Human Cytomegalovirus variant peptides adapt by decreasing their total coordination upon binding to a T cell receptor

Abstract

The tertiary structure of the native Cytomegalovirus peptide (NLV) presented by HLA-A2 and bound to the RA14 T cell receptor was used as a reference for the calculation of atomic coordination differences of both the NLV as well as of a number of singly substituted NLV variants in the absence of TCR. Among the pMHC complexes, the native peptide was found to exhibit the highest total coordination difference in respect to the reference structure, suggesting that it experienced the widest structural adaptation upon recognition by the TCR. In addition, the peptide on the isolated NLV-MHC complex was over-coordinated as compared to the rest of the variants. Moreover, the trend was found to account for a set of measured dissociation constants and critical concentrations for target-cell lysis for all variants in complexation with RA14: functionally, all variant peptides were established to be either weak agonists or null peptides, while, at the same time, our current study established that they were also under-coordinated in respect to NLV. It could, thus, be argued that the most ‘efficient’ structural adaptation upon pMHC recognition by the TCR requires of the peptide to undergo the widest under-coordination possible. The main structural characteristic which differentiated the NLV in respect to the variants was a the presence of 16 oxygen atoms (waters) in the former׳s second coordination shell which accounted for over-coordination of roughly 100% and 30% in the O–O and C–O partials respectively. In fact, in the absence of second shell oxygens, the NLV peptide was decidedly under-coordinated in respect to all of the variants, as also suggested by the C–C partial.

The coordination of unprotonated peptide tertiary structure as a metric of pMHC–TCR functional avidity

“…Additionally, gas-phase molecular orbital interactions on protonated tertiary structures revealed that the atomic coordination of agonist peptides resulted in the presence of a stable ammonium group on their N termini which was altogether unattainable for antagonists, and this finding was consistent across the range of conditions studied in regard to peptide formal charge and protonation of side chain groups [5,6] . Interestingly, we also attained data indicating that the atomic coordination of the peptide on the isolated pMHC (in the absence of TCR) may also serve as a metric of functional avidity, as we reported for the case of human cytomegalovirus (HCMV) variants [7] .…”

“…For all peptide structures, the Pair Distribution Function (PDF) and the Radial Distribution Function (RDF) and were calculated as described in our precursor work [5–7] , followed by integration of the RDF which yielded the total and partial atomic coordination. The procedure involved the initial calculation of the histogram of interatomic distances.…”

“…For every pair of atoms i and j ( i ≠ j ) on the peptide, their interatomic distance was calculated as where x , y and z are atomic Cartesian coordinates. Calculation of the peptide Pair Distribution Function (PDF, symbolized as g(r)) is in respect to the real space coordinate, r ; for the calculation, real space itself is segmented into bins, each bin of a size (width) equal to 0.1 °A Choice of the most appropriate bin size is a matter of experimentation and is particular to the system under investigation [5–7] . On the basis of the interatomic distances, the corresponding histogram, h ( r ), may then be constructed as where N is the number of peptide atoms and δ is the Dirac delta function.…”

Atomic Coordination Reflects Peptide Immunogenicity

“…Previously we established that cumulative coordination difference of the protonated variant peptides in respect to the index is correlated to immunological identity (Antipas and Germenis, 2015a , b , c , d ) and, more precisely, that cumulative under-coordination is characteristic of the antagonist; at this point we inquire if this might additionally hold true for unprotonated structures and the results are shown in Figure 4 , for the cases of the isolated peptides, the cleft environment up to 7 Å from each peptide and the entire pMHC-TCR complex. Both the total PDF (Figure 4A ) and the C-C partial (Figure 4B ) were found to be correlated to peptide immunological identity (i.e., antagonist peptides were under-coordinated in respect to Tax), in agreement with our previous results of protonated structures; in contrast, he rest of the PDF partials (Figures 4C–F ) were not relevant.…”

“…Coordination refers to atomic structure and expresses the tendency of atoms to be surrounded by other atoms (the coordination number indicates the number of atoms surrounding a reference atom). The calculation of atomic coordination is based on the initial formulation of a histogram of interatomic interactions, via calculation of the distances between all atom pairs and the assignment of these distances to bins of a predefined size (e.g., 0.1 Å; choice of the most appropriate bin size is a matter of experimentation (Antipas and Germenis, 2015a , b , c , d ) but does not affect the results if chosen to be sufficiently small). By convention, the ith bin is assigned all interatomic distances, R, within the range r < R < r + Δr, where r = i * Δ r and Δr is the bin size.…”