Solution NMR is a powerful tool for structural characterization of proteins and protein complexes not exceeding 200-300 amino acid residues, but difficulties in obtaining large quantities of properly refolded, isotopically enriched protein make this approach challenging for the m04 protein. However, we have been able to obtain virtually complete backbone resonance assignments as well as limited amide-amide NOE data for this system. Recent advances in modeling techniques using the program Rosetta in principle make it possible to model the structure of the protein on the basis of this chemical shift and limited NOE information. The physically realistic energy function implicit to Rosetta can discriminate native from non-native protein conformations and the chemical shift and NOE information strongly reduce the permissible region of conformational space. Refined models for m04 have been derived from this approach, revealing a structure that is roughly similar to the common Igg fold, but with numerous novel elements. Based on sequence homology, the new structure is believed to be representative of all members of the m02-m06 protein family. The m06 protein indeed is found to be structurally homologus to m04, but engages with the MHC-I in a manner that is distinctly different from m04, and appears in competition with binding of beta-microglobulin.
| Natarajan, Kannan; Jiang, Jiansheng; May, Nathan A et al. (2018) The Role of Molecular Flexibility in Antigen Presentation and T Cell Receptor-Mediated Signaling. Front Immunol 9:1657 |
| Natarajan, Kannan; McShan, Andrew C; Jiang, Jiansheng et al. (2017) An allosteric site in the T-cell receptor C? domain plays a critical signalling role. Nat Commun 8:15260 |
| Shen, Yang; Bax, Ad (2015) Homology modeling of larger proteins guided by chemical shifts. Nat Methods 12:747-50 |
| Sgourakis, Nikolaos G; May, Nathan A; Boyd, Lisa F et al. (2015) A Novel MHC-I Surface Targeted for Binding by the MCMV m06 Immunoevasin Revealed by Solution NMR. J Biol Chem 290:28857-68 |
| Sgourakis, Nikolaos G; Natarajan, Kannan; Ying, Jinfa et al. (2014) The structure of mouse cytomegalovirus m04 protein obtained from sparse NMR data reveals a conserved fold of the m02-m06 viral immune modulator family. Structure 22:1263-1273 |
