title: Fundamental reaction pathway and free energy profile of proteasome inhibition by syringolin A (SylA).
abstract: In this study, molecular dynamics (MD) simulations and first-principles quantum mechanical/molecular mechanical free energy (QM/MM-FE) calculations have been performed to uncover the fundamental reaction pathway of proteasome with a representative inhibitor syringolin A (SylA). The calculated results reveal that the reaction process consists of three steps. The first step is a proton transfer process, activating Thr1-O(γ) directly by Thr1-N(z) to form a zwitterionic intermediate. The next step is a nucleophilic attack on the olefin carbon of SylA by the negatively charged Thr1-O(γ) atom. The last step is a proton transfer from Thr1-N(z) to another olefin carbon of SylA to complete the inhibition reaction process. The calculated free energy profile demonstrates that the second step should be the rate-determining step and has the highest free energy barrier of 24.6 kcal mol(-1), which is reasonably close to the activation free energy (∼22.4-23.0 kcal mol(-1)) derived from the available experimental kinetic data. In addition, our computational results indicate that no water molecule can assist the rate-determining step, since the second step is not involved in a proton transfer process. The obtained mechanistic insights should be valuable for understanding the inhibition process of proteasome by SylA and structurally related inhibitors at a molecular level, and thus provide a solid mechanistic base and valuable clues for future rational design of novel, more potent inhibitors of proteasome.
authors.affiliation: Department of Chemistry, Zhengzhou University, Daxue Road, Zhengzhou, Henan 450052, China.
authors.forename: Donghui
authors.initials: D
authors.lastname: Wei
authors.forename: Mingsheng
authors.initials: M
authors.lastname: Tang
authors.forename: Chang-Guo
authors.initials: CG
authors.lastname: Zhan
mesh_terms: D056004:Molecular Dynamics Simulation; D010456:Peptides, Cyclic / Q000737:chemistry / Q000494:pharmacology*; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism*; D061988:Proteasome Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D011789:Quantum Theory; D012441:Saccharomyces cerevisiae / Q000201:enzymology*; D013816:Thermodynamics
chemical_list: D010456:Peptides, Cyclic; D061988:Proteasome Inhibitors; C407267:syringolin A; D046988:Proteasome Endopeptidase Complex