Makowska Joanna, Rodziewicz-Motowidło Sylwia, Bagińska Katarzyna, Vila Jorge A, Liwo Adam, Chmurzyński Lech, Scheraga Harold A
Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland.
Proc Natl Acad Sci U S A. 2006 Feb 7;103(6):1744-9. doi: 10.1073/pnas.0510549103. Epub 2006 Jan 30.
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 (P(II)) 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 P(II) 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 3J(HN Eta alpha), respectively. The computed ensemble-averaged radius of gyration Rg (7.4 +/- 1.0) A is in excellent agreement with that measured by small-angle x-ray scattering (SAXS) whereas, if the XAO peptide were in the P(II) conformation, Rg would be 11.6 A. 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 P(II) structure, reflecting a shifting conformational equilibrium rather than an all-or-none transition. The "P(II) 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.
基于丙氨酸的肽Ac-XX(A)7OO-NH2，简称为XAO（其中X、A和O分别表示二氨基丁酸、丙氨酸和鸟氨酸），最近有人提出它在低温下具有明确的多聚脯氨酸II（P(II)）构象。根据本文报道的广泛的核磁共振（NMR）和圆二色性（CD）研究结果以及理论计算，我们提供的证据表明，相反，这种肽没有任何显著量的有序P(II)结构，而是以一种构象集合的形式存在，在N端和C端区域有扭曲的弯曲。通过使用amber程序套件进行分子动力学/模拟退火计算获得构象集合，分别从旋转框架核Overhauser效应（ROE）体积和邻位耦合常数3J(HN Eta alpha)获得时间平均距离和二面角约束。计算得到的集合平均回转半径Rg（7.4±1.0）Å与小角X射线散射（SAXS）测量的结果非常吻合，而如果XAO肽处于P(II)构象，Rg将为11.6 Å。根据pH值、肽浓度和温度，XAO的CD光谱在217 nm区域可能有或没有具有正椭圆率的最大值，这是P(II)结构的特征，反映了构象平衡的移动而不是全或无的转变。因此，“P(II)构象”应被视为肽和蛋白质中单个氨基酸残基可及的构象状态之一，而不是折叠早期大多数链的结构。
