Designing specific protein-protein interactions using computation, experimental library screening, or integrated methods

Abstract

Given the importance of protein-protein interactions for nearly all biological processes, the design of protein affinity reagents for use in research, diagnosis or therapy is an important endeavor. Engineered proteins would ideally have high specificities for their intended targets, but achieving interaction specificity by design can be challenging. There are two major approaches to protein design or redesign. Most commonly, proteins and peptides are engineered using experimental library screening and/or in vitro evolution. An alternative approach involves using protein structure and computational modeling to rationally choose sequences predicted to have desirable properties. Computational design has successfully produced novel proteins with enhanced stability, desired interactions and enzymatic function. Here we review the strengths and limitations of experimental library screening and computational structure-based design, giving examples where these methods have been applied to designing protein interaction specificity. We highlight recent studies that demonstrate strategies for combining computational modeling with library screening. The computational methods provide focused libraries predicted to be enriched in sequences with the properties of interest. Such integrated approaches represent a promising way to increase the efficiency of protein design and to engineer complex functionality such as interaction specificity.

Figure 1

Examples of different types of protein–protein interactions where the protein fold is conserved but the specificity can be varied. A representative complex is shown for each class of interaction: A: Complex between SH3 domain from the Abl tyrosine kinase (green) and a proline-rich peptide (red). (PDB ID: 1ABO). B: Complex between SH2 domain from the SAP protein (green) and a phosphotyrosine peptide (red) (PDB ID: 1D4W). C: Complex between Erbin PDZ domain (green) and the C-terminal tail of the ErbB2 receptor (red) (PDB ID: 1MFG). D: Complex between the bZIP coiled-coil motifs of FOS (green) and JUN (red) (PDB ID: 1FOS). E: Complex between anti-apoptotic protein Mcl-1 (green) and the BH3 region of Bim (red) (PDB ID: 2PQK). F: Complex of a homodimer formed by the N-terminal domain of a particular Dscam isoform (PDB ID: 2V5M). Figure generated using PyMol (Delano Scientific).