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Electrostatics structure prediction and the energy landscapes for protein folding and binding

机译:静电学结构预测以及蛋白质折叠和结合的能级

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摘要

While being long in range and therefore weakly specific, electrostatic interactions are able to modulate the stability and folding landscapes of some proteins. The relevance of electrostatic forces for steering the docking of proteins to each other is widely acknowledged, however, the role of electrostatics in establishing specifically funneled landscapes and their relevance for protein structure prediction are still not clear. By introducing Debye‐Hückel potentials that mimic long‐range electrostatic forces into the Associative memory, Water mediated, Structure, and Energy Model (AWSEM), a transferable protein model capable of predicting tertiary structures, we assess the effects of electrostatics on the landscapes of thirteen monomeric proteins and four dimers. For the monomers, we find that adding electrostatic interactions does not improve structure prediction. Simulations of ribosomal protein S6 show, however, that folding stability depends monotonically on electrostatic strength. The trend in predicted melting temperatures of the S6 variants agrees with experimental observations. Electrostatic effects can play a range of roles in binding. The binding of the protein complex KIX‐pKID is largely assisted by electrostatic interactions, which provide direct charge‐charge stabilization of the native state and contribute to the funneling of the binding landscape. In contrast, for several other proteins, including the DNA‐binding protein FIS, electrostatics causes frustration in the DNA‐binding region, which favors its binding with DNA but not with its protein partner. This study highlights the importance of long‐range electrostatics in functional responses to problems where proteins interact with their charged partners, such as DNA, RNA, as well as membranes.
机译:静电相互作用的范围很广,因此特异性较弱,但它能够调节某些蛋白质的稳定性和折叠态。静电力对操纵蛋白质彼此对接的作用已广为人知,但是,静电在建立特定的漏斗状景观中的作用及其与蛋白质结构预测的作用仍不清楚。通过将模拟长距离静电力的Debye-Hückel势引入缔合记忆,水介导的结构和能量模型(AWSEM)(一种能够预测三级结构的可转移蛋白质模型),我们评估了静电对自然界景观的影响。十三种单体蛋白和四个二聚体。对于单体,我们发现添加静电相互作用不会改善结构预测。然而,核糖体蛋白S6的模拟表明折叠稳定性单调取决于静电强度。 S6变体的预测解链温度的趋势与实验观察结果一致。静电作用可以在结合中发挥多种作用。蛋白质复合物KIX-pKID的结合在很大程度上受到静电相互作用的帮助,静电相互作用可提供对天然状态的直接电荷-电荷稳定作用,并有助于结合态的漏斗化。相反,对于包括DNA结合蛋白FIS在内的其他几种蛋白质,静电会导致DNA结合区域受挫,这有利于其与DNA结合而不与蛋白伴侣结合。这项研究强调了长距离静电对蛋白质与其DNA,RNA和膜等带电伙伴相互作用的功能响应的重要性。

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