Residue-specific force field based on the protein coil library. RSFF1: Modification of OPLS-AA/L

Journal of Physical Chemistry B

Volumn 118, Issue 25, 2014, Pages 6983-6998

  Jiang, Fan ^a   Zhou, Chen Yang ^b   Wu, Yun Dong ^a,b  

^a PEKING UNIVERSITY   (China)

^b PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BIOINFORMATICS; MOLECULAR DYNAMICS; PEPTIDES;

CONFORMATIONAL DISTRIBUTION; ENERGY DECOMPOSITION; EXPLICIT WATER; FORCE FIELD PARAMETRIZATION; MOLECULAR DYNAMICS SIMULATIONS; NATIVE STATE; PROTEIN STRUCTURES; SECONDARY STRUCTURES;

ASCORBIC ACID;

BACTERIAL PROTEIN; DIPEPTIDE; HOMEODOMAIN PROTEIN; IGG FC-BINDING PROTEIN, STREPTOCOCCUS; PEPTIDE; PROTEIN; TRP-CAGE PEPTIDE; TRPZIP2 PROTEIN; WATER;

CHEMISTRY; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; STATIC ELECTRICITY; THEORETICAL MODEL;

BACTERIAL PROTEINS; DIPEPTIDES; HOMEODOMAIN PROTEINS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, THEORETICAL; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; STATIC ELECTRICITY; WATER;

EID: 84903486909     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp5017449     Document Type: Article

References (87)

