How do biomolecular systems speed up and regulate rates?

Physical Biology

Volumn 2, Issue 3, 2005, Pages

  Zhou, Huan Xiang ^a  

^a Florida State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR MOTOR;

CATALYSIS; CELL VIABILITY; CHEMICAL REACTION; CONFORMATIONAL TRANSITION; ELECTRIC CONDUCTIVITY; ENZYME BINDING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MECHANICS; PHASE TRANSITION; PHYSICAL MODEL; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; REVIEW;

EID: 26944492613     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/2/3/R01     Document Type: Review

References (146)

1. Jucovic M and Hartley R W 1996 Protein-protein interaction: a genetic selection for compensating mutations at the barnase-barstar interface Proc. Natl Acad. Sci. USA 93 2343-7
2. Terlau H, Shon K-J, Grilley M, Stocker M, Stuhmer W and Baldomero O M 1996 Strategy for rapid immobilization of prey by a fish-hunting marine snail Nature 381 148-51
3. Doi M and Edwards S F 1986 The Theory of Polymer Dynamics (Oxford: Clarendon) p 391
4. Kramers H A 1940 Brownian motion in a field of force and the diffusion model of chemical reactions Physica 7 284-304
5. Hänggi P, Talkner P and Borkovec M 1990 Reaction-rate theory: fifty years after Kramers Rev. Mod. Phys. 62 251-342
6. Zhou H-X 1989 The exponential nature of barrier crossings studied by Langevin dynamics Chem. Phys. Lett. 164 285-90
7. Szabo A, Schulten K and Schulten Z 1980 First passage time approach to diffusion controlled reactions J. Chem. Phys. 72 4350-7
8. Bicout D J and Szabo A 1997 First passage times, correlation functions, and reaction rates J. Chem. Phys. 106 10292-8
9. Du R, Pande V S, Grosberg A Y, Tanaka T and Shakhnovich E 1998 On the transition coordinate for protein folding J. Chem. Phys. 108 334-50
10. Gardiner C W 1985 Handbook of Stochastic Methods 2nd edn (Berlin: Springer) p 442
11. Zhou H-X 2001 Disparate ionic-strength dependencies of on and off rates in protein-protein association Biopolymers 59 427-33
12. Szabo A and Shoup D 1982 Role of diffusion in ligand binding to macromolecules and cell-bound receptors Biophys. J. 40 33-9
13. Debye P 1942 Reaction rate in ionic solutions Trans. Electrochem. Soc. 82 265-72
14. Smoluchowski M 1917 Versuch einer mathematischen Theorie der Koagulationskinetik kolloider Lösungen Z. Phys. Chem. 92 129-68
15. Shoup D, Lipari G and Szabo A 1981 Diffusion-controlled bimolecular reaction rates. The effect of rotational diffusion and orientation constraints Biophys. J. 36 697-714
16. Zhou H-X 1993 Brownian dynamics study of the influences of electrostatic interaction and diffusion on protein-protein association kinetics Biophys. J. 64 1711-26
17. Schlosshauer M and Baker D 2002 A general expression for bimolecular association rates with orientational constraints J. Phys. Chem. B 106 12079-83
18. Doi M 1975 Theory of diffusion-controlled reaction between non-simple molecules: I Chem. Phys. 11 107-13
19. Doi M 1975 Theory of diffusion-controlled reaction between non-simple molecules: II Chem. Phys. 11 115-21
20. Wilemski G and Fixman M 1973 General theory of diffusion-controlled reactions J. Chem. Phys. 58 4009-19
21. Zhou H-X and Szabo A 1996 Theory and simulation of the time-dependent rate coefficients of diffusion-influenced reactions Biophys. J. 71 2440-57
22. Temkin S I and Yakobson B I 1984 Diffusion-controlled reactions of chemically anisotropic molecules J. Phys. Chem. 88 2679-82
23. Berg O G 1985 Orientation constraints in diffusion-limited macromolecular association. The role of surface diffusion as a rate-enhancing mechanism Biophys. J. 47 1-14
