信号核苷和核苷酸的核糖环构象调查。
Survey of ribose ring pucker of signaling nucleosides and nucleotides.
作者信息
Salmaso Veronica, Jacobson Kenneth A
机构信息
Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
出版信息
Nucleosides Nucleotides Nucleic Acids. 2020;39(1-3):322-341. doi: 10.1080/15257770.2019.1658115. Epub 2019 Aug 28.
The ribose of protein-bound nucleosides and nucleotides displays preferred conformations (usually either North or South), which can be exploited to design enhanced analogs having chemically fixed conformations. We introduce a computational protocol for assembling data from the protein database (PDB) on the ribose and ribose-like conformation of small molecule ligands when complexed with purinergic signaling proteins (including receptors, enzymes and transporters, and related intracellular pathways). Some targets prefer exclusively North (adenosine and P2Y receptors, CD73, adenosine kinase ATP/ADP-binding site, adenosine deaminase), others prefer South (P2Y receptor, E-NTPDase2) or East (adenosine kinase substrates), while others (P2XRs) allow various conformations.
蛋白质结合的核苷和核苷酸中的核糖呈现出优选的构象（通常为北式或南式），可利用这些构象来设计具有化学固定构象的增强类似物。我们引入了一种计算协议，用于收集蛋白质数据库（PDB）中关于小分子配体与嘌呤能信号蛋白（包括受体、酶和转运蛋白以及相关细胞内途径）复合时的核糖和类核糖构象的数据。一些靶点仅偏好北式构象（腺苷和P2Y受体、CD73、腺苷激酶ATP/ADP结合位点、腺苷脱氨酶），另一些偏好南式构象（P2Y受体、E-NTPDase2）或东式构象（腺苷激酶底物），而其他靶点（P2XRs）则允许多种构象。
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