Dynamic analysis of sumo conjugation cascade by molecular modeling and simulations

Abstract

Ubiquitin (Ub) and ubiquitin like modifiers (Ubls) are proteins, which facilitate post-translational modification (PTM) of proteins. A PTM involves Ub/Ubl conjugation on to a specific target. In order to modify targets, Ub/Ubls are conjugating generally- their C-termini to the catalytic lysine residue of target. The mechanism of conjugation is a three step cascade, which is mediated by Ubiquitin-like protein activating enzyme (E1), Ubiquitin-like protein conjugating enzyme (E2) and Ubiquitin-like protein ligase (E3). SUMO-1 is an Ub/Ubl family member and it takes role in the signaling, metabolic and transcriptional regulation of the cell. Thus its malfunctioning results in various diseases like Parkinson disease, Alzheimer disease or cancer. Sumoylation has the general mechanistic structure of Ub/Ubl conjugation. Nevertheless in sumoylation, E2 has also the ability to recognize the target. For some specific cases it can even conjugate SUMO-1 on to the target without the presence of an E3. Thus, for such cases, whether E3 is required for conjugation is controversial. In order to understand the role of the E3 and E2’s target specificity in sumoylation, Molecular Dynamics (MD) simulations are carried out for the systems of Ubc9(E2)-RanBP2(E3)-SUMO- 1-RanGAP1(Target) and Ubc9-SUMO-1-RanGAP1. The dynamic analyses revealed that RanBP2 restricts the conformational space of the SUMO-1 and RanGAP1, which could ease the accessibility of the probable conformations of Ubc9 binding region and the catalytic LKSE motif of RanGAP1 for the catalysis. It is also observed that RanBP2 packs SUMO-1 and Ubc9 in a close geometry to constrain the microenvironment of the catalytic sites. With this packing, the loop around Asp33, which is a strictly conserved residue of Ubc9, access a unique conformational state, where Asp33 bends itself towards RanGAP1. Interestingly, the loop around Asp33 displays correlations with the catalytic sites of both Ubc9 and RanGAP1, when it is in this conformational state. Without RanBP2, however, the loop looses this conformational state and SUMO-1 directs it’s Gly68, which is highly conserved too, towards Ubc9. As Gly68 of SUMO-1 anchors on to Ubc9, it also reflects correlations with the catalytic site and Ubc9 binding surface of RanGAP1. With this motion, the system adjusts itself to mimic the packing action imposed by RanBP2. This observation suggests a functional significance of Asp33 of Ubc9 and Gly68 of SUMO-1, which should be studied by further experiments. The present results in general suggest that RanBP2 may both restrict the conformational space of the catalytic sites and impose an allosteric effect on the system of Ubc9-SUMO-1-RanGAP1.