Measuring the successes and deficiencies of constant pH molecular dynamics: A blind prediction study

Proteins: Structure, Function and Bioinformatics

Volumn 79, Issue 12, 2011, Pages 3381-3388

  Williams, Sarah L ^a   Blachly, Patrick G ^a   Mccammon, J Andrew ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Constant pH molecular dynamics (CpHMD); Implicit salvation; Monte Carlo; PK a prediction

Indexed keywords

BACTERIAL PROTEIN; NUCLEASE; SOLVENT; STAPHYLOCOCCUS NUCLEASE; UNCLASSIFIED DRUG;

ACCURACY; ANALYTICAL ERROR; ARTICLE; CONFORMATIONAL TRANSITION; CONSTANT PH MOLECULAR DYNAMICS; CONTROLLED STUDY; MOLECULAR DYNAMICS; PH; PKA; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN INTERACTION; PROTON TRANSPORT; SIMULATION; STAPHYLOCOCCUS;

COMPUTER SIMULATION; HYDROGEN-ION CONCENTRATION; MICROCOCCAL NUCLEASE; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MUTATION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTONS; STATIC ELECTRICITY;

EID: 81055156171     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23136     Document Type: Article

References (52)

1. Antosiewicz J, McCammon JA, Gilson MK. Prediction of pH-dependent properties of proteins. J Mol Biol 1994; 238: 415-436.
2. a's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry 1990; 29: 10219-10225.
3. as in proteins. Proteins: Struct Funct Genet 1993; 15: 252-265.
4. Mehler EL, Guarnieri F. A self-consistent microenvironment modulated screened Coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins. Biophys J 1999; 77: 3-22.
5. Wisz MS, Hellinga HW. An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants. Proteins: Struct Funct Genet 2003; 51: 360-377.
6. Pokala N, Handel TM. Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation. Protein Sci 2004; 13: 925-936.
7. Archontis G, Simonson T. Proton binding to proteins: a free-energy component analysis using a dielectric continuum model. Biophys J 2005; 88: 3888-3904.
8. 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.
9. as in proteins. Biophys J 2002; 83: 1731-1748.
10. a's of ionizable residues in proteins: semi-microscopic and microscopic approaches. J Phys Chem B 1997; 101: 4458-4472.
11. a of Glu 7 and 35 in hen egg white lysozyme and Glu 106 in human carbonic anhydrase II. J Am Chem Soc 1991; 113: 3572-3575.
12. a values using QM and QM/MM methods. J Phys Chem A 2005; 109: 6634-6643.
13. Riccardi D, Schaefer P, Yang Y, Yu HB, Ghosh N, Prat-Resina X, Konig P, Li GH, Xu DG, Guo H, Elstner M, Cui Q. Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. J Phys Chem B 2006; 110: 6458-6469.
14. Mongan J, Case DA, McCammon JA. Constant pH molecular dynamics in generalized Born implicit solvent. J Comput Chem 2004; 25: 2038-2048.
15. Baptista AM, Teixeira VH, Soares CM. Constant-pH molecular dynamics using stochastic titration. J Chem Phys 2002; 117: 4184-4200.
16. Machuqueiro M, Baptista AM. Acidic range titration of HEWL using a constant-pH molecular dynamics method. Proteins: Struct Funct Bioinf 2008; 72: 289-298.
17. Dlugosz M, Antosiewicz JM. Constant-pH molecular dynamics simulations: a test case of succinic acid. Chem Phys 2004; 302: 161-170.
18. Dlugosz M, Antosiewicz JM, Robertson AD. Constant-pH molecular dynamics study of protonation-structure relationship in a heptapeptide derived from ovomucoid third domain. Phys Rev E 2004; 69: 021915.1-021915.10.
19. Baptista AM, Martel PJ, Petersen SB. Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration. Proteins: Struct Funct Genet 1997; 27: 523-544.
20. 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.
21. Borjesson U, Hunenberger PH. pH-dependent stability of a decalysine α-helix studied by explicit-solvent molecular dynamics simulations at constant pH. J Phys Chem B 2004; 108: 13551-13559.
