Large scale characterization of the LC13 TCR and HLA-B8 structural landscape in reaction to 172 altered peptide ligands: a molecular dynamics simulation study

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.

Figure 1. Visualisation of the individual components of the TCR/peptide/MHC interaction.

Rendering is based on PDB accession code 1mi5 . Blue: peptide; White cartoon and transparent surface: MHC; Red: CDR1; Green: CDR2; Yellow: CDR3. The upper CDRs belong to the TCR α-chain while the lower ones belongs to the TCR β-chain. The α ₃ region of the MHC, the β ₂ microglobulin, and the variable and constant regions of the TCR are not visualized but were also included in our study.

Figure 2. Comparison of the peptide/MHC and pMHC/TCR binding affinity distributions between groupM and groupL.

(A) Binding affinity between the peptide and MHC measured by XScore. Although there are differences in the distributions, only 54% of the permutation tests show less overlap. The difference in the mean-values is larger but also not above our 90% threshold (see methods). (B) Binding affinity between the pMHC and TCR measured by Irad. (C) Binding affinity between the pMHC and TCR measured by ZRank.

Figure 3. Hydrogen bond footprints of the 100 ns MD simulations of groupM and groupL.

The normalized frequency of occurring H-bonds over simulation time is shown. The frequency is zero if no H-bond is present in any frame of any of the simulations of the group. The frequency is one if one H-bond is present in each frame of every simulation of the group. The value can exceed one if in average more than one H-bond is present in a residue. (A) H-bonds between the peptide and the MHC. (B) H-bonds between the peptide and the TCR. (C) H-bonds between the two chains of the TCR and the MHC. The six CDRs are marked with dashed lines. (D) H-bonds between the MHC and the two TCR chains. The helices are marked with dashed lines.

Figure 4. Solvent accessible surface areas (nm²) of the TCRpMHC interface during the 100 ns simulations.

(A–F) The six CDRs of the TCR. (G) Peptide bound between MHC and TCR. (H) Helix 1 of the MHC. (I) Helix 2 of the MHC.

Figure 5. RMSF of the CDRs, peptide and MHC helices over simulation time.

The solid lines indicate the mean values of groupM (red) and groupL (blue). The dotted lines are the mean +/− the standard error of the mean. The results are based on the backbone atoms only. If all atoms are taken into account the overall shape of the RMSF plots is similar, however, slightly more unstable (data not shown). (A–F) RMSF of the 6 CDRs. (G) RMSF of the peptide. (H,I) RMSF of the two MHC helices.

Figure 6. Distances in the TCRpMHC interface (nanometer) as measured over simulation time.

(A–C) Distributions of the distances between the central kink residue of helix 1 and the three CDRs of the TCR β-chain (D–F) Distributions of the distances between the central kink residue of helix 2 and the three CDRs of the TCR α-chain (G–I) Distributions of the distances at the begin, middle, and end of the MHC binding groove (J,K) Distributions of the distances between the central residue of the peptide and the two CDR3s (L,M) Distributions of the distances between the first residue of the peptide and the two CDR3s (N,O) Distributions of the distances between the last residue of the peptide and the two CDR3s (P) Distribution of the distances between peptide mean and the mean of both CDR3s (Q) 3D representation of the 16 distances. Orange: TCR α-chain; black: TCR β-chain; white: MHC; blue: peptide; red: distances illustrated in A–P. The MHC helix 2 and the C-terminal end of the peptide are depicted in the foreground.

Figure 7. Relative orientation of the TCR chains as measured by the ABangle package.

(A) BA: torsion angle between Vα and Vβ chain (B) BC1: tilting angle of Vβ (C) BC2: twisting-like angle of Vβ (D) AC1: tilting angle of Vα (E) AC2: twisting-like angle of Vα (F) DC: distance between the variable part of the α and β-chain in nanometer.