Protein Dynamics: A Theoretical Perspective

Advances in Molecular and Cell Biology

Volumn 22, Issue C, 1997, Pages 339-390

  Kazmirski, Steven L ^a   Daggett, Valerie ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0343870703     PISSN: 15692558     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1569-2558(08)60481-6     Document Type: Article

References (179)

1. Affleck R., Haynes C.A., and Clark D.S. Solvent dielectric effects on protein dynamics. Proc. Natl. Acad. Sci. USA 89 (1992) 1567-1570
2. Al-Karadaghi S., Cedergren-Zeppezaner E.S., Petrantos K., Hovmöller S., Terry H., Dauter Z., and Wilson K.S. Refined crystal structure of liver alcohol dehydrogenase-NADH complex at 1.8 Å resolution. Acta Crystallogr, D. 50 (1994) 793-807
3. Alber, T., Gilbert, W. A., Ringe Ponzi, D., & Petsko, G. A. (1982). In: Mobility and Function of Proteins and Nucleic Acids. (Ciba Foundation symposium 93), pp 4-24, Pitman, London.
4. Alexandrescu A.T., Ulrich E.L., and Markley J.L. Hydrogen-1 NMR evidence for three interconverting forms of staphylococcal nuclease: Effects of mutations and solution conditions on their distribution. Biochem. 28 (1989) 204-211
5. Alonso D.O.V., and Daggett V. Molecular dynamics simulations of protein unfolding and limited refolding: Characterization of partially unfolded states of ubiquitin in 60% methanol and in water. J. Mol. Biol. 247 (1995) 501-520
6. Alonso, D. O. V., & Daggett, V. (1997). Simulations of hydrophobic collapse. Submitted for publication.
7. Artymiuk P.J., Blake C.C.F., Grace D.E.P., Oatley S.J., Phillips D.C., and Sternberg M.J.E. Crystallographic studies of the dynamic properties of lysozyme. Nature 280 (1979) 563-568
8. Auffinger P., and Beveridge D.L. A simple test for evaluating the truncation effects in simulations of systems involving charged groups. Chem. Phys. Lett. 234 (1995) 413-415
9. Austin R.H., Beeson K.W., Eisenstein L., Frauenfelder H., and Gunsalus I.C. Dynamics of ligand binding to myoglobin. Proc. Natl. Acad. Sci. USA 44 (1975) 98-104
10. Axelsen P.H., Harel M., Silman I., and Sussman J.L. Structure and dynamics of the active site gorge of acetylcholinesterase: Synergistic use of molecular dynamics simulation and X-ray crystallography. Protein Sci. 3 (1994) 188-197
11. Barrick D., and Baldwin R.L. Three states analysis of sperm whale apomyoglobin folding. Biochem. 32 (1993) 3790-3796
12. Björkstén J., Soares C.M., Nilsson O., and Tapia O. On the stability and plastic properties of the interior L3 loop in R. capsulatus portn. A molecular dynamics study. Protein Eng. 7 (1994) 487-493
13. Bone S., and Pethig R. Dielectric studies of protein hydration and hydration-induced flexibility. J. Mol. Biol. 181 (1985) 323-326
14. Bromberg S., and Dill K.A. Side-chain entropy and packing in proteins. Prot. Sci. 3 (1994) 997-1009
15. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., and Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4 (1983) 187-217
16. Brooks C.L. Characterization of "native" apomyoglobin by molecular dynamics simulation. J. Mol. Biol. 227 (1992) 375-380
17. Brooks C.L., and Nilsson L. Promotion of helix formation in peptides dissolved in alcohol and water-alcohol mixtures. J. Am. Chem. Soc. 115 (1993) 11034-11035
18. Brunne R.M., Liepinsh E., Otting G., Wüthrich K., and van Gunsteren W.F. Hydration of proteins: A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J. Mol. Biol. 231 (1993) 1040-1048
19. Burke P.A., Griffin R.G., and Klibanov A.M. Solid-state nuclear magnetic resonance investigation of solvent dependence of tyrosyl ring motion in an enzyme. Biotechnol. Bioeng. 42 (1993) 87-94
20. Buus S., Sette A., and Grey H.M. The interaction between protein-derived immunogenic peptides and Ia. Immunol. Rev. 98 (1987) 115-141
21. Carlson M.L., Regan R., Elber R., Li H., Phillips G.N., Olson J.S., and Gibson Q.H. Nitric oxide recombination to double mutants of myoglobin: Role of ligand diffusion in a fluctuating heme pocket. Biochemistry 33 (1994) 10597-10606
