Ulmschneider Martin B, Sansom Mark S P, Di Nola Alfredo
Department of Chemistry, University of Rome La Sapienza, I-00185 Rome, Italy.
Biophys J. 2006 Mar 1;90(5):1650-60. doi: 10.1529/biophysj.105.065367. Epub 2005 Dec 9.
A computational method to calculate the orientation of membrane-associated alpha-helices with respect to a lipid bilayer has been developed. It is based on a previously derived implicit membrane representation, which was parameterized using the structures of 46 alpha-helical membrane proteins. The method is validated by comparison with an independent data set of six transmembrane and nine antimicrobial peptides of known structure and orientation. The minimum energy orientations of the transmembrane helices were found to be in good agreement with tilt and rotation angles known from solid-state NMR experiments. Analysis of the free-energy landscape found two types of minima for transmembrane peptides: i), Surface-bound configurations with the helix long axis parallel to the membrane, and ii), inserted configurations with the helix spanning the membrane in a perpendicular orientation. In all cases the inserted configuration also contained the global energy minimum. Repeating the calculations with a set of solution NMR structures showed that the membrane model correctly distinguishes native transmembrane from nonnative conformers. All antimicrobial peptides investigated were found to orient parallel and bind to the membrane surface, in agreement with experimental data. In all cases insertion into the membrane entailed a significant free-energy penalty. An analysis of the contributions of the individual residue types confirmed that hydrophobic residues are the main driving force behind membrane protein insertion, whereas polar, charged, and aromatic residues were found to be important for the correct orientation of the helix inside the membrane.
已开发出一种计算方法，用于计算膜相关α螺旋相对于脂质双层的取向。该方法基于先前推导的隐式膜表示，其使用46种α螺旋膜蛋白的结构进行参数化。通过与一组已知结构和取向的6种跨膜肽和9种抗菌肽的独立数据集进行比较，对该方法进行了验证。发现跨膜螺旋的最小能量取向与固态NMR实验中已知的倾斜角和旋转角高度一致。对自由能景观的分析发现，跨膜肽有两种类型的最小值：i）螺旋长轴与膜平行的表面结合构型，以及ii）螺旋以垂直取向跨越膜的插入构型。在所有情况下，插入构型也包含全局能量最小值。用一组溶液NMR结构重复计算表明，膜模型能够正确区分天然跨膜构象与非天然构象。所有研究的抗菌肽都被发现与膜表面平行取向并结合，这与实验数据一致。在所有情况下，插入膜都会带来显著的自由能惩罚。对单个残基类型贡献的分析证实，疏水残基是膜蛋白插入背后的主要驱动力，而极性、带电和芳香族残基对于螺旋在膜内的正确取向很重要。
