Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches

From folding to function: complex macromolecular reactions unraveled one-by-one with optical tweezers

(2021) Pétur O. Heidarsson et al.   Essays in Biochemistry

Pathogenic mutations in the kinesin-3 motor KIF1A diminish force generation and movement through allosteric mechanisms

(2021) Breane G. Budaitis et al.   JOURNAL OF CELL BIOLOGY

Probing Interdomain Linkers and Protein Supertertiary Structure In Vitro and in Live Cells with Fluorescent Protein Resonance Energy Transfer

(2021) Sujit Basak et al.   JOURNAL OF MOLECULAR BIOLOGY

Ensemble Switching Unveils a Kinetic Rheostat Mechanism of the Eukaryotic Thiamine Pyrophosphate Riboswitch

(2021) Junyan Ma et al.   RNA

Mechanical Model for Catch-Bond-Mediated Cell Adhesion in Shear Flow

(2020) Long Li et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

POLARIS: Path of Least Action Analysis on Energy Landscapes

(2020) Evan Seitz et al.   Journal of Chemical Information and Modeling

Specific Conformational Dynamics and Expansion Underpin a Multi-Step Mechanism for Specific Binding of p27 with Cdk2/Cyclin A

(2020) Maksym Tsytlonok et al.   JOURNAL OF MOLECULAR BIOLOGY

Publisher Correction: Processive extrusion of polypeptide loops by a Hsp100 disaggregase

(2020) Mario J. Avellaneda et al.   NATURE

Resolving dynamics and function of transient states in single enzyme molecules

(2020) Hugo Sanabria et al.   Nature Communications

Templated folding of intrinsically disordered proteins

(2020) Angelo Toto et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Finding an Optimal Pathway on a Multidimensional Free-Energy Landscape

(2020) Haohao Fu et al.   Journal of Chemical Information and Modeling

Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation

(2020) Nandini Sharma et al.   Science Advances

Single-Molecule Studies of Protein Folding with Optical Tweezers

(2020) Carlos Bustamante et al.   Annual Review of Biochemistry

Recurrent mismatch binding by MutS mobile clamps on DNA localizes repair complexes nearby

(2020) Pengyu Hao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of Ligand Binding on the Energy Landscape of Acyl-CoA-Binding Protein

(2020) Punam Sonar et al.   BIOPHYSICAL JOURNAL

FRET and optical trapping reveal mechanisms of actin-activation of the power stroke and phosphate-release in myosin V

(2020) Laura K. Gunther et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

How fast are the motions of tertiary-structure elements in proteins?

(2020) Gilad Haran et al.   JOURNAL OF CHEMICAL PHYSICS

Expectation maximized molecular dynamics: Toward efficient learning of rarely sampled features in free energy surfaces from unbiased simulations

(2020) Pallab Dutta et al.   JOURNAL OF CHEMICAL PHYSICS

Ribosome-mediated polymerization of long chain carbon and cyclic amino acids into peptides in vitro

(2020) Joongoo Lee et al.   Nature Communications

Retrieving functional pathways of biomolecules from single-particle snapshots

(2020) Ali Dashti et al.   Nature Communications

Dynamic Instability from Non-equilibrium Structural Transitions on the Energy Landscape of Microtubule

(2020) Shannon F. Stewman et al.   Cell Systems

Recent advances in single-molecule fluorescence microscopy render structural biology dynamic

(2020) Luka Bacic et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Unraveling protein’s structural dynamics: from configurational dynamics to ensemble switching guides functional mesoscale assemblies

(2020) Exequiel Medina et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques

(2019) Petra Rovó et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Allostery in Its Many Disguises: From Theory to Applications

(2019) Shoshana J. Wodak et al.   STRUCTURE

Molecular mechanism of cytoplasmic dynein tension sensing

(2019) Lu Rao et al.   Nature Communications

Super-Resolution Microscopy of Chromatin

(2019) Birk   Genes

Role of hydration water in the onset of protein structural dynamics

(2019) Giorgio Schirò et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Single-Molecule Analysis and Engineering of DNA Motors

(2019) Sonisilpa Mohapatra et al.   CHEMICAL REVIEWS

Mechanism of ribosome stalling during translation of a poly(A) tail

(2019) Viswanathan Chandrasekaran et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Activation of PKA via asymmetric allosteric coupling of structurally conserved cyclic nucleotide binding domains

(2019) Yuxin Hao et al.   Nature Communications

Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones

(2019) Salvatore Assenza et al.   eLife

50+ Years of Protein Folding

(2018) A. V. Finkelstein   BIOCHEMISTRY-MOSCOW

OUP accepted manuscript

(2018)   Briefings in Functional Genomics

Complex regulatory mechanisms mediated by the interplay of multiple post-translational modifications

(2018) Veronika Csizmok et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein Folding Free Energy Landscape along the Committor - the Optimal Folding Coordinate

