Constant-pH molecular dynamics using continuous titration coordinates

Proteins: Structure, Function and Genetics

Volumn 56, Issue 4, 2004, Pages 738-752

  Lee, Michael S ^a   Salsbury Jr , Freddie R ^b   Brooks III, Charles L ^c  

^a UNITED STATES ARMY MEDICAL RESEARCH INSTITUTE OF INFECTIOUS DISEASES   (United States)

^b WAKE FOREST UNIVERSITY   (United States)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

BPTI; Conformational change; Free energy; Ovomucoid; pKa; Proteins; RNase A

Indexed keywords

OVOMUCOID; PROTEIN; PROTON; RIBONUCLEASE A; SOLVENT;

ACCURACY; ARTICLE; ATOM; BORN IMPLICIT SOLVENT MODEL; CONFORMATIONAL TRANSITION; ENERGY TRANSFER; EXTENDED HAMILTONIAN MODEL; FORCE; FREE ENERGY; MODEL; MOLECULAR DYNAMICS; MOTION; PH; PKA; PRIORITY JOURNAL; PROTEIN CONFORMATION; SIMULATION; THEORETICAL MODEL; THERMODYNAMICS; TITRIMETRY;

APROTININ; COMPUTER SIMULATION; HYDROGEN-ION CONCENTRATION; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MURAMIDASE; RIBONUCLEASE, PANCREATIC; THERMODYNAMICS; TITRIMETRY; TRYPSIN INHIBITOR, KAZAL PANCREATIC;

EID: 4043132337     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20128     Document Type: Article

References (70)

