Theoretical perspectives on biological machines

Myosin V executes steps of variable length via structurally constrained diffusion

(2020) David Hathcock et al.   eLife

Mechanisms for achieving high speed and efficiency in biomolecular machines

(2019) Jason A. Wagoner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heat Oscillations Driven by the Embryonic Cell Cycle Reveal the Energetic Costs of Signaling

(2019) Jonathan Rodenfels et al.   DEVELOPMENTAL CELL

Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular Machines

(2019) D. Thirumalai et al.   CHEMICAL REVIEWS

Is F1-ATPase a Rotary Motor with Nearly 100% Efficiency? Quantitative Analysis of Chemomechanical Coupling and Mechanical Slip

(2019) Tomonari Sumi et al.   NANO LETTERS

Processivity, velocity and universal characteristics of nucleic acid unwinding by helicases

(2019) S. Chakrabarti et al.   BIOPHYSICAL JOURNAL

Energy budget of Drosophila embryogenesis

(2019) Yonghyun Song et al.   CURRENT BIOLOGY

How kinesin waits for ATP affects the nucleotide and load dependence of the stepping kinetics

(2019) Ryota Takaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Antiparallel Dimerization of Myosin X Imparts Bundle Selectivity for Processive Motility

(2018) Matthew A. Caporizzo et al.   BIOPHYSICAL JOURNAL

Current fluctuations and transport efficiency for general Langevin systems

(2018) Andreas Dechant et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

The cytoplasmic dynein transport machinery and its many cargoes

(2018) Samara L. Reck-Peterson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase

(2018) Wen Ma et al.   eLife

Molecular mechanisms of the interhead coordination by interhead tension in cytoplasmic dyneins

(2018) Qian Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics of Allosteric Transitions in Dynein

(2018) Yonathan Goldtzvik et al.   STRUCTURE

Nonequilibrium Energetics of Molecular Motor Kinesin

(2018) Takayuki Ariga et al.   PHYSICAL REVIEW LETTERS

Theoretical Investigation of Distributions of Run Lengths for Biological Molecular Motors

(2017) Yunxin Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Drastic Compensation of Electronic and Solvation Effects on ATP Hydrolysis Revealed through Large-Scale QM/MM Simulations Combined with a Theory of Solutions

(2017) Hideaki Takahashi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Bistability, Oscillations, and Bidirectional Motion of Ensemble of Hydrodynamically Coupled Molecular Motors

(2017) P. Malgaretti et al.   PHYSICAL REVIEW LETTERS

Generic Properties of Stochastic Entropy Production

(2017) Simone Pigolotti et al.   PHYSICAL REVIEW LETTERS

Elucidating interplay of speed and accuracy in biological error correction

(2017) Kinshuk Banerjee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parsing the roles of neck-linker docking and tethered head diffusion in the stepping dynamics of kinesin

(2017) Zhechun Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kinematics of the lever arm swing in myosin VI

(2017) Mauro L. Mugnai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intraflagellar transport velocity is governed by the number of active KIF17 and KIF3AB motors and their motility properties under load

(2017) Bojan Milic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reexamining the origin of the directionality of myosin V

(2017) Raphael Alhadeff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular chaperones maximize the native state yield on biological times by driving substrates out of equilibrium

(2017) Shaon Chakrabarti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simulating the dynamics of the mechanochemical cycle of myosin-V

(2017) Shayantani Mukherjee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allocating dissipation across a molecular machine cycle to maximize flux

(2017) Aidan I. Brown et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microtubule-Based Transport and the Distribution, Tethering, and Organization of Organelles

(2017) Kari Barlan et al.   Cold Spring Harbor Perspectives in Biology

Kinesin motility driven by subdomain dynamics

(2017) Wonmuk Hwang et al.   eLife

Mitochondrial flashes regulate ATP homeostasis in the heart

(2017) Xianhua Wang et al.   eLife

The Kinesin-1 Chemomechanical Cycle: Stepping Toward a Consensus

(2016) William O. Hancock   BIOPHYSICAL JOURNAL

Molecular Motors: Power Strokes Outperform Brownian Ratchets

(2016) Jason A. Wagoner et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantifying the Heat Dissipation from a Molecular Motor’s Transport Properties in Nonequilibrium Steady States

