Mazhibiyeva Akerke, Pham Tri T, Pats Karina, Lukac Martin, Molnár Ferdinand
Laboratory of Computational Structural Biology, Department of Biology, Nazarbayev University, Kabanbay Batyr 53, Astana, 010000, Kazakhstan.
Laboratory of Mechanobiology, Department of Biology, Nazarbayev University, Kabanbay Batyr 53, Astana, 010000, Kazakhstan.
Comput Struct Biotechnol J. 2025 May 15;27:1998-2013. doi: 10.1016/j.csbj.2025.05.010. eCollection 2025.
AlphaFold 2 has revolutionized protein structure prediction, yet systematic evaluations of its performance against experimental structures for specific protein families remain limited. Here we present the first comprehensive analysis comparing AlphaFold 2-predicted and experimental nuclear receptor structures, examining root-mean-square deviations, secondary structure elements, domain organization, and ligand-binding pocket geometry. While AlphaFold2 achieves high accuracy in predicting stable conformations with proper stereochemistry, it shows limitations in capturing the full spectrum of biologically relevant states, particularly in flexible regions and ligand-binding pockets. Statistical analysis reveals significant domain-specific variations, with ligand-binding domains showing higher structural variability (CV = 29.3%) compared to DNA-binding domains (CV = 17.7%). Notably, Alphafold 2 systematically underestimates ligand-binding pocket volumes and captures only single conformational states in homodimeric receptors where experimental structures show functionally important asymmetry. These findings provide critical insights for structure-based drug design targeting nuclear receptors and establish a framework for evaluating Alphafold 2 predictions across other protein families.
AlphaFold 2彻底改变了蛋白质结构预测，但针对特定蛋白质家族，将其预测性能与实验结构进行系统评估的研究仍然有限。在此，我们首次对AlphaFold 2预测的核受体结构与实验结构进行了全面分析，研究了均方根偏差、二级结构元件、结构域组织和配体结合口袋几何形状。虽然AlphaFold 2在预测具有正确立体化学的稳定构象方面具有较高的准确性，但在捕捉所有生物学相关状态方面存在局限性，尤其是在柔性区域和配体结合口袋中。统计分析揭示了显著的结构域特异性差异，与DNA结合结构域（变异系数=17.7%）相比，配体结合结构域表现出更高的结构变异性（变异系数=29.3%）。值得注意的是，AlphaFold 2系统地低估了配体结合口袋的体积，并仅捕捉到同二聚体受体中的单一构象状态，而实验结构显示出功能上重要的不对称性。这些发现为针对核受体的基于结构的药物设计提供了关键见解，并建立了一个评估AlphaFold 2在其他蛋白质家族预测结果的框架。
