Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins.
Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins.
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DOI：
10.3390/molecules26030634
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发表时间：
2021-01-26
期刊：
影响因子：
--
通讯作者：
Whitten ST
中科院分区：
文献类型：
--
作者：
Paiz EA;Lewis KA;Whitten ST
当从蛋白质线圈文库构建时，α和多脯氨酸II(PPII)盆地是拉马钱德兰地图上人口最多的两个区域，蛋白质线圈文库是一种广泛使用的变性状态模型，由蛋白质数据库中发现的不规则结构片段构建而成。这表明α和PPII构象是存在于生物蛋白质溶液中的变性结构系综的主要成分，这一观察结果在一定程度上得到了对短肽的结构研究的支持，因此未折叠的多肽。尽管短肽中常见氨基酸的内在构象倾向已经通过实验确定，并通过对蛋白质线圈文库的调查进行估计，但到目前为止，这些内在构象倾向定量复制内在无序蛋白质(IDPs)结构行为的能力一直难以建立。最近，我们证明了IDPs在水中平均流体力学尺寸的序列依赖性以及热对线圈尺寸的影响，提供了与α和PPII主干构象的偏差相关的序列依赖性和热力学能量。在这里，我们将基于多肽的固有构象倾向研究和蛋白质线圈文库的调查结果与基于序列的热效应对IDP流体力学大小的分析的结果进行比较，表明获得了对蛋白质变性状态的共同结构和热力学描述。
The α and polyproline II (PPII) basins are the two most populated regions of the Ramachandran map when constructed from the protein coil library, a widely used denatured state model built from the segments of irregular structure found in the Protein Data Bank. This indicates the α and PPII conformations are dominant components of the ensembles of denatured structures that exist in solution for biological proteins, an observation supported in part by structural studies of short, and thus unfolded, peptides. Although intrinsic conformational propensities have been determined experimentally for the common amino acids in short peptides, and estimated from surveys of the protein coil library, the ability of these intrinsic conformational propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs), an increasingly important class of proteins in cell function, has thus far proven elusive to establish. Recently, we demonstrated that the sequence dependence of the mean hydrodynamic size of IDPs in water and the impact of heat on the coil dimensions, provide access to both the sequence dependence and thermodynamic energies that are associated with biases for the α and PPII backbone conformations. Here, we compare results from peptide-based studies of intrinsic conformational propensities and surveys of the protein coil library to those of the sequence-based analysis of heat effects on IDP hydrodynamic size, showing that a common structural and thermodynamic description of the protein denatured state is obtained.
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影响因子：
6.8
作者：
Eliezer, David
通讯作者：
Eliezer, David
影响因子：
15
作者：
Chen, K;Liu, ZG;Kallenbach, NR
通讯作者：
Kallenbach, NR
DOI：
10.1002/prot.340220410
发表时间：
1995-08-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND GENETICS
影响因子：
--
作者：
GOMEZ, J;HILSER, VJ;FREIRE, E
通讯作者：
FREIRE, E
影响因子：
8
作者：
Ferreon, JC;Hilser, VJ
通讯作者：
Hilser, VJ
DOI：
10.1002/prot.1
发表时间：
1996-06-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND GENETICS
影响因子：
--
作者：
DAquino, JA;Gomez, J;Freire, E
通讯作者：
Freire, E