Molecular dynamics simulations to provide insights into epitopes coupled to the soluble and membrane-bound MHC-II complexes

Abstract

Epitope recognition by major histocompatibility complex II (MHC-II) is essential for the activation of immunological responses to infectious diseases. Several studies have demonstrated that this molecular event takes place in the MHC-II peptide-binding groove constituted by the α and β light chains of the heterodimer. This MHC-II peptide-binding groove has several pockets (P1-P11) involved in peptide recognition and complex stabilization that have been probed through crystallographic experiments and in silico calculations. However, most of these theoretical calculations have been performed without taking into consideration the heavy chains, which could generate misleading information about conformational mobility both in water and in the membrane environment. Therefore, in absence of structural information about the difference in the conformational changes between the peptide-free and peptide-bound states (pMHC-II) when the system is soluble in an aqueous environment or non-covalently bound to a cell membrane, as the physiological environment for MHC-II is. In this study, we explored the mechanistic basis of these MHC-II components using molecular dynamics (MD) simulations in which MHC-II was previously co-crystallized with a small epitope (P7) or coupled by docking procedures to a large (P22) epitope. These MD simulations were performed at 310 K over 100 ns for the water-soluble (MHC-IIw, MHC-II-P(7w), and MHC-II-P(22w)) and 150 ns for the membrane-bound species (MHC-IIm, MHC-II-P(7m), and MHC-II-P(22m)). Our results reveal that despite the different epitope sizes and MD simulation environments, both peptides are stabilized primarily by residues lining P1, P4, and P6-7, and similar noncovalent intermolecular energies were observed for the soluble and membrane-bound complexes. However, there were remarkably differences in the conformational mobility and intramolecular energies upon complex formation, causing some differences with respect to how the two peptides are stabilized in the peptide-binding groove.

Figure 1. Steps depicting the construction of the membrane-bound systems (MHC-II_m, MHC-II-P_7m and MHC-II-P_22m).

A) The receptor (MHC-II) and the ligand (P₂₂). B) The MHC-II-P₂₂ complex. C) The MHC-II-P_22m complex embedded in a POPC membrane.

Figure 2. Membrane equilibrium after embedding MHC-II_m (black line), MHC-II-P_7m (red line), and MHC-II-P_22m (blue line) in a POPC membrane.

The surface area (A) and (B) area per lipid (A_lip) as a function of the simulation time show that both properties converged to stable values after 50 ns.

Figure 3. RMSF analysis of the water-soluble and membrane-bound MHC-II-P₇ complex.

A-B) The soluble peptide-free (MHC-II_w, black line) and peptide-bound (MHC-II-P_7w, red line) species. C-D) The membrane-bound peptide-free (MHC-II_m, black line) and peptide-bound (MHC-II-P_7m, red line) complexes.

Figure 4. RMSF analysis of the soluble and membrane-bound MHC-II-P₂₂ complex.

A-B) The soluble peptide-free (MHC-II_w, black line) and peptide-bound (MHC-II-P_22w, red line) complexes. C-D) The membrane-bound peptide-free (MHC-II_m, black line) and peptide-bound (MHC-II-P_22m, red line) complexes.

Figure 5. Average structures of the pMHC-II complexes.

A) MHC-II-P_22w, B) MHC-II-P_22m, C) MHC-II-P_7w and D) MHC-II-P_7m.

Figure 6. pMHC-II complexes color-coded according to their B-factors.

A-B) MHC-II-P_7w complex. C-D) MHC-II-P_7m. E-F) MHC-II-P_22w and G-H) MHC-II-P_22m. Complexes are drawn in cartoon representation and color-coded according to the B-factor of Cα atom, from blue (lowest B factor: less than 30 Ų) to red (highest B factor: greater than 50 Ų). B-factors were obtained from the average RMSF values.

Figure 7. Schematic MHC-II-P₇ representation.

A) Map of the interactions that stabilize the soluble MHC-II-P_7w complex. B) Map of the interactions that stabilize the membrane-bound MHC-II-P_7m. The residues of P₇ are represented by a single circle. Only the side chains of P₇ involved in hydrogen bonds or hydrophobic contacts are shown explicitly. MHC-II residues participating in hydrogen bonds (green dotted lines) are represented by a single box, and hydrophobic contacts are represented by red half circles.

Figure 8. Schematic representation of the non-covalent interactions between MHC-II and P₂₂.

A) Map of the interactions that stabilize the soluble MHC-II-P_22-w complex. B) Map of the interactions that stabilize the membrane-bound MHC-II-P_22m. The residues of P₂₂ are represented by a single circle. Only the side chains of P₂₂ involved in hydrogen bonds or hydrophobic contacts are shown explicitly. MHC-II residues participating in hydrogen bonds (green dotted lines) are represented by a single box, and hydrophobic contacts are represented by red half circles.