Structural and Dynamical Insights on HLA-DR2 Complexes That Confer Susceptibility to Multiple Sclerosis in Sardinia: A Molecular Dynamics Simulation Study

<div><p>Sardinia is a major Island in the Mediterranean with a high incidence of multiple sclerosis, a chronic autoimmune inflammatory disease of the central nervous system. Disease susceptibility in Sardinian population has been associated with five alleles of major histocompatibility complex (MHC) class II DRB1 gene. We performed 120 ns of molecular dynamics simulation on one predisposing and one protective alleles, unbound and in complex with the two relevant peptides: Myelin Basic Protein and Epstein Barr Virus derived peptide. In particular we focused on the MHC peptide binding groove dynamics. The predisposing allele was found to form a stable complex with both the peptides, while the protective allele displayed stability only when bound with myelin peptide. The local flexibility of the MHC was probed dividing the binding groove into four compartments covering the well known peptide anchoring pockets. The predisposing allele in the first half cleft exhibits a narrower and more rigid groove conformation in the presence of myelin peptide. The protective allele shows a similar behavior, while in the second half cleft it displays a narrower and more flexible groove conformation in the presence of viral peptide. We further characterized these dynamical differences by evaluating H-bonds, hydrophobic and stacking interaction networks, finding striking similarities with super-type patterns emerging in other autoimmune diseases. The protective allele shows a defined preferential binding to myelin peptide, as confirmed by binding free energy calculations. All together, we believe the presented molecular analysis could help to design experimental assays, supports the molecular mimicry hypothesis and suggests that propensity to multiple sclerosis in Sardinia could be partly linked to distinct peptide-MHC interaction and binding characteristics of the antigen presentation mechanism.</p> </div

Binding free energies calculations for peptide-MHC complexes.

<p>Predisposing (*15:01) and protective (*16:01) alleles bound to MBP and EBNA-1. In column 2 is reported the binding free energies (kcal/mol), in column 3 is reported their corresponding IC₅₀ values and in column 4 is reported the IC₅₀ scaled by the allele specific MBP IC₅₀.</p

RMSD time plot.

<p>C-alpha root mean square deviation variation with respect to initial frame obtained during long MD simulations, on the selected binding residues of (A) *15:01 allele and (B) *16:01 allele.</p

Configurational entropies.

<p>Entropy contributions to the free energies calculated on binding site residues for the free and bound MHC.</p

MBP-MHC H-bonds.

<p>Persistence of hydrogen bonds formed between MBP 85–98 peptide and the chain β1 5–90 residues of allele *15:01 (in blue) and *16:01 (in green), during long MD simulation of 120 ns.</p

MHC-peptide Interaction Network.

<p>Persistent H-bonds (in green, ball representation), hydrophobic (in grey, surf representation) and stacking (in pink, ball-stick representation) interactions present during MD simulations for (A)*15:01-MBP (B)*15:01-EBNA-1 (C) *16:01-MBP and (D)*16:01-EBNA-1 complexes.</p

Peptide-MHC class II simulation lengths.

<p>Summary of MHC-peptide complexes modeled with different force fields (C27-FF and A99-FF). MD simulation on free MHC system was done using only C27-FF.</p

Peptide structure inside binding groove.

<p>(A) MBP 85–98 epitope, (B) EBNA-1 400–413 epitope.</p

Pockets and four compartments of MHC class II binding groove.

<p>(A) The MHC cleft is shown using cartoon representation. The backbone of MBP peptide is shown in cartoon and the C-alpha atoms in sphere representations. The residues forming the pockets are shown in Van der Waals representation. (B) Region D1 (in red), D2 (blue), D3 (green) and D4 (yellow).</p

Local binding groove distance distribution plot.

<p>Normalized probability distribution of center of mass distance of heavy atoms between the flanking residues of chain A and chain B along different sections of binding groove (D1, D2, D3 and D4), for (A) *15:01 allele and (B) *16:01 allele.</p