Institute of Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia, United States of America.
PLoS One. 2011 Jan 5;6(1):e15920. doi: 10.1371/journal.pone.0015920.
The quality of X-ray crystallographic models for biomacromolecules refined from data obtained at high-resolution is assured by the data itself. However, at low-resolution, >3.0 Å, additional information is supplied by a forcefield coupled with an associated refinement protocol. These resulting structures are often of lower quality and thus unsuitable for downstream activities like structure-based drug discovery.
An X-ray crystallography refinement protocol that enhances standard methodology by incorporating energy terms from the HINT (Hydropathic INTeractions) empirical forcefield is described. This protocol was tested by refining synthetic low-resolution structural data derived from 25 diverse high-resolution structures, and referencing the resulting models to these structures. The models were also evaluated with global structural quality metrics, e.g., Ramachandran score and MolProbity clashscore. Three additional structures, for which only low-resolution data are available, were also re-refined with this methodology.
The enhanced refinement protocol is most beneficial for reflection data at resolutions of 3.0 Å or worse. At the low-resolution limit, ≥4.0 Å, the new protocol generated models with Cα positions that have RMSDs that are 0.18 Å more similar to the reference high-resolution structure, Ramachandran scores improved by 13%, and clashscores improved by 51%, all in comparison to models generated with the standard refinement protocol. The hydropathic forcefield terms are at least as effective as Coulombic electrostatic terms in maintaining polar interaction networks, and significantly more effective in maintaining hydrophobic networks, as synthetic resolution is decremented. Even at resolutions ≥4.0 Å, these latter networks are generally native-like, as measured with a hydropathic interactions scoring tool.
对于从高分辨率获得的数据进行生物大分子的 X 射线晶体学模型的质量由数据本身保证。然而，在低分辨率（>3.0Å）下，通过力场与相关的精修协议提供了额外的信息。这些得到的结构通常质量较低，因此不适合下游活动，如基于结构的药物发现。
描述了一种改进标准方法的 X 射线晶体学精修协议，该协议通过合并来自 HINT（疏水性相互作用）经验力场的能量项来增强标准方法。通过对 25 个不同高分辨率结构的合成低分辨率结构数据进行精修，并将得到的模型与这些结构进行参考，对该协议进行了测试。还使用全局结构质量指标，例如 Ramachandran 分数和 MolProbity clashscore 对模型进行了评估。对另外三个只有低分辨率数据的结构也用这种方法进行了重新精修。
该改进的精修协议对于分辨率为 3.0Å 或更差的反射数据最有益。在低分辨率极限（≥4.0Å）下，新协议生成的模型的 Cα 位置与参考高分辨率结构的 RMSD 更相似，差异为 0.18Å，Ramachandran 分数提高了 13%，clashscore 提高了 51%，与使用标准精修协议生成的模型相比。疏水力场项在维持极性相互作用网络方面至少与库仑静电项一样有效，在维持疏水性网络方面更为有效，随着合成分辨率的降低。即使在分辨率≥4.0Å 下，这些网络通常也具有类似天然的性质，这可以通过疏水性相互作用评分工具来衡量。
