Calculation of mutational free energy changes in transition states for protein folding
Calculation of mutational free energy changes in transition states for protein folding
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DOI：
10.1016/s0006-3495(03)74556-1
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发表时间：
2003-08-01
影响因子：
3.4
通讯作者：
Vendruscolo, M
中科院分区：
文献类型：
--
作者：
Lindorff-Larsen, K;Paci, E;Vendruscolo, M
实验和计算方法的最新进展使得有可能相当准确地确定其形成是一些小蛋白质折叠速率限制的结构-过渡态系综，或TSE。我们提出了一种方法来分析和验证这种结构的全原子模型。该方法是基于实验数据的比较与计算的TSE的自由能的变化所产生的特定突变。使用最初开发用于预测天然蛋白质稳定性的突变变化的方法，在过渡态结构的集合的所有成员中单独建模每个突变。我们首先将这种方法应用于六种蛋白质，我们已经确定了TSE的技术，使用实验突变数据（F值）的限制，在结构的确定和找到一个高度显着的相关性之间的计算自由能的变化和那些来自实验动力学数据。然后，我们使用的程序来分析由分子动力学模拟的展开确定的过渡态结构，再次找到一个高的相关性。最后，我们使用的方法来估计几个疏水核心突变体的Fyn SH3的折叠速率的变化。两者合计，这些结果表明，这里开发的程序是一种工具，用于分析，评估和提高蛋白质折叠过渡态结构的质量的一般有效性。
Recent advances in experimental and computational methods have made it possible to determine with considerable accuracy the structures whose formation is rate limiting for the folding of some small proteins - the transition state ensemble, or TSE. We present a method to analyze and validate all-atom models of such structures. The method is based on the comparison of experimental data with the computation of the change in free energy of the TSE resulting from specific mutations. Each mutation is modeled individually in all members of an ensemble of transition state structures using a method originally developed to predict mutational changes in the stability of native proteins. We first apply this method to six proteins for which we have determined the TSEs with a technique that uses experimental mutational data (F-values) as restraints in the structure determination and find a highly significant correlation between the calculated free energy changes and those derived from experimental kinetic data. We then use the procedure to analyze transition state structures determined by molecular dynamics simulations of unfolding, again finding a high correlation. Finally, we use the method to estimate changes in folding rates of several hydrophobic core mutants of Fyn SH3. Taken together, these results show that the procedure developed here is a tool of general validity for analyzing, assessing, and improving the quality of the structures of transition states for protein folding.