Single-Molecule Biophysics (eBook)

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