(Q30428863)

15 October 2017

Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristol phosphatidylocholine. I. Structure and dynamics (English)

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molecular dynamics simulation

15 October 2017

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author name string

Woolf TB

series ordinal

1

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PMC publication ID

1181140

15 October 2017

language of work or name

English

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publication date

1 November 1997

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15 October 2017

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15 October 2017

73

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15 October 2017

5

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15 October 2017

2376-2392

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On simulating lipid bilayers with an applied surface tension: periodic boundary conditions and undulations

15 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

What is the surface tension of a lipid bilayer membrane?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Commentary: surface tension of biomembranes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Approaching the mechanism of protein transport across the ER membrane.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Molecular dynamics investigation of the structure of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Molecular dynamics study of early picosecond events in the bacteriorhodopsin photocycle: dielectric response, vibrational cooling and the J, K intermediates

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Electron-crystallographic refinement of the structure of bacteriorhodopsin

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Molecular dynamics study of the M412 intermediate of bacteriorhodopsin

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Automated method for modeling seven-helix transmembrane receptors from experimental data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Interaction of small peptides with lipid bilayers

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Molecular dynamics study of the proton pump cycle of bacteriorhodopsin

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

The probable arrangement of the helices in G protein-coupled receptors.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Area/lipid of bilayers from NMR.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Domain closure in lactoferrin. Two hinges produce a see-saw motion between alternative close-packed interfaces

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Molecular dynamics simulations of a lipid bilayer and of hexadecane: an investigation of membrane fluidity

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

A method for alpha-helical integral membrane protein fold prediction.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Seven-helix bundles: molecular modeling via restrained molecular dynamics.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Molecular dynamics study of the 13-cis form (bR548) of bacteriorhodopsin and its photocycle

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Structure and Fluctuations of Bacteriorhodopsin in the Purple Membrane: A Molecular Dynamics Study

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

A continuum theory for the prediction of lateral and rotational positioning of alpha-helices in membrane proteins: bacteriorhodopsin.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

An analysis of incorrectly folded protein models. Implications for structure predictions.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Hydrophobic organization of membrane proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Structure-function studies on bacteriorhodopsin. VIII. Substitutions of the membrane-embedded prolines 50, 91, and 186: the effects are determined by the substituting amino acids.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Conformation of proline residues in bacteriorhodopsin

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Proline kinks in transmembrane alpha-helices

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Proline residues in transmembrane helices: structural or dynamic role?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Proline in alpha-helix: stability and conformation studied by dynamics simulation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Unfolding of an ?-helix in water

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Bacteriorhodopsin can be refolded from two independently stable transmembrane helixes and the complementary five-helix fragment

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Domain closure in mitochondrial aspartate aminotransferase

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Modeling of the structure of bacteriorhodopsin. A molecular dynamics study

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Forces involved in the assembly and stabilization of membrane proteins

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Structural comparison suggests that thermolysin and related neutral proteases undergo hinge-bending motion during catalysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Thermodynamic measurements of the contributions of helix-connecting loops and of retinal to the stability of bacteriorhodopsin

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Bacteriorhodopsin: a light-driven proton pump in Halobacterium Halobium

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Temperature-dependent aggregation of bacteriorhodopsin in dipalmitoyl- and dimyristoylphosphatidylcholine vesicles

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Characterization of proline-containing right-handed alpha-helix by molecular dynamics studies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Picosecond timescale rigid-helix and side-chain motions in deoxymyoglobin.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Dramatic differences in the motions of the mouth of open and closed cytochrome P450BM-3 by 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=1181140

Molecular dynamics simulations of isolated helices of myoglobin

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Packing interactions of aib-containing helices: Molecular modeling of parallel dimers of simple hydrophobic helices and of alamethicin

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

Conformations of proline residues in membrane environments

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

A thermodynamic scale for the helix-forming tendencies of the commonly occurring amino acids

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1181140

The cotranslational integration of membrane proteins into the phospholipid bilayer is a multistep process

26 November 2018

1 reference

12 December 2020

Geometry of proline-containing alpha-helices in proteins

1 reference

12 December 2020

Proline residues in transmembrane helices of channel and transport proteins: a molecular modelling study

1 reference

12 December 2020

The effect of environment on the stability of an integral membrane helix: Molecular dynamics simulations of surfactant protein C in chloroform, methanol and water

1 reference

12 December 2020

Intrahelical hydrogen bonding of serine, threonine and cysteine residues within alpha-helices and its relevance to membrane-bound proteins

1 reference

12 December 2020

Molecular dynamics simulation of the stability of a 22-residue alpha-helix in water and 30% trifluoroethanol

1 reference

12 December 2020

Solute diffusion in lipid bilayer membranes: an atomic level study by molecular dynamics simulation

1 reference

12 December 2020

Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer

1 reference

12 December 2020

Prediction of the positioning of the seven transmembrane alpha-helices of bacteriorhodopsin. A molecular simulation study

1 reference

12 December 2020

Molecular dynamics study of bacteriorhodopsin and artificial pigments

1 reference

12 December 2020

Conformational studies on peptides with proline in the right-handed alpha-helical region

1 reference

12 December 2020

Kinked structures of isolated nicotinic receptor M2 helices: a molecular dynamics study

1 reference

12 December 2020

Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban

1 reference

12 December 2020

Membrane protein folding and oligomerization: the two-stage model

1 reference

12 December 2020

The glycophorin A transmembrane domain dimer: Sequence-specific propensity for a right-handed supercoil of helixes

1 reference

12 December 2020

Characterization of proline-containing alpha-helix (helix F model of bacteriorhodopsin) by molecular dynamics studies

1 reference

12 December 2020

Differential helix propensity of small apolar side chains studied by molecular dynamics simulations

1 reference

12 December 2020

Modeling of transmembrane seven helix bundles

1 reference

12 December 2020

10.1016/S0006-3495(97)78267-5

Identifiers

DOI

1 reference

15 October 2017

1 reference

PMC publication ID

1181140

15 October 2017

PubMed publication ID

9370432

1 reference

PMC publication ID

1181140