Chapter 6 Implicit Solvent Simulations of Biomolecules in Cellular Environments

Annual Reports in Computational Chemistry

Volumn 4, Issue , 2008, Pages 107-121

  Feig, Michael ^a   Tanizaki, Seiichiro ^b   Sayadi, Maryam ^c  

^a Michigan State University   (United States)

^b UNIVERSITY OF TEXAS AT ARLINGTON   (United States)

^c MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

Generalized Born; Langevin; membrane; molecular crowding; thermostat

Indexed keywords

EID: 54849421535     PISSN: 15741400     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1574-1400(08)00006-6     Document Type: Chapter

References (93)

1. Roux B., and Simonson T. Implicit solvent models. Biophys. Chem. 78 (1999) 1-20
2. Feig M. Kinetics from implicit solvent simulations of biomolecules as a function of viscosity. J. Chem. Theory Comput. 3 (2007) 1734-1748
3. Zagrovic B., and Pande V. Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study. J. Comput. Chem. 24 (2003) 1432-1436
4. Sugita Y., and Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314 (1999) 141-151
5. Feig M., and Brooks III C.L. Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr. Opin. Struct. Biol. 14 (2004) 217-224
6. Gnanakaran S., Nymeyer H., Portman J., Sanbonmatsu K.Y., and Garcia A.E. Peptide folding simulations. Curr. Opin. Struct. Biol. 13 (2003) 168-174
7. Im W., Chen J.H., and Brooks C.L. Peptide and protein folding and conformational equilibria: Theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. Adv. Protein Chem. 72 (2006) 173
8. Onufriev A., Bashford D., and Case D.A. Exploring protein native states and large-scale conformational changes with a modified Generalized Born model. Proteins 55 (2004) 383-394
9. Tanizaki S., and Feig M. Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model. J. Phys. Chem. B 110 (2006) 548-556
10. Ruscio J.Z., and Onufriev A. A computational study of nucleosomal DNA flexibility. Biophys. J. 91 (2006) 4121-4132
11. Ewald P.P. Die Berechnung optischer und elektrostatischer Gitterpotentiale. Ann. Physik 64 (1921) 253-287
12. Darden T.A., York D., and Pedersen L.G. Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
13. Lee M.S., Salsbury Jr. F.R., and Brooks III C.L. Novel Generalized Born methods. J. Chem. Phys. 116 (2002) 10606-10614
14. Krol M. Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer. J. Comput. Chem. 24 (2003) 531-546
15. Zimmerman S.B., and Minton A.P. Macromolecular crowding-Biochemical, biophysical, and physiological consequences. Annu. Rev. Biophys. Biomol. Struct. 22 (1993) 27-65
16. Friedel M., Sheeler D.J., and Shea J.-E. Effects of confinement and crowding on the thermodynamics and kinetics of folding of a minimalist β-barrel protein. J. Chem. Phys. 118 (2003) 8106-8113
17. Despa F., Fernandez A., and Berry R.S. Dielectric modulation of biological water. Phys. Rev. Lett. 93 (2004)
18. Brooks C.L., Berkowitz M., and Adelman S.A. Generalized Langevin theory for many-body problems in chemical-dynamics-Gas-surface collisions, vibrational-energy relaxation in solids, and recombination reactions in liquids. J. Chem. Phys. 73 (1980) 4353-4364
19. Wesson L., and Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci. 1 (1992) 227-235
20. Lazaridis T., and Karplus M. Effective energy function for proteins in solution. Proteins 35 (1999) 133-152
21. Ferrara P., Apostolakis J., and Caflish A. Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins 46 (2002) 24-33
22. Sharp K.A., and Honig B. Electrostatic interactions in macromolecules: Theory and applications. Annu. Rev. Biophys. Chem. 19 (1990) 301-332
23. Gilson M.K., Sharp K.A., and Honig B.H. Calculating the electrostatic potential of molecules in solution: Method and error assessment. J. Comput. Chem. 9 (1987) 327-335
