Conformational preferences of modified uridines: comparison of AMBER derived force fields.
作者： Indrajit Deb , Joanna Sarzynska , Lennart Nilsson , Ansuman Lahiri
DOI: 10.1021/CI400582A
关键词: RNA 、 Force field (chemistry) 、 Computational chemistry 、 Molecular dynamics 、 Nucleic acid structure 、 Pseudouridine 、 Chemistry 、 Molecular conformation 、 Dihydrouridine 、 Thermodynamics
摘要: The widespread occurrence of modified residues in RNA sequences necessitates development accurate parameters for these modifications reliable modeling structure and dynamics. A comprehensive set the 107 naturally occurring was proposed by Aduri et al. (J. Chem. Theory Comput. 2007, 3, 1464-1475) AMBER FF99 force field. In this work, we tested on a uridine residues, namely, dihydrouridine, 2-thiouridine, 4-thiouridine, pseudouridine, uridine-5-oxyacetic acid, performing molecular dynamics replica exchange simulations nucleosides. Although our using field did not, general, reproduce experimentally observed conformational characteristics well, combination parameter with recent revisions showed noticeable improvement some
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sci-hub.se 参考文章(86)
Darrell R. Davis, Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies) American Society of Microbiology. pp. 85- 102 ,(1998) , 10.1128/9781555818296.CH5
Leonard P. M. ORBONS, Cornelis ALTONA, Conformational analysis of the B and Z forms of the d(m5C-G)3 and d(br5C-G)3 hexamers in solution. A 300-MHz and 500-MHz NMR study. FEBS Journal. ,vol. 160, pp. 141- 148 ,(1986) , 10.1111/J.1432-1033.1986.TB09950.X
M. Sundaralingam, S. T. Rao, J. Abola, Molecular Conformation of Dihydrouridine: Puckered Base Nucleoside of Transfer RNA Science. ,vol. 172, pp. 725- 727 ,(1971) , 10.1126/SCIENCE.172.3984.725
Nicolas Foloppe, Alexander D MacKerell, Jr, None, All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data Journal of Computational Chemistry. ,vol. 21, pp. 86- 104 ,(2000) , 10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G
Itaru Okamoto, Shiqi Cao, Hiroto Tanaka, Kohji Seio, Mitsuo Sekine, Synthesis of 4-Thiopseudoisocytidine and 4-Thiopseudouridine as Components of Triplex-forming Oligonucleotides Chemistry Letters. ,vol. 38, pp. 174- 175 ,(2009) , 10.1246/CL.2009.174
F. E. Hruska, K. K. Ogilvie, A. A. Smith, H. Wayborn, Molecular Conformation of 4-Thiouridine in Aqueous Solution Canadian Journal of Chemistry. ,vol. 49, pp. 2449- 2452 ,(1971) , 10.1139/V71-400
Wayne A Decatur, Maurille J Fournier, rRNA modifications and ribosome function. Trends in Biochemical Sciences. ,vol. 27, pp. 344- 351 ,(2002) , 10.1016/S0968-0004(02)02109-6
C. Altona, Conformational analysis of nucleic acids. Determination of backbone geometry of single‐helical RNA and DNA in aqueous solution Recueil des Travaux Chimiques des Pays-Bas. ,vol. 101, pp. 413- 433 ,(2010) , 10.1002/RECL.19821011201
P AGRIS, Wobble position modified nucleosides evolved to select transfer RNA codon recognition: a modified-wobble hypothesis. Biochimie. ,vol. 73, pp. 1345- 1349 ,(1991) , 10.1016/0300-9084(91)90163-U
Hanna Sierzputowska-Gracz, Elzbieta Sochacka, Andrzej Malkiewicz, Kenneth Kuo, Charles W. Gehrke, Paul F. Agris, Chemistry and structure of modified uridines in the anticodon, wobble position of transfer RNA are determined by thiolation Journal of the American Chemical Society. ,vol. 109, pp. 7171- 7177 ,(1987) , 10.1021/JA00257A044