Dynamic distance disorder in proteins is caused by trapping
Dynamic distance disorder in proteins is caused by trapping
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DOI：
10.1021/jp057497p
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发表时间：
2006-05-18
影响因子：
3.3
通讯作者：
Karplus, Martin
中科院分区：
文献类型：
--
作者：
Luo, Guobin;Andricioaei, Ioan;Karplus, Martin
通过分子动力学模拟研究了单分子电子传递速率的变化所证明的蛋白质的动态紊乱。计算了NAD(P) H：黄素氧化还原酶（Fre）与黄素腺嘌呤二核苷酸（FAD）配合物在供体-受体距离波动时的平均力势，结果与电子转移实验结果一致。计算得到的距离波动的自相关函数在飞秒到纳秒时间尺度上，在低温下具有简单的指数行为，在高温下具有拉伸指数行为。这表明，计算出的动态无序是由蛋白质能量图上势阱的广泛捕获时间引起的，并提出了在更长的时间尺度上实验观察到的拉伸指数行为的相应起源。
Dynamic disorder in proteins, as demonstrated by variations in single-molecule electron transfer rates, is investigated by molecular dynamics simulations. The potential of mean force for the fluctuating donor-acceptor distance is calculated for the NAD( P) H: flavin oxidoreductase ( Fre) complex with flavin adenine dinucleotide ( FAD) and is found to be in agreement with that estimated from electron transfer experiments. The calculated autocorrelation function of the distance fluctuations has a simple exponential behavior at low temperatures and stretched exponential behavior at higher temperatures on femtosecond to nanosecond time scales. This indicates that the calculated dynamic disorder arises from a wide range of trapping times in potential wells on the protein energy landscape and suggests a corresponding origin for the stretched exponential behavior observed experimentally on longer time scales.