Breed J, Biggin P C, Kerr I D, Smart O S, Sansom M S
Laboratory of Molecular Biophysics, University of Oxford, UK.
Biochim Biophys Acta. 1997 Apr 26;1325(2):235-49. doi: 10.1016/s0005-2736(96)00262-3.
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 H-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 > or = 5 helices per bundle were open. Continuum electrostatics calculations suggested that the N = 6 pore is cation-selective, whereas pores with N > or = 7 helices per bundle were predicted to be somewhat less ion-selective.
短杆菌肽通道被模拟为跨膜螺旋的近似平行束，每束包含4至8个螺旋。初始模型通过真空受限分子动力学（MD）模拟生成，并通过在中心孔内部和孔口存在水分子的情况下进行60皮秒的MD模拟进行优化。螺旋束通过孔内水分子和Gln-7侧链之间的氢键网络得以稳定。基于孔径分布预测了通道电导，结果表明每束4个螺旋的束形成了一个封闭的孔，而每束螺旋数N≥5的孔是开放的。连续介质静电学计算表明，每束6个螺旋的孔具有阳离子选择性，而每束螺旋数N≥7的孔预计离子选择性稍低。
