Biomolecular simulations at constant pH

Current Opinion in Structural Biology

Volumn 15, Issue 2, 2005, Pages 157-163

  Mongan, John ^a   Case, David A ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEPTAPEPTIDE; SOLVENT;

CALCULATION; MATHEMATICAL COMPUTING; PH; PKA; POISSON DISTRIBUTION; PRESSURE; PRIORITY JOURNAL; PROTON TRANSPORT; REVIEW; SIMULATION; TEMPERATURE; THERMODYNAMICS;

EID: 17044422037     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2005.02.002     Document Type: Review

References (55)

1. J. Wyman, and S.J. Gill Binding and Linkage 1990 University Science Books Mill Valley, CA, USA
2. R.A. Alberty Thermodynamics of Biochemical Reactions 2003 John Wiley New York
3. J.B. Matthew, Gurd FRN, E.B. Garcia-Moreno, M.A. Flanagan, K.L. March, and S.J. Shire pH-dependent processes in proteins CRC Crit Rev Biochem 18 1985 91 197
4. P. Beroza, and D.A. Case Calculations of proton-binding thermodynamics in proteins Methods Enzymol 295 1998 170 189
5. a behavior.
6. B. García-Moreno, and C.A. Fitch Structural interpretation of pH and salt-dependent processes in proteins with computational methods Methods Enzymol 380 2004 20 51 This is another good and up-to-date survey of pH-dependent processes in proteins.
7. A. Warshel, F. Sussman, and G. King Free energy changes in solvated proteins: microscopic calculations using a reversible charging process Biochemistry 25 1986 8368 8372
8. L.R. Pratt G. Hummer Simulation and Theory of Electrostatic Interactions in Solution 1999 American Institute of Physics Melville, NY, USA
9. M. Bergdorf, C. Peter, and P.H. Hünenberger Influence of cut-off truncation and artificial periodicity of electrostatic interactions in molecular simulations of solvated ions: a continuum electrostatics study J Chem Phys 119 2003 9129 9144
10. T. Darden, D. Pearlman, and L.G. Pedersen Ionic charging free energies: spherical versus periodic boundary conditions J Chem Phys 109 1998 10921 10935
11. a shifts without truncation of electrostatic interactions: an explicit solvent calculation for succinic acid J Phys Chem 100 1996 6389 6392
12. a values. Both explicit solvent and GB models are examined.
13. R.M. Levy, M. Belhadj, and D.B. Kitchen Gaussian fluctuation formula for electrostatic free-energy changes J Chem Phys 95 1991 3627 3633
14. T. Simonson Gaussian fluctuations and linear response in an electron transfer protein Proc Natl Acad Sci USA 99 2002 6544 6549
15. T. Simonson Electrostatics and dynamics of proteins Rep Prog Phys 66 2003 737 787 This paper provides a very thorough overview of commonly used models to account for electrostatic interactions in proteins.
16. N.A. Baker Poisson-Boltzmann methods for biomolecular electrostatics Methods Enzymol 383 2004 94 118
17. C. Lim, D. Bashford, and M. Karplus Absolute pKa calculations with continuum dielectric methods J Phys Chem 95 1991 5610 5620
18. W.H. Richardson, C. Peng, D. Bashford, L. Noodleman, and D.A. Case Incorporating solvation effects into density functional theory: calculation of absolute acidities Int J Quantum Chem 61 1997 207 217
19. J.J. Klicic, R.A. Friesner, S.Y. Liu, and W.C. Guida Accurate prediction of acidity constants in aqueous solution via density functional theory and self-consistent reaction field methods J Phys Chem A 106 2002 1327 1335
20. D.M. Chipman Computation of pKa from dielectric continuum theory J Phys Chem A 106 2002 7413 7422
21. J. Tomasi Thirty years of continuum solvation chemistry: a review, and prospects for the near future Theor Chem Acc 112 2004 184 203 The author provides a survey of the use of continuum solvent models in combination with quantum mechanical descriptions of the solute.
22. C. Tanford, and J.G. Kirkwood Theory of titration curves. I. General equations for impenetrable spheres J Am Chem Soc 79 1957 5333 5339
23. D. Bashford, and M. Karplus pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model Biochemistry 29 1990 10219 10225
24. C.N. Schutz, and A. Warshel What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins 44 2001 400 417
25. A. Warshel Computer Modelling of Chemical Reactions in Enzymes and Solutions 1991 John Wiley & Sons New York
26. a's of ionizable residues in proteins: semi-microscopic and microscopic approaches J Phys Chem B 101 1997 4458 4472
27. •].
28. E.G. Alexov, and M.R. Gunner Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties Biophys J 74 1997 2075 2093
