This list contains references from the content that can be linked to their source. For a full set of references and notes please see the PDF or HTML where available.
N. Agmon (1984). Diffusion with back reaction. Journal of Chemical Physics 81, 2811–2817.
N. Agmon & J. J. Hopfield (1983). Transient kinetics of chemical reactions with bounded diffusion perpendicular to the reaction coordinate: intramolecular processes with slow conformational changes. Journal of Chemical Physics 78, 6947–6959.
X. Ai , Z. Zhou , Y. Bai & W. Y. Choy (2006). 15N NMR spin relaxation dispersion study of the molecular crowding effects on protein folding under native conditions. Journal of the American Chemical Society 128, 3916–3917.
E. Alm , A. V. Morozov , T. Kortemme & D. Baker (2002). Simple physical models connect theory and experiment in protein folding kinetics. Journal of Molecular Biology 322, 463–476.
R. Alsallaq & H.-X. Zhou (2007a). Energy landscape and transition state of protein–protein association. Biophysical Journal 92, 1486–1502.
R. Alsallaq & H.-X. Zhou (2007b). Prediction of protein-protein association rates from a transition-state theory. Structure 15, 215–224.
R. Alsallaq & H. X. Zhou (2008). Electrostatic rate enhancement and transient complex of protein-protein association. Proteins-Structure Function and Bioinformatics 71, 320–335.
G. Altobelli & S. Subramaniam (2000). Kinetics of association of anti-lysozyme monoclonal antibody D44.1 and hen-egg lysozyme. Biophysical Journal 79, 2954–2965.
N. M. Antikainen , R. D. Smiley , S. J. Benkovic & G. G. Hammes (2005). Conformation coupled enzyme catalysis: single-molecule and transient kinetics investigation of dihydrofolate reductase. Biochemistry 44, 16835–16843.
R. D. Astumian (1997). Thermodynamics and kinetics of a Brownian motor. Science 276, 917–922.
A. Baerga-Ortiz , A. R. Rezaie & E. A. Komives (2000). Electrostatic dependence of the thrombin–thrombomodulin interaction. Journal of Molecular Biology 296, 651–658.
G. I. Bell (1978). Models of the specific adhesion of cells to cells. Science 200, 618–627.
A. Berezhkovskii & A. Szabo (2005). One-dimensional reaction coordinates for diffusive activated rate processes in many dimensions. Journal of Chemical Physics 122, 14503.
A. M. Berezhkovskii & S. M. Bezrukov (2004). Optimizing transport of metabolites through large channels: molecular sieves with and without binding. Biophysical Journal 88, L17–L19.
A. M. Berezhkovskii , E. Pollak & V. Y. Zitserman (1992). Activated rate processes: generalization of the Kramers–Grote–Hynes and Langer theories. Journal of Chemical Physics 97, 2422–2437.
O. G. Berg (1985). Orientation constraints in diffusion-limited macromolecular association. The role of surface diffusion as a rate-enhancing mechanism. Biophysical Journal 47, 1–14.
O. G. Berg & M. Ehrenberg (1982). Association kinetics with coupled three- and one-dimensional diffusion. Chain-length dependence of the association rate to specific DNA sites. Biophysical Chemistry 15, 41–51.
O. G. Berg , R. B. Winter & P. H. Von Hippel (1981). Diffusion-driven mechanisms of protein translocation on nucleic acids. I. Models and theory. Biochemistry 20, 6929–6948.
M. Berkowitz , J. D. Morgan , J. A. Mccammon & S. H. Northrup (1983). Diffusion-controlled reactions: a variational formula for the optimum reaction coordinate. Journal of Chemical Physics 79, 5563–5565.
S. Berneche & B. Roux (2003). A microscopic view of ion conduction through the K+ channel. Proceedings of the National Academy of Sciences of the United States of America 100, 8644–8648.
D. J. Bicout & A. Szabo (1997). First passage times, correlation functions, and reaction rates. Journal of Chemical Physics 106, 10292–10298.
M. Bier (2003). Processive motor protein as an overdamped Brownian stepper. Physical Review Letters 91, 148101.
P. C. Blainey , A. M. Van Oijen , A. Banerjee , G. L. Verdine & X. S. Xie (2006). A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proceedings of the National Academy of Sciences of the United States of America 103, 5752–5757.
J. D. Bryngelson & P. G. Wolynes (1989). Intermediates and barrier crossing in a random energy model (with applications to protein folding). Journal of Physical Chemistry 93, 6902–6915.
N.-V. Buchete & G. Hummer (2008). Coarse master equations for peptide folding dynamics. Journal of Physical Chemistry B 112, 6057–6069.
C. Bustamante , D. Keller & G. Oster (2001). The physics of molecular motors. Accounts of Chemical Research 34, 412–420.
S. Candia , M. L. Garcia & R. Latorre (1992). Mode of action of iberiotoxin, a potent blocker of the large conductance Ca2+-activated K+ channel. Biophysical Journal 63, 583–590.
Y. Cao , R. Kuske & H. Li (2008). Direct observation of Markovian behavior of the mechanical unfolding of individual proteins. Biophysical Journal 95, 782–788.
M. Carrion-Vazquez , A. F. Oberhauser , S. B. Fowler , P. E. Marszalek , S. E. Broedel , J. Clarke & J. M. Fernandez (1999). Mechanical and chemical unfolding of a single protein: a comparison. Proceedings of the National Academy of Sciences of the United States of America 96, 3694–3699.
