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

Tamiki Komatsuzaki (Editor), Masaru Kawakami (Editor), Satoshi Takahashi (Editor), Haw Yang (Editor), Robert J. Silbey (Editor), Stuart A. Rice (Series Editor), Aaron R. Dinner (Series Editor)
ISBN: 978-1-118-05780-3
512 pages
November 2011
Advances in Chemical Physics, Volume 146, Single Molecule Biophysics: Experiments and Theory (1118057805) cover image
Discover the experimental and theoretical developments in optical single-molecule spectroscopy that are changing the ways we think about molecules and atoms

The Advances in Chemical Physics series provides the chemical physics field with a forum for critical, authoritative evaluations of advances in every area of the discipline. This latest volume explores the advent of optical single-molecule spectroscopy, and how atomic force microscopy has empowered novel experiments on individual biomolecules, opening up new frontiers in molecular and cell biology and leading to new theoretical approaches and insights. Organized into two parts—one experimental, the other theoretical—this volume explores advances across the field of single-molecule biophysics, presenting new perspectives on the theoretical properties of atoms and molecules. Single-molecule experiments have provided fresh perspectives on questions such as how proteins fold to specific conformations from highly heterogeneous structures, how signal transductions take place on the molecular level, and how proteins behave in membranes and living cells.This volume is designed to further contribute to the rapid development of single-molecule biophysics research.

Filled with cutting-edge research reported in a cohesive manner not found elsewhere in the literature, each volume of the Advances in Chemical Physics series serves as the perfect supplement to any advanced graduate class devoted to the study of chemical physics.

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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

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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.

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