Protein complexes can now be analysed in-vivo using a new technique.

As a performer of life activities, proteins exert their specific biological functions through interactions such as the formation of protein complexes. The localization effects, crowding effects, and microenvironments of intracellular organelles are essential for maintaining the structure and function of protein complexes.

Recently, a research team led by Professor Zhang Lihua of the Dalian Institute of Chemical Physics (DICP) of the Chinese Academy of Sciences (CAS) developed a cleavable cross-linker based on glycosidic bonds. Data analysis throughput and accuracy of identification of cross-linking information with good, biocompatible amphibians. It enables in vivo cross-linking of protein complexes in living cells and achieves accurate and large-scale analysis. The study has been published in Angewandte Chemie International Edition On March 30th.

Cross-linked chemiluminescence mass spectrometry (CXMS), particularly in vivo CXMS, is a large-scale analysis of the in situ formation and interaction interface of protein complexes in living cells. However, in vivo CXMS in living cells faces challenges such as high cell perturbation and complex spectra retrieval of crosslinked peptides.

In this study, the researchers incorporated glycosidic bonds into the design of functional crosslinks based on the high biocompatibility of glucose molecules and the mass spectrometric splitting property of glycosidic bonds. They screened and obtained trehalose, a highly biocompatible molecule, as the skeleton molecule and developed a mass spectrometry-cleavable cross-linker, trehalose disuccinimidyl succinate (TDS).

This cross-linker showed superior maintenance of cell viability compared to the currently reported membrane-permeable chemical cross-linkers and enabled efficient cross-linking of protein complexes in cells under low perturbation conditions.

The authors found that the low-energy glycosidic bond-selective fragmentation mode of high-energy peptide bond mass spectrometry reduces the analysis complexity of the spectra of crosslinked peptide fragments, which greatly improves the efficiency and accuracy of crosslinked peptide identification.

They identified the conformation of 1,453 proteins corresponding to more than 3,500 crosslinked peptide pairs, and 843 protein-protein interaction information from Hela cells.

“We have thoroughly realized the cross-linking and global analysis of protein complexes in living cells, and provided an important toolkit for exploring interaction sites to regulate protein function in the microenvironment of living cells,” said Professor Zhang.