J. Chahine , R. J. Oliveira , V. B. Leite & J. Wang (2007). Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding. Proceedings of the National Academy of Sciences of the United States of America 104, 14646–14651.
D. Chandler (1978). Statistical mechanics of isomerization dynamics in liquids and transition-state approximation. Journal of Chemical Physics 68, 2959–2970.
G. Chen , J. D. Wen & I. Tinoco JR (2007). Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA. RNA 13, 2175–2188.
M. S. Cheung , D. Klimov & D. Thirumalai (2005). Molecular crowding enhances native state stability and refolding rates of globular proteins. Proceedings of the National Academy of Sciences of the United States of America 102, 4753–4758.
J. D. Chodera , N. Singhal , V. S. Pande , K. A. Dill & W. C. Swope (2007). Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. Journal of Chemical Physics, 126, 155101.
J. D. Chodera , W. C. Swope , J. W. Pitera & K. A. Dill (2006). Long-time protein folding dynamics from short-time molecular dynamics simulations. Multiscale Modeling and Simulation 5, 1214–1226.
M. Cieplak , M. Henkel , J. Karbowski & J. R. Banavar (1998). Master equation approach to protein folding and kinetic traps. Physical Review Letters 80, 3650–3653.
F. C. Collins & G. E. Kimball (1949). Diffusion-controlled reaction rates. Journal of Colloid Science 4, 425–437.
M. D'Abramo , A. Di Nola & A. Amadei (2009). Kinetics of carbon monoxide migration and binding in solvated myoglobin as revealed by molecular dynamics simulations and quantum mechanical calculations. The Journal of Physical Chemistry B 113, 16346–16353.
R. J. Darling , U. Kuchibhotla , W. Glaesner , R. Micanovic , D. R. Witcher & J. M. Beals (2002). Glycosylation of erythropoietin affects receptor binding kinetics: role of electrostatic interactions. Biochemistry 41, 14524–14531.
P. Debye (1942). Reaction rate in ionic solutions. Transactions of the Electrochemical Society 82, 265–272.
M. Doi (1975a). Theory of diffusion-controlled reaction between non-simple molecules. I. Chemical Physics 11, 107–113.
W. Dong , F. Baros & J. C. Andre (1989). Diffusion-controlled reactions. I. Molecular dynamics simulation of a noncontinuum model. Journal of Chemical Physics 91, 4643–4650.
R. Du , V. S. Pande , A. Y. Grosberg , T. Tanaka & E. S. Shakhnovich (1998). On the transition coordinate for protein folding. Journal of Chemical Physics 108, 334–350.
O. K. Dudko , G. Hummer & A. Szabo (2006). Intrinsic rates and activation free energies from single-molecule pulling experiments. Physical Review Letters 96, 108101.
O. K. Dudko , G. Hummer & A. Szabo (2008). Theory, analysis, and interpretation of single-molecule force spectroscopy experiments. Proceedings of the National Academy of Sciences of the United States of America 105, 15755–15760.
A. H. Elcock , R. R. Gabdoulline , R. C. Wade & J. A. Mccammon (1999). Computer simulation of protein–protein association kinetics: acetylcholinesterase-fasciculin. Journal of Molecular Biology 291, 149–162.
B. P. English , W. Min , A. M. Van Oijen , K. T. Lee , G. Luo , H. Sun , B. J. Cherayil , S. C. Kou & X. S. Xie (2006). Ever-fluctuating single enzyme molecules: Michaelis–Menten equation revisited. Nature Chemical Biology 2, 87–94.
L. Escobar , M. J. Root & R. Mackinnon (1993). Influence of protein surface charge on the bimolecular kinetics of a potassium channel peptide inhibitor. Biochemistry 32, 6982–6987.
E. Evans & K. Ritchie (1997). Dynamic strength of molecular adhesion bonds. Biophysical Journal 72, 1541–1555.
M. G. Evans & M. Polanyi (1935). Some applications of the transition state method to the calculation of reaction velocities, especially in solution. Transactions of the Faraday Society 31, 875–894.
H. Eyring (1935). The activated complex in chemical reactions. Journal of Chemical Physics 3, 107–115.
O. Flomenbom , K. Velonia , D. Loos , S. Masuo , M. Cotlet , Y. Engelborghs , J. Hofkens , A. E. Rowan , R. J. Nolte , M. Van Der Auweraer , F. C. De Schryver & J. Klafter (2005). Stretched exponential decay and correlations in the catalytic activity of fluctuating single lipase molecules. Proceedings of the National Academy of Sciences of the United States of America 102, 2368–2372.
J. Foote & H. N. Eisen (1995). Kinetic and affinity limits on antibodies produced during immune responses. Proceedings of the National Academy of Sciences of the United States of America 92, 1254–1256.
R. R. Gabdoulline , U. Kummer , L. F. Olsen & R. C. Wade (2003). Concerted simulations reveal how peroxidase compound III formation results in cellular oscillations. Biophysical Journal 85, 1421–1428.
R. R. Gabdoulline & R. C. Wade (1997). Simulation of the diffusional association of barnase and barstar. Biophysical Journal 72, 1917–1929.
R. R. Gabdoulline & R. C. Wade (2001). Protein–protein association: investigation of factors influencing association rates by Brownian dynamics simulations. Journal of Molecular Biology 306, 1139–1155.
