Spinach on the ceiling: A theoretical chemist's return to biology

Annual Review of Biophysics and Biomolecular Structure

Volumn 35, Issue , 2006, Pages 1-47

  Karplus, Martin ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITÉ LOUIS PASTEUR   (France)

Author keywords

Molecular dynamics; NMR coupling constants; Reaction kinetics; Trajectory calculations

Indexed keywords

CHEMICAL REACTION KINETICS; LIFE EVENT; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FOLDING; REVIEW;

AUSTRIA; BIOLOGY; HISTORY, 20TH CENTURY; HISTORY, 21ST CENTURY; MOLECULAR BIOLOGY; UNITED STATES;

SPINACIA OLERACEA;

EID: 33745054630     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.33.110502.133350     Document Type: Review

References (127)

1. Alder BJ, Wainwright TE. 1957. Phase transition for a hard sphere system. J. Chem. Phys. 27:1208-9
2. Anfinsen CB. 1973. Principles that govern folding of protein chains. Science 181:223-30
3. Artymiuk PJ, Blake CCF, Grace DEP, Oatley SJ, Phillips DC, Sternberg MJE. 1979. Crystallographic studies of the dynamic properties of lysozyme. Nature 280:563-68
4. 2-. J. Chem. Phys. 50:478-88
5. Berendsen H. 1976. Report of CECAM Workshop: models for protein dynamics. Orsay, May 24-July 17
6. Beuhler RJ, Bernstein RB, Kramer KH. 1966. Observation of reactive asymmetry of methyl iodide crossed beam study of reaction of rubidium with oriented methyl iodide molecules. J. Am. Chem. Soc. 88:5331-32
7. Bradshaw WH, Conrad HE, Corey EJ, Gunsalus IC, Lednicer D. 1959. Microbiological degradation of (+)-camphor. J. Am. Chem. Soc. 81:5507
8. Brooks BR, Karplus M. 1983. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. USA 80:6571-75
9. Brooks BR, Karplus M. 1985. Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proc. Natl. Acad. Sci. USA 82:4995-99
10. Brooks CL III, Karplus M, Pettitt BM. 1988. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. New York: Wiley
11. Brünger AT, Brooks CL III, Karplus M. 1985. Active site dynamics of ribonuclease. Proc. Natl. Acad. Sci. USA 82:8458-62
12. Brünger AT, Clore GM, Gronenborn AM, Karplus M. 1986. Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proc. Natl. Acad. Sci. USA 83:3801-5
13. Brünger AT, Huber R, Karplus M. 1987. Trypsinogen-trypsin transition: a molecular dynamics study of induced conformational change in the activation domain. Biochemistry 26:5153-62
14. Brünger AT, Karplus M. 1991. Molecular dynamics simulations with experimental restraints. Ar. Chem. Res. 24:54-61
15. Brünger AT, Kuriyan J, Karplus M. 1987. Crystallographic R factor refinement by molecular dynamics. Science 235:458-60
16. Case DA, Karplus M. 1979. Dynamics of ligand binding to heme proteins. J. Mol. Biol. 132:343-68
17. Caves TC, Karplus M. 1969. Perturbed Hartree-Fock theory. I. Diagrammatic double-perturbation analysis. J. Chem. Phys. 50:3649-61
18. Colonna-Cesari F, Perahia D, Karplus M, Ecklund H, Brändén CI, Tapia O. 1986. Interdomain motion in liver alcohol dehydrogenase: structural and energetic analysis of the hinge bending mode. J. Biol. Chem. 261:15273-80
19. Conroy H. 1960. Nuclear magnetic resonance in organic structural elucidation. Adv. Org. Chem. Vol. II, p. 265
20. Cusack S, Smith J, Finney J, Karplus M, Trewhella J. 1986. Low frequency dynamics of proteins studied by neutron time-of-flight spectroscopy. Physica 136B:256-59
