A quantitative paradigm for water-assisted proton transport through proteins and other confined spaces

A CLC-ec1 mutant reveals global conformational change and suggests a unifying mechanism for the CLC Cl–/H+ transport cycle

(2020) Tanmay S Chavan et al.   eLife

Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale

(2020) C. Li et al.   BIOPHYSICAL JOURNAL

Water-Assisted Proton Transport in Confined Nanochannels

(2020) Xinyou Ma et al.   Journal of Physical Chemistry C

Variational Approach for Learning Markov Processes from Time Series Data

(2019) Hao Wu et al.   JOURNAL OF NONLINEAR SCIENCE

Network analysis of a proposed exit pathway for protons to the P-side of cytochrome c oxidase

(2018) Xiuhong Cai et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design

(2018) Wei Chen et al.   JOURNAL OF CHEMICAL PHYSICS

Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics

(2018) Christoph Wehmeyer et al.   JOURNAL OF CHEMICAL PHYSICS

Multiscale Kinetic Modeling Reveals an Ensemble of Cl–/H+ Exchange Pathways in ClC-ec1 Antiporter

(2018) Heather B. Mayes et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

No evidence that carotenoid pigments boost either immune or antioxidant defenses in a songbird

(2018) Rebecca E. Koch et al.   Nature Communications

Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux

(2018) Zhi Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Predicting reaction coordinates in energy landscapes with diffusion anisotropy

(2017) Pratyush Tiwary et al.   JOURNAL OF CHEMICAL PHYSICS

Identification of simple reaction coordinates from complex dynamics

(2017) Robert T. McGibbon et al.   JOURNAL OF CHEMICAL PHYSICS

Analyzing and Driving Cluster Formation in Atomistic Simulations

(2017) Gareth A. Tribello et al.   Journal of Chemical Theory and Computation

Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochromecoxidase

(2017) Ruibin Liang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter

(2016) Sangyun Lee et al.   BIOPHYSICAL JOURNAL

Simulation of Proton Transport in Proton Exchange Membranes with Reactive Molecular Dynamics

(2016) C. Arntsen et al.   Fuel Cells

Perspective: How good is DFT for water?

(2016) Michael J. Gillan et al.   JOURNAL OF CHEMICAL PHYSICS

Proton Wire Dynamics in the Green Fluorescent Protein

(2016) Ai Shinobu et al.   Journal of Chemical Theory and Computation

Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins

(2016) Sangyun Lee et al.   Journal of Chemical Theory and Computation

The Origin of Coupled Chloride and Proton Transport in a Cl–/H+ Antiporter

(2016) Sangyun Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Basis for Differential Anion Binding and Proton Coupling in the Cl–/H+ Exchanger ClC-ec1

(2016) Tao Jiang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ultrafast proton transport in sub-1-nm diameter carbon nanotube porins

(2016) Ramya H. Tunuguntla et al.   Nature Nanotechnology

Acid activation mechanism of the influenza A M2 proton channel

(2016) Ruibin Liang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiscale simulations reveal key features of the proton-pumping mechanism in cytochromecoxidase

(2016) Ruibin Liang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spectral gap optimization of order parameters for sampling complex molecular systems

(2016) Pratyush Tiwary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation

(2015) Frank Noé et al.   Journal of Chemical Theory and Computation

Grotthuss mechanisms: from proton transport in proton wires to bioprotonic devices

(2015) Takeo Miyake et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model

(2014) Edina Rosta et al.   Journal of Chemical Theory and Computation

A Time-Independent Free Energy Estimator for Metadynamics

(2014) Pratyush Tiwary et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hydrated Excess Protons Can Create Their Own Water Wires

(2014) Yuxing Peng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Well-Tempered Metadynamics Converges Asymptotically

(2014) James F. Dama et al.   PHYSICAL REVIEW LETTERS

Multiscale simulation reveals a multifaceted mechanism of proton permeation through the influenza A M2 proton channel

(2014) Ruibin Liang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activation and Proton Transport Mechanism in Influenza A M2 Channel

(2013) Chenyu Wei et al.   BIOPHYSICAL JOURNAL

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Changing hydration level in an internal cavity modulates the proton affinity of a key glutamate in cytochrome c oxidase

(2013) P. Goyal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiscale reactive molecular dynamics

(2012) Chris Knight et al.   JOURNAL OF CHEMICAL PHYSICS

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

(2012) Takefumi Yamashita et al.   Journal of Chemical Theory and Computation

Water wires in atomistic models of the Hv1 proton channel

(2011) Mona L. Wood et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Glu-286 Rotation and Water Wire Reorientation Are Unlikely the Gating Elements for Proton Pumping in Cytochrome c Oxidase

(2011) Shuo Yang et al.   BIOPHYSICAL JOURNAL

Sensors and regulators of intracellular pH

(2009) Joseph R. Casey et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CLC Chloride Channels and Transporters: From Genes to Protein Structure, Pathology and Physiology

(2008) Thomas J. Jentsch   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

A Secondary Gate As a Mechanism for Inhibition of the M2 Proton Channel by Amantadine

(2008) Myunggi Yi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS