计算化学家面临的RNA挑战。
RNA challenges for computational chemists.
作者信息
Yildirim Ilyas, Turner Douglas H
机构信息
Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, USA.
出版信息
Biochemistry. 2005 Oct 11;44(40):13225-34. doi: 10.1021/bi051236o.
Abstract
Some experimental results for the thermodynamics of RNA folding cannot be explained by simple pairwise hydrogen-bonding models. Such effects include the stabilities of isoguanosine-isocytidine (iG-iC) base pairs and of various 2 x 2 nucleotide internal loops. Presumably, these results can be explained by base stacking effects, which can be partitioned into Coulombic and overlap effects. We review experimental measurements that provide benchmarks for testing the approximations and theories used for modeling nucleic acids. Quantitative agreement between experiment and theory will indicate understanding of the interactions determining RNA stability and structure.
摘要
一些关于RNA折叠热力学的实验结果无法用简单的成对氢键模型来解释。这些效应包括异鸟苷-异胞苷（iG-iC）碱基对以及各种2×2核苷酸内环的稳定性。据推测，这些结果可以用碱基堆积效应来解释，碱基堆积效应可分为库仑效应和重叠效应。我们回顾了一些实验测量，这些测量为测试用于核酸建模的近似方法和理论提供了基准。实验与理论之间的定量一致性将表明对决定RNA稳定性和结构的相互作用有了理解。
相似文献
1
RNA challenges for computational chemists.计算化学家面临的RNA挑战。
Biochemistry. 2005 Oct 11;44(40):13225-34. doi: 10.1021/bi051236o.
2
Stability and structure of RNA duplexes containing isoguanosine and isocytidine.含有异鸟苷和异胞苷的RNA双链体的稳定性和结构
J Am Chem Soc. 2001 Feb 21;123(7):1267-74. doi: 10.1021/ja002623i.
3
Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs.RNA中局部结构的堆积效应：当侧翼GC对被异鸟嘌呤-异胞嘧啶对取代时串联GA对结构的变化。
J Phys Chem B. 2007 Jun 21;111(24):6718-27. doi: 10.1021/jp068732m. Epub 2007 Apr 6.
4
Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for G.U pairs: one hydrogen bond for each G.U pair in r(GGCGUGCC)(2) and two for each G.U pair in r(GAGUGCUC)(2).核磁共振光谱和分子模型表明，G.U碱基对可能存在不同的氢键模式：在r(GGCGUGCC)(2)中每个G.U碱基对有一个氢键，而在r(GAGUGCUC)(2)中每个G.U碱基对有两个氢键。
Biochemistry. 2000 Aug 1;39(30):8970-82.
5
Coarse-grained model for predicting RNA folding thermodynamics.预测 RNA 折叠热力学的粗粒度模型。
J Phys Chem B. 2013 May 2;117(17):4901-11. doi: 10.1021/jp401087x. Epub 2013 Apr 16.
6
The energetics of small internal loops in RNA.RNA中较小内部环的能量学
Biopolymers. 1999;52(4):157-67. doi: 10.1002/1097-0282(1999)52:4<157::AID-BIP1001>3.0.CO;2-E.
7
Solution structure of an RNA internal loop with three consecutive sheared GA pairs.具有三个连续剪切GA对的RNA内部环的溶液结构
Biochemistry. 2005 Mar 1;44(8):2845-56. doi: 10.1021/bi048079y.
8
Effects of nucleotide bromination on the stabilities of Z-RNA and Z-DNA: a molecular mechanics/thermodynamic perturbation study.核苷酸溴化对Z-RNA和Z-DNA稳定性的影响：一项分子力学/热力学微扰研究
Biopolymers. 1989 Nov;28(11):1939-57. doi: 10.1002/bip.360281111.
9
Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases.DNA和RNA碱基的电子性质、氢键、堆积及阳离子结合
Biopolymers. 2001;61(1):3-31. doi: 10.1002/1097-0282(2001)61:1<3::AID-BIP10048>3.0.CO;2-4.
10
Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs.短RNA螺旋上未配对末端核苷酸的热力学与较大RNA中螺旋末端的堆积相关。
J Mol Biol. 1999 Jul 30;290(5):967-82. doi: 10.1006/jmbi.1999.2906.
引用本文的文献
1
The Role of Bond Functions in Describing Intermolecular Electron Correlation for Van der Waals Dimers: A Study of (CH) and Ne.键函数在描述范德华二聚体分子间电子相关中的作用：对（CH）和 Ne 的研究。
Int J Mol Sci. 2024 Jan 25;25(3):1472. doi: 10.3390/ijms25031472.
