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Roles of electrostatic interaction in proteins

Published online by Cambridge University Press:  17 March 2009

Haruki Nakamura
Haruki Nakamura
Affiliation:
Protein Engineering Research Institute, Furuedai, Suita, Osaka 565. Japan
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Extract

Electrostatic effects play an essential role in specific molecular recognition and molecular assembly in many biologically important molecules. The specific electric field at the active site also regulates the catalytic reaction of a protein. Moreover, intramolecular or inter-subunit electrostatic interactions, such as saltbridges, hydrogen bonds, and charge-dipole interactions, are considered to work to stabilize protein molecules. Those electrostatic roles recently observed in proteins are reviewed with a description of the origins and principles of electrostatic forces, and analyses will be made using simple models to illuminate the physical basis.

Type
Research Article
Information
Quarterly Reviews of Biophysics , Volume 29 , Issue 1 , February 1996 , pp. 1 - 90
Copyright
Copyright © Cambridge University Press 1996

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References

REFERENCES

Akke, M. & Forsen, S. (1990) Protein stability and electrostatic interactions between solvent exposed charged side chains, PROTEINS: Struct. Funct. Genet. 8, 23–29.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Anderson, J.Ullo, J. J. & Yip, S. (1987) Molecular dynamics simulation of dielectric properties of water, J. Chem. Phys. 87, 1725–1732.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Arnold, E., Jacobo-Molina, A.Nanni, R. G.Williams, R. L.Lu, X.Ding, J., Clark, A. D. Jr.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.CrossRefGoogle ScholarPubMed
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.Google Scholar
Astumian, R. D. & Bier, M. (1994) Fluctuation driven ratchets: Molecular motors, Phys. Rev. Lett. 72, 1766–1769.CrossRefGoogle ScholarPubMed
Baker, E. N. & Hubbard, R. E. (1984) Hydrogen bonding in globular proteins, Prog. Biophys. molec. Biol. 44, 97–179.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Barlow, D. J. & Thornton, J. M. (1983) Ion-pairs in proteins, J. Mol. Biol. 168, 867–885.CrossRefGoogle ScholarPubMed
Barlow, D. J. & Thornton, J. M. (1986) The distribution of charged groups in proteins, Biopolymers 25, 1717–1733.CrossRefGoogle ScholarPubMed
Bashford, D., Case, D. A., Dalvit, C., Tennant, L. & Wright, P. E. (1993) Electrostatic cacluations of side-chain pK a values in myoglobin and comparison with NMR data for histidines, Biochemistry 32, 8045–8056.CrossRefGoogle ScholarPubMed
Bashford, D. & Gerwert, K. (1992) Electrostatic calculations of the p a values of ionizable groups in bacteriorhodopsin, J. Mol. Biol. 224, 473–486.CrossRefGoogle Scholar
Bashford, D. & Karplus, M. (1990) pK a's of ionizable groups in proteins: Atomic details from a continuum electrostatic model, Biochemisty 29, 10219–10225.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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. Pullman, B.), pp. 331–342. Dordrecht: Reidel.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Blundell, T.Jenkins, J., Pearl, L., Sewell, T., & Pedersen, V. (1985) The high resolution structure of endothiapepsin, in Aspartic Proteinases and Their Inhibitors (ed. Kostka, V.), pp. 151–161. Berlin: Walter de Gruyter.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Brenner, B., Yu, L. C. and Podolsky, R. J. (1984) X-ray diffraction evidence for crossbridge formation in relaxed muscle fibers at various ionic strength, Biophys. J. 46, 299–306.CrossRefGoogle Scholar
