Roles of electrostatic interaction in proteins

Quarterly Reviews of Biophysics

Volumn 29, Issue 1, 1996, Pages 1-90

  Nakamura, Haruki ^a  

^a BIOMOL ENG RESEARCH INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ENDONUCLEASE; PROTEIN; RESOLVASE; RIBONUCLEASE H; SOLVENT;

DIELECTRIC CONSTANT; DNA BINDING; ELECTRICITY; ESCHERICHIA COLI; HOLLIDAY JUNCTION; HYDROGEN BOND; IONIZATION; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR RECOGNITION; NONHUMAN; ONCOGENE C MYB; PKA; POSITIVE FEEDBACK; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN STABILITY; REVIEW;

EID: 84962439356     PISSN: 00335835     EISSN: None     Source Type: Journal    
DOI: 10.1017/s0033583500005746     Document Type: Review

References (211)

1. AKKE, M. & FORSEN, S. (1990) Protein stability and electrostatic interactions between solvent exposed charged side chains, PROTEINS: Struct. Funct. Genet. 8, 23-29.
2. ANDERSON, D. E., BECKTEL, W. J. & DAHLQUIST, F. W. (1990) pH-induced denaturation of proteins: A simple salt bridge contributes 3-5 kcal/mol to the free energy of folding of T4 lysozyme, Biochemistry 29, 2403-2408.
3. ANDERSON, J., ULLO, J. J. & YIP, S. (1987) Molecular dynamics simulation of dielectric properties of water, J. Chem. Phys. 87, 1725-1732.
4. ÅQVIST, J., LUECKE, H., QUIOCHO, F. A. & WARSHEL, A. (1991) Dipoles localized at helix termini of proteins stabilize charges, Proc. Natl. Acad. Sci. USA 88, 2026-2030.
5. ARIYOSHI, M., VASSYLYEV, D. G., IWASAKI, H., NAKAMURA, H., SHINAGAWA, H. & MORIKAWA, K. (1994) Atomic structure of the RuvC resolvase: A Holliday junction-specific endonuclease from E. coli, Cell 78, 1063-1072.
6. ARNOLD, E., JACOBO-MOLINA, A., NANNI, R. G., WILLIAMS, R. L., LU, X., DING, J., CLARK JR., A. D., ZHANG, A., FERRIS, A. L., CLARK, P., HIZI, A. & HUGHES, S. H. (1992) Structure of HIV-1 reverse transcriptase/DNA complex at 7 Å resolution showing active site locations, Nature 357, 85-89.
7. ARUTYUNYAN, E. G., KURANOVA, I. P., VAINSHTEIN, B. K. & STEIGEMANN, W. (1980) X-ray structural investigation of leghemoglobin. Structure of acetate-ferrileghemoglobin at a resolution of 2.0 Å, Sov. Phys. Crystallogr. 25, 43-58.
8. ASTUMIAN, R. D. & BIER, M. (1994) Fluctuation driven ratchets: Molecular motors, Phys. Rev. Lett. 72, 1766-1769.
9. BAKER, E. N. & HUBBARD, R. E. (1984) Hydrogen bonding in globular proteins, Prog. Biophys. molec. Biol. 44, 97-179.
10. BANNER, D. W., BLOOMER, A. C., PETSKO, G. A., PHILLIPS, D. C., POGSON, C. I., WILSON, I. A., CORRAN, P. H., FURTH, A. J., MILMAN, J. D., OFFORD, R. E., PRIDDLE, J. D. & WALEY, S. G. (1975) Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5 Å resolution using amino acid sequence data, Nature 255, 609-614.
11. BARLOW, D. J. & THORNTON, J. M. (1983) Ion-pairs in proteins, J. Mol. Biol. 168, 867-885.
12. BARLOW, D. J. & THORNTON, J. M. (1986) The distribution of charged groups in proteins, Biopolymers 25, 1717-1733.
13. a values in myoglobin and comparison with NMR data for histidines, Biochemistry 32, 8045-8056.
14. a values of ionizable groups in bacteriorhodopsin, J. Mol. Biol. 224, 473-486.
15. a's of ionizable groups in proteins: Atomic details from a continuum electrostatic model, Biochemisty 29, 10219-10225.
16. BASHFORD, D. & KARPLUS, M. (1991) Multiple-site titration curves of proteins: An analysis of exact and approximate methods for their calculation, J. Phys. Chem. 95, 9556-9561.
17. BENNETT, R. J. & WEST, S. C. (1995) RuvC protein resolves Holliday junctions via cleavage of the continuous (noncrossover) strands, Proc. Natl. Acad. Sci. USA 92, 5635-5639.
18. BERENDSEN, H. J. C., POSTMA, J. P. M., VAN GUNSTEREN, W. F. & HERMANS, J. (1981) Interaction models for water in relation to protein hydration, in Intermolecular Forces (ed. B. Pullman), pp. 331-342. Dordrecht: Reidel.
19. BIERZYNSKI, A., KIM, P. S. & BALDWIN, R. L. (1982) A salt bridge stabilizes the helix formed by isolated C-peptide of RNase A, Proc. Natl. Acad. Sci. USA 79, 2470-2474.
20. BLUNDELL, T., JENKINS, J., PEARL, L., SEWELL, T., & PEDERSEN, V. (1985) The high resolution structure of endothiapepsin, in Aspartic Proteinases and Their Inhibitors (ed. V. Kostka), pp. 151-161. Bėrlin: Walter de Gruyter.
