dc.contributor.authorHartono, Yossa Dwi
dc.contributor.authorIto, Mika
dc.contributor.authorVilla, Alessandra
dc.contributor.authorNilsson, Lennart
dc.identifier.citationHartono, 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.7b10878en_US
dc.description.abstractTautomerism 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.en_US
dc.format.extent9 p.en_US
dc.relation.ispartofseriesJournal of Physical Chemistry Ben_US
dc.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.en_US
dc.subjectScience::Biological sciencesen_US
dc.titleComputational study of uracil tautomeric forms in the ribosome : the case of uracil and 5-oxyacetic acid uracil in the first anticodon position of tRNAen_US
dc.typeJournal Article
dc.contributor.schoolSchool of Biological Sciencesen_US
dc.description.versionPublished versionen_US

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