(2018) Sergei V. Krivov   Journal of Chemical Theory and Computation

Utilizing Coarse-Grained Modeling and Monte Carlo Simulations to Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions

(2018) Carolina Cragnell et al.   JOURNAL OF MOLECULAR BIOLOGY

Replica-Based Protein Structure Sampling Methods: Compromising between Explicit and Implicit Solvents

(2018) Martin Kulke et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A non-equilibrium approach to allosteric communication

(2018) Gerhard Stock et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Nonequilibrium Scaling Behavior in Driven Soft Biological Assemblies

(2018) Federica Mura et al.   PHYSICAL REVIEW LETTERS

Broken detailed balance and non-equilibrium dynamics in living systems: a review

(2018) F S Gnesotto et al.   REPORTS ON PROGRESS IN PHYSICS

Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer

(2018) Eitan Lerner et al.   SCIENCE

Accurate Protein-Folding Transition-Path Statistics from a Simple Free-Energy Landscape

(2018) William M. Jacobs et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95

(2018) Inna S. Yanez Orozco et al.   Nature Communications

Perspective: Identification of collective variables and metastable states of protein dynamics

(2018) Florian Sittel et al.   JOURNAL OF CHEMICAL PHYSICS

Stationary state distribution and efficiency analysis of the Langevin equation via real or virtual dynamics

(2017) Dezhang Li et al.   JOURNAL OF CHEMICAL PHYSICS

Identification and Validation of Reaction Coordinates Describing Protein Functional Motion: Hierarchical Dynamics of T4 Lysozyme

(2017) Matthias Ernst et al.   Journal of Chemical Theory and Computation

Operando XAS Study of the Surface Oxidation State on a Monolayer IrOx on RuOx and Ru Oxide Based Nanoparticles for Oxygen Evolution in Acidic Media

(2017) Anders F. Pedersen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Single-molecule FRET studies on the cotranscriptional folding of a thiamine pyrophosphate riboswitch

(2017) Heesoo Uhm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Environmental perturbations lead to extensive directional shifts in RNA processing

(2017) Allison L. Richards et al.   PLoS Genetics

Threshold effect of growth rate on population variability ofEscherichia colicell lengths

(2017) Manasi S. Gangan et al.   Royal Society Open Science

SnapShot: Timescales in Cell Biology

(2016) Maya Shamir et al.   CELL

Applications of Discrete Molecular Dynamics in biology and medicine

(2016) Elizabeth A Proctor et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Perspective: Mechanochemistry of biological and synthetic molecules

(2016) Dmitrii E. Makarov   JOURNAL OF CHEMICAL PHYSICS

Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit

(2016) Bin W. Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Single-molecule imaging of non-equilibrium molecular ensembles on the millisecond timescale

(2016) Manuel F Juette et al.   NATURE METHODS

Broken detailed balance at mesoscopic scales in active biological systems

(2016) Christopher Battle et al.   SCIENCE

Localized force application reveals mechanically sensitive domains of Piezo1

(2016) Jason Wu et al.   Nature Communications

Perfect timing: splicing and transcription rates in living cells

(2016) Tara Alpert et al.   Wiley Interdisciplinary Reviews-RNA

Landscape and flux theory of non-equilibrium dynamical systems with application to biology

(2015) Jin Wang   ADVANCES IN PHYSICS

MEPSA: minimum energy pathway analysis for energy landscapes: Fig. 1.

(2015) Iñigo Marcos-Alcalde et al.   BIOINFORMATICS

Free Energy Surface of an Intrinsically Disordered Protein: Comparison between Temperature Replica Exchange Molecular Dynamics and Bias-Exchange Metadynamics

(2015) Gül H. Zerze et al.   Journal of Chemical Theory and Computation

Simultaneous Single-Molecule Force and Fluorescence Sampling of DNA Nanostructure Conformations Using Magnetic Tweezers

(2015) Felix E. Kemmerich et al.   NANO LETTERS

Intrinsically disordered proteins in cellular signalling and regulation

(2015) Peter E. Wright et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

A Monte Carlo Method for Generating Side Chain Structural Ensembles

(2015) Asmit Bhowmick et al.   STRUCTURE

Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer

(2015) Van K Duesterberg et al.   eLife

Intrinsically Disordered Proteins and Intrinsically Disordered Protein Regions

(2014) Christopher J. Oldfield et al.   Annual Review of Biochemistry

Reconstructing Folding Energy Landscapes by Single-Molecule Force Spectroscopy

(2014) Michael T. Woodside et al.   Annual Review of Biophysics

Single-molecule studies of riboswitch folding

(2014) Andrew Savinov et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Single-Molecule Studies of Intrinsically Disordered Proteins

(2014) Marco Brucale et al.   CHEMICAL REVIEWS

Exploring the topography of the stress-modified energy landscapes of mechanosensitive molecules

