Evidence map›Paper›PMID 21806035›Full record

ArticleLangmuir : the ACS journal of surfaces and colloids2011

All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer.

Jason D Perlmutter, William J Drasler, Wangshen Xie, Jiali Gao, Jean-Luc Popot, Jonathan N Sachs

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Langmuir : the ACS journal of surfaces and colloids, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.

0numbers the graph read from it
0cells of the map it votes in
25citing papers in PubMed
3.9field-weighted citation impact, top 6% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

25 citing papers in PubMed, 62 citations in OpenAlex.

  1. Review
  2. Review
  3. Article
  4. The Martini Model in Materials Science.Advanced materials (Deerfield Beach, Fla.) · 2021
    Article
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  8. Review
  9. Article
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  14. Review
  15. Article
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  17. Article
  18. Amphipols for each season.The Journal of membrane biology · 2014
    Review
  19. Article
  20. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors at 3 institutions in 2 countries.

Jason D PerlmutterDepartment of Biomedical Engineering, 312 Church Street SE, University of Minnesota, Minneapolis, Minnesota 55455, USA.
William J Drasler
Wangshen Xie
Jiali Gao
Jean-Luc Popot
Jonathan N Sachs
Centre National de la Recherche Scientifique · FRTwin Cities Orthopedics · USUniversity of Minnesota · US

Funding

BIOMOLECULAR INTERACTIONS AND ENZYMATIC PROCESSESR01GM046736 · NIGMS · UNIVERSITY OF MINNESOTA TWIN CITIES · PI JIALI GAO · 1993 to 2026
$6.5M
KINESIN PHOSPHORYLATIONR01GM046376 · NIGMS · UNIVERSITY OF CALIFORNIA DAVIS · PI SCHOLEY, JONATHAN M · 1991 to 1994
–
NIGMS NIH HHS GM46376NIGMS NIH HHS R01 GM046736
6 · The paper itself

Abstract

Amphipathic polymers called amphipols (APols) have been developed as an alternative to detergents for stabilizing membrane proteins (MPs) in aqueous solutions. APols provide MPs with a particularly mild environment and, as a rule, keep them in a native functional state for longer periods than do detergents. Amphipol A8-35, a derivative of polyacrylate, is widely used and has been particularly well studied experimentally. In aqueous solutions, A8-35 molecules self-assemble into well-defined globular particles with a mass of ∼40 kDa and a R(g) of ∼2.4 nm. As a first step towards describing MP/A8-35 complexes by molecular dynamics (MD), we present three sets of simulations of the pure APol particle. First, we performed a series of all-atom MD (AAMD) simulations of the particle in solution, starting from an arbitrary initial configuration. Although AAMD simulations result in stable cohesive particles over a 45 ns simulation, the equilibration of the particle organization is limited. This motivated the use of coarse-grained MD (CGMD), allowing us to investigate processes on the microsecond time scale, including de novo particle assembly. We present a detailed description of the parametrization of the CGMD model from the AAMD simulations and a characterization of the resulting CGMD particles. Our third set of simulations utilizes reverse coarse-graining (rCG), through which we obtain all-atom coordinates from a CGMD simulation. This allows a higher-resolution characterization of a configuration determined by a long-timescale simulation. Excellent agreement is observed between MD models and experimental, small-angle neutron scattering data. The MD data provides new insight into the structure and dynamics of A8-35 particles, which is possibly relevant to the stabilizing effects of APols on MPs, as well as a starting point for modeling MP/A8-35 complexes.

Indexed as

Molecular Dynamics SimulationAcrylic ResinsMembrane ProteinsModels, MolecularAcrylic ResinsMembrane Proteins

Identifiers

PMID21806035
PMCPMC3214636
OpenAlexW2070231716

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.