29. R.E. Georgescu, E.G. Alexov, and M.R. Gunner Combining conformational flexibility and continuum electrostatics for calculating pKas in proteins Biophys J 83 2002 1731 1748
30. E. Alexov Role of the protein side-chain fluctuations on the strength of pair-wise electrostatic interactions: comparing experimental with computed pKas Proteins 50 2003 94 103
31. A. Koumanov, A. Karshikoff, E.P. Friis, and T.V. Borchert Conformational averaging in pK calculations: improvement and limitations in prediction of ionization properties of proteins J Phys Chem B 105 2001 9339 9344
32. a behavior.
33. A. Onufriev, D.A. Case, and G.M. Ullmann A novel view of pH titration in biomolecules Biochemistry 40 2001 3413 3419
34. D. Poland Free energy of proton binding in proteins Biopolymers 69 2003 60 71
35. C. Tanford, and R. Roxby Interpretation of protein titration curves Biochemistry 11 1972 2192 2198
36. D. Bashford, and M. Karplus Multiple-site titration curves of proteins: an analysis of exact and approximate methods for their calculation J Phys Chem 95 1991 9556 9561
37. P. Beroza, D.R. Fredkin, M.Y. Okamura, and G. Feher Protonation of interacting residues in a protein by Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides Proc Natl Acad Sci USA 88 1991 5804 5808
38. A.M. Baptista, P.J. Martel, and S.B. Petersen Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration Proteins 27 1997 523 544
39. U. Börjesson, and P.H. Hünenberger Explicit-solvent molecular dynamics simulation at constant pH: methodology and application to small amines J Chem Phys 114 2001 9706 9719
40. A.M. Baptista Comment on "Explicit-solvent molecular dynamics simulation at constant pH: methodology and application to small amines" J Chem Phys 116 2002 7766 7768
41. U. Börjesson, and P.H. Hünenberger pH-dependent stability of a decalysine α-helix studied by explicit-solvent molecular dynamics simulations at constant pH J Phys Chem B 108 2004 13551 13559 This paper provides an example of the ways in which a continuous protonation variable can be used in conjunction with MD simulations.
42. M.S. Lee, F.R. Salsbury, and C.L. Brooks Constant-pH molecular dynamics using continuous titration coordinates Proteins 56 2004 738 752 This paper reports an ingenious way to use continuous titration coordinates and yet bias the simulations to allow the populations of the physical end states to be extracted in reasonable time. The underlying dynamics are based on a GB model.
43. X. Kong, and C.L. Brooks III λ-dynamics: a new approach to free energy calculations J Chem Phys 105 1996 2414 2423
44. J.E. Mertz, and B.M. Pettitt Molecular dynamics at a constant pH Supercomputer Appl High Perform Comput 8 1994 47 53
45. A.M. Baptista, V.H. Teixeira, and C.M. Soares Constant-pH molecular dynamics using stochastic titration J Chem Phys 117 2002 4184 4200
46. ••].
47. •• ] illustrate how protonation states in an MD simulation can be updated (at relatively infrequent intervals) from the distribution one predicts from PB analysis.
48. M. Feig, and C.L. Brooks III Recent advances in the development and application of implicit solvent models in biomolecule simulations Curr Opin Struct Biol 14 2004 217 224
49. J. Mongan, D.A. Case, and J.A. McCammon Constant pH molecular dynamics in generalized Born implicit solvent J Comput Chem 25 2004 2038 2048 This approach uses MC sampling to update protonation states very frequently, using a GB model both for dynamics and for estimating protonation change energies. For lysozyme, the results are roughly converged after 1 ns of simulation and are mostly independent of which crystal form is used as the starting structure.
50. a estimates.
51. R. Burgi, P.A. Kollman, and W.F. van Gunsteren Simulating proteins at constant pH: an approach combining molecular dynamics and Monte Carlo simulation Proteins 47 2002 469 480
52. H. Nymyer, S. Gnanakran, and A.E. García Atomic simulations of protein folding, using the replica exchange algorithm Methods Enzymol 383 2004 119 149
53. C. Simmerling, T. Fox, and P.A. Kollman Use of locally enhanced sampling in free energy calculations: testing and application of the alpha to beta anomerization of glucose J Am Chem Soc 120 1998 5771 5782
54. D. Hamelberg, J. Mongan, and J.A. McCammon Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules J Chem Phys 120 2004 11919 11929
55. S.T. Wlodek, J. Antosiewicz, and J.A. McCammon Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories Protein Sci 6 1997 373 382