Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations

Briefings in Bioinformatics
Bernhard KnappCharlotte M Deane

Abstract

The interaction between T-cell receptors (TCRs) and major histocompatibility complex (MHC)-bound epitopes is one of the most important processes in the adaptive human immune response. Several hypotheses on TCR triggering have been proposed. Many of them involve structural and dynamical adjustments in the TCR/peptide/MHC interface. Molecular Dynamics (MD) simulations are a computational technique that is used to investigate structural dynamics at atomic resolution. Such simulations are used to improve understanding of signalling on a structural level. Here we review how MD simulations of the TCR/peptide/MHC complex have given insight into immune system reactions not achievable with current experimental methods. Firstly, we summarize methods of TCR/peptide/MHC complex modelling and TCR/peptide/MHC MD trajectory analysis methods. Then we classify recently published simulations into categories and give an overview of approaches and results. We show that current studies do not come to the same conclusions about TCR/peptide/MHC interactions. This discrepancy might be caused by too small sample sizes or intrinsic differences between each interaction process. As computational power increases future studies will be able to and should ha...Continue Reading

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Citations

Dec 4, 2015·Journal of Chemical Information and Modeling·Bernhard Knapp, Charlotte M Deane
Aug 26, 2016·Biophysical Journal·Samuel DemharterPeter Minary
Jun 16, 2017·Journal of Chemical Theory and Computation·Bernhard KnappCharlotte M Deane
Nov 1, 2017·Nucleic Acids Research·Jinwoo LeemCharlotte M Deane
Oct 21, 2015·Scientific Reports·Alistair BaileyTim Elliott
Sep 10, 2019·PLoS Computational Biology·Bernhard KnappCharlotte M Deane
Aug 17, 2020·Proceedings of the National Academy of Sciences of the United States of America·Wonmuk HwangEllis L Reinherz
Jul 26, 2017·Frontiers in Immunology·R Charlotte EcclestonPeter V Coveney
Sep 2, 2017·Frontiers in Cellular and Infection Microbiology·Gisela Canedo-MarroquínAlexis M Kalergis
Feb 26, 2019·Scientific Reports·Jose Luis Dominguez, Bernhard Knapp
Mar 6, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Jayvee R AbellaLydia E Kavraki
Dec 25, 2019·Journal of Biomolecular Structure & Dynamics·Sunil Kumar Tripathi, Dinakar M Salunke
Dec 27, 2019·Computational Biology and Chemistry·Asuman BunsuzPemra Ozbek
Jun 29, 2021·Journal of Biomolecular Structure & Dynamics·Arne StrandJohann Deisenhofer
Aug 11, 2021·Journal of Chemical Information and Modeling·David R Bell, Serena H Chen
Jul 11, 2019·Journal of Chemical Information and Modeling·Rodrigo OchoaPilar Cossio
Oct 26, 2018·Journal of Chemical Theory and Computation·Bernhard KnappCharlotte M Deane
May 10, 2019·Journal of Chemical Information and Modeling·Samuel DemharterPeter Minary
May 5, 2018·Journal of Medicinal Chemistry·Cecilia LindgrenAnna Linusson
Nov 19, 2021·Journal of Chemical Theory and Computation·David R BellGuojing Cong

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