Deconvolution of conformational exchange from Raman spectra of aqueous RNA nucleosides.
Deconvolution of conformational exchange from Raman spectra of aqueous RNA nucleosides.
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DOI：
10.1038/s42004-020-0298-x
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发表时间：
2020-05-06
影响因子：
5.9
通讯作者：
Almond, Andrew
中科院分区：
文献类型：
--
作者：
Wilson, Alex L.;Outeiral, Carlos;Dowd, Sarah E.;Doig, Andrew J.;Popelier, Paul L. A.;Waltho, Jonathan P.;Almond, Andrew
核糖核酸（rna）是分子生物学中心法则的关键。虽然拉曼光谱在研究RNA构象动力学方面具有很大的潜力，但目前的计算拉曼预测和分配方法在系统大小和包含构象交换方面受到限制。在这里，提出了一个框架，预测拉曼光谱使用的混合子光谱对应的主要构象计算使用经典和从头算分子动力学。实验优化允许嘌呤和嘧啶分别以syn和anti为主，核糖在等效的南种群和北种群之间交换。这些测量结果与核糖核苷的拉曼光谱以及以前的实验和计算结果非常吻合。该框架提供了核糖核苷溶液种群和RNA亚基构象交换的测量。它补充了其他实验技术，可以扩展到其他分子，如蛋白质和碳水化合物，使生物学见解和提供一个新的分析工具。单核糖核苷酸的构象灵活性使得解释它们的振动谱具有挑战性。本文采用经典分子动力学和从头算分子动力学相结合的方法计算了不同单核苷酸构象对实验拉曼光谱的贡献。
Ribonucleic acids (RNAs) are key to the central dogma of molecular biology. While Raman spectroscopy holds great potential for studying RNA conformational dynamics, current computational Raman prediction and assignment methods are limited in terms of system size and inclusion of conformational exchange. Here, a framework is presented that predicts Raman spectra using mixtures of sub-spectra corresponding to major conformers calculated using classical and ab initio molecular dynamics. Experimental optimization allowed purines and pyrimidines to be characterized as predominantly syn and anti, respectively, and ribose into exchange between equivalent south and north populations. These measurements are in excellent agreement with Raman spectroscopy of ribonucleosides, and previous experimental and computational results. This framework provides a measure of ribonucleoside solution populations and conformational exchange in RNA subunits. It complements other experimental techniques and could be extended to other molecules, such as proteins and carbohydrates, enabling biological insights and providing a new analytical tool. The conformational flexibility of monoribonucleotides can make interpreting their vibrational spectra challenging. Here a combination of classical and ab initio molecular dynamics is used to calculate the contributions of different monoribonucleotide conformers to experimental Raman spectra.
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DOI：
10.1107/s2059798318009324
发表时间：
2018-09-01
期刊：
Acta crystallographica. Section D, Structural biology
影响因子：
--
作者：
Afonine PV;Klaholz BP;Moriarty NW;Poon BK;Sobolev OV;Terwilliger TC;Adams PD;Urzhumtsev A
通讯作者：
Urzhumtsev A
影响因子：
2.9
作者：
HOOVER, WG
通讯作者：
HOOVER, WG
影响因子：
4.4
作者：
BECKE, AD
通讯作者：
BECKE, AD
DOI：
10.1126/science.1202692
发表时间：
2011-05-20
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Dunkle JA;Wang L;Feldman MB;Pulk A;Chen VB;Kapral GJ;Noeske J;Richardson JS;Blanchard SC;Cate JH
通讯作者：
Cate JH
影响因子：
4.4
作者：
JORGENSEN, WL;CHANDRASEKHAR, J;KLEIN, ML
通讯作者：
KLEIN, ML