A cooperative knock-on mechanism underpins Ca2+-selective cation permeation in TRPV channels

Atomistic Details of Charge/Space Competition in the Ca2+ Selectivity of Ryanodine Receptors

(2021) Chunhong Liu et al.   Journal of Physical Chemistry Letters

Heat-dependent opening of TRPV1 in the presence of capsaicin

(2021) Do Hoon Kwon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Ca2+ permeation mechanism of the ryanodine receptor revealed by a multi-site ion model

(2020) Aihua Zhang et al.   Nature Communications

Phylogenetics Identifies Two Eumetazoan TRPM Clades and an Eighth TRP Family, TRP Soromelastatin (TRPS)

(2020) Nathaniel J Himmel et al.   MOLECULAR BIOLOGY AND EVOLUTION

High‐resolution structures of transient receptor potential vanilloid channels: Unveiling a functionally diverse group of ion channels

(2020) Mark K. Goor et al.   PROTEIN SCIENCE

Evolutionary analyses reveal independent origins of gene repertoires and structural motifs associated to fast inactivation in calcium-selective TRPV channels

(2020) Lisandra Flores-Aldama et al.   Scientific Reports

Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating

(2020) Keri A. McKiernan et al.   PLoS Computational Biology

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

Structural and Evolutionary Insights Point to Allosteric Regulation of TRP Ion Channels

(2019) Jacob K. Hilton et al.   ACCOUNTS OF CHEMICAL RESEARCH

CHAP: A Versatile Tool for the Structural and Functional Annotation of Ion Channel Pores

(2019) Gianni Klesse et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural basis of temperature sensation by the TRP channel TRPV3

(2019) Appu K. Singh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

TRP Channels as Potential Drug Targets

(2018) Magdalene M. Moran   Annual Review of Pharmacology and Toxicology

Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels

(2018) Wojciech Kopec et al.   Nature Chemistry

Ion Permeation Mechanism in Epithelial Calcium Channel TRVP6

(2018) Serzhan Sakipov et al.   Scientific Reports

Structures of TRPV2 in distinct conformations provide insight into role of the pore turret

(2018) Timothy L. Dosey et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural insights on TRPV5 gating by endogenous modulators

(2018) Taylor E. T. Hughes et al.   Nature Communications

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules

(2017) Seonghoon Kim et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Intracellular Ca 2+ Sensing: Its Role in Calcium Homeostasis and Signaling

(2017) Rafaela Bagur et al.   MOLECULAR CELL

Opening of the human epithelial calcium channel TRPV6

(2017) Luke L. McGoldrick et al.   NATURE

Crystal structure of the epithelial calcium channel TRPV6

(2016) Kei Saotome et al.   NATURE

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Engineering vanilloid-sensitivity into the rat TRPV2 channel

(2016) Feng Zhang et al.   eLife

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

(2015) Hui Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Evolution of TRP channels inferred by their classification in diverse animal species

(2015) Guangda Peng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Ion Selectivity Strategies of Sodium Channel Selectivity Filters

(2014) Todor Dudev et al.   ACCOUNTS OF CHEMICAL RESEARCH

Exact Test of Independence Using Mutual Information

(2014) Shawn Pethel et al.   Entropy

CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations

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

Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions

(2014) Miriam Kohagen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Calcium Binding to Calmodulin by Molecular Dynamics with Effective Polarization

(2014) Miriam Kohagen et al.   Journal of Physical Chemistry Letters

Ion permeation in K+ channels occurs by direct Coulomb knock-on

(2014) D. A. Kopfer et al.   SCIENCE

Different Inward and Outward Conduction Mechanisms in NaVMs Suggested by Molecular Dynamics Simulations

(2014) Song Ke et al.   PLoS Computational Biology

Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels

(2013) Ludovic Sauguet et al.   EMBO JOURNAL

Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel

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

Python for Scientists and Engineers

(2011) K. Jarrod Millman et al.   COMPUTING IN SCIENCE & ENGINEERING

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

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

OPM database and PPM web server: resources for positioning of proteins in membranes

(2011) Mikhail A. Lomize et al.   NUCLEIC ACIDS RESEARCH

On the selective ion binding hypothesis for potassium channels

(2011) I. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites

(2010) M. G. Derebe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Properties of the intracellular transient receptor potential (TRP) channel in yeast, Yvc1

(2009) Yiming Chang et al.   FEBS LETTERS

Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles

(2009) Christopher L. McClendon et al.   Journal of Chemical Theory and Computation

Mechanism of potassium-channel selectivity revealed by Na+ and Li+ binding sites within the KcsA pore

(2009) Ameer N Thompson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

K+/Na+ Selectivity in K Channels and Valinomycin: Over-coordination Versus Cavity-size constraints

(2007) Sameer Varma et al.   JOURNAL OF MOLECULAR BIOLOGY