DNA-protein binding mediated by a solvent site-dipole field

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• 作者：Nobuyuki Hamasaki ; Hiroo Miyagawa ; Daisuke Mitomo ; Akihiko Yamagisi and Junichi Higo
• 刊名：Chemical Physics Letters
• 出版年：2006
• 出版时间：11 November 2006
• 年：2006
• 卷：431
• 期：1-3
• 页码：160-163
• 全文大小：362 K

文摘

We performed a molecular dynamics simulation to study the binding process between DNA and the third DNA binding region of HMG-I(Y) in explicit water. Starting from a configuration where the two biomolecules were positioned spatially apart to each other, they approached and bound to each other during the simulation. In this process, a solvent site-dipole field was formed in the inter-biomolecular zone, as if the field connects the biomolecules. This indicates that the directional motions of water molecules were restrained in the zone, and suggests that the solvent site-dipole field may mediate the molecular binding.