(2016) Wonseok Hwang et al.   Journal of Physical Chemistry Letters

Direct observation of intermediate states during the stepping motion of kinesin-1

(2016) Hiroshi Isojima et al.   Nature Chemical Biology

Pif1 is a force-regulated helicase

(2016) Jing-Hua Li et al.   NUCLEIC ACIDS RESEARCH

Discrete Step Sizes of Molecular Motors Lead to Bimodal Non-Gaussian Velocity Distributions under Force

(2016) Huong T. Vu et al.   PHYSICAL REVIEW LETTERS

Broken Detailed Balance of Filament Dynamics in Active Networks

(2016) J. Gladrow et al.   PHYSICAL REVIEW LETTERS

Dissipation Bounds All Steady-State Current Fluctuations

(2016) Todd R. Gingrich et al.   PHYSICAL REVIEW LETTERS

Universal Trade-Off Relation between Power and Efficiency for Heat Engines

(2016) Naoto Shiraishi et al.   PHYSICAL REVIEW LETTERS

Broken detailed balance at mesoscopic scales in active biological systems

(2016) Christopher Battle et al.   SCIENCE

Collective dynamics of processive cytoskeletal motors

(2016) R. Tyler McLaughlin et al.   Soft Matter

Kinetic Adaptations of Myosins for Their Diverse Cellular Functions

(2016) Sarah M. Heissler et al.   TRAFFIC

Effects of Obstacles on the Dynamics of Kinesins, Including Velocity and Run Length, Predicted by a Model of Two Dimensional Motion

(2016) Woochul Nam et al.   PLoS One

Helicase Processivity and Not the Unwinding Velocity Exhibits Universal Increase with Force

(2015) David L. Pincus et al.   BIOPHYSICAL JOURNAL

Thermodynamic Uncertainty Relation for Biomolecular Processes

(2015) Andre C. Barato et al.   PHYSICAL REVIEW LETTERS

Myosin VI deafness mutation prevents the initiation of processive runs on actin

(2015) Olena Pylypenko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kinetics of nucleotide-dependent structural transitions in the kinesin-1 hydrolysis cycle

(2015) Keith J. Mickolajczyk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Colloquium: Random first order transition theory concepts in biology and physics

(2015) T. R. Kirkpatrick et al.   REVIEWS OF MODERN PHYSICS

Direct observation of structure-function relationship in a nucleic acid-processing enzyme

(2015) M. J. Comstock et al.   SCIENCE

Structural dynamics of myosin 5 during processive motion revealed by interferometric scattering microscopy

(2015) Joanna Andrecka et al.   eLife

The Winch Model Can Explain both Coordinated and Uncoordinated Stepping of Cytoplasmic Dynein

(2014) Andreja Šarlah et al.   BIOPHYSICAL JOURNAL

Allosteric Communication in the Dynein Motor Domain

(2014) Gira Bhabha et al.   CELL

Evolution and Classification of Myosins, a Paneukaryotic Whole-Genome Approach

(2014) Arnau Sebé-Pedrós et al.   Genome Biology and Evolution

Structure of human cytoplasmic dynein-2 primed for its power stroke

(2014) Helgo Schmidt et al.   NATURE

Catalytic strategy used by the myosin motor to hydrolyze ATP

(2014) F. A. Kiani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Formation and structures of GroEL:GroES2 chaperonin footballs, the protein-folding functional form

(2014) X. Fei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cytoplasmic dynein transports cargos via load-sharing between the heads

(2014) Vladislav Belyy et al.   Nature Communications

DNA unwinding heterogeneity by RecBCD results from static molecules able to equilibrate

(2013) Bian Liu et al.   NATURE

Spontaneous Detachment of the Leading Head Contributes to Myosin VI Backward Steps

(2013) Keigo Ikezaki et al.   PLoS One

Electrostatic origin of the unidirectionality of walking myosin V motors

(2013) S. Mukherjee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design principles governing the motility of myosin V

