Bezpalaya Ekaterina, Kurilova Svetlana, Vorobyeva Nataliya, Rodina Elena
Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia.
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia.
Life (Basel). 2025 Jan 15;15(1):100. doi: 10.3390/life15010100.
Inorganic pyrophosphatases, or PPases, are ubiquitous enzymes whose activity is necessary for a large number of biosynthetic reactions. The catalytic function of PPases is dependent on certain conformational changes that have been previously characterized based on the comparison of the crystal structures of various complexes. The current work describes the conformational dynamics of a structural model of human mitochondrial pyrophosphatase hPPA2 using molecular dynamics simulation, all-atom principal component analysis, and coarse-grained normal mode analysis. In addition to the wild-type enzyme, four mutant variants of hPPA2 were characterized that correspond to the natural pathogenic variants causing severe mitochondrial dysfunction and cardio pathologies. As a result, we identified the global type of flexible motion that seems to be shared by other dimeric PPases. This motion is discussed in terms of the allosteric behavior of the protein. Analysis of the observed conformational dynamics revealed the formation of a binding site for anionic ligands in the active site that could be relevant to enzyme catalysis. Based on the comparison of the wild-type and mutant PPases dynamics, we suggest the possible molecular mechanisms of the functional incompetence of hPPA2 caused by mutations. The results of this work allow for deeper insight into the structural basis of PPase function and the possible effects of pathogenic mutations on the protein structure and function.
无机焦磷酸酶，即PPases，是普遍存在的酶，其活性对于大量生物合成反应而言是必需的。PPases的催化功能依赖于某些构象变化，这些变化先前已基于各种复合物晶体结构的比较得以表征。当前的工作利用分子动力学模拟、全原子主成分分析和粗粒度正常模式分析，描述了人线粒体焦磷酸酶hPPA2结构模型的构象动力学。除了野生型酶之外，还对hPPA2的四个突变变体进行了表征，这些变体对应于导致严重线粒体功能障碍和心脏疾病的天然致病变体。结果，我们确定了似乎为其他二聚体PPases所共有的全局柔性运动类型。从蛋白质的别构行为角度对这种运动进行了讨论。对观察到的构象动力学的分析揭示了活性位点中阴离子配体结合位点的形成，这可能与酶催化作用相关。基于野生型和突变型PPases动力学的比较，我们提出了由突变导致的hPPA2功能丧失的可能分子机制。这项工作的结果有助于更深入地了解PPase功能的结构基础以及致病突变对蛋白质结构和功能的可能影响。
