Abstract
Hydrogen bonds are crucial factors that stabilize a complex ribonucleic acid (RNA) molecule's three-dimensional (3D) structure. Minute conformational changes can result in variations in the hydrogen bond interactions in a particular structure. Furthermore, networks of hydrogen bonds, especially those found in tight clusters, may be important elements in structure stabilization or function and can therefore be regarded as potential tertiary motifs. In this paper, we describe a graph theoretical algorithm implemented as a web server that is able to search for unbroken networks of hydrogen-bonded base interactions and thus provide an accounting of such interactions in RNA 3D structures. This server, COGNAC (COnnection tables Graphs for Nucleic ACids), is also able to compare the hydrogen bond networks between two structures and from such annotations enable the mapping of atomic level differences that may have resulted from conformational changes due to mutations or binding events. The COGNAC server can be accessed at http://mfrlab.org/grafss/cognac.
Highlights
The three-dimensional (3D) structures of complex ribonucleic acid (RNA) molecules are as crucial for their function as they are for proteins
The majority of such structural annotations have focused on the alignment of RNA 3D structures to detect similarities in folding and sub-folding [6,7,8] and these approaches are not unlike those used in protein fold comparisons where an often used method involves superpositions of the atoms forming the structures’ backbones
We describe a server that is able to map hydrogen bonds between RNA bases and from this accounting of such interactions, allow for the annotation of RNA base interaction clusters that may potentially be structural motifs; in addition, it may yield potential insights regarding the functional or structure stabilization roles for clusters of interacting bases
Summary
The three-dimensional (3D) structures of complex ribonucleic acid (RNA) molecules are as crucial for their function as they are for proteins. Upon selection of the type of representative graph(s) for the connection table, another interface appears prompting the user to provide a specific base as the graph’s node or to leave the base as a wildcard option (Figure 2C). This interface uses JSmol (http://wiki.jmol.org) windows to enable users to orientate the bases in order to facilitate a visual aided approach toward envisioning possible hydrogen bonding interactions that may occur. For the comparison of similar structures, a listing that highlights the differences between two structures is provided with a further visualization option of comparing the structures in adjacent synchronized Jmol or JSmol windows
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