22. 1H NMR spectroscopy. Proc. Natl. Acad. Sci. USA 86 (1989) 2195-2198
23. Clarage J.B., Romo T., Andrews B.K., Pettitt B.M., and Phillips G.N. A sampling problem in molecular dynamics simulations of macromolecules. Proc. Natl. Acad. Sci. USA 92 (1995) 3288-3292
24. Cocco M.J., and Lecomte J.T.J. Structural features of the protoporphyrin apomyoglobin complex-A proton NMR spectroscopy study. Biochem. 29 (1990) 11057-11067
25. Comell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., and Kollman P.A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117 (1995) 5179-5197
26. Czerminski R., and Elber R. Computational studies of ligand diffusion in globins: I. Leghemoglobin. Proteins: Structure, Function and Genetics 10 (1991) 70-80
27. Daggett V., and Levitt M. Realistic simulations of native-protein dynamics in solution and beyond. Annu. Rev. Biophys. Biomol. Struct. 22 (1993) 353-380
28. Daggett V., and Levitt M. Protein unfolding pathways explored through molecular dynamics simulations. J. Mol. Biol. 232 (1993) 600-619
29. Daggett V., Schröder S., and Kollman P. Catalytic pathway of serine proteases: Classical and quantum mechanical calculations. J. Am. Chem. Soc. 113 (1991) 8926-8935
30. Debouck C., Gorniak J.G., Strickler J.E., Meek T.D., Metcalf B.W., and Rosenberg M. Human immunodeficiency virus protease expressed in Escherichia coli exhibits autoprocessing and specific maturation of the gag precursor. Proc. Natl. Acad. Sci. USA 84 (1987) 8903-8906
31. Deisenhofer J., Epp. O., Sinning I., and Michel H. Crystallographic refinement at 2. 3 Å resolution and refined model of the photosynthetic reaction centre from Rhodopseudomonas viridis. J. Mol. Biol. 246 (1995) 429-457
32. Denisov V.P., and Halle B. Dynamics of the internal and external hydration of globular protein. J. Am. Chem. Soc. 116 (1994) 10324-10325
33. Denisov V.P., and Halle B. Protein hydration dynamics in aqueous solution: A comparison of bovine pancreatic trypsin inhibitor and ubiquitin by oxygen-17 spin relaxation dispersion. J. Mol. Biol. 245 (1995) 682-697
34. Denisov V.P., and Halle B. Hydrogen exchange and protein hydration: The deuteron spin relaxation dispersions of bovine pancreatic trypsin inhibitor and ubiquitin. J. Mol. Biol. 245 (1995) 698-709
35. Derrida B. Random-energy model: An exactly solvable model of disordered systems. Phys. Rev. B. 24 (1981) 2613
36. Diaz J.M., Wroblowski B., and Engelborghs Y. Molecular dynamics simulation of the solution structures of Ha-ras-p21 GDP and GTP complexes: Flexibility, possible hinges, and levers of the conformational transition. Biochem. 34 (1995) 12038-12047
37. Doucet J., and Benoit J.P. Molecular dynamics studied by analysis of the X-ray diffuse scattering from lysozyme crystals. Nature 325 (1987) 643-646
38. Dykes D.C., Friedman F.K., Dykes S.L., Murphy R.B., Brandt-Rauf P.W., and Pincus M.R. Molecular dynamics of the H-ras gene-encoded p21 protein: Identification of flexible regions and possible effector domains. J. Biomol. Struct. Dynamics 11 (1993) 443-458
39. Elber R., and Karplus M. Multiple conformational states of proteins: A molecular dynamics analysis of myoglobin. Science 235 (1987) 318-321
40. Elber R., and Karplus M. Enhanced sampling in molecular dynamics: Use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin. J. Am. Chem. Soc. 112 (1990) 9161-9175
41. Epstein D.M., Benkovic S.J., and Wright P.E. Dynamics of the dihydrofolate reductase-folate complex: Catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features. Biochem. 34 (1995) 11037-11048
42. Evans P.A., Kautz R.A., Fox R.O., and Dobson C.M. A magnetization-transfer nuclear magnetic resonance study of the folding of staphylococcal nuclease. Biochem. 28 (1989) 362-370
43. Falzone C.J., Wright P.E., and Benkovic S.J. Evidence for two interconverting protein isomers in the methotrexate complex of dihydrofolate reductase from Escherichia coli. Biochem. 30 (1991) 2148-2191
