Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK.
Viruses. 2023 Jun 10;15(6):1348. doi: 10.3390/v15061348.
DNA-mimicking proteins encoded by viruses can modulate processes such as innate cellular immunity. An example is Ung-family uracil-DNA glycosylase inhibition, which prevents Ung-mediated degradation via the stoichiometric protein blockade of the Ung DNA-binding cleft. This is significant where uracil-DNA is a key determinant in the replication and distribution of virus genomes. Unrelated protein folds support a common physicochemical spatial strategy for Ung inhibition, characterised by pronounced sequence plasticity within the diverse fold families. That, and the fact that relatively few template sequences are biochemically verified to encode Ung inhibitor proteins, presents a barrier to the straightforward identification of Ung inhibitors in genomic sequences. In this study, distant homologs of known Ung inhibitors were characterised via structural biology and structure prediction methods. A recombinant cellular survival assay and in vitro biochemical assay were used to screen distant variants and mutants to further explore tolerated sequence plasticity in motifs supporting Ung inhibition. The resulting validated sequence repertoire defines an expanded set of heuristic sequence and biophysical signatures shared by known Ung inhibitor proteins. A computational search of genome database sequences and the results of recombinant tests of selected output sequences obtained are presented here.
病毒编码的模拟 DNA 的蛋白质可以调节诸如先天细胞免疫等过程。一个例子是 Ung 家族尿嘧啶-DNA 糖基化酶抑制，它通过 Ung DNA 结合裂缝的等摩尔蛋白阻断来防止 Ung 介导的降解。在尿嘧啶-DNA 是病毒基因组复制和分布的关键决定因素的情况下，这一点很重要。不相关的蛋白质折叠支持 Ung 抑制的常见物理化学空间策略，其特征是在不同折叠家族中存在明显的序列可塑性。事实上，相对较少的模板序列在生物化学上被证实编码 Ung 抑制剂蛋白，这给在基因组序列中直接鉴定 Ung 抑制剂带来了障碍。在这项研究中，通过结构生物学和结构预测方法对已知 Ung 抑制剂的远同源物进行了表征。使用重组细胞存活测定和体外生化测定筛选远缘变体和突变体，以进一步探索支持 Ung 抑制的基序中的可容忍序列可塑性。由此产生的经过验证的序列库定义了一个扩展的、由已知 Ung 抑制剂蛋白共享的启发式序列和生物物理特征集。本文介绍了对基因组数据库序列的计算搜索以及对选定输出序列的重组测试结果。
