Evidence map›Paper›PMID 20338183›Full record

ArticleJournal of molecular biology2010

Computational predictions of the mutant behavior of AraC.

Monica Berrondo, Jeffrey J Gray, Robert Schleif

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of molecular biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.8field-weighted citation impact, top 29% 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

3 citing papers in PubMed, 8 citations in OpenAlex.

  1. Review
  2. Article
  3. 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.

Monica BerrondoChemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA.
Jeffrey J Gray
Robert Schleif
Johns Hopkins University · US

Funding

Prediction of the Structure of Therapeutic Antibodies with their AntigensR01GM078221 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI GRAY, JEFFREY J · 2006 to 2020
$4.0M
REGULATORY MECHANISMS OF THE E COLI ARABINOSE OPERONR37GM018277 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI SCHLEIF, ROBERT F. · 1994 to 2004
$2.3M
REGULATORY MECHANISMS OF THE E COLI ARABINOSE OPERONR01GM018277 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI SCHLEIF, ROBERT F. · 1985 to 2009
$2.2M
Protein switches created by domain insertion: modeling, prediction, and design.F31GM081901 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI BERRONDO, MONICA · 2007 to 2009
$118k
BIOPHYSICS OF THE NUCLEOPROTEIN ACCESSORY PROTEIN NHP6AF32GM018277 · NIGMS · FOX CHASE CANCER CENTER · PI KATZ, DARIN S · 1996 to 1997
–
NIGMS NIH HHS F31 GM081901NIGMS NIH HHS F32 GM018277NIGMS NIH HHS GM018277NIGMS NIH HHS GM078221NIGMS NIH HHS GM081901NIGMS NIH HHS R01 GM018277NIGMS NIH HHS R01 GM078221NIGMS NIH HHS R37 GM018277
6 · The paper itself

Abstract

An algorithm implemented in Rosetta correctly predicts the folding capabilities of the 17-residue N-terminal arm of the AraC gene regulatory protein when arabinose is bound to the protein and the dramatically different structure of this arm when arabinose is absent. The transcriptional activity of 43 mutant AraC proteins with alterations in the arm sequences was measured in vivo and compared with their predicted folding properties. Seventeen of the mutants possessed regulatory properties that could be directly compared with folding predictions. Sixteen of the 17 mutants were correctly predicted. The algorithm predicts that the N-terminal arm sequences of AraC homologs fold to the Escherichia coli AraC arm structure. In contrast, it predicts that random sequences of the same length and many partially randomized E. coli arm sequences do not fold to the E. coli arm structure. The high level of success shows that relatively "simple" computational methods can in some cases predict the behavior of mutant proteins with good reliability.

Indexed as

ArabinoseAraC Transcription FactorComputer SimulationEscherichia coliEscherichia coli ProteinsGene ExpressionGene Expression ProfilingModels, BiologicalModels, MolecularMutant ProteinsProtein BindingProtein ConformationProtein FoldingArabinoseAraC protein, E coliAraC Transcription FactorEscherichia coli ProteinsMutant Proteins

Identifiers

PMID20338183
PMCPMC2873782
OpenAlexW2038880196

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.