Evidence map›Paper›PMID 37662233›Full record

ArticlebioRxiv : the preprint server for biology2023

3D modeling of CpG DNA binding with matrix lumican shows leucine-rich repeat motif involvement as in TLR9-CpG DNA interactions.

Tansol Choi, George Maiti, Shukti Chakravarti

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

Article in bioRxiv : the preprint server for biology, 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
–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

0 citing papers in PubMed, 0 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

3 authors at 1 institution in 1 country.

Tansol ChoiDepartment of Ophthalmology, NYU Grossman School of Medicine, New York, NY 10016, USA.
George MaitiDepartment of Ophthalmology, NYU Grossman School of Medicine, New York, NY 10016, USA.
Shukti ChakravartiDepartment of Ophthalmology, NYU Grossman School of Medicine, New York, NY 10016, USA.
New York University · US

Funding

TGF beta and AKT signal-driven pathogenesis in keratoconusR01EY026104 · NEI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI Shukti Chakravarti · 2016 to 2026
$4.2M
Extracellular matrix proteoglycans regulate toll-like receptors 4 and 9 - Equipment SupplementR01EY030917 · NEI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI CHAKRAVARTI, SHUKTI · 2020 to 2023
$1.8M
NEI NIH HHS R01 EY026104NEI NIH HHS R01 EY030917
6 · The paper itself

Abstract

Lumican is an extracellular matrix proteoglycan, known to regulate toll-like receptor (TLR) signaling in innate immune cells. In experimental settings, lumican suppresses TLR9 signaling by binding to, and sequestering its synthetic ligand, CpG-DNA, in non-signal permissive endosomes. However, the molecular details of lumican interactions with CpG-DNA are obscure. Here, the 3-D structure of the 22 base-long CpG-DNA (CpG ODN_2395) bound to lumican or TLR9 were modeled using homology modeling and docking methods. Some of the TLR9-CpG ODN_2395 features predicted by our model are consistent with the previously reported TLR9-CpG DNA crystal structure, substantiating our current analysis. Our modeling indicated a smaller buried surface area for lumican-CpG ODN_2395 (1803 Å

Indexed as

CollagenCpG DNAExtracellular matrixInflammationLRR motifsLumicanProtein-DNA dockingTLR9

Identifiers

PMID37662233
PMCPMC10473624
OpenAlexW4386056178

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.