22. Lee MS, Salsbury FR, Brooks CL. Constant-pH molecular dynamics using continuous titration coordinates. Proteins: Struct Funct Bioinf 2004; 56: 738-752.
23. Khandogin J, Brooks CL. Constant pH molecular dynamics with proton tautomerism. Biophys J 2005; 89: 141-157.
24. Khandogin J, Chen JH, Brooks CL. Exploring atomistic details of pH-dependent peptide folding. Proc Natl Acad Sci USA 2006; 103: 18546-18550.
25. Williams SL, de Oliveira CAF, McCammon JA. Coupling constant pH molecular dynamics with accelerated molecular dynamics. JChem Theory Comput 2010; 6: 560-568.
26. Meng YL, Roitberg AE. Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model. J Chem Theory Comput 2010; 6: 1401-1412.
27. Mongan J, Case DA. Biomolecular simulations at constant pH. Curr Opin Struct Biol 2005; 15: 157-163.
28. Chen JH, Brooks CL, Khandogin J. Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol 2008; 18: 140-148.
29. Baker NA, Bashford D, Case DA. Implicit solvent electrostatics in biomolecular simulation. In: Leimkuhler B, Chipot C, Elber R, Laaksonen A, Mark A, Schlick T, Schütte C, Skeel R, editors. New algorithms for macromolecular simulation, Vol. 49. New York: Springer; 2006. pp. 263-295.
30. http://amylase.ucd.ie/pKacoop/
31. a values of Asp and Glu residues in staphylococcal nuclease. Proteins: Struct Funct Bioinf 2009; 77: 570-588.
32. Isom DG, Cannon BR, Castaneda CA, Robinson A, Garcia-Moreno BE. High tolerance for ionizable residues in the hydrophobic interior of proteins. Proc Natl Acad Sci USA 2008; 105: 17784-17788.
33. Isom DG, Castaneda CA, Cannon BR, Velu PD, Garcia-Moreno BE. Charges in the hydrophobic interior of proteins. Proc Natl Acad Sci USA 2010; 107: 16096-16100.
34. Isom DG, Castaneda CA, Cannon BR, Garcia-Moreno BE. Large shifts in pK(a) values of lysine residues buried inside a protein. Proc Natl Acad Sci USA 2011; 108: 5260-5265.
35. Harms MJ, Schlessman JL, Sue GR, Garcia-Moreno BE. In press.
36. Cannon BR, Isom DG, Garcia-Moreno BE. In press.
37. Chimenti MS, Khangulov VS, Robinson AC, Heroux A, Majumdar A, Schlessman JL, Garcia-Moreno BE. In press.
38. a values in myoglobin and comparison with NMR data for histidines. Biochemistry 1993; 32: 8045-8056.
39. Kyte J. Structure in protein chemistry. New York: Garland Publishing Inc.; 1995. p. 64.
40. Onufriev A, Case DA, Ullmann GM. A novel view of pH titration in biomolecules. Biochemistry 2001; 40: 3413-3419.
41. Cantor CR, Schimmel PR. Biophysical chemistry. Part III. The behavior of biological macromolecules. San Francisco: W.H. Freeman and Co.; 1980. pp. 863-866.
42. Fitch CA, Whitten ST, Hilser VJ, Garcia-Moreno BE. Molecular mechanisms of pH-driven conformational transitions of proteins: insights from continuum electrostatics calculations of acid unfolding. Proteins: Struct Funct Bioinf 2006; 63: 113-126.
43. Wang JM, Cieplak P, Kollman PA. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 2000; 21: 1049-1074.
44. Onufriev A, Case DA, Bashford D. Effective Born radii in the generalized Born approximation: the importance of being perfect. JComput Chem 2002; 23: 1297-1304.
45. Onufriev A, Bashford D, Case DA. Modification of the generalized Born model suitable for macromolecules. J Phys Chem B 2000; 104: 3712-3720.
46. Onufriev A, Bashford D, Case DA. Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins: Struct Funct Bioinf 2004; 55: 383-394.
47. Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977; 23: 327-341.
48. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984; 81: 3684-3690.
49. MATLAB, Version 7.11.0. Natick, Massachusetts: The MathWorks Inc.; 2010.
50. a values. Proteins: Struct Funct Bioinf 2005; 61: 704-721.
51. Chen J, Im W, Brooks CL. Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. J Am Chem Soc 2006; 128: 3728-3736.
52. a values by constant-pH molecular dynamics being hindered by inherited problems? Proteins: Struct Funct Bioinf. 2011; 79: 3437-3447.