Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

Transient water wires mediate selective proton transport in designed channel proteins

Journal Article · · Nature Chemistry

Not provided.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Organization:
USDOE
DOE Contract Number:
AC02-06CH11357
OSTI ID:
2423712
Journal Information:
Nature Chemistry, Journal Name: Nature Chemistry Journal Issue: 7 Vol. 15; ISSN 1755-4330
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English

References (103)

An aqueous H+ permeation pathway in the voltage-gated proton channel Hv1 journal June 2010
De novo design of a transmembrane Zn 2+ -transporting four-helix bundle journal December 2014
Conformational Changes of an Ion Channel Detected Through Water−Protein Interactions Using Solid-State NMR Spectroscopy journal January 2010
Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus journal January 2009
Oxygen and proton pathways in cytochrome c oxidase journal January 1998
Coupling of Phosphorylation to Electron and Hydrogen Transfer by a Chemi-Osmotic type of Mechanism journal July 1961
Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport journal November 2015
Features and development of Coot journal March 2010
Packing of apolar side chains enables accurate design of highly stable membrane proteins journal March 2019
A defined structural unit enables de novo design of small-molecule–binding proteins journal September 2020
Chance and design—Proton transfer in water, channels and bioenergetic proteins journal August 2006
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles journal August 2012
PLUMED 2: New feathers for an old bird journal February 2014
Water orientation and dynamics in the closed and open influenza B virus M2 proton channels journal March 2021
Phaser crystallographic software journal July 2007
Thermodynamic Properties of Internal Water Molecules in the Hydrophobic Cavity around the Catalytic Center of Cytochrome c Oxidase journal December 2004
De Novo Computational Design of Retro-Aldol Enzymes journal March 2008
Endosomal pH in neuronal signaling and synaptic transmission: role of Na+/H+ exchanger NHE5 journal January 2014
Single-chain heteropolymers transport protons selectively and rapidly journal January 2020
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy journal November 2003
Combinatorial methods for small-molecule placement in computational enzyme design journal October 2006
Changing hydration level in an internal cavity modulates the proton affinity of a key glutamate in cytochrome c oxidase journal November 2013
Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins journal January 2016
A Secondary Gate As a Mechanism for Inhibition of the M2 Proton Channel by Amantadine journal July 2008
Principles for designing ideal protein structures journal November 2012
Bottom-up de novo design of functional proteins with complex structural features journal January 2021
Combinatorial Approach for Exploring Conformational Space and Activation Barriers in Computer-Aided Enzyme Design journal April 2020
Ultrafast proton transport in sub-1-nm diameter carbon nanotube porins journal April 2016
De novo design of picomolar SARS-CoV-2 miniprotein inhibitors journal September 2020
Solution structure and dynamics of a de novo designed three-helix bundle protein journal May 1999
Model bias in macromolecular crystal structures journal November 1992
Proton Transport through Influenza A Virus M2 Protein Reconstituted in Vesicles journal January 2008
Charge Delocalization in Proton Channels, I: The Aquaporin Channels and Proton Blockage journal January 2007
XDS journal January 2010
Computational design of transmembrane pores journal August 2020
The vacuolar (H+)-ATPases — nature's most versatile proton pumps journal February 2002
The Grotthuss mechanism journal October 1995
Matplotlib: A 2D Graphics Environment journal January 2007
Characterization of different water pools in solid-state NMR protein samples journal September 2009
A second generation multistate empirical valence bond model for proton transport in aqueous systems journal September 2002
Crystallizing Membrane Proteins for Structure Determination: Use of Lipidic Mesophases journal June 2009
Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase journal June 2016
Coupling Amplification in 2D MAS NMR and Its Application to Torsion Angle Determination in Peptides journal November 1997
Hydrophobic gasket mutation produces gating pore currents in closed human voltage-gated proton channels journal August 2019
Proton and cation transport activity of the M2 proton channel from influenza A virus journal August 2010
Multiscale Reactive Molecular Dynamics for Absolute p K a Predictions and Amino Acid Deprotonation journal May 2014
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules book January 2011
Resolving the Structural Debate for the Hydrated Excess Proton in Water journal November 2021
Probing membrane protein structure using water polarization transfer solid-state NMR journal October 2014
GROMACS: Fast, flexible, and free journal January 2005
Osmotic water transport through carbon nanotube membranes journal July 2003
