Holyoake John, Domene Carmen, Bright Joanne N, Sansom Mark S P
Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
Eur Biophys J. 2004 May;33(3):238-46. doi: 10.1007/s00249-003-0355-2. Epub 2003 Oct 22.
Bacterial homologues of mammalian potassium channels provide structures of two states of a gated K channel. Thus, the crystal structure of KcsA represents a closed state whilst that of MthK represents an open state. Using homology modelling and molecular dynamics simulations we have built a model of the transmembrane domain of KcsA in an open state and have compared its conformational stability with that of the same domain of KcsA in a closed state. Approximate Born energy calculations of monovalent cations within the two KcsA channel states suggest that the intracellular hydrophobic gate in the closed state provides a barrier of height approximately 5 kT to ion permeation, whilst in the open state the barrier is absent. Simulations (10 ns duration) in an octane slab (a simple membrane mimetic) suggest that closed- and open-state models are of comparable conformational stability, both exhibiting conformational drifts of approximately 3.3 A Calpha RMSD relative to the respective starting models. Substantial conformational fluctuations are observed in the intracellular gate region during both simulations (closed state and open state). In the simulation of open-state KcsA, rapid ( < 5 ns) exit of all three K+ ions occurs through the intracellular mouth of the channel. Helix kink and swivel motion is observed at the molecular hinge formed by residue G99 of the M2 helix. This motion is more substantial for the open- than for the closed-state model of the channel.
哺乳动物钾通道的细菌同源物提供了门控钾通道两种状态的结构。因此，KcsA的晶体结构代表关闭状态，而MthK的晶体结构代表开放状态。利用同源建模和分子动力学模拟，我们构建了开放状态下KcsA跨膜结构域的模型，并将其构象稳定性与关闭状态下KcsA相同结构域的构象稳定性进行了比较。对两种KcsA通道状态下单价阳离子的近似玻恩能量计算表明，关闭状态下的细胞内疏水门对离子渗透提供了约5 kT高度的屏障，而在开放状态下则不存在该屏障。在辛烷板（一种简单的膜模拟物）中的模拟（持续时间10 ns）表明，关闭状态和开放状态模型具有相当的构象稳定性，相对于各自的起始模型，两者均表现出约3.3 Å Cα均方根偏差的构象漂移。在两种模拟（关闭状态和开放状态）过程中，均在细胞内门区域观察到大量的构象波动。在开放状态KcsA的模拟中，所有三个K+离子通过通道的细胞内口快速（<5 ns）流出。在由M2螺旋的G99残基形成的分子铰链处观察到螺旋扭结和旋转运动。对于通道的开放状态模型，这种运动比关闭状态模型更显著。
