Sagnella D E, Laasonen K, Klein M L
Department of Chemistry, University of Pennsylvania, Philadelphia 19104, USA.
Biophys J. 1996 Sep;71(3):1172-8. doi: 10.1016/S0006-3495(96)79321-9.
Proton transfer in biological systems is thought to often proceed through hydrogen-bonded chains of water molecules. The ion channel, gramicidin A (gA), houses within its helical structure just such a chain. Using the density functional theory based ab initio molecular dynamics Car-Parrinello method, the structure and dynamics of proton diffusion through a polyglycine analog of the gA ion channel has been investigated. In the channel, a proton, which is initially present as hydronium (H3O+), rapidly forms a strong hydrogen bond with a nearest neighbor water, yielding a transient H5O2+ complex. As in bulk water, strong hydrogen bonding of this complex to a second neighbor solvation shell is required for proton transfer to occur. Within gA, this second neighbor shell included not only a channel water molecule but also a carbonyl of the channel backbone. The present calculations suggest a transport mechanism in which a priori carbonyl solvation is a requirement for proton transfer.
生物系统中的质子转移通常被认为是通过水分子的氢键链进行的。离子通道短杆菌肽A（gA）在其螺旋结构中就包含这样一条链。使用基于密度泛函理论的从头算分子动力学Car-Parrinello方法，研究了质子通过gA离子通道的聚甘氨酸类似物扩散的结构和动力学。在通道中，最初以水合氢离子（H3O+）形式存在的质子迅速与最近邻的水分子形成强氢键，产生一个瞬态的H5O2+络合物。与在体水中一样，这种络合物与第二近邻溶剂化壳层形成强氢键是质子转移发生的必要条件。在gA内部，这个第二近邻壳层不仅包括一个通道水分子，还包括通道主链的一个羰基。目前的计算表明了一种传输机制，其中先验的羰基溶剂化是质子转移的必要条件。
