Tagging proteins: sumoylation mechanism by molecular modeling and molecular dynamics simulations

Abstract

Sumoylation, the covalent attachment of SUMO (Small Ubiquitin Like Modifier) to target proteins is a posttranslational modification that can alter intracellular localization, interactions with other proteins or result in modifications by other post-translational modifiers. Malfunctioning of sumoylation pathway is concerned with many neurological diseases, such as Huntington’s disease, Parkinson’s disease and more. Besides, sumoylation is a part of cancer related pathways. Like other ubiquitin like modifier (Ubl) conjugation mechanisms, the covalent attachment of SUMO to target proteins involves three classes of enzymes: Ubiquitin-like protein activating enzyme (E1), Ubiquitin-like protein conjugating enzyme (E2) and Ubiquitin-like protein ligase (E3). Sumoylation is different than other Ubl conjunction paths in a way that, the E2 ligase, Ubc9, can function with lower reaction efficiency in the absence of an E3 ligase. One of the target proteins that Ubc9 can uniquely sumoylate with high reaction efficiency is RanGAP1. This work is based on the Ubc9-SUMO-RanGAP1-RanBP2 system. Presense of RanBP2 is thought to possess an allosteric effect on Ubc9 and SUMO, thereby increasing the efficiency of the transfer of the bond from Ubc9 to Ran- GAP1. Molecular Dynamics (MD) simulations Ubc9-SUMO-RanGAP1-RanBP2 and Ubc9-SUMO-RanGAP1 complexes are carried out at 300 K including the isopeptide bond between Gly97 of SUMO and 524Lys of RanGAP1. To obtain coherent results, parallel simulations of both structures are carried out. Expectedly, RanBP2 behaves as an E3 ligase for the system and allosterically enhances the conformational stability of the Ubc9-SUMO-RanGAP1 structure. Coupling of SUMO and RanGAP1 is found to dependent on couplings of Loop 2 with Thr511-Leu522 and Leu555-Pro566 regions of RanGAP1. Furthermore, the presence of RanBP2 is shown to impose a packing motion for the Loop 2 region, which is Lys30-Met36 region of Ubc9 (Karaca et al., 2010). Asp33 residue is observed to maintain a unique conformational state, where Asp33 bends towards RanGAP1. In order to clarify the role of Asp33 of Ubc9, Asp33Ala mutant is designed. With the mutation, the significance of Asp33 residue, more importantly the significance of Loop 2 region is highlighted.