A self-consistent, microenvironment modulated screened Coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins

Biophysical Journal

Volumn 77, Issue 1, 1999, Pages 3-22

  Mehler, Ernest L ^a,b   Guarnieri, Frank ^a  

^a CITY UNIVERSITY OF NEW YORK   (United States)

^b MOUNT SINAI MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC ACID; EGG WHITE; GLUTAMIC ACID; LYSOZYME; PROTEIN;

AMINO ACID ANALYSIS; ARTICLE; CHEMICAL MODIFICATION; CRYSTAL; CRYSTAL STRUCTURE; DIELECTRIC CONSTANT; ELECTRIC POTENTIAL; ELECTRICITY; HYDROPHILICITY; HYDROPHOBICITY; PH; PKA; PROTEIN ANALYSIS; PROTEIN CONFORMATION;

EID: 0033012333     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)76868-2     Document Type: Article

References (86)

1. Alexov, E. G., and M. R. Gunner. 1997. Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties. Biophys. J. 74:2075-2093.
2. Antosiewicz, J., J. A. McCammon, and M. K. Gilson. 1994. Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238:415-436.
3. Antosiewicz, J., J. A. McCammon, and M. K. Gilson. 1996. The determinants of pKas in proteins. Biochemistry. 35:7819-7833.
4. a values of acidic residues of hen and turkey lysozymes by two-dimensional NMR. Biophys. J. 66:1180-1184.
5. a's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochem. 29: 10219-10225.
6. Bashford, D., and M. Karplus. 1991. Multiple-site titration curves of proteins: an analysis of exact and approximate methods for their calculation. J. Phys. Chem. 95:9556-9561.
7. Bernstein, F. C., T. F. Koetzle, G, J. B. Williams, E. F. Meyer, M. D. Brice, J. R. Rogers, D. Kennard, T. Simanouchi, and M. Tatsumi. 1977. The protein data bank: a computer-based archival file for macromolecular structure. J. Mol. Biol. 112:535-542.
8. Beroza, P., and D. A. Case. 1996. Including side chain flexibility in continuum electrostatic calculations of protein titration. J. Phys. Chem. 100:20156-20163.
9. Beroza, P., D. R. Fredkin, M. Y. Okamura, and G. Feher. 1991. Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides. Proc. Natl. Acad. Sci. USA. 88:5804-5808.
10. Birss, F. W., and S. Fraga. 1963. Self-consistent-field theory. I. General treatment. J. Chem. Phys. 38:2552-2557.
11. Bode, W., A. Z. Wei, R. Huber, E. Meyer, J. Travis, and S. Neumann. 1986. X-ray crystal structure of the complex of human leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor. EMBO J. 5:2453-2458.
12. Born, M. 1920. Volumen und Hydrationswärme der Ionen. Z. Phys. 1:45-48.
13. Böttcher, C. J. F. 1938. The dielectric constant of dipole liquids. Physica. 5:635-639.
14. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4:187-217.
15. Bucher, M., and T. L. Porter. 1986. Analysis of the Born model for hydration of ions. J. Phys. Chem. 90:3406-3411.
16. Collura, V. P., P. J. Greaney, and B. Robson. 1994. A method for rapidly assessing and refining simple solvent treatments in molecular modelling. Example studies on the antigen-combining loop H2 from FAB fragment McP603. Prot. Eng. 7:221-233.
17. Conway, B. E., J. O. M. Bockris, and I. A. Ammar. 1951. The dielectric constant of the solution in the diffuse and Helmholtz double layers at a charged interface in aqueous solution. Trans. Faraday Soc. 47:756-767.
18. Cornette, J. L., K. B. Cease, H. Margalit, J. L. Spouge, J. A. Berzofsky, and C. DeLisi. 1987. Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. J. Mol. Biol. 195: 659-685.
19. Debye, P. 1929. Polar Molecules, Dover, New York.
20. Debye, P., and L. Pauling. 1925. The inter-ionic attraction theory of ionized solutes. IV. The influence of variation of dielectric constant on the limiting law for small concentrations. J. Am. Chem. Soc. 47: 2129-2134.
