Protein–protein interaction: from mechanism to protein design

Abstract

] 68 Tel. 972 8 934 Fax. 972 8 934 E-mail: Studying the mechanism of protein-protein interactions For studying the mechanism of protein-protein association, we introduced a thermodynamic framework for the association reaction, which enabled us to present a general formulation for the calculation of rates of association for mutant protein complexes. Moreover, we established a design protocol, which enables us to specifically alter rates of association, without affecting the rates of dissociation of a protein complex. This formulation was used for the successful design of a protein complex which binds 250 fold faster and tighter compared to the native proteins. Using computer simulations we demonstrated that the energy profile during association resembles in shape a funnel, with the final complex being at the energy minima. For faster associating protein complexes the energy funnel deepens and its volume increases. Currently, we are investigating the relevance of faster association in the biological environment both by mimicking the crowded environment and by relating faster binding with enhanced biological activity. In parallel we investigated the forces which stabilize a protein complex once it is formed. The use of single mutations or even double-mutant cycles is not sufficient for this purpose, as the The complexity of life requires proteins to be able to transfer specific signals, build multi-unit machines, control the function of enzymes and regulate production and activities. Many of these tasks are performed through specific protein-protein interactions. This is feasible due to the almost unlimited potential for generating unique binding sites on proteins, characterized by their shape and surface chemistry. Despite the high degree of specificity, high-affinity protein-protein interactions are formed at rates close to the diffusion limit. We were intrigued to investigate the mechanism of protein-protein interactions, and to apply the gained knowledge towards protein design. Our research is conducted on a number of protein-protein interactions. Basic research into the mechanism of complex formation and stability is conducted on the interaction between TEM1-β-lactamase with its protein inhibitor BLIP. Structure-function studies are conducted on the interaction between different type I interferons and their receptors, using either the soluble extracellular domains of the receptors (for in vitro studies), or intact receptors (for in situ work). Protein-design is carried out on the interactions between growth-hormone and its receptor and between ras and its effectors. In addition we carry out bioinformatics work on a database of protein-protein interactions with known structures. Fig. 1 Structure of the interferon-receptor complex as determined from distance-constraint docking gideon_schraiber.id 26.12.2001, 15:17 68