phys. Chem. B 2004, 108 (21), 6582-6594.
17. Kim, Y. S.; Wang, J. P.; Hochstrasser, R. M. Two-dimensional infrared spectroscopy of the alanine dipeptide in aqueous solution. J. Phys. Chem. B 2005, 109 (15), 7511-7521.
18. Grdadolnik, J.; Grdadolnik, S. G.; Avbelj, F. Determination of conformational preferences of dipeptides using vibrational spectroscopy. J. Phys. Chem. B 2008, 112, 2712-2718.
19. Beachy, M. D.; Chasman, D.; Murphy, R. B.; Halgren, T. A.; Friesner, R. A. Accurate ab Initio Quantum Chemical Determination of the Relative Energetics of Peptide Conformations and Assessment of Empirical Force Fields. J. Am. Chem. Soc. 1997, 119, 5908-5920.
20. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, J. D.; Evanseck, M. J.; 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.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. J. Phys. Chem. B 1998, 102, 3586-3616.
21. MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III. Improved treatment of the protein backbone in empirical force fields. J. Am. Chem. Soc. 2004, 126, 698-699.
22. Mackerell, A. D. Empirical force fields for biological macromolecules: Overview and issues. J. Comput. Chem. 2004, 25 (13), 1584-1604.
23. Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C; Wang, B.; Woods, R. J. The Amber Biomolecular Simulation Programs. J. Comput. Chem. 2005, 26 (16), 1668-1688.
24. MacKerell, A. D., Jr.; Feig, M.; Brooks, C. L., III. Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 2004, 25, 1400-1415.
25. Feig, M.; MacKerell, A. D.; Brooks, C. L. Force field influence on the observation of pi-helical protein structures in molecular dynamics simulations. J. Phys. Chem. B 2003, 107 (12), 2831-2836.
26. Berman, H. M.; Westbrook, J.; Feng, .Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyal, I. N.; Bourne, P. E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242.
27. Macias, A. T.; MacKerell, A. D. CH/pi interactions involving aromatic amino acids: Refinement of the CHARMM tryptophan force field. J. Comput. Chem. 2005, 26 (14), 1452-1463.
28. Jorgensen, W. L. Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water. J. Am. Chem. Soc. 1981, 103, 335-340.
29. Roux, B. Valence selectivity of the gramicidin channel: A molecular dynamics free energy perturbation study. Biophys. J. 1996, 71, 3177-3185.
30. Darden, T. A.; York, D.; Pedersen, L. G. Particle Mesh Ewald: An Nlog(N) Method for Ewald Sums in Large Systems. J. Chem. Phys. 1993, 98, 10089-10092.
31. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes. J. Comput. Phys. 1977, 23 (3), 327-341.
32. Nose, S. A Molecular Dynamics Method for Simulations in the Canonical Ensemble. Mol. Phys. 1984, 52, 255-268.
33. Brooks, B, R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comput. Chem. 1983, 4, 187-217.
34. Feig, M.; Karanicolas, J.; Brooks, C. L., III. MMTSB Tool Set: Enhanced Sampling and Multiscale Modeling Methods for Applications in Structural Biology. J. Mol. Graphics Modell. 2004, 22, 377-395.
35. Wang, G.; Dunbrack, R. L. PISCES: a protein sequence culling server. Bioinformatics 2003, 19, 1589-1591.
36. Chou, P. Y.; Fasman, G. D. Prediction of protein conformation. Biochemistry 1974, 13, 222-245.
37. Guzzo, A. The influence of amino-acid sequence on protein structure. Biophys. J. 1965, 5, 809-822.
38. Lewis, P. N.; Go, N.; Go, M.; Kotelchuck, D.; Scheraga, H. A. Helix Probability Profiles of Denatured Proteins and Their Correlation with Native Structures. Proc. Natl. Acad. Sci. U.S.A. 1970, 65, 810-815.
39. Stellwagen, E.; Shalongo, W. Evidence for Glutamate Self-Capping Within a Peptide Helix. Biopolymers (Peptide Sci.) 1997, 43, 413-418.
40. Tanizaki, S.; Clifford, J. W.; Connelly, B, D.; Feig, M. Conformational Sampling of Peptides in Cellular Environments. Biophys. J. 2008, 94, 747-759.
41. Ben-Naim, A. Statistical potentials extracted from protein structures: Are these meaningful potentials. J. Chem. Phys. 1997, 107 (9), 3698-3706.