21. BOLIN, J. T., FILMAN, D. J., MATTHEWS, D. A., HAMLIN, R. C. & KRAUT, J. (1982) Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 Å resolution, J. Biol. Chem. 257, 13650-13662.
22. BOWIE, J. U., LUTHY, R. & EISENBERG, D. (1991) A method to identify protein sequences that fold into a known three-dimensional structure, Science 253, 164-170.
23. BRADLEY, E. K., THOMASON, J. F., COHEN, F. E., KOSEN, P. A. & KUNTZ, I. D. (1990) Studies of synthetic helical peptides using circular dichroism and nuclear magnetic resonance, J. Mol. Biol. 215, 607-622.
24. BRENNER, B., SHOENBERG, M., CHALOVICH, J. M., GREENE, L. E. AND EISENBERG, E. (1982) Evidence for cross-bridge attachment in relaxed muscle at low ionic strength, Proc. Natl. Acad. Sci. USA 79, 7288-7291.
25. BRENNER, B., YU, L. C. AND PODOLSKY, R. J. (1984) X-ray diffraction evidence for cross-bridge formation in relaxed muscle fibers at various ionic strength, Biophys. J. 46, 299-306.
26. BROOKS, C. L., KARPLUS, M. & PETTITT, B. M. (1988) Proteins: A theoretical perspective of dynamics, structure, and thermodynamics. New Yorok: John Wiley & Sons.
27. BRUCCOLERI, R. E. (1993) Grid positioning independence and the reduction of self-energy in the solution of the Poisson-Boltzmann equation, J. Comput. Chem. 14, 1417-1422.
28. CARTER, P. & WELLS, J. A. (1988) Dissecting the catalytic triad of a serine protease, Nature 332, 564-568.
29. CHOU, P. Y. & FASMAN, G. D. (1974) Conformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins, Biochemistry 13, 211-222.
30. CROUCH, R. J., & DIRKSEN, M.-L. (1982) Ribonuclease H, In Nuclease (eds, S. Linn & R. J. Roberts), pp. 211-241. New York: Cold Spring Harbor Laboratory.
31. DAO-PIN, S., SAUER, U., NICHOLSON, H. & MATTHEWS, B. W. (1991) Contribution of engineered surface salt bridges to the stability of T4 lysozyme determined by directed mutagenesis, Biochemistry 30, 7142-7153.
32. DAVIES, J. F., II, HOSTOMSKA, Z., HOSTOMSKY, Z., JORDAN, S. R. & MATTHEWS, D. (1991) Crystal structure of the ribonuclease H domain of HIV-I reverse transcriptase, Science 252, 88-95.
33. DE DIOS, A. C., PEARSON, J. G. & OLDFIELD, E. (1993) Secondary and tertiary structural effects on protein NMR chemical shifts: An ab initio approach, Science 260, 1491-1496.
34. DILL, K. (1990) Dominant forces in protein folding, Biochemistry 29, 7133-7155.
35. DOI, T., RECKTENWALD, A., KARAKI, Y., KIKUCHI, M., MORIKAWA, K., IKEHARA, M., INAOKA, T., HORI, N. & OHTSUKA, E. (1992) Role of the basic amino acid cluster and Glu-23 in pyrimidine dimer glycosylase activity of T4 endonuclease V, Proc. Natl. Acad. Sci. USA 89, 9420-9424.
36. DOOLITTLE, R. F., FENG, D.-F., JOHNSON, M. S. & MCCLURE, M. A. (1989) Origins and evolutionary relationships of retroviruses, Q. Rev. Biol. 64, 1-30.
37. ERNST, J.A, CLUBB, R. T., ZHOU, H.-X., GRONENBORN, A. M. & CLORE, G. M. (1995) Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR, Science 267, 1813-1817.
38. ERWIN, C. R., BARNETT, B. L., OLIVER, J. D. & SULLIVAN, J. F. (1990) Effects of engineered salt bridges on the stability of subtilisin BPN′, Protein Eng. 4, 87-97.
39. FEDOROFF, O. Y., SALAZAR, M. & REID, B. R. (1993) Structure of a DNA:RNA hybrid duplex. Why RNase H does not cleave pure RNA, J. Mol. Biol. 233, 509-523.
40. FELDMAN, Y. & KOZLOVICH, N. (1995) Time domain dielectric spectroscopy study of macromolecular solutions, Trends in Polym. Sci. 3, 53-60.
41. FERSHT, A. R. (1984) Basis of biological specificity, Trends in Biochem. Sci. 9, 145-147.
42. FERSHT, A. R. (1985) Enzyme Structure and Mechanism, pp. 156. New York: Freeman, W. H.
43. FIELD, M. J., BASH, P. A. & KARPLUS, M. (1990) A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations, J. Comput. Chem. 11, 700-733.
44. FINKELSTEIN, A. V. & PTITSYN, O. B. (1987) Why do globular proteins fit the limited set of folding patterns? Prog. Biophys. molec. Biol. 50, 171-190.
45. FRAUENFELDER, H., PETSKO, G. A. & TSERNOGLOU, D. (1979) Temperature-dependent X-ray diffraction as a probe of protein structural dynamics, Nature 280, 558-563.
46. FRIEDMAN, H. L. (1975) Image approximation to the reaction field, Mol. Phys. 29, 1533-1543.
47. FRÖHLICH, H. (1960) Theory of Dielectrics-Dielectric constant and dielectric loss, 2nd edn. Oxford: Clarendon Press.
48. GILSON, M. K. & HONIG, B. H. (1987) Calculation of electrostatic potentials in an enzyme active site, Nature 330, 84-86.
