A theoretical model investigation of peptide bond formation involving two water molecules in ribosome supports the two-step and eight membered ring mechanism

作者：Wang, Qiang; Gao, Jun^*; Zhang, Dongju; Liu, Chengbu

来源：Chemical Physics, 2015, 450: 1-11.

DOI：10.1016/j.chemphys.2015.01.011

• Peptide bond formation
• Ribosome
• Two-step
• Eight-membered transition state

The ribosome is the macromolecular machine that catalyzes protein synthesis. The kinetic isotope effect analysis reported by Strobel group supports the two-step mechanism. However, the destination of the proton originating from the nucleophilic amine is uncertain. A computational simulation of different mechanisms including water molecules is carried out using the same reaction model and theoretical level. Formation the tetrahedral intermediate with proton transfer from nucleophilic nitrogen, is the rate-limiting step when two water molecules participate in peptide bond formation. The first water molecule forming hydrogen bonds with O9' and H15' in the A site can decrease the reaction barriers. Combined with results of the solvent isotope effects analysis, we conclude that the three-proton transfer mechanism in which water molecule mediate the proton shuttle between amino and carbon oxygen in rate-limiting step is the favorable mechanism. Our results will shield light on a better understand the reaction mechanism of ribosome.

• 出版日期2015-4-1
• 单位华中农业大学; 山东大学