Antigen Processing At The Atomic Level: Md Simulations Of Mhci And Its Peptide-Loading Complex

Antigens exposed at the cell surface by major histocompatibility complex class I (MHCI) proteins enable self/non-self recognition by cytotoxic T cells, protecting the organism against viral infections and cancer-causing mutations. To perform their role, MHCI must first be loaded with an antigenic peptide inside the endoplasmic reticulum (ER), a process controlled by a multi-protein assembly called the peptide-loading complex (PLC). In the absence of any experimental structure of the PLC, we used molecular dynamics (MD) simulations to study its individual components, their assembly and their function. We have predicted the structure of the tapasin • MHCI interface, and shown how tapasin both protects empty MHCI from unfolding and catalyses the selection of high-affinity peptides through a molecular tug-of-war mechanism: tapasin pulls on a region of the MHCI peptide binding groove to open it, while the peptide simultaneously tries to close the groove. Low-affinity contenders “lose” this challenge and are exchanged until a high-affinity one binds to and closes the groove, thereby initiating complex break-down. We have also shown how tapasin recruits the transporter associated with antigen processing (TAP) into the PLC via transmembrane interactions. In addition, by truncating antigens or removing them from the MHCI binding groove, we made a spatially resolved map of MHCI plasticity, revealing how peptide loading status affects key structural regions contacting tapasin. Finally, we have integrated the previous elements to build a computational model of the full PLC. Our MD simulations explain experimental kinetics and mutagenesis data, and represent the first in-depth, atomic-level study of the mechanism underlying the PLC, an important step towards a better understanding of adaptive immunity.