44. 562. Nat. Struct. Biol. 1 (1994) 30-35
45. 562. Biochemistry 30 (1991) 7711-7717
46. Ferrin T.E., Huang C.C., Jarvis L.E., and Langridge R. The MIDAS display system. J. Mol. Graph. 6 (1988) 13-27
47. Fersht A. Enzyme Structure and Mechanism (1985), W.H. Freeman & Company, New York.
48. Filipovic D., Paulsen M.D., Loida P.J., Sligar S.G., and Ornstein R.L. Ethylbenzene hydroxylation by cytochrome P450cam, Biochem. Biophys. Res. Commun. 189 (1992) 488-495
49. Fischer G., Bang H., and Mech C. Determination of enzymatic catalysis for the cis-trans-isomerization of peptide binding in proline-containing peptides. Biomed. Biochim. Acta 43 (1984) 1101-1111
50. Fischer G., Wittmann-Liebold B., Lang K., Kiefhaber T., and Schmid F.X. Cyclophilin and peptidyl-prolyl cis-trans isomerase are probably identical proteins. Nature 337 (1989) 476-478
51. Fitzpatrick P.A., Steinmetz A.C.U., Ringe D., and Klibanov A.M. Enzyme crystal structure in a neat organic solvent. Proc. Natl. Acad. Sci. USA 90 (1993) 8653-8657
52. Forrester K., Almoguera C., Han K., Grizzle W.E., and Perucho M. Detection of high incidence of K-ras oncogenes during human colon tumorigenesis. Nature 327 (1987) 298-303
53. Frauenfelder H., and Gratton E. Protein dynamics and hydration. Methods Enz. 127 (1986) 207-216
54. Frauenfelder H., and Wolynes P.G. Biomolecules: Where the physics of complexity and simplicity meet. Phys. Today Vol. 47 (1994) 58-64
55. Frauenfelder H., Petsko G.A., and Tsemoglou D. Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature 280 (1979) 558-563
56. H-ras.: An experimental and theoretical study. Biochem. 33 (1994) 3237-3244
57. Gibson Q.H., Regan R., Elber R., Olson J.S., and Carver T.E. Distal pocket residues affect picosecond ligand recombination in myoglobin: An experimental and molecular dynamics study of position 29 mutants. J. Biol. Chem. 267 (1992) 22022-22034
58. Gilson M.K., and Honig B.H. The dielectric constant of a folded protein. Biopolymers 25 (1986) 2097-2119
59. Gilson M.K., Straatsma T.P., McCammon J.A., Ripoll D.R., Faerman C.H., Axelsen P.H., Silman I., and Sussman J.L. Open "back door" in a molecular dynamics simulation of acetylcholinesterase. Science 263 (1994) 1276-1278
60. Graves M.C., Meidel M.C., Pan Y.C., Manneberg M., Lahm H.W., and Gruninger-Leitch F. Identification of a human immunodeficiency virus-1 protease cleavage site within the 66,000 Dalton subunit of reverse transcriptase. Biochem. Biophys. Res. Commun. 168 (1990) 30-36
61. Greene B.I., Hochstrasser R.M., Weisman R.B., and Eaton W.A. Spectroscopic studies of oxy-and carbonmonoxyhemoglobin after pulsed optical excitation. Proc. Natl. Acad. Sci. USA 75 (1978) 5255-5259
62. Guenot J., and Kollman P.A. Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation. J. Comp. Chem. 14 (1993) 295-311
63. Gustchina A., and Weber I.T. Comparison of inhibitor binding in HIV-1 protease and in non-viral aspartic proteases: The role of the flap. FEBS Lett. 269 (1990) 269-272
64. Hagler A.T., Huler E., and Lifson S. Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. J. Am. Chem. Soc. 96 (1974) 5319-5335
65. Hall D., and Pavitt N. An appraisal of molecular force fields for the representation of polypeptides. J. Comp. Chem. 5 (1984) 441-450
66. Hall S.S. Protein images update natural history. Science 267 (1995) 620-624
67. Harding M.W., Galat A., Uehling D.E., and Schreiber S.L. A receptor for the immunosuppressant FK506 is a cis-trans peptidyl-prolyl isomerase. Nature 341 (1989) 758-760
68. Harpaz Y., ElMasry N., Fersht A.R., and Henrick K. Direct observation of better hydration at the N terminus of an α-helix with glycine rather than alanine as the N-cap residue. Proc. Natl. Acad. Sci. USA 91 (1994) 311-315
69. Hartmann H., Parak F., Steigemann W., Petsko G.A., Ringe Ponzi D., and Frauenfelder H. Conformational substates in a protein: Structure and dynamics of metmyoglobin at 80 K. Proc. Natl. Acad. Sci. USA 79 (1982) 4967-4971
