Incorporating global features of RNA motifs in predictions for an ensemble of secondary structures for encapsidated MS2 bacteriophage RNA

Abstract

The secondary structure of encapsidated MS2 genomic RNA poses an interesting RNA folding challenge. Cryoelectron microscopy has demonstrated that encapsidated MS2 RNA is well-ordered. Models of MS2 assembly suggest that the RNA hairpin-protein interactions and the appropriate placement of hairpins in the MS2 RNA secondary structure can guide the formation of the correct icosahedral particle. The RNA hairpin motif that is recognized by the MS2 capsid protein dimers, however, is energetically unfavorable, and thus free energy predictions are biased against this motif. Computer programs called Crumple, Sliding Windows, and Assembly provide useful tools for prediction of viral RNA secondary structures when the traditional assumptions of RNA structure prediction by free energy minimization may not apply. These methods allow incorporation of global features of the RNA fold and motifs that are difficult to include directly in minimum free energy predictions. For example, with MS2 RNA the experimental data from SELEX experiments, crystallography, and theoretical calculations of the path for the series of hairpins can be incorporated in the RNA structure prediction, and thus the influence of free energy considerations can be modulated. This approach thoroughly explores conformational space and generates an ensemble of secondary structures. The predictions from this new approach can test hypotheses and models of viral assembly and guide construction of complete three-dimensional models of virus particles.

The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch

“…The birth of a specialized machine designed for MD simulation-Anton [36], [37] has increased the timescale limitation up to 200 times compared to simulations with conventional High Performance Computing (HPC) machines. Recent advances in software development and RNA structure modeling have improved the building of RNA models [38]–[48]. Together with enhanced sampling techniques [49]–[52] these modeling tools extend the accessible conformational space beyond that available within even the extended MD timescales.…”

Crumple: A Method for Complete Enumeration of All Possible Pseudoknot-Free RNA Secondary Structures

“…The ability to compute the complete set of possible structures with Crumple expands the potential applications of approaches such as Barmap to modeling RNA folding. The output of Crumple can also be used with programs such as Sliding Windows and Assembly [8], [9] to explore possible conformations of longer sequences, with local cotranscriptional folding. Thus, Crumple offers a useful alternative to traditional RNA folding methods.…”

“…Concatenation of the 14mer to make 28mers and 42mers creates test cases that include multibranch loops. The Crumple algorithm has been applied to or tested on the following biological sequences: a section of the 5′ untranslated region of the HIV-1 RNA [8], satellite tobacco mosaic virus RNA [8], MS2 bacteriophage RNA [9], a section of the 3′untranslated region of Alfalfa Mosaic Virus RNA, 4 guide RNA from Trypanosome brucei , and a bacterial noncoding RNA MicA. In all cases, the minimum free energy structures predicted by rnafold, mfold, or RNAStructure were present in the Crumple output (Figure S1).…”

“…Crumple can provide a larger set of structures that may allow additional insights into folding pathways. Crumple can also provide input for programs such as Sliding Windows and Assembly when the assumption of local cotranscriptional folding may apply [8], [9]. Complete enumeration of all possible solutions to the RNA folding problem allows a mathematically rigorous perspective.…”

A novel delivery platform based on Bacteriophage MS2 virus-like particles

“…CP molecules first form a dimer. The dimer can bind to an RNA hairpin and then undergoes an allosteric conformational change in the FG loop region (Bleckley and Schroeder, 2012), forming an asymmetric A/B dimer rather than a symmetric C/C dimer (Borodavka et al, 2012;Rolfsson et al, 2010; , 2007). The FG loops of the B conformation of CP surround the fivefold vertices of the icosahedron, and the A and C conformations interdigitate at the threefold vertices of the icosahedron, thus forming an icosahedron of 60 A/B dimers and 30 C/C dimers Valegård et al, 1990).…”