Analysis and evaluation of channel models: simulations of alamethicin. (Q30332186)

18 September 2017

Analysis and evaluation of channel models: simulations of alamethicin. (English)

1 reference

18 September 2017

D Peter Tieleman

1

1 reference

18 September 2017

Berk Hess

series ordinal

2

1 reference

18 September 2017

Mark S P Sansom

series ordinal

3

1 reference

18 September 2017

language of work or name

English

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publication date

1 November 2002

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18 September 2017

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18 September 2017

83

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18 September 2017

5

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18 September 2017

2393-2407

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OmpA: a pore or not a pore? Simulation and modeling studies

18 September 2017

1 reference

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Simulation approaches to ion channel structure-function relationships

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

X-ray structure of a ClC chloride channel at 3.0 A reveals the molecular basis of anion selectivity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Voltage-dependent pore formation and antimicrobial activity by alamethicin and analogues

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions

3 June 2018

1 reference

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Voltage-dependent insertion of alamethicin at phospholipid/water and octane/water interfaces

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Hinges, swivels and switches: the role of prolines in signalling via transmembrane alpha-helices

3 June 2018

1 reference

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Helical membrane protein folding, stability, and evolution

3 June 2018

1 reference

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A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels

3 June 2018

1 reference

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

3 June 2018

1 reference

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Structure and dynamics of the pore-lining helix of the nicotinic receptor: MD simulations in water, lipid bilayers, and transbilayer bundles

3 June 2018

1 reference

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Protonation of lysine residues inverts cation/anion selectivity in a model channel

3 June 2018

1 reference

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Continuum solvent model calculations of alamethicin-membrane interactions: thermodynamic aspects

3 June 2018

1 reference

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Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer

3 June 2018

1 reference

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Exploring models of the influenza A M2 channel: MD simulations in a phospholipid bilayer

3 June 2018

1 reference

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Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane

3 June 2018

1 reference

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Membrane protein folding and stability: physical principles

3 June 2018

1 reference

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Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

An alamethicin channel in a lipid bilayer: molecular dynamics simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Exploration of the structural features defining the conduction properties of a synthetic ion channel

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Alamethicin helices in a bilayer and in solution: molecular dynamics simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel

3 June 2018

1 reference

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Electrostatics and the ion selectivity of ligand-gated channels

3 June 2018

1 reference

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A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer

3 June 2018

1 reference

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

3 June 2018

1 reference

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A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Intrinsic rectification of ion flux in alamethicin channels: studies with an alamethicin dimer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

HOLE: a program for the analysis of the pore dimensions of ion channel structural models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Alamethicin channels - modelling via restrained molecular dynamics simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Helix bending in alamethicin: molecular dynamics simulations and amide hydrogen exchange in methanol

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

A novel method for structure-based prediction of ion channel conductance properties.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Structure and functions of channel-forming peptides: magainins, cecropins, melittin and alamethicin

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Water in channel-like cavities: structure and dynamics.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Probability of alamethicin conductance states varies with nonlamellar tendency of bilayer phospholipids.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Alamethicin: A Peptide Model for Voltage Gating and Protein-Membrane Interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Structure and function of channel-forming peptaibols

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

The pore dimensions of gramicidin A.

3 June 2018

1 reference

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Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

The lowest conductance state of the alamethicin pore

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Open channel noise. I. Noise in acetylcholine receptor currents suggests conformational fluctuations

3 June 2018

1 reference

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The biophysics of peptide models of ion channels

3 June 2018

1 reference

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Model ion channels: gramicidin and alamethicin

3 June 2018

1 reference

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Convergence of sampling in protein simulations.

3 June 2018

1 reference

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Proline-induced hinges in transmembrane helices: possible roles in ion channel gating

26 November 2018

1 reference

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Structure-based prediction of the conductance properties of ion channels

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302328

Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects.

26 November 2018

1 reference

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Electrostatic effects in macromolecules: fundamental concepts and practical modeling

26 November 2018

1 reference

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Molecular dynamics with coupling to an external bath

26 November 2018

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GROMACS: A message-passing parallel molecular dynamics implementation

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MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures

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Synthetic amphiphilic peptide models for protein ion channels

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Alamethicin and related peptaibols--model ion channels

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Probing alamethicin channels with water-soluble polymers. Size-modulated osmotic action

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inferred from DOI database lookup

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Identifiers

DOI

10.1016/S0006-3495(02)75253-3

1 reference

18 September 2017

1 reference

18 September 2017

PubMed publication ID

12414676

1 reference