Topological descriptions of protein folding
Topological descriptions of protein folding
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DOI：
10.1073/pnas.1808312116
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发表时间：
2019-05-07
影响因子：
11.1
通讯作者：
Wong, Helen
中科院分区：
文献类型：
--
作者：
Flapan, Erica;He, Adam;Wong, Helen
自近二十年前发现深结蛋白以来，打结蛋白如何折叠一直存在争议。计算和实验方法都被用来研究蛋白质结的形成。受Bolinger等人[Bolinger D，et al.（2010）PLoS Comput Biol 6：e1000731]对6（1）-打结α-卤酸脱卤酶（Dehl）蛋白质折叠的计算机模拟的启发，我们引入了结折叠的拓扑描述，其可以描述所有目前已知的蛋白质结类型形成的途径，并预测未来可能鉴定的结类型。我们分析了来自蛋白质结的晶体结构的指纹数据，作为特定蛋白质结可能根据我们理论的特定途径折叠的证据。我们的研究结果证实了Taylor的3（1）-结蛋白和4（1）-结酮酸还原异构酶的结折叠的扭曲发夹理论，并提出了41-结光敏色素和5（2）-和6（1）-结蛋白的替代折叠机制。
How knotted proteins fold has remained controversial since the identification of deeply knotted proteins nearly two decades ago. Both computational and experimental approaches have been used to investigate protein knot formation. Motivated by the computer simulations of Bolinger et al. [Bolinger D, et al. (2010) PLoS Comput Biol 6:e1000731] for the folding of the 6(1)-knotted alpha-haloacid dehalogenase (Dehl) protein, we introduce a topological description of knot folding that could describe pathways for the formation of all currently known protein knot types and predicts knot types that might be identified in the future. We analyze fingerprint data from crystal structures of protein knots as evidence that particular protein knots may fold according to specific pathways from our theory. Our results confirm Taylor's twisted hairpin theory of knot folding for the 3(1)-knotted proteins and the 4(1)-knotted ketol-acid reductoisomerases and present alternative folding mechanisms for the 41-knotted phytochromes and the 5(2)- and 6(1)-knotted proteins.