Baştuğ Turgut, Kuyucak Serdar
Department of Materials Science and Nanotechnology, Faculty of Engineering, TOBB University of Economy and Technology, Ankara, Turkey.
School of Physics, University of Sydney, Sydney, NSW, 2006, Australia.
Biophys Rev. 2012 Sep;4(3):271-282. doi: 10.1007/s12551-012-0084-9. Epub 2012 Sep 1.
Membrane proteins control the traffic across cell membranes and thereby play an essential role in cell function from transport of various solutes to immune response via molecular recognition. Because it is very difficult to determine the structures of membrane proteins experimentally, computational methods have been increasingly used to study their structure and function. Here we focus on two classes of membrane proteins-ion channels and transporters-which are responsible for the generation of action potentials in nerves, muscles, and other excitable cells. We describe how computational methods have been used to construct models for these proteins and to study the transport mechanism. The main computational tool is the molecular dynamics (MD) simulation, which can be used for everything from refinement of protein structures to free energy calculations of transport processes. We illustrate with specific examples from gramicidin and potassium channels and aspartate transporters how the function of these membrane proteins can be investigated using MD simulations.
膜蛋白控制着跨细胞膜的物质运输，从而在细胞功能中发挥着至关重要的作用，涵盖了从各种溶质的运输到通过分子识别进行免疫反应等多个方面。由于通过实验确定膜蛋白的结构非常困难，因此计算方法越来越多地被用于研究它们的结构和功能。在这里，我们聚焦于两类膜蛋白——离子通道和转运蛋白，它们负责在神经、肌肉和其他可兴奋细胞中产生动作电位。我们描述了计算方法如何被用于构建这些蛋白的模型以及研究其运输机制。主要的计算工具是分子动力学（MD）模拟，它可用于从优化蛋白质结构到运输过程的自由能计算等各个方面。我们通过短杆菌肽、钾通道和天冬氨酸转运蛋白的具体例子来说明如何使用MD模拟来研究这些膜蛋白的功能。