21. Demchuk, E., and R. C. Wade. 1996. Improving the continuum dielectric approach to calculating pKa's of ionizable groups in proteins. J. Phys. Chem. 100:17373-17387.
22. Ehrenson, S. 1989. Continuum radial dielectric functions for ion and dipole solution systems. J. Comp. Chem. 10:77-93.
23. Fukamizo, T., T. Torikata, T. Nagayama, T. Minematsu, and K. Hayashi. 1983. Enzymatic activity of avian egg-white lysozymes. J. Biochem. (Tokyo). 94:115-122.
24. Gallagher, T., P. Alexander, P. Bryan, and G. L. Gilliland. 1994. Two crystal structures of the BI immunoglobulin-binding domain of streptococcal protein G and comparison with NMR. Biochemistry. 33: 4721-4729.
25. Ghose, A. K., and G. M. Crippen. 1986. Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships I. Partition coefficients as a measure of hydrophobicity. J. Comp. Chem. 7:565-577.
26. Gilson, M. K. 1993. Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins Struct. Func. Genet. 15:266-282.
27. Guarnieri, F., A. B. Schmidt, and E. L. Mehler. 1998. A screened Coulomb potential based implicit solvent model: formulation and parameter development. Int. J. Quantum Chem. 69:57-64.
28. Harvey, S. C., and P. Hoekstra. 1972. Dielectric relaxation spectra of water adsorbed on lysozyme. J. Phys. Chem. 76:2987-2994.
29. Hassan, S. A., F. Guarnieri, and E. Mehler. 1999. A screened Coulomb potential based implicit solvent model: parametrization and prediction of structures of small peptides. Biophys. J. 76:A198.
30. Howlin, B., D. S. Moss, and Harris, G. W. 1989. Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body/TLS model. Acta Crys. A. 45:851.
31. Hyland, L. J., T. A. Tomaszek, Jr., and T. D. Meek. 1991. Human immunodeficiency virus-1 protease. 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism. Biochemistry. 30:8454-8463.
32. Ido, E., H. Han, F. J. Kezdy, and J. J. Tang. 1991. Kinetic studies of human immunodeficiency virus type 1 protease and its active-site hydrogen bond mutant A28S. J. Biol. Chem. 266:24359-24366.
33. Inagaki, F., Y. Kawano, I. Shamada, K. Takahashi, and T. Miyazawa. 1981. Nuclear magnetic resonance study of the microenvironments of histidine residues of ribonuclease T1 and carboxymethylated ribonuclease T1. J. Biochem. 89:1185-1195.
34. Juffer, A. H., P. Argos, and H. J. Vogel. 1997. Calculating acid-dossociation constants of proteins using the boundary element method. J. Phys. Chem. 101:7664-7673.
35. Katayanagi, K., M. Miyagawa, M. Matsushima, M. Ishikawa, S. Kanaya, H. Nakamura, M. Ikehara, T. Matsuzaki, and K. Morikawa. 1992. Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution. J. Mol. Biol. 223:1029-1052.
36. 9k. J. Mol. Biol. 259:828-839.
37. Khare, D., P. Alexander, J. Antosiewicz, P. Bryan, M. Gilson, and J. Orban. 1997. Pka measurements from nuclear magnetic resonance for the B1 and B2 immunoglobulin G-binding domains of protein G: comparison with calculated values for nuclear magnetic resonance and x-ray structures. Biochemistry. 36:3580-3589.
38. King, G., F. S. Lee, and A. Warshel. 1991. Microscopic simulations of macroscopic dielectric constants of solvated proteins. J. Chem. Phys. 91:3647-3661.
39. Klapper, I., R. Hagstrom, R. Fine, K. Sharp, and B. Honig. 1986. Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins Struct. Func. Genet. 1:47-59.
40. Kostrewa, D., H.-W. Choe, U. Heinemann, and W. Saenger. 1989. Crystal structure of guanosine-free ribonuclease T1, complexed with vanadate, suggests conformational change upon substrate binding. Biochemistry. 28:7592-7600.
