Evolution of coronavirus frameshifting elements: Competing stem networks explain conservation and variability.

The frameshifting RNA element (FSE) in coronaviruses (CoVs) regulates the programmed -1 ribosomal frameshift (-1 PRF) mechanism common to many viruses. The FSE is of particular interest as a promising drug candidate. Its associated pseudoknot or stem loop structure is thought to play a large role in frameshifting and thus viral protein production. To investigate the FSE structural evolution, we use our graph theory-based methods for representing RNA secondary structures in the RNA-As-Graphs (RAG) framework to calculate conformational landscapes of viral FSEs with increasing sequence lengths for representative 10 Alpha and 13 Beta-CoVs. By following length-dependent conformational changes, we show that FSE sequences encode many possible competing stems which in turn favor certain FSE topologies, including a variety of pseudoknots, stem loops, and junctions. We explain alternative competing stems and topological FSE changes by recurring patterns of mutations. At the same time, FSE topology robustness can be understood by shifted stems within different sequence contexts and base pair coevolution. We further propose that the topology changes reflected by length-dependent conformations contribute to tuning the frameshifting efficiency. Our work provides tools to analyze virus sequence/structure correlations, explains how sequence and FSE structure have evolved for CoVs, and provides insights into potential mutations for therapeutic applications against a broad spectrum of CoV FSEs by targeting key sequence/structural transitions.

Competing Intramolecular Hydrogen Bond Strengths and Intermolecular Interactions in the 4-Aminobutanol-Water Complex.

We seek to determine the effect of competing intermolecular hydrogen bonds from water on the preferred conformation of 4-aminobutanol (4AB) monomers stabilized by intramolecular hydrogen bonds. Toward this end, the rotational spectrum of the 4-aminobutanol-H2O complex was recorded using Fourier transform microwave spectroscopy and fit to the rotational, quadrupole coupling, and centrifugal distortion constants of the Watson S-reduction Hamiltonian. The experimental results are consistent with a 4AB-water complex that preserves the intramolecular hydrogen bond within the 4AB monomer and forms a single intermolecular bond with water acting as a donor. The experimental monomer structure agrees well with the lowest energy conformation calculated at the MP2/6-311++G(d,p) level of theory. Upon complex formation and the introduction of competing intermolecular bonds from water, only small changes in the OH···N intramolecular hydrogen bond and backbone torsional angles of the 4-aminobutanol monomer are observed. Similar small changes were observed for the shorter chain 3-aminopropanol amino alcohol monomer when complexed with water, in contrast to the 2-aminoethanol-H2O complex. In the latter, a large change in the backbone torsional angle and a breaking of the intramolecular hydrogen bond were observed. Thus, extending the methylene chain results in an increase in the strength of the intramolecular hydrogen bond in unbranched amino alcohols.

Isotopic Dependence of the Hydrogen-Transfer-Triggered Methyl-Group Rotation in Deuterated 5-Methyltropolone.

We present here the first experimental study of the microwave spectrum of deuterated 5-methyltropolone, a molecule which exhibits two large-amplitude motions: an intramolecular hydrogen transfer (deuterium transfer in the current case of deuterated 5-methyltropolone) and a methyl torsion. The main goal of this study was to get information on the isotopic dependence of the main tunneling parameters of 5-methyltropolone in the framework of the two dimensional tunneling formalism, which previously has shown some counterintuitive results for isotopic dependence of tunneling parameters in 2-methylmalonaldehyde. Measurements were carried out by Fourier-transform microwave spectroscopy in the 9 GHz to 26 GHz frequency range. Theoretical analysis was carried out using a tunneling-rotational Hamiltonian based on a G12 m extended-group-theory formalism. Our global fit of 384 transitions to 17 molecular parameters gave a weighted root-mean-square deviation of 0.8. The current study on the isotopic dependence of the main tunneling parameters in 5-methyltropolone supports the assumption of possible "leakage" between tunneling parameters in the two-dimensional tunneling formalism in use.