The rovibrational spectrum of BeH, MgH and CaH at high temperatures in the X 2Σ+X\,{}^2\Sigma^+ state: a theoretical study

Accurate line lists for three molecules, BeH, MgH and CaH, in their ground electronic states are presented. These line lists are suitable for temperatures relevant to exoplanetary atmospheres and cool stars (up to 2000K). A combination of empirical and \textit{ab initio} methods is used. The rovibrational energy levels of BeH, MgH and CaH are computed using the programs Level and DPotFit in conjunction with `spectroscopic' potential energy curves (PECs). The PEC of BeH is taken from the literature, while the PECs of CaH and MgH are generated by fitting to the experimental transition energy levels. Both spin-rotation interactions (except for BeH, for which it is negligible) and non-adiabatic corrections are explicitly taken into account. Accurate line intensities are generated using newly computed \textit{ab initio} dipole moment curves for each molecule using high levels of theory. Full line lists of rotation-vibration transitions for $^9$BeH, $^{24}$MgH, $^{25}$MgH, $^{26}$MgH and $^{40}$CaH are made available in an electronic form as supplementary data to this article and at \url{www.exomol.com}.Comment: MNRAS (in press

Next generation sequencing and de novo transcriptomics to study gene evolution

Background: Studying gene evolution in non-model species by PCR-based approaches is limited to highly conserved genes. The plummeting cost of next generation sequencing enables the application of de novo transcriptomics to any species.Results: Here we describe how to apply de novo transcriptomics to pursue the evolution of a single gene of interest. We follow a rapidly evolving seed protein that encodes small, stable peptides. We use software that needs limited bioinformatics background and assemble four de novo seed transcriptomes. To demonstrate the quality of the assemblies, we confirm the predicted genes at the peptide level on one species which has over ten copies of our gene of interest. We explain strategies that favour assembly of low abundance genes, what assembly parameters help capture the maximum number of transcripts, how to develop a suite of control genes to test assembly quality and we compare several sequence depths to optimise cost and data volume.Conclusions: De novo transcriptomics is an effective approach for studying gene evolution in species for which genome support is lacking

The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction

High-affinity, high-selectivity protein-protein interactions that are critical for cell survival present an evolutionary paradox: How does selectivity evolve when acquired mutations risk a lethal loss of high-affinity binding? A detailed understanding of selectivity in such complexes requires structural information on weak, noncognate complexes which can be difficult to obtain due to their transient and dynamic nature. Using NMR-based docking as a guide, we deployed a disulfide-trapping strategy on a noncognate complex between the colicin E9 endonuclease (E9 DNase) and immunity protein 2 (Im2), which is seven orders of magnitude weaker binding than the cognate femtomolar E9 DNase-Im9 interaction. The 1.77 A crystal structure of the E9 DNase-Im2 complex reveals an entirely noncovalent interface where the intersubunit disulfide merely supports the crystal lattice. In combination with computational alanine scanning of interfacial residues, the structure reveals that the driving force for binding is so strong that a severely unfavorable specificity contact is tolerated at the interface and as a result the complex becomes weakened through "frustration." As well as rationalizing past mutational and thermodynamic data, comparing our noncognate structure with previous cognate complexes highlights the importance of loop regions in developing selectivity and accentuates the multiple roles of buried water molecules that stabilize, ameliorate, or aggravate interfacial contacts. The study provides direct support for dual-recognition in colicin DNase-Im protein complexes and shows that weakened noncognate complexes are primed for high-affinity binding, which can be achieved by economical mutation of a limited number of residues at the interface