Tamiki Komatsuzaki & M. Kawakami 
Single-Molecule Biophysics [PDF ebook] 
Experiment and Theory, Volume 146

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.

Table of Content

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 Kcs A 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

About the author

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.