Simulations of substrate transport in the multidrug transporter EmrD (Q35949089)

11 August 2017

Simulations of substrate transport in the multidrug transporter EmrD (English)

1 reference

11 August 2017

Joseph Baker

1

1 reference

11 August 2017

Stephen H Wright

series ordinal

2

1 reference

11 August 2017

Florence Tama

series ordinal

3

1 reference

11 August 2017

language of work or name

English

0 references

publication date

20 March 2012

1 reference

11 August 2017

1 reference

11 August 2017

80

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11 August 2017

6

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11 August 2017

1620-1632

1 reference

A gate-free pathway for substrate release from the inward-facing state of the Na⁺-galactose transporter

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Substrate binding and translocation of the serotonin transporter studied by docking and molecular dynamics simulations.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

The substrate-driven transition to an inward-facing conformation in the functional mechanism of the dopamine transporter

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Simulation of spontaneous substrate binding revealing the binding pathway and mechanism and initial conformational response of GlpT.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Structural basis of substrate selectivity in the glycerol-3-phosphate: phosphate antiporter GlpT.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Proton transport pathway in the ClC Cl-/H+ antiporter

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Bacterial multidrug transport through the lens of the major facilitator superfamily

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Ins and outs of major facilitator superfamily antiporters.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Very fast prediction and rationalization of pKa values for protein-ligand complexes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Salt-bridge dynamics control substrate-induced conformational change in the membrane transporter GlpT.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Opening and closing of the periplasmic gate in lactose permease

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Substrate binding and formation of an occluded state in the leucine transporter

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

R.E.DD.B.: a database for RESP and ESP atomic charges, and force field libraries

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Sugar binding induces an outward facing conformation of LacY.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Automated builder and database of protein/membrane complexes for molecular dynamics simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Single-molecule FRET reveals sugar-induced conformational dynamics in LacY.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Sugar transport across lactose permease probed by steered molecular dynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Multiple molecular mechanisms for multidrug resistance transporters

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Site-directed alkylation and the alternating access model for LacY.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Comparison of multiple Amber force fields and development of improved protein backbone parameters

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Sugar binding and protein conformational changes in lactose permease

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Promiscuity in multidrug recognition and transport: the bacterial MFS Mdr transporters.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Lessons from lactose permease

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Structure of the multidrug transporter EmrD from Escherichia coli

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Automatic atom type and bond type perception in molecular mechanical calculations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Molecular dynamics studies of the archaeal translocon

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

On the putative co-transport of drugs by multidrug resistance proteins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Very fast empirical prediction and rationalization of protein pKa values

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Scalable molecular dynamics with NAMD

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Molecular dynamics study of gating in the mechanosensitive channel of small conductance MscS

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Computational studies of membrane channels

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Structural mechanism of the simultaneous binding of two drugs to a multidrug-binding protein

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Development and testing of a general amber force field

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Crystal structures of QacR-diamidine complexes reveal additional multidrug-binding modes and a novel mechanism of drug charge neutralization

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Structure and mechanism of the lactose permease of Escherichia coli

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Mystery of multidrug transporters: the answer can be simple

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Acidic residues in the lactococcal multidrug efflux pump LmrP play critical roles in transport of lipophilic cationic compounds

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Analysis of a complete library of putative drug transporter genes in Escherichia coli

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

The secondary multidrug transporter LmrP contains multiple drug interaction sites.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Structural basis of multidrug recognition by BmrR, a transcription activator of a multidrug transporter

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Major facilitator superfamily

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Mutations affecting substrate specificity of the Bacillus subtilis multidrug transporter Bmr.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Proton-dependent multidrug efflux systems

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Multidrug resistance in Lactococcus lactis: evidence for ATP-dependent drug extrusion from the inner leaflet of the cytoplasmic membrane.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

VMD: visual molecular dynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

The pore dimensions of gramicidin A.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Uncoupler-resistant mutants of bacteria

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

Energetics and mechanism of drug transport mediated by the lactococcal multidrug transporter LmrP.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

An E. coli gene emrD is involved in adaptation to low energy shock.

11 July 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24056

Bioenergetics of the staphylococcal multidrug export protein QacA. Identification of distinct binding sites for monovalent and divalent cations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24056

Determinants of substrate recognition by the Escherichia coli multidrug transporter MdfA identified on both sides of the membrane.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24056

Promiscuity in the geometry of electrostatic interactions between the Escherichia coli multidrug resistance transporter MdfA and cationic substrates

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24056

Evidence for simultaneous binding of dissimilar substrates by the Escherichia coli multidrug transporter MdfA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24056

Helix dynamics in a membrane transport protein: comparative simulations of the glycerol-3-phosphate transporter and its constituent helices

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24056

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24056

Structure and dynamics of phospholipid bilayers using recently developed general all-atom force fields.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24056

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24056

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions

21 January 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3349012

24 September 2018

https://api.crossref.org/works/10.1002%2FPROT.24056

Asymmetric Stability among the Transmembrane Helices of Lactose Permease†

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24056

Mechanism of Gating and Ion Conductivity of a Possible Tetrameric Pore in Aquaporin-1

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24056

Conformational change in an MFS protein: MD simulations of LacY

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22434745

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.24056

1 reference

11 August 2017

1 reference

11 August 2017

PubMed publication ID

22434745

1 reference