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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains
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Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

机译：通过分子动力学与多肽链的联合残基模型从头开始模拟蛋白质折叠路径

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摘要

We report the application of Langevin dynamics to the physics-based united-residue (UNRES) force field developed in our laboratory. Ten trajectories were run on seven proteins [PDB ID codes 1BDD (α; 46 residues), 1GAB (α; 47 residues), 1LQ7 (α; 67 residues), 1CLB (α; 75 residues), 1E0L (β; 28 residues), and 1E0G (α+β; 48 residues), and 1IGD (α+β; 61 residues)] with the UNRES force field parameterized by using our recently developed method for obtaining a hierarchical structure of the energy landscape. All α-helical proteins and 1E0G folded to the native-like structures, whereas 1IGD and 1E0L yielded mostly nonnative α-helical folds although the native-like structures are lowest in energy for these two proteins, which can be attributed to neglecting the entropy factor in the current parameterization of UNRES. Average folding times for successful folding simulations were of the order of nanoseconds, whereas even the ultrafast-folding proteins fold only in microseconds, which implies that the UNRES time scale is approximately three orders of magnitude larger than the experimental time scale because the fast motions of the secondary degrees of freedom are averaged out. Folding with Langevin dynamics required 2-10 h of CPU time on average with a single AMD Athlon MP 2800+ processor depending on the size of the protein. With the advantage of parallel processing, this process leads to the possibility to explore thousands of folding pathways and to predict not only the native structure but also the folding scenario of a protein together with its quantitative kinetic and thermodynamic characteristics.
机译：我们报告了兰格文动力学在我们实验室开发的基于物理的联合残基（UNRES）力场中的应用。在7种蛋白质上运行10条轨迹[PDB ID码1BDD（α; 46个残基），1GAB（α; 47个残基），1LQ7（α; 67个残基），1CLB（α; 75个残基），1E0L（β; 28个残基） ，和1E0G（α+β； 48个残基）和1IGD（α+β； 61个残基）]，并使用我们最近开发的用于获得能级结构的方法对UNRES力场进行了参数化。所有α-螺旋蛋白和1E0G均折叠为天然样结构，而1IGD和1E0L产生的大部分为非天然α-螺旋折叠，尽管这两种蛋白的天然样结构能量最低，这可归因于忽略了熵因子在UNRES的当前参数化中。成功折叠模拟的平均折叠时间约为纳秒，而即使超快速折叠的蛋白质也仅折叠几微秒，这意味着UNRES时间尺度比实验时间尺度大约大三个数量级，因为第二自由度被平均化。使用单个Langevin动态折叠需要一个AMD Athlon MP 2800+处理器平均需要2-10小时的CPU时间，具体取决于蛋白质的大小。利用并行处理的优势，该过程导致探索数千种折叠途径并预测蛋白质的天然结构以及其折叠情况及其定量动力学和热力学特征的可能性。

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