Evidence map›Paper›PMID 34302678›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2021

Poor Person's pH Simulation of Membrane Proteins.

Chitrak Gupta, Umesh Khaniya, John W Vant, Mrinal Shekhar, Junjun Mao, M R Gunner, Abhishek Singharoy

Abstract read
PubMed Publisher
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. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
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

1 citing paper in PubMed.

  1. Article
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

7 authors.

Chitrak GuptaThe School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.
Umesh KhaniyaDepartment of Physics, City College of New York, New York, NY, USA.
John W VantThe School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.
Mrinal ShekharCenter for Development of Therapeutics, Broad Institute, Cambridge, MA, USA.
Junjun MaoLevich Institute, City College of New York, New York, NY, USA.
M R GunnerDepartment of Physics, City College of New York, New York, NY, USA.
Abhishek SingharoyThe School of Molecular Sciences, Arizona State University, Tempe, AZ, USA. asinghar@asu.edu.

Funding

WHOLE CELL SIMULATIONP41GM104601 · NIGMS · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI TAJKHORSHID, EMAD · 2012 to 2021
$19.0M
Femtosecond nano-crystallography of membrane proteinsR01GM095583 · NIGMS · ARIZONA STATE UNIVERSITY-TEMPE CAMPUS · PI FROMME, PETRA · 2010 to 2023
$4.3M
Commodity Hardware Acceleration of Popular Modeling Software for Structural BioloR01GM098243 · NIGMS · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI SCHULTEN, KLAUS · 2011 to 2014
$1.2M
NIGMS NIH HHS P41 GM104601NIGMS NIH HHS R01 GM095583NIGMS NIH HHS R01 GM098243
6 · The paper itself

Abstract

pH conditions are central to the functioning of all biomolecules. However, implications of pH changes are nontrivial on a molecular scale. Though a rigorous microscopic definition of pH exists, its implementation in classical molecular dynamics (MD) simulations is cumbersome, and more so in large integral membrane systems. In this chapter, an integrative pipeline is described that combines Multi-Conformation Continuum Electrostatics (MCCE) computations with MD simulations to capture the effect of transient protonation states on the coupled conformational changes in transmembrane proteins. The core methodologies are explained, and all the software required to set up this pipeline are outlined with their key parameters. All associated analyses of structure and function are provided using two case studies, namely those of bioenergetic complexes: NADH dehydrogenase (complex I) and V

Indexed as

Hydrogen BondingHydrogen-Ion ConcentrationLigandsMembrane ProteinsNADH DehydrogenaseProtein ConformationProtonsSignal TransductionStatic ElectricityVacuolar Proton-Translocating ATPasesLigandsMembrane ProteinsNADH DehydrogenaseProtonsVacuolar Proton-Translocating ATPasesComplex IHydrogen bond networkMolecular dynamicsMulti-Conformation Continuum ElectrostaticsPotential of mean forceProton transferV-ATPase

Identifiers

PMID34302678

What OpenQuestion holds

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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.