Alamethicin channels - modelling via restrained molecular dynamics simulations
Alamethicin channels - modelling via restrained molecular dynamics simulations
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DOI：
10.1016/s0005-2736(96)00262-3
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发表时间：
1997-04-26
影响因子：
3.4
通讯作者：
Sansom, MSP
中科院分区：
文献类型：
--
作者：
Breed, J;Biggin, PC;Sansom, MSP
丙甲霉素通道已被建模为近似平行的跨双层螺旋束，每束包含N = 4至8个螺旋。通过在真空中约束的分子动力学（MD）模拟生成初始模型，并通过60 ps MD模拟与水分子存在于中心孔内和口处进行细化。螺旋束通过孔内水分子和Gln-7侧链之间的II-键网络稳定。通道电导预测的基础上的孔隙半径分布，并建议N = 4束形成闭塞孔，而孔与N大于或等于5螺旋每束是开放的。连续静电学计算表明，N=6孔是阳离子选择性的，而每束N大于或等于7螺旋的孔被预测为离子选择性稍低。
Alamethicin channels have been modelled as approximately parallel bundles of transbilayer helices containing between N = 4 and 8 helices per bundle. Initial models were generated by in vacuo restrained molecular dynamics (MD) simulations, and were refined by 60 ps MD simulations with water molecules present within and at the mouths of the central pore. The helix bundles were stabilized by networks of II-bonds between intra-pore water molecules and Gln-7 side-chains. Channel conductances were predicted on the basis of pore radius profiles, and suggested that the N = 4 bundle formed an occluded pore, whereas pores with N greater than or equal to 5 helices per bundle were open. Continuum electrostatics calculations suggested that the N=6 pore is cation-selective, whereas pores with N greater than or equal to 7 helices per bundle were predicted to be somewhat less ion-selective.