Exploring the different states of wild-type T-cell receptor and mutant conformational changes towards understanding the antigen recognition

Abstract

Recognition of proteolytic peptide fragments presented by major histocompatibility complex (MHC) on target cells by T-cell receptor (TCR) is among the most important interactions in the adaptive immune system. Several computational studies have been performed to investigate conformational and dynamical properties of TCRs for enhanced immunogenicity. Here, we present the large-scale molecular dynamics (MD) simulation studies of the two comprehensive systems consisting of the wild-type and mutant IG4 TCR in complex with the tumor epitope NY-ESO peptide (SLLMWITQC) and analyzed for mapping conformational changes of TCR in the states prior to antigen binding, upon antigen binding and after the antigen was released. All of the simulations were performed with different states of TCRs for each 1000 ns of simulation time, providing six simulations for time duration of 6000 ns (6µs). We show that rather than undergoing most critical conformational changes upon antigen binding, the high proportion of complementarity-determining region (CDR) loops change by comparatively small amount. The hypervariable CDRα3 and CDRβ3 loops showed significant structural changes. Interestingly, the TCR β chain loops showed the least changes, which is reliable with recent implications that β domain of TCR may propel antigen interaction. The mutant shows higher rigidity than wild-type even in released state; expose an induced fit mechanism occurring from the re-structuring of CDRα3 loop and can allow enhanced binding affinity of the peptide antigen. Additionally, we show that CDRα3 loop and peptide contacts are an adaptive feature of affinity enhanced mutant TCR.

Communicated by Ramaswamy H. Sarma

The wild-type has sampled significantly larger conformational changes than the mutant even in the released state.

Keywords:

• T-cell receptors
• Complementarity-determining region
• Molecular dynamics simulations
• Conformational changes
• Binding affinity

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

We acknowledge financial support from the Department of Biotechnology, Ministry of Science & Technology, Government of India. Sunil Kumar Tripathi is funded by a Young Investigator (YI) award from the Regional Centre for Biotechnology, Faridabad, India.