1. Karplus, M.; McCammon, J. A. Molecular Dynamics Simulations of Biomolecules Nat. Struct. Biol. 2002, 9, 646-652
2. Dror, R. O.; Dirks, R. M.; Grossman, J. P.; Xu, H.; Shaw, D. E. Biomolecular Simulation: A Computational Microscope for Molecular Biology Annu. Rev. Biophys. 2012, 41, 429-452
3. Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Shaw, D. E. How Fast-Folding Proteins Fold Science 2011, 334, 517-520
4. Mirjalili, V.; Feig, M. Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles J. Chem. Theory Comput. 2013, 9, 1294-1303
5. Durrant, J. D.; McCammon, J. A. Molecular Dynamics Simulations and Drug Discovery BMC Biol. 2011, 9, 71
6. Piana, S.; Klepeis, J. L.; Shaw, D. E. Assessing the Accuracy of Physical Models Used in Protein-Folding Simulations: Quantitative Evidence from Long Molecular Dynamics Simulations Curr. Opin. Struc. Biol. 2014, 24, 98-105
7. Oostenbrink, C.; Villa, A.; Mark, A. E.; van Gunsteren, W. F. A Biomolecular Force Field Based on The Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6 J. Comput. Chem. 2004, 25, 1656-1676
8. Jorgensen, W. L.; Tirado-Rives, J. Potential Energy Functions for Atomic-Level Simulations of Water and Organic and Biomolecular Systems Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 6665-6670
9. Xu, Z.; Luo, H. H.; Tieleman, D. P. Modifying The OPLS-AA Force Field to Improve Hydration Free Energies for Several Amino Acid Side Chains Using New Atomic Charges and an Off-Plane Charge Model for Aromatic Residues J. Comput. Chem. 2007, 28, 689-697
10. Tong, Y.; Mei, Y.; Li, Y. L.; Ji, C. G.; Zhang, J. Z. Electrostatic Polarization Makes a Substantial Contribution to the Free Energy of Avidin-Biotin Binding J. Am. Chem. Soc. 2010, 132, 5137-5142
11. Xie, W.; Orozco, M.; Truhlar, D. G.; Gao, J. X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water J. Chem. Theory. Comput. 2009, 5, 459-467
12. Ponder, J. W.; Wu, C.; Ren, P.; Pande, V. S.; Chodera, J. D.; Schnieders, M. J.; Haque, I.; Mobley, D. L.; Lambrecht, D. S.; DiStasio, R. A., Jr. Current Status of the AMOEBA Polarizable Force Field J. Phys. Chem. B 2010, 114, 2549-2564
13. Wang, J.; Cieplak, P.; Li, J.; Wang, J.; Cai, Q.; Hsieh, M.; Lei, H.; Luo, R.; Duan, Y. Development of Polarizable Models for Molecular Mechanical Calculations II: Induced Dipole Models Significantly Improve Accuracy of Intermolecular Interaction Energies J. Phys. Chem. B 2011, 115, 3100-3111
14. 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 Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179-5197
15. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616
16. Jorgensen, W. L.; Maxwell, D. S.; TiradoRives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids J. Am. Chem. Soc. 1996, 118, 11225-11236
17. Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides J. Phys. Chem. B 2001, 105, 6474-6487
18. Mackerell, A. D.; Feig, M.; Brooks, C. L. 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
19. MacKerell, A. D.; Feig, M.; Brooks, C. L. Improved Treatment of the Protein Backbone in Empirical Force Fields J. Am. Chem. Soc. 2004, 126, 698-699
20. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T. A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed-Phase Quantum Mechanical Calculations J. Comput. Chem. 2003, 24, 1999-2012
21. 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 2006, 65, 712-725
22. Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; Shaw, D. E. Improved Side-Chain Torsion Potentials for the Amber ff99sb Protein Force Field Proteins 2010, 78, 1950-1958
23. Hu, H.; Elstner, M.; Hermans, J. Comparison Of A QM/MM Force Field and Molecular Mechanics Force Fields in Simulations of Alanine and Glycine "Dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in Water in Relation to the Problem of Modeling the Unfolded Peptide Backbone in Solution Proteins 2003, 50, 451-463
24. Okur, A.; Strockbine, B.; Hornak, V.; Simmerling, C. Using PC Clusters to Evaluate the Transferability of Molecular Mechanics Force Fields for Proteins J. Comput. Chem. 2003, 24, 21-31
25. Yoda, T.; Sugita, Y.; Okamoto, Y. Secondary-Structure Preferences of Force fields for Proteins Evaluated by Generalized-Ensemble Simulations Chem. Phys. 2004, 307, 269-283
26. Wang, T.; Wade, R. C. Force Field Effects on a β-Sheet Protein Domain Structure in Thermal Unfolding Simulations J. Chem. Theory Comput. 2006, 2, 140-148
27. Todorova, N.; Legge, F. S.; Treutlein, H.; Yarovsky, I. Systematic Comparison of Empirical Forcefields for Molecular Dynamic Simulation of Insulin J. Phys. Chem. B 2008, 112, 11137-11146
28. Freddolino, P. L.; Park, S.; Roux, B.; Schulten, K. Force Field Bias in Protein Folding Simulations Biophys. J. 2009, 96, 3772-3780
29. Matthes, D.; de Groot, B. L. Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes Biophys. J. 2009, 97, 599-608
