Richardson Jane S, Videau Lizbeth L, Williams Christopher J, Hintze Bradley J, Lewis Steven M, Richardson David C
Department of Biochemistry, Duke University, Durham, North Carolina, USA.
Duke Institute of Health Innovation, Duke University Medical Center, Durham, North Carolina, USA.
Protein Sci. 2025 Jun;34(6):e70157. doi: 10.1002/pro.70157.
While cis peptides preceding proline can occur about 5% of the time, cis peptides preceding any other residue ("cis-nonPro" peptides) are an extremely rare feature in protein structures, of considerable importance for two opposite reasons. On one hand, their genuine occurrences are mostly found at sites critical to biological function, from the active sites of carbohydrate enzymes to rare adjacent-residue disulfide bonds. On the other hand, a cis-nonPro can easily be misfit into weak or ambiguous electron density, which led to a high incidence of unjustified cis-nonPro over the 2006-2015 decade. This paper uses high-resolution crystallographic data and especially stringent quality-filtering at the residue level to identify genuine occurrences of cis-nonPro and to survey both individual examples and broad patterns of their functionality. We explain the procedure developed to identify genuine cis-nonPro examples with almost no false positives. We then survey a large sample of the varied functional roles and structural contexts of cis-nonPro, including the uses of specific amino acids for particular purposes. We emphasize aspects not previously covered: that cis-nonPro essentially always (except for vicinal disulfides) occurs in well-ordered structure, and especially the great concentration of occurrence in proteins that process or bind carbohydrates (identified by occurrence on the CAZy website).
虽然脯氨酸之前的顺式肽段出现的概率约为5%，但其他任何残基之前的顺式肽段（“顺式-非脯氨酸”肽段）在蛋白质结构中却是极为罕见的特征，因其具有两个相反的重要原因。一方面，它们真正出现的位置大多在对生物功能至关重要的位点，从碳水化合物酶的活性位点到罕见的相邻残基二硫键。另一方面，顺式-非脯氨酸很容易被误判为弱或模糊的电子密度，这导致在2006 - 2015年这十年间，不合理的顺式-非脯氨酸出现的频率很高。本文利用高分辨率晶体学数据，特别是在残基水平上进行严格的质量筛选，以识别顺式-非脯氨酸的真正出现情况，并研究其单个实例及其功能的广泛模式。我们解释了所开发的用于识别几乎没有假阳性的真正顺式-非脯氨酸实例的程序。然后，我们调查了大量顺式-非脯氨酸的不同功能作用和结构背景的样本，包括特定氨基酸用于特定目的的情况。我们强调了以前未涵盖的方面：顺式-非脯氨酸基本上总是（除了邻位二硫键）出现在有序结构中，特别是在处理或结合碳水化合物的蛋白质中出现的高度集中情况（通过CAZy网站上的出现情况来确定）。