24. Warwicker J., and Watson H.C. Calculation of the electric potential in the active site cleft due to α-helix dipoles. J. Mol. Biol. 157 (1982) 671-679
25. Feig M., Onufriev A., Lee M.S., Im W., Case D.A., and Brooks III C.L. Performance comparison of Generalized Born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J. Comput. Chem. 25 (2004) 265-284
26. Zhou Y.C., Feig M., and Wei G.W. Highly accurate biomolecular electrostatics in continuum dielectric environments. J. Comput. Chem. 29 (2008) 87-97
27. Still W.C., Tempczyk A., Hawley R.C., and Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112 (1990) 6127-6129
28. Sitkoff D., Sharp K.A., and Honig B. Accurate calculation of hydration free-energies using macroscopic solvent models. J. Phys. Chem. 98 (1994) 1978-1988
29. Tan C., Tan Y.H., and Luo R. Implicit nonpolar solvent models. J. Phys. Chem. B 111 (2007) 12263-12274
30. Wagoner J.A., and Baker N.A. Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms. Proc. Natl. Acad. Sci. USA 103 (2006) 8331-8336
31. Gallicchio E., and Levy R.M. AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J. Comput. Chem. 25 (2004) 479-499
32. Chen J., and Brooks III C.L. Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. Phys. Chem. Chem. Phys. 10 (2008) 471-481
33. Stern H.A., and Feller S.E. Calculation of the dielectric permittivity profile for a nonuniform system: Application to a lipid bilayer simulation. J. Chem. Phys. 118 (2003) 3401-3412
34. Sigalov G., Scheffel P., and Onufriev A. Incorporating variable dielectric environments into the Generalized Born model. J. Chem. Phys. 122 (2005)
35. Feig M., Im W., and Brooks III C.L. Implicit solvation based on Generalized Born theory in different dielectric environments. J. Chem. Phys. 120 (2004) 903-911
36. Kirkwood J.G. Theory of solutions of molecules containing widely separated charges with special application to zwitterions. J. Chem. Phys. 2 (1934) 351-361
37. Bashford D., and Case D.A. Generalized Born models of macromolecular solvation effects. Ann. Rev. Phys. Chem. 51 (2000) 129-152
38. Lee M.S., Feig M., Salsbury Jr. F.R., and Brooks III C.L. New analytical approximation to the standard molecular volume definition and its application to Generalized Born calculations. J. Comput. Chem. 24 (2003) 1348-1356
39. Brown F.L.H., and Brannigan G. A consistent model for thermal fluctuations and protein-induced deformations in lipid bilayers. Biophys. J. 90 (2006) 1501-1520
40. Feig M., and Brooks III C.L. Evaluating CASP4 predictions with physical energy functions. Proteins 49 (2002) 232-245
41. Kollman P.A., Massova I., Reyes C., Kuhn B., Huo S., Chong L., Lee M., Lee T., Duan Y., Wang W., Donini O., Cieplak P., Srinivasan J., Case A.D., and Cheatham III T.E. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts Chem. Res. 33 (2000) 889-897
42. Li X.F., Hassan S.A., and Mehler E.L. Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effect: Calculation of structural and dynamic properties. Proteins 60 (2005) 464-484
43. Huang A., and Stultz C.M. Conformational sampling with implicit solvent models: Application to the PHF6 peptide in tau protein. Biophys. J. 92 (2007) 34-45
44. Fan H., Mark A.E., Zhu J., and Honig B. Comparative study of Generalized Born models: Protein dynamics. Proc. Natl. Acad. Sci. USA 102 (2005) 6760-6764
45. Watanabe Y.S., Kim J.G., Fukunishi Y., and Nakamura H. Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation. Chem. Phys. Lett. 400 (2004) 258-263
46. Baumketner A., and Shea J.E. The thermodynamics of folding of a beta hairpin peptide probed through replica exchange molecular dynamics simulations. Theor. Chem. Acc. 116 (2006) 262-273
47. Bursulaya B.D., and Brooks III C.L. Comparative study of the folding free-energy landscape of a three-stranded β-sheet protein with explicit and implicit solvent models. J. Phys. Chem. B 104 (2000) 12378-12383