21. 20a. Dalton L. 2003. Karplus Equation. Chem. Eng. News 81:37-39
22. Deisenhofer J, Steigemann W. 1975. Crystallographic refinement and the structure of the bovine pancreatic trypsin inhibitor at 1.5 Å resolution. Acta Crystallogr. B 31:238-50
23. Dobson CM. 2003. Protein folding and misfolding. Nature 426:884-90
24. Dobson CM, Karplus M. 1986. Internal motion of proteins: nuclear magnetic resonance measurements and dynamic simulations. Methods Enzymol. 131:362-89
25. Dobson CM, Sali A, Karplus M. 1998. Protein folding: a perspective from theory and experiment. Angew. Chem. Int. Ed. 37:868-93
26. Elber R, Karplus M. 1990. 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. 112:9161-75
27. Farkas A, Farkas L. 1935. Experiments on heavy hydrogen. V. The elementary reactions of light and heavy hydrogen. The thermal conversion of ortho-deuterium and the interaction of hydrogen and deuterium. Proc. R. Soc. London A 152:124-51
28. Feynman RP, Leighton RB, Sands M. 1963. The Feynman Lectures in Physics. Addison-Wesley
29. Field MJ, Bash PA, Karplus M. 1990. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comp. Chem. 11:700-33
30. Frauenfelder H, Hartmann H, Karplus M, Kuntz ID Jr, Kuriyan J, et al. 1987. Thermal expansion of a protein. Biochemistry 26:254-61
31. Frauenfelder H, Petsko GA, Tsernoglou D. 1979. Temperature-dependent x-ray diffraction as a probe of protein structural dynamics. Nature 280:558-63
32. 3. J. Chem. Phys. 64:2461-59
33. Gao J, Kuczera K, Tidor B, Karplus M. 1989. Hidden thermodynamics of mutant proteins: a molecular dynamics analysis. Science 244:1069-72
34. 1ATPase. Cell 123:195-205
35. Gelin BR. 1976. Application of empirical energy functions to conformational problems in biochemical systems. PhD thesis. Harvard Univ.
36. Gelin BR, Karplus M. 1975. Sidechain torsional potentials and motion of amino acids in proteins: bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. USA 72:2002-6
37. Gelin BR, Karplus M. 1977. Mechanism of tertiary structural change in hemoglobin. Proc. Natl. Acad. Sci. USA 74:801-5
38. Gilardi R, Karle IL, Karle J, Sperling W. 1971. Crystal structure of visual chromophores, 11-cis and all-trans retinal. Nature 232:187
39. 2. J. Chem. Phys. 49:3602-9
40. Harvey SC, Prabhakaran M, Mao B, McCammon JA. 1984. Phenylalanine transfer RNA: molecular dynamics simulation. Science 223:1189-91
41. Hemley RJ, Dinur U, Vaida V, Karplus M. 1985. Theoretical study of the ground and excited singlet states of styrene. J. Am. Chem. Soc. 107:836-44
42. Hirschfelder JA, Eyring H, Topley B. 1936. Reactions involving hydrogen molecules and atoms. J. Chem. Phys. 4:170-77
43. Honig B, Hudson B, Sykes BD, Karplus M. 1971. Ring orientation in β-ionone and retinals. Proc. Natl. Acad. Sci. USA 68:1289-93
44. Honig B, Karplus M. 1971. Implications of torsional potential of retinal isomers for visual excitation. Nature 229:558-60
45. Honig B, Warshel A, Karplus M. 1975. Theoretical studies of the visual chromophore. Acc. Chem. Res. 8:92-100
46. Hvidt A, Nielsen SO. 1966. Hydrogen exchange in proteins. Adv. Protein Chem. 21:287-86
47. Ichiye T, Karplus M. 1983. Fluorescence depolarization of tryptophan residues in proteins: a molecular dynamics study. Biochemistry 22:2884-93
48. Imai K, Osawa E. 1989. An extension of multiparameteric Karplus equation. Tetrahedron Lett. 30:4251-54
