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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Phylogeny of protein-folding trajectories reveals a unique pathway to native structure.
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Phylogeny of protein-folding trajectories reveals a unique pathway to native structure.

机译：蛋白质折叠轨迹的系统发育揭示了天然结构的独特途径。

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摘要

To scrutinize how a protein folds at atomic resolution, we performed 200 molecular dynamics simulations (each of 50 ns) of the miniprotein Trp-cage on the computational grid. Within the trajectories, 58 folding and 31 unfolding events were identified and subjected to extensive comparison and classification. Based on an analogy with biological sequences, the folding and unfolding trajectories (arrays of sequential snapshots of structures) were aligned by dynamic programming allowing gaps. A phylogenetic tree derived from the alignments revealed four distinct groups of the trajectories, characterized by the Trp side-chain motions and the main-chain motions. It was found that only one group attained the native structure and that the other three led to pseudonative structures having the correct main-chain trace but different nonnative Trp side-chain rotamers, indicating that those four folded structures were each attained through a unique folding pathway.
机译：为了检查蛋白质在原子分辨率下如何折叠，我们在计算网格上执行了200个分子模拟动力学（每个50 ns）小蛋白Trp笼。在这些轨迹中，确定了58个折叠事件和31个展开事件，并进行了广泛的比较和分类。根据与生物序列的类比，通过动态编程对齐折叠和展开轨迹（结构顺序快照的阵列），以留出空隙。从比对得出的系统发育树揭示了四个不同的轨迹组，其特征在于Trp侧链运动和主链运动。发现只有一组获得了天然结构，其他三组导致了具有正确主链痕迹但具有不同非天然Trp侧链旋转异构体的假本位结构，表明这四个折叠结构均通过独特的折叠途径获得。

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