Analyzing the flexibility of RNA structures by constraint counting |
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Authors: | Fulle Simone Gohlke Holger |
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Institution: | Department of Biological Sciences, Molecular Bioinformatics Group, J. W. Goethe-University, Frankfurt, Germany |
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Abstract: | RNA requires conformational dynamics to undergo its diverse functional roles. Here, a new topological network representation of RNA structures is presented that allows analyzing RNA flexibility/rigidity based on constraint counting. The method extends the FIRST approach, which identifies flexible and rigid regions in atomic detail in a single, static, three-dimensional molecular framework. Initially, the network rigidity of a canonical A-form RNA is analyzed by counting on constraints of network elements of increasing size. These considerations demonstrate that it is the inclusion of hydrophobic contacts into the RNA topological network that is crucial for an accurate flexibility prediction. The counting also explains why a protein-based parameterization results in overly rigid RNA structures. The new network representation is then validated on a tRNAASP structure and all NMR-derived ensembles of RNA structures currently available in the Protein Data Bank (with chain length ≥40). The flexibility predictions demonstrate good agreement with experimental mobility data, and the results are superior compared to predictions based on two previously used network representations. Encouragingly, this holds for flexibility predictions as well as mobility predictions obtained by constrained geometric simulations on these networks. Potential applications of the approach to analyzing the flexibility of DNA and RNA/protein complexes are discussed. |
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Keywords: | MD molecular dynamics FIRST floppy inclusion and rigid substructure topography 3D three-dimensional FRODA framework rigidity optimized dynamics algorithm DOF degree(s) of freedom dof independent internal degree(s) of freedom PDB Protein Data Bank GNM Gaussian Network Model NOE nuclear Overhauser enhancement RMSD root mean-square deviation |
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