SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals.

SARS-CoV-2 has a zoonotic origin and was transmitted to humans via an undetermined intermediate host, leading to infections in humans and other mammals. To enter host cells, the viral spike protein (S-protein) binds to its receptor, ACE2, and is then processed by TMPRSS2. Whilst receptor binding contributes to the viral host range, S-protein:ACE2 complexes from other animals have not been investigated widely. To predict infection risks, we modelled S-protein:ACE2 complexes from 215 vertebrate species, calculated changes in the energy of the complex caused by mutations in each species, relative to human ACE2, and correlated these changes with COVID-19 infection data. We also analysed structural interactions to better understand the key residues contributing to affinity. We predict that mutations are more detrimental in ACE2 than TMPRSS2. Finally, we demonstrate phylogenetically that human SARS-CoV-2 strains have been isolated in animals. Our results suggest that SARS-CoV-2 can infect a broad range of mammals, but few fish, birds or reptiles. Susceptible animals could serve as reservoirs of the virus, necessitating careful ongoing animal management and surveillance.

cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly.

MOTIVATION: Many bioinformatics areas require us to assign domain matches onto stretches of a query protein. Starting with a set of candidate matches, we want to identify the optimal subset that has limited/no overlap between matches. This may be further complicated by discontinuous domains in the input data. Existing tools are increasingly facing very large data-sets for which they require prohibitive amounts of CPU-time and memory. RESULTS: We present cath-resolve-hits (CRH), a new tool that uses a dynamic-programming algorithm implemented in open-source C++ to handle large datasets quickly (up to ∼1 million hits/second) and in reasonable amounts of memory. It accepts multiple input formats and provides its output in plain text, JSON or graphical HTML. We describe a benchmark against an existing algorithm, which shows CRH delivers very similar or slightly improved results and very much improved CPU/memory performance on large datasets. AVAILABILITY AND IMPLEMENTATION: CRH is available at https://github.com/UCLOrengoGroup/cath-tools; documentation is available at http://cath-tools.readthedocs.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Systematic computational prediction of protein interaction networks.

Determining the network of physical protein associations is an important first step in developing mechanistic evidence for elucidating biological pathways. Despite rapid advances in the field of high throughput experiments to determine protein interactions, the majority of associations remain unknown. Here we describe computational methods for significantly expanding protein association networks. We describe methods for integrating multiple independent sources of evidence to obtain higher quality predictions and we compare the major publicly available resources available for experimentalists to use.

The actin-associating protein Tm5NM1 blocks mesenchymal motility without transition to amoeboid motility.

Cell migration is an integral component of metastatic disease. The ability of cells to transit between mesenchymal and amoeboid modes of migration has complicated the development of successful therapies designed to target cell migration as a means of inhibiting metastasis. Therefore, investigations of the mechanisms that regulate cell migration and render cells stationary are necessary. Tropomyosins are actin-associating proteins that regulate the activity of several effectors of actin filament dynamics. Previously, we have shown that the tropomyosin isoform Tm5NM1 stabilizes actin filaments and inhibits cell migration in a two-dimensional culture system. Here, we show that Tm5NM1 inhibits the mesenchymal migration of multiple cell lines in an isoform-specific manner. Tm5NM1 stimulates the downregulation of Src kinase activity and a rounded or elliptical morphology in three-dimensional collagen gels, and cells have dramatically reduced capacity to form pseudopodia. Importantly, we find that Tm5NM1 inhibits both the mesenchymal to amoeboid and amoeboid to mesenchymal transitions. Collectively, our data suggest that mimicking the action of Tm5NM1 overexpression represents an approach for effectively inhibiting the mesenchymal mode of migration.

VUV irradiation effects on proteins in high-flux synchrotron radiation circular dichroism spectroscopy.

Synchrotron radiation circular dichroism (SRCD) spectroscopy is emerging as an important new tool in structural molecular biology. Previously we had shown that in lower-flux SRCD instruments, such as UV1 at ISA and beamline 3.1 at the SRS, vacuum ultraviolet (VUV) radiation damage to proteins was not evident after exposure over a period of hours. No effects were detected in either the protein primary or the secondary structures. However, with the development of high-flux beamlines, such as CD12 at the SRS, this issue has been revisited because of changes observed in the SRCD spectra of consecutive scans of protein samples obtained on this high-flux beamline. Experiments have been designed to distinguish between two different possible mechanisms: (i) photoionization causing free radicals or secondary electrons producing degradation of the protein, and (ii) local heating of the sample resulting in protein denaturation. The latter appears to be the principal source of the signal deterioration.

CDtool-an integrated software package for circular dichroism spectroscopic data processing, analysis, and archiving.

