Exploring the RING-catalyzed ubiquitin transfer mechanism by MD and QM/MM calculations

• Published in: PloS one 2014-07, Vol.9 (7), p.e101663-e101663
• Main Authors: Zhen, Yunmei, Qin, Guangrong, Luo, Cheng, Jiang, Hualiang, Yu, Kunqian, Chen, Guanghui
• Format: Article
• Language: English
• Subjects: Biology and Life Sciences; Catalysis; Chemistry; Computer applications; Computer simulation; Conformation; Energy; Enzymes; Laboratories; Ligases; Lysine; Mathematical models; Models, Molecular; Molecular dynamics; Molecular Dynamics Simulation; Molecular modelling; Physics; Protein Binding; Protein Conformation; Proteins; Proteomics; Quantum mechanics; R&D; Research & development; RING Finger Domains; Simulation; Small Ubiquitin-Related Modifier Proteins - chemistry; Small Ubiquitin-Related Modifier Proteins - metabolism; Substrate Specificity; Substrates; Three dimensional models; Ubiquitin; Ubiquitin - chemistry; Ubiquitin - metabolism; Ubiquitin-Conjugating Enzymes - chemistry; Ubiquitin-Conjugating Enzymes - metabolism; Ubiquitin-protein ligase; Ubiquitin-Protein Ligases - chemistry; Ubiquitin-Protein Ligases - metabolism; Ubiquitination
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0101663

Ubiquitylation is a universal mechanism for controlling cellular functions. A large family of ubiquitin E3 ligases (E3) mediates Ubiquitin (Ub) modification. To facilitate Ub transfer, RING E3 ligases bind both the substrate and ubiquitin E2 conjugating enzyme (E2) linked to Ub via a thioester bond to form a catalytic complex. The mechanism of Ub transfer catalyzed by RING E3 remains elusive. By employing a combined computational approach including molecular modeling, molecular dynamics (MD) simulations, and quantum mechanics/molecular mechanics (QM/MM) calculations, we characterized this catalytic mechanism in detail. The three-dimensional model of dimeric RING E3 ligase RNF4 RING, E2 ligase UbcH5A, Ub and the substrate SUMO2 shows close contact between the substrate and Ub transfer catalytic center. Deprotonation of the substrate lysine by D117 on UbcH5A occurs with almost no energy barrier as calculated by MD and QM/MM calculations. Then, the side chain of the activated lysine gets close to the thioester bond via a conformation change. The Ub transfer pathway begins with a nucleophilic addition that forms an oxyanion intermediate of a 4.23 kcal/mol energy barrier followed by nucleophilic elimination, resulting in a Ub modified substrate by a 5.65 kcal/mol energy barrier. These results provide insight into the mechanism of RING-catalyzed Ub transfer guiding the discovery of Ub system inhibitors.