Y. Q. Gao , W. Yang & M. Karplus (2005). A structure-based model for the synthesis and hydrolysis of ATP by F1-ATPase. Cell 123, 195–205.
S. Gianni , A. Engstrom , M. Larsson , N. Calosci , F. Malatesta , L. Eklund , C. C. Ngang , C. Travaglini-Allocatelli & P. Jemth (2005). The kinetics of PDZ domain-ligand interactions and implications for the binding mechanism. Journal of Biological Chemistry 280, 34805–34812.
D. T. Gillespie (1977). Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81, 2340–2361.
S. A. N. Goldstein & C. Miller (1993). Mechanism of charybdotoxin block of a voltage-gated K+ channel. Biophysical Journal 65, 1613–1619.
I. V. Gopich & A. B. Doktorov (1996). Kinetics of diffusion-influenced reversible reaction A+B <-> C in solutions. Journal of Chemical Physics 105, 2320–2332.
I. V. Gopich & A. Szabo (2002). Kinetics of reversible diffusion influenced reactions: the self-consistent relaxation time approximation. Journal of Chemical Physics 117, 507–517.
I. Goychuk & P. Hanggi (2002). Ion channel gating: a first-passage time analysis of the Kramers type. Proceedings of the National Academy of Sciences of the United States of America 99, 3552–3556.
W. J. Greenleaf , K. L. Frieda , D. A. Foster , M. T. Woodside & S. M. Block (2008). Direct observation of hierarchical folding in single riboswitch aptamers. Science 319, 630–633.
R. F. Grote & J. T. Hynes (1980). The stable states picture of chemical reactions. II. Rate constants for condensed and gas phase reaction models. Journal of Chemical Physics 73, 2715–2732.
S. E. Halford & J. F. Marko (2004). How do site-specific DNA-binding proteins find their targets? Nucleic Acids Research 32, 3040–3052.
P. Hanggi , P. Talkner & M. Borkovec (1990). Reaction rate theory: 50 years after Kramers. Reviews of Modern Physics 62, 251–341.
L. Hemsath , R. Dvorsky , D. Fiegen , M. F. Carlier & M. R. Ahmadian (2005). An electrostatic steering mechanism of Cdc42 recognition by Wiskott–Aldrich syndrome proteins. Molecular Cell 20, 313–324.
T. L. Hill (1975). Effect of rotation on diffusion-controlled rate of ligand-protein association. Proceedings of the National Academy of Sciences of the United States of America 72, 4918–4922.
T. L. Hoffman , C. C. Labranche , W. Zhang , G. Canziani , J. Robinson , I. Chaiken , J. A. Hoxie & R. W. Doms (1999). Stable exposure of the coreceptor-binding site in a CD4-independent HIV-1 envelope protein. Proceedings of the National Academy of Sciences of the United States of America 96, 6359–6364.
G. Hummer & I. G. Kevrekidis (2003). Coarse molecular dynamics of a peptide fragment: free energy, kinetics, and long-time dynamics computations. Journal of Chemical Physics 118, 10762–10773.
R. J. Johnson , J. G. Mccoy , C. A. Bingman , G. N. Phillips JR & R. T. Raines (2007). Inhibition of human pancreatic ribonuclease by the human ribonuclease inhibitor protein. Journal of Molecular Biology 368, 434–449.
W. Junge (1999). ATP synthase and other motor proteins. Proceedings of the National Academy of Sciences of the United States of America 96, 4735–4737.
J. C. Keck (1960). Variational theory of chemical reaction rates applied to three-body recombination. Journal of Chemical Physics 32, 1035–1050.
M. S. Kellermayer , S. B. Smith , H. L. Granzier & C. Bustamante (1997). Folding-unfolding transitions in single titin molecules characterized with laser tweezers. Science 276, 1112–1116.
C. Kiel & L. Serrano (2009). Cell type-specific importance of ras-c-raf complex association rate constants for MAPK signaling. Science Signaling 2, ra38.
J. S. Kim & A. Yethiraj (2009). Effect of macromolecular crowding on reaction rates: a computational and theoretical study. Biophysical Journal 96, 1333–1340.
K. Kinosita JR, K. Adachi & H. Itoh (2004). Rotation of F1-ATPase: how an ATP-driven molecular machine may work. Annual Review of Biophysics and Biomolecular Structure 33, 245–268.
A. B. Kolomeisky & M. E. Fisher (2007). Molecular motors: a theorist's perspective. Annual Review of Physical Chemistry 58, 675–695.
A. V. Korennykh , J. A. Piccirilli & C. C. Correll (2006). The electrostatic character of the ribosomal surface enables extraordinarily rapid target location by ribotoxins. Nature Structural and Molecular Biology 13, 436–443.
S. C. Kou , B. J. Cherayil , W. Min , B. P. English & X. S. Xie (2005). Single-molecule Michaelis-Menten equations. Journal of Physical Chemistry B 109, 19068–19081.
H. A. Kramers (1940). Brownian motion in a field of force and the diffusion model of chemical reactions. Physica 7, 284–304.
S. V. Krivov & M. Karplus (2002). Free energy disconnectivity graphs: application to peptide models. Journal of Chemical Physics 117, 10894–10903.
Y. Y. Kuttner , N. Kozer , E. Segal , G. Schreiber & G. Haran (2005). Separating the contribution of translational and rotational diffusion to protein association. Journal of the American Chemical Society 127, 15138–15144.
