Analysis of Atg proteins involved in the formation of the Atg1 complex, their interaction with the Atg8 protein during autophagosome maturation

Abstract

Aim. Relying on the data from numerous researches on the representatives of ATG proteins from H.sapiens and S.cerevisiae organisms, we decided to explore the difference between ATG proteins from plant organism. Subsequent stages comprised the determination of in silico phosphorylation effects on the native structure of the protein model and the possible influences on the stability of the three-dimensional complex by the molecular dynamics method. Methods. Methodologically, one can highlight the process of models elaboration on known sequences in AlphaFold 2.0 program and subsequent mechanistic review of molecular mobility of the obtained conformational models through the molecular dynamics in Gromacs 4.5 program and Charmm36 force field. Results. As a result of the model development and exploring the process of ATG-protein complexation, the geometrical specificities of the structures under investigation revealed the binding sites on the surface of the Atg1 complex components. We also suggested some areas for the intermolecular interactions based on the already published data on experimentl mutagenesis. Additively, we performed an analysis of the molecular dynamics simulations in the case of phosphorylation and its effect on the conformational mobility of these objects. Conclusions. Applying the computer simulation modelling methods we created the Atg1 complex elements and then analyzed these four proteins participating in the process.