70. Hartsough D.S., and Merz K.M. Protein flexibility in aqueous and nonaqueous solutions. J. Am. Chem. Soc. 114 (1992) 10113-10116
71. Hartsough D.S., and Merz K.M. Protein dynamics and solvation in aqueous and nonaqueous environments. J. Am. Chem. Soc. 115 (1993) 6529-6537
72. Henderson L.E., Copeland T.D., Sowder R.C., Schultz A.M., and Oroszlan S. In: Bolognesi D. (Ed). Human Retroviruses, Cancer, and AIDS: Approaches to Prevention and Therapy (1988), Alan R. Liss, Inc., New York. 135-147
73. Henry E.R. Molecular dynamics simulations of heme reorientational motions in myoglobin. Biophys. J. 64 (1993) 869-885
74. Herron J.N., Terry A.H., Johnston S., He X.M., Guddat L.W., Voss E.W., and Edmundson A.B. High resolution structures of the 4-4-20 Fab-fluorescein complex in two solvent systems: Effects of solvent on structure and antigen-binding affinity. Biophys. J. 67 (1994) 2167-2183
75. Hong M.K., Braunstein D., Cowen B.R., Frauenfelder H., Iben I.E.T., Mourant J.R., Ormos P., Scholl R., Schulte A., Steinbach P.J., Xie A.-H., and Young R.D. Conformational substates and motions in myoglobin. External influences on structure and dynamics. Biophys. J. 58 (1990) 429-436
76. Howard A.E., and Kollman P.A. Molecular dynamics studies of a DNA-binding protein: 1. A comparison of the trp repressor and trp aporepressor aqueous simulations. Protein Sci. 1 (1992) 1173-1184
77. Hughson F.M., Wright P.E., and Baldwin R.L. Structural characterization of a partly folded apomyoglobin intermediate. Science 249 (1990) 1544-1548
78. Jap B.K., and Walian P.J. Biophysics of the structure and function of porins. Q. Rev. Biophys. 23 (1990) 367-403
79. Jaskólski M., Tamasselli A.G., Sawyer T.K., Staples D.G., Henrikson R.L., Schneider J., Kent S.B., and Wlodawer A. Structure at 2.5 Å resolution of chemically synthesized human immunodeficiency virus type 1 protease complexed with a hydroxyethylene-based inhibitor. Biochem. 30 (1991) 1600-1609
80. Jewsbury P., and Kitagawa T. The distal residue-CO interaction in carbonmonoxy myoglobins: A molecular dynamics study of two distal histidine tautomers. Biophys. J. 67 (1994) 2236-2250
81. Karplus M., and Petsko G.A. Molecular dynamics simulations in biology. Nature 347 (1990) 631-639
82. Kendrew J.C., Bodo G., Dintzis H.M., Parrish R.G., Wyckoff H., and Phillips D.C. A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature 181 (1958) 662-666
83. Kim Y., and Prestagard J.H. Demonstration of a conformational equilibrium in acyl carrier protein from spinach using rotating frame nuclear magnetic resonance spectroscopy. J. Am. Chem. Soc. 112 (1990) 3707-3709
84. Kitchen D.B., Hirata F., Westbrook J.D., Levy R., Kotke D., and Yarmush M. Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water. J. Comp. Chem. 11 (1990) 1169-1180
85. Kitson D.H., Avbelj F., Moult J., Nguyen D.T., Mertz J.E., Hadzi D., and Hagler A.T. On achieving better than 1-Å accuracy in a simulation of a large protein: Streptomyces griseus protease A. Proc. Natl. Acad. Sci. USA 90 (1993) 8920-8924
86. Klig L.S., Carey J., and Yanofsky C. trp repressor interactions with the trp aro H and trp R operators. Comparisons of repressor binding in vitro and repression in vivo. J. Mol. Biol. 202 (1988) 769-777
87. Komeiji Y., Uebayasi M., Someya J., and Yamato I. Molecular dynamics simulation of trp-aporepressor in a solvent. Protein Eng. 4 (1991) 871-875
88. 9k: NMR studies of minor (cis-Pro43) isoform and the Pro43Gly mutant. Biochem. 29 (1990) 4400-4409
89. Kraulis P. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structure. J. Appl. Crystallogr. 24 (1991) 946-950
90. Kuczera K., Kuriyan J., and Karplus M. Temperature dependence of the structure and dynamics of myoglobin: A simulation approach. J. Mol. Biol. 213 (1990) 351-373