Brooks, C. L., Karplus, M. & Pettitt, B. M. (1988) Proteins: A theoretical perspective of dynamics, structure, and thermodynamics. New Yorok: John Wiley & Sons.Google Scholar
Bruccoleri, R. E. (1993) Grid positioning independence and the reduction of selfenergy in the solution of the Poisson-Boltzmann equation, J. Comput. Chem. 14, 1417–1422.CrossRefGoogle Scholar
Carter, P. & Wells, J. A. (1988) Dissecting the catalytic triad of a serine protease, Nature 332, 564–568.Google Scholar
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.CrossRefGoogle ScholarPubMed
Crouch, R. J., & Dirksen, M.-L. (1982) Ribonuclease H, In Nuclease (eds Linn, S. & Roberts, R. J.), pp. 211–241. New York: Cold Spring Harbor Laboratory.Google Scholar
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.Google Scholar
IIDavies, J. F., 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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Dill, K. (1990) Dominant forces in protein folding, Biochemistry 29, 7133–7155.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Feldman, Y. & Kozlovich, N. (1995) Time domain dielectric spectroscopy study of macromolecular solutions, Trends in Polym. Sci. 3, 53–60.Google Scholar
Fersht, A. R. (1984) Basis of biological specificity, Trends in Biochem. Sci. 9, 145–147.CrossRefGoogle Scholar
Fersht, A. R. (1985) Enzyme Structure and Mechanism, pp. 156. New York: Freeman, W. H.Google Scholar
Field, M. J., Bash, P. A. & Karplus, M. (1990) A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations, J. Comput. Chem. II, 700–733.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Frauenfelder, H., Petsko, G. A. & Tsernoglou, D. (1979) Temperature-dependent X-ray diffraction as a probe of protein structural dynamics, Nature 280, 558–563.CrossRefGoogle ScholarPubMed
Friedman, H. L. (1975) Image approximation to the reaction field, Mol. Phys. 29, 1533–1543.CrossRefGoogle Scholar
FrÖhlich, H. (1960) Theory of Dielectrics-Dielectric constant and dielectric loss, 2nd edn.Oxford: Clarendon Press.Google Scholar
Gilson, M. K. & Honig, B. H. (1987) Calculation of electrostatic potentials in an enzyme active site, Nature 330, 84–86.CrossRefGoogle Scholar
Gilson, M. K. & Honig, B. H. (1988) Energetics of charge-charge interactions in proteins, PROTEINS: Struct. Funct. Genet. 3, 32–52.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.Google Scholar
Hansen, J. P. & McDonald, I. R. (1986) Theory of simple liquids, 2nd ed., London: Academic Press.Google Scholar
Hendsch, Z. & Tidor, B. (1994) Do salt bridges stabilize proteins ? A continuum electrostatic analysis, Protein Science 3, 211–226.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Holm, L. & Sander, C. (1991) Database algorithm for generating protein backbone and side-chain co-ordinates from Ca trace. Application to model building and detection of co-ordinate errors, J. Mol. Biol. 218, 183–194.CrossRefGoogle Scholar
Holmes, K. C., Popp, D., Gebhard, W. & Kabsch, W. (1990) Atomic model of the actin filament, Nature 347, 44–49.CrossRefGoogle ScholarPubMed
Honig, B. & Nicholls, A. (1995) Classical electrostatics in biology and chemistry, Science 268, 1144–1149.CrossRefGoogle ScholarPubMed
Honig, B., Sharp, K. & Yang, A.-S. (1993) Macroscopic models of aqueous solutions: Biological and chemical applications, J. Phys. Chem. 97, 1101–1109.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Ihara, S., OOI, T. & Takahashi, S. (1982) Effects of salts on the nonequivalent stability of the a-helices of isomeric block copolypeptides, Biopolymers 21, 131–145.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Israelachvili, J. N. (1985) Intermolecular and Surface Forces. London: Academic Press.Google Scholar
