Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/106400
Title: Computational study of uracil tautomeric forms in the ribosome : the case of uracil and 5-oxyacetic acid uracil in the first anticodon position of tRNA
Authors: Hartono, Yossa Dwi
Ito, Mika
Villa, Alessandra
Nilsson, Lennart
Keywords: Uracil
Science::Biological sciences
Ribosome
Issue Date: 2017
Source: Hartono, Y. D., Ito, M., Villa, A., & Nilsson, L. (2018). Computational study of uracil tautomeric forms in the ribosome : the case of uracil and 5-oxyacetic acid uracil in the first anticodon position of tRNA. Journal of Physical Chemistry B, 122(3), 1152-1160. doi:10.1021/acs.jpcb.7b10878
Series/Report no.: Journal of Physical Chemistry B
Abstract: Tautomerism is important in many biomolecular interactions, not least in RNA biology. Crystallographic studies show the possible presence of minor tautomer forms of transfer-RNA (tRNA) anticodon bases in the ribosome. The hydrogen positions are not resolved in the X-ray studies, and we have used ab initio calculations and molecular dynamics simulations to understand if and how the minor enol form of uracil (U), or the modified uracil 5-oxyacetic acid (cmo5U), can be accommodated in the tRNA–messenger-RNA interactions in the ribosome decoding center. Ab initio calculations on isolated bases show that the modification affects the keto–enol equilibrium of the uracil base only slightly; the keto form is dominant (>99.99%) in both U and cmo5U. Other factors such as interactions with the surrounding nucleotides or ions would be required to shift the equilibrium toward the enol tautomer. Classical molecular simulations show a better agreement with the X-ray structures for the enol form, but free energy calculations indicate that the most stable form is the keto. In the ribosome, the enol tautomers of U and cmo5U pair with a guanine forming two hydrogen bonds, which do not involve the enol group. The oxyacetic acid modification has a minor effect on the keto–enol equilibrium.
URI: https://hdl.handle.net/10356/106400
http://hdl.handle.net/10220/49608
ISSN: 1520-6106
DOI: 10.1021/acs.jpcb.7b10878
Rights: © 2017 American Chemical Society. This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SBS Journal Articles

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