Niesen Michiel J M, Wang Connie Y, Van Lehn Reid C, Miller Thomas F
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America.
PLoS Comput Biol. 2017 Mar 22;13(3):e1005427. doi: 10.1371/journal.pcbi.1005427. eCollection 2017 Mar.
We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations. A protocol for mapping amino-acid sequences to coarse-grained beads enables the direct simulation of trajectories for the co-translational insertion of arbitrary polypeptide sequences into the Sec translocon. The model reproduces experimentally observed features of membrane protein integration, including the efficiency with which polypeptide domains integrate into the membrane, the variation in integration efficiency upon single amino-acid mutations, and the orientation of transmembrane domains. The central advantage of the model is that it connects sequence-level protein features to biological observables and timescales, enabling direct simulation for the mechanistic analysis of co-translational integration and for the engineering of membrane proteins with enhanced membrane integration efficiency.
我们提出了一种粗粒度模拟模型，该模型能够模拟蛋白质通过Sec转运体进行转运和膜整合的分钟级动力学，同时保留足够的化学和结构细节，以捕捉驱动这些过程的许多序列特异性相互作用。该模型包括直接从实验结构获得的核糖体和Sec转运体的精确几何表示，以及从近200微秒基于残基的粗粒度分子动力学模拟中参数化的相互作用。一种将氨基酸序列映射到粗粒度珠子的方案能够直接模拟任意多肽序列共翻译插入Sec转运体的轨迹。该模型再现了膜蛋白整合的实验观察特征，包括多肽结构域整合到膜中的效率、单个氨基酸突变时整合效率的变化以及跨膜结构域的方向。该模型的核心优势在于它将序列水平的蛋白质特征与生物学观测值和时间尺度联系起来，能够直接模拟共翻译整合的机制分析以及工程改造具有更高膜整合效率的膜蛋白。
