Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

Nucleic Acids Research
Christian SchudomaDirk Walther

Abstract

The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by <25% in sequence identity fold into very similar structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLoo...Continue Reading

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Citations

Dec 7, 2011·Proceedings of the National Academy of Sciences of the United States of America·Parin SripakdeevongRhiju Das
Apr 30, 2010·Bioinformatics·Christian SchudomaDirk Walther
Jun 13, 2012·Bioinformatics·Jan HoinkaTeresa M Przytycka
Feb 9, 2011·Nucleic Acids Research·Magdalena RotherJanusz M Bujnicki
Sep 29, 2011·Nucleic Acids Research·Andrey ChursovDmitrij Frishman
Nov 6, 2013·Acta Crystallographica. Section D, Biological Crystallography·Marco MarciaAnna Marie Pyle
Jun 17, 2010·BMC Bioinformatics·Emidio Capriotti, Marc A Marti-Renom
Aug 24, 2013·RNA·Anton I PetrovNeocles B Leontis
Jun 2, 2011·RNA·Christian SchudomaDirk Walther
Nov 13, 2012·PloS One·Liang Liu, Shi-Jie Chen
Nov 14, 2013·Nucleic Acids Research·Grzegorz ChojnowskiJanusz M Bujnicki
Jun 1, 2011·Biomolecular Concepts·Christian Schudoma
May 29, 2016·Nucleic Acids Research·James RollNeocles Leontis
Aug 6, 2016·PLoS Computational Biology·Jun LiWei Wang
Sep 26, 2020·Nucleic Acids Research·Mubarak I Umar, Chun Kit Kwok
Jun 7, 2018·Nucleic Acids Research·Eric Augusto ItoFabrício Martins Lopes
Jun 8, 2017·BMC Bioinformatics·Shermin PeiMichelle M Meyer
Jul 10, 2018·Nucleic Acids Research·Yijie WangTeresa M Przytycka
Apr 3, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Jian ZhangWei Wang
Nov 13, 2019·Biochemistry·Katherine E RichardsonBrent M Znosko

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Software Mentioned

Mfold
MANIP
iFoldRNA
MySQL
ROSETTA
Paradise
seqid
FARNA
Annotate
MC

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