Exploring combined spin-labeling approach for structural studies of mRNA in the human ribosome.

IF 3.1 2区 化学 Q3 CHEMISTRY, PHYSICAL
Mikhail Kolokolov, Alexey Malygin, Dmitri Graifer, Mariya Meschaninova, Mariya Vorobyeva, Matvey Fedin, Olesya Krumkacheva, Elena Bagryanskaya
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Abstract

In this study, we investigated the structural variability of mRNA in the human ribosome by comparing two spin-labeling strategies: one involving an mRNA analog bearing two spin labels attached to the ribose-phosphate backbone and the other placing labels at the nucleotide bases. The use of two strategies of spin labeling of mRNAs allowed us to study for the first time the effect of the structure and location of spin labels on the measured interspin distances in human ribosome complexes. Experiments using dipolar EPR spectroscopy, supported by molecular dynamics calculations, demonstrated that labels introduced at nucleotide bases provide a higher resolution between mRNA conformations in the ribosome mRNA channel, compared to labels introduced at the ribose-phosphate backbone. Although ribose-phosphate labeling turned out to be less informative on its own for studying mRNA conformations in the ribosome than the previously used base labeling, it can find application in other complex studies of the structure of RNAs and their complexes.

探索人类核糖体中 mRNA 结构研究的组合自旋标记法。
在这项研究中,我们通过比较两种自旋标记策略研究了人类核糖体中 mRNA 的结构变异性:一种策略是在核糖-磷酸骨架上贴上两个自旋标签的 mRNA 类似物,另一种策略是在核苷酸碱基上贴标签。利用两种 mRNA 自旋标记策略,我们首次研究了自旋标记的结构和位置对人类核糖体复合物中测得的棘间距离的影响。在分子动力学计算的支持下,利用双极 EPR 光谱进行的实验表明,与在核糖-磷酸骨架上引入的标签相比,在核糖体 mRNA 通道中核苷酸碱基上引入的标签能提供 mRNA 构象间更高的分辨率。虽然在研究核糖体中的 mRNA 构象时,核糖-磷酸标记本身的信息量不如以前使用的碱基标记,但它可以应用于其他 RNA 及其复合物结构的复杂研究中。
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来源期刊
Journal of Chemical Physics
Journal of Chemical Physics 物理-物理:原子、分子和化学物理
CiteScore
7.40
自引率
15.90%
发文量
1615
审稿时长
2 months
期刊介绍: The Journal of Chemical Physics publishes quantitative and rigorous science of long-lasting value in methods and applications of chemical physics. The Journal also publishes brief Communications of significant new findings, Perspectives on the latest advances in the field, and Special Topic issues. The Journal focuses on innovative research in experimental and theoretical areas of chemical physics, including spectroscopy, dynamics, kinetics, statistical mechanics, and quantum mechanics. In addition, topical areas such as polymers, soft matter, materials, surfaces/interfaces, and systems of biological relevance are of increasing importance. Topical coverage includes: Theoretical Methods and Algorithms Advanced Experimental Techniques Atoms, Molecules, and Clusters Liquids, Glasses, and Crystals Surfaces, Interfaces, and Materials Polymers and Soft Matter Biological Molecules and Networks.
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