Evidence map›Paper›PMID 25478971›Full record

ArticleJournal of structural biology2015

Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization.

R Lasala, N Coudray, A Abdine, Z Zhang, M Lopez-Redondo, R Kirshenbaum, J Alexopoulos, Z Zolnai, D L Stokes, I Ubarretxena-Belandia

Open access · greenAbstract read
In one paragraph

Article in Journal of structural biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
1.3field-weighted citation impact, top 21% 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

8 citing papers in PubMed, 12 citations in OpenAlex.

  1. Article
  2. Photocyclic behavior of rhodopsin induced by an atypical isomerization mechanism.Proceedings of the National Academy of Sciences of the United States of America · 2017
    Article
  3. Structure of the SLC4 transporter Bor1p in an inward-facing conformation.Protein science : a publication of the Protein Society · 2017
    Article
  4. Article
  5. Review
  6. Review
  7. Article
  8. 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

10 authors at 4 institutions in 1 country.

R LasalaNew York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA.
N CoudrayNew York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA.
A AbdineDepartment of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA.
Z ZhangNew York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA.
M Lopez-RedondoSkirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.
R KirshenbaumDepartment of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA.
J AlexopoulosSkirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.
Z ZolnaiDepartment of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA.
D L StokesNew York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA; Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.
I Ubarretxena-BelandiaNew York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA; Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA. Electronic address: Iban.Ubarretxena@mssm.edu.
New York Structural Biology Center · USIcahn School of Medicine at Mount Sinai · USNew York University · USUniversity of Wisconsin–Madison · US

Funding

UNIVERSITY OF WASHINGTONU54GM094598 · NIGMS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI STOKES, DAVID L. · 2010 to 2014
$8.3M
High-throughput Pipeline for Electron CrystallographyR01GM095747 · NIGMS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI STOKES, DAVID L. · 2010 to 2013
$1.2M
Acquisition of an electron cryo-microscope for structural biologyS10RR026473 · NCRR · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI UBARRETXENA, IBAN · 2011 to 2011
$500k
NCRR NIH HHS S10 RR026473NIGMS NIH HHS R01 GM095747NIGMS NIH HHS R01GM095747NIGMS NIH HHS U54 GM094598NIGMS NIH HHS U54GM094598
6 · The paper itself

Abstract

Electron crystallography is well suited for studying the structure of membrane proteins in their native lipid bilayer environment. This technique relies on electron cryomicroscopy of two-dimensional (2D) crystals, grown generally by reconstitution of purified membrane proteins into proteoliposomes under conditions favoring the formation of well-ordered lattices. Growing these crystals presents one of the major hurdles in the application of this technique. To identify conditions favoring crystallization a wide range of factors that can lead to a vast matrix of possible reagent combinations must be screened. However, in 2D crystallization these factors have traditionally been surveyed in a relatively limited fashion. To address this problem we carried out a detailed analysis of published 2D crystallization conditions for 12 β-barrel and 138 α-helical membrane proteins. From this analysis we identified the most successful conditions and applied them in the design of new sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Using these matrices we have run 19 crystallization screens for 16 different membrane proteins totaling over 1300 individual crystallization conditions. Six membrane proteins have yielded diffracting 2D crystals suitable for structure determination, indicating that these new matrices show promise to accelerate the success rate of membrane protein 2D crystallization.

Indexed as

CrystallizationDetergentsHydrogen-Ion ConcentrationLipidsMembrane ProteinsDetergentsLipidsMembrane Proteins96-well formatElectron cryomicroscopyElectron crystallographyHigh-throughput screeningMembrane proteinMembrane protein reconstitutionTwo-dimensional (2D) crystal

Identifiers

PMID25478971
PMCPMC4419781
OpenAlexW2018821149

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.