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Finding 3D motifs in ribosomal RNA structures.

Apostolico A, Ciriello G, Guerra C, Heitsch CE, Hsiao C, Williams LD - Nucleic Acids Res. (2009)

Bottom Line: Furthermore, it provides a new way of characterizing complex 3D motifs, notably junctions, that have been defined and identified in the secondary structure but have not been analyzed and classified in three dimensions.We demonstrate the relevance and utility of our approach by applying it to the Haloarcula marismortui large ribosomal unit.Pending the implementation of a dedicated web server, the code accompanying this article, written in JAVA, is available upon request from the contact author.

View Article: PubMed Central - PubMed

Affiliation: College of Computing, Georgia Institute of Technology, Atlanta, GA 30332-0280, USA.

ABSTRACT
The identification of small structural motifs and their organization into larger subassemblies is of fundamental interest in the analysis, prediction and design of 3D structures of large RNAs. This problem has been studied only sparsely, as most of the existing work is limited to the characterization and discovery of motifs in RNA secondary structures. We present a novel geometric method for the characterization and identification of structural motifs in 3D rRNA molecules. This method enables the efficient recognition of known 3D motifs, such as tetraloops, E-loops, kink-turns and others. Furthermore, it provides a new way of characterizing complex 3D motifs, notably junctions, that have been defined and identified in the secondary structure but have not been analyzed and classified in three dimensions. We demonstrate the relevance and utility of our approach by applying it to the Haloarcula marismortui large ribosomal unit. Pending the implementation of a dedicated web server, the code accompanying this article, written in JAVA, is available upon request from the contact author.

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A 3-junction that forms a wrapped band. Note that all angles are similar.
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Figure 4: A 3-junction that forms a wrapped band. Note that all angles are similar.

Mentions: As already discussed, the classification made for the k*-junctions only weakly applies to the 3-junctions since we did not find a clear correspondence between the sequence of angles and the eccentricity of the junction. To see this consider the case of three similar angles. In this case, both the circular conformation and the wrapped band are possible. Indeed having only three fragments implies that the centroids of the two fragments at the opposite bends of the band are connected by one of the segments forming the three angles. This produces three similar angles as in the circle conformation (Figure 4).Figure 4.


Finding 3D motifs in ribosomal RNA structures.

Apostolico A, Ciriello G, Guerra C, Heitsch CE, Hsiao C, Williams LD - Nucleic Acids Res. (2009)

A 3-junction that forms a wrapped band. Note that all angles are similar.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651809&req=5

Figure 4: A 3-junction that forms a wrapped band. Note that all angles are similar.
Mentions: As already discussed, the classification made for the k*-junctions only weakly applies to the 3-junctions since we did not find a clear correspondence between the sequence of angles and the eccentricity of the junction. To see this consider the case of three similar angles. In this case, both the circular conformation and the wrapped band are possible. Indeed having only three fragments implies that the centroids of the two fragments at the opposite bends of the band are connected by one of the segments forming the three angles. This produces three similar angles as in the circle conformation (Figure 4).Figure 4.

Bottom Line: Furthermore, it provides a new way of characterizing complex 3D motifs, notably junctions, that have been defined and identified in the secondary structure but have not been analyzed and classified in three dimensions.We demonstrate the relevance and utility of our approach by applying it to the Haloarcula marismortui large ribosomal unit.Pending the implementation of a dedicated web server, the code accompanying this article, written in JAVA, is available upon request from the contact author.

View Article: PubMed Central - PubMed

Affiliation: College of Computing, Georgia Institute of Technology, Atlanta, GA 30332-0280, USA.

ABSTRACT
The identification of small structural motifs and their organization into larger subassemblies is of fundamental interest in the analysis, prediction and design of 3D structures of large RNAs. This problem has been studied only sparsely, as most of the existing work is limited to the characterization and discovery of motifs in RNA secondary structures. We present a novel geometric method for the characterization and identification of structural motifs in 3D rRNA molecules. This method enables the efficient recognition of known 3D motifs, such as tetraloops, E-loops, kink-turns and others. Furthermore, it provides a new way of characterizing complex 3D motifs, notably junctions, that have been defined and identified in the secondary structure but have not been analyzed and classified in three dimensions. We demonstrate the relevance and utility of our approach by applying it to the Haloarcula marismortui large ribosomal unit. Pending the implementation of a dedicated web server, the code accompanying this article, written in JAVA, is available upon request from the contact author.

Show MeSH