Protein β-turn classification remains an area of ongoing development in structural biology research. While the commonly used nomenclature defining type I, type II and type IV β-turns was introduced in the 1970s and 1980s, refinements of β-turn type definitions have been introduced as recently as 2019 by Dunbrack, Jr and co-workers who expanded the number of β-turn types to 18 (Shapovalov et al, PLOS Computat. Biol., 15, e1006844, 2019). Based on their analysis of 13 030 turns from 1074 ultrahigh resolution (≤1.2 Å) protein structures, they used a new clustering algorithm to expand the definitions used to classify protein β-turns and introduced a new nomenclature system. We recently encountered a specific problem when classifying β-turns in crystal structures of pentapeptide repeat proteins (PRPs) determined in our lab that are largely composed of β-turns that often lie close to, but just outside of, canonical β-turn regions. To address this problem, we devised a new scheme that merges the Klyne-Prelog stereochemistry nomenclature and definitions with the Ramachandran plot. The resulting Klyne-Prelog-modified Ramachandran plot scheme defines 1296 distinct potential β-turn classifications that cover all possible protein β-turn space with a nomenclature that indicates the stereochemistry of i + 1 and i + 2 backbone dihedral angles. The utility of the new classification scheme was illustrated by re-classification of the β-turns in all known protein structures in the PRP superfamily and further assessed using a database of 16 657 high-resolution protein structures (≤1.5 Å) from which 522 776 β-turns were identified and classified.

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蛋白质结构中β-转角分类新方案的介绍

蛋白质 β-转角分类仍然是结构生物学研究中不断发展的一个领域。虽然定义 I 型、II 型和 IV 型β-转角的常用命名法是在 1970 年代和 1980 年代引入的，但直到 2019 年，Dunbrack, Jr 及其同事才引入了对 β-转角类型定义的改进，他们扩展了β-转角类型的数量增加到 18（Shapovalov 等人，PLOS Computat. Biol., 15, e1006844, 2019）。基于他们对来自 1074 个超高分辨率（≤1.2 Å）蛋白质结构的 13030 个转角的分析，他们使用了一种新的聚类算法来扩展用于对蛋白质 β-转角进行分类的定义，并引入了一种新的命名系统。我们最近在对我们实验室确定的五肽重复蛋白 (PRP) 晶体结构中的 β 转角进行分类时遇到了一个特定问题，这些蛋白质主要由 β 转角组成，这些 β 转角通常位于典型的 β 转角区域附近，但正好位于其之外。为了解决这个问题，我们设计了一个新方案，将 Klyne-Prelog 立体化学命名法和定义与 Ramachandran 图合并。由此产生的 Klyne-Prelog 修改的 Ramachandran 绘图方案定义了 1296 个不同的潜在 β-转角分类，这些分类涵盖了所有可能的蛋白质 β-转角空间，其命名法表明了蛋白质的立体化学i  + 1 和i  + 2 骨架二面角。新分类方案的实用性通过对 PRP 超家族中所有已知蛋白质结构中的 β 转角重新分类来说明，并使用包含 16 657 个高分辨率蛋白质结构（≤1.5 Å）的数据库进一步评估，其中 522 776 β-转角被识别和分类。