Evuation of salt bridge structure and energetics in peptides using explicit, implicit, and hybrid solvation models

Journal of Chemical Theory and Computation

Volumn 4, Issue 3, 2008, Pages 488-498

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

^a STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 58149269532     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct7002308     Document Type: Article

References (65)

1. Tai, K. Conformational sampling for the impatient. Biophys. Chem. 2004, 107 (3), 213-220.
2. Roitberg, A.; Simmerling, C. Special issue: Conformational sampling. J. Mol. Graphics Modell. 2004, 22 (5), 317-317.
3. Smith, L. J.; Daura, X.; van Gunsteren, W. F. Assessing equilibration and convergence in biomoleeular simulations. Proteins: Struct., Funct., Genet. 2002, 48 (3), 487-496.
4. Hansmann, U. H. E. Parallel tempering algorithm for conformational studies of biological molecules. Chem. Phys. Lett. 1997, 281 (1-3), 140-150.
5. Swendsen, R. H.; Wang, J. S. Replica Monte-Carlo Simulation of Spin-Glasses. Phys. Rev. Lett. 1986, 57 (21), 2607-2609.
6. Tesi, M. C.; vanRensburg, E. J. J.; Orlandini, E.; Whittington, S. G. Monte Carlo study of the interacting self-avoiding walk model in three dimensions. J. Stat. Phys. 1996, 82 (1-2), 155-181.
7. Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 1999, 314 (1-2), 141-151.
8. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. Equation of State Calculations by Fast Computing Machines. J. Chem. Phys. 1953, 21 (6), 1087-1092.
9. Feig, M.; Karanicolas, J.; Brooks, C. L. MMTSB Fool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J. Mol. Graphics Modell. 2004, 22 (5), 377-395.
10. Garcia, A. E.; Sanbonmatsu, K. Y. Exploring the energy landscape of a beta hairpin in explicit solvent. Proteins: Struct., Funct., Genet. 2001, 42 (3), 345-354.
11. Garcia, A. E.; Sanbonmatsu, K. Y. alpha-Helical stabilization by side chain shielding of backbone hydrogen bonds. Proc. Natl. Acad. Sci. U.S.A. 2002, 99 (5), 2782-2787.
12. Karanicolas, J.; Brooks, C. L. The structural basis for biphasic kinetics in the folding of the WW domain from a forminbinding protein: Lessons for protein design? Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (7), 3954-3959.
13. Kinnear, B. S.; Jarrold, M. F.; Hansmann, U. H. E. All-atom generalized-ensemble simulations of small proteins. J. Mol. Graphics Modell. 2004, 22 (5), 397-403.
14. Pitera, J. W.; Swope, W. Understanding folding and design: Replica-exchangc simulations of "Trp-cage" miniproteins. Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (13), 7587-7592.
15. Roe, D. R.; Hornak, V.; Simmerling, C. Folding cooperativity in a three-stranded beta-sheet model. J. Mol. Biol. 2005, 352 (2), 370-381.
16. Sugita. Y.; Kitao, A.; Okamoto, Y. Multidimensional replicaexchange method for free-energy calculations. J. Chem. Phys. 2000, 113 (15), 6042-6051.
17. Zhou, R. H.; Berne, B. J.; Germain, R. The free energy landscape for beta hairpin folding in explicit water. Proc. Natl. Acad. Sci. U.S.A. 2001, 98 (26), 14931-14936.
18. Baumketner, A.; Shea, J. E. The structure of the Alzheimer amyloid beta 10-35 peptide probed through replicaexchange molecular dynamics simulations in explicit solvent. J. Mol. Biol. 2007, 366 (1), 275-285.
19. Paschek, D.; Nymeyer, H.; Garcia, A. E. Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: On the structure and possible role of internal water. J. Struct. Biol. 2007, 157 (3), 524-533.
20. Periole, X.; Mark, A. E. Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent. J. Chem. Phys. 2007, 126 (1).
21. Cheng, X.; Cui, G.; Hornak, V.; Simmerling, C. Modified Replica Exchange Simulation Methods for Local Structure Refinement. J. Phys. Chem. B 2005, 109 (16), 8220-8230.
