Evidence map›Paper›PMID 31958546›Full record

ArticleBiochimica et biophysica acta. General subjects2020

The lac repressor hinge helix in context: The effect of the DNA binding domain and symmetry.

Danielle Seckfort, Gillian C Lynch, B Montgomery Pettitt

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Biochimica et biophysica acta. General subjects, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.3field-weighted citation impact, top 44% 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

2 citing papers in PubMed, 4 citations in OpenAlex.

  1. Article
  2. 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

3 authors at 1 institution in 1 country.

Danielle SeckfortStructural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston 77030, TX, USA; Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston 77555, TX, USA.
Gillian C LynchDepartment of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston 77555, TX, USA.
B Montgomery PettittStructural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston 77030, TX, USA; Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston 77555, TX, USA. Electronic address: mpettitt@utmb.edu.
The University of Texas Medical Branch at Galveston · US

Funding

Theory of Proteins and Peptides in SolutionR01GM037657 · NIGMS · UNIVERSITY OF TEXAS MED BR GALVESTON · PI PETTITT, BERNARD MONTGOMERY · 1988 to 2023
$5.5M
NIGMS NIH HHS R01 GM037657
6 · The paper itself

Abstract

The Lac system of genes has been an important model system in understanding gene regulation. When the dimer lac repressor protein binds to the correct DNA sequence, the hinge region of the protein goes through a disorder to order transition. The hinge region is disordered when binding to nonoperator sequences. This region of the protein must pay a conformational entropic penalty to order when it is bound to operator DNA. Structural studies show that this region is flexible. Previous simulations showed that this region is disordered when free in solution without the DNA binding domain present. Our simulations corroborate that this region is extremely flexible in solution, but we find that the presence of the DNA binding domain proximal to the hinge helix and salt make the ordered conformation more favorable even without DNA present.

Indexed as

DNA, BacterialEscherichia coliLac RepressorsMolecular Dynamics SimulationProtein ConformationThermodynamicsDNA, BacterialLac RepressorsDisordered proteinsDisorder to order transitionLacIMD simulationsMetadynamicsProteinSalt stability

Identifiers

PMID31958546
PMCPMC7366509
OpenAlexW2998945527

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.