Peptide fragment studies on the folding elements of dihydrofolate reductase from Escherichia coli
Peptide fragment studies on the folding elements of dihydrofolate reductase from Escherichia coli
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DOI：
10.1002/prot.20675
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发表时间：
2006-02-01
影响因子：
2.9
通讯作者：
Iwakura, M
中科院分区：
文献类型：
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作者：
Arai, M;Iwakura, M
蛋白质可折叠的必要条件之一是存在一套完整的“折叠元件”（FE），这些元件是分布在氨基酸序列上的短的连续肽段。蛋白质折叠的FE-组装模型已经被提出，其中FE在折叠早期通过FE-FE相互作用在引导结构形成中起作用。然而，两个主要的问题仍然有待澄清的作用，在确定蛋白质的折叠。FEs是可以单独形成类天然结构的AFU吗？仅仅存在没有相互连接的FE是蛋白质可折叠的充分条件吗？在这里，我们解决这些问题，使用对应于从大肠杆菌DHFR的FE肽片段。我们通过CD测量表明，FE肽在天然条件下是未折叠的，并且其中一些具有朝向非天然螺旋的倾向。MD模拟还显示了非天然的螺旋倾向的肽，和螺旋内容估计从模拟是很好的相关性估计从CD在TFE。因此，DHFR的FEs不是AFU，这表明FEs在非局部相互作用中的重要性。我们还表明，FE肽的等摩尔混合物不诱导任何结构形成。因此，FE之间的相互连接，这将加强非局部FE-FE相互作用，也是蛋白质可折叠的必要条件之一。
One of the necessary conditions for a protein to be foldable is the presence of a complete set of "folding elements" (FEs) that are short, contiguous peptide segments distributed over an amino acid sequence. The FE-assembly model of protein folding has been proposed, in which the FEs play a role in guiding structure formation through FE-FE interactions early in folding. However, two major issues remain to be clarified regarding the roles of the FEs in determining protein foldability. Are the FEs AFUs that can form nativelike structures in isolation? Is the presence of only the FEs without mutual connections a sufficient condition for a protein to be foldable? Here, we address these questions using peptide fragments corresponding to the FEs of DHFR from Escherichia coli. We show by CD measurement that the FE peptides are unfolded under the native conditions, and some of them have the propensities toward non-native helices. MD simulations also show the non-native helical propensities of the peptides, and the helix contents estimated from the simulations are well correlated with those estimated from the CD in TFE. Thus, the FEs of DHFR are not AFUs, suggesting the importance of the FEs in nonlocal interactions. We also show that equimolar mixtures of the FE peptides do not induce any structural formation. Therefore, mutual connections between the FEs, which should strengthen the nonlocal FE-FE interactions, are also one of the necessary conditions for a protein to be foldable.