Protein-nucleic acid recognition: simulation of base and "model" amino acids complexes in DMSO by the Monte Carlo method.
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 energetically 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.
Danilov
V I
VI
Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine.
Slyusarchuk
O N
ON
Poltev
V I
VI
Alderfer
J L
JL
D000596:Amino Acids; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004121:Dimethyl Sulfoxide; D008958:Models, Molecular; D009010:Monte Carlo Method; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins; D004247:DNA; D004121:Dimethyl Sulfoxide