Department of Physics and Astronomy, University of Denver , Denver, Colorado 80208, United States.
J Chem Theory Comput. 2017 Oct 10;13(10):5065-5075. doi: 10.1021/acs.jctc.7b00545. Epub 2017 Sep 28.
Thermophilic proteins denature at much higher temperature compared to their mesophilic homologues, in spite of high structural and sequential similarity. Computational approaches to understand this puzzle face three major challenges: (i) unfolded ensembles are usually neglected, (ii) simulation studies of the folded states are often too short, and (iii) the majority of investigations focus on a few protein pairs, obscuring the prevalence of different strategies across multiple protein systems. We address these concerns by carrying out all-atom simulations to characterize physicochemical properties of both the folded and the disordered ensemble in multiple (12) thermophilic-mesophilic homologous protein pairs. We notice two clear trends in most pairs (10 out of 12). First, specific distribution of charges in the native basin-sampled from multimicrosecond long Molecular Dynamics (MD) simulation trajectories-leads to more favorable electrostatic interaction energy in thermophiles compared to mesophiles. Next, thermophilic proteins have lowered electrostatic interaction in their unfolded state-generated using Monte Carlo (MC) simulation-compared to their mesophilic counterparts. The net contribution of interaction energy to folding stability, however, remains more favorable in thermophiles compared to mesophiles. The overall contribution of electrostatics quantified by combining the net interaction energy and the solvation penalty of folding-due to differential charge burial in the folded and the unfolded ensemble-is also mostly favorable in thermophilic proteins compared to mesophiles. The systems that deviate from this trend provide interesting test cases to learn more about alternate design strategies when modification of charges is not viable due to functional reasons. The unequal contribution of the unfolded state to the stability in thermophiles and mesophiles highlights the importance of modeling the disordered ensemble to understand thermophilic adaptation as well as protein stability, in general. Our integrated approach-combining finite element analysis with MC and MD-can be useful in designing charge mutations to alter protein stability.
尽管具有高度的结构和序列相似性，但与中温同源物相比，嗜热蛋白在更高的温度下变性。为了理解这个难题，计算方法面临三个主要挑战：（i）通常忽略展开的集合，（ii）折叠状态的模拟研究通常太短，以及（iii）大多数研究集中在少数蛋白质对上，掩盖了多种蛋白质系统中不同策略的普遍性。我们通过进行全原子模拟来解决这些问题，以描述多个（12）嗜热-中温同源蛋白对中折叠和无序集合的物理化学性质。我们注意到大多数对（10 对中的 12 对）中的两个明显趋势。首先，在来自多微秒长分子动力学（MD）模拟轨迹的天然盆地中采样的特定电荷分布导致与中温生物相比，嗜热生物中的静电相互作用能更有利。接下来，与中温蛋白相比，在其展开状态下（使用 Monte Carlo（MC）模拟生成），嗜热蛋白的静电相互作用降低。然而，与中温蛋白相比，折叠稳定性的相互作用能净贡献仍然更有利。通过将净相互作用能与折叠的溶剂化罚分（由于折叠和展开集合中的电荷差异掩埋）结合起来定量的静电贡献，与中温蛋白相比，嗜热蛋白也更有利。偏离此趋势的系统提供了有趣的测试案例，可以了解在由于功能原因电荷修饰不可行时，替代设计策略的更多信息。在嗜热生物和中温生物中，展开状态对稳定性的贡献不均等，这突出了建模无序集合以理解嗜热适应以及一般蛋白质稳定性的重要性。我们的综合方法-结合有限元分析与 MC 和 MD-可用于设计电荷突变以改变蛋白质稳定性。
