Hello friends of OPIG,
From my last blopig blog post [link: https://www.blopig.com/blog/2019/10/comparative-analysis-of-the-cdr-loops-of-antigen-receptors/], I summarised our findings that TCR CDRs are more flexible than their antibody counterparts. Because of this observation, we believe that it is more appropriate to represent TCR binding sites using an ensemble of conformations.
Continue readingAllow me to present our recently accepted paper: Comparative analysis of the CDR loops of antigen receptors, to appear in Frontiers in Immunology [1]. In the blog post I will give a quick five-minute summary of the key messages in this work.
Continue readingAt this week’s journal club I presented my latest results on the effect of the constant regions of antibodies (ABs) and T-cell receptors (TCRs) on the dynamics of the overall system. Not including constant regions in such simulations is a commonly used simplification that is found throughout the literature. This is mainly due a massive saving in computational runtime as illustrated below: 
The constant regions contain about 210 residues but an additional speed up comes from the much smaller solvation box. If a cubic solvation box is used then the effect is even more severe:
But the question is: “Is is OK to remove the constant regions of an AB or TCR and simulate without them?”.
Using replica simulations we found that simulations with and without constant regions lead to (on average) significantly different results. The detail of our analysis will soon be submitted to a scientific journal. The current working title is “Why constant regions are essential in antibody and T-cell receptor Molecular Dynamics simulations”.