Molecular Dynamics Simulations Reveal Distinct Conformational Changes of Three Cullins in Cullin-Ring E3 Ubiquitin Ligases

Abstract

Cullin-RING E3 ubiquitin ligases (CRLs) facilitate ubiquitin transfer from E2 to the substrate, thus tagging the substrate for degradation. CRL contain four components: substrate binding protein, adaptor, cullin and Rbx protein. Our previous studies[1-3] showed that substrate binding proteins and Rbx proteins are flexible allowing the shortening of the distance between E2 and the substrate for initiation of ubiquitination, or the increase of the distance for accommodating the polyubiquitin chain. However, the role of cullin in the function of ubiquitination remains unclear. Is cullin a rigid scaffold or does it have the flexibility for conformational control of ubiquitination? Why are there seven cullins in the human genome? With highly conserved structure and sequence, how do these cullins specifically facilitate ubiquitination for different substrates? To answer these questions, we performed MD simulations on three cullins with available crystal structures, cul1, cul4A and cul5. In all three cases, we observed large conformational change during the 60 ns simulations. These conformational changes either shorten or increase the distance between E2 and the substrate to facilitate mono- or polyubiquitination, suggesting that cullins allosterically regulate the ubiquitination process. We further observed that rotation hinges and degree of flexibilities are significantly different for these three cullins, which may be attributed to the long loops in different positions for these three cullins. We propose that the long loops may specifically regulate the conformational control of ubiquitination for different cullins with different substrates. Funded by NCI NIH contract HHSN261200800001E.1. Liu, J.; Nussinov, R.; Biophys J., 2010, 99(3), 736-44.2. Liu, J.; Nussinov, R.; J Mol Biol., 2010, 396(5), 1508-233. Liu, J.; Nussinov, R.; PLoS. Comput. Biol. 2009, 5(10), e1000527.