A theoretical thermochemical study of solute-solvent dielectric effects in the displacement of codon-anticodon base pairs |
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Authors: | M Monajjemi M H Razavian F Mollaamin F Naderi B Honarparvar |
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Institution: | (1) Islamic Azad University, Tehran, Iran;(2) Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran;(3) Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran;(4) Department of Chemistry, Qom Branch, Islamic Azad University, Qom, Iran;(5) Department of Chemistry, Islamic Azad University, Shahriar-Shareh Gods Branch, Tehran, Iran |
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Abstract: | Quantum-chemical solvent effect theories describe the electronic structure of a molecular subsystem embedded in a solvent
or other molecular environment. The solvation of biomolecules is important in molecular biology, since numerous processes
involve proteins interacting in changing solvent-solute systems. In this theoretical study, we focus on mRNA-tRNA base pairs
as a fundamental step in protein synthesis influenced by hydrogen bonding between two antiparallel trinucleotides, namely,
the mRNA codon and tRNA anticodon. We use the mean reaction field theories, which describe electrostatic and polarization
interactions between solute and solvent in the AAA, UUU, AAG, and UUC triplex sequences optimized in various solvent media
such as water, dimethylsulfoxide, methanol, ethanol, and cyclopean using the self-consistent reaction field model. This process
depends on either the reaction potential function of the solvent or charge transfer operators that appear in solute-solvent
interaction. Because of codon and anticodon biological criteria, we performed nonempirical quantum-mechanical calculations
at the BLYP and B3LYP/3-21G, 6-31G, and 6-31G* levels of theory in the gas phase and five solvents at three temperatures.
Finally, to obtain more information, we calculated thermochemical parameters to find that the dielectric constant of solvents
plays an important role in the displacement of amino acid sequences on codon-anticodon residues in proteins, which can cause
some mutations in humans. |
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