91. Kuczera K., Lambry J.-C., Martin J.-L., and Karplus M. Nonexponential relaxation after ligand dissociation from myoglobin: A molecular dynamics simulation. Proc. Natl. Acad. Sci. USA 90 (1993) 5805-5807
92. Kuriyan J., Wilz S., Karplus M., and Petsko G.A. X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5 Å resolution. J. Mol. Biol. 192 (1986) 133-154
93. 562: The highly-ordered limit of molten globules. Folding and Design 1 (1996) 335-346
94. Lapatto R., Blundell T., Hemmings A., Overington J., Wilderspin A., Wood S., Merson D.R., Whittle P.J., Danley D.E., Geoghegan K.F., Hawrylik S.J., Lee S.E., Scheld K.G., and Hobart P.M. X-ray analysis of HIV-1 proteinase at 2.7 Å resolution confirms structural homology among retroviral enzymes. Nature 342 (1989) 299-302
95. Lasky L.A., Nakamura G., Smith D.H., Fennie C., Shimasaki C., Patzer E., Berman P., Gregory T., and Capon D.J. Delineation of a region of the human immunodeficiency virus type 1 gp120 glycoprotein critical for interaction with the CD4 receptor. Cell 50 (1987) 975-985
96. 5: The role of a neutral histidine at the N-cap position. J. Am. Chem. Soc. 113 (1991) 9663-9665
97. Levitt M. Molecular dynamics of native proteins. I. Computer simulations of trajectories. J. Mol. Biol. 168 (1993) 595-620
98. Levitt M., Hirshberg M., Sharon R., and Daggett V. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Computer Physics Commun. 91 (1995) 215-231
99. Levitt, M., Hirshberg, M., Sharon, R., Laidig, K.E. & Daggett, V. (1997). Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution. J. Phys. Chem., in press.
100. Levitt M., and Sharon R. Accurate simulation of protein dynamics in solution. Proc. Natl. Acad. Sci. USA 85 (1988) 7557-7561
101. Li, A., & Daggett, V. (1995). Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular dynamics: Comparison to X-ray crystallographic and NMR data. Prot. Eng., in press.
102. Li H., Elber R., and Straub J.E. Molecular dynamics simulation of NO recombination to myoglobin mutants. J. Biol. Chem. 268 (1993) 17908-17916
103. Lii J.-H., and Allinger N.L. The MM3 force field for amides, polypeptides, and proteins. J. Comp. Chem. 12 (1991) 186-199
104. Lim K., and Herron J.N. Molecular dynamics of the anti-fluorescein 4-4-20 antigen-binding fragment. 1. Computer simulations. Biochem. 34 (1995) 6962-6974
105. Lim K., Jameson D.M., Gentry C.A., and Herron J.N. Molecular dynamics of the anti-fluorescein 4-4-20 antigen-binding fragment. 2. Time-resolved fluorescence spectroscopy. Biochem. 34 (1995) 6975-6984
106. Lim M., Jackson T.A., and Anfinrud P.A. Nonexponential protein relaxation: Dynamics of conformational change in myoglobin. Proc. Natl. Acad. Sci. USA 90 (1993) 5801-5804
107. Lim M., Jackson T.A., and Anfinrud P.A. Binding of CO to myoglobin from a heme pocket docking site to form nearly linear Fe-C-O. Science 269 (1995) 962-966
108. Loida P.J., Sligar S.G., Paulsen M.D., Arnold G.E., and Ornstein R.L. Stereoselective hydroxylation of norcamphor by cytochrome P450cam: Experimental verification of molecular dynamics simulations. J. Biol. Chem. 270 (1995) 5326-5330
109. Loncharich R.J., and Brooks B.R. The effects of truncating long-range forces on protein dynamics. Proteins: Structure, Function, and Genetics 6 (1989) 32-45
110. Loncharich R.J., and Brooks B.R. Temperature dependence of dynamics of hydrated myoglobin: Comparison of force field calculations with neutron scattering data. J. Mol. Biol. 215 (1990) 439-455
111. Madden D.R., Gorga J.C., Strominger J.L., and Wiley D.C. The structure of HLA-B27 reveals nonamer self-peptides bound in an extended conformation. Nature 353 (1991) 321-325
112. 5 at 2.0 Å resolution. Cold Spring Harbor Symp. Quant. Biol. 36 (1972) 387-395
113. 562 for Escherichia coli at 2.5 Å resolution. J. Biol. Chem. 254 (1979) 1699-1706
114. McCammon J.A., and Harvey S.C. Dynamics of Proteins and Nucleic Acids (1987), Cambridge University Press, Cambridge.
