(Q30165296)

18 September 2017

OmpA: a pore or not a pore? Simulation and modeling studies (English)

1 reference

18 September 2017

Peter J Bond

1

1 reference

18 September 2017

José D Faraldo-Gómez

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

0 references

publication date

1 August 2002

1 reference

18 September 2017

13

1 reference

based on heuristic

inferred from page(s)

published in

Biophysical Journal

1 reference

18 September 2017

83

1 reference

18 September 2017

2

1 reference

18 September 2017

763-775

1 reference

Setting up and optimization of membrane protein simulations.

18 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

The mechanism of glycerol conduction in aquaglyceroporins.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Solution NMR studies of the integral membrane proteins OmpX and OmpA from Escherichia coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Molecular dynamics simulations of wild-type and mutant forms of the Mycobacterium tuberculosis MscL 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=1302185

Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Structure and assembly of beta-barrel membrane proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Structural determinants of MscL gating studied by 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=1302185

Structure of outer membrane protein A transmembrane domain by NMR spectroscopy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Probing the interface between membrane proteins and membrane lipids by X-ray crystallography

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Ion channels, permeation, and electrostatics: insight into the function of KcsA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Ion channel formation by N-terminal domain: a common feature of OprFs of Pseudomonas and OmpA of Escherichia coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

The amino terminus of Pseudomonas aeruginosa outer membrane protein OprF forms channels in lipid bilayer membranes: correlation with a three-dimensional model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Structure and function of bacterial outer membrane proteins: barrels in a nutshell

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Simulations of ion channels--watching ions and water move

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Molecular dynamics of the KcsA K(+) channel in a bilayer membrane

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

High-resolution structure of the OmpA membrane domain

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Membrane simulations: bigger and better?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Refolded outer membrane protein A of Escherichia coli forms ion channels with two conductance states in planar lipid bilayers

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Dynamic properties of Na+ ions in models of ion channels: a molecular dynamics 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=1302185

Structure of the outer membrane protein A transmembrane domain

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Electrostatics and the ion selectivity of ligand-gated channels

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

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=1302185

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=1302185

Annexins: from structure to function.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

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=1302185

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=1302185

VMD: visual molecular 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=1302185

Backbone-dependent rotamer library for proteins. Application to side-chain prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

The pore dimensions of gramicidin A.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

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=1302185

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Pore-forming activity of OmpA protein of Escherichia coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Energetics of ion conduction through the K+ 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=1302185

Molecular dynamics study of aquaporin-1 water channel in a lipid bilayer.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Evidence for association of lipopolysaccharide with Pseudomonas fluorescens strain MF0 porin OprF.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Water and potassium dynamics inside the KcsA K(+) channel.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

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=1302185

Lipid properties and the orientation of aromatic residues in OmpF, influenza M2, and alamethicin systems: molecular dynamics simulations

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

IMPALA: a simple restraint field to simulate the biological membrane in molecular structure studies.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Proposal for a peptidoglycan-associating alpha-helical motif in the C-terminal regions of some bacterial cell-surface proteins

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

The C-terminal sequence conservation between OmpA-related outer membrane proteins and MotB suggests a common function in both gram-positive and gram-negative bacteria, possibly in the interaction of these domains with peptidoglycan

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Ionophore properties of OmpA of Escherichia coli.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Fluctuation and Cross-correlation Analysis of Protein Motions Observed in Nanosecond Molecular Dynamics Simulations

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

OmpA protein of Escherichia coli outer membrane occurs in open and closed channel forms

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1302185

Prediction of membrane protein orientation in lipid bilayers: a theoretical approach

26 November 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975207-7

Molecular dynamics with coupling to an external bath

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975207-7

GROMACS: A message-passing parallel molecular dynamics implementation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975207-7

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975207-7

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975207-7

Climatic impact of tropical lowland deforestation on nearby montane cloud forests

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975207-7

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975207-7

Effective diffusion coefficients of K+ and Cl- ions in ion channel models

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2802%2975207-7

10.1016/S0006-3495(02)75207-7

7 January 2021

Identifiers

DOI

1 reference

18 September 2017

1 reference

18 September 2017

PubMed publication ID

12124263

1 reference