Single-molecule approach to dispersed kinetics and dynamic disorder: Probing conformational fluctuation and enzymatic dynamics

This article reviews our efforts in understanding dynamical fluctuations of both conformation and enzymatic reactivity in single biomolecules. The single-molecule approach is shown to be particularly powerful for studies of dispersed kinetics and dynamic disorder. New single-molecule observations have revealed conformational transitions occurring on a broad range of timescales, 100 μs–10 s, offering new clues for understanding energy landscape of proteins, as well as the structural and chemical dynamics therein.

[1]  C. Seidel,et al.  Monitoring conformational dynamics of a single molecule by selective fluorescence spectroscopy. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[2]  N. Kampen,et al.  Stochastic processes in physics and chemistry , 1981 .

[3]  David Keller,et al.  Single-molecule studies of the effect of template tension on T7 DNA polymerase activity , 2000, Nature.

[4]  P. Wolynes,et al.  Spin glasses and the statistical mechanics of protein folding. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Kiwamu Saito,et al.  Imaging of single fluorescent molecules and individual ATP turnovers by single myosin molecules in aqueous solution , 1995, Nature.

[6]  Robert J. Chichester,et al.  Single Molecules Observed by Near-Field Scanning Optical Microscopy , 1993, Science.

[7]  C. P. Lindsey,et al.  Detailed comparison of the Williams–Watts and Cole–Davidson functions , 1980 .

[8]  J. Ricard,et al.  Regulatory Behavior of Monomeric Enzymes , 1974 .

[9]  Eugene I. Shakhnovich,et al.  Relaxation to Equilibrium in the Random Energy Model , 1989 .

[10]  R. Zwanzig.  Nonequilibrium statistical mechanics , 2001, Physics Subject Headings (PhySH).

[11]  Robert Zwanzig,et al.  Rate processes with dynamical disorder , 1990 .

[12]  S. Mukamel,et al.  Stochastic-trajectories and nonPoisson kinetics in single-molecule spectroscopy , 1999 .

[13]  X. Zhuang,et al.  Correlating Structural Dynamics and Function in Single Ribozyme Molecules , 2002, Science.

[14]  Hiroyasu Itoh,et al.  Resolution of distinct rotational substeps by submillisecond kinetic analysis of F1-ATPase , 2001, Nature.

[15]  S. Weiss.  Fluorescence spectroscopy of single biomolecules. , 1999, Science.

[16]  R. Rigler,et al.  Conformational transitions monitored for single molecules in solution. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[17]  E. Neria,et al.  Molecular dynamics of an enzyme reaction: proton transfer in TIM , 1997 .

[18]  P. Kollman,et al.  Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. , 1998, Science.

[19]  H. Peter Lu,et al.  Single-molecule Enzymology* , 1999, The Journal of Biological Chemistry.

[20]  Gregory K. Schenter,et al.  Statistical Analyses and Theoretical Models of Single-Molecule Enzymatic Dynamics , 1999 .

[21]  R. Hochstrasser,et al.  Nonexponential kinetics of a single tRNAPhe molecule under physiological conditions. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Gerhard Hummer,et al.  Multi-basin dynamics of a protein in a crystal environment , 1997 .

[23]  J. Klafter,et al.  Anomalous Diffusion and Relaxation Close to Thermal Equilibrium: A Fractional Fokker-Planck Equation Approach , 1999 .

[24]  Ron Elber,et al.  Long time dynamics of complex systems. , 2002, Accounts of chemical research.

[25]  P. Wolynes,et al.  The energy landscapes and motions of proteins. , 1991, Science.

[26]  M. Karplus,et al.  Nonexponential relaxation after ligand dissociation from myoglobin: a molecular dynamics simulation. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Haw Yang,et al.  Probing single-molecule dynamics photon by photon , 2002 .

[28]  C Frieden,et al.  Slow transitions and hysteretic behavior in enzymes. , 1979, Annual review of biochemistry.

[29]  Michael F. Shlesinger,et al.  Time‐Scale Invariance in Transport and Relaxation , 1991 .

[30]  R. Astumian,et al.  Protein conformational fluctuations and free-energy transduction , 2002 .

[31]  D. Beratan,et al.  Electron transfer mechanisms. , 1998, Current opinion in chemical biology.

[32]  H. Frauenfelder,et al.  Conformational substates in proteins. , 1988, Annual review of biophysics and biophysical chemistry.

[33]  D. Sherrington.  Stochastic Processes in Physics and Chemistry , 1983 .

[34]  J. Brochon.  Maximum entropy method of data analysis in time-resolved spectroscopy. , 1994, Methods in enzymology.

[35]  J. Ross,et al.  Nonlinear kinetics and new approaches to complex reaction mechanisms. , 1999, Annual review of physical chemistry.

[36]  Statistics of dwell times in a reaction with randomly fluctuating rates , 2001 .

[37]  Jianshu Cao,et al.  Direct measurements of memory effects in single-molecule kinetics , 2002 .

[38]  S. Bezrukov,et al.  Examining noise sources at the single-molecule level: 1/f noise of an open maltoporin channel. , 2000, Physical review letters.

