(Q37033955)

17 August 2017

Ion binding sites and their representations by reduced models (English)

1 reference

17 August 2017

Benoît Roux

1

1 reference

PMC publication ID

3718881

17 August 2017

language of work or name

English

0 references

publication date

30 April 2012

1 reference

Journal of Physical Chemistry B

17 August 2017

1 reference

17 August 2017

116

1 reference

17 August 2017

23

1 reference

17 August 2017

6966-6979

1 reference

Ion selectivity from local configurations of ligands in solutions and ion channels.

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Protonation of key acidic residues is critical for the K⁺-selectivity of the Na/K pump

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Probing the thermodynamics of competitive ion binding using minimum energy structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Ion selectivity in channels and transporters

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Two mechanisms of ion selectivity in protein binding sites

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Exploring the ion selectivity properties of a large number of simplified binding site models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Statistical determinants of selective ionic complexation: ions in solvent, transport proteins, and other "hosts".

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Ion selectivity in the KcsA potassium channel from the perspective of the ion binding site

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Computations of standard binding free energies with molecular dynamics simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Structural transitions in ion coordination driven by changes in competition for ligand binding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Control of ion selectivity in LeuT: two Na+ binding sites with two different mechanisms

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Tuning ion coordination architectures to enable selective partitioning

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Principles of selective ion transport in channels and pumps

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Calculation of absolute protein-ligand binding free energy from computer simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

On the calculation of absolute macromolecular binding free energies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

The statistical-thermodynamic basis for computation of binding affinities: a critical review

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Negative Conductance Caused by Entry of Sodium and Cesium Ions into the Potassium Channels of Squid Axons

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

On the utilization of energy minimization to the study of ion selectivity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Determinants of K+ vs Na+ selectivity in potassium channels.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Grand canonical Monte Carlo simulations of water in protein environments.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Density functional theory investigations on the chemical basis of the selectivity filter in the K+ channel protein.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Factors governing the Na(+) vs K(+) selectivity in sodium ion channels

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Hydration structure and free energy of biomolecularly specific aqueous dications, including Zn2+ and first transition row metals

20 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3718881

Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 2. Tests with simple spherical systems

20 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22494321

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22494321

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Quasichemical theory with a soft cutoff

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22494321

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/JP3007365

1 reference

17 August 2017

1 reference

PMC publication ID

3718881

17 August 2017

PubMed publication ID

22494321

1 reference

PMC publication ID

3718881