1. Yao J, Feher VA, Espejo BF, Reymond MT, Wright PE, Dyson HJ. Stabilization of a Type IV turn in a family of linear peptides in water solution. J Mol Biol 1994;243:736-753.
2. Kirshenbaum K, Daggett V. pH-dependent conformations of the amyloid beta(1-28) peptide fragment explored using molecular dynamics. Biochemistry 1995;34:7629-7639.
3. Alonso DO, DeArmond SJ, Cohen FE, Daggett V. Mapping the early steps in the pH-induced conformational conversion of the prion protein. Proc Natl Acad Sci USA 2001;98:2895-2899.
4. Ripoli DR, Vorobjev YN, Liwo A, Vila JA, Scheraga HA. Coupling between folding and ionization equilibria: effects of pH on the conformational preferences of polypeptides. J Mol Biol 1996;264: 770-783.
5. Ripoli DR, Vila JA, Villegas ME, Scheraga HA. On the pH-conformational dependence of the unblocked SYPYD peptide. J Mol Biol 1999;292:431-440.
6. Vila JA, Ripoli DR, Scheraga HA. Influence of lysine content and pH on the stability of alanine-based copolypeptides. Biopolymers 2001;58:235-246.
7. Bashford D Gerwert K. Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin. J Mol Biol 1992; 224:473-486.
8. Antosiewicz J, McCammon JA, Gilson MK. Prediction of pH-dependent properties of proteins. J Mol Biol 1994;238:415-436.
9. Sham YY, Chu ZT, Warshel A. Consistent calculations of pKa's of ionizable residues in proteins: semi-microscopic and microscopic approaches. J Phys Chem B1997;101:4458-4472.
10. van Vlijmen HWT, Schaefer M, Karplus M. Improving the accuracy of protein pKa calculations: conformational averaging vs. the average structure. Proteins 1998;33:145-148.
11. Koumanov A, Karshikoff A, Friis EP, Borchert TV. Conformational averaging in pK calculations: improvement and limitations in prediction of ionization properties of proteins. J Phys Chem B 2001;105:9339-9344.
12. Gorfe AA, Ferrara P, Caflisch A, Marti DN, Bosshard HR, Jelesarov I. Calculation of protein ionization equilibria with conformational sampling: pKa of a model leucine zipper, GCN4 and barnase. Proteins 2002;46:41-60.
13. Simonson T, Brooks CL III. Charge screening and the dielectric constant of proteins: insights from molecular dynamics. J Am Chem Soc 1996;118:8452-8458.
14. Schutz CN, Warshel A. What are the dielectric "constants" of proteins and how to validate electrostatic models. Proteins 2001; 44:400-417.
15. King G, Lee FS, Warshel A. Microscopic simulations of macroscopic dielectric constants of solvated proteins. J Chem Phys 1991;95:4366-4377.
16. Dominy BN, Minoux H, Brooks CL III. Electrostatic basis for the stability of thermophilic proteins. Proteins 2004. In press.
17. Sitkoff D, Sharp KA, Honig B. Accurate calculation of hydration free-energies using macroscopic solvent models. J Phys Chem 1994;98:1978-1988.
18. Russell ST, Warshel A. Calculations of electrostatic energies in proteins: the energetics of ionized groups in bovine pancreatic trypsin inhibitor. J Mol Biol 1985;185:389-404.
19. Lee FS, Chu ZT, Warshel A. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs. J Comp Chem 1993;14:161-185.
20. Warshel A, Sussman F, King G. Free energy ofcharges in solvated proteins: microscopic calculations using a reversible charging process. Biochemistry 1986;25:8368-8372.
21. Bürgi R, Kollman PA, van Gunsteren WF. Simulating proteins at constant pH: an approach combining molecular dynamics and Monte Carlo simulation. Proteins 2002;47:469-480.
22. Baptista AM, Martel PJ, Petersen SB. Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration. Proteins 1997;27:523-544.
23. Baptista AM, Teixeira VH, Soares CM. Constant-pH molecular dynamics using stochastic titration. J Chem Phys 2002;117:4184-4200.
24. Borjesson U, Hunenberger PH. Explicit-solvent molecular dynamics simulation at constant pH: methodology and application to small amines. J Chem Phys 2001;114:9706-9719.
25. Mertz JE, Pettitt BM. Molecular dynamics at a constant pH. Supercomputer Applic High Perf Comput 1994;8:47-53.
26. Aqvist J, Warshel A. Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches. Chem Rev 1993;93:2523-2544.
27. Sham YY, Muegge I, Warshel A. Simulating proton translocations in proteins: probing proton transfer pathways in the Rhodobacter sphaeroides reaction center. Proteins 1999;36:484-500.
28. Warshel A. Computer modeling of chemical reactions in enzymes and solutions. New York: Wiley; 1991.
29. Kong X, Brooks CL III. λ-Dynamics: a new approach to free energy calculations. J Chem Phys 1996;105:2414-2423.
30. Guo Z, Brooks CL III, Kong X. Efficient and flexible algorithm for free energy calculations using the λ-dynamics approach. J Phys Chem B 1998;102:2032-2036.
31. Warshel A. Calculations ofenzymic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry 1981;20:3167.
32. Onufriev A, Case DA, Ullmann GM. A novel view ofpH titration in biomolecules. Biochemistry 2001;40:3413-3419.
33. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 1983;4: 187-217.
34. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-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.
35. Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 1990;112:6127-6129.
36. Lee MS, Feig M, Salsbury FR Jr, Brooks CL III. New analytic approximation to the standard molecular volume model and its application to generalized Born calculations. J Comp Chem 2003; 24:1348-1356.