49. GILSON, M. K. & HONIG, B. H. (1988) Energetics of charge-charge interactions in proteins, PROTEINS: Struct. Funct. Genet. 3, 32-52.
50. GILSON, M. K., SHARP, K. & HONIG, B. H. (1987) Calculating the electrostatic potential of molecules in solution: Method and error assessment, J. Comput. Chem. 9, 327-335.
51. GO, N., NOGUCHI, T. & NISHIKAWA, T. (1983) Dynamics of a small globular protein in terms of low-frequency vivrational modes, Proc. Natl. Acad. Sci. USA 80, 3696-3700.
52. HANSEN, J. P. & MCDONALD, I. R. (1986) Theory of simple liquids, 2nd ed., London: Academic Press.
53. HENDSCH, Z. & TIDOR, B. (1994) Do salt bridges stabilize proteins ? A continuum electrostatic analysis, Protein Science 3, 211-226.
54. HOL, W. G. J., HALIE, L. M. & SANDER, C. (1981) Dipoles of the α-helix and β-sheet: their role in protein folding, Nature 294, 532-536.
55. HOL, W. G. J., VAN DUIJNEN, P. T. & BERENDSEN, H. J. C. (1978) The α-helix dipole and the properties of proteins, Nature 273, 443-446.
56. α trace. Application to model building and detection of co-ordinate errors, J. Mol. Biol. 218, 183-194.
57. HOLMES, K. C., POPP, D., GEBHARD, W. & KABSCH, W. (1990) Atomic model of the actin filament, Nature 347, 44-49.
58. HONIG, B. & NICHOLLS, A. (1995) Classical electrostatics in biology and chemistry, Science 268, 1144-1149.
59. HONIG, B., SHARP, K. & YANG, A.-S. (1993) Macroscopic models of aqueous solutions: Biological and chemical applications, J. Phys. Chem. 97, 1101-1109.
60. HOROVITZ, A., SERRANO, L., AVRON, B., BYCROFT, M. & FERSHT, A. R. (1990) Strength and co-operativity of contributions of surface salt bridges to protein stability, J. Mol. Biol. 216, 1031-1044.
61. HOSHI, H., SAKURAI, M., INOUE, Y. & CHUJO, R. (1987) Medium effects on the molecular electronic structure. I. The formulation of a theory for the estimation of a molecular electronic structure surrounded by an anisotropic medium, J. Chem. Phys. 87, 1107-1115.
62. HSU, I-N., DELBAERE, L. T. J., JAMES, M. N. G. & HOFMANN, T. (1977) Penicillopepsin from Penicillium janthinellum crystal structure at 2.8 Å and sequence homology with porcine pepsin, Nature 266, 140-145.
63. IHARA, S., OOI, T. & TAKAHASHI, S. (1982) Effects of salts on the nonequivalent stability of the α-helices of isomeric block copolypeptides, Biopolymers 21, 131-145.
64. INOUE, H., HAYASE, Y. IWAI, S. & OHTSUKA, E. (1987) Sequence-dependent hydrolysis of RNA using modified oligonucleotide splints and RNase H, FEBS Lett. 215, 327-330.
65. ISHIKAWA, K., OKUMURA, M., KATAYANAGI, K., KIMURA, S., KANAYA, S., NAKAMURA, H. & MORIKAWA, K. (1993) Crystal structure of ribonuclease H from Thermus thermophilus HB8 refined at 2.8 Å resolution, J. Mol. Biol. 230, 529-542.
66. ISRAELACHVILI, J. N. (1985) Intermolecular and Surface Forces. London: Academic Press.
67. JACOBO-MOLINA, A. DING, J., NANNI, R. G., CLARK JR., A. D., LU, X., TANTILLO, C., WILLIAMS, R. L., KAMER, G., FERRIS, A. K. CLARK, P., HIZI, A., HUGHES, S. H. & ARNOLD, E. (1993) Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 Å resolution shows bend DNA, Proc. Natl. Acad. Sci. USA, 90, 6320-6324.
68. JARDETZKY, O. & ROBERTS, G. C. K. (1981) NMR in Molecular Biology, pp. 281-284. New York: Academic Press.
69. JONES, D. T., TAYLOR, W. R. & THORNTON, J. M. (1992) A new approach to protein fold recognition, Nature 358, 86-89.
70. JONES, S. & THORNTON, J. M. (1995) Protein-protein interactions: A review of protein dimer structures, Prog. Biophys. molec. Biol. 63, 31-65.
71. KABSCH, W., MANNHERZ, H. G., SUCK, D., PAI, E. F. AND HOLMES, K. C. (1990) Atomic structure of the actin: DNase I complex, Nature 347, 37-44.
72. KABSCH, W. & SANDER, C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22, 2577-2637.
73. KANAYA, S., KOHARA, A., MIURA, Y., SEKIGUCHI, A., IWAI, S., INOUE, H., OHTSUKA, E., & IKEHARA, M. (1990) Identification of the amino acid residues involved in an active site of Escherichia coli ribonuclease H by site-directed mutagenesis, J. Biol. Chem. 265, 4615-4621.
74. KATAYANAGI, K., MIYAGAWA, M., MATSUSHIMA, M., ISHIKAWA, M., KANAYA, S., IKEHARA, M., MATSUZAKI, T. & MORIKAWA, K. (1990) Three-dimensional structure of ribonuclease H from E. coli, Nature 347, 306-309.
75. KATAYANAGI, K., MIYAGAWA, M., MATSUSHIMA, M., ISHIKAWA, M., KANAYA, S., NAKAMURA, H., IKEHARA, M., MATSUZAKI, T. & MORIKAWA, K. (1992) Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution, J. Mol. Biol. 223, 1029-1052.