30. Vymětal, J.; Vondrášek, J. Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides-The Alanine Dipeptide Case Study J. Phys. Chem. B 2010, 114, 5632-5642
31. Project, E.; Nachliel, E.; Gutman, M. Force Field-Dependant Structural Divergence Revealed During Long Time Simulations of Calbindin D9k J. Comput. Chem. 2010, 31, 1864-1872
32. Best, R. B.; Hummer, G. Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides J. Phys. Chem. B 2009, 113, 9004-9015
33. Piana, S.; Lindorff-Larsen, K.; Shaw, D. E. How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization? Biophys. J. 2011, 100, L47-L49
34. Mittal, J.; Best, R. B. Tackling Force-Field Bias in Protein Folding Simulations: Folding of Villin HP35 and Pin WW Domains in Explicit Water Biophys. J. 2010, 99, L26-L28
35. 2 Dihedral Angles J. Chem. Theory Comput. 2012, 8, 3257-3273
36. Nerenberg, P. S.; Head-Gordon, T. Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides J. Chem. Theory Comput. 2011, 7, 1220-1230
37. Li, D.; Brüschweiler, R. NMR-Based Protein Potentials Angew. Chem., Int. Ed. 2010, 49, 6778-6780
38. Nymeyer, H. Energy Landscape of the Trpzip2 Peptide J. Phys. Chem. B 2009, 113, 8288-8295
39. Day, R.; Paschek, D.; Garcia, A. E. Microsecond Simulations of the Folding/Unfolding Thermodynamics of the Trp-Cage Miniprotein Proteins 2010, 78, 1889-1899
40. Vymetal, J.; Vondrasek, J. Critical Assessment of Current Force Fields. Short Peptide Test Case J. Chem. Theory Comput. 2013, 9, 441-451
41. Jiang, F.; Han, W.; Wu, Y. D. Influence of Side Chain Conformations on Local Conformational Features of Amino Acids and Implication for Force Field Development J. Phys. Chem. B 2010, 114, 5840-5850
42. Jiang, F.; Han, W.; Wu, Y. D. The Intrinsic Conformational Features of Amino Acids from a Protein Coil Library and Their Applications in Force Field Development Phys. Chem. Chem. Phys. 2013, 15, 3413-3428
43. Swindells, M. B.; MacArthur, M. W.; Thornton, J. M. Intrinsic ø, ψ Propensities of Amino Acids, Derived from the Coil Regions of Known Structures Nat. Struct. Biol. 1995, 2, 596-603
44. Serrano, L. Comparison between the ø Distribution of the Amino Acids in the Protein Database and NMR Data Indicates that Amino Acids have Various ø Propensities in the Random Coil Conformation J. Mol. Biol. 1995, 254, 322-333
45. Fiebig, K. M.; Schwalbe, H.; Buck, M.; Smith, L. J.; Dobson, C. M. Toward a Description of the Conformations of Denatured States of Proteins. Comparison of a Random Coil Model with NMR Measurements J. Phys. Chem. 1996, 100, 2661-2666
46. Penkett, C. J.; Redfield, C.; Dodd, I.; Hubbard, J.; McBay, D. L.; Mossakowska, D. E.; Smith, R.; Dobson, C. M.; Smith, L. J. NMR Analysis of Main-Chain Conformational Preferences in an Unfolded Fibronectin-Binding Protein J. Mol. Biol. 1997, 274, 152-159
47. Avbelj, F.; Baldwin, R. L. Role of Backbone Solvation and Electrostatics in Generating Preferred Peptide Backbone Conformations: Distributions of phi Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 5742-5747
48. Fitzkee, N. C.; Fleming, P. J.; Rose, G. D. The Protein Coil Library: A Structural Database of Nonhelix, Nonstrand Fragments Derived from the PDB Proteins 2005, 58, 852-854
49. Jha, A. K.; Colubri, A.; Zaman, M. H.; Koide, S.; Sosnick, T. R.; Freed, K. F. Helix, Sheet, and Polyproline II Frequencies and Strong Nearest Neighbor Effects in a Restricted Coil Library Biochemistry 2005, 44, 9691-9702
50. Avbelj, F.; Grdadolnik, S. G.; Grdadolnik, J.; Baldwin, R. L. Intrinsic Backbone Preferences Are Fully Present in Blocked Amino Acids Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 1272-1277
51. Poon, C.; Samulski, E. T.; Weise, C. F.; Weisshaar, J. C. Do Bridging Water Molecules Dictate the Structure of a Model Dipeptide in Aqueous Solution? J. Am. Chem. Soc. 2000, 122, 5642-5643
52. Shi, Z.; Olson, C. A.; Rose, G. D.; Baldwin, R. L.; Kallenbach, N. R. Polyproline II Structure in a Sequence of Seven Alanine Residues Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 9190-9195
53. Shi, Z.; Chen, K.; Liu, Z.; Kallenbach, N. R. Conformation of the Backbone in Unfolded Proteins Chem. Rev. 2006, 106, 1877-1897
54. Grdadolnik, J.; Golič Grdadolnik, S.; Avbelj, F. Determination of Conformational Preferences of Dipeptides Using Vibrational Spectroscopy J. Phys. Chem. B 2008, 112, 2712-2718
55. Schweitzer-Stenner, R. Distribution of Conformations Sampled by the Central Amino Acid Residue in Tripeptides Inferred from Amide I Band Profiles and NMR Scalar Coupling Constants J. Phys. Chem. B 2009, 113, 2922-2932
56. Grdadolnik, J.; Mohacek-Grosev, V.; Baldwin, R. L.; Avbelj, F. Populations of the Three Major Backbone Conformations in 19 Amino Acid Dipeptides Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 1794-1798
57. McGregor, M. J.; Islam, S. A.; Sternberg, M. J. Analysis of the Relationship between Side-Chain Conformation and Secondary Structure In Globular Proteins J. Mol. Biol. 1987, 198, 295-310