Jacobo-Molina, A.Ding, J., Nanni, R. G., Clark, A. D. Jr., 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. Set. USA, 90, 6320–6324.CrossRefGoogle Scholar
Jardetzky, O. & Roberts, G. C. K. (1981) NMR in Molecular Biology, pp. 281–284. New York: Academic Press.Google Scholar
Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992) A new approach to protein fold recognition, Nature 358, 86–89.CrossRefGoogle ScholarPubMed
Jones, S. & Thornton, J. M. (1995) Protein-protein interactions: A review of protein dimer structures, Prog. Biophys. molec. Biol. 63, 31–65.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Kabsch, W. & Sander, C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22, 2577–2637.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.Google Scholar
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.CrossRefGoogle Scholar
Katayanagi, K., Okumura, M. & Morikawa, K. (1993) Crystal structure of Escherichia coli RNase H1 in complex with Mg2+ at 2·8 Å resolution: Proof for a single Mg2+-binding site, PROTEINS: Struct. Fund. Genet. 17, 337–346.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
King, G., Lee, F. S. & Warshel, A. (1991) Microscopic simulations of macroscopic dielectric constants of solvated proteins, J. Chem. Phys. 95, 4366–4377.CrossRefGoogle Scholar
King, G. & Warshel, A. (1989) A surface constrained all-atom solvent model for effective simulations of polar solutions, J. Chem. Phys. 91, 3647–3661CrossRefGoogle Scholar
Kirkwood, J. G. (1934) Theory of solutions of molecules containing widely separated charges with special application to Zwitterions. J. Chem. Phys. 2, 351–361.CrossRefGoogle Scholar
Klapper, I., Hagstrom, R., Fine, R., Sharp, K. & Honig, B. (1986) PROTEINS: Struct. Fund. Genet. 1, 47–59.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Levitt, M., Sander, C. & Stern, P. S. (1985) Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme, J. Mol. Biol. 181, 423–447.CrossRefGoogle Scholar
Linderstrøm-Lang, K. (1924) On the ionisation of proteins, C. R. Trav. Lab. Carlsberg 15, 1–29.Google Scholar
Lockhart, D. J. & Kim, P. S. (1992) Internal Stark effect measurement of the electric field at the amino terminus of an a helix, Science 257, 947–951.CrossRefGoogle Scholar
Lockhart, D. J. & Kim, P. S. (1993) Electrostatic screening of charge and dipole interactions with the helix backbone, Science 260, 198–202.CrossRefGoogle ScholarPubMed
Lumb, K. J. & Kim, P. S. (1995) Measurement of interhelical electrostatic interactions in the GCN4 leucine zipper, Science 268, 436–439.CrossRefGoogle ScholarPubMed
Makhatadze, G. I. & Privalov, P. L. (1993) Contribution of hydration to protein folding thermodynamics I. The enthalpy of hydration, J. Mol. Biol. 232, 639–659CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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, Ada Crystallogr. 39B, 480–490.CrossRefGoogle Scholar
Marqusee, S. & Baldwin, R. L. (1987) Helix stabilization by Glu−…Lys+ salt bridges in short peptides of de novo design, Proc. Natl. Acad. Set. USA 84, 8898–8902.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
Matthew, J. B. & Richards, F. M. (1982) Anion binding and pH-dependent electrostatic effects in ribonuclease, Biochemistry 21, 4989–4999.CrossRefGoogle ScholarPubMed
McCammon, J. A., Gelin, B. R. & Karplus, M. (1977) Dynamics of folded proteins, Nature 267, 585–590.CrossRefGoogle ScholarPubMed
McCammon, J. A. & Harvey, S. C. (1987) Dynamics of proteins and nucleic acids. Cambridge: Cambridge Univ. Press.CrossRefGoogle Scholar
McDonald, I. K. & Thornton, J. M. (1994) Satisfying hydrogen bonding potential in proteins, J. Mol. Biol. 238, 777–793.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Milligan, R. A., Whittaker, M. and Safer, D. (1990) Molecular structure of F-actin and location of surface binding sites, Nature 348, 217–222.CrossRefGoogle ScholarPubMed