76. 2+-binding site, PROTEINS: Struct. Funct. Genet. 17, 337-346.
77. KIDERA, A., INAKA, K., MATSUSHIMA, M. & GO, N. (1992) Normal mode refinement: Crystallographic refinement of protein dynamic structure II. Application to human lysozyme, J. Mol. Biol. 225, 477-486.
78. KING, G., LEE, F. S. & WARSHEL, A. (1991) Microscopic simulations of macroscopic dielectric constants of solvated proteins, J. Chem. Phys. 95, 4366-4377.
79. KING, G. & WARSHEL, A. (1989) A surface constrained all-atom solvent model for effective simulations of polar solutions, J. Chem. Phys. 91, 3647-3661
80. KIRKWOOD, J. G. (1934) Theory of solutions of molecules containing widely separated charges with special application to Zwitterions, J. Chem. Phys. 2, 351-361.
81. KLAPPER, I., HAGSTROM, R., FINE, R., SHARP, K. & HONIG, B. (1986) PROTEINS: Struct. Funct. Genet. 1, 47-59.
82. KOHDA, D., SAWADA, T., & INAGAKI, F. (1991) Characterization of pH titration shifts for all the nonlabile proton resonances in a protein by two-dimensional NMR: The case of mouse Epidermal growth factor, Biochemistry 30, 4896-4900.
83. KOHLSTAEDT, L. A., WANG, J., FRIEDMAN, J. M., RICE, P. A. & STEITZ, T. A. (1992) Crystal structure at 3.5 Å resolution of HIV-1 reverse transcriptase complexed with an inhibitor, Science 256, 1783-1790.
84. KOMATSU, K., NAKAMURA, H., NAKAGAWA, S. & UMEYAMA, H. (1984) Electrostatic forces in the inhibition of dihydrofolate reductase by methotrexate. A field potential study, Chem. Pharm. Bull. 32, 3313-3316.
85. LEE, F. S. & WARSHEL, A. (1992) A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations, J. Chem. Phys. 97, 3100-3107.
86. LEVITT, M., SANDER, C. & STERN, P. S. (1985) Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme, J. Mol. Biol. 181, 423-447.
87. LINDERSTROM-LANG, K. (1924) On the ionisation of proteins, C. R. Trav. Lab. Carlsberg 15, 1-29.
88. LOCKHART, D. J. & KIM, P. S. (1992) Internal Stark effect measurement of the electric field at the amino terminus of an α helix, Science 257, 947-951.
89. LOCKHART, D. J. & KIM, P. S. (1993) Electrostatic screening of charge and dipole interactions with the helix backbone, Science 260, 198-202.
90. LUMB, K. J. & KIM, P. S. (1995) Measurement of interhelical electrostatic interactions in the GCN4 leucine zipper, Science 268, 436-439.
91. MAKHATADZE, G. I. & PRIVALOV, P. L. (1993) Contribution of hydration to protein folding thermodynamics I. The enthalpy of hydration, J. Mol. Biol. 232, 639-659
92. MARQUART, M., DEISENHOFER, J., HUBER, R. & PALM, W. (1980) Crystallographic refinement and atomic models of the intact immunoglobulin molecule Kol and its antigen-binding fragment at 3.0 Å and 1.9 Å resolution, J. Mol. Biol. 141, 369-391.
93. MARQUART, M., WALTER, J., DEISENHOFER, J., BODE, W. & HUBER, R. (1983) The geometry of the reactive site and of the peptide groups in trypsin, tripsinogen and its complex with inhibitors, Acta Crystallogr. 398, 480-490.
94. + salt bridges in short peptides of de novo design, Proc. Natl. Acad. Sci. USA 84, 8898-8902.
95. MATSUO, Y., NAKAMURA, H. & NISHIKAWA, K. (1995) Detection of protein 3D-1D compatibility characterized by the evaluation of side-chain packing and electrostatic interaction, J. Biochem. (Tokyo) 118, 137-148.
96. MATTHEW, J. B. & RICHARDS, F. M. (1982) Anion binding and pH-dependent electrostatic effects in ribonuclease, Biochemistry 21, 4989-4999.
97. MCCAMMON, J. A., GELIN, B. R. & KARPLUS, M. (1977) Dynamics of folded proteins, Nature 267, 585-590.
98. MCCAMMON, J. A. & HARVEY, S. C. (1987) Dynamics of proteins and nucleic acids. Cambridge: Cambridge Univ. Press.
99. McDONALD, I. K. & THORNTON, J. M. (1994) Satisfying hydrogen bonding potential in proteins, J. Mol. Biol. 238, 777-793.
100. MCLACHLAN, A. D. AND STEWART, M. (1976) The 14-fold periodicity in α-tropomyosin and the interaction with actin, J. Mol. Biol. 103, 271-298.
101. MIERTUS, S., SCROCCO, E. & TOMASI, J. (1981) Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects, Chem. Phys. 55, 117-129.
102. MILLIGAN, R. A., WHITTAKER, M. AND SAFER, D. (1990) Molecular structure of F-actin and location of surface binding sites, Nature 348, 217-222.
103. MITCHINSON, C. & BALDWIN, R. L. (1986) The design and production of semisynthetic ribonucleases with increased thermostability by incorporation of S-peptide analogous with enhanced helical stability, PROTEINS: Struct. Funct. Genet. 1, 23-33.
104. MIURA, N., HAYASHI, Y., SHINYASHIKI, N. & MASHIMO, S. (1995) Observation of unfreezable water in aqueous solution of globular protein by microwave dielectric measurement, Biopolymers 36, 9-16.
