Hydration and DNA recognition by homeodomains
Hydration and DNA recognition by homeodomains
复制标题
DOI：
10.1016/s0092-8674(00)81306-9
复制
发表时间：
1996-06-28
期刊：
影响因子：
64.5
通讯作者：
Wuthrich, K
中科院分区：
文献类型：
--
作者：
Billeter, M;Guntert, P;Wuthrich, K
在环境温度和压力下，在明确的溶剂水中进行了2纳秒分子动力学（MD）模拟，以补充实验核磁共振（NMR）数据的结构和动力学的这种复杂的一个nanosecond同源结构域-DNA复合物。除了直接的蛋白质-DNA接触，MD轨迹属性的一个重要作用，为特定的DNA识别水分子介导的分子间接触。模拟提供了一个详细的描述的途径水合水分子交换进出的蛋白质-DNA界面，并表明这些“内部”的沃茨的停留时间是在纳秒的时间尺度上，附近的低端的范围内确定的NMR。
A 2-nanosecond molecular dynamics (MD) simulation of an Antennapedia homeodomain-DNA complex in explicit solvent water at ambient temperature and pressure was performed to supplement experimental nuclear magnetic resonance (NMR) data on the structure and dynamics of this complex. In addition to direct protein-DNA contacts, the MD trajectory attributes an essential role for specific DNA recognition to hydration water molecules that mediate intermolecular contacts. The simulation provides a detailed description of the pathways of hydration water molecules exchanging in and out of the protein-DNA interface and indicates that the residence times of these ''interior'' waters are on the nanosecond time scale, near the lower end of the range determined by NMR.