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. Fund. Genet. 1, 23–33.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
Morikami, K., Nakai, T., Kidera, A., Saito, M. & Nakamura, H. (1992) PRESTO: A vectorized molecular mechanics program for biopolymers, Computers Chem. 16, 243–248.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Nakamura, H. (1991) Theoretical studies of electrostatic aspects of proteins, in Recent Advances in Biochemistry (eds. Byun, S. M., Lee, S. Y. & Yang, C. H.), pp. 29–42. Seoul: The Biochemical Society of the Republic of Korea.Google Scholar
Nakamura, H. (1988) Numerical calculations of reaction fields of protein-solvent systems, J. Phys. Soc.Jpn. 57, 3702–3705.CrossRefGoogle Scholar
Nakamura, H. (1993) Reproduction of correct electrostatic field by charges and dipoles on a closed surface, J. Mol. Graph. 11, 30–36.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Nakamura, H., Komatsu, K. & Umeyama, H. (1985b) Electrostatic complementarities between guest ligands and host enzymes, J. Phys. Soc. Jpn. 54, 3257–3260.CrossRefGoogle Scholar
Nakamura, H., Nagashima, S. & Wakabayashi, T. (1994) Electrostatic field around the actin filemant, in Synchrotron Radiation in the Biosciences (eds. Chance, B., Deisenhofer, J.Ebashi, S.Goodhead, D. T.Helliwell, J. R.Huxley, H. E.Iizuka, T.Kirz, J.Mitsui, T.Rubenstein, E.Sakabe, N.Sasaki, T.Schmahl, G.Stuhrmann, H. B.W¨trich, K. & Zaccai, G.), pp. 502–508. New York: Oxford Univ. Press.Google Scholar
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.CrossRefGoogle Scholar
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, 11535–11539CrossRefGoogle ScholarPubMed
Nakamura, H., Sakamoto, T. & Wada, A. (1988) A theoretical study of the dielectric constant of proteins, Protein Eng. 2, 177–183.CrossRefGoogle Scholar
Nakamura, H. & Wada, A. (1985) Nature of the charge distribution in proteins III, Electric multipole structures, J. Phys. Soc. Jpn. 54, 4047–4052.CrossRefGoogle Scholar
Neumann, M. (1985) The dielectric constant of water. Computer simulations with the MCY potential, J. Chem. Phys. 82, 5663–5672.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Noguchi, T. & Go, N. (1985) Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins, Biopolymers 24, 527–546.Google Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Oobatake, M. & Ooi, T. (1993) Hydration and heat stability effects on protein unfolding, Prog. Biophys. molec. Biol. 59, 237–284.CrossRefGoogle ScholarPubMed
Pabo, C. O. & Sauer, R. T. (1992) Transcription factors: structural families and principles of DNA recognition, Ann. Rev. Biochem. 61, 1053–1095.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Parsons, S. M., & Raftery, M. A. (1972) Ionization behavior of the catalytic carboxyls of lysozyme. Effects of ionic strength, Biochemistry 11, 1623–1629.CrossRefGoogle ScholarPubMed
Perutz, M. F. (1978) Electrostatic effects in proteins, Science 201, 1187–1191.CrossRefGoogle ScholarPubMed
Perutz, M. F. & Raidt, H. (1975) Stereochemical basis of heat stability in bacterial ferredoxins and in haemoglobin A2, Nature 255, 256–259.CrossRefGoogle ScholarPubMed
Petsko, G. A. & Ringe, D. (1984) Fluctuations in protein structure from X-ray diffraction, Ann. Rev. Biophys. Bioeng. 13, 331–371.CrossRefGoogle ScholarPubMed
Phillips, G. N., Fillers, J. P. & Cohen, C. (1986) Tropomyosin crystal structure and muscle regulation, J. Mol. Biol. 192, 111–131.CrossRefGoogle ScholarPubMed
Phillips, S. E. V. & Schoenborn, B. P. (1981) Neutron diffraction reveals oxygenhistidine hydrogen bond in oxymyoglobin, Nature 292, 81–82.CrossRefGoogle ScholarPubMed