105. MOMANY, F. A., MCGUIRE, R. F., BURGESS, A. W. & SCHERAGA, H. A. (1975) Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids, J. Phys. Chem. 79, 2361-2381.
106. MORIKAMI, K., NAKAI, T., KIDERA, A., SAITO, M. & NAKAMURA, H. (1992) PRESTO: A vectorized molecular mechanics program for biopolymers, Computers Chem. 16, 243-248.
107. MORIKAWA, K., MATSUMOTO, O., TSUJIMOTO, M., KATAYANAGI, K., ARIYOSHI, M., DOI, T., IKEHARA, M. & OHTSUKA, E. (1992) X-ray structure of T4 endonuclease V: An excision repair enzyme specific for a pyrimidine dimer, Science 256, 523-526.
108. NAKAMURA, H. (1991) Theoretical studies of electrostatic aspects of proteins, in Recent Advances in Biochemistry (eds. S. M. Byun, S. Y. Lee & C. H. Yang), pp. 29-42. Seoul: The Biochemical Society of the Republic of Korea.
109. NAKAMURA, H. (1988) Numerical calculations of reaction fields of protein-solvent systems, J. Phys. Soc. Jpn. 57, 3702-3705.
110. NAKAMURA, H. (1993) Reproduction of correct electrostatic field by charges and dipoles on a closed surface, J. Mol. Graph. 11, 30-36.
111. NAKAMURA, H., KOMATSU, K., NAKAGAWA, S. & UMEYAMA, H. (1985a) Visualization of electrostatic recognition by enzymes for their ligands and cofactors, J. Mol. Graph. 3, 2-11.
112. NAKAMURA, H., KOMATSU, K. & UMEYAMA, H. (1985b) Electrostatic complementarities between guest ligands and host enzymes, J. Phys. Soc. Jpn. 54, 3257-3260.
113. NAKAMURA, H., NAGASHIMA, S. & WAKABAYASHI, T. (1994) Electrostatic field around the actin filemant, in Synchrotron Radiation in the Biosciences (eds. B. Chance, J. Deisenhofer, S. Ebashi, D. T. Goodhead, J. R. Helliwell, H. E. Huxley, T. Iizuka, J. Kirz, T. Mitsui, E. Rubenstein, N. Sakabe, T. Sasaki, G. Schmahl, H. B. Stuhrmann, K. Wütrich & G. Zaccai), pp. 502-508. New York: Oxford Univ. Press.
114. NAKAMURA, H. & NISHIDA, S. (1987) Numerical calculations of electrostatic potentials of protein-solvent systems by the self-consistent boundary method, J. Phys. Soc. Jpn., 56, 1609-1622.
115. NAKAMURA, H., ODA, Y., IWAI, S., INOUE, H., OHTSUKA, E., KANAYA, S., KIMURA, S., KATSUDA, C., KATAYANAGI, K., MORIKAWA, K., MIYASHIRO, H. & IKEHARA, M. (1991) How does RNase H recognize a DNA-RNA hybrid? Proc. Natl. Acad. Sci. USA 88, 11535-11539
116. NAKAMURA, H., SAKAMOTO, T. & WADA, A. (1988) A theoretical study of the dielectric constant of proteins, Protein Eng. 2, 177-183.
117. NAKAMURA, H. & WADA, A. (1985) Nature of the charge distribution in proteins III, Electric multipole structures, J. Phys. Soc. Jpn. 54, 4047-4052.
118. NEUMANN, M. (1985) The dielectric constant of water. Computer simulations with the MCY potential, J. Chem. Phys. 82, 5663-5672.
119. NICHOLSON, H., BECKTEL, W. J. & MATTHEWS, B. W. (1988) Enhanced protein thermostability from designed mutations that interact with α-helix dipoles, Nature 336, 651-656.
120. NISHIKAWA, K. & MATSUO, Y. (1993) Development of pseudo-energy potentials for assessing protein 3D-1D compatibility and detecting weak homologies, Protein Eng. 6, 811-820.
121. NOGUCHI, T. & GO, N. (1985) Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins, Biopolymers 24, 527-546.
122. ODA, Y., YAMAZAKI, T., NAGAYAMA, K., KANAYA, S., KURODA, Y. & NAKAMURA, H. (1994) Individual ionization constants of all the carboxyl groups in ribonuclease HI from Escherichia coli determined by NMR, Biochemistry 33, 5275-5284.
123. OGATA, K., MORIKAWA, S., NAKAMURA, H., HOJO, H., YOSHIMURA, S., ZHANG, R., AIMOTO, S., AMETANI, Y., HIRATA, Z., SARAI, A., ISHII, S. & NISHIMURA, Y. (1995) Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb, Nature Struct. Biol. 2, 309-320.
124. OGATA, K., MORIKAWA, S., NAKAMURA, H., SEKIKAWA, A., INOUE, T., KANAI, H., SARAI, A., ISHII, S. & NISHIMURA, Y. (1994) Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices, Cell 79, 639-648.
125. OOBATAKE, M. & OOI, T. (1993) Hydration and heat stability effects on protein unfolding, Prog. Biophys. molec. Biol. 59, 237-284.
126. PABO, C. O. & SAUER, R. T. (1992) Transcription factors: structural families and principles of DNA recognition, Ann. Rev. Biochem. 61, 1053-1095.
127. PAI, E.F, KRENGEL, U., PETSKO, G. A., GOODY, R. S., KABSCH, W. & WITTINGHOFER, A. (1990) Refined crystal structure of the triphosphate conformation of H-ras P21 at 1.35 Å resolution: implications for the mechanism of GTP hydrolysis, EMBO J. 9, 2351-2359.
