Evidence map›Paper›PMID 26073186›Full record

ArticleNature communications2015

A network of molecular switches controls the activation of the two-component response regulator NtrC.

Dan K Vanatta, Diwakar Shukla, Morgan Lawrenz, Vijay S Pande

Abstract read
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In one paragraph

Article in Nature communications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.

0numbers the graph read from it
0cells of the map it votes in
26citing 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

26 citing papers in PubMed.

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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

4 authors.

Dan K VanattaDepartment of Chemistry, Stanford University, Stanford, California 94305, USA.
Diwakar Shukla1] Department of Chemistry, Stanford University, Stanford, California 94305, USA [2] SIMBIOS NIH Center for Biomedical Computation, Stanford University, Stanford, California 94305,USA [3] Department of Chemical and Bimolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illionios 61801, USA.
Morgan LawrenzDepartment of Chemistry, Stanford University, Stanford, California 94305, USA.
Vijay S Pande1] Department of Chemistry, Stanford University, Stanford, California 94305, USA [2] SIMBIOS NIH Center for Biomedical Computation, Stanford University, Stanford, California 94305,USA.

Funding

Physics-based Simulation of Biological Structures(RMI)U54GM072970 · NIGMS · STANFORD UNIVERSITY · PI ALTMAN, RUSS BIAGIO · 2004 to 2013
$33.5M
Topology, nucleation, and the protein folding barrierR01GM062868 · NIGMS · STANFORD UNIVERSITY · PI PANDE, VIJAY S · 2002 to 2018
$5.5M
NIGMS NIH HHS R01 GM062868NIGMS NIH HHS R01GM62828NIGMS NIH HHS U54 GM072970
6 · The paper itself

Abstract

Recent successes in simulating protein structure and folding dynamics have demonstrated the power of molecular dynamics to predict the long timescale behaviour of proteins. Here, we extend and improve these methods to predict molecular switches that characterize conformational change pathways between the active and inactive state of nitrogen regulatory protein C (NtrC). By employing unbiased Markov state model-based molecular dynamics simulations, we construct a dynamic picture of the activation pathways of this key bacterial signalling protein that is consistent with experimental observations and predicts new mutants that could be used for validation of the mechanism. Moreover, these results suggest a novel mechanistic paradigm for conformational switching.

Indexed as

Molecular Dynamics SimulationProtein Interaction MapsBacterial ProteinsMarkov ChainsModels, MolecularPII Nitrogen Regulatory ProteinsProtein Structure, TertiaryBacterial ProteinsPII Nitrogen Regulatory Proteins

Identifiers

PMID26073186

What OpenQuestion holds

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Registered trials

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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.