[39]  P. W. Anderson,et al.  A Mathematical Model for the Narrowing of Spectral Lines by Exchange or Motion , 1954 .

[40]  E. Pike,et al.  On the numerical inversion of the Laplace transform and similar Fredholm integral equations of the first kind , 1978 .

[41]  M. Toda,et al.  In: Statistical physics II , 1985 .

[42]  X. Zhuang,et al.  A single-molecule study of RNA catalysis and folding. , 2000, Science.

[43]  K. Neet,et al.  [8] Hysteretic enzymes , 1980 .

[44]  H. Gutfreund,et al.  The foundations of enzyme action. , 1967, Essays in biochemistry.

[45]  N. Agmon,et al.  Conformational Cycle of a Single Working Enzyme , 2000 .

[46]  The Manipulation of Single Biomolecules , 2001 .

[47]  X. Xie,et al.  Statistical approaches for probing single-molecule dynamics photon-by-photon , 2002 .

[48]  S. F. Chekmarev,et al.  Potential energy surfaces and conformational transitions in biomolecules: a successive confinement approach applied to a solvated tetrapeptide. , 2002, Physical review letters.

[49]  A. H. Klahn,et al.  References and Notes , 2022 .

[50]  Kurt Warncke,et al.  Nature of biological electron transfer , 1992, Nature.

[51]  Edward S. Yeung,et al.  Differences in the chemical reactivity of individual molecules of an enzyme , 1995, Nature.

[52]  Norman J. Dovichi,et al.  STUDIES ON SINGLE ALKALINE PHOSPHATASE MOLECULES : REACTION RATE AND ACTIVATION ENERGY OF A REACTION CATALYZED BY A SINGLE MOLECULE AND THE EFFECT OF THERMAL DENATURATION : THE DEATH OF AN ENZYME , 1996 .

[53]  W. E. Moerner,et al.  ADP-induced rocking of the kinesin motor domain revealed by single-molecule fluorescence polarization microscopy , 2001, Nature Structural Biology.

[54]  L. Stryer.  Fluorescence energy transfer as a spectroscopic ruler. , 1978, Annual review of biochemistry.

[55]  J. Gelles,et al.  χ-Sequence recognition and DNA translocation by single RecBCD helicase/nuclease molecules , 2001, Nature.

[56]  Single channel recording in mouse sperm. , 1997 .

[57]  David Chandler,et al.  Transition path sampling: throwing ropes over rough mountain passes, in the dark. , 2002, Annual review of physical chemistry.

[58]  Sunney Xie,et al.  Single‐Molecule Approach to Enzymology , 2001 .

[59]  H Frauenfelder,et al.  Dynamics of ligand binding to myoglobin. , 1975, Biochemistry.

[60]  M. Shlesinger,et al.  Beyond Brownian motion , 1996 .

[61]  Wolynes,et al.  Intermittency of single molecule reaction dynamics in fluctuating environments. , 1995, Physical review letters.

[62]  C D Kroenke,et al.  Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. , 2001, Methods in enzymology.

[63]  Peter G. Wolynes,et al.  Analyzing single molecule trajectories on complex energy landscapes using replica correlation functions , 1999 .

[64]  Arieh Warshel,et al.  Molecular dynamics simulations of biological reactions. , 2002, Accounts of chemical research.

[65]  J. Winkler,et al.  Electron Transfer In Proteins , 1997, QELS '97., Summaries of Papers Presented at the Quantum Electronics and Laser Science Conference.

[66]  D. O'connor,et al.  Time-Correlated Single Photon Counting , 1984 .

[67]  D. Chandler,et al.  Introduction To Modern Statistical Mechanics , 1987 .

[68]  K. Rubinson.  Steady-state kinetics of solitary batrachotoxin-treated sodium channels. Kinetics on a bounded continuum of polymer conformations. , 1992, Biophysical journal.

[69]  R. Marcus,et al.  Electron transfers in chemistry and biology , 1985 .

[70]  Martin Karplus,et al.  Molecular dynamics simulations of biomolecules. , 2002, Nature structural biology.

[71]  E. Shakhnovich,et al.  The folding thermodynamics and kinetics of crambin using an all-atom Monte Carlo simulation. , 2000, Journal of molecular biology.

[72]  W. Eaton,et al.  Nonexponential structural relaxations in proteins , 1996 .

[73]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[74]  Luciano Pietronero,et al.  FRACTALS IN PHYSICS , 1990 .

[75]  Mark J. Schnitzer,et al.  Kinesin hydrolyses one ATP per 8-nm step , 1997, Nature.

[76]  B. Sakmann,et al.  Single-Channel Recording , 1995, Springer US.

[77]  George H. Weiss,et al.  Theory of single-molecule fluorescence spectroscopy of two-state systems , 1999 .

[78]  Eitan Geva,et al.  Two-state dynamics of single biomolecules in solution , 1998 .

[79]  Graham Williams,et al.  Non-symmetrical dielectric relaxation behaviour arising from a simple empirical decay function , 1970 .