J. S. Langer (1969). Statistical theory of decay of metastable states. Annals of Physics 54, 258–275.
P. Lauger , W. Stephan & E. Frehland (1980). Fluctuations of barrier structure in ionic channels. Biochimica et Biophysica Acta 602, 167–180.
T. A. Laurence , Y. Kwon , A. Johnson , C. W. Hollars , M. O'Donnell , J. A. Camarero & D. Barsky (2008). Motion of a DNA sliding clamp observed by single molecule fluorescence spectroscopy. Journal of Biological Chemistry 283, 22895–22906.
M. J. Law , M. E. Linde , E. J. Chambers , C. Oubridge , P. S. Katsamba , L. Nilsson , I. S. Haworth & I. A. Laird-Offringa (2006). The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA. Nucleic Acids Research 34, 275–285.
J. D. Lear (2003). Proton conduction through the M2 protein of the influenza A virus; a quantitative, mechanistic analysis of experimental data. FEBS Letters 552, 17–22.
J. L. Lebowitz , E. Helfand & E. Praestgaard (1965). Scaled particle theory of fluid mixtures. Journal of Chemical Physics 43, 774–779.
S. Lee & M. Karplus (1987). Kinetics of diffusion-influenced bimolecular reactions in solution. I. General formalism and relaxation kinetics of fast reversible reactions. Journal of Chemical Physics 86, 1883–1903.
D. G. Levitt (1986). Interpretation of biological ion channel flux data-reaction-rate versus continuum theory. Annual Review of Biophysics and Biophysical Chemistry 15, 29–57.
C. G. Li , Y. Q. Wang & G. J. Pielak (2009). Translational and rotational diffusion of a small globular protein under crowded conditions. Journal of Physical Chemistry B 113, 13390–13392.
J. Liphardt , B. Onoa , S. B. Smith , I. J. Tinoco & C. Bustamante (2001). Reversible unfolding of single RNA molecules by mechanical force. Science 292, 733–737.
H. P. Lu , L. Xun & X. S. Xie (1998). Single-molecule enzymatic dynamics. Science 282, 1877–1882.
N. N. Lukzen , A. B. Doktorov & A. I. Burshtein (1986). Non-markovian theory of diffusion-controlled excitation transfer. Chemical Physics 102, 289–304.
B. T. Marshall , K. K. Sarangapani , J. Lou , R. P. Mcever & C. Zhu (2005). Force history dependence of receptor–ligand dissociation. Biophysical Journal 88, 1458–1466.
J. Martin , M. Mayhew , T. Langer & U. Hartl (1993). The reaction cycle of GroEL and GroES in chaperonin-assisted protein folding. Nature 366, 228–233.
J. Mathé , H. Visram , V. Viasnoff , Y. Rabin & A. Meller (2004). Nanopore unzipping of individual DNA hairpin molecules. Biophysical Journal 87, 3205–3212.
S. R. Mcguffee & A. H. Elcock (2006). Atomically detailed simulations of concentrated protein solutions: the effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems. Journal of the American Chemical Society 128, 12098–12110.
V. I. Melnikov & S. V. Meshkov (1986). Theory of activated rate processes: exact solution of the Kramers problem. Journal of Chemical Physics 85, 1018–1027.
R. Merkel , P. Nassoy , A. Leung , K. Ritchie & E. Evans (1999). Energy landscapes of receptor–ligand bonds explored with dynamic force spectroscopy. Nature 397, 50–53.
C. Merlo , K. A. Dill & T. R. Weikl (2005). Φ values in protein-folding kinetics have energetic and structural components. Proceedings of the National Academy of Sciences of the United States of America 102, 10171–10175.
C. Miller (1990). Diffusion-controlled binding of a peptide neurotoxin to its K+ channel receptor. Biochemistry 29, 5320–5325.
W. Min , I. V. Gopich , B. P. English , S. C. Kou , X. S. Xie & A. Szabo (2006). When does the Michaelis–Menten equation hold for fluctuating enzymes? Journal of Physical Chemistry B 110, 20093–20097.
W. Min , G. Luo , B. J. Cherayil , S. C. Kou & X. S. Xie (2005). Observation of a power-law memory kernel for fluctuations within a single protein molecule. Physical Review Letters 94, 198302.
W. Min & X. S. Xie (2006). Kramers model with a power-law friction kernel: dispersed kinetics and dynamic disorder of biochemical reactions. Physical Review E 73, 010902.
D. D. Minh , C. E. Chang , J. Trylska , V. Tozzini & J. A. Mccammon (2006). The influence of macromolecular crowding on HIV-1 protease internal dynamics. Journal of the American Chemical Society 128, 6006–6007.
J. Mittal & R. B. Best (2010). Dependence of protein folding stability and dynamics on the density and composition of macromolecular crowders. Biophysical Journal 98, 315–320.
O. Miyashita , J. N. Onuchic & M. Y. Okamura (2004). Transition state and encounter complex for fast association of cytochrome c2 with bacterial reaction center. Proceedings of the National Academy of Sciences of the United States of America 101, 16174–16179.
V. Muñoz , E. R. Henry , J. Hofrichter & W. A. Eaton (1998). A statistical mechanical model for β-hairpin kinetics. Proceedings of the National Academy of Sciences of the United States of America 95, 5872–5879.