115. Momany F.A., McGuire R.F., Burgess A.W., and Scheraga H.A. 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 (1975) 2361-2381
116. Momany F.A., McGuire R.F., Yan J.F., and Scheraga H.A. Energy parameters in polypeptides. III. Semiempirical molecular orbital calculations for hydrogen bonded model peptides. J. Phys. Chem. 74 (1970) 2424-2438
117. 5: Presence of a stable native core. Biochemistry 29 (1990) 1984-1989
118. 5. Biochemistry 32 (1993) 199-207
119. 5: NMR studies of the histidine residues. Biochemistry 30 (1991) 8357-8365
120. Nakagawa S., Yu H.-A., Karplus M., and Umeyana H. Active site dynamics of acyl-chymotrypsin. Proteins: Structure, Function, and Genetics 16 (1993) 172-194
121. Neumann M., Steinhauser O., and Pawley G.S. Consistent calculation of the static and frequency-dependent dielectric constant in computer simulations. Mol. Phys. 52 (1984) 97-113
122. Northrup S.H., Wensel T.G., Meares C.F., Wendoloski J.J., and Matthew J.B. Electrostatic field around cytochrome c: Theory and energy transfer experiment. Proc. Natl. Acad. Sci. USA 87 (1990) 9503-9507
123. Obmolova G.U., Safonova T.N., Teplyakov A.V., Popov A.N., Kuranova I.P., Harutyunyan E.G., and Vainshtein B.K. X-ray structure of ferrous complexes of the yellow lupin leghemoglobin with CO and NO at 1.8 angstroms resolution. Biorg. Khim. 14 (1988) 1509-1520
124. Ochi H., Hata Y., Tanaka N., Kakudo M., Sakurai T., Aihara S., and Morita Y. Structure of rice ferricytochrome c at 2.0 Å resolution. J. Mol. Biol. 166 (1983) 407-418
125. Orozco M., Tirado-Rives J., and Jorgensen W.L. Mechanism for the rotamase activity of FK506 binding protein from molecular dynamics simulations. Biochem. 32 (1993) 12864-12874
126. Otting G., and Liepinsh E. Protein hydration viewed by high-resolution NMR spectroscopy: Implication for magnetic resonance image contrast. Acc. Chem. Res. 28 (1995) 171-177
127. Otting G., and Wüthrich K. Studies of protein hydration in aqueous solution by direct NMR observation of individual protein-bound water molecules. J. Am. Chem. Soc. 111 (1989) 1871-1875
128. 5. Primary structure of the heme-containing moiety. J. Biol. Chem. 251 (1976) 6767-6774
129. Paulsen M.D., and Ornstein R.L. Predicting the product specificity and coupling of cytochrome P450cam. J. Comput. Aided Mol. Des. 6 (1992) 449-460
130. Paulsen M.D., and Ornstein R.L. Substrate mobility in thiocamphor-bound cytochrome P450cam: An explanation of the conflict between the observed product profile and the X-ray structure. Protein Eng. 6 (1993) 359-365
131. Paulsen M.D., Filipovic D., Sligar S.G., and Ornstein R.L. Controlling the regiospecificity and coupling of cytochrome P450cam: T185F mutant increases coupling and abolishes 3-hydroxynorcamphor product. Protein Sci. 2 (1993) 357-365
132. Perutz M.F., and Mathews F.S. An x-ray study of azide methaemoglobin. J. Mol. Biol. 21 (1966) 199-202
133. Perutz M.F., Rossmann M.G., Cullis A.F., Muirhead H., Will G., and North A.C.T. Structure of haemoglobin. A three-dimensional fourier synthesis at 5.5 Å resolution, obtained by x-ray analysis. Nature 185 (1960) 416-422
134. Petrich J.W., Lambry J.-C., Kuczera K., Karplus M., Poyart C., and Martin J.-L. Ligand binding and protein relaxation in heme proteins: A room temperature analysis of NO geminate recombination. Biochem. 30 (1991) 3975-3987
135. Phillips G.N., and Pettitt B.M. Structure and dynamics of the water around myoglobin. Prot. Sci. 4 (1995) 149-158
136. Ptaszek L.M., Vijayakumar S., Ravishanker G., and Beveridge D.L. Molecular dynamics studies of the human CD4 protein. Biopolymers 34 (1994) 1145-1153