22. Fukunishi, H.; Watanabe, O.; Fakada, S. On the Hamiltonian replica exchange method for efficient sampling of biomoleeular systems: Application to protein structure prediction. J. Chem. Phys. 2002, 116 (20), 9058-9067.
23. Kofke, D. A. On the acceptance probability of replicaexchange Monte Carlo trials. J. Chem. Phys. 2002, 117 (15), 6911-6914.
24. Rathore, N.; Chopra, M.; de Pablo, J. J. Optimal allocation of replicas in parallel tempering simulations. J. Chem. Phys. 2005, 122 (2), 024111.
25. Jang, S. M.; Shin, S.; Pak, Y. Replica-exchange method using the generalized effective potential. Phys. Rev. Lett. 2003, 91 (5), 058305.
26. Mitsutake, A.; Sugita, Y.; Okamoto, Y. Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test. J. Chem. Phys. 2003, 118 (14), 6664-6675.
27. Sugita, Y.; Okamoto, Y. Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape. Chem. Phys. Lett. 2000, 329 (3-4), 261-270.
28. Okur, A.; Wiekstrom, L.; Layten, M.; Geney, R.; Song, K.; Hornak, V.; Simmerling, C. Improved efficiency of replica exchange simulations through use of a hybrid explicit/implicit solvation model. J. Chem. Theory Comput. 2006, 2 (2), 420-433.
29. Okur, A.; Roe, D. R.; Cui, G. L.; Hornak, V.; Simmerling, C. Improving convergence of replica-exchange simulations through coupling to a high-temperature structure reservoir. J. Chem. Theory Comput. 2007, 3 (2), 557-568.
30. Roitberg, A. E.; Okur, A.; Simmerling, C. Coupling of replica exchange simulations to a non-Boltzmann structure reservoir. J. Phys. Chem. B 2007, 111 (10), 2415-2418.
31. Affentranger, R.; Tavernelli, I.; Di Iorio, E. E. A novel Hamiltonian replica exchange MD protocol to enhance protein conformational space sampling. J. Chem. Theory Comput. 2006, 2 (2), 217-228.
32. Lyman, E.; Zuckerman, D. M. Resolution exchange simulation with incremental coarsening. J. Chem. Theory Comput. 2006, 2 (3), 656-666.
33. Li, H.; Li, G.; Berg, B. A.; Yang, W. Finite reservoir replica exchange to enhance canonical sampling in ragged energy surfaces. J. Chem. Phys. 2006, 125 (14), 144902.
34. Li, H.; Yang, W. Sampling enhancement for the quantum mechanical potential based molecular dynamics simulations: a general algorithm and its extension for free energy calculation on rugged energy surface. J. Chem. Phys. 2007, 126 (11), 114104.
35. Min, D.; Li, H.; Li, G.; Bitetti-Putzer, R.; Yang, W. Synergistic approach to improve "alchemical" free energy calculation in ragged energy surface. J. Chem. Phys. 2007, 126 (14), 144109.
36. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. J. Am. Chem. Soc. 1990, 112 (16), 6127-6129.
37. Nymeyer, H.; Garcia, A. E. Simulation of the folding equilibrium of alpha-helical peptides: A comparison of the generalized born approximation with explicit solvent. Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (24), 13934-13939.
38. Zhou, R. H.; Berne, B. J. Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water? Proc. Natl. Acad. Sci. U.S.A. 2002, 99 (20), 12777-12782.
39. Roe, D. R.; Okur, A.; Wickstrom, L.; Hornak, V.; Simmerling, C. Secondary structure bias in generalized born solvent models: Comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation. J. Phys. Chem. B 2007, 111 (7), 1846-1857.
40. Simmerling, C.; Strockbine, B.; Roitberg, A. E. All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 2002, 124 (38), 11258-11259.
41. Zhou, R. H. Free energy landscape of protein folding in water: Explicit vs. implicit solvent. Proteins: Struct., Funct., Genet. 2003, 53 (2), 148-161.
42. Ghosh. A.; Rapp. C. S.; Friesner, R. A. Generalized born model based on a surface integral formulation. J. Phys. Chem. B 1998, 102 (52), 10983-10990.