41. Kuramitsu, S., and K. Hamaguchi. 1980. Analysis of the acid-base titration curve of hen lysozyme. J. Biochem. 87:1215-1219.
42. Leo, A., P. Y. C. Jow, C. Silipo, and C. Hansch. 1975. Calculation of hydrophobic constant (log P) from π and f-constants. J. Med. Chem. 18:865-868.
43. Lorentz, H. A. 1952. Theory of Electrons. Dover, New York.
44. Luo, N., E. Mehler, and R. Osman. 1999. Specificity and catalysis of uracil DNA glycosylase. A molecular dynamics study of reactant and product complexes with DNA. Biochemistry. In press.
45. Luo, R., M. S. Head, J. Moult, and M. K. Gilson. 1998. pKa shifts in small molecules and HIV protease: electrostatics and conformation. J. Amer. Chem. Soc. 120:6138-6146.
46. MacKerell, A. D. J., D. Bashfod, M. Bellot, R. L. J. Dunbrack, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, B. Roux, M. Schlenkrich, J. Smith, R. Stote, J. Straub, J. Wiorkiewicz-Kuczera, and M. Karplus. 1992. Self-consistent parametrization of bio molecules for molecular modeling and condensed phase simulations. Biophys. J. 6:A143.
47. MacKerell, A. D. J., J. Wiorkiewicz-Kuczera, and M. Karplus. 1995. An all-atom empirical Emergy function for the simulation of nucleic acids. J. Amer. Chem. Soc. 117:11946-11975.
48. Mannhold, R., R. F. Rekker, C. Sonntag, A. M. ter Laak, K. Dross, and E. E. Polymeropouos. 1995. Comparative evaluation of the predictive power of calculation procedures for molecular lipophilicity. J. Pharm. Sci. 84:1410-1419.
49. March, K. L., D. G. Maskalick, R. D. England, S. H. Friend, and F. R. N. Gurd. 1982. Analysis of electrostatic interactions and their relationship to conformation and stability of bovine pancreatic trypsin inhibitor. Biochem. 21:5241-5251.
50. Marquart, M., J. Deisenhofer, W. Bode, and R. Huber. 1983. The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors. Acta Crys. Sect. B. 39:480.
51. Mehler, E. L. 1977. Self-consistent nonorthogonal group function approximation for polyatomic systems. I. Closed shells. J. Chem. Phys. 67: 2728-2739.
52. Mehler, E. L. 1996a. The Lorentz-Debye-Sack theory and dielectric screening of electrostatic effects in proteins and nucleic acids. In Molecular Electrostatic Potential: Concepts and Applications, J. S. Murray and K. Sen, editors. Elsevier Science, Amsterdam, The Netherlands. 371-405.
53. Mehler, E. L. 1996b. A self-consistent, free energy based approximation to calculate pH dependent electrostatic effects in proteins. J. Phys. Chem. 100:16006-16018.
54. Mehler, E. L., and E. Eichele. 1984. Electrostatic effects in water-accessible regions of proteins. Biochemistry. 23:3887-3891.
55. Mehler, E. L., and T. J. Solmajer. 1991. Electrostatic effects in proteins: comparison of dielectric and charge models. Prot. Eng. 4:903-910.
56. Oda, Y., T. Yamazaki, K. Nagayama, S. Kanaya, Y. Kuroda, and H. Nakamura. 1994. Individual ionization constants of all the carboxyl groups in ribonuclease HI from Escherichia coli determined by NMR. Biochemistry. 33:5275-5284.
57. Oda, Y., M. Yoshida, and S. Kanaya. 1993. Role of Histidine-124 in the catalytic function of ribonuclease HI from Escherichia coli. J. Biol. Chem. 268:88-92.
58. Onsager, L. 1936. Electric moments of molecules in liquids. J. Amer. Chem. Soc. 58:1486-1493.
59. Pennock, B. D., and H. P. Schwan. 1969. Further observations on the electrical properties of hemoglobin-bound water. J. Phys. Chem. 73: 2600-2610.
60. Ponnuswamy, P. K., M. Prabhakaran, and P. Manavalan. 1980. Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins. Biochim. Biophys. Acta. 623:301-316.
61. Ramanadham, M., L. C. Sieker, and L. H. Jensen. 1981. Structure of triclinic lysozyme and it Cu(2+) complex at 2 angstroms resolution. Acta Crys. A. 37:33.
