Department of Chemistry, City College of New York/CUNY, New York, New York, USA.
Biophys J. 2013 Feb 5;104(3):633-42. doi: 10.1016/j.bpj.2012.12.038.
Protegrin is an antimicrobial peptide with a β-hairpin structure stabilized by a pair of disulfide bonds. It has been extensively studied by solid-state NMR and computational methods. Here we use implicit membrane models to examine the binding of monomers on the surface and in the interior of the membrane, the energetics of dimerization, the binding to membrane pores, and the stability of different membrane barrel structures in pores. Our results challenge a number of conclusions based on previous experimental and theoretical work. The burial of monomers into the membrane interior is found to be unfavorable for any membrane thickness. Because of its imperfect amphipathicity, protegrin binds weakly, at most, on the surface of zwitterionic membranes. However, it binds more favorably onto toroidal pores. Anionic charge on the membrane facilitates the binding due to electrostatic interactions. Solid-state NMR results have suggested a parallel NCCN association of monomers in dimers and association of dimers to form octameric or decameric β-barrels. We find that this structure is not energetically plausible for binding to bilayers, because in this configuration the hydrophobic sides of two monomers point in opposite directions. In contrast, the antiparallel NCCN and especially the parallel NCNC octamers are stable and exhibit a favorable binding energy to the pore. The results of 100-ns simulations in explicit bilayers corroborate the higher stability of the parallel NCNC barrel compared with the parallel NCCN barrel. The ability to form pores in zwitterionic membranes provides a rationalization for the peptide's cytotoxicity. The discrepancies between our results and experiment are discussed, and new experiments are proposed to resolve them and to test the validity of the models.
防御素是一种具有β发夹结构的抗菌肽，由一对二硫键稳定。它已经通过固态 NMR 和计算方法进行了广泛的研究。在这里，我们使用隐式膜模型来研究单体在膜表面和内部的结合、二聚体的形成能、与膜孔的结合以及不同膜桶结构在孔中的稳定性。我们的结果挑战了一些基于以前的实验和理论工作的结论。单体嵌入膜内部的掩埋被发现不利于任何膜厚度。由于其不完全的两亲性，防御素最多只能在两性离子膜的表面上弱结合。然而，它在环形孔上的结合更为有利。膜上的阴离子电荷由于静电相互作用而促进了结合。固态 NMR 结果表明单体在二聚体中的 NCCN 平行缔合以及二聚体缔合形成八聚体或十聚体β桶。我们发现，这种结构在与双层结合时在能量上是不可行的，因为在这种构象中，两个单体的疏水面指向相反的方向。相比之下，反平行 NCCN 特别是平行 NCNC 八聚体是稳定的，并且表现出对孔的有利结合能。在明式双层中进行的 100ns 模拟的结果证实了平行 NCNC 桶与平行 NCCN 桶相比具有更高的稳定性。在两性离子膜中形成孔的能力为肽的细胞毒性提供了合理化解释。我们讨论了我们的结果与实验之间的差异，并提出了新的实验来解决这些差异，并测试模型的有效性。