R. D. Murrell-Lagnado & R. W. Aldrich (1993). Energetics of Shaker K channel's block by inactivation peptides. Journal of General Physiology 102, 977–1003.
W. Naumann (1994). Competitive reversible binding: a theoretical study of density effects on the long-time relaxation. Journal of Chemical Physics 101, 10953–10960.
A. Nitzan (1987). Non-Markovian theory of activated rate processes. VI. Unimolecular reactions in condensed phases. Journal of Chemical Physics 86, 2734–2749.
F. Noe & S. Fischer (2008). Transition networks for modeling the kinetics of conformational change in macromolecules. Current Opinion in Structural Biology 18, 154–162.
H. J. Nolte , T. L. Rosenberry & E. Neumann (1980). Effective charge on acetylcholinesterase active sites determined from the ionic strength dependence of association rate constants with cationic ligands. Biochemistry 19, 3705–3711.
S. H. Northrup & H. P. Erickson (1992). Kinetics of protein–protein association explained by Brownian dynamics computer simulation. Proceedings of the National Academy of Sciences of the United States of America 89, 3338–3342.
S. H. Northrup & J. T. Hynes (1980). The stable states picture of chemical reactions. I. Formulation for rate constants and initial condition effects. Journal of Chemical Physics 73, 2700–2714.
S. H. Northrup , J. C. L. Reynolds , C. M. Miller , K. J. Forrest & J. O. Boles (1986). Diffusion-controlled association rate of cytochrome c and cytochrome c peroxidase in a simple electrostatic model. Journal of the American Chemical Society 108, 8162–8170.
Y. Okada & N. Hirokawa (2000). Mechanism of the single-headed processivity: diffusional anchoring between the K-loop of kinesin and the C terminus of tubulin. Proceedings of the National Academy of Sciences of the United States of America 97, 640–645.
L. Onsager (1931). Reciprocal relations in irreversible processes. II. Physical Review 38, 2265–2279.
T. Pape , W. Wintermeyer & M. Rodnina (1998). Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome. The EMBO Journal 17, 7490–7497.
C. Park & R. T. Raines (2001). Quantitative analysis of the effect of salt concentration on enzymatic catalysis. Journal of the American Chemical Society 123, 11472–11479.
E. Pollak (1986). Theory of activated rate processes: a new derivation of Kramers' expression. Journal of Chemical Physics 85, 865–867.
E. Pollak , H. Grabert & P. Hanggi (1989). Theory of activated rate processes for arbitrary frequency dependent friction: solution of the turnover problem. Journal of Chemical Physics 91, 4073–4087.
A. N. Pryor , T. Selwood , L. S. Leu , M. A. Andracki , B. H. Lee , M. Rao , T. Rosenberry , B. P. Doctor , I. Silman & D. M. Quinn (1992). Simple general acid-base catalysis of physiological acetylcholinesterase reactions. Journal of the American Chemical Society 114, 3896–3900.
H. Qian (1997). A simple theory of motor protein kinetics and energetics. Biophysical Chemistry 67, 263–267.
H. Qian (2000). A simple theory of motor protein kinetics and energetics. II. Biophysical Chemistry 83, 35–43.
H. Qian (2008). Cooperativity and specificity in enzyme kinetics: a single-molecule time-based perspective. Biophysical Journal 95, 10–17.
S. Qin , D. D. Minh , J. A. Mccammon & H.-X. Zhou (2010). Method to predict crowding effects by postprocessing molecular dynamics trajectories: application to the flap dynamics of HIV-1 protease. Journal of Physical Chemistry Letters 1, 107–110.
S. Qin & H.-X. Zhou (2009). Dissection of the high rate constant for the binding of a ribotoxin to the ribosome. Proceedings of the National Academy of Sciences of the United States of America 106, 6974–6979.
S. Qin & H.-X. Zhou (2010). Generalized fundamental measure theory for atomistic modeling of macromolecular crowding. Physical Review E 81, 031919.
S. Qin & H. X. Zhou (2008). Prediction of salt and mutational effects on the association rate of U1A protein and U1 small nuclear RNA stem/loop II. Journal of Physical Chemistry B 112, 5955–5960.
Z. Radic , P. D. Kirchhoff , D. M. Quinn , J. A. Mccammon & P. Taylor (1997). Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase. Journal of Biological Chemistry 272, 23265–23277.
P. H. Richter & M. Eigen (1974). Diffusion controlled reaction rates in spheroidal geometry. Application to repressor–operator association and membrane bound enzymes. Biophysical Chemistry 2, 255–263.
M. Rief , M. Gautel , F. Oesterhelt , J. M. Fernandez & H. E. Gaub (1997). Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276, 1109–1112.
A. D. Riggs , S. Bourgeois & M. Cohn (1970). The lac repressor–operator interaction. III. Kinetic studies. Journal of Molecular Biology 53, 401–417.
H. Risken (1989). The Fokker–Planck Equation, 2nd edn.Berlin: Springer-Verlag.
M. V. Rodnina , K. B. Gromadski , U. Kothe & H. J. Wieden (2005). Recognition and selection of tRNA in translation. FEBS Letters 579, 938–942.
O. Schaad , H. X. Zhou , A. Szabo , W. A. Eaton & E. R. Henry (1993). Simulation of the kinetics of ligand binding to a protein by molecular dynamics: geminate rebinding of nitric oxide to myoglobin. Proceedings of the National Academy of Sciences of the United States of America 90, 9547–9551.
