Hassan Ayaz, Lima Filipe C D A, Crespilho Frank N
São Carlos Institute of Chemistry, University of São Paulo (USP), São Carlos, SP 13566-590, Brazil.
IRCBM, COMSATS University Islamabad (CUI), 1.5 KM Defence Road Off Raiwand Road, Lahore 54000, Pakistan.
Biochemistry. 2025 Feb 18;64(4):782-790. doi: 10.1021/acs.biochem.4c00621. Epub 2025 Feb 4.
Endonuclease III (EndoIII), a key enzyme in the base excision repair (BER) pathway, contains a [4Fe4S] cluster that facilitates DNA repair through DNA-mediated charge transfer. Recent findings indicate that the redox state of this cluster influences EndoIII's binding affinity for DNA, modulating the enzyme's activity. In this study, we investigated the structural and electronic changes of the [4Fe4S] cluster upon binding to double-stranded DNA (dsDNA) using Fourier transform infrared spectroscopy, density functional theory calculations, and machine learning models. Our results reveal shifts in Fe-S bond vibrational modes, suggesting stabilization of the oxidized [4Fe4S] cluster in proximity to negatively charged DNA. A machine learning model, trained on the spectral features of the EndoIII/DNA complex, predicted the enzyme-DNA binding distance, providing further insights into the structural changes upon binding. We correlated the electrochemical stabilization potential of 150 mV in the [4Fe4S] cluster with the enzyme's DNA-binding properties, demonstrating how the cluster's redox state plays a crucial role in both structural stability and DNA repair.
核酸内切酶III（EndoIII）是碱基切除修复（BER）途径中的关键酶，含有一个[4Fe4S]簇，通过DNA介导的电荷转移促进DNA修复。最近的研究结果表明，该簇的氧化还原状态影响EndoIII对DNA的结合亲和力，从而调节酶的活性。在本研究中，我们使用傅里叶变换红外光谱、密度泛函理论计算和机器学习模型，研究了[4Fe4S]簇与双链DNA（dsDNA）结合时的结构和电子变化。我们的结果揭示了Fe-S键振动模式的变化，表明氧化态的[4Fe4S]簇在带负电荷的DNA附近得到稳定。一个基于EndoIII/DNA复合物光谱特征训练的机器学习模型预测了酶与DNA的结合距离，为结合时的结构变化提供了进一步的见解。我们将[4Fe4S]簇中150 mV的电化学稳定电位与酶的DNA结合特性相关联，证明了该簇的氧化还原状态如何在结构稳定性和DNA修复中发挥关键作用。
