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The Synthesis of [Sn10SiSiMe334]2- Using a Metastable SnI Halide Solution Synthesized via a Co-condensation Technique
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The Hypervariable Loops of Free TCRs Sample Multiple Distinct Metastable Conformations in Solution.

James E Crooks1, Christopher T Boughter1, L Ridgway Scott2

  • 1Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, United States.

Frontiers in Molecular Biosciences
|November 29, 2018
PubMed
Summary

T cell receptor (TCR) dynamics reveal multiple states for antigen-binding loops in solution. These findings explain how TCRs search for and bind peptide-MHC complexes, impacting immune cell recognition.

Keywords:
T cell receptor dynamicsadaptive immunityindependent component (IC) analysisinnate immunitymarkov state modelsmolecular dynamics (MD)

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Area of Science:

  • Immunology
  • Structural Biology
  • Computational Biology

Background:

  • T cell receptor (TCR) interaction with peptide-MHC (pMHC) complexes is crucial for adaptive immunity.
  • While crystal structures show TCR-pMHC interactions, the dynamic conformational states of TCRs in solution remain poorly understood.
  • Understanding TCR dynamics is key to elucidating antigen recognition mechanisms.

Purpose of the Study:

  • To investigate the dynamic conformational states of T cell receptor Complementarity Determining Region (CDR) loops in solution.
  • To correlate these solution dynamics with TCR binding to peptide-MHC (pMHC) complexes.
  • To compare the dynamics of conventional αβ T cell receptors with invariant Natural Killer T cell receptors (iNKTCRs).

Main Methods:

  • All-atom molecular dynamics simulations of the 2C T cell receptor in explicit water.
  • Construction of Markov State Models for CDR3α and CDR3β loops.
  • Comparative simulations of the invariant Natural Killer T cell receptor (NKT15).

Main Results:

  • Markov State Models revealed multiple metastable conformational states for CDR3α and CDR3β loops in solution.
  • Simulated states reproduced known crystal conformations of CDR3β and identified novel conformations.
  • These findings suggest that bound TCR states arise from searching pre-existing equilibrium conformational states.
  • Invariant NKTCRs exhibit distinct but more restricted dynamic states compared to conventional TCRs.

Conclusions:

  • TCR CDR loops exist in multiple dynamic states in solution, facilitating pMHC binding.
  • The conformational flexibility of TCRs is essential for their promiscuous antigen recognition.
  • Distinct dynamic properties of iNKTCRs reflect their specialized recognition of CD1d ligands.