(2013) M. Hinczewski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation

(2012) Ornchuma Itsathitphaisarn et al.   CELL

Efficiency of molecular machines with continuous phase space

(2012) N. Golubeva et al.   EPL

The myosin superfamily at a glance

(2012) M. A. Hartman et al.   JOURNAL OF CELL SCIENCE

Hidden complexity in the isomerization dynamics of Holliday junctions

(2012) Changbong Hyeon et al.   Nature Chemistry

The energy–speed–accuracy trade-off in sensory adaptation

(2012) Ganhui Lan et al.   Nature Physics

Efficiencies of a molecular motor: a generic hybrid model applied to the F1-ATPase

(2012) Eva Zimmermann et al.   NEW JOURNAL OF PHYSICS

Tubulin Acetylation Alone Does Not Affect Kinesin-1 Velocity and Run Length In Vitro

(2012) Wilhelm J. Walter et al.   PLoS One

Energetic costs of cellular computation

(2012) P. Mehta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stochastic thermodynamics, fluctuation theorems and molecular machines

(2012) Udo Seifert   REPORTS ON PROGRESS IN PHYSICS

Toward a molecular understanding of RNA remodeling by DEAD-box proteins

(2012) Rick Russell et al.   RNA Biology

Simultaneous Observation of the Lever Arm and Head Explains Myosin VI Dual Function

(2012) Keigo Ikezaki et al.   Small

Dissecting the Kinematics of the Kinesin Step

(2012) Zhechun Zhang et al.   STRUCTURE

Plant-Specific Myosin XI, a Molecular Perspective

(2012) Motoki Tominaga et al.   Frontiers in Plant Science

Principles of Unconventional Myosin Function and Targeting

(2011) M. Amanda Hartman et al.   Annual Review of Cell and Developmental Biology

Lever-Arm Mechanics of Processive Myosins

(2011) Yujie Sun et al.   BIOPHYSICAL JOURNAL

Chemomechanical Coupling and Motor Cycles of Myosin V

(2011) Veronika Bierbaum et al.   BIOPHYSICAL JOURNAL

A Physical Model Reveals the Mechanochemistry Responsible for Dynein's Processive Motion

(2011) Denis Tsygankov et al.   BIOPHYSICAL JOURNAL

Prediction of Hydrodynamic and Other Solution Properties of Rigid Proteins from Atomic- and Residue-Level Models

(2011) A. Ortega et al.   BIOPHYSICAL JOURNAL

Detailed Tuning of Structure and Intramolecular Communication Are Dispensable for Processive Motion of Myosin VI

(2011) Mary Williard Elting et al.   BIOPHYSICAL JOURNAL

Revisiting the Central Dogma One Molecule at a Time

(2011) Carlos Bustamante et al.   CELL

Stochastic thermodynamics of single enzymes and molecular motors

(2011) U. Seifert   EUROPEAN PHYSICAL JOURNAL E

A universal pathway for kinesin stepping

(2011) Bason E Clancy et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Efficiency of Autonomous Soft Nanomachines at Maximum Power

(2011) Udo Seifert   PHYSICAL REVIEW LETTERS

Thermodynamic efficiency and mechanochemical coupling of F1-ATPase

(2011) S. Toyabe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequential Establishment of Stripe Patterns in an Expanding Cell Population

(2011) C. Liu et al.   SCIENCE

Cytoplasmic Dynein Moves Through Uncoordinated Stepping of the AAA+ Ring Domains

(2011) M. A. DeWitt et al.   SCIENCE

Capturing the essence of folding and functions of biomolecules using coarse-grained models

(2011) Changbong Hyeon et al.   Nature Communications

Structural and Functional Insights into the Myosin Motor Mechanism

(2010) H. Lee Sweeney et al.   Annual Review of Biophysics

Switch between Large Hand-Over-Hand and Small Inchworm-like Steps in Myosin VI

(2010) So Nishikawa et al.   CELL

Cellular Heterogeneity: Do Differences Make a Difference?

