Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulations (Q30481344)

14 August 2017

Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulations (English)

1 reference

14 August 2017

Andrea Catte

1

1 reference

14 August 2017

James C Patterson

2

1 reference

14 August 2017

Denys Bashtovyy

3

1 reference

14 August 2017

Martin K Jones

4

1 reference

14 August 2017

Feifei Gu

5

1 reference

14 August 2017

Ling Li

6

1 reference

14 August 2017

Aldo Rampioni

7

1 reference

14 August 2017

Durba Sengupta

8

1 reference

14 August 2017

Timo Vuorela

9

1 reference

14 August 2017

Perttu Niemelä

10

1 reference

14 August 2017

Mikko Karttunen

11

1 reference

14 August 2017

Siewert Jan Marrink

12

1 reference

14 August 2017

Ilpo Vattulainen

13

1 reference

14 August 2017

Jere P Segrest

14

1 reference

14 August 2017

language of work or name

English

0 references

publication date

7 December 2007

1 reference

14 August 2017

14

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inferred from page(s)

published in

Biophysical Journal

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14 August 2017

94

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14 August 2017

6

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14 August 2017

2306-2319

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

14 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Crystallographic R factor refinement by molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

The MARTINI force field: coarse grained model for biomolecular simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Novel changes in discoidal high density lipoprotein morphology: a molecular dynamics study.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Coarse grained protein-lipid model with application to lipoprotein particles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Insertion and assembly of membrane proteins via simulation.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Atomistic simulation studies of cholesteryl oleates: model for the core of lipoprotein particles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

ATP-binding cassette transporter A1: a cell cholesterol exporter that protects against cardiovascular disease

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Apolipoprotein structural organization in high density lipoproteins: belts, bundles, hinges and hairpins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Apolipoprotein structure and dynamics.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

HDL as a target in the treatment of atherosclerotic cardiovascular disease

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

A three-dimensional molecular model of lipid-free apolipoprotein A-I determined by cross-linking/mass spectrometry and sequence threading.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Formation and Metabolism of Prebeta-Migrating, Lipid-Poor Apolipoprotein A-I

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Influence of the HDL receptor SR-BI on lipoprotein metabolism and atherosclerosis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

High density lipoprotein structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Simulation of MscL gating in a bilayer under stress.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Comparative models for human apolipoprotein A-I bound to lipid in discoidal high-density lipoprotein particles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

ApoA-I structure on discs and spheres. Variable helix registry and conformational states

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Detailed molecular model of apolipoprotein A-I on the surface of high-density lipoproteins and its functional implications.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Structural models of human apolipoprotein A-I: a critical analysis and review

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

The impact of phospholipid transfer protein (PLTP) on HDL metabolism

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Lecithin cholesterol acyltransferase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Structure of low density lipoprotein (LDL) particles: basis for understanding molecular changes in modified LDL.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

The conformation of apolipoprotein A-I in high-density lipoproteins is influenced by core lipid composition and particle size: a surface plasmon resonance study

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Structure and function of apolipoprotein A-I and high-density lipoprotein

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Remodelling of high density lipoproteins by plasma factors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Molecular dynamics on a model for nascent high-density lipoprotein: role of salt bridges

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

A proposed architecture for lecithin cholesterol acyl transferase (LCAT): identification of the catalytic triad and molecular modeling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Predicting the structure of apolipoprotein A-I in reconstituted high-density lipoprotein disks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Crystal structure of truncated human apolipoprotein A-I suggests a lipid-bound conformation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

The molecular pathology of lecithin:cholesterol acyltransferase (LCAT) deficiency syndromes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

VMD: visual molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Conformation of the oleate chains in crystals of cholesteryl oleate at 123 K.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

The charge and structural stability of apolipoprotein A-I in discoidal and spherical recombinant high density lipoprotein particles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Apolipoproteins and the structural organization of plasma lipoproteins: human plasma high density lipoprotein-3

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Intermolecular contact between globular N-terminal fold and C-terminal domain of ApoA-I stabilizes its lipid-bound conformation: studies employing chemical cross-linking and mass spectrometry.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Role of cholesterol and polyunsaturated chains in lipid-protein interactions: molecular dynamics simulation of rhodopsin in a realistic membrane environment.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Double belt structure of discoidal high density lipoproteins: molecular basis for size heterogeneity

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Alpha-helix formation is required for high affinity binding of human apolipoprotein A-I to lipids

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: diffusion, free energy of hydration, and structural properties.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

The spatial organization of apolipoprotein A-I on the edge of discoidal high density lipoprotein particles: a mass specrometry study

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Molecular dynamics simulations on discoidal HDL particles suggest a mechanism for rotation in the apo A-I belt model

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Evidence that phospholipids play a key role in pre-beta apoA-I formation and high-density lipoprotein remodeling

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Influence of phospholipid depletion on the size, structure, and remodeling of reconstituted high density lipoproteins

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Evidence that cholesteryl ester transfer protein-mediated reductions in reconstituted high density lipoprotein size involve particle fusion

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2257918

Preparation and characterization of spheroidal, reconstituted high-density lipoproteins with apolipoprotein A-I only or with apolipoprotein A-I and A-II.

26 November 2018

1 reference

12 December 2020

Early incorporation of cell-derived cholesterol into pre-beta-migrating high-density lipoprotein

1 reference

12 December 2020

The conformation of apolipoprotein A-I in discoidal and spherical recombinant high density lipoprotein particles. 13C NMR studies of lysine ionization behavior

1 reference

12 December 2020

Interactions of synthetic peptide analogs of the class A amphipathic helix with lipids. Evidence for the snorkel hypothesis

1 reference

12 December 2020

Effect of cholesterol on the charge and structure of apolipoprotein A-I in recombinant high density lipoprotein particles

1 reference

12 December 2020

A detailed molecular belt model for apolipoprotein A-I in discoidal high density lipoprotein

1 reference

12 December 2020

Simulation of the Spontaneous Aggregation of Phospholipids into Bilayers

1 reference

12 December 2020

Characterization of lipoprotein particles isolated by immunoaffinity chromatography. Particles containing A-I and A-II and particles containing A-I but no A-II

1 reference

12 December 2020

Triglyceride-enrichment of high density lipoproteins enhances their remodelling by phospholipid transfer protein

1 reference

12 December 2020

10.1529/BIOPHYSJ.107.115857

Identifiers

DOI

1 reference

14 August 2017

1 reference

14 August 2017

PubMed publication ID

18065479

1 reference