Asaithambi Killivalavan, Biswas Iman, Suguna Kaza
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
Curr Res Struct Biol. 2022 May 26;4:175-191. doi: 10.1016/j.crstbi.2022.05.003. eCollection 2022.
Ddi1 is a multidomain protein that belongs to the ubiquitin receptor family of proteins. The Ddi1 proteins contain a highly conserved retroviral protease (RVP)-like domain along with other domains. The severity of opportunistic infections, caused by parasitic protozoa in AIDS patients, was found to decline when HIV protease inhibitors were used in antiretroviral therapy. Parasite growth was shown to be suppressed by a few of the inhibitors targeting Ddi1 present in these parasites. In this study, the binding of HIV protease inhibitors to the RVP domain of Ddi1 from and ; and the binding of ubiquitin to the ubiquitin-associated domain of Ddi1 from these two parasites were established using Biolayer Interferometry. The crystal structures of the RVP domains of Ddi1 from and were determined; they form homodimers similar to those observed in HIV protease and the reported structures of the same domain from , and humans. The native form of the domain showed an open dimeric structure and a normal mode analysis revealed that it can take up a closed conformation resulting from relative movements of the subunits. Based on the crystal structure of the RVP domain of Ddi1 from , a seven residue peptide inhibitor was designed and it was shown to bind to the RVP domain of Ddi1 from by Biolayer Interferometry. This peptide was modified using computational methods and was shown to have a better affinity than the initial peptide.
Ddi1是一种多结构域蛋白，属于泛素受体蛋白家族。Ddi1蛋白包含一个高度保守的逆转录病毒蛋白酶（RVP）样结构域以及其他结构域。在抗逆转录病毒疗法中使用HIV蛋白酶抑制剂时，发现艾滋病患者由寄生原生动物引起的机会性感染的严重程度有所下降。已表明这些寄生虫中存在的一些靶向Ddi1的抑制剂可抑制寄生虫生长。在本研究中，使用生物层干涉术确定了HIV蛋白酶抑制剂与来自[具体物种1]和[具体物种2]的Ddi1的RVP结构域的结合；以及泛素与这两种寄生虫的Ddi1的泛素相关结构域的结合。确定了来自[具体物种1]和[具体物种2]的Ddi1的RVP结构域的晶体结构；它们形成同二聚体，类似于在HIV蛋白酶中观察到的以及来自[具体物种3]、[具体物种4]和人类的同一结构域的报道结构。该结构域的天然形式显示出开放的二聚体结构，正常模式分析表明它可以由于亚基的相对运动而呈现封闭构象。基于来自[具体物种1]的Ddi1的RVP结构域的晶体结构，设计了一种七肽抑制剂，并通过生物层干涉术表明它可与来自[具体物种2]的Ddi1的RVP结构域结合。使用计算方法对该肽进行了修饰，结果表明其亲和力比初始肽更好。
