Allosteric effects and regulation of signaling: the ubiquitin E3 ligases

Abstract

Allosteric communications are important for cellular signaling1, including ubiquitin systems. In E3 ubiquitin ligases, substrate binding proteins, e.g. VHL-box, SOCS-box or the F-box proteins, recruit substrates for ubiquitination via conformational selection and population shift2,3, accurately positioning and orienting the substrates for ubiquitin transfer. Yet, how does the E3 machinery precisely position the substrate? What is the role of allostery in regulation of signaling for ubiquitin or ubiquitin-like systems? To address these questions, we performed molecular dynamics simulations for different ubiquitin or ubiquitin-like systems. We simulated seven substrate binding proteins. All have two domains: one binds to the substrate; the other to E3 ligase modules Skp1/Elongin C. We found that in all cases the flexible inter-domain linker serves as a hinge rotating the substrate binding domain, optimally and accurately positioning it for ubiquitin transfer. We further observed that the linker flexibility could be regulated allosterically by binding events of either domain. For one of these substrate binding proteins, pVHL, a tumor suppressor protein which forms part of the E3 ubiquitin ligase complex and regulates the degradation of the hypoxia inducible factor, we designed five allosterically-stabilizing mutants to stabilize the inter-domain interface4. We proposed that drugs mimicking the mutants' allosteric effects may rescue pVHL function in the von Hippel-Lindau disease. Ubiquitin-like E3 ligases are also observed to allosterically regulate degradation. Sumoylation involves covalent attachment of SUMO (Small Ubiquitin-Like Modifier) to target proteins. The E3 ligase, RanBP2, was observed to allosterically regulate sumoylation process.1. Tsai CJ, del Sol A, Nussinov R. J Mol Biol. 378:1-11, 2008.2. Ma B, Kumar S, Tsai CJ, Nussinov R. Protein Eng. Des. Sel. 12:713-720, 1999.3. Boehr DD, Wright PE. Science 320:1429-30, 2008.4. Liu J, Nussinov R. Proc Natl Acad Sci USA 105:901-6, 2008.