A computational approach for the annotation of hydrogen-bonded base interactions in crystallographic structures of the ribozymes

A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and...

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Bibliographic Details
Main Authors: Hamdani, Hazrina Yusof, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas, Artymiuk, Peter J., Firdaus-Raih, Mohd
Format: Conference Proceeding
Language:English
Subjects:
Annotations
Automation
CHEMICAL BONDS
COMPLEXES
Crystal structure
CRYSTALLOGRAPHY
DIAGRAMS
GRAPH THEORY
HYDROGEN
Hydrogen bonding
Hydrogen bonds
INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY
MOLECULAR STRUCTURE
Nucleic acids
Ribonucleic acid
RIBOSOMES
RNA
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Summary:A fundamental understanding of the atomic level interactions in ribonucleic acid (RNA) and how they contribute towards RNA architecture is an important knowledge platform to develop through the discovery of motifs from simple arrangements base pairs, to more complex arrangements such as triples and larger patterns involving non-standard interactions. The network of hydrogen bond interactions is important in connecting bases to form potential tertiary motifs. Therefore, there is an urgent need for the development of automated methods for annotating RNA 3D structures based on hydrogen bond interactions. COnnection tables Graphs for Nucleic ACids (COGNAC) is automated annotation system using graph theoretical approaches that has been developed for the identification of RNA 3D motifs. This program searches for patterns in the unbroken networks of hydrogen bonds for RNA structures and capable of annotating base pairs and higher-order base interactions, which ranges from triples to sextuples. COGNAC was able to discover 22 out of 32 quadruples occurrences of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1FFK) and two out of three occurrences of quintuple interaction reported by the non-canonical interactions in RNA (NCIR) database. These and several other interactions of interest will be discussed in this paper. These examples demonstrate that the COGNAC program can serve as an automated annotation system that can be used to annotate conserved base-base interactions and could be added as additional information to established RNA secondary structure prediction methods.
ISSN:0094-243X
1551-7616
DOI:10.1063/1.4931240