Luo Guobin, Andricioaei Ioan, Xie X Sunney, Karplus Martin
Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
J Phys Chem B. 2006 May 18;110(19):9363-7. doi: 10.1021/jp057497p.
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.
通过分子动力学模拟研究了蛋白质中的动态无序，这是由单分子电子转移速率的变化所证明的。计算了与黄素腺嘌呤二核苷酸（FAD）形成的NAD(P)H：黄素氧化还原酶（Fre）复合物中供体-受体距离波动的平均力势，并发现其与从电子转移实验估计的结果一致。在飞秒到纳秒的时间尺度上，计算得到的距离波动自相关函数在低温下具有简单的指数行为，在较高温度下具有拉伸指数行为。这表明计算出的动态无序源于蛋白质能量景观上势阱中广泛的捕获时间，并为在更长时间尺度上实验观察到的拉伸指数行为提出了相应的起源。