128. PARSONS, S. M., & RAFTERY, M. A. (1972) Ionization behavior of the catalytic carboxyls of lysozyme. Effects of ionic strength, Biochemistry 11, 1623-1629.
129. PERUTZ, M. F. (1978) Electrostatic effects in proteins, Science 201, 1187-1191.
130. PERUTZ, M. F. & RAIDT, H. (1975) Stereochemical basis of heat stability in bacterial ferredoxins and in haemoglobin A2, Nature 255, 256-259.
131. PETSKO, G. A. & RINGE, D. (1984) Fluctuations in protein structure from X-ray diffraction, Ann. Rev. Biophys. Bioeng. 13, 331-371.
132. PHILLIPS, G. N., FILLERS, J. P. & COHEN, C. (1986) Tropomyosin crystal structure and muscle regulation, J. Mol. Biol. 192, 111-131.
133. PHILLIPS, S. E. V. & SCHOENBORN, B. P. (1981) Neutron diffraction reveals oxygen-histidine hydrogen bond in oxymyoglobin, Nature 292, 81-82.
134. PRIVALOV, P. L. & GILL, S. J. (1988) Stability of protein structure and hydrophobic interaction, Adv. Protein Chem. 39, 191-234.
135. PRIVALOV, P. L. & MAKHATADZE, G. I. (1993) Contribution of hydration to protein folding thermodynamics II. The entropy and Gibbs energy of hydration, J. Mol. Biol. 232, 660-679.
136. RAYMENT, I., HOLDEN, H. M., WHITTAKER, M., YOHN, C. B., LORENZ, M., HOLMES, K. & MILLIGAN, R. A. (1993a) Structure of the actin-myosin complex and its implication for muscle contraction, Science 261, 58-65.
137. RAYMENT, I., RYPNIEWSKI, W. R., SCHMIDT-BASE, K., SMITH, R., TOMCHICK, D. R., BENNING, M. M., WINKELMANN, D. A., WESENBERG, G. & HOLDEN, H. M. (1993b) Three-dimensional structure of myosin subfragment-1: A molecular motor, Science 261, 50-58.
138. REYNOLDS, C. A., KING, P. M. & RICHARDS, W. G. (1988) Computed redox potentials and the design of bioreductive agents, Nature 334, 80-82
139. RICHARDS, W. G., KING, P. M. & REYNOLDS, C. (1989) A. Solvent effects, Protein Eng. 2, 319-327.
140. RICHARDSON, J. S. & RICHARDSON, D. C. (1988) Amino acid preference for specific locations at the ends of α helices, Science 240, 1648-1652.
141. 13C nuclear magnetic resonance studies at 90.5 MHz of the basic pancreatic trypsin inhibitor, Biochemistry 17, 2263-2269.
142. ROGERS, N. K. & STERNBERG, M. J. E. (1984) Electrostatic interactions in globular proteins, J. Mol. Biol. 174, 527-542.
143. ROUSSELET, J., SALOME, L., AJDARI, A. & PROST, J. (1994) Directional motion of brownian particles induced by a periodic asymmetric potential, Nature 370, 446-448.
144. RUEGG, C., AMMER, D. & LERCH, K. (1982) Comparison of amino acid sequence and thermostability of tyrosinase from three wild type strains of Neurospora crassa, J. Biol. Chem. 257, 6420-6426.
145. RULLMANN, J. A. C., BELLIDO, M. N. & VAN DUIJNEN, P. TH. (1989) The active site of papain: All-atom study of interactions with protein matrix and solvent, J. Mol. Biol. 206, 101-118
146. RUSSEL, A. J., THOMAS, P. G. & FERSHT, A. R. (1987) Electrostatic effects of modification of charged groups in the active site cleft of subtilisin by protein engineering, J. Mol. Biol. 193, 803-813.
147. SAITO, M. (1992) Molecular dynamics simulations of proteins in water without the truncation of long-range Coulomb interactions, Mol. Simul. 8, 321-333.
148. SAITO, M. (1994) Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation, J. Chem. Phys. 101, 4055-4061.
149. SAITO, M. & TANIMURA, R. (1995) Relative melting temperatures of RNase HI mutant proteins from MD simulation/free energy calculations, Chem. Phys. Lett. 236, 156-161.
150. SAKAMOTO, T., NAKAMURA, H., UEDAIRA, H. & WADA, A. (1989) High-frequency dielectric relaxation of water bound to hydrophilic silica gels, J. Phys. Chem. 93, 357-366.
151. SALI, D., BYCROFT, M. & FERSHT, A. R. (1988) Stabilization of protein structure by interaction of α-helix dipole with a charged side chain, Nature 335, 740-743.
152. SALI, D., BYCROFT, M. & FERSHT, A. R. (1991) Surface electrostatic interaction contributes little to stability of barnase, J. Mol. Biol. 220, 779-788.
153. SCHIRMER, T. & EVANS, P. R. (1990) Structural basis of the allosteric behaviour of phosphofructokinase, Nature 343, 140-145.
154. SCHOENBERG, M. (1988) Characterization of the myosin adenosine triphosphate (M-ATP) cross bridge in rabbit and frog skeletal muscle fibers, Biophys. J. 54, 135-148.
