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Nucleic Acids Research Advance Access originally published online on September 29, 2006
Nucleic Acids Research 2006 34(19):5361-5368; doi:10.1093/nar/gkl580
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Nucleic Acids Research, 2006, Vol. 34, No. 19 5361-5368
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Molecular dynamics simulations of human Formula: the role of modified bases in mRNA recognition

Nina E. McCrate, Mychel E. Varner, Kenneth I. Kim and Maria C. Nagan*

Division of Science, Truman State University, 100 East Normal, Kirksville MO 63501, USA

*To whom correspondence should be addressed. Tel: +1 660 785 4084; Fax: +1 660 785 4045; Email: mnagan{at}truman.edu

Received May 18, 2006. Revised July 21, 2006. Accepted July 24, 2006.

Accuracy in translation of the genetic code into proteins depends upon correct tRNA–mRNA recognition in the context of the ribosome. In human Formula three modified bases are present in the anticodon stem–loop—2-methylthio-N6-threonylcarbamoyladenosine at position 37 (ms2t6A37), 5-methoxycarbonylmethyl-2-thiouridine at position 34 (mcm5s2U34) and pseudouridine ({psi}) at position 39—two of which, ms2t6A37 and mcm5s2U34, are required to achieve wild-type binding activity of wild-type human Formula [C. Yarian, M. Marszalek, E. Sochacka, A. Malkiewicz, R. Guenther, A. Miskiewicz and P. F. Agris (2000) Biochemistry, 39, 13390–13395]. Molecular dynamics simulations of nine tRNA anticodon stem–loops with different combinations of nonstandard bases were performed. The wild-type simulation exhibited a canonical anticodon stair-stepped conformation. The ms2t6 modification at position 37 is required for maintenance of this structure and reduces solvent accessibility of U36. Ms2t6A37 generally hydrogen bonds across the loop and may prevent U36 from rotating into solution. A water molecule does coordinate to {psi}39 most of the simulation time but weakly, as most of the residence lifetimes are <40 ps.


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