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首页> 外文期刊>Physica, A. Statistical mechanics and its applications >Folding/unfolding kinetics of lattice proteins studied using a simple statistical mechanical model for protein folding, I: Dependence on native structures and amino acid sequences
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Folding/unfolding kinetics of lattice proteins studied using a simple statistical mechanical model for protein folding, I: Dependence on native structures and amino acid sequences

机译：使用简单的蛋白质折叠统计机械模型研究晶格蛋白质的折叠/展开动力学，I：对天然结构和氨基酸序列的依赖

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The folding/unfolding kinetics of a three-dimensional lattice protein was studied using a simple statistical mechanical model for protein folding that we developed earlier. We calculated a characteristic relaxation rate for the free energy profile starting from a completely unfolded structure (or native structure) that is assumed to be associated with a folding rate (or an unfolding rate). The chevron plot of these rates as a function of the inverse temperature was obtained for four lattice proteins, namely, proteins a1, a2, b1, and b2, in order to investigate the dependency of the folding and unfolding rates on their native structures and amino acid sequences. Proteins a1 and a2 fold to the same native conformation, but their amino acid sequences differ. The same is the case for proteins b1 and b2, but their native conformation is different from that of proteins a1 and a2. However, the chevron plots of proteins a1 and a2 are very similar to each other, and those of proteins b1 and b2 differ considerably. Since the contact orders of proteins b1 and b2 are identical, the differences in their kinetics should be attributed to the amino acid sequences and consequently to the interactions between the amino acid residues. A detailed analysis revealed that long-range interactions play an important role in causing the difference in the folding rates. The chevron plots for the four proteins exhibit a chevron rollover under both strongly folding and strongly unfolding conditions. The slower relaxation time on the broad and flat free energy surfaces of the unfolding conformations is considered to be the main origin of the chevron rollover, although the free energy surfaces have features that are rather complicated to be described in detail here. Finally, in order to concretely examine the relationship between changes in the free energy profiles and the chevron plots, we illustrate some examples of single amino acid substitutions that increase the folding rate.
机译：使用我们之前开发的简单的蛋白质折叠统计机械模型，研究了三维晶格蛋白质的折叠/展开动力学。我们从完全展开的结构（或自然结构）开始计算了自由能曲线的特征弛豫率，该结构被认为与折叠率（或展开率）相关。为了研究折叠和解折叠速率对其天然结构和氨基的依赖性，针对四种晶格蛋白（即蛋白a1，a2，b1和b2）获得了这些速率随逆温度变化的人字形图。酸序列。蛋白质a1和a2折叠成相同的天然构象，但它们的氨基酸序列不同。蛋白质b1和b2的情况相同，但它们的天然构象与蛋白质a1和a2的构象不同。但是，蛋白质a1和a2的人字形图非常相似，而蛋白质b1和b2的人字形图有很大差异。由于蛋白质b1和b2的接触顺序相同，因此其动力学差异应归因于氨基酸序列，因此应归因于氨基酸残基之间的相互作用。详细的分析表明，长距离相互作用在引起折叠速率差异中起着重要作用。四种蛋白质的人字形图在强折叠和强折叠条件下均显示出人字形翻转。尽管自由能表面具有相当复杂的特征，在此将对其进行详细描述，但是在展开构象的宽而平坦的自由能表面上，较慢的弛豫时间被认为是人字形翻转的主要原因。最后，为了具体检查自由能曲线的变化与人字形图之间的关系，我们举例说明了增加折叠率的单个氨基酸取代的一些例子。

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