Jewell Shannon, Nguyen Thanh Binh, Ascher David B, Robertson Avril A B
School of Chemistry and Molecular Bioscience, University of Queensland, Brisbane, Australia.
Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Australia.
Comput Struct Biotechnol J. 2024 Sep 22;23:3506-3513. doi: 10.1016/j.csbj.2024.09.013. eCollection 2024 Dec.
Nucleotide-binding oligomerization domain, leucine rich repeat containing X1 (NLRX1) is a negative regulator of the nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) pathway, with a significant role in the context of inflammation. Altered expression of NLRX1 is prevalent in inflammatory diseases leading to interest in NLRX1 as a drug target. There is a lack of structural information available for NLRX1 as only the leucine-rich repeat domain of NLRX1 has been crystallised. This lack of structural data limits progress in understanding function and potential druggability of NLRX1. We have modelled full-length NLRX1 by combining experimental, homology modelled and AlphaFold2 structures. The full-length model of NLRX1 was used to explore protein dynamics, mutational tolerance and potential functions. We identified a new RNA binding site in the previously uncharacterized N-terminus, which served as a basis to model protein-RNA complexes. The structure of the adenosine triphosphate (ATP) binding domain revealed a potential catalytic functionality for the protein as a member of the ATPase Associated with Diverse Cellular Activity family of proteins. Finally, we investigated the interactions of NLRX1 with small molecule activators in development, revealing a binding site that has not previously been discussed in literature. The model generated here will help to catalyse efforts towards creating new drug molecules to target NLRX1 and may be used to inform further studies on functionality of NLRX1.
核苷酸结合寡聚化结构域富含亮氨酸重复序列蛋白X1（NLRX1）是活化B细胞核因子κB（NFκB）通路的负调节因子，在炎症反应中起重要作用。NLRX1表达改变在炎症性疾病中很常见，这引发了人们将NLRX1作为药物靶点的兴趣。由于只有NLRX1的富含亮氨酸重复序列结构域被结晶，目前缺乏NLRX1的结构信息。这种结构数据的缺乏限制了对NLRX1功能和潜在可成药性的理解。我们通过结合实验结构、同源建模结构和AlphaFold2结构对全长NLRX1进行了建模。利用NLRX1的全长模型探索了蛋白质动力学、突变耐受性和潜在功能。我们在以前未表征的N端鉴定了一个新的RNA结合位点，该位点为蛋白质-RNA复合物建模提供了基础。三磷酸腺苷（ATP）结合结构域的结构揭示了该蛋白质作为与多种细胞活动相关的ATP酶家族成员的潜在催化功能。最后，我们研究了NLRX1与小分子激活剂在发育过程中的相互作用，揭示了一个此前文献中未讨论过的结合位点。此处生成的模型将有助于推动针对NLRX1开发新药物分子的研究，并可用于为进一步研究NLRX1的功能提供参考。
