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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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Angles at the narrow side of the band: (a) if a connecting fragment occurs at the bend, we have a very small angle (∼ 20°/30°), (b) if a helix departs from that side, we have two acute angles (∼ 60°/80°).
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Figure 3: Angles at the narrow side of the band: (a) if a connecting fragment occurs at the bend, we have a very small angle (∼ 20°/30°), (b) if a helix departs from that side, we have two acute angles (∼ 60°/80°).

Mentions: We consider first k-junctions with k > 3, in the following denoted as k*-junction; as we discuss in the next section, the case of the 3-junctions needs to be treated separately. The angles induced by triplets of centroids, as defined above, are able to reveal the eccentricity of the junction. If we imagine the junction as a flexible loop it is easy to see that the more this loop resembles a circle, the more uniform will be the angles formed by the centroids. In contrast, if the loop resembles a squeezed ellipse or band, it will generate a set of obtuse angles, along the long sides of the band, and few (2 or 3) small angles at the bends (the two typical cases are shown in Figure 3). Thus from the sequence of inter-fragments angles, we can identify two main conformation: low eccentricity EL which indicates a circular junction and high eccentricity EH which indicates a band. We define also an intermediate state, denoted as EM.Figure 3.


Finding 3D motifs in ribosomal RNA structures.

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

Angles at the narrow side of the band: (a) if a connecting fragment occurs at the bend, we have a very small angle (∼ 20°/30°), (b) if a helix departs from that side, we have two acute angles (∼ 60°/80°).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: Angles at the narrow side of the band: (a) if a connecting fragment occurs at the bend, we have a very small angle (∼ 20°/30°), (b) if a helix departs from that side, we have two acute angles (∼ 60°/80°).
Mentions: We consider first k-junctions with k > 3, in the following denoted as k*-junction; as we discuss in the next section, the case of the 3-junctions needs to be treated separately. The angles induced by triplets of centroids, as defined above, are able to reveal the eccentricity of the junction. If we imagine the junction as a flexible loop it is easy to see that the more this loop resembles a circle, the more uniform will be the angles formed by the centroids. In contrast, if the loop resembles a squeezed ellipse or band, it will generate a set of obtuse angles, along the long sides of the band, and few (2 or 3) small angles at the bends (the two typical cases are shown in Figure 3). Thus from the sequence of inter-fragments angles, we can identify two main conformation: low eccentricity EL which indicates a circular junction and high eccentricity EH which indicates a band. We define also an intermediate state, denoted as EM.Figure 3.

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
Related in: MedlinePlus