155. SCHULZ, G. E. & SCHIRMER, R. H. (1979) Principles of protein structure. New York: Springer-Verlag.
156. SERRANO, L. & FERSHT, A. R. (1989) Capping and α-helix stability, Nature 342, 296-299.
157. SERRANO, L., HOROVITZ, A., AVRON, B., BYCROFT, M. & FERSHT, A. R. (1990) Estimating the contribution of engineered surface electrostatic interactions to protein stability by using double-mutant cycles, Biochemistry 29, 9434-9352.
158. SHARP, K. (1991) Incorporating solvent and ion screening into molecular dynamics using the finite-difference Poisson-Boltzmann method, J. Comput. Chem. 12, 454-468.
159. SHARP, K., JEAN-CHARLES, A. & HONIG, B. (1992) A local dielectric constant model for solvation free energies which accounts for solute polarizability, J. Phys. Chem. 96, 3822-3828.
160. SHERIDAN, R. P., LEVY, R. M. & SALEMME, F. R. (1982) α-helix dipole model and electrostatic stabilization of 4-α-helical proteins, Proc. Natl. Acad. Sci. USA 79, 4545-4549.
161. SHIRE, S. J., HANANIA, G. I. H. & GURD, F. R. N. (1974) Electrostatic effects in myoglobin. Hydrogen ion equilibria in sperm whale ferrimyoglobin, Biochemistry 13, 2967-2979.
162. SHOEMAKER, K. R., KIM, P. S., BREMS, D. N., MARQUSEE, S., YORK, E. J., CHAIKEN, I. M., STEWART, J. M. & BALDWIN, R. L. (1985) Nature of the charged-group effect on the stability of the C-peptide helix, Proc. Natl. Acad. Sci. USA 82, 2349-2353.
163. SHOEMAKER, K. R., KIM, P. S., YORK, E. J., STEWART, J. M. & BALDWIN, R. L. (1987) Tests of the helix dipole model for stabilization of α-helics, Nature 326, 563-567.
164. SIMONSON, T., PERAHIA, D. & BRICOGNE, G. (1991) Intramolecular dielectric screening in proteins, J. Mol. Biol. 218, 859-886.
165. - exchange reaction and gas phase protonation of polyethers, J. Comput. Chem. 7, 718-730
166. SIPPL, M. J. (1990) Calculation of conformational ensembles from potentials of mean force: An approach to the knowledge-based prediction of local structures in globular proteins, J. Mol. Biol. 213, 850-883.
167. SIPPL, M. J. (1995) Knowledge-based potentials for proteins, Curr. Opin. Struct. Biol. 5, 229-235.
168. SMITH, W. W., BURNETT, R. M., DARLING, G. D. & LUDWIG, M. L. (1977) Structure of the semiquinone form of flavodoxin from clostridium MP. Extention of 1.8 Å resolution and some comparisons with the oxidized state, J. Mol. Biol. 117, 195-225.
169. SPEEDY, R. J. & ANGELL, C. A. (1976) Isothermal compressibility of supercooled water and evidence for a thermodynamic singularity at -45 °C, J. Chem. Phys. 65, 851-858.
170. STERNBERG, M. J. E., HAYES, F. R., RUSSEL, A. J., THOMAS, P. G. & FERSHT, A. R. (1987) Prediction of electrostatic effects of engineering of protein charges, Nature 330, 86-88.
171. STILL, W. C., TEMPCZYK, A., HAWLEY, R. C. & HENDRICKSON, T. (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics, J. Am. Chem. Soc. 112, 6127-6129.
172. SUTOH, K. (1982) Identification of myosin-binding sites on the actin sequence, Biochemistry 21, 3654-3661.
173. SUTOH, K., ANDO, M., SUTOH, K. AND TOYOSHIMA, Y. Y. (1991) Site-directed mutations of Dictyostelium actin: Disruption of a negative charge cluster at the N terminus, Proc. Natl. Acad. Sci. USA 88, 7711-7714.
174. TAKAHASHI, S., KIM, E.-H., HIBINO, T. & OOI, T. (1989) Comparison of α-helix stability in peptides having a negatively or positively charged residue block attached either to the N- or C-terminus of an α-helix: The electrostatic contribution and anisotropic stability of the α-helix, Biopolymers 28, 995-1009.
175. a values, Biopolymers 32, 897-909.
176. TAKANO, T. (1977) Structure of myoglobin refined at 2.0 Å resolution II. Structure of deoxymyoglobin from sperm whale, J. Mol. Biol. 110, 569-584.
177. TAKASHIMA, S. & ASAMI, K. (1993) Calculation and measurement of the dipole moment of small proteins: Use of Protein Data Bank, Biopolymers 33, 59-68.
178. TANFORD, C. (1957) Theory of protein titration curves. II. Calculations for simple models at low ionic strength, J. Am. Chem. Soc. 79, 5340-5347.
179. TANFORD, C. & KIRKWOOD, J. G. (1957) Theory of protein titration curves. I. General equations for impenetrable spheres, J. Am. Chem. Soc. 79, 5333-5339.
180. TANFORD, C. & ROXBY, R. (1972) Interpretation of protein titration curves. Application to lysozyme, Biochemistry 11, 2192-2198.
181. TAYLOR, W. R. & ORENGO, C. A. (1989) Protein structure alignment, J. Mol. Biol. 208, 1-22.
182. TEPLYAKOV, A. V., KURANOVA, I. P., HARUTYUNYAN, E. H., VAINSHTEIN, B. K., FROMMEL, C., HOHNE, W. E. & WILSON, K. S. (1990) Crystal structure of thermitase at 1.4 Å resolution, J. Mol. Biol. 214, 261-279.
