Interplay between drying and stability of a TIM barrel protein: a combined simulation-experimental study.
Interplay between drying and stability of a TIM barrel protein: a combined simulation-experimental study.
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DOI：
10.1021/ja310544t
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发表时间：
2013-02-06
影响因子：
15
通讯作者：
Matthews, C. Robert
中科院分区：
文献类型：
--
作者：
Das, Payel;Kapoor, Divya;Halloran, Kevin T.;Zhou, Ruhong;Matthews, C. Robert
最近的分子动力学模拟表明，纳米尺度的脱湿对蛋白质的稳定性、功能和折叠动力学具有重要作用。利用αTS TIM桶状蛋白的协同模拟-实验方法，揭示了疏水氨基酸簇内干燥的发生及其在蛋白质稳定性和结构实验指标上的表现，验证了这一假设。在模拟中发现，在异亮氨酸、亮氨酸和缬氨酸（ILV）这三个支链脂肪氨基酸簇中产生的空腔经历了强烈的水密度波动或间歇性脱湿转变。用疏水程度较低的丙氨酸单独取代大ILV簇n端上的10个残基，显示出对脱湿的影响减弱或减弱，这取决于突变位点。我们的模拟还表明，用等构和极性天冬酰胺取代埋在地下的亮氨酸增强了N端和c端簇的润湿性。实验结果表明，天冬酰胺变异体的原生态和中间态的稳定性、二级结构和致密性与中间态中大n端簇的优先干燥一致。相比之下，包含小c端簇的区域在中间只经历部分干燥，其结构和稳定性不受天冬酰胺取代的影响。令人惊讶的是，在n端簇中，为适应亮氨酸被天冬酰胺取代所需要的结构扭曲揭示了原生盆地中存在可替代的稳定褶皱。这项模拟与实验相结合的研究证明了疏水ILV簇中的干燥对αTS TIM桶的折叠和稳定性的关键作用。
Recent molecular dynamics simulations have suggested important roles for nanoscale dewetting on the stability, function, and folding dynamics of proteins. Using a synergistic simulation-experimental approach on the αTS TIM barrel protein, we validate this hypothesis by revealing the occurrence of drying inside hydrophobic amino acid clusters and its manifestation on experimental measures of protein stability and structure. Cavities created within three clusters of branched aliphatic amino acids, isoleucines, leucines and valines (ILV), were found to experience strong water density fluctuations or intermittent dewetting transitions in simulations. Individually substituting 10 residues in the large ILV cluster at the N-terminus with the less hydrophobic alanine showed a weakening or diminishing effect on dewetting that depended on the site of the mutation. Our simulations also demonstrated that replacement of buried leucines with the isosteric and polar asparagine enhanced the wetting of the N- and C-terminal clusters. Experimental results on the stability, secondary structure and compactness of the native and intermediate states for the asparagine variants are consistent with the preferential drying of the large N-terminal cluster in the intermediate. By contrast, the region encompassing the small C-terminal cluster only experiences partial drying in the intermediate and its structure and stability are unaffected by the asparagine substitution. Surprisingly, the structural distortions required to accommodate the replacement of leucine by asparagine in the N-terminal cluster revealed the existence of alternative stable folds in the native basin. This combined simulation-experimental study demonstrates the critical role of drying in hydrophobic ILV clusters to the folding and stability of the αTS TIM barrel.
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DOI：
10.1073/pnas.92.7.2657
发表时间：
1995-03-28
影响因子：
11.1
作者：
KIEFHABER, T;BALDWIN, RL
通讯作者：
BALDWIN, RL
影响因子：
2.9
作者：
Bilsel, O;Zitzewitz, JA;Matthews, CR
通讯作者：
Matthews, CR
影响因子：
5.6
作者：
Forsyth, William R.;Bilsel, Osman;Matthews, C. Robert
通讯作者：
Matthews, C. Robert
DOI：
10.1073/pnas.1934837100
发表时间：
2003-10-14
影响因子：
11.1
作者：
Huang, X;Margulis, CJ;Berne, BJ
通讯作者：
Berne, BJ
影响因子：
64.8
作者：
Liu, P;Huang, XH;Berne, BJ
通讯作者：
Berne, BJ