Theoretical Studies On The Mechanism Of Novel Protein Labeling And Protein Chemical Synthesis Reactions

Labeling and synthesizing protein through chemical methods have been essential strategies for exploring the structures and functions of proteins.In recent years,many protein labeling and synthesis reactions have been developed and successfully applied.Understanding of reaction mechanism can help to improve the reaction and develop new reactions.This dissertation reports our investigations of the detailed mechanism of the recently developed CBT-Cys click reaction and serine/threonine ligation reaction by density functional theory.In chapter 1,chemical protein labeling methods and chemical protein synthesis methods were briefly introducted.In chapter 2,the background and methods of computational chemistry were briefly introduced.In chapter 3,systematic theoretical study was carried out to fully understand the detailed mechanism of CBT-Cys click reaction.It was found that the most favorable mechanism included C-S bond formation,C-N bond formation,C-N bond cleavage,and several facile proton transfer steps.The rate-determining step was the C-N bond cleavage step.Except for the C-S bond formation step,all the steps occurred with the assistance of phosphoric acid.In chapter 4,the mechanism of serine/threonine ligation reaction was investigated by density functional theory.It was found that the reaction sequentially proceeds through imine capture,5-endo-trig cyclization and [1,5] O-to-N acyl transfer steps,all of which occurred with the assistance of pyridinium.The imine capture and 5-endo-trig cyclization steps were reversible whereas the [1,5] O-to-N acyl transfer step was irreversible.The [1,5] O-to-N acyl transfer step proceeded through a stepwise addition-elimination mechanism with the C-O bond cleavage as the rate-determining step of the overall reaction.The diastereoselectivity for the exclusive formation of the S-configured N,O-benzylidene acetal-linked peptide originated from the disfavored steric repulsion between the leaving phenolic oxygen and the side chain of the C-terminal peptide in the R-configured C-O bond cleavage transition state in the acyl transfer step.A suitable ring size as well as a good leaving group in acyl transfer were responsible for the high efficiency of the serine/threonine ligation reaction.At the end,we summarized the research work and looked forward to the development trend of computational chemistry and the successful development of novel protein labeling and synthesis reactions.These results provided in-depth understanding of the mechanism of the CBT-Cys click reaction and the serine/threonine linkage reaction and elucidated the intrisic reasons for the experimental observations.The research can not only help people deeply understand the mechanism of similar reactions,but also provide theoretical foundations for bioorganic chemists to experimentally develop new reactions.We hope that the research results of this dissertation can contribute to the development of bioorganic chemistry.