(Q41960466)

14 October 2017

Aggregation of lipid-anchored full-length H-Ras in lipid bilayers: simulations with the MARTINI force field (English)

1 reference

14 October 2017

0 references

Hualin Li

1

1 reference

14 October 2017

Alemayehu A Gorfe

series ordinal

2

1 reference

14 October 2017

language of work or name

English

0 references

publication date

26 July 2013

1 reference

14 October 2017

1 reference

14 October 2017

8

1 reference

14 October 2017

7

1 reference

14 October 2017

e71018

1 reference

Creative Commons Attribution 4.0 International

14 October 2017

start time

26 July 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Using the Wimley-White Hydrophobicity Scale as a Direct Quantitative Test of Force Fields: The MARTINI Coarse-Grained Model

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Martini Force Field Parameters for Glycolipids.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

NMR-based functional profiling of RASopathies and oncogenic RAS mutations.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Defining the membrane-associated state of the PTEN tumor suppressor protein.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

N-Ras forms dimers at POPC membranes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Coarse-grain simulations reveal movement of the synaptobrevin C-terminus in response to piconewton forces.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Formation and domain partitioning of H-ras peptide nanoclusters: effects of peptide concentration and lipid composition

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

What drives the clustering of membrane-bound Ras?

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Organization, dynamics, and segregation of Ras nanoclusters in membrane domains

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Revealing conformational substates of lipidated N-Ras protein by pressure modulation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Solution structure of the state 1 conformer of GTP-bound H-Ras protein and distinct dynamic properties between the state 1 and state 2 conformers

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Role of lipids in spheroidal high density lipoproteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Conformational states of human rat sarcoma (Ras) protein complexed with its natural ligand GTP and their role for effector interaction and GTP hydrolysis

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Polarizable water model for the coarse-grained MARTINI force field

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Ras membrane orientation and nanodomain localization generate isoform diversity

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Location, tilt, and binding: a molecular dynamics study of voltage-sensitive dyes in biomembranes.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

The molecular face of lipid rafts in model membranes.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Mechanisms of Ras membrane organization and signalling: Ras on a rocker.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Water-membrane partition thermodynamics of an amphiphilic lipopeptide: an enthalpy-driven hydrophobic effect

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Fast procedure for reconstruction of full-atom protein models from reduced representations.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Ras nanoclusters: molecular structure and assembly

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Free energy profile of H-ras membrane anchor upon membrane insertion

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

H-ras protein in a bilayer: interaction and structure perturbation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Flexibility of ras lipid modifications studied by 2H solid-state NMR and molecular dynamics simulations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

The lipidated membrane anchor of full length N-Ras protein shows an extensive dynamics as revealed by solid-state NMR spectroscopy

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

H-ras, K-ras, and inner plasma membrane raft proteins operate in nanoclusters with differential dependence on the actin cytoskeleton

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Lipid modifications of a Ras peptide exhibit altered packing and mobility versus host membrane as detected by 2H solid-state NMR.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Ras signaling from plasma membrane and endomembrane microdomains

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

The Ras superfamily at a glance

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Three separable domains regulate GTP-dependent association of H-ras with the plasma membrane

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Signaling specificity by Ras family GTPases is determined by the full spectrum of effectors they regulate

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Ras proteins: different signals from different locations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Membrane insertion of a lipidated ras peptide studied by FTIR, solid-state NMR, and neutron diffraction spectroscopy

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Ras-effector interactions: after one decade

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Direct visualization of Ras proteins in spatially distinct cell surface microdomains

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Guanine nucleotide exchange factors for Rho GTPases: turning on the switch

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

The guanine nucleotide-binding switch in three dimensions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Identification and characterization of RA-GEF-2, a Rap guanine nucleotide exchange factor that serves as a downstream target of M-Ras

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Four human ras homologs differ in their abilities to activate Raf-1, induce transformation, and stimulate cell motility

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Comparative protein modeling by satisfaction of spatial restraints

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

VMD: visual molecular dynamics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

All ras proteins are polyisoprenylated but only some are palmitoylated

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

The MARTINI Coarse-Grained Force Field: Extension to Proteins.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Multi-scale simulation of the simian immunodeficiency virus fusion peptide.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Membrane lateral structure: the influence of immobilized particles on domain size

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Molecular view of cholesterol flip-flop and chemical potential in different membrane environments.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Structure and dynamics of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Visualizing association of N-ras in lipid microdomains: influence of domain structure and interfacial adsorption

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

The linker domain of the Ha-Ras hypervariable region regulates interactions with exchange factors, Raf-1 and phosphoinositide 3-kinase

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

The role of G-domain orientation and nucleotide state on the Ras isoform-specific membrane interaction

18 August 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0071018

The Lipid Modifications of Ras that Sense Membrane Environments and Induce Local Enrichment

21 January 2018

2 references

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0071018

21 January 2018

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3724741

Structural Model of the Membrane-Bound C Terminus of Lipid-Modified Human N-Ras Protein

3 November 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0071018

G Protein-Coupled Receptors Self-Assemble in Dynamics Simulations of Model Bilayers

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0071018

Suitability of the MARTINI Force Field for Use with Gas-Phase Protein Complexes

21 January 2018

1 reference

12 December 2020

From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations

1 reference

12 December 2020

Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields

1 reference

12 December 2020

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

1 reference

12 December 2020

Ras isoforms vary in their ability to activate Raf-1 and phosphoinositide 3-kinase

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0071018

Identifiers

DOI

1 reference

14 October 2017

0 references

1 reference

14 October 2017

PubMed publication ID

23923044

1 reference