Molecular Dynamics Simulation of Lipid-Modified Signaling Proteins.

Vinay V Nair, Alemayehu A Gorfe

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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact, top 87% 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

0 citing papers in PubMed, 0 citations in OpenAlex.

No citing paper in PubMed yet.

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

2 authors at 1 institution in 1 country.

Vinay V NairDepartment of Integrative Biology & Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.

Alemayehu A GorfeDepartment of Integrative Biology & Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA. Alemayehu.G.Abebe@uth.tmc.edu.

The University of Texas Health Science Center at Houston · US

Funding

Decoding the structures and lipid binding specificity of small GTPase membrane anchorsR01GM124233 · NIGMS · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI GORFE, ALEMAYEHU A., HANCOCK, JOHN F · 2018 to 2021

$1.3M

NIGMS NIH HHS R01 GM124233

6 · The paper itself

Abstract

In this chapter, we provide a practical guide on how to plan, execute, and interpret atomistic and coarse-grained molecular dynamics (MD) simulations of lipid-modified proteins in model membranes. After outlining some key practical considerations when planning such simulations, we survey resources and techniques to obtain force field parameters for nonconventional amino acids, such as posttranslationally lipid-modified amino acids that are unique to this class of proteins. We then describe the protocols to build, setup, and run the simulations, followed by a brief comment on the analysis and interpretation of the simulations. Finally, examples of insights that could be gained from atomistic and coarse-grained MD simulations of lipidated proteins will be provided, using RAS proteins as illustrative examples. Throughout the chapter, we highlight the main advantages and limitations of simulating RAS and related lipid-modified G-proteins in biomimetic membranes.

Indexed as

Amino AcidsBiochemical PhenomenaLipid BilayersMolecular Dynamics SimulationSignal TransductionAmino AcidsLipid BilayersG-proteinsLipidated proteinsLipid bilayerMembraneMolecular dynamics simulation

Identifiers

PMID34302675

DOI10.1007/978-1-0716-1468-6_9

PMCPMC8961723

OpenAlexW3185337138

What OpenQuestion holds

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LicenceTDM

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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.