Single Molecule Biophysics: Experiments and Theori Advances in Chemical Physics, Volume 146

Volume Editors Tamiki Komatsuzaki is a Professor in the Molecule and Life Nonlinear Sciences Laboratory, Research Institute for Electronic Science at Hokkaido University in Japan. His research interests include origin of selectivity and stochasticity of reactions, single-molecule biophysics, as well as protein landscape and complexity in kinetics and dynamics. Masaru Kawakami is an Associate Professor at the Japan Advanced Institute of Science and Technology (JAIST) School of Material Science. He specializes in biophysics, single-molecule measurement, protein folding, and structural biology, and his research focuses on single-molecule dynamics of biomolecules. Satoshi Takahashi is a Professor at the Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Japan. His research focuses on protein folding and functional dynamics. Haw Yang is an Associate Professor in the Department of Chemistry at Princeton University. His current research focuses on high-resolution quantitative single-molecule protein dynamics and real-time 3D single-particle tracking spectroscopy. Robert J. Silbey is the Class of 1942 Professor of Chemistry at MIT. His research involves theoretical studies of single-molecule spectroscopy at low temperatures, energy and electron transfer and relaxation in molecular aggregates, the optical and electronic properties of conjugated oligomers and polymers, and the transport of charge in organic systems. Series Editors Stuart A. Rice received his master's and doctorate from Harvard University and was a junior fellow at Harvard for two years before joining the faculty of the University of Chicago in 1957, where he is currently the Frank P. Hixon Distinguished Service Professor Emeritus. Aaron R. Dinner received his bachelor's degree and doctorate from Harvard University, after which he conducted postdoctoral research at the University of Oxford and the University of California, Berkeley. He joined the faculty at the University of Chicago in 2003.

Preface xiii Part One Developments on Single-Molecule Experiments Staring at a Protein: Ensemble and Single-Molecule Investigations on Protein-Folding Dynamics 3 By Satoshi Takahashi and Kiyoto Kamagata Single-Molecule FRET of Protein-Folding Dynamics 23 By Daniel Nettels and Benjamin Schuler Quantitative Analysis of Single-Molecule FRET Signals and its Application to Telomere DNA 49 By Kenji Okamoto and Masahide Terazima Force to Unbind Ligand-Receptor Complexes and the Internal Rigidity of Globular Proteins Probed by Single-Molecule Force Spectroscopy 71 By Atsushi Ikai, Rehana Afrin, and Hiroshi Sekiguchi Recent Advances in Single-Molecule Biophysics with the Use of Atomic Force Microscopy 89 By Masaru Kawakami and Yukinori Taniguchi Dynamical Single-Molecule Observations of Membrane Protein Using High-Energy Probes 133 By Yuji C. Sasaki Single-Molecular Gating Dynamics for the KcsA Potassium Channel 147 By Shigetoshi Oiki, Hirofumi Shimizu, Masayuki Iwamoto, and Takashi Konno Static and Dynamic Disorder in IN VITRO Reconstituted Receptor-Adaptor Interaction 195 By Hiroaki Takagi, Miki Morimatsu, and Yasushi Sako Part Two Developments on Single-Molecule Theories and Analyses Change-Point Localization and Wavelet Spectral Analysis of Single-Molecule Time Series 219 By Haw Yang Theory of Single-Molecule FRET Efficiency Histograms 245 By Irina V. Gopich and Attila Szabo Multidimensional Energy Landscapes in Single-Molecule Biophysics 299 By Akinori Baba and Tamiki Komatsuzaki Generalized Michaelis-Menten Equation for Conformation Modulated Monomeric Enzymes 329 By Jianlan Wu and Jianshu Cao Making it Possible: Constructing a Reliable Mechanism from a Finite Trajectory 367 By Ophir Flomenbom Free Energy Landscapes of Proteins: Insights from Mechanical Probes 395 By Zu Thur Yew, Peter D. Olmsted, and Emanuele Paci Mechanochemical Coupling Revealed by the Fluctuation Analysis of Different Biomolecular Motors 419 By Hiroaki Takagi and Masatoshi Nishikawa Author Index 437 Subject Index 467