Characterization of the unfolded state of repeat proteins.

Hfsp Journal Pub Date : 2008-12-01 Epub Date: 2008-11-12 DOI:10.2976/1.3021145
Amit Mor, Gilad Haran, Yaakov Levy
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引用次数: 6

Abstract

The unfolded state ensemble of proteins has been described as a structurally featureless state. While this approach is supported by the fact that many unfolded proteins follow the scaling law behavior of a random coil, there is evidence that the unfolded states of various proteins are stabilized by native or non-native interactions. Recently, the existence of extensive non-native structure was reported for a repeat protein, which resulted in a scaling law exponent that is significantly smaller than that of a random polymer [Cortajarena et al., J. Mol. Biol. 382(1), 203-212 (2008)]. It was concluded that the high compactness of this protein stems from a significant fraction of interacting PP(II) helical segments in the unfolded state. In this study, we aim at providing possible molecular understanding of this anomalous compactness of the unfolded state and to investigate its origin. Using a hierarchy of computational models, we ask whether in general the unfolded state of a repeat protein is likely to be intrinsically more compact than the unfolded state of globular proteins, or whether this phenomenon depends mostly on the occurrence of a specific sequence that promotes PP(II) conformations. Our results suggest that the formation of the PP(II) conformation is indeed essential, yet the recurring sequence of repeat proteins promotes the interactions between these PP(II) segments and the formation of non-native interactions in the unfolded state.

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重复序列蛋白未折叠状态的表征。
蛋白质的未折叠状态集合被描述为一种结构上没有特征的状态。虽然这种方法得到了许多未折叠蛋白质遵循随机线圈的比例定律行为的事实的支持,但有证据表明,各种蛋白质的未折叠状态通过天然或非天然相互作用而稳定。最近,报道了重复蛋白存在广泛的非天然结构,这导致标度律指数显著小于无规聚合物的标度律指标[Cortajarena等人,J.Mol.Biol.382(1),203-212(2008)]。得出的结论是,这种蛋白质的高度致密性源于在未折叠状态下的大量相互作用的PP(II)螺旋段。在这项研究中,我们的目的是提供可能的分子理解,这种异常紧凑的展开状态,并研究其起源。使用计算模型的层次结构,我们询问重复蛋白的未折叠状态是否在本质上比球状蛋白的未展开状态更紧密,或者这种现象是否主要取决于促进PP(II)构象的特定序列的出现。我们的研究结果表明,PP(II)构象的形成确实是必要的,但重复蛋白的重复序列促进了这些PP(Ⅱ)片段之间的相互作用,并在未折叠状态下形成非天然相互作用。
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Hfsp Journal
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