São Carlos Institute of Chemistry, University of São Paulo, 13560-970, São Paulo, Brazil.
Goiano Federal Institute of Education, Science and Technology, Campus Rio Verde, 75901-970, Goiás, Brazil.
Sci Rep. 2020 Feb 6;10(1):1931. doi: 10.1038/s41598-020-58531-4.
Endonuclease III (EndoIII) is a DNA glycosylase that contains the [4Fe4S] cluster, which is essential for the protein to bind to damaged DNA in a process called base excision repair (BER). Here we propose that the change in the covalency of Fe-S bonds of the [4Fe4S] cluster caused by double-stranded (ds)-DNA binding is accompanied by a change in their strength, which is due to alterations of the electronic structure of the cluster. Micro-FTIR spectroscopy in the mid-IR region and FTIR spectroscopy in the far IR (450 and 300 cm) were used independently to study the structural changes in EndoIII and the behavior of the [4Fe4S] cluster it contains, in the native form and upon its binding to ds-DNA. Structural changes in the DNA itself were also examined. The characteristics vibrational modes, corresponding to Fe-S (sulfide) and Fe-S (thiolate) bonds were identified in the cluster through far IR spectroscopy as well through quantum chemistry calculations. Based on the experimental results, these vibrational modes shift in their spectral positions caused by negatively charged DNA in the vicinity of the cluster. Modifications of the Fe-S bond lengths upon DNA binding, both of the Fe-S (sulfide) and Fe-S (thiolate) bonds in the [4Fe4S] cluster of EndoIII are responsible for the stabilization of the cluster towards higher oxidation state (3+), and hence its redox communication along the ds-DNA helix.
内切核酸酶 III（EndoIII）是一种含有[4Fe4S]簇的 DNA 糖苷酶，该簇对于该蛋白在碱基切除修复（BER）过程中与受损 DNA 结合至关重要。在这里，我们提出双链 DNA（ds-DNA）结合引起的[4Fe4S]簇中铁-硫键的共价键变化伴随着它们强度的变化，这是由于簇的电子结构发生了变化。中红外区的微傅里叶变换红外光谱（micro-FTIR）和远红外区（450 和 300 cm）的傅里叶变换红外光谱（FTIR）分别被独立用于研究内切核酸酶 III 的结构变化及其所包含的[4Fe4S]簇的行为，包括在天然状态下以及与 ds-DNA 结合时的状态。还研究了 DNA 本身的结构变化。通过远红外光谱以及量子化学计算，在簇中识别出对应于 Fe-S（硫化物）和 Fe-S（硫醇盐）键的特征振动模式。基于实验结果，这些振动模式在其光谱位置上发生了偏移，这是由于带负电荷的 DNA 靠近簇引起的。在 DNA 结合时，Fe-S（硫化物）和 Fe-S（硫醇盐）键的长度发生了变化，这使得[4Fe4S]簇中的 EndoIII 稳定在更高的氧化态（3+），从而实现了沿 ds-DNA 螺旋的氧化还原通讯。