49. Irikura KK, Tidor B, Brooks BR, Karplus M. 1985. Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference. Science 229:571-72
50. Islam SA, Karplus M, Weaver DL. 2002. Application of the diffusion-collision model to the folding of three-helix bundle proteins. J. Mol. Biol. 318:199-215
51. Islam SA, Karplus M, Weaver DL. 2004. The role of sequence and structure in protein folding kinetics: the diffusion-collision model applied to proteins L and G. Structure 12:1833-45
52. Karplus M. 1952. Bird activity in the continuous daylight of arctic summer. Ecology 33:129
53. Karplus M. 1956. Charge distribution in the hydrogen molecule. J. Chem. Phys. 25:605-6
54. Karplus M. 1959. Contact electron-spin interactions of nuclear magnetic moments. J. Chem. Phys. 30:11-15
55. Karplus M. 1959. Interpretation of the electron-spin resonance spectrum of the methyl radical. J. Chem. Phys. 30:15-18
56. Karplus M. 1960. Theory of proton coupling constants in unsaturated molecules. J. Am. Chem. Soc. 82:4431
57. Karplus M. 1960. Weak interactions in molecular quantum mechanics. Rev. Mod. Phys. 32:455-60
58. Karplus M. 1963. Vicinal proton coupling in nuclear magnetic resonance. J. Am. Chem. Soc. 85:2870
59. Karplus M. 1968. Structural implications of reaction kinetics. In Structural Chemistry and Molecular Biology: A Volume Dedicated to Linus Pauling by His Students, Colleagues, and Friends, ed. A Rich, N Davidson, pp. 837-47. San Francisco: Freeman
60. Karplus M. 1982. Dynamics of proteins. Ber. Bunsen-Ges. Phys. Chem. 86:386-95
61. Karplus M. 1996. Theory of vicinal coupling constants. In Encyclopedia of Nuclear Magnetic Resonance. Vol. 1: Historical Perspectives, ed. DM Grant, RK Harris, pp. 420-22. New York: Wiley
62. Karplus M. 1997. The Levinthal Paradox: yesterday and today. Fold. Des. 2:569-76
63. Karplus M. 2002. Molecular dynamics simulations of biomolecules. Acc. Chem. Res. 35:321-23
64. Karplus M, Fraenkel GK. 1961. Theoretical interpretation of carbon-13 hyperfine interactions in electron spin resonance spectra. J. Chem. Phys. 35:1312-23
65. Karplus M, Godfrey M. 1966. Quasiclassical trajectory analysis for the reaction of potassium atoms with oriented methyl iodide molecules. J. Am. Chem. Soc. 88:5332
66. Karplus M, Kuppermann A, Isaacson LM. 1958. Quantum-mechanical calculation of one-electron properties. I. General formulation. J. Chem. Phys. 29:1240-46
67. Karplus M, Kuriyan J. 2005. Molecular dynamics and protein function. Proc. Natl. Acad. Sci. USA 102:6679-85
68. Karplus M, Lawler RG, Fraenkel GK. 1965. Electron spin resonance studies of deuterium isotope effects. A novel resonance-integral perturbation. J. Am. Chem. Soc. 87:5260
69. Karplus M, McCammon JA. 2002. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9:646-52
70. Karplus M, Porter RN. 1970. Atoms and Molecules: An Introduction for Students of Physical Chemistry. Menlo Park, CA: Benjamin Cummins
71. 2). J. Chem. Phys. 43:3259-87
72. Karplus M, Weaver DL. 1976. Protein-folding dynamics. Nature 260:404-6
73. Karplus M, Weaver DL. 1994. Folding dynamics: the diffusion-collision model and experimental data. Protein Sci. 3:650-68
74. Karplus R, Kroll NM. 1950. Fourth-order corrections in quantum electrodynamics and the magnetic moment of the electron. Phys. Rev. 77:536-49
