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首页> 美国卫生研究院文献>Proceedings of the National Academy of Sciences of the United States of America >Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins
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Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins

机译：Polyproline II构象是许多局部构象状态之一而不是未折叠的肽和蛋白质的整体构象

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摘要

The alanine-based peptide Ac-XX(A)7OO-NH2, referred to as XAO (where X, A, and O denote diaminobutyric acid, alanine, and ornithine, respectively), has recently been proposed to possess a well defined polyproline II (PII) conformation at low temperatures. Based on the results of extensive NMR and CD investigations combined with theoretical calculations, reported here, we present evidence that, on the contrary, this peptide does not have any significant amount of organized PII structure but exists in an ensemble of conformations with a distorted bend in the N- and C-terminal regions. The conformational ensemble was obtained by molecular dynamics/simulated annealing calculations using the amber suite of programs with time-averaged distance and dihedral-angle restraints obtained from rotating-frame nuclear Overhauser effect (ROE) volumes and vicinal coupling constants 3JHNΗα, respectively. The computed ensemble-averaged radius of gyration Rg (7.4 ± 1.0) Å is in excellent agreement with that measured by small-angle x-ray scattering (SAXS) whereas, if the XAO peptide were in the PII conformation, Rg would be 11.6 Å. Depending on the pH, peptide concentration, and temperature, the CD spectra of XAO do or do not possess the maximum with positive ellipticity in the 217-nm region, which is characteristic of the PII structure, reflecting a shifting conformational equilibrium rather than an all-or-none transition. The “PII conformation” should, therefore, be considered as one of the accessible conformational states of individual amino acid residues in peptides and proteins rather than as a structure of most of the chain in the early stage of folding.
机译：最近有人提出基于丙氨酸的肽Ac-XX（A）700-NH2被称为XAO（其中X，A和O分别代表二氨基丁酸，丙氨酸和鸟氨酸），具有定义明确的聚脯氨酸II （PII）低温构象。根据此处报道的大量NMR和CD研究结果以及理论计算的结果，我们提供了证据，相反，该肽没有明显的有组织的PII结构，但是存在弯曲扭曲的构象整体在N和C端区域。通过分子动力学/模拟退火计算，使用琥珀色程序组，通过时间平均距离和二面角约束，从旋转框架核Overhauser效应（ROE）体积和邻域耦合常数 3 获得了构象集合体。 sup>JHNΗα。计算得到的集合平均回转半径Rg（7.4±1.0）Å与通过小角度X射线散射（SAXS）测量的集合平均半径非常一致，而如果XAO肽为PII构型，则Rg为11.6Å 。根据pH，肽浓度和温度的不同，XAO的CD光谱在217 nm区域是否具有最大的正椭圆率，这是PII结构的特征，反映了构象平衡的变化而不是全部。 -或无过渡。因此，“ PII构象”应被认为是肽和蛋白质中单个氨基酸残基可及的构象状态之一，而不是折叠初期大部分链的结构。

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