Department of Physics , Virginia Tech , Blacksburg , Virginia 24060 , United States.
Early Stage Pharmaceutical Development , Genentech Inc. , South San Francisco , California 94080 , United States.
J Chem Theory Comput. 2019 Apr 9;15(4):2620-2634. doi: 10.1021/acs.jctc.8b01123. Epub 2019 Mar 26.
Unconstrained atomistic simulations of intrinsically disordered proteins and peptides (IDP) remain a challenge: widely used, "general purpose" water models tend to favor overly compact structures relative to experiment. Here we have performed a total of 93 μs of unrestrained MD simulations to explore, in the context of IDPs, a recently developed "general-purpose" 4-point rigid water model OPC, which describes liquid state of water close to experiment. We demonstrate that OPC, together with a popular AMBER force field ff99SB, offers a noticeable improvement over TIP3P in producing more realistic structural ensembles of three common IDPs benchmarks: 55-residue apo N-terminal zinc-binding domain of HIV-1 integrase ("protein IN"), amyloid β-peptide (Aβ) (residues 1-42), and 26-reside H4 histone tail. As a negative control, computed folding profile of a regular globular miniprotein (CLN025) in OPC water is in appreciably better agreement with experiment than that obtained in TIP3P, which tends to overstabilize the compact native state relative to the extended conformations. We employed Aβ peptide to investigate the possible influence of the solvent box size on simulation outcomes. We advocate a cautious approach for simulations of IDPs: we suggest that the solvent box size should be at least four times the radius of gyration of the random coil corresponding to the IDP. The computed free energy landscape of protein IN in OPC resembles a shallow "tub" - conformations with substantially different degrees of compactness that are within 2 k T of each other. Conformations with very different secondary structure content coexist within 1 k T of the global free energy minimum. States with higher free energy tend to have less secondary structure. Computed low helical content of the protein has virtually no correlation with its degree of compactness, which calls into question the possibility of using the helicity as a metric for assessing performance of water models for IDPs, when the helicity is low. Predicted radius of gyration ( R ) of H4 histone tail in OPC water falls in-between that of a typical globular protein and a fully denatured protein of the same size; the predicted R is consistent with two independent predictions. In contrast, H4 tail in TIP3P water is as compact as the corresponding globular protein. The computed free energy landscape of H4 tail in OPC is relatively flat over a significant range of compactness, which, we argue, is consistent with its biological function as facilitator of internucleosome interactions.
无约束的原子模拟对无序蛋白质和肽(IDP)仍然是一个挑战:广泛使用的“通用”水模型往往偏向于相对于实验过于紧凑的结构。在这里,我们总共进行了 93 μs 的无约束 MD 模拟,以在 IDP 的背景下探索最近开发的“通用”4 点刚性水模型 OPC,该模型接近实验描述了水的液态。我们证明,OPC 与流行的 AMBER 力场 ff99SB 一起,在产生更真实的三个常见 IDP 基准结构集合方面,相对于 TIP3P 有显著的改进:55 残基 apo N-末端锌结合域 HIV-1 整合酶(“蛋白 IN”)、淀粉样β肽(Aβ)(残基 1-42)和 26 残基 H4 组蛋白尾部。作为负对照,在 OPC 水中计算的规则球状小蛋白(CLN025)的折叠曲线与实验相比,明显优于在 TIP3P 中获得的折叠曲线,后者相对于扩展构象往往会过度稳定紧凑的天然状态。我们使用 Aβ 肽来研究溶剂盒大小对模拟结果的可能影响。我们提倡对 IDP 进行模拟的谨慎方法:我们建议溶剂盒的大小至少应该是与 IDP 对应的无规卷曲的回转半径的四倍。在 OPC 中,蛋白 IN 的自由能景观类似于一个浅的“管” - 构象,彼此之间的紧凑度有很大的不同,彼此之间的距离在 2 kT 以内。具有非常不同二级结构含量的构象在全球自由能最小值的 1 kT 以内共存。具有较高自由能的状态往往具有较少的二级结构。计算得到的蛋白低螺旋含量与紧凑度几乎没有相关性,这使得在螺旋度较低时,使用螺旋度作为评估 IDP 水模型性能的指标变得值得怀疑。在 OPC 水中,H4 组蛋白尾部的预测回转半径(R)介于典型球状蛋白和相同大小的完全变性蛋白之间;预测的 R 与两个独立的预测一致。相比之下,TIP3P 水中的 H4 尾部与相应的球状蛋白一样紧凑。在 OPC 中,H4 尾部的自由能景观在相当大的紧凑范围内相对平坦,我们认为这与其作为核小体相互作用促进剂的生物学功能一致。