title: Coupling between side chain interactions and binding pocket flexibility in HLA-B*44:02 molecules investigated by molecular dynamics simulations.
abstract: MHC class I molecules present antigenic peptides to cytotoxic T-cells at the cell surface. Peptide loading of class I molecules in the endoplasmatic reticulum can involve interaction with the tapasin chaperone protein. The human class I allotype HLA-B*44:02 with an Asp at position 116 at the floor of the F pocket (which binds the peptide C-terminal residues) depends on tapasin for efficient peptide loading. However, HLA-B*44:05 (identical to B*44:02 except for tyrosine 116) can efficiently load peptides in the absence of tapasin. Both allotypes adopt very similar structures in the presence of the same peptide. Molecular dynamics simulations indicate a significantly higher conformational flexibility of the F pocket in the absence of a peptide for B*44:02 compared to B*44:05. Free energy simulations to open the F pocket indicate a molecular side chain switch mechanism that underlies the global opening motion. This side chain switch involves the rearrangement of salt bridges and hydrogen bonding of the basic arginine 97 with three acidic aspartate residues 114, 116 and 156 near the F pocket. A replica exchange simulation to specifically accelerate side chain motions demonstrates that the same side chain rearrangements induce global opening motions of the F pocket. In case of B*44:05 the free energy barrier for F pocket opening was significantly higher compared to B*44:02 and no associated side chain rearrangement was observed. Such coupling of local side chain rearrangements with global conformational changes might be the basis for allosteric changes in other class I allotypes as well as for allosteric changes in other proteins.
authors.affiliation: Physik-Department T38, Technische Universität München, James Franck Street 1, 85748 Garching, Germany.
authors.forename: Katja
authors.initials: K
authors.lastname: Ostermeir
authors.affiliation: Molecular Life Science, Jacobs University Bremen, Campus Ring 1, 28357 Bremen, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Springer
authors.affiliation: Physik-Department T38, Technische Universität München, James Franck Street 1, 85748 Garching, Germany. Electronic address: martin.zacharias@ph.tum.de.
authors.forename: Martin
authors.initials: M
authors.lastname: Zacharias
mesh_terms: D000596:Amino Acids / Q000378:metabolism*; D001665:Binding Sites; D059948:HLA-B44 Antigen / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D059948:HLA-B44 Antigen; D010455:Peptides
keywords: Accelerated sampling; Free energy calculation; MHC class I molecule; Peptide editing, Molecular simulation; Peptide loading