M. Schlierf & M. Rief (2006). Single-molecule unfolding force distributions reveal a funnel-shaped energy landscape. Biophysical Journal 90, L33–L35.
M. Schlosshauer & D. Baker (2002). A general expression for bimolecular association rates with orientational constraints. Journal of Physical Chemistry B 106, 12079–12083.
M. Schlosshauer & D. Baker (2004). Realistic protein–protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein Science 13, 1660–1669.
J. Schonbrun & K. A. Dill (2003). Fast protein folding kinetics. Proceedings of the National Academy of Sciences of the United States of America 100, 12678–12682.
R. Schranner & P. H. Richter (1978). Rate enhancement by guided diffusion. Chain length dependence of repressor-operator association rates. Biophysical Chemistry 8, 135–150.
G. Schreiber & A. R. Fersht (1993). Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering. Biochemistry 32, 5145–5150.
G. Schreiber & A. R. Fersht (1996). Rapid, electrostatically assisted association of proteins. Nature Structural Biology 3, 427–431.
G. Schreiber , G. Haran & H.-X. Zhou (2009). Fundamental aspects of protein-protein association kinetics. Chemical Reviews 109, 839–860.
J. M. Schurr (1979). One-dimensional diffusion coefficient of proteins absorbed on DNA. Hydrodynamic considerations. Biophysical Chemistry 9, 413–414.
B. E. Shapiro & H. Qian (1997). A quantitative analysis of single protein–ligand complex separation with the atomic force microscope. Biophysical Chemistry 67, 211–219.
R. Shapiro , M. Ruiz-Gutierrez & C.-Z. Chen (2000). Analysis of the interactions of human ribonuclease inhibitor with angiogenin and ribonuclease A by mutagenesis: importance of inhibitor residues inside versus outside the C-terminal ‘hot spot’. Journal of Molecular Biology 302, 497–519.
B. J. Shen , T. Hage & W. Sebald (1996). Global and local determinants for the kinetics of interleukin-4/interleukin-4 receptor alpha chain interaction. A biosensor study employing recombinant interleukin-4-binding protein. European Journal of Biochemistry 240, 252–261.
J. Shi , J. Dertouzos , A. Gafni , D. Steel & B. A. Palfey (2006). Single-molecule kinetics reveals signatures of half-sites reactivity in dihydroorotate dehydrogenase A catalysis. Proceedings of the National Academy of Sciences of the United States of America 103, 5775–5780.
D. Shoup , G. Lipari & A. Szabo (1981). Diffusion-controlled bimolecular reaction rates. The effect of rotational diffusion and orientation constraints. Biophysical Journal 36, 697–714.
D. Shoup & A. Szabo (1982). Role of diffusion in ligand binding to macromolecules and cell-bound receptors. Biophysical Journal 40, 33–39.
J. L. Skinner & P. G. Wolynes (1978). Relaxation processes and chemical kinetics. Journal of Chemical Physics 69, 2143–2150.
K. Solc & W. H. Stockmayer (1971). Kinetics of diffusion-controlled reaction between chemically asymmetric molecules. I. General theory. Journal of Chemical Physics 54, 2981–2988.
K. Solc & W. H. Stockmayer (1973). Kinetics of diffusion-controlled reaction between chemically asymmetric molecules. II. Approximate steady-state solution. International Journal of Chemical Kinetics 5, 733–752.
A. Spaar , C. Dammer , R. R. Gabdoulline , R. C. Wade & V. Helms (2006). Diffusional encounter of barnase and barstar. Biophysical Journal 90, 1913–1924.
R. C. Stewart & R. Van Bruggen (2004). Association and dissociation kinetics for CheY interacting with the P2 domain of CheA. Journal of Molecular Biology 336, 287–301.
M. Stoer & F. Wagner (1997). A simple min-cut algorithm. Journal of the ACM 44, 585–591.
J. E. Straub , M. Borkovec & B. J. Berne (1986). Non-Markovian activated rate processes: comparison of current theories with numerical simulation data. Journal of Chemical Physics 84, 1788–1794.
R. Swaminathan , C. P. Hoang & A. S. Verkman (1997). Photobleaching recovery and anisotropy decay of green fluorescent protein GFP-S65T in solution and cells: cytoplasmic viscosity probed by green fluorescent protein translational and rotational diffusion. Biophysical Journal 72, 1900–1907.
A. Szabo (1989). Theory of diffusion-influenced fluorescence quenching. Journal of Physical Chemistry 93, 6929–6939.
A. Szabo (1991). Theoretical approaches to reversible diffusion-influenced reactions: monomer–excimer kinetics. Journal of Chemical Physics 95, 2481–2490.
A. Szabo , K. Schulten & Z. Schulten (1980). First passage time approach to diffusion controlled reactions. Journal of Chemical Physics 72, 4350–4357.
A. Szabo , D. Shoup , S. H. Northrup & J. A. Mccammon (1982). Stochastically gated diffusion-influenced reactions. Journal of Chemical Physics 77, 4484–4493.
S. I. Temkin & B. I. Yakobson (1984). Diffusion-controlled reactions of chemically anisotropic molecules. Journal of Physical Chemistry 88, 2679–2682.
H. Terlau , K.-J. Shon , M. Grilley , M. Stocker , W. Stuhmer & O. M. Baldomero (1996). Strategy for rapid immobilization of prey by a fish-hunting marine snail. Nature 381, 148–151.