48. Yoda T., Sugita Y., and Okamoto Y. Cooperative folding mechanism of a beta-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation. Proteins 66 (2007) 846-859
49. Chen J.H., Im W.P., and Brooks C.L. Balancing solvation and intramolecular interactions: Toward a consistent Generalized Born force field. J. Am. Chem. Soc. 128 (2006) 3728-3736
50. Zagrovic B., Sorin E.J., and Pande V. β-Hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 313 (2001) 151-169
51. Chen C.J., and Xiao Y. Molecular dynamics simulations of folding processes of a beta-hairpin in an implicit solvent. Phys. Biol. 3 (2006) 161-171
52. Nymeyer H., and Garcia A.E. Simulation of the folding equilibrium of α-helical peptides: A comparison of the Generalized Born approximation with explicit solvent. Proc. Natl. Acad. Sci. USA 100 (2003) 13934-13939
53. Karanicolas J., and Brooks III C.L. Integrating folding kinetics and protein function: Biphasic kinetics and dual binding specificity in a WW domain. Proc. Natl. Acad. Sci. USA 101 (2004) 3432-3437
54. Jagielska A., and Scheraga H.A. Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: All-atom molecular dynamics in implicit solvent. J. Comput. Chem. 28 (2007) 1068-1082
55. Yang M., Yordanov B., Levy Y., Brüschweiler R., and Huo S. The sequence-dependent unfolding pathway plays a critical role in the amyloidogenicity of transthyretin. Biochemistry 45 (2006) 11992-12002
56. Formaneck M.S., and Cui Q. The use of a Generalized Born model for the analysis of protein conformational transitions: A comparative study with explicit solvent simulations for chemotaxis Y protein (CheY). J. Comput. Chem. 27 (2006) 1923-1943
57. Onufriev A., Case D.A., and Bashford D. Structural details, pathways, and energetics of unfolding apomyoglobin. J. Mol. Biol. 325 (2003) 555-567
58. Murcia M., Faraldo-Gomez J.D., Maxfield F.R., and Roux B. Modeling the structure of the StART domains of MLN64 and StAR proteins in complex with cholesterol. J. Lipid Res. 47 (2006) 2614-2630
59. Chocholousova J., and Feig M. Implicit solvent simulations of DNA and DNA-protein complexes: Agreement with explicit solvent vs. experiment. J. Phys. Chem. B 110 (2006) 17240-17251
60. Tsui V., and Case D.A. Molecular dynamics simulations of nucleic acids with a Generalized Born solvation model. J. Am. Chem. Soc. 122 (2000) 2489-2498
61. Feig M., Chocholousova J., and Tanizaki S. Extending the horizon: Towards the efficient modeling of large biomolecular complexes in atomic detail. Theor. Chem. Acc. 116 (2006) 194-205
62. Gong X.Q., Zhang C.F., Feig M., and Burton Z.F. Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II. Mol. Cell 18 (2005) 461-470
63. Hajjar E., Perahia D., Débat H., Nespoulous C., and Robert C.H. Odorant binding and conformational dynamics in the odorant-binding protein. J. Biol. Chem. 281 (2006) 29929-29937
64. Mongan J., and Case D.A. Biomolecular simulations at constant pH. Curr. Opin. Struct. Biol. 15 (2005) 157-163
65. Lee M.S., Salsbury F.R.J., and Brooks III C.L. Constant pH molecular dynamics using continuous titration coordinates. Proteins 56 (2004) 738-752
66. Khandogin J., Chen J.H., and Brooks III C.L. Exploring atomistic details of pH-dependent peptide folding. Proc. Natl. Acad. Sci. USA 103 (2006) 18546-18550
67. Chen Y.Z., Chen X., and Deng Y.F. Simulating botulinum neurotoxin with constant pH molecular dynamics in Generalized Born implicit solvent. Comput. Phys. Commun. 177 (2007) 210-213
68. Chen J.H., Won H.S., Im W., Dyson H.J., and Brooks III C.L. Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling. J. Biomol. NMR 31 (2005) 59-64
69. Chen J., and Brooks III C.L. Can molecular dynamics simulations provide high-resolution refinement of protein structure?. Proteins 67 (2007) 922-930
