ArticlePLoS computational biology2014
Large scale characterization of the LC13 TCR and HLA-B8 structural landscape in reaction to 172 altered peptide ligands: a molecular dynamics simulation study.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Article
- TheProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Peptide cargo tunes a network of correlated motions in human leucocyte antigens.The FEBS journal · 2020Article
- T cell receptor interactions with human leukocyte antigen govern indirect peptide selectivity for the cancer testis antigen MAGE-A4.The Journal of biological chemistry · 2020Article
- Methods for sequence and structural analysis of B and T cell receptor repertoires.Computational and structural biotechnology journal · 2020Review
- MHC binding affects the dynamics of different T-cell receptors in different ways.PLoS computational biology · 2019Article
- NMR: an essential structural tool for integrative studies of T cell development, pMHC ligand recognition and TCR mechanobiology.Journal of biomolecular NMR · 2019Article
- How peptide/MHC presence affects the dynamics of the LC13 T-cell receptor.Scientific reports · 2019Article
- Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring.Molecular immunology · 2018Article
- The Hypervariable Loops of Free TCRs Sample Multiple Distinct Metastable Conformations in Solution.Frontiers in molecular biosciences · 2018Article
- Article
- Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes.Current topics in medicinal chemistry · 2018Review
- Dynamical footprint of cross-reactivity in a human autoimmune T-cell receptor.Scientific reports · 2017Article
- DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles.BMC structural biology · 2017Article
- Modeling Functional Motions of Biological Systems by Customized Natural Moves.Biophysical journal · 2016Article
- Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo.Bioinformatics (Oxford, England) · 2016Article
- Matched Peptides: Tuning Matched Molecular Pair Analysis for Biopharmaceutical Applications.Journal of chemical information and modeling · 2015Article
- Quantitative Analysis of the Association Angle between T-cell Receptor Vα/Vβ Domains Reveals Important Features for Epitope Recognition.PLoS computational biology · 2015Article
- Examining variable domain orientations in antigen receptors gives insight into TCR-like antibody design.PLoS computational biology · 2014Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The interplay between T cell receptors (TCRs) and peptides bound by major histocompatibility complexes (MHCs) is one of the most important interactions in the adaptive immune system. Several previous studies have computationally investigated their structural dynamics. On the basis of these simulations several structural and dynamical properties have been proposed as effectors of the immunogenicity. Here we present the results of a large scale Molecular Dynamics simulation study consisting of 100 ns simulations of 172 different complexes. These complexes consisted of all possible point mutations of the Epstein Barr Virus peptide FLRGRAYGL bound by HLA-B*08:01 and presented to the LC13 TCR. We compare the results of these 172 structural simulations with experimental immunogenicity data. We found that simulations with more immunogenic peptides and those with less immunogenic peptides are in fact highly similar and on average only minor differences in the hydrogen binding footprints, interface distances, and the relative orientation between the TCR chains are present. Thus our large scale data analysis shows that many previously suggested dynamical and structural properties of the TCR/peptide/MHC interface are unlikely to be conserved causal factors for peptide immunogenicity.
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