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Homology modeling and ligand interaction of Cytochrome b protein

Keywords: Homology modeling , cytochrome b , Modeller9v7 , FlexX , PROCHECK

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Abstract:

Cytochrome b is a component of respiratory chain complex III, also known as the bc1 complex or ubiquinol-cytochrome c reductase. These complexes are involved in electron transport and the generation of ATP and thus play a vital role in the cell. The cytochrome bc1 complex is a membrane-bound enzyme that catalyses the transfer of electrons from ubiquinol to cytochrome c, coupling this process to the translocation of protons across the inner mitochondrial membrane. The function of proteins is generally determined by its three-dimensional (3D) structure. Thus, it would be useful to know the 3D structure of the thousands of protein sequences that are emerging from many genome projects. Structural studies on bio-molecules have changed our perception of the biological world in the last twenty years. A number of efforts have been made on structure prediction. One such technique that has found a wide appreciation is Homology modeling which aims at predicting the 3D structure of biomolecules, relying heavily on resources such as pattern/function and sequence. However, the three-dimensional structure of cytochrome b subunit protein (Accession number C4PKA1) from Homo sapiens remains unknown. In the present study, effort was made to generate the three-dimensional (3D) structure of the cytochrome b based on available template (1BGY) structural homologues from Protein Data Bank and the model validated with standard parameters (Procheck). With the predicted model, the ligand was subjected to docking study using FlexX docking tool. Flexible docking was carried out with the HEM - Protoporphyrin X [Heme] as ligand; which was found to bind at His267, Ile268 and Val343 residues on given generated protein. We therefore concluded that the above mentioned residues were the key residue sites for ligand binding. The predicted model showed better results than the template structure with 0% disallowed regions. This study will be used in broad screening of the protein in the respiratory process and can be further implemented in future drug designing.

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