A key event in the developing and mature immune system is the recognition of MHC bound peptide antigens by means of antigen receptors expressed by T cells. Although it is thought that this recognition event is highly specific, crossreactivity is also an essential feature of this recognition. Both specificity and crossreactivity are not well understood at a structural level, partly due to the current difficulty of gathering structural information for a large number of MHC-bound peptides. This project plans to combine hydrogen- deuterium exchange experiments with nuclear magnetic resonance techniques to develop a rapid method to obtain information as to how the peptide backbone is oriented in the MHC binding groove (the focus of Aim 1). In pursuing this overall goal the planned studies will also uncover novel aspects of the structure and structural dynamics of MHC bound peptides. A comparison of hydrogen deuterium exchange data with X-ray crystallographic data will uncover at which points in their backbone peptides are hydrogen bonded to the MHC molecules and at which points they are associated with mobile water molecules that are part of the binding interface (Aim 2). The existence of such mobile water molecules had been postulated in our previous computational studies. Water networks may also facilitate structural flexibility of the bound peptide. The focus of Aim 3 is to distinguish between static and dynamic models of structural heterogeneity of MHC bound peptides.
In Aim 4 we will apply computational methods to the interpretation of hydrogen exchange data to develop a more complete methodology to predict the conformation and conformational heterogeneity of MHC bound peptides. The project will facilitate future studies of the structural basis of molecular mimicry and autoimmunity. Future studies on vaccine design and the assessment of vaccine risk will also be aided by a rapid method to obtain structural information of MHC-bound peptides. The studies will provide an opportunity for undergraduate and graduate students to learn important techniques, such as expression of recombinant proteins, NMR spectroscopy, mass spectroscopy, and computational techniques. ? ? ?