(2014) Sai Sriharsha M. Konda et al.   JOURNAL OF CHEMICAL PHYSICS

Probing Protein Multidimensional Conformational Fluctuations by Single-Molecule Multiparameter Photon Stamping Spectroscopy

(2014) Maolin Lu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A second molecular biology revolution? The energy landscapes of biomolecular function

(2014) Ruth Nussinov et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Magnetic Tweezers for the Measurement of Twist and Torque

(2014) Jan Lipfert et al.   Jove-Journal of Visualized Experiments

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular Catch Bonds and the Anti-Hammond Effect in Polymer Mechanochemistry

(2013) Sai Sriharsha M. Konda et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein Folding Under Mechanical Forces: A Physiological View

(2013) Yalda Javadi et al.   PHYSIOLOGY

Nonequilibrium landscape theory of neural networks

(2013) H. Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution

(2013) Andrea Haller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From mechanical folding trajectories to intrinsic energy landscapes of biopolymers

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

Filtered FCS: Species Auto- and Cross-Correlation Functions Highlight Binding and Dynamics in Biomolecules

(2012) Suren Felekyan et al.   CHEMPHYSCHEM

Synergistic Applications of MD and NMR for the Study of Biological Systems

(2012) Olivier Fisette et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization

(2012) David Shirvanyants et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring the Energy Landscape of Nucleic Acid Hairpins Using Laser Temperature-Jump and Microfluidic Mixing

(2012) Ranjani Narayanan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer

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

Energy landscape analysis of native folding of the prion protein yields the diffusion constant, transition path time, and rates

(2012) H. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Supertertiary structure of the synaptic MAGuK scaffold proteins is conserved

(2012) J. J. McCann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function

(2012) Giulio Quarta et al.   PLoS Computational Biology

Equilibrium Sampling in Biomolecular Simulations

(2011) Daniel M. Zuckerman   Annual Review of Biophysics

Mitochondrial ATP synthase: architecture, function and pathology

(2011) An I. Jonckheere et al.   JOURNAL OF INHERITED METABOLIC DISEASE

Experimental validation of free-energy-landscape reconstruction from non-equilibrium single-molecule force spectroscopy measurements

(2011) Amar Nath Gupta et al.   Nature Physics

Discrete molecular dynamics

(2011) Elizabeth A. Proctor et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Trapping Conformational States Along Ligand-Binding Dynamics of Peptide Deformylase: The Impact of Induced Fit on Enzyme Catalysis

(2011) Sonia Fieulaine et al.   PLOS BIOLOGY

Mitotic force generators and chromosome segregation

(2010) Gul Civelekoglu-Scholey et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Fluctuation-dissipation theorem in nonequilibrium steady states

(2010) U. Seifert et al.   EPL

The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cells

(2010) Martina Huranová et al.   JOURNAL OF CELL BIOLOGY

Full distance-resolved folding energy landscape of one single protein molecule

(2010) J. C. M. Gebhardt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the pH-optimum of activity and stability of proteins

(2010) Kemper Talley et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Riboswitches and the RNA World

(2010) R. R. Breaker   Cold Spring Harbor Perspectives in Biology

How do proteins gain new domains?

(2010) Joseph A Marsh et al.   GENOME BIOLOGY

Size and Shape of Protein Molecules at the Nanometer Level Determined by Sedimentation, Gel Filtration, and Electron Microscopy

(2009) Harold P. Erickson   BIOLOGICAL PROCEDURES ONLINE

Mechanical Signaling on the Single Protein Level Studied Using Steered Molecular Dynamics

(2009) Georgi Z. Genchev et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Long-timescale molecular dynamics simulations of protein structure and function

(2009) John L Klepeis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Comparison of Three Perturbation Molecular Dynamics Methods for Modeling Conformational Transitions

(2009) He Huang et al.   Journal of Chemical Theory and Computation

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Transcription Dynamics

(2009) Gordon L. Hager et al.   MOLECULAR CELL

Coordinate-dependent diffusion in protein folding

(2009) R. B. Best et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Scale-free flow of life: on the biology, economics, and physics of the cell

(2009) Alexei Kurakin   Theoretical Biology and Medical Modelling

Exploring the Free Energy Landscape: From Dynamics to Networks and Back

(2009) Diego Prada-Gracia et al.   PLoS Computational Biology

Free-Energy Landscape of Enzyme Catalysis†

(2008) Stephen J. Benkovic et al.   BIOCHEMISTRY

Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations

(2008) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule nonequilibrium periodic Mg2+-concentration jump experiments reveal details of the early folding pathways of a large RNA

(2008) X. Qu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Disclosure of the mycobacterial outer membrane: Cryo-electron tomography and vitreous sections reveal the lipid bilayer structure

(2008) C. Hoffmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics

(2008) Feng Ding et al.   STRUCTURE