75. Karplus S, Karplus M. 1972. Nuclear magnetic resonance determination of the angle ψ in peptides. Proc. Natl. Acad. Sci. USA 69:3204-6
76. Deleted in proof
77. Kirkwood JG, Oppenheim I. 1961. Chemical Thermodynamics. New York: McGraw Hill
78. Kline AD, Braun W, Wüthrich K. 1988. Determination of the complete 3-dimensional structure of the alpha-amylase inhibitor tendamistat in aqueous-solution by nuclear magnetic resonance and distance geometry. J. Mol. Biol. 204:675-724
79. Kuppermann A, Karplus M, Isaacson LM. 1959. The quantum-mechanical calculation of one-electron properties. II. One-and two-center moment integrals. Zeit. Nat. 14a:311-18
80. Kuppermann A, Schatz GC. 1975. Quantum-mechanical reactive scattering: accurate 3-dimensional calculation. J. Chem. Phys. 62:2502-4
81. Kuriyan J, Weis WI. 1991. Rigid protein motion as a model for crystallographic temperature factors. Proc. Natl. Acad. Sci. USA 88:2773-77
82. Lawler RG, Bolton JR, Karplus M, Fraenkel GK. 1967. Deuterium isotope effects in the electron spin resonance spectra of naphthalene negative ions. J. Chem. Phys. 47:2149-65
83. Lee A-W, Karplus M, Poyart C, Bursaux E. 1988. Analysis of proton release in oxygen binding by hemoglobin: implications for the cooperative mechanism. Biochemistry 27:1285-301
84. Levitt M, Lifson S. 1969. Refinement of protein conformations using a macromolecular energy minimization procedure. J. Mol. Biol. 46:269-79
85. Levy RM, Karplus M, Wolynes PG. 1981. NMR relaxation parameters in molecules with internal motion: exact Langevin trajectory results compared with simplified relaxation models. J. Am. Chem. Soc. 103:5998-6011
86. Lifson S, Warshel A. 1969. Consistent force field for calculations of conformations vibrational spectra and enthalpies of cycloalkanes and n-alkane molecules. J. Chem. Phys. 49:5116-29
87. Linderstrom-Lang K. 1955. Deuterium exchange between peptides and water. Chem. Soc. Spec. Publ. 2, p. 1.
88. Liu B. 1973. Ab-initio potential-energy surface for linear H-3. J. Chem. Phys. 58:1925-37
89. Ma J, Sigler PB, Xu Z, Karplus M. 2000. A dynamic model for the allosteric mechanism of GroEL. J. Mol. Biol. 302:303-13
90. McCammon JA, Gelin BR, Karplus M. 1977. Dynamics of folded proteins. Nature 267:585-90
91. Mierke DF, Huber T, Kessler H. 1994. Coupling-constants again: experimental restraints in structure refinement. J. Comp. Aided Mol. Des. 8:29-40
92. Miranker A, Karplus M. 1991. Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins Struct. Funct. Genet. 11:29-34
93. Moffitt W. 1954. Atomic valence states and chemical binding. Rep. Prog. Phys. 17:173-200
94. Monod J, Wyman J, Changeux JP. 1965. On nature of allosteric transitions: a plausible model. J. Mol. Biol. 12:88-118
95. Morokuma K, Eu BC, Karplus M. 1969. Collision dynamics and the statistical theories of chemical reactions. I. Average cross section from transition-state theory. J. Chem. Phys. 51:5193-203
96. Morokuma K, Karplus M. 1971. Collision dynamics and the statistical theories of chemical reactions. II. Comparison of reaction probabilities. J. Chem. Phys. 55:63-75
97. Nadler W, Brünger AT, Schulten K, Karplus M. 1987. Molecular and stochastic dynamics of proteins. Proc. Natl. Acad. Sci. USA 84:7933-37
98. 2. J. Mol. Biol. 188:455-75
99. Olejniczak ET, Dobson CM, Levy RM, Karplus M. 1984. Motional averaging of proton nuclear Overhauser effects in proteins. Predictions from a molecular dynamics simulation of lysozyme. J. Am. Chem. Soc. 106:1923-30
