Poxleitner M, Seitz-Beywl J, Heinzinger K
Max-Planck-Institut für Chemie (Otto-Hahn-Institut), Mainz, Bundesrepublik Deutschland.
Z Naturforsch C J Biosci. 1993 Jul-Aug;48(7-8):654-65. doi: 10.1515/znc-1993-7-820.
Molecular Dynamics (MD) simulations were performed on a gramicidin A dimer model representing a transmembrane channel. Different from previous simulations the peptide was in contact with bulk water at both ends of the dimer to guarantee a realistic description of the hydration of the biomolecule. The flexible BJH model for water was employed in the simulations and the gramicidin-water, gramicidin-ion and ion-water potentials used are based on molecular orbital calculations. The water structure near the gramicidin was investigated first by a simulation without ions, while for the energy profiles of the ion transport through the channel a potassium or a sodium ion was added. These investigations provide a detailed and conclusive picture on a molecular level of the role of water in the ion transport through a gramicidin A channel and can explain the experimental results on the selectivity between alkali ions, their double or even triple occupancy, the exclusion or permeability of anions depending upon cation concentration and the consequences of differences in the ionic charge. The investigation demonstrate that the water molecules around the gramicidin behave as an integral part of the peptide and the functionality is the result of the whole complex biomolecule-water.
对代表跨膜通道的短杆菌肽A二聚体模型进行了分子动力学（MD）模拟。与之前的模拟不同，该肽在二聚体的两端都与大量水接触，以确保对生物分子水合作用的真实描述。模拟中采用了灵活的BJH水模型，所使用的短杆菌肽-水、短杆菌肽-离子和离子-水势均基于分子轨道计算。首先通过无离子模拟研究了短杆菌肽附近的水结构，而对于离子通过通道的能量分布，则添加了钾离子或钠离子。这些研究在分子水平上详细而确凿地描绘了水在通过短杆菌肽A通道的离子运输中的作用，并可以解释关于碱金属离子选择性、其双重甚至三重占据、阴离子根据阳离子浓度的排斥或渗透性以及离子电荷差异后果的实验结果。研究表明，短杆菌肽周围的水分子表现为肽的一个组成部分，其功能是整个生物分子-水复合物的结果。