2
Extending density functional theory with near chemical accuracy beyond pure water.用超越纯水的近化学精度扩展密度泛函理论。
Nat Commun. 2023 Feb 13;14(1):799. doi: 10.1038/s41467-023-36094-y.
3
Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides.预测和分析修饰核苷酸的 RNA 近邻参数。
Nucleic Acids Res. 2020 Sep 18;48(16):8901-8913. doi: 10.1093/nar/gkaa654.
4
An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch.氢键、离子氛围和动力学的复杂平衡促进了新霉素感应核糖开关 U 形转弯中尿嘧啶到胞嘧啶的无缝替换。
Nucleic Acids Res. 2018 Jul 27;46(13):6528-6543. doi: 10.1093/nar/gky490.
5
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.分子模拟捕捉到的 RNA 结构动力学：全面概述。
Chem Rev. 2018 Apr 25;118(8):4177-4338. doi: 10.1021/acs.chemrev.7b00427. Epub 2018 Jan 3.
6
Physics-based all-atom modeling of RNA energetics and structure.基于物理学的RNA能量学与结构的全原子建模
Wiley Interdiscip Rev RNA. 2017 Sep;8(5). doi: 10.1002/wrna.1422.
7
Blind tests of RNA nearest-neighbor energy prediction.RNA最近邻能量预测的盲测。
Proc Natl Acad Sci U S A. 2016 Jul 26;113(30):8430-5. doi: 10.1073/pnas.1523335113. Epub 2016 Jul 8.
8
RNA design rules from a massive open laboratory.从大规模开放实验室中获得的 RNA 设计规则。
Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2122-7. doi: 10.1073/pnas.1313039111. Epub 2014 Jan 27.
9
Computational approaches to predicting the impact of novel bases on RNA structure and stability.预测新碱基对RNA结构和稳定性影响的计算方法。
ACS Chem Biol. 2013 Nov 15;8(11):2354-9. doi: 10.1021/cb4006062. Epub 2013 Oct 8.
10
Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position.摆动碱基对几何形状对密码子简并性的作用：反密码子摆动位置的嘌呤碱基。
J Mol Model. 2012 Aug;18(8):3805-20. doi: 10.1007/s00894-012-1385-4. Epub 2012 Mar 8.
本文引用的文献
1
Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA.水中芳香堆积的影响因素：在DNA背景下的评估
J Am Chem Soc. 2000 Feb 10;122(10):2213-2222. doi: 10.1021/ja9934854.
2
The Monte Carlo method.蒙特卡罗方法。
J Am Stat Assoc. 1949 Sep;44(247):335-41. doi: 10.1080/01621459.1949.10483310.
3
Ions and RNA folding.离子与RNA折叠。
Annu Rev Biophys Biomol Struct. 2005;34:221-43. doi: 10.1146/annurev.biophys.34.040204.144511.
4
Conformational determinants of tandem GU mismatches in RNA: insights from molecular dynamics simulations and quantum mechanical calculations.RNA中串联GU错配的构象决定因素：来自分子动力学模拟和量子力学计算的见解
Biochemistry. 2005 Feb 8;44(5):1433-43. doi: 10.1021/bi047932q.
5
BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences.贝叶斯折叠：结合热力学、共变和化学数据用于比对RNA序列的合理二级结构折叠。
RNA. 2004 Sep;10(9):1323-36. doi: 10.1261/rna.5168504.
6
The thermodynamics of DNA structural motifs.DNA结构基序的热力学
Annu Rev Biophys Biomol Struct. 2004;33:415-40. doi: 10.1146/annurev.biophys.32.110601.141800.
7
An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots.一种用于计算包括假结在内的核酸碱基配对概率的算法。
J Comput Chem. 2004 Jul 30;25(10):1295-304. doi: 10.1002/jcc.20057.
8
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.将化学修饰约束纳入用于预测RNA二级结构的动态规划算法中。
Proc Natl Acad Sci U S A. 2004 May 11;101(19):7287-92. doi: 10.1073/pnas.0401799101. Epub 2004 May 3.
9
Pronounced instability of tandem IU base pairs in RNA.RNA中串联IU碱基对明显不稳定。
Nucleic Acids Res. 2004 Mar 22;32(5):1824-8. doi: 10.1093/nar/gkh501. Print 2004.
10
A guide to ions and RNA structure.离子与RNA结构指南。
RNA. 2004 Mar;10(3):335-43. doi: 10.1261/rna.5205404.
Zotero 插件