(Q42269231)

19 October 2017

Energetics of ion permeation, rejection, binding, and block in gramicidin A from free energy simulations (English)

1 reference

19 October 2017

Serdar Kuyucak

2

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author name string

Turgut Baştuğ

series ordinal

1

1 reference

PMC publication ID

1459526

19 October 2017

language of work or name

English

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publication date

13 March 2006

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19 October 2017

10

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inferred from page(s)

published in

Biophysical Journal

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19 October 2017

90

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19 October 2017

11

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19 October 2017

3941-3950

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

19 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

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=1459526

Role of protein flexibility in ion permeation: a case study in 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=1459526

Computer simulations 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=1459526

Ionic permeation free energy in gramicidin: a semimicroscopic perspective

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

Energetics of ion conduction through the gramicidin 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=1459526

Gramicidin A channel as a test ground for molecular dynamics force fields

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

Continuum electrostatics fails to describe ion permeation in the gramicidin 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=1459526

Trial by ordeal: ionic free energies in gramicidin

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

Computational studies of the gramicidin 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=1459526

Simulation approaches to ion channel structure-function relationships

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

Structures of gramicidins A, B, and C incorporated into sodium dodecyl sulfate micelles

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

Mechanisms of permeation and selectivity in calcium 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=1459526

Structure of lipid bilayers

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

26 October 2017

Modeling of ion channels

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

Cation transport: an example of structural based selectivity

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

Valence selectivity of the gramicidin channel: a molecular dynamics free energy perturbation 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=1459526

A semi-microscopic Monte Carlo study of permeation energetics in a gramicidin-like channel: the origin of cation selectivity

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

VMD: visual 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=1459526

The use of physical methods in determining gramicidin channel structure and function

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

Molecular Dynamics Simulations of the Gramicidin 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=1459526

Structure and dynamics of ion transport through 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=1459526

The gramicidin A transmembrane channel: a proposed pi(L,D) helix

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

Free energy via molecular simulation: applications to chemical and biomolecular systems

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

Equilibrium binding constants for the group I metal cations with gramicidin-A determined by competition studies and T1+-205 nuclear magnetic resonance spectroscopy

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

Interpretation of biological ion channel flux data--reaction-rate versus continuum theory

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

Theoretical perspectives on ion-channel electrostatics: continuum and microscopic approaches

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

Molecular determinants of channel function

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

The determination of binding constants of micellar-packaged gramicidin A by 13C-and 23Na-NMR.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1459526

The divalent cation-binding sites of gramicidin A transmembrane ion-channel

17 August 2018

1 reference

12 December 2020

Molecular dynamics simulations of biomolecules

1 reference

12 December 2020

Ion pair binding of Ca2+ and Cl- ions in micellar-packaged gramicidin A

1 reference

12 December 2020

Ca2+-Gramicidin a interactions and blocking effects on the ionic channel

1 reference

12 December 2020

Location of ion-binding sites in the gramicidin channel by X-ray diffraction

1 reference

12 December 2020

Monovalent cation transport: lack of structural deformation upon cation binding

1 reference

12 December 2020

10.1529/BIOPHYSJ.105.074633

Identifiers

DOI

1 reference

19 October 2017

1 reference

PMC publication ID

1459526

19 October 2017

PubMed publication ID

16533834

1 reference

PMC publication ID

1459526