III. 思考球状蛋白质的几何框架：蛋白质中的转角
III. Geometrical framework for thinking about globular proteins: turns in proteins
AI总结：
本文基于沿链戳触相互作用的几何框架，将蛋白质转角解释为局部、孤立且约束部分松弛的成对戳触接触，并系统划分其结构类别与氨基酸偏好。
摘要：
我们最近表明，沿链“戳触”成对相互作用的概念，提供了一个基于对称性和几何学的统一框架，可用于理解蛋白质二级与三级结构的形成。研究发现，α-螺旋和β-折叠是特殊几何结构，它们以重复方式具有系统性的戳触接触；其中，沿α-螺旋的接触是局部的，而β-折叠内一对相邻链之间的接触是非局部的。成对戳触相互作用也支配三级结构的形成，但其作用较弱，并且不存在二级结构形成中那样的特殊几何约束。在此，我们证明蛋白质转角——蛋白质中最普遍的非重复结构元件——是局部的（如α-螺旋中那样）且孤立（非重复）的戳触成对接触实例，其几何约束得到部分松弛。对蛋白质转角（有时也称为 reverse turns、β-turns、β-bends、hairpin bends、3₁₀ bends、kinks、widgets 等）的这一简单而纯粹几何的定义，提供了一个统一它们的简明框架。我们给出了一项系统分析的结果，并识别了它们的结构类别及其各自的氨基酸偏好。
英文摘要：
We have shown recently that the notion of poking pairwise interactions along a chain provides a unifying framework for understanding the formation of both secondary and the tertiary protein structure based on symmetry and geometry. $α$-helices and $β$-sheets are found to be special geometries that have systematic poking contacts in a repetitive manner with the contacts being local along the $α$-helix and non-local along a pair of adjacent strands within a $β$-sheet. Pairwise poking interactions also govern tertiary structure formation, but they are weaker and there are no special geometrical constraints as in secondary structure formation. Here we demonstrate that protein turns, the most prevalent non-repetitive structural element in proteins, are instances of local (as in $α$-helices) and isolated (non-repetitive) poking pairwise contacts for which the geometrical constraints are partially relaxed. This simple and purely geometrical definition of protein turns (also sometimes known as reverse turns, $β$-turns, $β$-bends, hairpin bends, $3_{10}$ bends, kinks, widgets, ...) provides a simple framework for unifying them. We present the results of a systematic analysis and identify their structural classes as well as their respective amino acid preferences.
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