Increasing temperature accelerates protein unfolding without changing the pathway of unfolding
Increasing temperature accelerates protein unfolding without changing the pathway of unfolding
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DOI：
10.1016/s0022-2836(02)00672-1
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发表时间：
2002-09-06
影响因子：
5.6
通讯作者：
Daggett, V
中科院分区：
文献类型：
--
作者：
Day, R;Bennion, BJ;Daggett, V
传统上，我们依靠极高的温度（498 K, 225°c）在可用的时间尺度内研究蛋白质的展开过程。用显式溶剂进行分子动力学模拟。然而，计算机硬件的最新进展使我们能够将热变性研究扩展到更低的温度。本文描述了凝乳胰蛋白酶抑制剂2在298k至498k 7种温度下的模拟结果。模拟长度从94纳秒到20纳秒不等，总模拟时间为344纳秒，或0.34毫秒。在298 K下，蛋白质在整个50 ns模拟中非常稳定。在348 K时，对应于实验观察到的C12熔化温度，蛋白质在前25 ns展开，在20 ns探索部分展开的构象，然后在最后35 ns重新折叠。在其熔化温度以上，完全热变性发生在一个活化过程中。早期展开的特征是蛋白质核心的滑动或呼吸运动，导致核心减弱和二级结构的一些损失的展开过渡状态。在展开转变之后，随着蛋白质传递到完全变性的集合，核心接触迅速丢失。虽然在不同温度下，展开过程中事件的总体特征和顺序都是守恒的，但在这些事件发生的时间尺度上存在着实质性的差异。我们得出结论，498 K模拟适合以最小的计算费用阐明蛋白质展开的细节。(C) 2002 Elsevier Science Ltd.版权所有。
We have traditionally relied on extremely elevated temperatures (498 K, 225degreesC) to investigate the unfolding process of proteins within the time-scale available. to molecular dynamics simulations with explicit solvent. However, recent advances in computer hardware have allowed us to extend our thermal denaturation studies to much lower temperatures. Here we describe the results of simulations of chymotrypsin inhibitor 2 at seven temperatures, ranging from 298 K to 498 K. The simulation lengths vary from 94 ns to 20 ns, for a total simulation time of 344 ns, or 0.34 mus. At 298 K, the protein is very stable over the full 50 ns simulation. At 348 K, corresponding to the experimentally observed melting temperature of C12, the protein unfolds over the first 25 ns, explores partially unfolded conformations for 20 ns, and then refolds over the last 35 ns. Above its melting temperature, complete thermal denaturation occurs in an activated process. Early unfolding is characterized by sliding or breathing motions in the protein core, leading to an unfolding transition state with a weakened core and some loss of secondary structure. After the unfolding transition, the core contacts are rapidly lost as the protein passes on to the fully denatured ensemble. While the overall character and order of events in the unfolding process are well conserved across temperatures, there are substantial differences in the timescales over which these events take place. We conclude that 498 K simulations are suitable for elucidating the details of protein unfolding at a minimum of computational expense. (C) 2002 Elsevier Science Ltd. All rights reserved.