Department of Chemistry, University of California, Irvine, California.
Department of Chemical Engineering & Materials Science, University of California, Irvine, California.
Biopolymers. 2019 Jun;110(6):e23266. doi: 10.1002/bip.23266. Epub 2019 Mar 5.
Like polypeptides, peptoids, or N-substituted glycine oligomers, have intrinsic conformational preferences due to their amide backbones and close spacing of side chain substituents. However, the conformations that peptoids adopt are distinct from polypeptides due to several structural differences: the peptoid backbone is composed of tertiary amide bonds that have trans and cis conformers similar in energy, they lack a backbone hydrogen bond donor, and have an N-substituent. To better understand how these differences manifest in actual peptoid structures, we analyzed 46 high quality, experimentally determined peptoid structures reported in the literature to extract their backbone conformational preferences. One hundred thirty-two monomer dihedral angle pairs were compared to the calculated energy landscape for the peptoid Ramachandran plot, and were found to fall within the expected minima. Interestingly, only two regions of the backbone dihedral angles ϕ and ψ were found to be populated that are mirror images of each other. Furthermore, these two conformers are present in both cis and trans forms. Thus, there are four primary conformers that are sufficient to describe almost all known backbone conformations for peptoid oligomers, despite conformational constraints imposed by a variety of side chains, macrocyclization, or crystal packing forces. Because these conformers are predominant in peptoid structure, and are distinct from those found in protein secondary structures, we propose a simple naming system to aid in the description and classification of peptoid structure.
与多肽类似，肽类类似物或 N-取代甘氨酸寡聚物由于其酰胺骨架和侧链取代基的紧密间隔而具有内在的构象偏好。然而，由于几个结构差异，肽类类似物的构象与多肽不同：肽类骨架由三级酰胺键组成，这些键具有相似能量的顺式和反式构象，它们缺乏骨架氢键供体，并且具有 N-取代基。为了更好地理解这些差异在实际肽类结构中的表现，我们分析了文献中报道的 46 个高质量、实验确定的肽类结构，以提取其骨架构象偏好。将 132 个单体二面角对与肽类 Ramachandran 图的计算能量景观进行比较，发现它们落在预期的最小值内。有趣的是，只有两个骨架二面角 ϕ 和 ψ 区域被发现是彼此的镜像。此外，这两种构象同时存在于顺式和反式中。因此，尽管存在各种侧链、大环化或晶体堆积力的构象限制，但有四种主要构象足以描述几乎所有已知的肽类寡聚物的骨架构象。由于这些构象在肽类结构中占主导地位，并且与蛋白质二级结构中的构象不同，我们提出了一种简单的命名系统，以帮助描述和分类肽类结构。
