Water and hydrophobic gates in ion channels and nanopores

A Newly Available Tool for Functional Annotation of Ion Channel Structures Based on Molecular Dynamics Simulations

(2018) Gianni Klesse et al.   BIOPHYSICAL JOURNAL

How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1′ Pocket of Thermolysin

(2017) Stefan G. Krimmer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The lysosomal potassium channel TMEM175 adopts a novel tetrameric architecture

(2017) Changkeun Lee et al.   NATURE

Intrusion and extrusion of water in hydrophobic nanopores

(2017) Antonio Tinti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Water models for biomolecular simulations

(2017) Alexey V. Onufriev et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Engineered transmembrane pores

(2016) Mariam Ayub et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

A monodisperse transmembrane α-helical peptide barrel

(2016) Kozhinjampara R. Mahendran et al.   Nature Chemistry

Characterizing hydrophobicity of amino acid side chains in a protein environment via measuring contact angle of a water nanodroplet on planar peptide network

(2016) Chongqin Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinct regions that control ion selectivity and calcium-dependent activation in the bestrophin ion channel

(2016) George Vaisey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Annotation of Ion Channel Structures by Molecular Simulation

(2016) Jemma L. Trick et al.   STRUCTURE

Gating-like Motions and Wall Porosity in a DNA Nanopore Scaffold Revealed by Molecular Simulations

(2015) Vishal Maingi et al.   ACS Nano

Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries

(2015) Elizabeth Jefferys et al.   Journal of Chemical Theory and Computation

Modular Design of Self-Assembling Peptide-Based Nanotubes

(2015) Natasha C. Burgess et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Designing a Hydrophobic Barrier within Biomimetic Nanopores

(2014) Jemma. L. Trick et al.   ACS Nano

Stochastic transport through carbon nanotubes in lipid bilayers and live cell membranes

(2014) Jia Geng et al.   NATURE

Structure and selectivity in bestrophin ion channels

(2014) T. Yang et al.   SCIENCE

A hydrophobic barrier deep within the inner pore of the TWIK-1 K2P potassium channel

(2014) Prafulla Aryal et al.   Nature Communications

Self-Assembled DNA Nanopores That Span Lipid Bilayers

(2013) Jonathan R. Burns et al.   NANO LETTERS

Carbon nanotube membranes with ultrahigh specific adsorption capacity for water desalination and purification

(2013) Hui Ying Yang et al.   Nature Communications

Drying Transition in the Hydrophobic Gate of the GLIC Channel Blocks Ion Conduction

(2012) Fangqiang Zhu et al.   BIOPHYSICAL JOURNAL

Recent trends in nanopores for biotechnology

(2012) Daniel H Stoloff et al.   CURRENT OPINION IN BIOTECHNOLOGY

Designing biomimetic pores based on carbon nanotubes

(2012) R. Garcia-Fandino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations

(2011) Phillip J. Stansfeld et al.   Journal of Chemical Theory and Computation

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Electric-field-induced wetting and dewetting in single hydrophobic nanopores

(2011) Matthew R. Powell et al.   Nature Nanotechnology

Learning from Nature: Building Bio-Inspired Smart Nanochannels

(2009) Xu Hou et al.   ACS Nano

Bubbles, Gating, and Anesthetics in Ion Channels

(2008) Roland Roth et al.   BIOPHYSICAL JOURNAL

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Outer membrane protein G: Engineering a quiet pore for biosensing

(2008) M. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Water in Nonpolar Confinement: From Nanotubes to Proteins and Beyond

(2007) Jayendran C. Rasaiah et al.   Annual Review of Physical Chemistry