(Q35926185)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22824277%20AND%20SRC:MED&resulttype=core&format=json

8 February 2020

title

Accelerating membrane insertion of peripheral proteins with a novel membrane mimetic model (English)

1 reference

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8 February 2020

5

1 reference

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8 February 2020

Taras Pogorelov

2

1 reference

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8 February 2020

Mark J Arcario

3

1 reference

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8 February 2020

Geoff A Christensen

4

1 reference

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8 February 2020

author name string

Y Zenmei Ohkubo

1

1 reference

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8 February 2020

language of work or name

English

0 references

publication date

1 May 2012

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8 February 2020

1 reference

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8 February 2020

volume

102

1 reference

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8 February 2020

issue

9

1 reference

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8 February 2020

page(s)

2130-2139

1 reference

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Molecular determinants of phospholipid synergy in blood clotting

8 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Capturing spontaneous partitioning of peripheral proteins using a biphasic membrane-mimetic model

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Atomic view of calcium-induced clustering of phosphatidylserine in mixed lipid bilayers

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Polarizable water model for the coarse-grained MARTINI 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=3341550

Dynamical view of membrane binding and complex formation of human factor VIIa and tissue factor

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Recent estimates of the structure of the factor VIIa (FVIIa)/tissue factor (TF) and factor Xa (FXa) ternary complex

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Molecular dynamics simulations of the dimerization of transmembrane alpha-helices

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Membrane-bending mechanism of amphiphysin N-BAR domains

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

De novo design of antimicrobial polymers, foldamers, and small molecules: from discovery to practical applications

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Emerging roles for lipids in shaping membrane-protein function.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Four-scale description of membrane sculpting by BAR domains

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Crystal structure of human factor VIII: implications for the formation of the factor IXa-factor VIIIa complex

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Protein diffusion on charged membranes: a dynamic mean-field model describes time evolution and lipid reorganization.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

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=3341550

The MARTINI force field: coarse grained model for biomolecular 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=3341550

Single-molecule experiments in vitro and in silico

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Bilayer thickness and membrane protein function: an energetic perspective.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Membrane assembly of simple helix homo-oligomers studied via 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=3341550

Introduction to the membrane protein reviews: the interplay of structure, dynamics, and environment in membrane protein function

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Positioning of proteins in membranes: a computational approach

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Phosphatidic acid- and phosphatidylserine-binding 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=3341550

A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Balancing solvation and intramolecular interactions: toward a consistent generalized Born 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=3341550

Insertion and assembly of membrane proteins via simulation.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

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=3341550

Interfacial folding and membrane insertion of designed peptides studied by 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=3341550

Domain formation induced by the adsorption of charged proteins on mixed lipid membranes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in 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=3341550

The crystal structure of activated protein C-inactivated bovine factor Va: Implications for cofactor function

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Recent advances in the development and application of implicit solvent models in biomolecule 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=3341550

Structure and fluctuations of charged phosphatidylserine bilayers in the absence of salt

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Structural basis of membrane binding by Gla domains of vitamin K-dependent 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=3341550

Lipids on the frontier: a century of cell-membrane bilayers

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

C2 domain of protein kinase C alpha: elucidation of the membrane docking surface by site-directed fluorescence and spin labeling

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Mutagenesis of the gamma-carboxyglutamic acid domain of human factor VII to generate maximum enhancement of the membrane contact site

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Generalized-ensemble algorithms for molecular simulations of biopolymers

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Steered molecular dynamics and mechanical functions of 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=3341550

Conformation, localization, and integrin binding of talin depend on its interaction with phosphoinositides

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Structural basis of the membrane-targeting and unmasking mechanisms of the radixin FERM domain

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Enhancement of vitamin-K-dependent protein function by modification of the gamma-carboxyglutamic acid domain: studies of protein C and factor VII.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Manipulation of the membrane binding site of vitamin K-dependent proteins: enhanced biological function of human factor VII.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Docking phospholipase A2 on membranes using electrostatic potential-modulated spin relaxation magnetic resonance

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Modulation of GTPase activity of G proteins by fluid shear stress and phospholipid composition

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Concerted diffusion of lipids in raft-like membranes.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Distinct structural and adhesive roles of Ca2+ in membrane binding of blood coagulation factors

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Coarse-grained model simulations of mixed-lipid systems: composition and line tension of a stabilized bilayer edge.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Directed self-assembly of monodisperse phospholipid bilayer Nanodiscs with controlled size

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Lipid modulation of nicotinic acetylcholine receptor function: the role of membrane lipid composition and fluidity

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

A novel phosphatidylserine-binding peptide motif defined by an anti-idiotypic monoclonal antibody. Localization of phosphatidylserine-specific binding sites on protein kinase C and phosphatidylserine decarboxylase

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

The Local Phospholipid Environment Modulates the Activation of Blood Clotting

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Multiscale coarse graining of liquid-state systems

14 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3341550

Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel

14 November 2018

1 reference

12 December 2020

Atomistic simulation of hydrophobic matching effects on lipid composition near a helical peptide embedded in mixed-lipid bilayers

1 reference

12 December 2020

The actin-binding protein profilin binds to PIP2 and inhibits its hydrolysis by phospholipase C

1 reference

12 December 2020

Molecular dynamics simulation study of correlated motions in phospholipid bilayer membranes

1 reference

12 December 2020

Lipid-protein interactions in blood coagulation

1 reference

12 December 2020

Sequence-dependent interaction of β-peptides with membranes

1 reference

12 December 2020

A multiscale coarse-graining method for biomolecular systems

1 reference

12 December 2020

Tissue factor positions and maintains the factor VIIa active site far above the membrane surface even in the absence of the factor VIIa Gla domain. A fluorescence resonance energy transfer study

1 reference

12 December 2020

The membrane complex between transducin and dark-state rhodopsin exhibits large-amplitude interface dynamics on the sub-microsecond timescale: insights from all-atom MD simulations

1 reference

12 December 2020

Membrane poration by antimicrobial peptides combining atomistic and coarse-grained descriptions

1 reference

12 December 2020

10.1016/J.BPJ.2012.03.015

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22824277%20AND%20SRC:MED&resulttype=core&format=json

8 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22824277%20AND%20SRC:MED&resulttype=core&format=json

8 February 2020

PubMed publication ID

22824277

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22824277%20AND%20SRC:MED&resulttype=core&format=json