58. Chakrabarti, P.; Pal, D. The Interrelationships of Side-Chain and Main-Chain Conformations in Proteins Prog. Biophys. Mol. Biol. 2001, 76, 1-102
59. Sugita, Y.; Okamoto, Y. Replica-Exchange Molecular Dynamics Method for Protein Folding Chem. Phys. Lett. 1999, 314, 141-151
60. Thomas, P. D.; Dill, K. A. An Iterative Method for Extracting Energy-Like Quantities from Protein Structures Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 11628-11633
61. Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madura, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. Development of an Improved Four-Site Water Model for Biomolecular Simulations: TIP4P-Ew J. Chem. Phys. 2004, 120, 9665-9678
62. Prakash, M. K.; Barducci, A.; Parrinello, M. Replica Temperatures for Uniform Exchange and Efficient Roundtrip Times in Explicit Solvent Parallel Tempering Simulations J. Chem. Theory Comput. 2011, 7, 2025-2027
63. Bussi, G.; Donadio, D.; Parrinello, M. Canonical Sampling through Velocity Rescaling J. Chem. Phys. 2007, 126, 14101
64. Lin, I. C.; Tuckerman, M. E. Enhanced Conformational Sampling of Peptides via Reduced Side-Chain and Solvent Masses J. Phys. Chem. B 2010, 114, 15935-15940
65. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. LINCS: A Linear Constraint Solver for Molecular Simulations J. Comput. Chem. 1997, 18, 1463-1472
66. Berman, H.; Henrick, K.; Nakamura, H. Announcing the Worldwide Protein Data Bank Nat. Struct. Biol. 2003, 10, 980
67. Amir, E. D.; Kalisman, N.; Keasar, C. Differentiable, Multi-Dimensional, Knowledge-Based Energy Terms for Torsion Angle Probabilities and Propensities Proteins 2008, 72, 62-73
68. Smith, J. C.; Karplus, M. Empirical Force Field Study of Geometries and Conformational Transitions of Some Organic Molecules J. Am. Chem. Soc. 1992, 114, 801-812
69. Arnautova, Y. A.; Jagielska, A.; Scheraga, H. A. A New Force Field (ECEPP-05) for Peptides, Proteins, and Organic Molecules J. Phys. Chem. B 2006, 110, 5025-5044
70. Pal, T. K.; Sankararamakrishnan, R. Quantum Chemical Investigations on Intraresidue Carbonyl-Carbonyl Contacts in Aspartates of High-Resolution Protein Structures J. Phys. Chem. B 2010, 114, 1038-1049
71. Han, W.; Wu, Y.-D. Coarse-Grained Protein Model Coupled with a Coarse-Grained Water Model: Molecular Dynamics Study of Polyalanine-Based Peptides J. Chem. Theory Comput. 2007, 3, 2146-2161
72. Bartlett, G. J.; Choudhary, A.; Raines, R. T.; Woolfson, D. N. n→π* Interactions in Proteins Nat. Chem. Biol. 2010, 6, 615-620
73. HNα for Identification of Helical Secondary Structure J. Mol. Biol. 1984, 180, 741-751
74. Ludvigsen, S.; Andersen, K. V.; Poulsen, F. M. Accurate Measurements of Coupling Constants from Two-Dimensional Nuclear Magnetic Resonance Spectra of Proteins and Determination of ø-Angles J. Mol. Biol. 1991, 217, 731-736
75. α) Coupling Constants in 15N-Enriched Proteins J. Am. Chem. Soc. 1993, 115, 7772-7777
76. 13C Three-Bond J Couplings Measured by Three-Dimensional Heteronuclear NMR. How Planar Is the Peptide Bond? J. Am. Chem. Soc. 1997, 119, 6360-6368
77. 3 J Coupling Analysis for the Joint Calibration of Karplus Coefficients and Evaluation of Torsion Angles J. Biomol. NMR 1999, 14, 1-12
78. Case, D. A.; Scheurer, C.; Brüschweiler, R. Static and Dynamic Effects on Vicinal Scalar J Couplings in Proteins and Peptides: A MD/DFT Analysis J. Am. Chem. Soc. 2000, 122, 10390-10397
79. Vogeli, B.; Ying, J.; Grishaev, A.; Bax, A. Limits on Variations in Protein Backbone Dynamics from Precise Measurements of Scalar Couplings J. Am. Chem. Soc. 2007, 129, 9377-9385
80. Neidigh, J. W.; Fesinmeyer, R. M.; Andersen, N. H. Designing a 20-Residue Protein Nat. Struct. Biol. 2002, 9, 425-430
81. Cochran, A. G.; Skelton, N. J.; Starovasnik, M. A. Tryptophan Zippers: Stable, Monomeric β-Hairpins Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 5578-5583
82. Blanco, F. J.; Rivas, G.; Serrano, L. A Short Linear Peptide That Folds into a Native Stable β-Hairpin in Aqueous Solution Nat. Struct. Biol. 1994, 1, 584-590
83. Lindorff-Larsen, K.; Maragakis, P.; Piana, S.; Eastwood, M. P.; Dror, R. O.; Shaw, D. E. Systematic Validation of Protein Force Fields against Experimental Data PLoS One 2012, 7, e32131
84. Clarke, N. D.; Kissinger, C. R.; Desjarlais, J.; Gilliland, G. L.; Pabo, C. O. Structural Studies of the Engrailed Homeodomain Protein Sci. 1994, 3, 1779-1787
85. Matthes, D.; de Groot, B. L. Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes Biophys. J. 2009, 97, 599-608
86. Best, R. B.; Mittal, J. Free-Energy Landscape of the GB1 Hairpin in All-Atom Explicit Solvent Simulations with Different Force Fields: Similarities and Differences Proteins 2011, 79, 1318-1328
87. Muñoz, V.; Serrano, L. Development of the Multiple Sequence Approximation within the AGADIR Model of α-helix Formation: Comparison with Zimm-Bragg and Lifson-Roig Formalisms Biopolymers 1997, 41, 495-509