Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations (Q42182110)

18 October 2017

Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations (English)

1 reference

18 October 2017

Elizabeth J Denning

1 reference

18 October 2017

Thomas B Woolf

series ordinal

1 reference

18 October 2017

language of work or name

English

0 references

publication date

1 April 2010

1 reference

18 October 2017

1 reference

18 October 2017

1 reference

18 October 2017

1 reference

18 October 2017

1105-1119

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

18 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

A Comparison of Three Perturbation Molecular Dynamics Methods for Modeling Conformational Transitions

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Crystal structure of full-length KcsA in its closed conformation

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Probing the flexibility of large conformational changes in protein structures through local perturbations

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Cooperative transition between open and closed conformations in potassium channels

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Generation, comparison, and merging of pathways between protein conformations: gating in K-channels

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Molecular dynamics simulation of the Escherichia coli NikR protein: equilibrium conformational fluctuations reveal interdomain allosteric communication pathways

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

A Kv channel with an altered activation gate sequence displays both "fast" and "slow" activation kinetics.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

End-point targeted molecular dynamics: large-scale conformational changes in potassium channels

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Clustal W and Clustal X version 2.0

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Structural and thermodynamic properties of selective ion binding in a K+ channel

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Theoretical and computational models of biological ion channels

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Crystallographic study of the tetrabutylammonium block to the KcsA K+ channel

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Common mechanism of pore opening shared by five different potassium channels

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Investigating the putative glycine hinge in Shaker potassium channel.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Crystal structure of a mammalian voltage-dependent Shaker family K+ channel

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

In silico activation of KcsA K+ channel by lateral forces applied to the C-termini of inner helices

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Computational studies of membrane channels

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Calculating potentials of mean force from steered molecular dynamics simulations

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Filter flexibility and distortion in a bacterial inward rectifier K+ channel: simulation studies of KirBac1.1.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Tools for channels: moving towards molecular calculations of gating and permeation in ion channel biophysics

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

The Occupancy of Ions in the K+ Selectivity Filter: Charge Balance and Coupling of Ion Binding to a Protein Conformational Change Underlie High Conduction Rates

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Gating of MscL Studied by Steered Molecular Dynamics

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

A quantitative description of membrane current and its application to conduction and excitation in nerve

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Crystal structure of the potassium channel KirBac1.1 in the closed state

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

X-ray structure of a voltage-dependent K+ channel

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Open-state models of a potassium channel

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Crystal structure and mechanism of a calcium-gated potassium channel

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Scanning the intracellular S6 activation gate in the shaker K+ channel

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Intrinsic flexibility and gating mechanism of the potassium channel KcsA

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 A resolution

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Dynamic interaction of S5 and S6 during voltage-controlled gating in a potassium channel

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Comparative protein structure modeling of genes and genomes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Homology modeling and molecular dynamics simulation studies of an inward rectifier potassium channel

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Structure and dynamics of K channel pore-lining helices: a comparative simulation study

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Structural rearrangements underlying K+-channel activation gating

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

The pore dimensions of gramicidin A.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Dynamics of a small globular protein in terms of low-frequency vibrational modes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Kv channel gating requires a compatible S4-S5 linker and bottom part of S6, constrained by non-interacting residues

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Targeted molecular dynamics of an open-state KcsA channel

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Computer simulation of the KvAP voltage-gated potassium channel: steered molecular dynamics of the voltage sensor

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

A side chain in S6 influences both open-state stability and ion permeation in a voltage-gated K+ channel

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Computing ensembles of transitions from stable states: Dynamic importance sampling.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

The open state gating mechanism of gramicidin a requires relative opposed monomer rotation and simultaneous lateral displacement

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Kv channel S6 helix as a molecular switch: simulation studies.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Permeation and gating in proteins: kinetic Monte Carlo reaction path following.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Structural basis of TEA blockade in a model potassium channel

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Implicit solvation based on generalized Born theory in different dielectric environments

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

A mutant KcsA K(+) channel with altered conduction properties and selectivity filter ion distribution

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

KcsA closed and open: modelling and simulation studies

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Generalized born model with a simple smoothing function.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Proline-induced distortions of transmembrane helices.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2822122

Global twisting motion of single molecular KcsA potassium channel upon gating

17 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19950367

12 December 2020

inferred from PubMed ID database lookup

Energetics of pore opening in a voltage-gated K(+) channel

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19950367

12 December 2020

inferred from PubMed ID database lookup

Mechanism of intracellular block of the KcsA K+ channel by tetrabutylammonium: insights from X-ray crystallography, electrophysiology and replica-exchange molecular dynamics simulations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19950367

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1002/PROT.22632

1 reference

release_qum3ya4amvbkpawmhgwv4nwrrm

18 October 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/qum3ya4amvbkpawmhgwv4nwrrm

24 November 2022

mapped directly with Wikidata item

1 reference

18 October 2017

PubMed publication ID

19950367

1 reference