ISSN 2736-1756
Advanced Journal of Microbiology Research ISSN 2241-9837 Vol. 12 (2), pp. 001-011, February, 2018. © International Scholars Journals
Full Length Research Paper
Bio-nanomodeling of active site in oxidized azurin using by computational methods
F. Mollaamin1*, K. Shahani poor2, T. Nejadsattari3 and M. Monajjemi1,4
1Department of Chemistry, Science and Research Branch, Islamic Azad University, Tehran. Iran.
2Ph.D Student, Science and Research Branch, Islamic Azad University, Tehran, Iran.
3Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
Accepted 10 December, 2017
Abstract
A cluster model for active site of oxidized azurin was presented and investigated the geometric structure and thermochemical parameters. Quantum-mechanical calculations were performed at the HF and B3lYP/6-31G levels of theory in the gas phase and eight solvents at four temperatures. Also, nuclear shielding parameters of the active site of oxidized azurin have been taken into account using GIAO and CSGT methods at the HF and B3LYP/6-31G levels of theory in the gas phase and in different solvents such as water, DMSO, nitromethane, methanol, ethanol, acetone, dichloroethane and dichloromethane. The results were revealed that the NMR chemical shielding parameters are strongly affected by inducing different solvent media. According to these theoretical results of energy values, some important relationships have been found between the dielectric constant and structural stability of active site of oxidized azurin. Thus, it can be drastically concluded that the dielectric permittivity of the solvent is a key factor that determines the chemical behavior of active site azurin in solution.
Key words: Azurin, IR, nuclear magnetic resonance, blue copper proteins, solvent effect.