Braza Mac Kevin E, Demir Özlem, Ahn Surl-Hee, Morris Clare K, Calvó-Tusell Carla, McGuire Kelly L, de la Peña Avalos Bárbara, Carpenter Michael A, Chen Yanjun, Casalino Lorenzo, Aihara Hideki, Herzik Mark A, Harris Reuben S, Amaro Rommie E
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA.
Department of Chemical Engineering, University of California, Davis, Davis, CA.
bioRxiv. 2024 Dec 12:2024.12.11.628032. doi: 10.1101/2024.12.11.628032.
APOBEC3B (A3B) is implicated in DNA mutations that facilitate tumor evolution. Although structures of its individual N- and C-terminal domains (NTD and CTD) have been resolved through X-ray crystallography, the full-length A3B (fl-A3B) structure remains elusive, limiting understanding of its dynamics and mechanisms. In particular, the APOBEC3B C-terminal domain (A3Bctd) active site is frequently closed in models and structures. In this study, we built several new models of fl-A3B using integrative structural biology methods and selected a top model for further dynamical investigation. We compared dynamics of the truncated (A3Bctd) to the fl-A3B via conventional and Gaussian accelerated molecular dynamics (MD) simulations. Subsequently, we employed weighted ensemble methods to explore the fl-A3B active site opening mechanism, finding that interactions at the NTD-CTD interface enhance the opening frequency of the fl-A3B active site. Our findings shed light on the structural dynamics of fl-A3B, which may offer new avenues for therapeutic intervention in cancer.
载脂蛋白B编辑酶催化多肽样蛋白3B（APOBEC3B，A3B）与促进肿瘤进化的DNA突变有关。尽管已通过X射线晶体学解析了其单个N端和C端结构域（NTD和CTD）的结构，但全长A3B（fl-A3B）的结构仍然未知，这限制了对其动力学和机制的理解。特别是，在模型和结构中，APOBEC3B C端结构域（A3Bctd）的活性位点经常是关闭的。在本研究中，我们使用整合结构生物学方法构建了几个新的fl-A3B模型，并选择了一个顶级模型进行进一步的动力学研究。我们通过传统和高斯加速分子动力学（MD）模拟比较了截短型（A3Bctd）与fl-A3B的动力学。随后，我们采用加权系综方法探索fl-A3B活性位点的开放机制，发现NTD-CTD界面处的相互作用提高了fl-A3B活性位点的开放频率。我们的研究结果揭示了fl-A3B的结构动力学，这可能为癌症的治疗干预提供新途径。
