Three-dimensional models of immune cell surface proteins and identification of binding sites

The extracellular regions of many cell surface proteins of the immune system contain distinct domains that may be linked in many different ways and are often only loosely tethered to the transmembrane segment. In efforts to identify regions critical for binding, molecular models of these domains are used to select residues for mutagenesis and to map binding sites. Many immune cell surface proteins belong to protein superfamilies and display only limited sequence identity compared to proteins of known three-dimensional (3D) structure, often 30% or less. Therefore, detailed 3D structures are difficult to predict, and structure-based sequence analysis and model assessment are particularly important components of the model building process. In some cases, experimentally determined structures have made it possible to assess the accuracy of predictions, which illustrates the opportunities and shortcomings of the approach. Herein the model-based identification of binding sites in cell surface proteins is described and representative examples are discussed.