Kessel A, Cafiso D S, Ben-Tal N
Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.
Biophys J. 2000 Feb;78(2):571-83. doi: 10.1016/S0006-3495(00)76617-3.
Alamethicin is a 20-amino acid antibiotic peptide that forms voltage-gated ion channels in lipid bilayers. Here we report calculations of its association free energy with membranes. The calculations take into account the various free-energy terms that contribute to the transfer of the peptide from the aqueous phase into bilayers of different widths. The electrostatic and nonpolar contributions to the solvation free energy are calculated using continuum solvent models. The contributions from the lipid perturbation and membrane deformation effects and the entropy loss associated with peptide immobilization in the bilayer are estimated from a statistical thermodynamic model. The calculations were carried out using two classes of experimentally observed conformations, both of which are helical: the NMR and the x-ray crystal structures. Our calculations show that alamethicin is unlikely to partition into bilayers in any of the NMR conformations because they have uncompensated backbone hydrogen bonds and their association with the membrane involves a large electrostatic solvation free energy penalty. In contrast, the x-ray conformations provide enough backbone hydrogen bonds for the peptide to associate with bilayers. We tested numerous transmembrane and surface orientations of the peptide in bilayers, and our calculations indicate that the most favorable orientation is transmembrane, where the peptide protrudes approximately 4 A into the water-membrane interface, in very good agreement with electron paramagnetic resonance and oriented circular dichroism measurements. The calculations were carried out using two alamethicin isoforms: one with glutamine and the other with glutamate in the 18th position. The calculations indicate that the two isoforms have similar membrane orientations and that their insertion into the membrane is likely to involve a 2-A deformation of the bilayer, again, in good agreement with experimental data. The implications of the results for the biological function of alamethicin and its capacity to oligomerize and form ion channels are discussed.
短杆菌肽A是一种由20个氨基酸组成的抗生素肽，可在脂质双层中形成电压门控离子通道。在此，我们报告了其与膜的结合自由能的计算结果。这些计算考虑了有助于肽从水相转移到不同宽度双层膜中的各种自由能项。使用连续介质溶剂模型计算了溶剂化自由能的静电和非极性贡献。脂质扰动和膜变形效应的贡献以及与肽在双层膜中固定相关的熵损失是根据统计热力学模型估算的。计算使用了两类实验观察到的构象，二者均为螺旋构象：核磁共振（NMR）构象和X射线晶体结构。我们的计算表明，短杆菌肽A不太可能以任何NMR构象分配到双层膜中，因为它们具有未补偿的主链氢键，并且它们与膜的结合涉及较大的静电溶剂化自由能惩罚。相比之下，X射线构象为肽与双层膜结合提供了足够的主链氢键。我们测试了肽在双层膜中的多种跨膜和表面取向，我们的计算表明最有利的取向是跨膜取向，此时肽向水-膜界面突出约4埃，这与电子顺磁共振和取向圆二色性测量结果非常吻合。计算使用了两种短杆菌肽同工型：一种在第18位含有谷氨酰胺，另一种含有谷氨酸。计算表明这两种同工型具有相似的膜取向，并且它们插入膜中可能会使双层膜发生2埃的变形，这同样与实验数据吻合良好。文中讨论了这些结果对短杆菌肽A生物学功能及其寡聚化和形成离子通道能力的影响。
