Change in specific interactions between lactose repressor protein and DNA induced by ligand binding: molecular dynamics and molecular orbital calculations

Matsushita, Yushu; Murakawa, Takeru; Shimamura, Kanako; Ohyama, Tatsuya; Oishi, Masatsugu; Kurita, Noriyuki

doi:10.1080/08927022.2015.1036265

Cited by 6 publications

(1 citation statement)

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“…However, it is more realistic to use an explicit solvent model. Hence, FMO calculations have been performed with explicit models for an oligopeptide [8], proteins [9][10][11], ligands [12], protein/ligand complexes [13][14][15], double-stranded (ds) DNAs [16,17], and a protein/dsDNA complex [18]. To the list we would like to add a single-stranded DNA (ssDNA) and its complex with a protein.…”

Section: Introductionmentioning

confidence: 99%

Explicit solvation of a single-stranded DNA, a binding protein, and their complex: a suitable protocol for fragment molecular orbital calculation

Komeij

Okiyama²,

Mochizuki

et al. 2017

CBIJ

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Fragment molecular orbital (FMO) calculations were performed for explicitly solvated single-stranded DNA (ssDNA), ssDNA binding protein, and their complex in order to assess the solvent effects on the solutes and thereby to find optimal solvation conditions for FMO calculation. A series of solvated structures were generated with different solvent thicknesses. The structures were subjected to FMO calculation at MP2/6-31G* to obtain the net charges and internal energies of the solutes and the solute-solvent interaction energies as functions of the solvent thickness. In all cases, the properties showed complete or marginal convergence at ca. 6 Ǻ, regardless whether or not the system charge was neutralized. This suggested that the first and second solvent shells mainly determine the electronic structure of a solute while the outer solvent including ions has only minor effects, consistent with several preceding reports. In light of this, and considering safety as a factor, we conclude that a solvent shell thickness of ca. 8 Ǻ suffices for FMO calculation of the solutes.

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