100. Perutz M. 1971. Stereochemistry of cooperative effects in haemoglobin. Nature 232:408-13
101. Phillips DC. 1981. Closing remarks. In Biomolecular Stereodynamics, ed. RH Sarma, 2:497-48. Guilderland, NY: Adenine
102. 3. J. Chem. Phys. 40:1105-15
103. Post CB, Dobson CM. 2005. Meeting review frontiers in computational biophysics: a symposium in honor of Martin Karplus. Structure 13:949-52
104. Purins D, Karplus M. 1969. Spin delocalization and vibrational-electronic interaction in the toluene ion-radicals. J. Chem. Phys. 50:214-33
105. Rahman A. 1964. Correlations in motion of atoms in liquid argon. Phys. Rev. 136:A405-11
106. Sali A, Shakhnovich E, Karplus M. 1994. How does a protein fold? Nature 369:248-51
107. 2)":
108. Karplus M, Porter RN, Sharma RD (1965) J. Chem. Phys. 43:3259-3287.
109. Theor. Chem. Acc. 103:270-72
110. Schekkerman H, Tulp I, Piersma T, Visser GH. 2003. Mechanisms promoting higher growth rate in arctic than in temperate shorebirds. Ecophysiology 134:332-42
111. Scheraga HA. 1968. Calculations of the conformations of small molecules. Adv. Phys. Org. Chem. 6:103-84
112. Schulten K, Karplus M. 1972. On the origin of a low-lying forbidden transition in polyenes and related molecules. Chem. Phys. Lett. 14:305-9
113. Shavitt I, Karplus M. 1962. Multicenter integrals in molecular quantum mechanics. J. Chem. Phys. 36:550-51
114. 3. J. Chem. Phys. 48:2700-13
115. Shulman RG, Glarum SH, Karplus M. 1971. Electronic structure of cyanide complexes of hemes and heme protein. J. Mol. Biol. 57:93-115
116. Simonson T, Archontis G, Karplus M. 2002. Free energy simulations come of age: protein-ligand recognition. Acc. Chem. Res. 35:430-37
117. Smith J, Cusack S, Pezzeca U, Brooks BR, Karplus M. 1986. Inelastic neutron scattering analysis of low frequency motion in proteins: a normal mode study of the bovine pancreatic trypsin inhibitor. J. Chem. Phys. 85:3636-54
118. Stillinger FH, Rahman A. 1974. Improved simulation of liquid water by molecular-dynamics. J. Chem. Phys. 60:1545-57
119. Szabo A, Karplus M. 1972. A mathematical model for structure-function relations in hemoglobin. J. Mol. Biol. 72:163-97
120. Szent-Györgyi A. 1948. Nature of Life, A Study of Muscle. New York: Academic. 102 pp.
121. Taylor EH, Datz S. 1955. Study of chemical reaction mechanisms with molecular beams: the reaction of K with HBr. J. Chem. Phys. 23:1711-18
122. van der Vaart A, Ma J, Karplus M. 2004. The unfolding action of GroEL on a protein substrate. Biophys. J. 87:562-73
123. Wall FT, Porter RN. 1963. Sensitivity of exchange-reaction probabilities to potential-energy surface. J. Chem. Phys. 39:311
124. Warshel A, Karplus M. 1974. Calculation of ππ* excited state conformations and vibronic structure of retinal and related molecules. J. Am. Chem. Soc. 96:5677-89
125. Wong CF, McCammon JA. 1986. Dynamics and design of enzymes and inhibitors. J. Am. Chem. Soc. 108:3830-32
126. Yang W, Bitetti-Putzer R, Karplus M. 2004. Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence. J. Chem. Phys. 120:2618-28
127. Young MA, Gonfloni S, Superti-Furga G, Roux B, Kuriyan J. 2001. Dynamic coupling between the SH2 and SH3 domains of c-Src and hck underlies their inactivation by C-terminal tyrosin phosphorylation. Cell 105:115-26