Privalov, P. L. & Gill, S. J. (1988) Stability of protein structure and hydrophobic interaction, Adv. Protein Chem. 39, 191–234.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Rayment, I., Rypniewski, W. R., Schmidt-Base, K., Smith, R., Tomchick, D. R., Benning, M. M., Winkelmann, D. A., Wesenberg, G. & Holden, H. M. (1993 b) Three-dimensional structure of myosin subfragment-1: A molecular motor, Science 261, 50–58.CrossRefGoogle ScholarPubMed
Reynolds, C. A., King, P. M. & Richards, W. G. (1988) Computed redox potentials and the design of bioreductive agents, Nature 334, 80–82CrossRefGoogle ScholarPubMed
Richards, W. G., King, P. M. & Reynolds, C. (1989) A. Solvent effects, Protein Eng. 2, 319–327.CrossRefGoogle Scholar
Richardson, J. S. & Richardson, D. C. (1988) Amino acid preference for specific locations at the ends of α helices, Science 240, 1648–1652.CrossRefGoogle ScholarPubMed
Richarz, R., & Wüthrich, K. (1978) High-field 13C nuclear magnetic resonance studies at 90·5 MHz of the basic pancreatic trypsin inhibitor, Biochemistry 17, 2263–2269.CrossRefGoogle ScholarPubMed
Rogers, N. K. & Sternberg, M. J. E. (1984) Electrostatic interactions in globular proteins, J. Mol. Biol. 174, 527–542.CrossRefGoogle ScholarPubMed
Rousselet, J., Salome, L., Ajdari, A. & Prost, J. (1994) Directional motion of brownian particles induced by a periodic asymmetric potential, Nature 370, 446–448.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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, 101–118CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Saito, M. (1992) Molecular dynamics simulations of proteins in water without the truncation of long-range Coulomb interactions, Mol. Simul. 8, 321–333.CrossRefGoogle Scholar
Saito, M. (1994) Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation, J. Chem. Phys. 101, 4055–4061.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
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.Google ScholarPubMed
Sali, D., Bycroft, M. & Fersht, A. R. (1991) Surface electrostatic interaction contributes little to stability of barnase, J. Mol. Biol. 220, 779–788.Google ScholarPubMed
Schirmer, T. & Evans, P. R. (1990) Structural basis of the allosteric behaviour of phosphofructokinase, Nature 343, 140–145.CrossRefGoogle ScholarPubMed
Schoenberg, M. (1988) Characterization of the myosin adenosine triphosphate (MATP) cross bridge in rabbit and frog skeletal muscle fibers, Biophys. J. 54, 135–148.CrossRefGoogle Scholar
Schulz, G. E. & Schirmer, R. H. (1979) Principles of protein structure. New York: Springer-Verlag.CrossRefGoogle Scholar
Serrano, L. & Fersht, A. R. (1989) Capping and α-helix stability, Nature 342, 296–299.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Sharp, K. (1991) Incorporating solvent and ion screening into molecular dynamics using the finite-difference Poisson-Boltzmann method, J. Comput. Chem. 12, 454–468.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Simonson, T., Perahia, D. & Bricogne, G. (1991) Intramolecular dielectric screening in proteins, J. Mol. Biol. 218, 859–886.CrossRefGoogle ScholarPubMed
Singh, U. C. & Kollman, P. A. (1986) A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3C1+Cl− exchange reaction and gas phase protonation of poly ethers, J. Comput. Chem. 7, 718–730CrossRefGoogle Scholar
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, 859–883.CrossRefGoogle Scholar
