title: Kinetics of peptide binding to the class II MHC protein I-Ek.
abstract: Class II MHC glycoproteins bind short (7-25 amino acid) peptides in an extended type II polyproline-like conformation and present them for immune recognition. Because empty MHC is unstable, measurement of the rate of the second-order reaction between peptide and MHC is challenging. In this report, we use dissociation of a pre-bound peptide to generate the active, peptide-receptive form of the empty class II MHC molecule I-Ek. This allows us to measure directly the rate of reaction between active, empty I-Ek and a set of peptides that vary in structure. We find that all peptides studied, despite having highly variable dissociation rates, bind with similar association rate constants. Thus, the rate-limiting step in peptide binding is minimally sensitive to peptide side-chain structure. An interesting complication to this simple model is that a single peptide can sometimes bind to I-Ek in two kinetically distinguishable conformations, with the stable peptide-MHC complex isomer forming much more slowly than the less-stable one. This demonstrates that an additional free-energy barrier limits the formation of certain specific MHC-peptide complex conformations.
authors.affiliation: Department of Chemistry, Stanford University, Stanford, California 94305, USA.
authors.forename: P M
authors.initials: PM
authors.lastname: Kasson
authors.forename: J D
authors.initials: JD
authors.lastname: Rabinowitz
authors.forename: L
authors.initials: L
authors.lastname: Schmitt
authors.forename: M M
authors.initials: MM
authors.lastname: Davis
authors.forename: H M
authors.initials: HM
authors.lastname: McConnell
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000944:Antigens, Differentiation, B-Lymphocyte / Q000737:chemistry / Q000378:metabolism; D001667:Binding, Competitive; D016466:CHO Cells; D010856:Columbidae; D006224:Cricetinae; D003574:Cytochrome c Group / Q000737:chemistry / Q000378:metabolism; D005973:Glutamine / Q000737:chemistry / Q000378:metabolism; D000949:Histocompatibility Antigens Class II / Q000737:chemistry / Q000378:metabolism*; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D046911:Macromolecular Substances; D008969:Molecular Sequence Data; D009952:Ornithine / Q000737:chemistry / Q000378:metabolism; D010455:Peptides / Q000138:chemical synthesis / Q000378:metabolism*; D011485:Protein Binding; D020033:Protein Isoforms / Q000737:chemistry / Q000378:metabolism
chemical_list: D000944:Antigens, Differentiation, B-Lymphocyte; D003574:Cytochrome c Group; D000949:Histocompatibility Antigens Class II; C024138:I-E-antigen; D046911:Macromolecular Substances; D010455:Peptides; D020033:Protein Isoforms; C045084:invariant chain; D005973:Glutamine; D009952:Ornithine