37. Grycuk T. Revision of the model system concept for the prediction of pKa's in proteins. J Phys Chem B 2002;106:1434-1445.
38. Baptista AM, Soares CM. Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium ofproteins. J Phys Chem B 2001;105:293-309.
39. Besler BH, Merz KM, Killman PA. Atomic charges derived from semiempirical methods. J Comp Chem 1990;11:431-439.
40. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Salvador P, Dannenberg JJ, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Baboul AG, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Andres JL, Gonzalez C, Head-Gordon M, Replogle ES, Pople JA. Gaussian 98 (Revision A.11.1). Pittsburgh, PA: Gaussian, Inc.; 2001.
41. Feig M, Mackerell AD Jr, Brooks CL III. Force field influence on the observation of pi-helical protein structures in molecular dynamics simulations. J Phys Chem B 2003;107:2831-2836.
42. Nosé, S. A Unified formation of the constant-temperature molecular-dynamics method. J Chem Phys 1984;81:511-519.
43. Hoover WG. Canonical dynamics-equilibrium phase-space distributions. Phys Rev A 1985;31:1695-1697.
44. Martyna GJ, Klein ML, Tuckerman M. Nosé-Hoover chains: the canonical ensemble via continuous dynamics. J Chem Phys 1992; 97:2635-2643.
45. Gilson MK, Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins 1988;4:7-18.
46. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
47. Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 1999;314:141-151.
48. Hoogstraten CG, Choe S, Westler WM, Markley JL. Comparison of the accuracy of protein solution structures derived from conventional network-edited NOESY data. Protein Sci 1995;4:2289-2299.
49. Parkin S, Rupp B, Hope H. Structure of bovine pancreatic trypsin inhibitor at 125K: definition of carboxyl terminal residues Gly57 and Ala 58. Acta Crystallogr D Biol Crystallogr 1996;52:18-29.
50. Vaney MC, Maignan S, RiesKautt M, Ducruix A. High-resolution structure (1.33 Å) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus: data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission. Acta Crystallogr D Biol Crystallogr 1996;52:505-517.
51. Wlodawer A, Svensson LA, Sjolin L, Gilliland GL. Structure of phosphate-free ribonuclease A refined at 1.26 Å. Biochemistry 1988;27:2705-2717.
52. 1 and implications for catalysis. J Mol Biol 1995;247:774-807.
53. Del Buono GS, Figuerido FE, Levy RM. Intrinsic pKas of ionizable residues in proteins-an explicit solvent calculation for lysozyme. Proteins 1994;20:85-97.
54. Onufriev A, Bashford D, Case DA. A modification of the generalized Born model suitable for macromolecules. J Phys Chem B 2000;104:3712-3720.
55. Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL III. Performance comparison of generalized Born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comp Chem 2004;25:265-284.
56. Nina M, Beglov D, Roux B. Atomic radii for continuum electrostatics based on molecular dynamics free energy simulations. J Phys Chem B 1997;101:5239-5248.
57. Lee MS, Olson MA. Evaluation of Poisson solution models using a hybrid explicit/implicit solvent method. Manuscript in preparation.
58. Calimet N, Schaefer M, Simonson T. Protein molecular dynamics with the generalized Born/ACE solvent model. Proteins 2001;45: 144-158.
59. King G, Warshel A. A surface constrained all-atom solvent model for effective simulations of polar solutions. J Chem Phys 1989;91: 3647-3661.
60. Sagnella DE, Tuckerman ME. An empirical valence bond model for proton transfer in water. J Chem Phys 1998;108:2073-2083.
61. Chipot C. Rational determination of charge distributions for free energy calculations. J Comp Chem 2003;24:409-415.
62. Patel S, Brooks CL III. CHARMM fluctuating charge force field for proteins: I. Parameterization and application to bulk organic liquid simulations. J Comput Chem 2004;25:1-15.
63. Stern HA, Kaminski GA, Banks JL, Zhou R, Berne BJ, Friesner RA. Fluctuating charge, polarizable dipole, and combined models: parameterization from ab initio quantum chemistry. J Phys Chem B 1999;103:4730-4737.
64. Banba S, Guo Z, Brooks CL III. New free energy based methods for ligand binding from detailed structure-function to multiple-ligand screening. In: Reddy MR, Erion MD, editors. Free energy calculations in rational drug design. Vol. 1. New York: Kluwer Academic/Plenum; 2001. p 195-223.
65. Nozaki Y, Tanford C. Examination of titration behavior. Methods Enzymol 1967;11:715-734.
66. Bashford D, Case DA, Dalvit C, Tennant L, Wright PE. Electrostatic calculations of side-chain pKa values in myoglobin and comparison with NMR data for histidines. Biochemistry 1993;32: 8045-8056.
67. Schaller W, Robertson AD. pH, ionic strength, and temperature dependencies of ionization equilibria for the carboxyl groups in turkey ovomucoid third domain. Biochemistry 1995;34:4714-4723.
68. Brown LR, Marco AD, Wagner G, Wuthrich K. A study of the lysyl residues in the basic pancreatic trypsin inhibitor using 1H nuclear magnetic resonance at 360 MHz. Eur J Biochem 1976;62:103-107.
69. Brown LR, Marco AD, Wagner G, Wuthrich K. The influence of a single salt bridge on static and dynamic features of the globular solution conformation of the basic pancreatic trypsin inhibitor. Eur J Biochem 1978;88:87-95.
70. 13C nuclear magnetic resonance studies at 90.5 MHz of the basic pancreatic trypsin inhibitor. Biochemistry 1978;17:2263-2269.