Ulmschneider Martin B, Koehler Leman Julia, Fennell Hayden, Beckstein Oliver
Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA,
J Membr Biol. 2015 Jun;248(3):407-17. doi: 10.1007/s00232-015-9808-7. Epub 2015 May 28.
The cellular translocon, present in all three domains of life, is one of the most versatile and important biological nanopores. This complex molecular apparatus is directly responsible for the secretion of globular proteins across membranes as well as the insertion of integral membrane proteins into lipid bilayers. Recently determined structures of the archaean SecY translocon reveal an hour-glass-shaped pore, which accommodates the nascent peptide chain during translocation. While these structures provide important insights into ribosome binding to the translocon, threading of the nascent chain into the channel, and lateral gate opening for releasing the folded helical peptide into the membrane bilayer, the exact folding pathway of the peptide inside the protein-conducting channel during translocation and prior to the lateral release into the bilayer remains elusive. In the present study, we use molecular dynamics simulations to investigate atomic resolution peptide folding in hour-glass-shaped pore models that are based on the SecY translocon channel structure. The theoretical setup allows systematic variation of key determinants of folding, in particular the degree of confinement of the peptide and the hydration level of the pore. A 27-residue hydrophobic peptide was studied that is preferentially inserted into membranes by the translocon. Our results show that both pore diameter as well as channel hydration are important determinants for folding efficiency and helical stability of the peptide, therefore providing important insights into translocon gating and lateral peptide partitioning.
存在于生命的所有三个域中的细胞转运体，是用途最广泛且最重要的生物纳米孔之一。这个复杂的分子装置直接负责球状蛋白跨膜分泌以及整合膜蛋白插入脂质双层。最近确定的古细菌SecY转运体结构揭示了一个沙漏形孔，在转运过程中容纳新生肽链。虽然这些结构为核糖体与转运体的结合、新生链穿入通道以及横向门打开以将折叠的螺旋肽释放到膜双层中提供了重要见解，但在转运过程中以及横向释放到双层之前，肽在蛋白质传导通道内的确切折叠途径仍然难以捉摸。在本研究中，我们使用分子动力学模拟来研究基于SecY转运体通道结构的沙漏形孔模型中的原子分辨率肽折叠。该理论设置允许对折叠的关键决定因素进行系统变化，特别是肽的受限程度和孔的水化水平。研究了一种27个残基的疏水肽，它优先通过转运体插入膜中。我们的结果表明，孔径和通道水化都是肽折叠效率和螺旋稳定性的重要决定因素，因此为转运体门控和肽的横向分配提供了重要见解。
