Evidence map›Paper›PMID 33850892›Full record

ArticleAnnals of translational medicine2021

Characterization of amino acid residues of T-cell receptors interacting with HLA-A*02-restricted antigen peptides.

Ying Zhu, Changxin Huang, Meng Su, Zuanmin Ge, Lanlan Gao, Yanfei Shi, Xuechun Wang, Jianfeng Chen

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

Article in Annals of translational medicine, 2021. 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
0.5field-weighted citation impact, top 39% 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

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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, 9 citations in OpenAlex.

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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

8 authors at 3 institutions in 1 country.

Ying ZhuDepartment of Oncology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.
Changxin HuangDepartment of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China.
Meng SuMaster Class, Zhejiang Chinese Medical University, Fourth School of Clinical Medicine, Hangzhou, China.
Zuanmin GeMaster Class, Hangzhou Normal University, School of Medicine, Hangzhou, China.
Lanlan GaoMaster Class, Hangzhou Normal University, School of Medicine, Hangzhou, China.
Yanfei ShiMaster Class, Hangzhou Normal University, School of Medicine, Hangzhou, China.
Xuechun WangMaster Class, Zhejiang Chinese Medical University, Fourth School of Clinical Medicine, Hangzhou, China.
Jianfeng ChenDepartment of Proctology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China.
Hangzhou Normal University · CNZhejiang Chinese Medical University · CNAffiliated Hospital of Hangzhou Normal University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe present study aimed to explore residues' properties interacting with HLA-A*02-restricted peptides on T-cell receptors (TCRs) and their effects on bond types of interaction and binding free energy.

methodsWe searched the crystal structures of HLA-A*02-restricted peptide-TCR complexes from the Protein Data Bank (PDB) database and subsequently collected relevant parameters. We then employed Schrodinger to analyze the bond types of interaction and Gromacs 2019 to evaluate the TCR-antigen peptide complex's molecular dynamics simulation. Finally, we compared the changes of bond types of interaction and binding free energy before and after residue substitution to ensure consistency of the conditions before and after residue substitution.

resultsThe main sites on the antigen peptides that formed the intermolecular interaction [hydrogen bond (HB) and pi stack] with TCRs were P4, P8, P2, and P6. The hydrophobicity of the amino acids inside or outside the disulfide bond of TCRs may be related to the intermolecular interaction and binding free energy between TCRs and peptides. Residues located outside the disulfide bond of TCR α or β chains and forming pi stack force played favorable roles in the complex intermolecular interaction and binding free energy. The residues of the TCR α or β chains that interacted with peptides were replaced by alanine (Ala) or glycine (Gly), and their intermolecular binding free energy of the complex had been improved. However, it had nothing to do with the formation of HB.

conclusionsThe findings of this study suggest that the hydrophobic nature of the amino acids inside or outside the disulfide bonds on the TCR may be associated with the intermolecular interaction and binding between the TCR and polypeptide. The residues located outside the TCR α or β single-chain disulfide bond and forming the pi-stack force showed a beneficial effect on the intermolecular interaction and binding of the complex. In addition, the part of the residues on the TCR α or β single chain that produced bond types of interaction with the polypeptide after being replaced by Ala or Gly, the intermolecular binding free energy of the complex was increased, regardless of whether HB was formed.

Indexed as

HLA-A*02-restricted antigensinteractionResidues of T-cell receptors (residues of TCRs)residue substitutionTCR-based immunotherapy

Identifiers

PMID33850892
PMCPMC8039679
OpenAlexW3139423142

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

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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.