Protein-Nucleic Acid Recognition: Simulation of Base and “Model” Amino Acids Complexes in DMSO by the Monte Carlo Method

Abstract

A computer simulation of guanine (G), cytosine (C), the G-C base pair, protonated C (CH⁺), acetic acid in neutral (AcOH) and deprotonated (AcO⁻) forms, G-AcO⁻, C-AcOH, and CH⁺⁻AcO⁻ complexes, solvated in DMSO was carried out by the Monte Carlo method. It is shown that the G-C base pair formation in DMSO is energetically favorable. The G-AcO⁻ complex formation is comparable with the formation of G-C base pair in energetical favorability. In this case the acetate anion can replace C in the G-C base pair. The formation of the C-AcOH complex is much less favorable than the formation of the G-C pair. However proton transfer from AcOH to C leads to the formation of the CH⁺-AcO⁻ complex, which is the most favorable of all complexes studied. Here the acetic acid can replace G in a G-C base pair. The formation of G-AcO⁻ and CH+-AcO⁻ specific complexes detected in DMSO with the help of experiment and theory is a competitive process with respect to the formation of G-C base pairs, and can be considered the primary step in the real mechanism of protein-nucleic acid recognition.