Topological Reaction Coordinate Captures the Folding Transition State Ensemble in a Pierced Lasso Protein
Topological Reaction Coordinate Captures the Folding Transition State Ensemble in a Pierced Lasso Protein
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拓扑反应坐标捕获穿孔套索蛋白中的折叠过渡态整体
DOI：
10.1021/acs.jpcb.3c06678
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发表时间：
2024
期刊：
影响因子：
--
通讯作者：
Haglund, Ellinor
中科院分区：
文献类型：
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作者：
Noel, Jeffrey K.;Haglund, Ellinor
具有穿孔套索拓扑结构(PLT)的蛋白质有一个由二硫键创建的共价环，而主链则回绕以穿线环。与打结的拓扑相比，这种线状拓扑具有独特的特征；值得注意的是，拓扑受化学环境控制，共价环即使在变性时也保持不变。在这项工作中，我们使用激素瘦素作为我们的PLT系统的模型，并使用基于结构的(Go-̅-Like)模型使用分子动力学模拟来研究其折叠。我们发现，还原的蛋白质具有两态折叠机制，具有过渡态系综(TSE)，这可以用反应配位Q来表征，反应配位Q是形成的天然接触的分数。相比之下，氧化后的蛋白质必须将部分多肽链穿过共价环，其折叠过程很难用Q来表征。相反，我们发现，监测环路上残基的拓扑坐标可以识别氧化瘦素的TSE。通过准确识别预测的TSE，现在可以可靠地计算PLT蛋白质的理论phi值，从而能够与实验测量进行比较。我们发现，环线限制导致非正则phi值均匀较小，因为这种PLT蛋白在TSE中具有平坦的能量景观。
Proteins with a pierced lasso topology (PLT) have a covalent loop created by a disulfide bond, and the backbone circles back to thread the loop. This threaded topology has unique features compared to knotted topologies; notably, the topology is controlled by the chemical environment and the covalent loop remains intact even when denatured. In this work, we use the hormone leptin as our model PLT system and study its folding using molecular dynamics simulations that employ a structure-based (Go̅-like) model. We find that the reduced protein has a two-state folding mechanism with a transition state ensemble (TSE) that can be characterized by the reaction coordinateQ, the fraction of native contacts formed. In contrast, the oxidized protein, which must thread part of the polypeptide chain through a covalent loop, has a folding process that is poorly characterized byQ. Instead, we find that a topological coordinate that monitors the residue crossing the loop can identify the TSE of oxidized leptin. By precisely identifying the predicted TSE, one may now reliably calculate theoretical phi-values for the PLT protein, thereby enabling a comparison with experimental measurements. We find the loop-threading constraint leads to noncanonical phi-values that are uniformly small because this PLT protein has a flat energy landscape through the TSE.