24. Pauling L 1948 Nature of forces between large molecules of biological interest Nature 161 707-9
25. Benkovic S J and Hammes-Schiffer S 2003 A perspective on enzyme catalysis Science 301 1196-202
26. Garcia-Viloca M, Gao J, Karplus M and Truhlar D G 2004 How enzymes work: analysis by modern rate theory and computer simulations Science 303 186-95
27. Zhou H-X 2001 The affinity-enhancing roles of flexible linkers in two-domain DNA-binding proteins Biochemistry 40 15069-73
28. Zhou H-X, Wlodek S T and McCammon J A 1998 Conformation gating as a mechanism for enzyme specificity Proc. Natl Acad. Sci. USA 95 9280-3
29. Raushel F M, Thoden J B and Holden H M 2003 Enzymes with molecular tunnels Acc. Chem. Res. 36 539-48
30. Knighton D R, Kan C-C, Howland E, Janson C A, Hostomska Z, Welsh K M and Matthews D A 1994 Structure of and kinetic channeling in bifunctional dihydrofolate reductase-thymidylate synthase Nat. Struct. Biol. 1 186-94
31. Elcock A H, Huber G A and McCammon J A 1997 Electrostatic channeling of substrates between enzyme active sites: comparison of simulation and experiment Biochemistry 36 16049-58
32. Miers J B, Postlewaite J C, Zyung T, Chen S, Roemig G R, Wen X, Dlott D D and Szabo A 1990 Diffusion can explain the nonexponential rebinding of carbon-monoxide to protoheme J. Chem. Phys. 93 8771-6
33. Atreya C E, Johnson E F, Williamson J, Chang S-Y, Liang P-H and Anderson K S 2003 Probing electrostatic channeling in protozoal bifunctional thymidylate synthase-dihydrofolate reductase using site-directed mutagenesis J. Biol. Chem. 278 28901-11
34. Atreya C E and Anderson K S 2004 Kinetic characterization of bifunctional thymidylate synthase-dihydrofolate reductase (TS-DHFR) from Cryptosporidium hominis. A paradigm shift for TS activity and channeling behavior J. Biol. Chem. 279 18314-22
35. Elcock A H 2002 Atomistic simulations of competition between substrates binding to an enzyme Biophys. J. 82 2326-32
36. Gruebele M 2002 Protein folding: the free energy surface Curr. Opin. Struct. Biol. 12 161-8
37. Akmal A and Muñoz V 2004 The nature of the free-energy barriers to two-state folding Proteins 57 142-52
38. Zwanzig R, Szabo A and Bagchi B 1992 Levinthal's paradox Proc. Natl Acad. Sci. USA 89 20-2
39. Zwanzig R 1995 Simple model of protein folding kinetics Proc. Natl Acad. Sci. USA 92 9801-4
40. Doyle R, Simons K, Qian H and Baker D 1997 Local interactions and the optimization of protein folding Proteins 29 282-91
41. Plaxco K W, Simons K T and Baker D 1998 Contact order, transition state placement and the refolding rates of single domain proteins J. Mol. Biol. 277 985-94
42. Shoemaker B A and Wolynes P G 1999 Exploring structures in protein folding funnels with free energy functionals: the denatured ensemble J. Mol. Biol. 287 657-74
43. Galzitskaya O V and Finkelstein A V 1999 A theoretical search for folding/unfolding nuclei in three-dimensional protein structures Proc. Natl Acad. Sci. USA 96 11299-304
44. Alm E and Baker D 1999 Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures Proc. Natl Acad. Sci. USA 96 11305-10
45. Muñoz V and Eaton W A 1999 A simple model for calculating the kinetics of protein folding from three-dimensional structures Proc. Natl Acad. Sci. USA 96 11311-6
46. Guerois R and Serrano L 2000 The SH3-fold family: experimental evidence and prediction of variations in the folding pathways J. Mol. Biol. 304 967-82
47. Bicout D J and Szabo A 2000 Entropic barriers, transition states, funnels, and exponential protein folding kinetics: a simple model Protein Sci. 9 452-65
48. Alm E, Morozov A V, Kortemme T and Baker D 2002 Simple physical models connect theory and experiment in protein folding kinetics J. Mol. Biol. 322 463-76