43. Liu, P.; Kim, B.; Friesner, R. A.; Berne, B. J. Replica exchange with solute tempering: A method for sampling biological systems in explicit water. Proc. Natl. Acad. Sci. U.S.A. 2005, 102 (39), 13749-13754.
44. Huang, X.; Hagen, M.; Kim, B.; Friesner, R. A.; Zhou, R.; Berne, B. J. Replica Exchange with Solute Tempering: Efficiency in Large Scale Systems. J. Phys. Chem. B 2007, 111 (19), 5405-5410.
45. Geney, R.; Layten, M.; Gomperts, R.; Hornak, V.; Simmerling, C. Investigation of Salt Bridge Stability in a Generalized Born Solvent Model. J. Chem. "Theory Comput. 2006, 2 (1), 115-127.
46. Wickstrom, L.; Okur, A.; Song, K.; Hornak, V.; Raleigh, D. P.; Simmerling, C. L. The Unfolded State of the Villin Headpiece Helical Subdomain: Computational Studies of the Role of Locally Stabilized Structure. J. Mol. Biol. 2006, 360 (5), 1094-1107.
47. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Struct., Funct., Bioinformatics 2006, 65 (3), 712-725.
48. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A 2Nd Generation Force- Field for the Simulation of Proteins, Nucleic-Acids, and Organic-Molecules. J. Am. Chem. Soc. 1995, 117 (19), 5179-5197.
49. Wang, J. M.; Cieplak, P.; Kollman, P. A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000, 21 (12), 1049-1074.
50. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79 (2), 926-935.
51. Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber biomolecular simulation programs. J. Comput. Chem. 2005, 26 (16), 1668-1688.
52. 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.
53. Berendsen, H. J. C.; Postma, J. P. M.; Vangunsteren, W. F.; Dinola, A.; Haak, J. R. Molecular-Dynamics with Coupling to an External Bath. J. Chem. Phys. 1984, 81 (8), 3684-3690.
54. Weber, W.; Hunenberger, P. H.; McCammon, J. A. Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: Influence of artificial periodicity on peptide conformation. J. Phys. Chem. B 2000, 104 (15). 3668-3675.
55. Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald - an N. Log(N) Method for Ewald Sums in Large Systems. J. Chem. Phys. 1993, 98 (12), 10089-10092.
56. Onufriev, A.; Bashford, D.; Case, D. A. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins: Struct., Funct., Bioinformatics 2004, 55 (2), 383-394.
57. Bondi, A. Van Der Waals Volumes + Radii. J. Phys. Chem. 1964, 68 (3), 441-478.
58. Tsui, V.; Case, D. A. Molecular dynamics simulations of nucleic acids with a generalized born solvation model. J. Am. Chem. Soc. 2000, 122 (11), 2489-2498.
59. Ponder, J. W.; Richards, F. M. An Efficient Newton-Like Method for Molecular Mechanics Energy Minimization of Large Molecules. J. Comput. Chem. 1987, 8 (7), 1016-1024.
60. Simmerling, C.; Elber, R.; Zhang, J. MOIL-View - A Program for Visualization of Structure and Dynamics of Biomolecules and STO - A Program for Computing Stochastic Paths. In Modelling of Biomolecular Structures and Mechanisms; Pullman et al., A., Ed.; Kluwer Academic Publishers: The Netherlands, 1995; pp 241-265.
61. McKnight, C. J.; Matsudaira, P. T.; Kim, P. S. NMR structure of the 35-residue villin headpiece subdomain. Nat. Struct. Biol. 1997, 4 (3), 180-4.
62. Kabsch, W.; Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22 (12), 2577-2637.
63. Okur, A.; Simmerling, C. Hybrid Implicit/Explicit Solvation Methods. In Annual Reports in Computational Chemistry; Elsevier: 2006; Vol. 2, pp 97-109.
64. Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. Pairwise Solute Descreening of Solute Charges from a Dielectric Medium. Chem. Phys. Lett. 1995, 246 (1-2), 122-129.
65. Singh, J.; Thornton, J. M. In Atlas of Protein Side-Chain Interactions; IRL Press: Oxford, 1992; Vol. I & II.