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Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling (2010)
| Venue: | Nucleic Acids Res |
| Citations: | 6 - 1 self |
BibTeX
@ARTICLE{Schudoma10sequence-structurerelationships,
author = {Christian Schudoma and Patrick May and Viktoria Nikiforova and Dirk Walther},
title = {Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling},
journal = {Nucleic Acids Res},
year = {2010},
pages = {970--980}
}
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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 similar-ity. 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. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.
Keyphrases
rna loop sequence-structure relationship loop homology rna molecule rna loop model building specific function homology present three-dimensional structure small fraction unique loop structure similar structure sequence identity rna structure rna loop structure sequence similar-ity comprehensive loop-structure data set isosteric relationship distinct cluster possible sequence clear evidence template structure sequence divergence-based selection rna loop homology design effort actual sequence unstructured loop region sequence structure relationship limited number loop-structure data set actual rna loop space rna sequence online database systematic analysis rna engineering rfam database