49. Makarov D, Keller C A, Plaxco K W and Metiu H 2002 How the folding rate constant of simple, single-domain proteins depends on the number of native contacts Proc. Natl Acad. Sci. USA 99 3535-9
50. Weikl T R, Palassini M and Dill K A 2004 Cooperativity in two-state protein folding kinetics Protein Sci. 13 822-9
51. Oliva F Y and Muñoz V 2004 A simple thermodynamic test to discriminate between two-state and downhill folding J. Am. Chem. Soc. 126 8596-7
52. Jacobsen H and Stockmayer W 1950 Intramolecular reaction in polycondensations: I. The theory of linear systems J. Chem. Phys. 18 1600-6
53. Wallin S and Chan H S 2005 A critical assessment of the topomer search model of protein folding using a continuum explicit-chain model with extensive conformational sampling Protein Sci. 14 1643-60
54. Berezhkovskii A and Szabo A 2004 Ensemble of transition states for two-state protein folding from the eigenvectors of rate matrices J. Chem. Phys. 121 9186-7
55. Matouschek A and Fersht A R 1991 Protein engineering in analysis of protein folding pathways and stability Methods Enzymol. 202 81-112
56. Merlo C, Dill K A and Weikl T R 2005 Φ values in protein-folding kinetics have energetic and structural components Proc. Natl Acad. Sci. USA 102 10171-5
57. Burton R E, Myers J K and Oas T G 1998 Protein folding dynamics: quantitative comparison between theory and experiment Biochemistry 37 5337-43
58. Mayor U, Johnson C M, Daggett V and Fersht A R 2000 Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation Proc. Natl Acad. Sci. USA 97 13518-22
59. Qiu L, Pabit S A, Roitberg A E and Hagen S J 2002 Smaller and faster: the 20-residue Trp-cage protein folds in 4 micros J. Am. Chem. Soc. 124 12952-3
60. Liu Z and Chan H S 2005 Desolvation is a likely origin of robust enthalpic barriers to protein folding J. Mol. Biol. 349 872-89
61. Kanehisa M I and Tsong T Y 1978 Mechanism of the multiphasic kinetics in the folding and unfolding of globular proteins J. Mol. Biol. 124 177-94
62. Cieplak M, Henkel M, Karbowski J and Banavar J R 1998 Master equation approach to protein folding and kinetic traps Phys. Rev. Lett. 80 3650-3
63. Ozkan S B, Dill K A and Bahar I 2002 Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model Protein Sci. 11 1958-70
64. Ozkan S B, Dill K A and Bahar I 2003 Computing the transition state populations in simple protein models Biopolymers 68 35-46
65. Schonbrun J and Dill K A 2003 Fast protein folding kinetics Proc. Natl Acad. Sci. USA 100 12678-82
66. Van Kampen N G 1992 Stochastic Processes in Physics and Chemistry (Amsterdam: North-Holland) p 465
67. Press W H, Flannery B P, Teukolsky S A and Vettering W T 1986 Numerical Recipes (Cambridge: Cambridge University Press) p 818
68. Chan H S and Dill K A 1993 Energy landscapes and the collapse dynamics of homopolymers J. Chem. Phys. 99 2116-27
69. Zhou H-X 2003 Theory for the rate of contact formation in a polymer chain with local conformational transitions J. Chem. Phys. 118 2010-5
70. Zhou H-X 2001 Single-chain versus dimeric protein folding: Thermodynamic and kinetic consequences of covalent linkage J. Am. Chem. Soc. 123 6730-1
71. Zhou H-X 2002 A model for the binding of the inactivation N-terminal to the ion pore of Shaker potassium channel: both electrostatic attraction and covalent linkage are required for rapid inactivation J. Phys. Chem. B 106 2393-7
72. Zhou H-X 2001 Loops in proteins can be modeled as worm-like chains J. Phys. Chem. B 105 6763-6
73. Karplus M and Weaver D L 1994 Protein folding dynamics: the diffusion-collision model and experimental data Protein Sci. 3 650-68
