An immune response is generated when a wide range of foreign particles (viruses, bacteria, peptides, etc.) enter our body. As the body mounts an effective immune response, a series of complex molecular and cellular events take place that protect us from these pathogens. For example, to activate the immune response against the antigenic peptides derived from these pathogens, T-cell receptors on the CD8⁺ and CD4⁺ T-cell surfaces interact with the peptide-bound major histocompatibility complex (MHC) molecules. The antigenic peptides bind in the grooves of MHC molecules, where a variety of structural features are orchestrated that enable the MHCs to target diverse antigenic peptides. The two classes—MHC-I and MHC-II—accommodate antigenic peptides of different lengths and present peptides derived from intracellular and extracellular pathogens, respectively. The initial assembly and folding of the MHC molecule in the endoplasmic reticulum and then its transport to the late endosomal compartment leaves a short peptide segment bound to the antigen-binding groove in the MHCs. This short peptide segment is released in a chaperone-catalyzed process called peptide exchange or peptide editing, and the antigenic peptide-bound MHC (pMHC) is then transported to the cell surface for recognition by T cell receptors on CD4⁺ T cells.

Over the years, extensive structural and biochemical studies have helped us to understand the detailed molecular mechanism underlying the interaction between MHC and antigenic peptides. For MHC-I, structural and molecular dynamics (MD) simulation studies have helped observe several critical metastable states involved in the peptide-loading process. These studies have shown that the N-terminal residues of the peptide guide the initial substrate loading. In pMHC-II, α-helices flank the peptide-binding groove, while the β-sheets form the binding floor. The bound peptide's N- and C-terminal ends sprawl out in the solvent through the open ends of the groove, while the 9 aa-long core peptide binds tightly in the groove. Furthermore, the peptide-binding region in the groove undergoes drastic structural rearrangement during the peptide exchange process. In addition, MD simulations on pMHC-II have captured several transient intermediate states that are probably involved in peptide recognition. However, understanding of the peptide-loading conformational dynamics at the atomic level was still elusive for MHC-II and needed further investigation before it was taken up by Lin-Tai Da and co-workers.

In the study titled “Loading dynamics of one SARS-CoV-2-derived peptide into MHC-II revealed by kinetic models” published in the May 2 issue of Biophysical Journal, Lin-Tai Da and co-workers carried out MD simulations on human leukocyte antigen (HLA)-DR1 (one of the most common MHC-II molecules in humans) and a peptide derived from the N-terminal domain of the SARS-CoV-2 spike protein. It has been previously shown that the chosen S-peptide interacts with HLA-DR1 at nanomolar affinity. The authors constructed a model S-peptide and HLA-DR1 complex based on a crystal structure and subjected it to energy minimization and 100-ns unbiased MD simulations (in triplicate) to equilibrate the structure of the complex. The equilibrated pMHC-II structure was then subjected to fifteen 20-ns steered MD (SMD) simulations along five pulling directions, with an assumption that peptide pulling and peptide loading share similar conformational space. One hundred 20-ns unbiased MD simulations were carried out to remove the biases introduced by pulling force in SMD simulations. Two hundred 100-ns MD trajectories were collected on selected conformations to unveil the molecular mechanism underlying the peptide-loading process. Thus, the MD simulation combined with Markov state models constructed by using a splitting and lumping strategy helped the authors obtain deeper insights into the structural dynamics of pMHC-II beyond a microsecond timescale. The study determined a dominant peptide-loading path and an alternative path. The study deciphered critical metastable states of the pMHC-II complex during the peptide-loading process from the solvent-exposed state to the bound state at the atomic level. The study also highlighted the key structural motifs in MHC-II that are responsible for assisting the substrate loading, the role of intrinsic flexibility of MHC-II, and key differences between the peptide recognition mechanisms of MHC-I and MHC-II. This work should thus pave the way for the design of peptide-based vaccines against SARS-CoV-2 in the future.