70. Roe D.R., Okur A., Wickstrom L., Hornak V., and 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 111 (2007) 1846-1857
71. Geney R., Layten M., Gomperts R., Hornak V., and Simmerling C. Investigation of salt bridge stability in a Generalized Born solvent model. J. Chem. Theory Comput. 2 (2006) 115-127
72. Hoover W.G., Aoki K., Hoover C.G., and De Groot S.V. Time-reversible deterministic thermostats. Physica D 187 (2004) 253-267
73. Nose S. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 52 (1984) 255-268
74. Gunsteren W.F.V., and Berendsen H.J.C. Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry. Ang. Chemie 29 (1990) 992-91023
75. Wyman J. Studies on the dielectric constant of protein solutions. I. Zein. J. Biol. Chem. 90 (1930) 443-476
76. Asami K., Hanai T., and Koizumi N. Dielectric properties of yeast cells. J. Membrane Biol. 28 (1976) 169-180
77. Rufus, E., Alex, Z.C., Mathew, L. Dielectric relaxation studies of biological tissues in the microwave frequency range, APMC 2005 Proceedings, 2005, 16062-5
78. Tanizaki S., Clifford J.W., Connelly B.D., and Feig M. Conformational sampling of peptides in cellular environments. Biophys. J. 94 (2008) 747-759
79. Im W., Feig M., and Brooks III C.L. An implicit membrane Generalized Born theory for the study of structure, stability, and interactions of membrane proteins. Biophys. J. 85 (2003) 2900-2918
80. Spassov V.Z., Yan L., and Szalma S. Introducing an implicit membrane in Generalized Born/solvent accessibility continuum solvent models. J. Phys. Chem. B 106 (2002) 8726-8738
81. Kessel A., Cafiso D.S., and Ben-Tal N. Continuum solvent model calculations of alamethicin-membrane interactions: Thermodynamic aspects. Biophys. J. 78 (2000) 571-583
82. Tanizaki S., and Feig M. A Generalized Born formalism for heterogeneous dielectric environments: Application to the implicit modeling of biological membranes. J. Chem. Phys. 122 (2005) 12470-12476
83. Ulmschneider M.B., Ulmschneider J.P., Sansom M.S.P., and Di Nola A. A Generalized Born implicit-membrane representation compared to experimental insertion free energies. Biophys. J. 92 (2007) 2338-2349
84. Marrink S.J., and Berendsen H.J.C. Permeation process of small molecules across lipid membranes studied by molecular dynamics simulations. J. Phys. Chem. 100 (1996) 16729-16738
85. Radzicka A., and Wolfenden R. Comparing the polarities of the amino-acids-Side-chain distribution coefficients between the vapor-phase, cyclohexane, 1-octanol, and neutral aqueous-solution. Biochemistry 27 (1988) 1664-1670
86. Bemporad D., Essex J.W., and Luttmann C. Permeation of small molecules through a lipid bilayer: A computer simulation study. J. Phys. Chem. B 108 (2004) 4875-4884
87. MacCallum J.L., Bennett W.F.D., and Tieleman D.P. Partitioning of amino acid side chains into lipid bilayers: Results from computer simulations and comparison to experiment. J. General Phys. 129 (2007) 371-377
88. Ulmschneider J.P., Ulmschneider M.B., and Di Nola A. Monte Carlo folding of trans-membrane helical peptides in an implicit Generalized Born membrane. Proteins 69 (2007) 297-308
89. Im W., and Brooks C.L. Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proc. Natl. Acad. Sci. USA 102 (2005) 6771-6776
90. Im W., and Brooks C.L. De novo folding of membrane proteins: An exploration of the structure and NMR properties of the fd coat protein. J. Mol. Biol. 337 (2004) 513-519
91. Lomize A.L., Pogozheva I.D., Lomize M.A., and Mosberg H.I. Positioning of proteins in membranes: A computational approach. Protein Sci. 15 (2006) 1318-1333
92. MacKerell Jr. A.D., 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., and Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102 (1998) 3586-3616
93. Jorgensen W.L., Maxwell D.S., and Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118 (1996) 11225-11236