137. Quillin M.L., Li T., Olson J.S., Phillips G.N., Dou Y., Ikeda-Saito M., Regan R., Carlson M., Gibson Q.H., Li H., and Elber R. Structural and functional effects of apolar mutations of the distal valine in myoglobin. J. Mol. Biol. 245 (1995) 416-436
138. Quinn D.M. Acetylcholinesterase: Enzyme structure, reaction dynamics, and virtual transition states. Chem. Rev. 87 (1987) 955-975
139. Raag R., and Poulos T.L. The structural basis for substrate-induced changes in redox potential and spin equilibrium in cytochrome P-450cam. Biochem. 28 (1989) 917-922
140. Raag R., and Poulos T.L. Crystal structures of cytochrome P-450cam complexed with camphane, thiocamphor, and adamantane: Factors controlling P-450 substrate hydroxylation. Biochem. 30 (1991) 2674-2684
141. Rasmussen B.F., Stock A.M., Ringe D., and Petsko G.A. Crystalline ribonuclease A loses function below the dynamic transition at 220 K. Nature 357 (1992) 423-424
142. Rees D.C. Experimental evaluation of the effective dielectric constant of proteins. J. Mol. Biol. 141 (1980) 323-326
143. Rognan D., Zimmermann N., Jung G., and Folkers G. Molecular dynamics study of a complex between the human histocompatibility antigen HLA-A2 and the IMP58-66 nonapeptide from influenza virus matrix protein. Eur. J. Biochem. 208 (1992) 101-113
144. Russell A.J., and Fersht A.R. Rational modification of enzyme catalysis by engineering surface charge. Nature 328 (1987) 496-500
145. Russell A.J., Thomas P.G., and Fersht A.R. Electrostatic effects on modification of charged groups in the active site cleft of subtilisin by protein engineering. J. Mol. Biol. 193 (1987) 803-813
146. Ryde U. Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion. Proteins: Structure, Function, and Genetics 21 (1995) 40-56
147. Ryde U. On the role of Glu-68 in alcohol dehydrogenase. Protein Sci. 4 (1995) 1124-1132
148. Schaad O., Zhou H.-X., Szabo A., Eaton W.A., and Henry E.R. Simulation of the kinetics of ligand binding to a protein by molecular dynamics: Geminate rebinding of nitric oxide to myoglobin. Proc. Natl. Acad. Sci. USA 90 (1993) 9547-9551
149. Scheraga H.A. Calculations of conformations of polypeptides. Advan. Phys. Org. Chem. 6 (1968) 103-183
150. Shank C.V., Ippen E.P., and Bersohn R. Time-resolved spectroscopy of hemoglobin and its complexes with subpicosecond optical pulses. Science 193 (1976) 50-51
151. Shaw G.L., Davis B., Keeler J., and Fersht A.R. Backbone dynamics of chymotrypsin inhibitor 2: Effect of breaking the active site bond and its implications for the mechanism of inhibition of serine proteases. Biochemistry 34 (1995) 2225-2233
152. Simonson T., and Perahia D. Internal and interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution. Proc. Natl. Acad. Sci. USA 92 (1995) 1082-1086
153. Smith P.E., Brunne R.M., Mark A.E., and van Gunsteren W.F. Dielectric properties of trypsin inhibitor and lysozyme calculated from molecular dynamics simulations. J. Phys. Chem. 97 (1993) 2009-2014
154. Soares C.M., Björkstén J., and Tapia O. L3 loop-mediated mechanisms of pore closing in porin: A molecular dynamics perturbation approach. Protein Eng. 8 (1995) 5-12
155. Steinbach P.J., and Brooks B.R. Protein hydration elucidated by molecular dynamics simulation. Proc. Natl. Acad. Sci. USA 90 (1993) 9135-9139
156. Steinbach P.J., and Brooks B.R. New spherical-cutoff methods for long-range forces in macromolecular simulation. J. Comp. Chem. 15 (1994) 667-683
157. Steinbach P.J., and Brooks B.R. Protein simulation below the glass-transition temperature. Dependence on cooling protocol. Chem. Phys. Lett. 226 (1994) 447-452
