Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA

Crystal structures reveal the molecular basis of ion translocation in sodium/proton antiporters

(2016) Mathieu Coincon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Crystal structures reveal the molecular basis of ion translocation in sodium/proton antiporters

(2016) Mathieu Coincon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Hydrophobic Gating in Ion Channels

(2015) Prafulla Aryal et al.   JOURNAL OF MOLECULAR BIOLOGY

pH-Dependent Population Shift Regulates BACE1 Activity and Inhibition

(2015) Christopher R. Ellis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Simulating the function of sodium/proton antiporters

(2015) Raphael Alhadeff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Keeping It Simple, Transport Mechanism and pH Regulation in Na+/H+Exchangers

(2014) Octavian Călinescu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Predicting proton titration in cationic micelle and bilayer environments

(2014) Brian H. Morrow et al.   JOURNAL OF CHEMICAL PHYSICS

Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange

(2014) Juyong Lee et al.   Journal of Chemical Theory and Computation

CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations

(2014) Emilia L. Wu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Crystal structure of the sodium–proton antiporter NhaA dimer and new mechanistic insights

(2014) Chiara Lee et al.   JOURNAL OF GENERAL PHYSIOLOGY

Recent development and application of constant pH molecular dynamics

(2014) Wei Chen et al.   MOLECULAR SIMULATION

Functional and structural dynamics of NhaA, a prototype for Na+ and H+ antiporters, which are responsible for Na+ and H+ homeostasis in cells

(2013) Etana Padan   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Differential Effects of Mutations on the Transport Properties of the Na+/H+Antiporter NhaA fromEscherichia coli

(2013) Thomas Mager et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A two-domain elevator mechanism for sodium/proton antiport

(2013) Chiara Lee et al.   NATURE

Thermodynamic Coupling of Protonation and Conformational Equilibria in Proteins: Theory and Simulation

(2012) Chuanyin Shi et al.   BIOPHYSICAL JOURNAL

Revealing the Ligand Binding Site of NhaA Na+/H+Antiporter and Its pH Dependence

(2012) Michal Maes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics

(2012) Jason M. Swails et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Transport Mechanism and pH Regulation of the Na+/H+Antiporter NhaA fromEscherichia coli

(2011) Thomas Mager et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange

(2011) Jason A. Wallace et al.   Journal of Chemical Theory and Computation

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

Site-directed tryptophan fluorescence reveals two essential conformational changes in the Na+/H+ antiporter NhaA

(2011) L. Kozachkov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease

(2011) M. R. Gunner et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Toward accurate prediction of pKa values for internal protein residues: The importance of conformational relaxation and desolvation energy

(2011) Jason A. Wallace et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Transmembrane Segment II of NhaA Na+/H+Antiporter Lines the Cation Passage, and Asp65Is Critical for pH Activation of the Antiporter

(2009) Katia Herz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field

(2009) Jakob P. Ulmschneider et al.   Journal of Chemical Theory and Computation

CHARMM: The biomolecular simulation program

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

Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions

(2009) Yun Luo et al.   Journal of Physical Chemistry Letters

Pore architecture and ion sites in acid-sensing ion channels and P2X receptors

(2009) Eric B. Gonzales et al.   NATURE

Multiscale simulations of protein landscapes: Using coarse-grained models as reference potentials to full explicit models

(2009) Benjamin M. Messer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Combined computational and biochemical study reveals the importance of electrostatic interactions between the “pH sensor” and the cation binding site of the sodium/proton antiporter NhaA ofEscherichia coli

(2009) Elena Olkhova et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structure-based Functional Study Reveals Multiple Roles of Transmembrane Segment IX and Loop VIII–IX in NhaA Na+/H+Antiporter ofEscherichia coliat Physiological pH

(2008) Tzvi Tzubery et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The enlightening encounter between structure and function in the NhaA Na+–H+ antiporter

(2008) Etana Padan   TRENDS IN BIOCHEMICAL SCIENCES