74. Du D, Zhu Y, Huang C Y and Gai F 2004 Understanding the key factors that control the rate of beta-hairpin folding Proc. Natl Acad. Sci. USA 101 15915-20
75. Muñoz V, Thompson P A, Hofrichter J and Eaton W A 1997 Folding dynamics and mechanism of beta-hairpin formation Nature 390 196-9
76. Muñoz V, Henry E R, Hofrichter J and Eaton W A 1998 A statistical mechanical model for β-hairpin kinetics Proc. Natl Acad. Sci. USA 95 5872-9
77. Dinner A R, Lazaridis T and Karplus M 1999 Understanding β-hairpin formation Proc. Natl Acad. Sci. USA 96 9068-73
78. Karanicolas J and Brooks C L III 2002 The origins of asymmetry in the folding transition states of protein L and protein G Protein Sci. 11 2351-61
79. Moran L B, Schneider J P, Kentsis A, Reddy G A and Sosnick T R 1999 Transition state heterogeneity in GCN4 coiled coil folding studied by using multisite mutations and crosslinking Proc. Natl Acad. Sci. USA 96 10699-704
80. Jacob M, Schindler T, Balbach J and Schmid F X 1997 Diffusion control in an elementary protein folding reaction Proc. Natl Acad. Sci. USA 94 5622-7
81. Plaxco K W and Baker D 1998 Limited internal friction in the rate-limiting step of a two-state protein folding reaction Proc. Natl Acad. Sci. USA 95 13591-6
82. Bhattacharyya R P and Sosnick T R 1999 Viscosity dependence of the folding kinetics of a dimeric and monomeric coiled coil Biochemistry 38 2601-9
83. Qiu L, Zachariah C and Hagen S J 2003 Fast chain contraction during protein folding: 'foldability' and collapse dynamics Phys. Rev. Lett. 90 168103
84. Qiu L and Hagen S J 2004 A limiting speed for protein folding at low solvent viscosity J. Am. Chem. Soc. 126 3398-9
85. Pabit S A, Roder H and Hagen S J 2004 Internal friction controls the speed of protein folding from a compact configuration Biochemistry 43 12532-8
86. Bicout D J, Berezhkovskii A M and Szabo A 2001 Irreversible bimolecular reactions of Lagevin particles J. Chem. Phys. 114 2293-303
87. Zhou H-X and Szabo A 1991 Comparison between molecular dynamics simulations and the Smoluchowski theory of reactions in a hard sphere liquid J. Chem. Phys. 95 5948-52
88. Hartl F U and Hayer-Hartl M 2002 Molecular chaperones in the cytosol: from nascent chain to folded protein Science 295 1852-8
89. Saibil H R and Ranson N A 2002 The chaperonin folding machine Trends Biochem. Sci. 27 627-32
90. Yifrach O and Horovitz A 1995 Nested cooperativity in the ATPase activity of the oligomeric chaperonin GroEL Biochemistry 34 5303-8
91. Rye H S, Burston S G, Fenton W A, Beechem J M, Xu Z, Sigler P B and Horwich A L 1997 Distinct actions of cis and trans ATP within the double ring of the chaperonin GroEL Nature 388 792-8
92. Kad N M, Ranson N A, Cliff M J and Clarke A R 1998 Asymmetry, commitment and inhibition in the GroE ATPase cycle impose alternating functions on the two GroEL rings J. Mol. Biol. 278 267-78
93. Farr G W, Furtak K, Rowland M B, Ranson N A, Saibil H R, Kirchhausen T and Horwich A L 2000 Multivalent binding of nonnative substrate proteins by the chaperonin GroEL Cell 100 561-73
94. Roseman A M, Chen S, White H, Braig K and Saibil H R 1996 The chaperonin ATPase cycle: mechanism of allosteric switching and movements of substrate-binding domains in GroEL Cell 87 241-51
95. Xu Z, Horwich A L and Sigler P B 1997 The crystal structure of the asymmetric BroEL-GroES-(ADP) chaperonin complex Nature 388 741-50
96. Zhou H-X and Dill K A 2001 Stabilization of proteins in confined spaces Biochemistry 40 11289-93
97. Schreiber G and Fersht A R 1996 Rapid, electrostatically assisted association of proteins Nature Struct. Biol. 3 427-31
