Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.

分子动力学 (MD) 模拟被广泛用于补充固有无序蛋白质 (IDP) 的整体平均实验。然而，MD 经常受到不准确的限制。在这里，我们表明使用哈密顿副本交换 MD (HREMD) 增强采样导致无偏和准确的集合，再现小角度散射和 NMR 化学位移实验，对于使用两个最近优化的力场的三个不同序列特性的 IDP，表明HREMD 对 IDP 的普遍适用性。我们进一步证明，与 HREMD 不同，标准 MD 可以重现实验 NMR 化学位移，但不能重现小角度散射数据，这表明化学位移不足以测试 IDP 集合的有效性。令人惊讶的是，我们发现尽管它们的顺序不同，对于短轮廓长度（< 10 个残基），所有三个 IDP 的链间统计数据相似。结果表明，为 IDP 生成准确无偏集成的主要障碍现已基本克服。