Evidence map›Paper›PMID 26512108›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2015

Transient conformers of LacY are trapped by nanobodies.

Irina Smirnova, Vladimir Kasho, Xiaoxu Jiang, Els Pardon, Jan Steyaert, H Ronald Kaback

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

Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
2.7field-weighted citation impact, top 10% 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

15 citing papers in PubMed, 26 citations in OpenAlex.

  1. Article
  2. Article
  3. Exploring cellular biochemistry with nanobodies.The Journal of biological chemistry · 2020
    Review
  4. Article
  5. Plant glucose transporter structure and function.Pflugers Archiv : European journal of physiology · 2020
    Review
  6. Article
  7. It takes two to tango: The dance of the permease.The Journal of general physiology · 2019
    Review
  8. Engineered occluded apo-intermediate of LacY.Proceedings of the National Academy of Sciences of the United States of America · 2018
    Article
  9. Crystal Structure of a ligand-bound LacY-Nanobody Complex.Proceedings of the National Academy of Sciences of the United States of America · 2018
    Article
  10. Article
  11. Nanobodies to Study G Protein-Coupled Receptor Structure and Function.Annual review of pharmacology and toxicology · 2017
    Review
  12. Emulating proton-induced conformational changes in the vesicular monoamine transporter VMAT2 by mutagenesis.Proceedings of the National Academy of Sciences of the United States of America · 2016
    Article
  13. Crystal structure of a LacY-nanobody complex in a periplasmic-open conformation.Proceedings of the National Academy of Sciences of the United States of America · 2016
    Article
  14. Article
  15. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

6 authors at 3 institutions in 2 countries.

Irina SmirnovaDepartment of Physiology, University of California, Los Angeles, CA 90095-7327;
Vladimir KashoDepartment of Physiology, University of California, Los Angeles, CA 90095-7327;
Xiaoxu JiangDepartment of Physiology, University of California, Los Angeles, CA 90095-7327;
Els PardonStructural Biology Research Center; VIB, 1050 Brussel, Belgium, Vrije Universiteit Brussel, 1050 Brussel, Belgium;
Jan SteyaertStructural Biology Research Center, VIB, 1050 Brussel, Belgium, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussel, Belgium; rkaback@mednet.ucla.edu jan.steyaert@vub.ac.be.
H Ronald KabackDepartment of Physiology, University of California, Los Angeles, CA 90095-7327; Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095-7327; Molecular Biology Institute, University of California, Los Angeles, CA 90095-7327 rkaback@mednet.ucla.edu jan.steyaert@vub.ac.be.
University of California, Los Angeles · USVIB-VUB Center for Structural Biology · BEVrije Universiteit Brussel · BE

Funding

NEW APPROACHES TO MEMBRANE PROTEIN STRUCTURESR01DK051131 · NIDDK · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI KABACK, HOWARD RONALD · 1996 to 2014
$5.2M
Dynamics of the Lactose Permease of Escherichia ColiR56DK051131 · NIDDK · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI KABACK, HOWARD RONALD · 2015 to 2015
$154k
NIDDK NIH HHS DK51131NIDDK NIH HHS R01 DK051131NIDDK NIH HHS R56 DK051131
6 · The paper itself

Abstract

The lactose permease of Escherichia coli (LacY), a highly dynamic membrane protein, catalyzes symport of a galactopyranoside and an H(+) by using an alternating access mechanism, and the transport cycle involves multiple conformational states. Single-domain camelid nanobodies (Nbs) developed against a LacY mutant immobilized in an outward (periplasmic)-open conformation bind to the flexible WT protein and stabilize the open-outward conformation(s). Here, we use site-directed, distance-dependent Trp quenching/unquenching of fluorescent probes inserted on opposite surfaces of LacY to assess the conformational states of the protein complexed with each of eight unique Nbs that bind exclusively to the periplasmic side and block transport, but increase the accessibility of the sugar-binding site. Nb binding involves conformational selection of LacY molecules with exposed binding epitopes. Each of eight Nbs induces quenching with three pairs of cytoplasmic Trp/fluorophore probes, indicating closing of cytoplasmic cavity. In reciprocal fashion, the same Nbs induce unquenching of fluorescence in three pairs of periplasmic probes due to opening of the periplasmic cavity. Because the extent of fluorescence change with various Nbs differs and the differences correlate with changes in the rate of sugar binding, it is also concluded that the Nbs stabilize several different outward-open conformations of LacY.

Indexed as

Escherichia coli ProteinsMonosaccharide Transport ProteinsProtein ConformationSingle-Domain AntibodiesSymportersEscherichia coli ProteinsLacY protein, E coliMonosaccharide Transport ProteinsSingle-Domain AntibodiesSymportersalternating accessconformerslactose permeasemembrane transport proteinsnanobodies

Identifiers

PMID26512108
PMCPMC4653160
OpenAlexW2199392553

What OpenQuestion holds

Textmetadata
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.