H. Tjong & H.-X. Zhou (2010). The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe. Biophysical Journal 98, 2273–2280.
M. Tokuyama (2009a). Self-diffusion in multi-component glass-forming systems. Physica A 388, 3083–3092.
M. Tokuyama (2009b). Universality in multicomponent glass-forming liquids near the glass transition. Physical Review E 80, 031503.
M. Tokuyama & I. Oppenheim (1994). Dynamics of hard-sphere suspensions. Physical Review E 50, R16–R19.
M. Tokuyama & I. Oppenheim (1995). On the theory of concentrated hard-sphere suspensions. Physica A 216, 85–119.
N. T. Uter , I. Gruic-Sovulj & J. J. Perona (2005). Amino acid-dependent transfer RNA affinity in a class I aminoacyl-tRNA synthetase. Journal of Biological Chemistry 280, 23966–23977.
A. M. Van Oijen , P. C. Blainey , D. J. Crampton , C. C. Richardson , T. Ellenberger & X. S. Xie (2003). Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder. Science 301, 1235–1238.
D. C. Vellom , Z. Radic , Y. Li , N. A. Pickering , S. Camp & P. Taylor (1993). Amino acid residues controlling acetylcholinesterase and butylcholinesterase specificity. Biochemistry 32, 12–17.
M. Vijayakumar , K. Y. Wong , G. Schreiber , A. R. Fersht , A. Szabo & H.-X. Zhou (1998). Electrostatic enhancement of diffusion-controlled protein–protein association: comparison of theory and experiment on barnase and barstar. Journal of Molecular Biology 278, 1015–1024.
D. Walker , G. R. Moore , R. James & C. Kleanthous (2003). Thermodynamic consequences of bipartite immunity protein binding to the ribosomal ribonuclease colicin E3. Biochemistry 42, 4161–4171.
R. Wallis , G. K. Moore , R. James & C. Kleanthous (1995). Protein–protein interactions in colicin E9 DNase-immunity protein complexes. 1. Diffusion-controlled association and femtomolar binding for the cognate complex. Biochemistry 34, 13743–13750.
Y. M. Wang , R. H. Austin & E. C. Cox (2006). Single molecule measurements of repressor protein 1D diffusion on DNA. Physical Review Letters 97, 048302.
D. Wassaf , G. Kuang , K. Kopacz , Q. L. Wu , Q. Nguyen , M. Toews , J. Cosic , J. Jacques , S. Wiltshire , J. Lambert , C. C. Pazmany , S. Hogan , R. C. Ladner , A. E. Nixon & D. J. Sexton (2006). High-throughput affinity ranking of antibodies using surface plasmon resonance microarrays. Analytical Biochemistry 351, 241–253.
T. R. Weikl , M. Palassini & K. A. Dill (2004). Cooperativity in two-state protein folding kinetics. Protein Science 13, 822–829.
H. Wendt , L. Leder , H. Harma , I. Jelesarov , A. Baici & H. R. Bosshard (1997). Very rapid, ionic strenghth-dependent association and folding of a heterodimeric leucine zipper. Biochemistry 36, 204–213.
G. Wieczorek & P. Zielenkiewicz (2008). Influence of macromolecular crowding on protein–protein association rates – a Brownian dynamics study. Biophysical Journal 95, 5030–5036.
E. Wigner (1937). Calculation of the rate of elementary association reactions. Journal of Chemical Physics 5, 720–725.
G. Wilemski & M. Fixman (1973). General theory of diffusion-controlled reactions. Journal of Chemical Physics 58, 4009–4019.
Y. Wu , Y. Q. Gao & M. Karplus (2007). A kinetic model of coordinated myosin V. Biochemistry 46, 6318–6330.
J. Xing , H. Wang , P. Dimroth , C. Von Balmoos & G. Oster (2004). Torque generation by the sodium Fo-ATPase. Biophysical Journal 87, 2148–2163.
T. Yamamoto (1960). Quantum statistical mechanical theory of the rate of exchange chemical reactions in the gas phase. Journal of Chemical Physics 33, 281–289.
G. Yang , C. Cecconi , W. A. Baase , I. R. Vetter , W. A. Breyer , J. A. Haack , B. W. Matthews , F. W. Dahlquist & C. Bustamante (2000). Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme. Proceedings of the National Academy of Sciences of the United States of America 97, 139–144.
M. Yang , S. Lee & K. J. Shin (1998). Kinetic theory of bimolecular reactions in liquid. III. Reversible association–dissociation: A+B <->C. Journal of Chemical Physics 108, 9069–9085.
M. Yi , T. A. Cross & H. X. Zhou (2009). Conformational heterogeneity of the M2 proton channel and a structural model for channel activation. Proceedings of the National Academy of Sciences of the United States of America 106, 13311–13316.
A. Yildiz , M. Tomishige , R. Vale & P. R. Selvin (2004). Kinesin walks hand-over-hand. Science 303, 676–678.
J.-M. Yuan , C.-L. Chyan , H.-X. Zhou , T.-Y. Chung , H. Peng , G. Ping & G. Yang (2008). The effects of macromolecular crowding on the mechanical stability of protein molecules. Protein Science 17, 2156–2166.
