Probing Relative Domain Mobility of Class-I Major Histocompability Complex Molecules through Residual Dipolar Couplings

Abstract

The highly polymorphic proteins of class I major histocompatibility complex (MHC-I) are 45 kDa multi-domain heterodimers that play a key role in orchestrating the human adaptive immune response. Their function is to present endogenous and exogenous peptide ligands to cytotoxic T cells and Natural Killer cells. Despite a wealth of X-ray structural information on these proteins and their complexes, dynamic studies by NMR have been restricted to the study of local (chemical shift-based) changes occurring at different timescales, using relaxation experiments recorded for amide probes. Recent work from our group using methyl probes has suggested the presence of an allosteric network on the MHC structure, which is modulated in different alleles with functional consequences for the recognition of peptides and molecular chaperones. However, the precise structural mechanism underlying how conformational changes at the peptide-binding groove induced by the binding of different ligands affect the distal α3 domain remains unclear. Here we have obtained full NMR backbone assignments for a common human MHC-I molecule, HLA-A∗02:01, bound to two different high-affinity peptides. Using transverse relaxation optimized spectroscopy-based methods (ARTSY), we collected residual dipolar couplings (RDCs) for both systems, and utilized this data as restraints for structural refinement towards a rigorous analysis of alignment tensors for the different protein domains, relative to an overall molecular frame. Our results suggest that the local conformation of the peptide-binding groove may affect the global structure of the molecule via subtle changes in relative domain orientation and mobility. Our NMR-based mechanism has important implications for how MHC-I molecules of different peptide occupancies interact with their CD8 co-receptors and molecular chaperones.