Biomedical Chemistry: Research and Methods 2024, 7(3), e00224

Strategy for Experimental Studies of Target Protein Interactomics

P.V. Ershov, Y.V. Mezentsev, E.O. Yablokov, L.A. Kaluzhskiy, O.V. Gnedenko*,
A.A. Gilep, A.S. Ivanov

Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121 Russia; *e-mail: gnedenko.oksana@gmail.com

Keywords: protein-protein interactions; affine selection; protein subinteractome; complexation; surface plasmon resonance; platform

DOI:10.18097/BMCRM00224

The whole version of this paper is available in Russian.

It is known that intermolecular interactions of proteins and peptides play a critical role in life processes. Such interactions can be either directly related to the implementation of various functions or play the role of a regulator. Currently, there is no doubt that the majority of proteins function as part of various molecular complexes, the formation of which occurs due to protein-protein interactions (PPIs), the totality of which can be defined as the “protein interactome”. Protein subinteractome studies are critical for studying the functions and regulatory mechanisms of unknown or poorly annotated proteins, understanding the architecture of intracellular molecular machines, and the design of PPI modulators. Previously, we used combinations of experimental approaches, as well as analytical and preparative methods, to study the subinteractomes of functionally different cellular proteins, which allowed us to identify the protein subinteractomes of several clinically significant human proteins. The purpose of this work was to conceptualize the principles of the experimental platform we developed for studying protein subinteractomes and to describe its features in detail.
Figure 1. Block-diagram of the experimental platform for the study of protein subinteractomes.
Figure 2. SPR analysis of the interaction of the protein material of liver tissue lysate SEC fractions with immobilized protein CXXC1 (Uniprot ID: Q9P0U4) on the biosensor chip. (A) – distribution of the total binding signals of the protein material in the range of 1000 - 2000 kDa, (I); 150 - 500 kDa (II); 15 - 100 kDa (III). (B) - distribution of binding signals of the protein material of liver tissue lysate SEC fractions with average molecular weights of 15, 30, 45, 75 and 100 kDa. One RU (Resonance Unit) corresponds to the binding of one 1 pg of the protein material on one mm2 of the biosensor chip surface.

CLOSE
Table 1. Structure of the experimental platform for studying the subinteractomes of target proteins.

FUNDING

The research was supported by the Russian Science Foundation grant No. 23-15-00149.

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