Theoretical study and the circular dichroism of the N-S acyl rearrangement in the intein-mediated protein
| Autor: | Chu, Pei-Chuan, 朱沛全 |
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| Rok vydání: | 2013 |
| Druh dokumentu: | 學位論文 ; thesis |
| Popis: | 101 Intein is a self-catalyzed protein segment, acting as one of the key complexes in the protein splicing process and mediating both of the cleavage and the ligation of protein sequences. The process begins with an N-S acyl shift followed by transesterification, forming a branched intermediate which leads to the formation of succinimide and the S-N rearrangement. Although this four-step reaction has been previously studied, the detailed mechanisms of the first step (N-S acyl shift) and the last step (S-N acyl shift) are still unconfirmed. We report the computational study and the synchrotron radiation circular dichroism (SRCD) analysis of the N-S acyl shift in protein splicing. The models were built based on the X-ray crystallographic and solution NMR structures. The geometries of each reaction stage were located using density functional theory and second order Møller–Plesset perturbation theory. The SRCD signal reveals that the intein maintains the identical structures in different salinity. The computational results show that the N-S acyl shift is a two-step reaction, which goes through an oxothiazolidine forming step followed by a ring-opening step. The formation of the oxothiazolidine intermediate is accompanied by an intramolecular proton transfer, whereas the opening of the heterocyclic ring occurs simultaneously with an intermolecular double-proton transfer. The first and the second activation energies calculated at the level of MP2 are 30.8 kcal/mol and 14.9 kcal/mol, respectively. The overall reaction energy is 7.1 kcal/mol. |
| Databáze: | Networked Digital Library of Theses & Dissertations |
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