Lasham Jonathan, Djurabekova Amina, Kolypetris Georgios, Zickermann Volker, Vonck Janet, Sharma Vivek
Department of Physics, University of Helsinki, 00014 Helsinki, Finland.
Department of Physics, University of Helsinki, 00014 Helsinki, Finland.
Biochim Biophys Acta Bioenerg. 2025 Jan 1;1866(1):149512. doi: 10.1016/j.bbabio.2024.149512. Epub 2024 Sep 24.
The charge states of titratable amino acid residues play a key role in the function of membrane-bound bioenergetic proteins. However, determination of these charge states both through experimental and computational approaches is extremely challenging. Cryo-EM density maps can provide insights on the charge states of titratable amino acid residues. By performing classical atomistic molecular dynamics simulations on the high resolution cryo-EM structures of respiratory complex I from Yarrowia lipolytica, we analyze the conformational and charge states of a key acidic residue in its ND1 subunit, aspartic acid D203, which is also a mitochondrial disease mutation locus. We suggest that in the native state of respiratory complex I, D203 is negatively charged and maintains a stable hydrogen bond to a conserved arginine residue. Alternatively, upon conformational change in the turnover state of the enzyme, its sidechain attains a charge-neutral status. We discuss the implications of this analysis on the molecular mechanism of respiratory complex I.
可滴定氨基酸残基的电荷状态在膜结合生物能蛋白的功能中起关键作用。然而，通过实验和计算方法确定这些电荷状态极具挑战性。冷冻电镜密度图可以提供有关可滴定氨基酸残基电荷状态的见解。通过对解脂耶氏酵母呼吸链复合体I的高分辨率冷冻电镜结构进行经典的原子分子动力学模拟，我们分析了其ND1亚基中一个关键酸性残基天冬氨酸D203的构象和电荷状态，该残基也是线粒体疾病的突变位点。我们认为，在呼吸链复合体I的天然状态下，D203带负电荷，并与一个保守的精氨酸残基保持稳定的氢键。另外，在酶的周转状态发生构象变化时，其侧链达到电荷中性状态。我们讨论了这一分析对呼吸链复合体I分子机制的影响。
