Theoretical Molecular Biophysics, Department of Physical and Theoretical Chemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstr. 36a, 14169 Berlin, Germany.
Molecules. 2018 Sep 14;23(9):2355. doi: 10.3390/molecules23092355.
The dilemma of reconciling the contradictory evidence regarding the conformation of long solvated peptide chains is the so-called "reconciliation problem". Clues regarding the stability of certain conformations likely lie in the electronic structure at the peptide⁻solvent interface, but the peptide⁻solvent interaction is not fully understood. Here, we study the influence of aqueous solvent on peptide conformations by using classical molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) energy calculations. The model systems include an 11-residue peptide, X 2 A 7 O 2 (XAO), where X, A, and O denote diaminobutyric acid, alanine, and ornithine, respectively, and a 9-mer (Arg-Pro-Pro-Gly-Phe-Ser-Ala-Phe-Lys). Spectroscopic and MD data present conflicting evidence regarding the structure of XAO in water; some results indicate that XAO adopts a polyproline II (P II ) conformation, whereas other findings suggest that XAO explores a range of conformations. To investigate this contradiction, we present here the results of MD simulations of XAO and the 9-mer in aqueous solution, combined with QM/MM energy calculations.
调和关于长溶剂化肽链构象的矛盾证据的困境是所谓的“调和问题”。关于某些构象稳定性的线索可能在于肽-溶剂界面的电子结构，但肽-溶剂相互作用尚未完全理解。在这里，我们通过使用经典分子动力学 (MD) 和量子力学/分子力学 (QM/MM) 能量计算来研究水溶剂对肽构象的影响。模型系统包括一个 11 残基肽，X 2 A 7 O 2 (XAO)，其中 X、A 和 O 分别表示二氨基丁酸、丙氨酸和鸟氨酸，以及一个 9 -mer（精氨酸-脯氨酸-脯氨酸-甘氨酸-苯丙氨酸-丝氨酸-丙氨酸-苯丙氨酸-赖氨酸）。光谱和 MD 数据对 XAO 在水中的结构提供了相互矛盾的证据；一些结果表明 XAO 采用聚脯氨酸 II (P II )构象，而其他发现则表明 XAO 探索了一系列构象。为了解决这个矛盾，我们在这里提出了 XAO 和 9-mer 在水溶液中的 MD 模拟结果，并结合了 QM/MM 能量计算。
