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PresentationsComparative analysis of molecular docking methods for modeling the interaction of the FtsZ protein peptide with the SepF and FtsA proteinsLomonosov Moscow State University, Faculty of Biology, Department of Biophysics, Russia, 119992, Moscow, Leninskie Gory, 1-24 Bacterial cell division is a fundamental biological process that enables cell growth and reproduction. It is mediated by a multiprotein complex known as the divisome. One of the central components of the divisome is the FtsZ protein, a structural and functional analogue of eukaryotic tubulin that forms a dynamic Z-ring at the site of future septation. To perform its functions, FtsZ interacts with a number of partner proteins, including FtsA and SepF, which play an important role in stabilizing the Z-ring and anchoring it to the cytoplasmic membrane. It is known that a significant portion of FtsZ's interactions with its partner proteins are mediated through its short C-terminal peptide region. This region is characterized by high conformational flexibility and is capable of binding to various protein surfaces, making it a convenient model system for studying protein–peptide interactions. This study investigates the interaction of the FtsZ peptide with the SepF and FtsA proteins using protein–protein and protein–peptide docking methods. The primary objective of the study is to analyze and compare various computational approaches and software tools used to model such interactions, as well as to assess their applicability to systems involving short and flexible peptides. Available experimental structures of the SepF and FtsA proteins with the FtsZ peptide fragment were used as initial models for docking calculations. The methods under consideration differ in the algorithms used to search the conformational space, the degree to which component flexibility is taken into account, and the types of scoring functions. Particular attention is paid to the specific features of modeling the interaction interfaces characteristic of the FtsZ–SepF and FtsZ–FtsA complexes. To analyze the resulting docking models, structural criteria were used, including an assessment of the geometric correspondence of the complexes, an analysis of intermolecular contacts, and the spatial organization of the interaction interface. These data were compared with the known structures of the complexes. This work was supported by the Russian Science Foundation (project no. 25-44-01015, https://rscf.ru/project/25-44-01015/).
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