While protein conformational heterogeneity plays an important role in many aspects of biological function, including ligand binding, its impact has been difficult to quantify. Macromolecular X-ray diffraction is commonly interpreted with a static structure, but it can provide information on both the anharmonic and harmonic contributions to conformational heterogeneity. Here, through multiconformer modeling of time- and space-averaged electron density, we measure conformational heterogeneity of 743 stringently matched pairs of crystallographic datasets that reflect unbound/apo and ligand-bound/holo states. When comparing the conformational heterogeneity of side chains, we observe that when binding site residues become more rigid upon ligand binding, distant residues tend to become more flexible, especially in non-solvent exposed regions. Among ligand properties, we observe increased protein flexibility as the number of hydrogen bonds decrease and relative hydrophobicity increases. Across a series of 13 inhibitor bound structures of CDK2, we find that conformational heterogeneity is correlated with inhibitor features and identify how conformational changes propagate differences in conformational heterogeneity away from the binding site. Collectively, our findings agree with models emerging from NMR studies suggesting that residual side chain entropy can modulate affinity and point to the need to integrate both static conformational changes and conformational heterogeneity in models of ligand binding.

中文翻译：

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配体结合重塑蛋白质侧链构象异质性

虽然蛋白质构象异质性在生物功能的许多方面都发挥着重要作用，包括配体结合，但其影响难以量化。大分子 X 射线衍射通常用静态结构来解释，但它可以提供关于非谐波和谐波对构象异质性的贡献的信息。在这里，通过对时间和空间平均电子密度的多构象建模，我们测量了 743 对严格匹配的晶体数据集的构象异质性，这些数据集反映了未结合/载脂蛋白和配体结合/全息状态。在比较侧链的构象异质性时，我们观察到，当配体结合后结合位点残基变得更加刚性时，远处的残基往往变得更加灵活，尤其是在非溶剂暴露区域。在配体特性中，我们观察到随着氢键数量的减少和相对疏水性的增加，蛋白质的灵活性增加。在 CDK2 的一系列 13 个抑制剂结合结构中，我们发现构象异质性与抑制剂特征相关，并确定构象变化如何将构象异质性的差异传播远离结合位点。总的来说，我们的研究结果与 NMR 研究中出现的模型一致，表明残余侧链熵可以调节亲和力，并指出需要在配体结合模型中整合静态构象变化和构象异质性。在 CDK2 的一系列 13 个抑制剂结合结构中，我们发现构象异质性与抑制剂特征相关，并确定构象变化如何将构象异质性的差异传播远离结合位点。总的来说，我们的研究结果与 NMR 研究中出现的模型一致，表明残余侧链熵可以调节亲和力，并指出需要在配体结合模型中整合静态构象变化和构象异质性。在 CDK2 的一系列 13 个抑制剂结合结构中，我们发现构象异质性与抑制剂特征相关，并确定构象变化如何将构象异质性的差异传播远离结合位点。总的来说，我们的研究结果与 NMR 研究中出现的模型一致，表明残余侧链熵可以调节亲和力，并指出需要在配体结合模型中整合静态构象变化和构象异质性。