XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement.
XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement.
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DOI：
10.1107/s2059798316002837
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发表时间：
2016-04
期刊：
影响因子：
--
通讯作者：
Westerhoff LM
中科院分区：
文献类型：
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作者：
Borbulevych O;Martin RI;Tickle IJ;Westerhoff LM
XModeScore使用基于量子力学的X射线精修，然后基于能量应变（或配体应变）和严格的差异电子密度分析的组合进行精修后评分，确定活性位点残基沿着任何结合的配体的正确原异构/互变异构状态或模式。获得蛋白质-配体复合物结构的理解沿着适当的质子化和明确的溶剂效应对于在结构引导的药物发现和基于结构的药物发现中获得有意义的结果是重要的。不幸的是，质子化和互变异构现象是难以建立与传统的方法，因为在实验检测的H原子由于众所周知的限制，X射线晶体学的困难。在目前的工作中，它表明，半经验的，基于量子力学的大分子晶体学的细化是敏感的质子化状态/互变异构体形式的配体和残基的选择，因此可以用来探索潜在的状态。描述了一种新的评分方法，称为XModeScore，它列举了可能的原异构/互变异构模式，细化每个模式对X射线衍射数据与半经验量子力学（PM 6）的哈密顿量和分数每个模式使用的能量应变（或配体应变）和严格的统计分析的差异电子密度分布的组合。它示出，使用XModeScore，它是可以始终区分正确的绑定的原异构/互变异构模式的基础上，常规的X-射线数据，即使在较低的分辨率约3 μ m。 将这些X射线结果与从三个不同实例的更昂贵和费力的中子衍射研究获得的结果进行比较：人碳酸酐酶Ⅱ乙酰唑胺配体的互变异构现象（PDB条目3 hs 4和4k 0 s），尿酸氧化酶8HX配体中的互变异构现象（PDB条目4 n9 s和4 n9 m）和在天冬氨酸蛋白酶的活性位点内发现的催化天冬氨酸的质子化状态（PDB条目2 jjj）。在每种情况下，应用于X射线衍射数据的XModeScore能够确定由中子衍射数据定义的正确质子化状态。还讨论了基于QM的细化与传统细化对XModeScore的影响。
XModeScore determines the correct protomeric/tautomeric state or mode of active-site residues along with any bound ligand(s) using quantum-mechanics-based X-ray refinement followed by post-refinement scoring based on a combination of energetic strain (or ligand strain) and rigorous difference electron-density analysis. Gaining an understanding of the protein–ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated that semiempirical, quantum-mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation-state/tautomer form of ligands and residues, and can therefore be used to explore potential states. A novel scoring method, called XModeScore, is described which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum-mechanics (PM6) Hamiltonian and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron-density distribution. It is shown that using XModeScore it is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 2jjj). In each case, XModeScore applied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinement versus conventional refinement on XModeScore is also discussed.