98. Riggs A D, Bourgeois S and Cohn M 1970 The lac repressor-operator interaction. 3. Kinetic studies J. Mol. Biol. 53 401-17
99. Sparrer H, Lilie H and Buchner J 1996 Dynamics of the GroEL-protein complex: effects of nucleotides and folding mutants J. Mol. Biol. 258 74-87
100. Clark A C and Frieden C 1997 GroEL-mediated folding of structurally homologous dihydrofolate reductases J. Mol. Biol. 268 512-25
101. Perrett S, Zahn R, Stenberg G and Fersht A R 1997 Importance of electrostatic interactions in the rapid binding of polypeptides to GroEL J. Mol. Biol. 269 892-901
102. Tsurapa G P, Ikura T, Makio T and Kuwajima K 1998 Refolding kinetics of staphyloccocal nuclease and its mutants in the presence of the chaperonin GroEL J. Mol. Biol. 277 733-45
103. Rye H S, Roseman A M, Chen S, Furtak K, Fenton W A, Saibil H R and Horwich A L 1999 GroEL-GroES cycling: ATP and nonnative polypeptide direct alternation of folding-active rings Cell 97 325-38
104. Burston S G, Ranson N A and Clarke A R 1995 The origins and consequences of asymmetry in the chaperonin reaction cycle J. Mol. Biol. 249 138-52
105. Shoemaker B A, Portman J J and Wolynes P G 2000 Speeding molecular recognition by using the folding funnel: the fly-casting mechanism Proc. Natl Acad. Sci. USA 97 8868-73
106. Zhou H-X 2004 Polymer models of protein stability, folding, and interactions Biochemistry 43 2141-54
107. Zhou H-X 1997 Enhancement of protein-protein association rate by interaction potential: accuracy of prediction based on local Boltzmann factor Biophys. J. 73 2441-5
108. Vijayakumar M, Wong K-Y, Schreiber G, Fersht A R, Szabo A and Zhou H-X 1998 Electrostatic enhancement of diffusion-controlled protein-protein association: comparison of theory and experiment on barnase and barstar J. Mol. Biol. 278 1015-24
109. Zhou H-X 2003 Association and dissociation kinetics of colicin E3 and immunity protein 3 convergence of theory and experiment Protein Sci. 12 2379-82
110. Zhou H-X 1996 Effect of interaction potentials in diffusion-influenced reactions with small reactive regions J. Chem. Phys. 105 7235-7
111. Adam G and Delbruck M 1968 Reduction of dimensionality in biological diffusion processes Structural Chemistry and Molecular Biology ed N Davidson (San Francisco: Freeman) pp 198-215
112. Richter P H and Eigen M 1974 Diffusion controlled reaction rates in spheroidal geometry. Application to represser-operator association and membrane bound enzymes Biophys. Chem. 2 255-63
113. Berg O G, Winter R B and von Hippel P H 1981 Diffusion-driven mechanisms of protein translocation on nucleic acids: 1. Models and theory Biochemistry 20 6929-48
114. Berg O G and Ehrenberg M 1982 Association kinetics with coupled three- and one-dimensional diffusion. Chain-length dependence of the association rate to specific DNA sites Biophys. Chem. 15 41-51
115. Zhou H-X and Szabo A 2004 Enhancement of association rates by nonspecific binding to DNA and cell membranes Phys. Rev. Lett. 93 178101
116. Zhou H-X 2005 A model for the mediation of processivity of DNA-targeting proteins by nonspecific binding: Dependence on DNA length and presence of obstacles Biophys. J. 88 1608-15
117. Terry B J, Jack W E and Modrich P 1985 Facilitated diffusion during catalysis by Eco RI endonuclease. Nonspecific interactions in Eco RI catalysis J. Biol. Chem. 260 13130-7
118. Stanford N P, Szczelkun M D, Marko J F and Halford S E 2000 One- and three-dimensional pathways for proteins to reach specific sites EMBO J. 19 6546-57
119. Bustamante C, Keller D and Oster G 2001 The physics of molecular motors Acc. Chem. Res. 34 412-20
120. Astumian R D and Bier M 1996 Mechanochemical coupling of the motion of molecular motors to ATP hydrolysis Biophys. J. 70 637-53
