Brookner Dennis E, Hekstra Doeke R
Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, USA.
School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
bioRxiv. 2024 Jan 2:2023.09.01.555333. doi: 10.1101/2023.09.01.555333.
Conformational change mediates the biological functions of macromolecules. Crystallographic measurements can map these changes with extraordinary sensitivity as a function of mutations, ligands, and time. The isomorphous difference map remains the gold standard for detecting structural differences between datasets. Isomorphous difference maps combine the phases of a chosen reference state with the observed changes in structure factor amplitudes to yield a map of changes in electron density. Such maps are much more sensitive to conformational change than structure refinement is, and are unbiased in the sense that observed differences do not depend on refinement of the perturbed state. However, even minute changes in unit cell properties can render isomorphous difference maps useless. This is unnecessary. Here we describe a generalized procedure for calculating observed difference maps that retains the high sensitivity to conformational change and avoids structure refinement of the perturbed state. We have implemented this procedure in an open-source python package, MatchMaps, that can be run in any software environment supporting PHENIX and CCP4. Through examples, we show that MatchMaps "rescues" observed difference electron density maps for poorly-isomorphous crystals, corrects artifacts in nominally isomorphous difference maps, and extends to detecting differences across copies within the asymmetric unit, or across altogether different crystal forms.
构象变化介导大分子的生物学功能。晶体学测量能够以非凡的灵敏度描绘这些变化，作为突变、配体和时间的函数。同晶型差异图仍然是检测数据集之间结构差异的金标准。同晶型差异图将选定参考状态的相位与结构因子振幅的观测变化相结合，以生成电子密度变化图。此类图对构象变化的敏感度远高于结构精修，并且在观测差异不依赖于受扰状态精修的意义上是无偏的。然而，即使晶胞属性的微小变化也可能使同晶型差异图变得无用。这是不必要的。在此，我们描述了一种计算观测差异图的通用程序，该程序保留了对构象变化的高灵敏度，并避免了受扰状态的结构精修。我们已在一个开源Python包MatchMaps中实现了此程序，该包可在任何支持PHENIX和CCP4的软件环境中运行。通过实例，我们展示了MatchMaps如何“挽救”同晶性差的晶体的观测差异电子密度图，校正名义上同晶型差异图中的伪影，并扩展到检测不对称单元内各拷贝之间或完全不同晶体形式之间的差异。
