Protein-protein interaction study by molecular computer modeling

Kovalenko, I.B.; Fedorov, V.A.; Khruschev, S.S.; Riznichenko, G.Y.; Rubin, A.B.

Авторы: Kovalenko I.B., Fedorov V.A., Khruschev S.S., Riznichenko G.Yu, Rubin A.B.
Журнал: Biophysical Reviews
Том: 15
Год издания: 2023
Издательство: Springer Verlag
Местоположение издательства: Germany
Первая страница: 1611
Последняя страница: 1611
DOI: 10.1007/s12551-023-01150-w
Аннотация: In most biological systems, protein molecules play a key role. Using the methods of X-ray diffraction analysis and nuclear magnetic resonance, the spatial structures of many different proteins and their complexes have been studied. However, it still remains unclear in detail to what extent electrostatic and hydrophobic interactions affect the rate of for- mation of protein complexes at various stages of molecular approach. The formation of a protein complex is a multi-stage process that requires taking into account many factors, such as long-range electro- static interactions between protein surfaces, geometric and chemical complementarity of binding regions, molecular mobility in the protein- protein interface, and hydrophobic interactions. We have developed an original approach that allows, thanks to the combined use of Brownian and molecular dynamics methods, to predict the structure of the formed complex and the molecular mechanisms that led to its formation. In this approach, the Brownian dynamics method is used to model the forma- tion of a collision complex by two proteins, taking into account diffu- sion processes and electrostatic interactions, and molecular dynamics is used to model the transformation of a preliminary complex into a final one, taking into account the mobility of atoms, conformational changes, and solvent molecules.This approach allowed us to reveal the role of electrostatic and hydro- phobic interactions in the formation of the complex of plastocyanin and cytochrome f proteins in cyanobacteria, green algae and higher plants, and to show that their role in complex formation changes along with evolutionary changes in protein sequences.The work was supported by the grant of the Russian Science Founda- tion #21-74-20035.
Добавил в систему: Федоров Владимир Андреевич

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