121. Zhou H-X and Chen Y-d 1996 Chemically driven motility of Brownian particles Phys. Rev. Lett. 77 194-7
122. Astumian R D 1997 Thermodynamics and kinetics of a Brownian motor Science 276 917-22
123. Elston T, Wang H and Oster G 1998 Energy transduction in ATP synthase Nature 391 510-3
124. Dimroth P, Wang H, Grabe M and Oster G 1999 Energy transduction in the sodium F-ATPase of Propionigenium modestum Proc. Natl Acad. Sci. USA 96 4924-9
125. Junge W 1999 ATP synthase and other motor proteins Proc. Natl Acad. Sci. USA 96 4735-7
126. Okada Y and Hirokawa N 2000 Mechanism of the single-headed processivity: diffusional anchoring between the K-loop of kinesin and the C terminus of tubulin Proc. Natl Acad. Sci. USA 97 640-5
127. Oster G and Wang H 2003 Rotary protein motors Trends Biochem. Sci. 13 114-21
128. Bier M 2003 Processive motor protein as an overdamped Brownian stepper Phys. Rev. Lett. 91 148101
129. Kinosita K Jr, Adachi K and Itoh H 2004 Rotation of F1-ATPase: how an ATP-driven molecular machine may work Annu. Rev. Biophys. Biomol. Struct. 33 245-68
130. Yildiz A, Tomishige M, Vale R and Selvin P R 2004 Kinesin walks hand-over-hand Science 303 676-8
131. Xing J, Wang H, Dimroth P, von Balmoos C and Oster G 2004 Torque generation by the sodium Fo-ATPase Biophys. J. 87 2148-63
132. Parsegian A 1969 Energy of an ion crossing a low dielectric membrane: solutions to four relevant electrostatic problems Nature 221 844-6
133. Roux B 2005 Ion conduction and selectivity in K+ channels Annu. Rev. Biophys. Biomol. Struct. 34 153-71
134. Ketchem R R, Roux B and Cross T A 1997 High resolution refinement of a solid-state NMR derived structure of gramicidin A in a lipid bilayer environment Structure 5 11655-69
135. Zhou Y, Morais-Cabral J H, Kaufman A and MacKinnon R 2001 Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 Å resolution Nature 414 43-8
136. Jiang Y, Lee A, Chen J, Cadene M, Chait B T and MacKinnon R 2002 Crystal structure and mechanism of a calcium-gated potassium channel Nature 417 515-22
137. Nishimura K, Kim S, Zhang L and Cross T A 2002 The closed state of a H+ channel helical bundle combining precise orientational and distance restraints from solid state NMR Biochemistry 41 13170-7
138. Jiang Y, Lee A, Chen J, Ruta V, Cadene M, Chalt B T and MacKinnon R 2003 X-ray structure of a voltage-dependent K+ channel Nature 423 33-41
139. Kuo A, Gulbis J M, Antcliff J F, Rahman T, Lowe E D, Zimmer J, Cuthbertson J, Ashcroft F M, Ezaki T and Doyle D A 2003 Crystal structure of the potassium channel KirBac1.1 in the closed state Science 300 1922-6
140. Levitt D G 1986 Interpretation of biological ion channel flux data-reaction-rate versus continuum theory Annu. Rev. Biophys. Biophys. Chem. 15 29-57
141. Berezhkovskii A M and Bezrukov S M 2004 Optimizing transport of metabolites through large channels: molecular sieves with and without binding Biophys. J. 88 L17-9
142. Roux B, Allen T, Berneche S and Im W 2004 Theoretical and computational models of biological ion channels Q. Rev. Biophys. 37 15-103
143. Zhou M and MacKinnon R 2004 A mutant KcsA K+ channel with altered conduction properties and selectivity filter ion distribution J. Mol. Biol. 338 839-46
144. Morais-Cabral J H, Zhou Y and MacKinnon R 2001 Energetic optimization of ion conduction rate by the K+ selectivity filter Nature 414 37-42
145. Berneche S and Roux B 2001 Energetics of ion conduction through the K+ channel Nature 414 73-7
146. Noskov S, Berneche S and Roux B 2004 Control of ion selectivity by electrostatic and dynamic properties of carbonyl ligands Nature 431 830-4