Sippl, M. J. (1995) Knowledge-based potentials for proteins, Curt. Opin. Struct. Biol. 5, 229–235.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Sutoh, K. (1982) Identification of myosin-binding sites on the actin sequence, Biochemistry 21, 3654–3661.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Takahashi, T., Nakamura, H. & Wada, A. (1992) Electrostatic forces in two lysozymes: Calculations and measurements of histidine pK a values, Biopolymers 32, 897–909.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Takashima, S. & Asami, K. (1993) Calculation and measurement of the dipole moment of small proteins: Use of Protein Data Bank, Biopolymers 33, 59–68.CrossRefGoogle Scholar
Tanford, C. (1957) Theory of protein titration curves. II. Calculations for simple models at low ionic strength, J. Am. Chem. Soc. 79, 5340–5347.CrossRefGoogle Scholar
Tanford, C. & Kirkwood, J. G. (1957) Theory of protein titration curves. I. General equations for impenetrable spheres, J. Am. Chem. Soc. 79, 5333–5339.CrossRefGoogle Scholar
Tanford, C. & Roxby, R. (1972) Interpretation of protein titration curves. Application to lysozyme, Biochemistry 11, 2192–2198.CrossRefGoogle ScholarPubMed
Taylor, W. R. & Orengo, C. A. (1989) Protein structure alignment, J. Mol. Biol. 208, 1–22.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
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, 773–782.CrossRefGoogle ScholarPubMed
Wada, A. (1976) The α-helix as an electric macro-dipole, Adv. Biophys. 9, 1–63.Google Scholar
Wada, A. & Nakamura, H. (1981) Nature of the charge distribution in proteins, Nature 293. 757–758.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Wagner, G. & Wthrich, K. (1986) Observation of internal mobility of proteins by nuclear magnetic resonance in solution, Methods Enzym. 131, 307–326.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
Waldburger, C. D., Schildbach, J. F. & Sauer, R. T. (1995) Are buried salt bridges important for protein stability and conformational specificity? Nature Struct. Biol. 2, 122–128.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
Warshel, A., Papazyan, A. & Kollman, P. A. (1995) On low-barrier hydrogen bonds and enzyme catalysis, Science 269, 102–103.CrossRefGoogle ScholarPubMed
Warshel, A. & Russell, S. T. (1984) Calculation of electrostatic interactions in biological systems and in solutions, Q. Rev. Biophys. 17, 283–422.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Weiner, S. J., Seibel, G. L. & Kollman, P. A. (1986) The nature of enzyme catalysis in trypsin, Proc. Natl. Acad. Sci. USA 83, 649–653CrossRefGoogle ScholarPubMed
Wintersberger, U. (1990) Ribonuclease H of retroviral and cellular origin, Pharmac. Ther. 48, 259–280.CrossRefGoogle ScholarPubMed
Wodak, S. J. & Rooman, M. J. (1993) Generating and testing protein folds, Curr. Opin. Struct. Biol. 3, 247–259.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
Yamazaki, T., Yoshida, M., Kanaya, S., Nakamura, H. & Nagayama, K. (1991) Assignments of backbone 1H, 13C, and 15N resonances and secondary structure of ribonuclease H from Escherichia coli by heteronuclear three-dimensional NMR spectroscopy, Biochemistry 30, 6036–6047.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Yang, A.-S., Gunner, M. R., Sampogna, R., Sharp, K. & Honig, B. (1993) On the calculation of K as in proteins, PROTEINS: Struct. Fund. Genet. 15, 252–265.CrossRefGoogle Scholar
Yang, A.-S. & Honig, B. (1993) On the pH dependence of protein stability, J. Mol. Biol. 231, 459–474.CrossRefGoogle Scholar
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.CrossRefGoogle Scholar
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.CrossRefGoogle ScholarPubMed
Yang, W. & Steitz, T. A. (1995) Recombining the structures of HIV integrase, RuvC and RNase H, Structure 3, 131–134.CrossRefGoogle ScholarPubMed
Zauhar, R. J. & Morgan, R. S. (1985) Anew method for computing the macromolecular electric potential, J. Mol. Biol. 186, 815–820.CrossRefGoogle Scholar