Homology modeling and molecular dynamics simulation of an alpha Methyl coenzyme M reductase from methanogenic archea

摘要

Methanogenic archeans are organisms of considerable ecological and biotechnological interest, which produce methane through a restricted metabolic pathway. In the present article, homology modeling and molecular dynamics (MD) simulations were employed to construct the three-dimensional structures of the alpha Methyl-coenzyme M reductase (MCR-α) of the Methanogenic archeans from Tucuruí hydroelectric dam in eastern Brazilian Amazonia. The models obtained of the archean MCR-α presented approximately 70% and 69% sequence identity in comparison with the MCR-α from Methanopyrus klanderi and Methanosarcina barkeri, respectively. The analysis of the homology modeling and MD simulation indicates that our theoretical prediction is consistent with known experimental data and show that 3D structures of the MCR-α from archeans of different orders tend to be well-conserved. In additional, the electrostatic surface potentials were obtained and compared for the MCR-α from the two different forms.