Elucidating Ligand Charge Effects in MR1 Cell-Surface Translocation Using Molecular Simulations

The major histocompatibility complex class I-related protein 1 (MR1) is an antigen-presenting protein that binds its ligand in the endoplasmic reticulum and presents the resulting complex on the cell surface to regulate mucosal-associated invariant T (MAIT) cell function. The MAIT cells play an important role in infection defense and tissue repair and are involved in various pathological conditions. Therefore, MR1 and its ligands, which act as MAIT cell activation triggers, have garnered increasing attention. Notably, MR1 levels on the cell surface vary greatly depending on its ligands. However, the ligand recognition mechanism of MR1, as well as the structure-activity relationship of its ligands, remains poorly understood. In this study, we conducted computational analyses on the interactions between MR1 and its ligands and determined the stability of the MR1-ligand complex structures to clarify the chemical properties of ligands involved in the regulation of MR1 levels on the cell surface. Our findings provide evidence that covalent and noncovalent ligands bind to MR1 in an anionic state rather than in a previously assumed neutral state, thereby stabilizing the resulting MR1-ligand complex. Furthermore, neutralization of the positive charge derived from Arg9 upon binding of anionic ligands was identified as a key factor that contributes to the enhancement of its levels on the cell surface. Our results lay a strong foundation for further studies delving into the molecular mechanisms of ligand recognition and cell-surface localization of MR1 and will facilitate the design of ligands that activate MAIT cells.