Z. Zhang , P. T. Rajagopalan , T. Selzer , S. J. Benkovic & G. G. Hammes (2004). Single-molecule and transient kinetics investigation of the interaction of dihydrofolate reductase with NADPH and dihydrofolate. Proceedings of the National Academy of Sciences of the United States of America 101, 2764–2769.
H.-X. Zhou (1989). The exponential nature of barrier crossings studied by Langevin dynamics. Chemical Physics Letters 164, 285–290.
H.-X. Zhou (1993). Brownian dynamics study of the influences of electrostatic interaction and diffusion on protein–protein association kinetics. Biophysical Journal 64, 1711–1726.
H.-X. Zhou (1996). Effect of interaction potentials in diffusion-influenced reactions with small reactive regions. Journal of Chemical Physics 105, 7235–7237.
H.-X. Zhou (1997). Enhancement of protein-protein association rate by interaction potential: accuracy of prediction based on local Boltzmann factor. Biophysical Journal 73, 2441–2445.
H.-X. Zhou (1998). Theory of the diffusion-influenced substrate binding rate to a buried and gated active site. Journal of Chemical Physics 108, 8146–8154.
H.-X. Zhou (2001a). Disparate ionic-strength dependencies of on and off rates in protein–protein association. Biopolymers 59, 427–433.
H.-X. Zhou (2001b). The affinity-enhancing roles of flexible linkers in two-domain DNA-binding proteins. Biochemistry 40, 15069–15073.
H.-X. Zhou (2001c). Single-chain versus dimeric protein folding: thermodynamic and kinetic consequences of covalent linkage. Journal of the American Chemical Society 123, 6730–6731.
H.-X. Zhou (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. Journal of Physical Chemistry B 106, 2393–2397.
H.-X. Zhou (2003a). Association and dissociation kinetics of colicin E3 and immunity protein 3: convergence of theory and experiment. Protein Science 12, 2379–2382.
H.-X. Zhou (2003b). Quantitative account of the enhanced affinity of two linked scFvs specific for different epitopes on the same antigen. Journal of Molecular Biology 329, 1–8.
H.-X. Zhou (2004). Protein folding and binding in confined spaces and in crowded solutions. Journal of Molecular Recognition 17, 368–375.
H.-X. Zhou (2005a). How do biomolecular systems speed up and regulate rates? Physical Biology 2, R1–R25.
H.-X. Zhou (2005b). A model for the mediation of processivity of DNA-targeting proteins by nonspecific binding: dependence on DNA length and presence of obstacles. Biophysical Journal 88, 1608–1615.
H.-X. Zhou (2008). A minimum-reaction-flux solution to master-equation models of protein folding. Journal of Chemical Physics 128, 195104.
H.-X. Zhou , J. M. Briggs & J. A. Mccammon (1996). A 240-fold electrostatic rate-enhancement for acetylcholinesterase–substrate binding can be predicted by the potential within the active site. Journal of the American Chemical Society 118, 13069–13070.
H.-X. Zhou , J. M. Briggs , S. Tara & J. A. Mccammon (1998a). Correlation between rate of enzyme–substrate diffusional encounter and average Boltzmann factor around active site. Biopolymers 45, 355–360.
H.-X. Zhou & Y.-D. Chen (1996). Chemically driven motility of Brownian particles. Physical Review Letters 77, 194–197.
H.-X. Zhou & M. K. Gilson (2009). Theory of free energy and entropy in noncovalent binding. Chemical Reviews 109, 4092–4107.
H.-X. Zhou & J. A. Mccammon (2010). The gates of ion channels and enzymes. Trends in Biochemical Sciences 35, 179–185.
H.-X. Zhou , G. Rivas & A. P. Minton (2008). Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annual Review of Biophysics 37, 375–397.
H.-X. Zhou & A. Szabo (1991). Comparison between molecular dynamics simulations and the Smoluchowski theory of reactions in a hard sphere liquid. Journal of Chemical Physics 95, 5948–5952.
H.-X. Zhou & A. Szabo (1996a). Theory and simulation of the time-dependent rate coefficients of diffusion-influenced reactions. Biophysical Journal 71, 2440–2457.
H.-X. Zhou & A. Szabo (1996b). Theory and simulation of stochastically-gated diffusion-influenced reactions. Journal of Physical Chemistry 100, 2597–2604.
H.-X. Zhou & A. Szabo (2004). Enhancement of association rates by nonspecific binding to DNA and cell membranes. Physical Review Letters 93.
H.-X. Zhou , S. T. Wlodek & J. A. Mccammon (1998b). Conformation gating as a mechanism for enzyme specificity. Proceedings of the National Academy of Sciences of the United States of America 95, 9280–9283.
H.-X. Zhou , K. Y. Wong & M. Vijayakumar (1997). Design of fast enzymes by optimizing interaction potential in active site. Proceedings of the National Academy of Sciences of the United States of America 94, 12372–12377.
H.-X. Zhou & R. Zwanzig (2002). Barrier crossing coupled to a small set of oscillators. Journal of Physical Chemistry A 106, 7562–7564.
S. B. Zimmerman & S. O. Trach (1991). Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli. Journal of Molecular Biology 222, 599–620.
R. Zwanzig (1988). Diffusion in a rough potential. Proceedings of the National Academy of Sciences of the United States of America 85, 2029–2030.
R. Zwanzig (1995). Simple model of protein folding kinetics. Proceedings of the National Academy of Sciences of the United States of America 92, 9801–9804.