PMID: 9185564Jul 1, 1997Paper

RNA base-amino acid interaction strengths derived from structures and sequences

Nucleic Acids Research
B LustigRobert L Jernigan

Abstract

We investigate RNA base-amino acid interactions by counting their contacts in structures and their implicit contacts in various functional sequences where the structures can be assumed to be preserved. These frequencies are cast into equations to extract relative interaction energetics. Previously we used this approach in considering the major groove interactions of DNA, and here we apply it to the more diverse interactions observed in RNA. Structures considered are the three different tRNA synthetase complexes, the U1A spliceosomal protein with an RNA hairpin and the BIV TAR-Tat complex. We use binding data for the base frequencies for the seryl, aspartyl and glutaminyl tRNA-synthetase and U1 RNA-protein complexes. We compare with the previously reported DNA major groove peptide contacts the results for atoms of RNA bases, usually in the major groove. There are strong similarities between the rank orders of interacting bases in the DNA and the RNA cases. The apparent strongest RNA interaction observed is between arginine and guanine which was also one of the strongest DNA interactions. The similar data for base atomic interactions, whether base paired or not, support the importance of strong atomic interactions over local stru...Continue Reading

References

Mar 1, 1976·Proceedings of the National Academy of Sciences of the United States of America·N C SeemanA Rich
Apr 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·J Tao, A D Frankel
Sep 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·A Sarai, Y Takeda
Jan 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·Y TakedaV M Rivera
Apr 5, 1986·Journal of Molecular Biology·T D SchneiderA Ehrenfeucht
Apr 14, 1995·Science·Y Shi, J M Berg
Oct 20, 1995·Journal of Molecular Biology·Y Mandel-GutfreundH Margalit
Apr 28, 1995·Journal of Medicinal Chemistry·E J MartinW H Moos
Jun 6, 1995·Proceedings of the National Academy of Sciences of the United States of America·R Tan, A D Frankel
Nov 8, 1994·Proceedings of the National Academy of Sciences of the United States of America·J R Desjarlais, J M Berg
May 1, 1994·Journal of Chemical Information and Computer Sciences·M A SianiJ M Blaney
Nov 25, 1995·Nucleic Acids Research·B Lustig, R L Jernigan
Sep 1, 1995·Protein Science : a Publication of the Protein Society·A WallqvistD G Covell
Jan 1, 1996·Nucleic Acids Research·M SprinzlS Steinberg
Jan 1, 1996·Nucleic Acids Research·J Gu, R Reddy
Apr 4, 1997·Journal of Molecular Biology·A S Brodsky, J R Williamson

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Citations

Oct 2, 2002·Journal of Biomolecular Structure & Dynamics·Mark HsiehBrooke Lustig
Jun 13, 2012·Nucleic Acids Research·Amita BarikRanjit Prasad Bahadur
Jun 23, 2006·RNA·Michael TerribiliniDrena Dobbs
Nov 2, 1999·Journal of Molecular Biology·L VitaglianoL Mazzarella
Feb 14, 2016·The Journal of Biological Chemistry·Sk Tofajjen HossainMurray P Deutscher
Jun 27, 1998·Journal of Molecular Biology·M ErardA Gatignol

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