CDtool is a software package written to facilitate circular dichroism (CD) spectroscopic studies on both conventional lab-based instruments and synchrotron beamlines. It takes format-independent input data from any type of CD instrument, enables a wide range of standard and advanced processing methods, and, in a single user-friendly graphics-based package, takes raw data through the entire processing procedure and, importantly, uses data-mining techniques to retain in the final output all the information associated with the processing. It permits the facile comparison of data obtained from different instruments without the need for reformatting and displays it in graphical formats suitable for publication. It also includes the ability to automatically archive the processed data. This latter feature may be especially useful in light of recent funding institution directives with regard to data sharing and archiving and requirements for "good practice" and "traceability" within the pharmaceutical industry. In addition, CDtool includes a means of interfacing with protein data bank coordinate files and calculating secondary structures from them using alternate definitions and algorithms. This feature, along with a function that permits the facile production of new reference databases, enables the creation of specialized databases for secondary structural analyses of specific types of proteins. Thus the CDtool software not only enables rapid data processing and analyses but also includes many enhanced features not available in other CD data processing/analysis packages.

Analyses of circular dichroism spectra of membrane proteins.

Circular dichroism (CD) spectroscopy is a valuable technique for the determination of protein secondary structures. Many linear and nonlinear algorithms have been developed for the empirical analysis of CD data, using reference databases derived from proteins of known structures. To date, the reference databases used by the various algorithms have all been derived from the spectra of soluble proteins. When applied to the analysis of soluble protein spectra, these methods generally produce calculated secondary structures that correspond well with crystallographic structures. In this study, however, it was shown that when applied to membrane protein spectra, the resulting calculations produce considerably poorer results. One source of this discrepancy may be the altered spectral peak positions (wavelength shifts) of membrane proteins due to the different dielectric of the membrane environment relative to that of water. These results have important consequences for studies that seek to use the existing soluble protein reference databases for the analyses of membrane proteins.

Lamb ductus venosus: evidence of a cytochrome P-450 mechanism in its contractile tension.

We have recently shown that a cytochrome P-450-based mechanism is important for the generation of contractile tension by the ductus arteriosus and have now examined whether the same mechanism operates in the ductus venosus. Carbon monoxide (CO/O2 ratio, 0.27) and cytochrome P-450 inhibitors [metyrapone; 4-phenylimidazole; 14-isocyano, 15-(methoxymethyleneoxy)-5Z,8Z,11Z- eicosatrienoic acid; alpha-naphthoflavone] were tested in vitro on the ductus venosus sphincter from mature fetal lambs. Each preparation was precontracted with indomethacin (2.8 x 10(-6) M). Carbon monoxide completely relaxed the ductus, and its action was reversed by illumination with monochromatic light. Peak photocontraction occurred at 450 nm. With the exception of alpha-naphthoflavone, all cytochrome P-450 inhibitors were also relaxant agents. Alpha-naphthoflavone (the sole type I inhibitor tested) produced instead a modest contraction that was often transient. Relaxation brought about by both carbon monoxide and drugs was fully reversed by the thromboxane A2 analog 9,11-epithio-11,12-methano-thromboxane A2 and by excess potassium (55 mM). Carbon monoxide was equally effective in the intact ductus and the ductus denuded of endothelium, whereas cytochrome P-450 inhibitors were marginally less effective in the latter preparation. These findings indicate that the ductus venosus sphincter, like the ductus arteriosus, relies on an intramural cytochrome P-450 mechanism to develop its contractile tone. The actual constrictor remains to be characterized in both vessels.

Further evidence implicating a cytochrome P-450-mediated reaction in the contractile tension of the lamb ductus arteriosus.

The authors have recently provided evidence implicating the cytochrome P-450 system in the generation of contractile tension of the ductus arteriosus. To confirm this possibility, carbon monoxide (CO/O2 ratio, 0.27) and cytochrome P-450 inhibitors [4-phenylimidazole; 14-isocyano,15-(methoxymethyleneoxy)-5Z,8Z,11 Z-eicosatrienoic acid; 9-hydroxyellipticine; alpha-naphthoflavone] were tested on the isolated ductus arteriosus from mature fetal lambs equilibrated at low (4-26 mm Hg) or high (229-694 mm Hg) O2 partial pressure (PO2). Carbon monoxide completely relaxed intact vessel wall preparations and preparations consisting of only the muscle. Carbon monoxide relaxation was reversed by illumination with monochromatic light and the peak for the photoactivated contraction occurred at 450 nm. 4-Phenylimidazole (100 and 1,000 microM) was also a relaxant agent, and its action was manifest at both low and high PO2. Unlike 4-phenylimidazole, the isonitrile compound (5 microM) and 9-hydroxyellipticine (10 and 100 microM) were relaxant only at low PO2 and were also less potent. At the same PO2, alpha-naphthoflavone (10 microM) barely reduced ductal tension. Treatment of the ductus with either a combination of superoxide dismutase (60 or 150 U/ml) and catalase (40 or 1,000 U/ml) or mannitol alone (80 mM) failed to alter the steady-state tone at low PO2 and the contractile response to O2. Arachidonic acid was tested on tissues pretreated with the dual cyclooxygenase and lipoxygenase inhibitor, BW755C (10 microM), and produced a weak relaxation at a concentration of 1 microM or higher. 5,6-Epoxytrienoic acid relaxed the untreated tissue, and its action was abolished by indomethacin (2.8 microM).(ABSTRACT TRUNCATED AT 250 WORDS)