Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland.
J Mol Graph Model. 2012 Feb;32:67-74. doi: 10.1016/j.jmgm.2011.10.004. Epub 2011 Oct 20.
Two variants of NMR-based conformational analyses of flexible peptides are compared using two examples meeting the formula Tyr-D-Daa-Phe-Daa-NH₂ (Daa=diamino acid): 1 combining D-Dab² (α,γ-diaminobutyryl) with Lys⁴, and 2 -D-Dap² (α,β-diaminopropionyl) with Orn⁴. The ω-amino groups of D-Daa² and Daa⁴ are coupled with C=O into the urea, restraining 1 and 2 with 16- and 14-membered rings and leading to potent and impotent μ/δ opioid peptides, respectively. To the current task, we took from an earlier work (Filip et al, J. Pept. Sci. 11 (2005) 347-352) the NMR NOE- and J-data in H₂O/D₂O; and the selection of the ensembles of 1 and 2, 822 and 788 conformational families, respectively, obtained by using the EDMC/ECEPP3 method. Here, we generated ensembles of 1 and 2 using AMBER molecular dynamics in explicit water to eventually selected 686 and 761 conformers for 1 and 2, respectively. We did numbers of fits for both types of the conformational ensembles of 1 and 2 to their NOE- and J-data using a common method i.e. maximum entropy approach (Groth et al, J. Biomol. NMR 15 (1999) 315-330). Both types of the well structurally diversified ensembles fit to quite different equilibria in regressions to common experimental NOE- and J-restraints using maximum entropy principle, which is a disappointing message. Intriguing is startlingly small standard deviation in J-couplings: σ(JNHαH) ≈ 0.01 Hz for LES-MD/AMBER ensemble, contrary to σ(JNHαH) = 0.8 - 1.1 Hz for the EDMC/ECEPP ensemble, over the wide range of entropy, i.e. relatively insensitive to it. A similar feature is not the case when comparing σ(NOE) in both methods. Hence, at minute entropy contributions, it follows that J does or does not transpose "overfitted" into the final σ(J) in the AMBER or ECEPP ensemble, respectively. Could this be an effect of softness of the AMBER flexible-valence force field compared to ECEPP rigid-geometry, and its effect on ensemble sampling? We do not know an answer.
比较了两种基于 NMR 的柔性肽构象分析变体，这两种变体都满足公式 Tyr-D-Daa-Phe-Daa-NH₂（Daa=二氨基酸）：1 是将 D-Dab²（α，γ-二氨基丁酰基）与 Lys⁴ 结合，2 是将 -D-Dap²（α，β-二氨基丙酰基）与 Orn⁴ 结合。D-Daa² 和 Daa⁴ 的 ω-氨基与 C=O 偶联形成脲，分别将 1 和 2 约束在 16-和 14 元环中，导致具有强效和弱效 μ/δ 阿片肽。对于当前的任务，我们从早期的一项工作（Filip 等人，J. Pept. Sci. 11（2005）347-352）中获取了 H₂O/D₂O 中的 NMR NOE 和 J 数据；并使用 EDMC/ECEPP3 方法选择了分别由 1 和 2 组成的集合，分别为 822 和 788 个构象家族。在这里，我们使用 AMBER 分子动力学在显式水中生成 1 和 2 的集合，最终为 1 和 2 分别选择了 686 和 761 个构象。我们使用通用方法即最大熵方法（Groth 等人，J. Biomol. NMR 15（1999）315-330）对 1 和 2 的构象集合进行了多次拟合，以拟合其 NOE 和 J 数据。两种类型的构象集合都通过最大熵原理在回归到共同的实验性 NOE 和 J 约束中表现出相当不同的平衡，这是一个令人失望的消息。令人惊讶的是，J 耦合的标准偏差非常小：对于 LES-MD/AMBER 集合，σ（JNHαH）≈0.01 Hz，而对于 EDMC/ECEPP 集合，σ（JNHαH）=0.8-1.1 Hz，范围很广，即对熵的变化相对不敏感。在比较两种方法的 σ（NOE）时，情况并非如此。因此，在熵的微小贡献下，可以得出结论，J 要么在 AMBER 或 ECEPP 集合中“过度拟合”为最终的 σ（J），要么不“过度拟合”。这可能是 AMBER 柔性价力场相对于 ECEPP 刚性几何形状的柔软度及其对集合采样的影响吗？我们不知道答案。
