Proper modelling of ligand binding requires an ensemble of bound and unbound states
Proper modelling of ligand binding requires an ensemble of bound and unbound states
复制标题
配体结合的正确建模需要结合和未结合状态的集合
DOI：
10.1101/078147
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发表时间：
2016
期刊：
影响因子：
--
通讯作者：
F. von Delft
中科院分区：
文献类型：
--
作者：
N. Pearce;F. von Delft
我们强调并证明了在晶体学数据集中通常发生的配体结合和未结合状态的叠加建模的重要性。生成的合奏，不仅描述了晶体中的主导状态是重要的低占有率配体的高质量的细化，以及提出一个模型，解释所有观察到的密度。小分子仅与晶格中的一小部分蛋白质结合，但通常按惯例避免对配体的占据细化;假设误差将由B因子充分建模，则占据被设置为1，并且弱配体密度通常被忽略或归因于无序。在执行占据细化的情况下，叠加的原子状态很少被建模。我们在这里表明，这些建模方法导致配体模型的质量下降，并可能影响结合的配体和蛋白质之间的相互作用的解释。相反，上级的准确性是通过建模的配体部分占用和叠加在一个配体自由的“基态”溶剂模型。使用参考数据集对晶体的叠加未结合部分进行显式建模，允许以最小的过度拟合恐惧对配体的占用进行约束细化。更好地表示晶体还可以获得更有意义的细化原子参数，如B因子，从而更深入地了解晶体中的动力学。我们提出了一个简单的方法和简单的指导方针，用于生成绑定和未绑定状态的合奏，假设代表未绑定状态（基态）的数据集可用。从不同的电子密度度量来看，系综模型始终优于相应的单态模型。此外，局部建模的叠加基态被发现一般是更重要的配体模型的质量比收敛的整体阶段。
Synopsis We emphasise and demonstrate the importance of modelling the superpositions of ligand-bound and unbound states that commonly occur in crystallographic datasets. Generation of an ensemble that describes not only the dominant state in the crystal is important for the high-quality refinement of low-occupancy ligands, as well as to present a model that explains all of the observed density. Abstract Small molecules bind to only a fraction of the proteins in the crystal lattice, but occupancy refinement of ligands is often avoided by convention; occupancies are set to unity, assuming that the error will be adequately modelled by the B-factors, and weak ligand density is generally ignored or attributed to disorder. Where occupancy refinement is performed, the superposed atomic state is rarely modelled. We show here that these modelling approaches lead to a degradation of the quality of the ligand model, and potentially affect the interpretation of the interactions between the bound ligand and the protein. Instead, superior accuracy is achieved by modelling the ligand as partially occupied and superposed on a ligand-free “ground-state” solvent model. Explicit modelling of the superposed unbound fraction of the crystal using a reference dataset allows constrained refinement of the occupancy of the ligand with minimal fear of over-fitting. Better representation of the crystal also leads to more meaningful refined atomic parameters such as the B-factor, allowing more insight into dynamics in the crystal. We present a simple approach and simple guidelines for generating the ensemble of bound and unbound states, assuming that datasets representing the unbound states (the ground state) are available. Judged by various electron density metrics, ensemble models are consistently better than corresponding single-state models. Furthermore, local modelling of the superposed ground state is found to be generally more important for the quality of the ligand model than convergence of the overall phases.