Nat methods: Study on the enzymatic kinetics of enzyme substrate interaction in complex system

On March 5, ye Mingliang and Zou Hanfa, researchers from Dalian Institute of chemistry, Chinese Academy of Sciences, led the research team of new materials and new technologies for biological separation and analysis to make progress in the study of enzymatic kinetics of enzyme substrate interaction in complex systems Relevant research results were published in the latest issue of nature methods in the form of response (nature methods, 2014, 11220-222) Protease is a tool enzyme for proteomics research It can be used to hydrolyze proteins in complex proteomics samples into peptide segments to achieve quantitative protein analysis and identification There are hundreds of thousands of different proteins in complex proteomic samples, and their abundances are quite different, some even differ by more than ten orders of magnitude Many researchers believe that high abundance protein has higher reaction speed because of its high concentration, so it will be first enzymolysis It is even thought that the high abundance protein can be removed by segmented enzymolysis In order to study the relationship between the rate of enzymatic hydrolysis and the abundance of protein, ye Mingming et al Used quantitative proteomics technology to study the kinetics of enzymatic hydrolysis of complex protein samples of pancreatic protein, obtained the dynamic data of enzymatic hydrolysis by quantitatively comparing the peptide segments produced at two time points of enzymatic hydrolysis The results showed that: (1) the digestion sites with different digestion rates were related to the amino acid residues around them If the surrounding residues were neutral, the digestion was faster, while if the surrounding residues were charged, the digestion was slower; (2) there was no obvious correlation between the digestion rate of peptide segments and the protein abundance, indicating that the high abundance protein was not enzymolysis first The results show that in the process of proteome digestion, the rate of digestion (consumption rate) of each protein is mainly related to the number and kinetic characteristics of the cleavage site of the protein, but not to its abundance In the study of proteomics, the enzymolysis of proteins and the screening of modified enzyme substrates are all involved in the enzymatic reaction of enzymes with a large number of substrates with different abundances This work pioneered the study of enzymatic kinetics in complex systems by using quantitative proteomics technology, and will play a role in improving the theoretical study of enzymatic kinetics based on Michaelis equation Nature methods doi: 10.1038/nmet.2850 protein division priority is independent of protein strengths Ming Liang Ye, Yanbo pan, Kai Cheng & Hanfa Zou Department of high-capacity proteins is an effective way to improve sensitivity in the identification of low-capacity proteins in shotgun proteomics A recent Brief Communication by Fonslow et al reported an interesting approach for improving proteome coverage by a method termed digestion and depletion of abundant proteins (DigDeAPr)1 Fonslow…