Evidence map›Paper›PMID 36940840›Full record

ArticleMethods (San Diego, Calif.)2023

Site-specific incorporation of biophysical probes into NF-ĸB with non-canonical amino acids.

Wei Chen, Tristan R Gunther, Hannah E R Baughman, Elizabeth A Komives

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

Article in Methods (San Diego, Calif.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
0.1field-weighted citation impact, top 57% 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

0 citing papers in PubMed, 1 citations in OpenAlex.

No citing paper in PubMed yet.

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

4 authors at 1 institution in 1 country.

Wei ChenDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA. Electronic address: wzc5386@psu.edu.
Tristan R GuntherDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
Hannah E R BaughmanDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
Elizabeth A KomivesDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA. Electronic address: ekomives@ucsd.edu.
University of California San Diego · US

Funding

UCSD/SDSU IRACDAK12GM068524 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI TREJO, JOANN · 2003 to 2025
$24.4M
STRUCTURE AND STABILITY OF IKB/NF-KB COMPLEXESP01GM071862 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI HOFFMANN, ALEXANDER · 2006 to 2016
$14.9M
MOLECULAR BIOPHYSICS TRAINING PROGRAMT32GM008326 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI KOMIVES, ELIZABETH A. · 1989 to 2020
$7.5M
Molecular Biophysics Training Grant at UC San DiegoT32GM139795 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Galia Debelouchina, ELIZABETH A. KOMIVES · 2021 to 2026
$3.0M
The landscape of NFκB transcription dynamicsR01GM141182 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI KOMIVES, ELIZABETH A., WOLYNES, PETER GUY · 2022 to 2025
$2.3M
NIGMS NIH HHS K12 GM068524NIGMS NIH HHS P01 GM071862NIGMS NIH HHS R01 GM141182NIGMS NIH HHS T32 GM008326NIGMS NIH HHS T32 GM139795
6 · The paper itself

Abstract

The transcription factor NF-ĸB is a central mediator of immune and inflammatory responses. To understand the regulation of NF-ĸB, it is important to probe the underlying thermodynamics, kinetics, and conformational dynamics of the NF-ĸB/IĸBα/DNA interaction network. The development of genetic incorporation of non-canonical amino acids (ncAA) has enabled the installation of biophysical probes into proteins with site specificity. Recent single-molecule FRET (smFRET) studies of NF-ĸB with site-specific labeling via ncAA incorporation revealed the conformational dynamics for kinetic control of DNA-binding mediated by IĸBα. Here we report the design and protocols for incorporating the ncAA p-azidophenylalanine (pAzF) into NF-ĸB and site-specific fluorophore labeling with copper-free click chemistry for smFRET. We also expanded the ncAA toolbox of NF-ĸB to include p-benzoylphenylalanine (pBpa) for UV crosslinking mass spectrometry (XL-MS) and incorporated both pAzF and pBpa into the full-length NF-ĸB RelA subunit which includes the intrinsically disordered transactivation domain.

Indexed as

Amino AcidsNF-kappa BAzidesBenzophenonesPhenylalanine4-azidophenylalanine4-benzoylphenylalanineAmino AcidsAzidesBenzophenonesNF-kappa BPhenylalanineClick chemistryCrosslinking mass spectrometryNF-ĸBNon-canonical amino acidsSingle-molecule FRETSite-specific labeling

Identifiers

PMID36940840
PMCPMC10688598
OpenAlexW4327919407

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.