Dror Ron O, Jensen Morten Ø, Shaw David E
D. E. Shaw Research, New York, NY 10036, USA.
Annu Int Conf IEEE Eng Med Biol Soc. 2009;2009:2340-2. doi: 10.1109/IEMBS.2009.5335057.
Recent advances in algorithms, software, and hardware for molecular dynamics (MD) simulations have brought previously inaccessible simulation timescales within reach, allowing the use of MD simulation to address a substantially broader set of questions regarding protein function. MD has proved particularly useful in elucidating the functional mechanisms of membrane proteins, whose dynamics are especially difficult to characterize experimentally. Here, we illustrate the utility of state-of-the-art high-performance MD simulations in the study of membrane proteins, using as examples a G-protein-coupled receptor, an aquaporin, and an antiporter. In each case, we used MD either to deduce an atomic-level mechanism for protein function or to reconcile apparent discrepancies among recent experimental observations.
分子动力学（MD）模拟在算法、软件和硬件方面的最新进展已使以前无法达到的模拟时间尺度变得可行，从而能够利用MD模拟来解决关于蛋白质功能的一系列更广泛的问题。事实证明，MD在阐明膜蛋白的功能机制方面特别有用，因为膜蛋白的动力学很难通过实验来表征。在这里，我们以一种G蛋白偶联受体、一种水通道蛋白和一种反向转运蛋白为例，来说明最先进的高性能MD模拟在膜蛋白研究中的实用性。在每种情况下，我们都使用MD来推断蛋白质功能的原子水平机制，或协调最近实验观察结果之间明显的差异。
