Several mutations in the gene for the mitochondrial single stranded DNA binding protein (SSBP1) have recently been implicated in human disease, but initial reports are insufficient to explain the molecular mechanism of disease, including the possible role of SSBP1 heterotetramers in heterozygous patients. Here we employed molecular simulations to model the dynamics of wild type and 31 variant SSBP1 tetramer systems, including 7 variant homotetramer and 24 representative heterotetramer systems. Our simulations indicate that all variants are stable and most have stronger intermonomer interactions, reduced solvent accessible surface areas, and a net loss of positive surface charge. We then used structural alignments and phosphate binding simulations to predict DNA binding surfaces on SSBP1. Our models suggest that nearly the entire surface of SSBP1, excluding flexible loops and protruding helices, is available for DNA binding, and we observed several potential DNA binding hotspots. Changes to the protein surface in variant SSBP1 tetramers potentially alter anchor points or wrapping paths, rather than abolishing binding altogether. Overall, our findings disqualify tetramer destabilization or gross disruption of DNA binding as mechanisms of disease. Instead, they are consistent with subtle changes to DNA binding, wrapping, or release that cause rare but consequential failures of mtDNA maintenance, which, in turn, are consistent with the late onset of disease in most of the reported SSBP1 cases.

线粒体单链 DNA 结合蛋白 ( SSBP1 ) 基因的几个突变) 最近与人类疾病有关，但初步报告不足以解释疾病的分子机制，包括 SSBP1 异四聚体在杂合子患者中的可能作用。在这里，我们采用分子模拟来模拟野生型和 31 个变体 SSBP1 四聚体系统的动力学，包括 7 个变体同源四聚体和 24 个具有代表性的异源四聚体系统。我们的模拟表明，所有变体都是稳定的，并且大多数变体具有更强的单体间相互作用、减少的溶剂可及表面积和正表面电荷的净损失。然后我们使用结构比对和磷酸盐结合模拟来预测 SSBP1 上的 DNA 结合表面。我们的模型表明，SSBP1 的几乎整个表面，不包括柔性环和突出的螺旋，都可用于 DNA 结合，我们观察到几个潜在的 DNA 结合热点。变体 SSBP1 四聚体中蛋白质表面的变化可能会改变锚点或包裹路径，而不是完全取消结合。总体而言，我们的研究结果取消了四聚体不稳定或 DNA 结合的严重破坏作为疾病机制的资格。相反，它们与 DNA 结合、包裹或释放的细微变化相一致，这些变化会导致 mtDNA 维持罕见但随之而来的失败，这反过来与大多数报告的 SSBP1 病例中的晚期疾病发病一致。我们的研究结果取消了四聚体不稳定或 DNA 结合的严重破坏作为疾病机制的资格。相反，它们与 DNA 结合、包裹或释放的细微变化相一致，这些变化会导致 mtDNA 维持罕见但随之而来的失败，这反过来与大多数报告的 SSBP1 病例中的晚期疾病发病一致。我们的研究结果取消了四聚体不稳定或 DNA 结合的严重破坏作为疾病机制的资格。相反，它们与 DNA 结合、包裹或释放的细微变化相一致，这些变化会导致 mtDNA 维持罕见但随之而来的失败，这反过来与大多数报告的 SSBP1 病例中的晚期疾病发病一致。