183. TOMIOKA, A., RIBI, H. O., TOKUNAGA, M., FURUNO, T., SASABE, H., MIYANO, K. AND WAKABAYASHI, T. (1991) Structural analysis of muscle thin filament, Adv. Biophys. 27, 169-183.
184. TOYOSHIMA, C. AND WAKABAYASHI, T. (1985) Three-dimensional image analysis of the complex of thin filaments and myosin molecules from skeletal muscle. IV. Reconstitution from minimal- and high-dose images of the actin-tropomyosin-myosin subfragment-1 complex, J. Biochem. (Tokyo) 97, 219-243.
185. VAN GUNSTEREN, W. F. & MARK, A. E. (1992) On the interpretation of biochemical data by molecular dynamics computer simulation, Eur. J. Biochem. 204, 947-961.
186. VASSYLYEV, D. G., KASHIWAGI, T., MIKAMI, Y., ARIYOSHI, M., IWAI, S., OHTSUKA, E. & MORIKAWA, K. (1995) Atomic model of a pyrimidine dimer specific excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition, Cell 83, 773-783.
187. WADA, A. (1976) The α-helix as an electric macro-dipole, Adv. Biophys. 9, 1-63.
188. WADA, A. & NAKAMURA, H. (1981) Nature of the charge distribution in proteins, Nature 293, 757-758.
189. WADA, A., NAKAMURA, H. & SAKAMOTO, T. (1985) Nature of the charge distribution in proteins II. Effect of atomic partial charges on ionic charges, J. Phys. Soc. Jpn. 54, 4042-4046.
190. WAGNER, G. & WTHRICH, K. (1986) Observation of internal mobility of proteins by nuclear magnetic resonance in solution, Methods Enzym. 131, 307-326.
191. WAKO, H. & GO, N. (1987) Algorithm for rapid calculation of hessian of conformational energy function of proteins by supercomputer, J. Comput. Chem. 8, 625-635.
192. WALDBURGER, C. D., SCHILDBACH, J. F. & SAUER, R. T. (1995) Are buried
193. WALKER, J. E., WONACOTT, A. J. & HARRIS, J. I. (1980) Heat stability of a tetrameric enzyme, D-Glyceraldehyde-3-phosphate dehydrogenase, Eur. J. Biochem. 180, 581-586.
194. WARSHEL, A. & LEVITT, M. (1976) Theoretical studies of enzymatic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme, J. Mol. Biol. 103, 227-239.
195. WARSHEL, A., PAPAZYAK, A. & KOLLMAN, P. A. (1995) On low-barrier hydrogen bonds and enzyme catalysis, Science 269, 102-103.
196. WARSHEL, A. & RUSSELL, S. T. (1984) Calculation of electrostatic interactions in biological systems and in solutions, Q. Rev. Biophys. 17, 283-422.
197. WARSHEL, A. & WEISS, R. M. (1980) An empirical valence bond approach for comparing reactions in solutions and in enzymes, J. Am. Chem. Soc. 102, 6218-6226
198. WARWICKER, J. & WATSON, H. C. (1982) Calculation of the electric potential in the active site cleft due to α-helix dipoles, J. Mol. Biol. 157, 671-679.
199. WEINER, S. J., KOLLMAN, P. A., CASE, D. A., SINGH, U. C., GHIO, C., ALAGONA, G., PROFETA, S., JR. AND WEINER, P. (1984) A new force field for molecular mechanical simulation of nucleic acids and proteins, J. Am. Chem. Soc. 106, 765-784.
200. WEINER, S. J., SEIBEL, G. L. & KOLLMAN, P. A. (1986) The nature of enzyme catalysis in trypsin, Proc. Natl. Acad. Sci. USA 83, 649-653
201. WINTERSBERGER, U. (1990) Ribonuclease H of retroviral and cellular origin, Pharmac. Ther. 48, 259-280.
202. WODAK, S. J. & ROOMAN, M. J. (1993) Generating and testing protein folds, Curr. Opin. Struct. Biol. 3, 247-259.
203. XU, S. G., KRESS, M. AND HUXLEY, H. E. (1987) X-ray diffraction studies of the structural state of cross-bridges in skinned frog sartorius muscle at low ionic strength, J. Muscle Res. Cell Motil. 8, 39-54.
204. 15N resonances and secondary structure of ribonuclease H from Escherichia coli by heteronuclear three-dimensional NMR spectroscopy, Biochemistry 30, 6036-6047.
205. YAMAZAKI, T., YOSHIDA, M. & NAGAYAMA, K. (1993) Complete assignments of magnetic resonances of ribonuclease H from Escherichia coli by double- and triple-resonance 2D and 3D NMR spectroscopies, Biochemistry 32, 5656-5669.
206. as in proteins, PROTEINS: Struct. Funct. Genet. 15, 252-265.
207. YANG, A.-S. & HONIG, B. (1993) On the pH dependence of protein stability, J. Mol. Biol. 231, 459-474.
208. YANG, A.-S. & HONIG, B. (1994) Structural origins of pH and ionic strength effects on protein stability; Acid denaturation of sperm whale apomyoglobin, J. Mol. Biol. 231, 459-474.
209. YANG, W., HENDRICKSON, W. A., CROUCH, R. J., & SATOW, Y. (1990) Structure of ribonuclease H phased at 2 Å resolution by MAD analysis of the selenomethionyl protein, Science 249, 1398-1405.
210. YANG, W. & STEITZ, T. A. (1995) Recombining the structures of HIV integrase, RuvC and RNase H, Structure 3, 131-134.
211. ZAUHAR, R. J. & MORGAN, R. S. (1985) A new method for computing the macromolecular electric potential, J. Mol. Biol. 186, 815-820.