KEREVİT GANGLİA TRANSKRİPTOMUNDAKİ OTOPETRİN BENZERİ BİR PROTON KANALININ MODELLENMESİ

Abstract

Crayfish is a frequently used model organism in neuroscience to understand the functions of ion channels and various neurotransmitters and neuromodulators. In silico modeling of the molecular structure of various proteins and their dynamic interactions with other proteins and ligands is increasingly yielding results that are compatible with experimental studies. Simulation has become an important tool that saves time and money in determining the interaction dynamics of the proteins in question and recommending various agonists or antagonists. In this thesis, the three-dimensional structure of the proton channel was determined by Alphafold using the complete sequences of a proton channel from the otopetrin family, which was determined for the first time by our research team. The relationship between structure and function was modeled by the NAMD molecular dynamics software using the CHARMM force field, and the proton transmission paths were determined by distribution of the positions where the ions are likely to be found in protein residues and aqueous solution.