158. Sticht H., Willbold D., and Rösch P. Molecular dynamics simulation of equine infectious anemia virus Tat protein in water and in 40% trifluoroethanol. J. Biomol. Struct, Dyn. 12 (1994) 19-36
159. 5: Implications for protein-protein recognition. Biochemistry 34 (1995) 9682-9693
160. 5. Biochemistry 35 (1996) 11596-11604
161. Takahashi N., Hayano T., and Suzuki M. Peptidyl-prolyl cis-trans isomerase is the cyclosporin A-binding protein cyclophilin. Nature 337 (1989) 473-475
162. Takano T. Structure of myoglobin refined at 2.0 Å resolution. I. Crystallographic refinement of metmyoglobin from sperm whale. J. Mol. Biol. 110 (1977) 537-568
163. Tilton R.F., Dewan J.C., and Petsko G.A. Effects of temperature on protein structure and dynamics: X-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320 K. Biochemistry 31 (1992) 2469-2481
164. Tirado-Rives J., and Jorgensen W.L. Molecular dynamics simulations of the unfolding of apomyoglobin in water. Biochemistry 32 (1993) 4175-4184
165. Townsend A.R.M., and Bodmer H. Antigen recognition by class I-restricted T lymphocytes. Ann. Rev. Immunol. 7 (1989) 601-624
166. Townsend A.R.M., Rothbard J., Gotch F.M., Bahadur G., Wraith D., and McMichael A.J. The epitopes of influenza nucleoprotein recognized by cytotoxic Tlymphocytes can be defined with short synthetic peptides. Cell 44 (1986) 959-968
167. Treutlein H., Schulten K., Brünger A., Karplus M., Deisenhofer J., and Michel H. Chromophore-protein interactions and the function of the photosynthetic reaction center: A molecular dynamics study. Proc. Natl. Acad. Sci. USA 89 (1992) 75-79
168. Tsou C.-L. Conformational flexibility of enzyme active sites. Science 262 (1993) 380-381
169. van Buuren A.R., and Berendsen H.J.C. Molecular dynamics simulation of the stability of a 22-residue α-helix in water and 30% trifluoroethanol. Biopolymers 33 (1993) 1159-1166
170. Verkhivker G., Elber R., and Gibson Q.H. Microscopic modeling of ligand diffusion through the protein leghemoglobin: Computer simulations and experiments. J. Am. Chem. Soc. 114 (1992) 7866-7878
171. Weiner S.J., Kollman P.A., Case D.A., Singh U.C., Ghio C., Alagona G., Profeta S., and Weiner P. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106 (1984) 765-784
172. Weiss M.S., and Schulz G.E. Structure of porin refined at 1.8 Å resolution. J. Mol. Biol. 227 (1992) 493-509
173. Wescott C.R., and Klibanov A.M. The solvent dependence of enzyme specificity. Biochim. Biophys. Acta. 1206 (1994) 1-9
174. Willis B.T.M., and Pryor A.W. Thermal vibrations in crystallography (1975), Cambridge University Press, Cambridge.
175. Wondrak E.M., Louis J.M., and Oroszlan S. The effect of salt on the Michaelis-Menten constant of the HIV-1 protease correlates with the Hofmeister series. FEBS Lett. 280 (1991) 344-346
176. Yennawar N.H., Yennawar H.P., and Farber G.K. X-ray crystal structure of γ-chymotrypsin in hexane. Biochemistry 33 (1994) 7326-7336
177. York D.M., Darden T.A., Pedersen L.G., and Anderson M.W. Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution. Biochemistry 32 (1993) 1443-1453
178. Zinkernagel R.M., and Doherty P.C. Restriction of in vitro T cell-mediated cytotoxicity in lymphocytic choriomeningitis within a syngeneic or semiallogeneic system. Nature 248 (1974) 701-702
179. Zinkernagel R.M., and Doherty P.C. MHC-restricted cytotoxicity T cells: Studies on the biological role of polymorphic major transplantation antigens determining T-cell restriction-specificity, function, and responsiveness. Adv. Immunol. 27 (1979) 51-177