Tang, Ke; Roca, Jorjethe; Chen, Rong; Ansari, Anjum; Liang, Jie published the artcile< Thermodynamics of unfolding mechanisms of mouse mammary tumor virus pseudoknot from a coarse-grained loop-entropy model>, Category: imidazoles-derivatives, the main research area is mammary tumor virus pseudoknot thermodn entropy model; Energy landscape; Fluorescence spectroscopy; Heat capacity; Loop entropy; PK3D; Pseudoknotted RNA; RNA folding; RNA hairpin; Unfolding mechanism.
Pseudoknotted RNA mols. play important biol. roles that depend on their folded structure. To understand the underlying principles that determine their thermodn. and folding/unfolding mechanisms, we carried out a study on a variant of the mouse mammary tumor virus pseudoknotted RNA (VPK), a widely studied model system for RNA pseudoknots. Our method is based on a coarse-grained discrete-state model and the algorithm of PK3D (pseudoknot structure predictor in three-dimensional space), with RNA loops explicitly constructed and their conformational entropic effects incorporated. Our loop entropy calculations are validated by accurately capturing previously measured melting temperatures of RNA hairpins with varying loop lengths. For each of the hairpins that constitutes the VPK, we identified alternative conformations that are more stable than the hairpin structures at low temperatures and predicted their populations at different temperatures Our predictions were validated by thermodn. experiments on these hairpins. We further computed the heat capacity profiles of VPK, which are in excellent agreement with available exptl. data. Notably, our model provides detailed information on the unfolding mechanisms of pseudoknotted RNA. Anal. of the distribution of base-pairing probability of VPK reveals a cooperative unfolding mechanism instead of a simple sequential unfolding of first one stem and then the other. Specifically, we find a simultaneous “”loosening”” of both stems as the temperature is raised, whereby both stems become partially melted and co-exist during the unfolding process.
Journal of Biological Physics published new progress about Algorithm. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Category: imidazoles-derivatives.
Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem