无偏分子动力学模拟得到的完全结构构象集的无规卷曲蛋白质。
Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations.
机构信息
Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA.
Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA.
出版信息
Commun Biol. 2021 Feb 23;4(1):243. doi: 10.1038/s42003-021-01759-1.
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无规卷曲蛋白质(IDP)的整体平均实验。然而,MD 常常受到不准确的限制。在这里,我们展示了使用哈密顿复制交换 MD(HREMD)增强采样可以得到无偏且准确的集合,该集合可以重现小角度散射和 NMR 化学位移实验,使用两种最近优化的力场,对三个序列性质不同的 IDP 进行了研究,这表明 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检验 IDP 集合的有效性。令人惊讶的是,我们发现,尽管它们的序列存在差异,但所有三种 IDP 的链间统计数据对于短的轮廓长度(<10 个残基)都是相似的。结果表明,现在已经在很大程度上克服了为 IDP 生成准确无偏集合的主要障碍。