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核磁共振辅助的RNA二级结构预测：纳入方向依赖性化学位移约束

Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints.

作者信息

Chen Jonathan L, Bellaousov Stanislav, Tubbs Jason D, Kennedy Scott D, Lopez Michael J, Mathews David H, Turner Douglas H

机构信息

Department of Chemistry, University of Rochester , Rochester, New York 14627, United States.

Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States.

出版信息

Biochemistry. 2015 Nov 17;54(45):6769-82. doi: 10.1021/acs.biochem.5b00833. Epub 2015 Nov 3.

DOI:10.1021/acs.biochem.5b00833
PMID:26451676
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4666457/
Abstract

Knowledge of RNA structure is necessary to determine structure-function relationships and to facilitate design of potential therapeutics. RNA secondary structure prediction can be improved by applying constraints from nuclear magnetic resonance (NMR) experiments to a dynamic programming algorithm. Imino proton walks from NOESY spectra reveal double-stranded regions. Chemical shifts of protons in GH1, UH3, and UH5 of GU pairs, UH3, UH5, and AH2 of AU pairs, and GH1 of GC pairs were analyzed to identify constraints for the 5' to 3' directionality of base pairs in helices. The 5' to 3' directionality constraints were incorporated into an NMR-assisted prediction of secondary structure (NAPSS-CS) program. When it was tested on 18 structures, including nine pseudoknots, the sensitivity and positive predictive value were improved relative to those of three unrestrained programs. The prediction accuracy for the pseudoknots improved the most. The program also facilitates assignment of chemical shifts to individual nucleotides, a necessary step for determining three-dimensional structure.

摘要

了解RNA结构对于确定结构-功能关系以及促进潜在治疗药物的设计至关重要。通过将来自核磁共振（NMR）实验的约束应用于动态规划算法，可以改进RNA二级结构预测。来自NOESY谱的亚氨基质子游走揭示了双链区域。分析了GU对的GH1、UH3和UH5、AU对的UH3、UH5和AH2以及GC对的GH1中质子的化学位移，以确定螺旋中碱基对5'到3'方向性的约束。将5'到3'方向性约束纳入到一个NMR辅助二级结构预测（NAPSS-CS）程序中。当在包括九个假结的18个结构上进行测试时，相对于三个无约束程序，其灵敏度和阳性预测值有所提高。对假结的预测准确性提高最为显著。该程序还便于将化学位移分配给单个核苷酸，这是确定三维结构的必要步骤。

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