Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
Department of Biochemistry, University of Oxford, South Parks Road, Oxford, United Kingdom.
PLoS Comput Biol. 2020 Jun 4;16(6):e1007919. doi: 10.1371/journal.pcbi.1007919. eCollection 2020 Jun.
Transmembrane helix association is a fundamental step in the folding of helical membrane proteins. The prototypical example of this association is formation of the glycophorin dimer. While its structure and stability have been well-characterized experimentally, the detailed assembly mechanism is harder to obtain. Here, we use all-atom simulations within phospholipid membrane to study glycophorin association. We find that initial association results in the formation of a non-native intermediate, separated by a significant free energy barrier from the dimer with a native binding interface. We have used transition-path sampling to determine the association mechanism. We find that the mechanism of the initial bimolecular association to form the intermediate state can be mediated by many possible contacts, but seems to be particularly favoured by formation of non-native contacts between the C-termini of the two helices. On the other hand, the contacts which are key to determining progression from the intermediate to the native state are those which define the native binding interface, reminiscent of the role played by native contacts in determining folding of globular proteins. As a check on the simulations, we have computed association and dissociation rates from the transition-path sampling. We obtain results in reasonable accord with available experimental data, after correcting for differences in native state stability. Our results yield an atomistic description of the mechanism for a simple prototype of helical membrane protein folding.
跨膜螺旋缔合是螺旋膜蛋白折叠的基本步骤。这种缔合的典型例子是糖蛋白二聚体的形成。虽然其结构和稳定性已经得到很好的实验表征，但详细的组装机制却很难获得。在这里，我们使用磷脂膜内的全原子模拟来研究糖蛋白的缔合。我们发现，最初的缔合导致形成非天然的中间产物，与具有天然结合界面的二聚体分离，需要跨越显著的自由能势垒。我们已经使用过渡态抽样来确定缔合机制。我们发现，形成中间状态的初始双分子缔合的机制可以通过许多可能的接触来介导，但似乎特别有利于两个螺旋的 C 末端之间形成非天然接触。另一方面，对于确定从中间状态到天然状态的进展至关重要的接触是那些定义天然结合界面的接触，这让人联想到天然接触在确定球状蛋白折叠中的作用。作为对模拟的检查，我们已经从过渡态抽样计算了缔合和离解速率。在对天然状态稳定性的差异进行校正后，我们得到的结果与现有实验数据基本一致。我们的结果为简单的螺旋膜蛋白折叠的原型提供了一个原子水平的机制描述。
