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Analysis of Tandem Repeat Protein Folding Using Nearest-Neighbor Models
Annual Review of Biophysics ( IF 12.4 ) Pub Date : 2021-05-06 , DOI: 10.1146/annurev-biophys-102220-083020
Mark Petersen 1, 2 , Doug Barrick 2
Affiliation  

Cooperativity is a hallmark of protein folding, but the thermodynamic origins of cooperativity are difficult to quantify. Tandem repeat proteins provide a unique experimental system to quantify cooperativity due to their internal symmetry and their tolerance of deletion, extension, and in some cases fragmentation into single repeats. Analysis of repeat proteins of different lengths with nearest-neighbor Ising models provides values for repeat folding () and inter-repeat coupling (ΔGi-1,i). In this article, we review the architecture of repeat proteins and classify them in terms of ΔGi and ΔGi-1,i; this classification scheme groups repeat proteins according to their degree of cooperativity. We then present various statistical thermodynamic models, based on the 1D-Ising model, for analysis of different classes of repeat proteins. We use these models to analyze data for highly and moderately cooperative and noncooperative repeat proteins and relate their fitted parameters to overall structural features.

中文翻译:


使用最近邻模型分析串联重复蛋白质折叠

协同性是蛋白质折叠的标志,但协同性的热力学起源很难量化。串联重复蛋白提供了一个独特的实验系统来量化协同性,因为它们的内部对称性和它们对缺失、延伸以及在某些情况下碎片成单个重复的耐受性。使用最近邻 Ising 模型分析不同长度的重复蛋白质提供了重复折叠的值() 和重复耦合 (Δ G i -1, i )。在本文中,我们回顾了重复蛋白质的结构,并根据 Δ G i和 Δ G i -1, i对它们进行分类;这种分类方案根据它们的协同程度对重复蛋白质进行分组。然后,我们提出了基于 1D-Ising 模型的各种统计热力学模型,用于分析不同类别的重复蛋白质。我们使用这些模型来分析高度和中度合作和非合作重复蛋白质的数据,并将它们的拟合参数与整体结构特征联系起来。

更新日期:2021-05-07
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