TY - JOUR
T1 - The electronic-structure theory of a large-molecular system in solution
T2 - Application to the intercalation of proflavine with solvated DNA
AU - Yoshida, Norio
AU - Kiyota, Yasuomi
AU - Hirata, Fumio
N1 - Funding Information:
This work is supported by the Grant-in Aid for Scientific Research on Innovative Area of ‘Molecular Science of Fluctuations toward Biological Functions’ from the MEXT in Japan . We are also grateful to the support by the grant from the Next Generation Supercomputing Project, Nanoscience Program of the ministry. All biological graphics in this paper were described by using UCSF chimera, an extensible molecular modeling system, http://www.cgl.ucsf.edu/chimera [53] . N.Y. also thanks Prof. Shankar P. Das for carefully reading the manuscript.
PY - 2011/2/15
Y1 - 2011/2/15
N2 - A new approach for investigating solvent effects on the electronic structure of solvated macromolecules is proposed. The method is constructed by combining the quantum and molecular mechanics (QM/MM) methods with the reference interaction site model (RISM) theory. The system treated with the method is divided into three regions, quantum and molecular mechanical regions of solute, and the solvent region. The two solute regions are treated by the ordinary QM/MM method, while the solvent region is handled with the RISM theory. The method is applied to investigate the intercalation of proflavine to two types of decameric B-DNA, namely [deca(dG-dC)]2 and [deca(dA-dT)]2. Our results indicate that the affinity of intercalation of proflavine to the dG-dC base sequence is higher than that of the dA-dT DNA base sequence, which is consistent with the experimental results. The drastic change of solvation structure due to the intercalation makes large positive change in the solvation free energy which is attributed to the dehydration penalty of PR, the screening of electrostatic interaction between PR and DNA, and the hydrophobic interaction of elongated DNA chain.
AB - A new approach for investigating solvent effects on the electronic structure of solvated macromolecules is proposed. The method is constructed by combining the quantum and molecular mechanics (QM/MM) methods with the reference interaction site model (RISM) theory. The system treated with the method is divided into three regions, quantum and molecular mechanical regions of solute, and the solvent region. The two solute regions are treated by the ordinary QM/MM method, while the solvent region is handled with the RISM theory. The method is applied to investigate the intercalation of proflavine to two types of decameric B-DNA, namely [deca(dG-dC)]2 and [deca(dA-dT)]2. Our results indicate that the affinity of intercalation of proflavine to the dG-dC base sequence is higher than that of the dA-dT DNA base sequence, which is consistent with the experimental results. The drastic change of solvation structure due to the intercalation makes large positive change in the solvation free energy which is attributed to the dehydration penalty of PR, the screening of electrostatic interaction between PR and DNA, and the hydrophobic interaction of elongated DNA chain.
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U2 - 10.1016/j.molliq.2010.04.019
DO - 10.1016/j.molliq.2010.04.019
M3 - Article
AN - SCOPUS:79952009095
SN - 0167-7322
VL - 159
SP - 83
EP - 92
JO - Journal of Molecular Liquids
JF - Journal of Molecular Liquids
IS - 1
ER -