62. Rekker, R. F. 1977. The Hydrophobic Fragmental Constant. Elsevier, Amsterdam, The Netherlands.
63. Rekker, R. F. 1979. The hydrophobic fragmental constant: an extension to a 1000 data point set. Eur. J. Med. Chem. 14:479-488.
64. Sack, V. H. 1926. The dielectric constant of electrolytes. Phys. Z. 27: 206-208.
65. Sack, V. H. 1927. The dielectric constants of solutions of electrolytes at small concentrations. Phys. Z. 28:199-210.
66. Schaller, W., and A. D. Robertson. 1995. pH, ionic strength, and temperature dependence of ionization equilibria for the carboxyl groups in turkey ovomucoid third domain. Biochemistry. 34:4714-4723.
67. Schwarzenbach, G. 1936. Der Einfluss einer Ionenladung auf die Acidität einer Säure. Z. Physik. Chem. A. 176:133-153.
68. Sham, Y. Y., Z. T. Chu, and A. Warshel. 1997. Consistent calculations of pKa's of ionizable residues in proteins: semi-microscopic and microscopic approaches. J. Phys. Chem. 101:4458-4472.
69. Sham, Y. Y., I. Muegge, and A. Warshel. 1998. The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins. Biophys. J. 74:1744-1753.
70. Shirley, B. A., P. Stanssen, J. Steyaert, and C. N. Pace. 1989. Conformational stability and activity of ribonuclease T1 and mutants. J. Biol. Chem. 264:11621-11625.
71. Suzuki, T., and Y. Kudo. 1990. Automatic log P estimation based on combined additive modeling methods. J. Comp.-Aided Mol. Design. 4:155-198.
72. 2+ in calbindin mutants: a Monte Carlo study. Biophys. Chem. 38:179-183.
73. 9k: a Monte Carlo simulation study. Biochem. 30:5209-5217.
74. Swint-Kruse, L., and A. D. Roberson. 1995. Hydrogen bonds and the pH dependence of ovomucoid third domain stability. Biochemistry. 35: 4724-4732.
75. Szebenyi, D. M. E., and K. Moffat. 1986. The refined structure of vitamin D-dependent calcium-binding protein from bovine intestine. J. Biol. Chem. 261:8761-8777.
76. Takashima, S., and H. P. Schwan. 1965. Dielectric dispersion of crystalline powders of amino acids, peptides and proteins. J. Phys. Chem. 69: 4176-4182.
77. Tanford, C. 1962. Contribution of hydrophobic interactions to the stability of the globular conformation of proteins. J. Am. Chem. Soc. 84: 4240-4247.
78. Tanford, C., and R. Roxby. 1972. Interpretation of protein titration curves. Application to lysozyme. Biochemistry. 11:2192-2198.
79. Thanki, N., J. K. Rao, S. I. Foundling, W. J. Howe, J. B. Moon, J. O. Hui, A. Tomasselli, G., R. L. Heinrikson, S. Thaisrivongs, and A. Wlodawer. 1992. Crystal structure of a complex of HIV-1 protease with a dihydroxyethylene-containing inhibitor: comparisons with molecular modeling. Protein Sci. 1:1061-1072.
80. a, proton transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry. 20:3167-3177.
81. Warwicker, J., and H. C. Watson. 1982. Calculation of the electric potential in the active site cleft due to α-helix dipoles. J. Mol. Biol. 157: 671-679.
82. Webb, T. J. 1926. The free energy of hydration of ions and the electrostriction of the solvent. J. Am. Chem. Soc. 48:2589-2603.
83. Wilson, K. P., B. A. Malcolm, and B. W. Matthews. 1992. Structural and thermodynamic analysis of compensating mutations within the core of chicken egg white lysozyme. J. Biol Chem. 267:10842.
84. as in proteins. Proteins Struct. Func. Genet. 15:252-265.
85. Yang, W., W. A. Hendrickson, R. J. Crouch, and Y. Satow. 1990. Structure of ribonuclease H phased at 2 Å resolution by MAD analysis of the selenomethionyl protein. Science. 249:1398-1405.
86. You, T. J., and D. Bashford. 1995. Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility. Biophys. J. 69:1721-1733.