Evidence map›Paper›PMID 25456817›Full record

ArticleStructure (London, England : 1993)2014

Structural characterization of a flexible two-domain protein in solution using small angle X-ray scattering and NMR data.

Alexander Lemak, Bin Wu, Adelinda Yee, Scott Houliston, Hsiau-Wei Lee, Aleksandras Gutmanas, Xianyang Fang, Maite Garcia, Anthony Semesi, Yun-Xing Wang and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Structure (London, England : 1993), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Review
  3. The Protein Data Bank Archive.Methods in molecular biology (Clifton, N.J.) · 2021
    Review
  4. Review
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

12 authors.

Alexander LemakPrincess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada.
Bin WuPrincess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada.
Adelinda YeePrincess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada.
Scott HoulistonPrincess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada.
Hsiau-Wei LeeComplex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
Aleksandras GutmanasPrincess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada.
Xianyang FangProtein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702, USA.
Maite GarciaPrincess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada.
Anthony SemesiPrincess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada.
Yun-Xing WangProtein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702, USA.
James H PrestegardComplex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
Cheryl H ArrowsmithPrincess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada. Electronic address: carrow@uhnresearch.ca.

Funding

University of Georgia ProjectU54GM094597 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI ROST, BURKHARD · 2010 to 2014
$36.9M
SAXS FacilityZICBC011535 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI WANG, YUN XING M · 2014 to 2025
$7.5M
Canadian Institutes of Health ResearchNIGMS NIH HHS U54 GM094597
6 · The paper itself

Abstract

Multidomain proteins in which individual domains are connected by linkers often possess inherent interdomain flexibility that significantly complicates their structural characterization in solution using either nuclear magnetic resonance (NMR) spectroscopy or small-angle X-ray scattering (SAXS) alone. Here, we report a protocol for joint refinement of flexible multidomain protein structures against NMR distance and angular restraints, residual dipolar couplings, and SAXS data. The protocol is based on the ensemble optimization method principle (Bernadó et al., 2007) and is compared with different refinement strategies for the structural characterization of the flexible two-domain protein sf3636 from Shigella flexneri 2a. The results of our refinement suggest the existence of a dominant population of configurational states in solution possessing an overall elongated shape and restricted relative twisting of the two domains.

Indexed as

Magnetic Resonance SpectroscopyProtein ConformationScattering, Small AngleX-Ray DiffractionCrystallography, X-RayModels, MolecularProtein Structure, Tertiary

Identifiers

PMID25456817
PMCPMC5046226

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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.