Proton transfer via a transient linear water-molecule chain in a membrane protein journal June 2011
Deprotonation of D96 in Bacteriorhodopsin Opens the Proton Uptake Pathway journal February 2013
Principles of conduction and hydrophobic gating in K+ channels journal March 2010
Accurate computational design of multipass transmembrane proteins journal March 2018
Promoting transparency and reproducibility in enhanced molecular simulations journal July 2019
Structure and drug binding of the SARS-CoV-2 envelope protein transmembrane domain in lipid bilayers journal November 2020
Drying Transition in the Hydrophobic Gate of the GLIC Channel Blocks Ion Conduction journal July 2012
Hydrated Excess Protons Can Create Their Own Water Wires journal September 2014
Catalysis and Electron Transfer in De Novo Designed Helical Scaffolds journal March 2020
De Novo Design of Xeno‐Metallo Coiled Coils journal December 2015
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field journal December 2015
OPM database and PPM web server: resources for positioning of proteins in membranes journal September 2011
Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy journal November 2005
Multiscale reactive molecular dynamics journal December 2012
Computationally Efficient Multiconfigurational Reactive Molecular Dynamics journal September 2012
Voltage-Gated Proton Channels and Other Proton Transfer Pathways journal April 2003
Water in Nonpolar Confinement: From Nanotubes to Proteins and Beyond journal May 2008
CHARMM-GUI Membrane Builder toward realistic biological membrane simulations journal August 2014
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data journal July 2013
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers journal September 2015
CHAP: A Versatile Tool for the Structural and Functional Annotation of Ion Channel Pores journal August 2019
Identification of the functional core of the influenza A virus A/M2 proton-selective ion channel journal July 2009
Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient journal June 2021
Oxygen Activation and Energy Conservation by Cytochrome c Oxidase journal January 2018
Fast Parallel Algorithms for Short-Range Molecular Dynamics journal March 1995
Overview of the CCP 4 suite and current developments journal March 2011
Structural determinants of water permeation through aquaporin-1 journal October 2000
Improved prediction of protein side-chain conformations with SCWRL4 journal December 2009
VMD: Visual molecular dynamics journal February 1996
Crystallizing membrane proteins using lipidic mesophases journal April 2009
X-ray crystal structure of voltage-gated proton channel journal March 2014
Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase journal May 2017
A quantitative paradigm for water-assisted proton transport through proteins and other confined spaces journal December 2021
Towards automated crystallographic structure refinement with phenix.refine journal March 2012
Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations journal September 2007
Water in Nanopores and Biological Channels: A Molecular Simulation Perspective journal August 2020
De novo design of a hyperstable non-natural protein–ligand complex with sub-Å accuracy journal August 2017
Mitochondrial ion circuits journal June 2010
Stochastic transport through carbon nanotubes in lipid bilayers and live cell membranes journal October 2014
Structures of the otopetrin proton channels Otop1 and Otop3 journal June 2019
H+-ATPase, a primary pump for accumulation of neurotransmitters, is a major constituent of brain synaptic vesicles journal November 1990
Constructing ion channels from water-soluble α-helical barrels journal May 2021
Water-gated mechanism of proton translocation by cytochrome c oxidase journal June 2003
De novo design of transmembrane β barrels journal February 2021
X-ray Crystal Structure of the Influenza A M2 Proton Channel S31N Mutant in Two Conformational States: An Open and Shut Case journal June 2019
CHARMM-GUI: A web-based graphical user interface for CHARMM journal March 2008
Proton uptake mechanism in bacteriorhodopsin captured by serial synchrotron crystallography journal July 2019
Characterization of a helical protein designed from first principles journal August 1988
Inverse coupling in leak and voltage-activated K+ channel gates underlies distinct roles in electrical signaling journal December 2008
Hydrophobic plug functions as a gate in voltage-gated proton channels journal December 2013
Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin journal May 2011
Hydrophobic Gating in Ion Channels journal January 2015

Similar Records

Water, Solute, and Ion Transport in De Novo-Designed Membrane Protein Channels
Journal Article · 2024 · ACS Nano · OSTI ID:2510967

Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel
Journal Article · 2021 · Journal of Chemical Theory and Computation · OSTI ID:1875799

Electron transfer activation of a second water channel for proton transport in [FeFe]-hydrogenase
Journal Article · 2014 · Journal of Chemical Physics · OSTI ID:1226574

Related Subjects