(2010) Steven J. Altschuler et al.   CELL

Coordination and collective properties of molecular motors: theory

(2010) Thomas Guérin et al.   CURRENT OPINION IN CELL BIOLOGY

Coordination of molecular motors: from in vitro assays to intracellular dynamics

(2010) Erika LF Holzbaur et al.   CURRENT OPINION IN CELL BIOLOGY

Multiple native states reveal persistent ruggedness of an RNA folding landscape

(2010) Sergey V. Solomatin et al.   NATURE

Video imaging of walking myosin V by high-speed atomic force microscopy

(2010) Noriyuki Kodera et al.   NATURE

A cytoplasmic dynein tail mutation impairs motor processivity

(2010) Kassandra M. Ori-McKenney et al.   NATURE CELL BIOLOGY

Robust processivity of myosin V under off-axis loads

(2010) Yusuke Oguchi et al.   Nature Chemical Biology

Myosin VI: an innovative motor that challenged the swinging lever arm hypothesis

(2010) James A. Spudich et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Direct observation of the myosin-Va power stroke and its reversal

(2010) James R Sellers et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-molecule stepping and structural dynamics of myosin X

(2010) Yujie Sun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Active and passive mechanisms of helicases

(2010) Maria Manosas et al.   NUCLEIC ACIDS RESEARCH

Physical origins of entropy production, free energy dissipation, and their mathematical representations

(2010) Hao Ge et al.   PHYSICAL REVIEW E

Nonequilibrium Energetics of a SingleF1-ATPase Molecule

(2010) Shoichi Toyabe et al.   PHYSICAL REVIEW LETTERS

Influence of lever structure on myosin 5a walking

(2010) O. A. Oke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomically detailed simulation of the recovery stroke in myosin by Milestoning

(2010) R. Elber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contribution of the myosin VI tail domain to processive stepping and intramolecular tension sensing

(2010) Alexander R. Dunn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rigor to Post-Rigor Transition in Myosin V: Link between the Dynamics and the Supporting Architecture

(2010) Riina Tehver et al.   STRUCTURE

Velocity, Processivity, and Individual Steps of Single Myosin V Molecules in Live Cells

(2009) Paolo Pierobon et al.   BIOPHYSICAL JOURNAL

On the Energetics of ATP Hydrolysis in Solution

(2009) Shina C. L. Kamerlin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Energy Conversion by Molecular Motors Coupled to Nucleotide Hydrolysis

(2009) Reinhard Lipowsky et al.   JOURNAL OF STATISTICAL PHYSICS

Kinesin superfamily motor proteins and intracellular transport

(2009) Nobutaka Hirokawa et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Kinesin’s backsteps under mechanical load

(2009) Changbong Hyeon et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Mechanochemical model for myosin V

(2009) E. M. Craig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translocation and Unwinding Mechanisms of RNA and DNA Helicases

(2008) Anna Marie Pyle   Annual Review of Biophysics

Intramolecular Strain Coordinates Kinesin Stepping Behavior along Microtubules

(2008) Ahmet Yildiz et al.   CELL

Efficiency of molecular motors at maximum power

(2008) T. Schmiedl et al.   EPL

Load and PiControl Flux through the Branched Kinetic Cycle of Myosin V

(2008) Neil M. Kad et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Kinetic Model for the Coupling between Allosteric Transitions in GroEL and Substrate Protein Folding and Aggregation

(2008) Riina Tehver et al.   JOURNAL OF MOLECULAR BIOLOGY

Non-hexameric DNA helicases and translocases: mechanisms and regulation

(2008) Timothy M. Lohman et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Statistical Mechanics of Interacting Run-and-Tumble Bacteria

(2008) J. Tailleur et al.   PHYSICAL REVIEW LETTERS

Load-dependent ADP binding to myosins V and VI: Implications for subunit coordination and function

(2008) Y. Oguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Force Generation in Kinesin Hinges on Cover-Neck Bundle Formation

(2008) Wonmuk Hwang et al.   STRUCTURE

A Myo6 Mutation Destroys Coordination between the Myosin Heads, Revealing New Functions of Myosin VI in the Stereocilia of Mammalian Inner Ear Hair Cells

(2008) Ronna Hertzano et al.   PLoS Genetics

Transport of Beads by Several Kinesin Motors

(2007) Janina Beeg et al.   BIOPHYSICAL JOURNAL