Ferrario Eugenio, Miggiano Riccardo, Rizzi Menico, Ferraris Davide M
University of Piemonte Orientale, Department of Pharmaceutical Sciences, Largo Donegani 2, 28100 Novara, Italy.
IXTAL srl, Via Bovio 6, 28100 Novara, Italy.
Comput Struct Biotechnol J. 2022 Jul 18;20:3874-3883. doi: 10.1016/j.csbj.2022.07.027. eCollection 2022.
Computational methods for protein structure prediction have made significant strides forward, as evidenced by the last development of the neural network AlphaFold, which outperformed the CASP14 competitors by consistently predicting the structure of target proteins. Here we show an integrated structural investigation that combines the AlphaFold and crystal structures of human -3-Hydroxy-l-proline dehydratase, an enzyme involved in hydroxyproline catabolism and whose structure had never been reported before, identifying a structural element, absent in the AlphaFold model but present in the crystal structure, that was subsequently proved to be functionally relevant. Although the AlphaFold model lacked information on protein oligomerization, the native dimer was reconstructed using template-based and computational approaches. Moreover, molecular phasing of the diffraction data using the AlphaFold model resulted in dimer reconstruction and straightforward structure solution. Our work adds to the integration of AlphaFold with experimental structural and functional data for protein analysis, crystallographic phasing and structure solution.
蛋白质结构预测的计算方法取得了显著进展，神经网络AlphaFold的最新发展证明了这一点，它通过持续预测目标蛋白质的结构，在CASP14竞赛中胜过了竞争对手。在这里，我们展示了一项综合结构研究，该研究结合了人类3-羟基-L-脯氨酸脱水酶的AlphaFold结构和晶体结构，这种酶参与羟脯氨酸分解代谢，其结构此前从未被报道过。我们鉴定出一个在AlphaFold模型中不存在但在晶体结构中存在的结构元件，随后证明该元件具有功能相关性。尽管AlphaFold模型缺乏关于蛋白质寡聚化的信息，但使用基于模板和计算的方法重建了天然二聚体。此外，使用AlphaFold模型对衍射数据进行分子相位分析，实现了二聚体重建和直接的结构解析。我们的工作为将AlphaFold与蛋白质分析、晶体学相位分析和结构解析的实验结构与功能数据进行整合增添了内容。
