We published several papers in the second half of 2016. Below is a summary of some of these publications. Congratulations to everyone involved!
Elaaf’s paper ‘Hydrophobic shielding drives catalysis of hydride transfer in a family of F420H2-dependent enzymes’ in Biochemistry presents work done combining quantum mechanics and molecular dynamics calculations to study the catalytic mechanism of the activation of pretomanid by the deazaflavin-dependent nitroreductase (Ddn) from Mycobacterium tuberculosis.
Josh, Jason and Will published ‘Rangefinder: a semisynthetic FRET sensor design algorithm’ in ACS Sensors describing and demonstrating the use of a computational algorithm for the rapid in silico screening of dye attachment sites for the design of FRET sensors.
Elena’s paper ‘Active site desolvation and thermostability tradeoffs in the evolution of catalytically diverse triazine hydrolases.’ in Biochemistry presents work showing how the desolation of a reactive glutamate residue by second-shell residues and thermostability trade-offs contribute to the evolution of triazine hydrolases.
Dongdi’s paper ‘Classification and substrate head-group specificity of membrane fatty acid desaturases.’ in Computational and Structural Biotechnology Journal presents a detailed classification membrane fatty acid desaturases with regard to their function and substrate head-group specificity. This work will aid the rapid prediction of the function and specificity of new and existing sequences within this superfamily, as well as forming a basis for future efforts to manipulate the substrate specificity of these proteins for biotechnology applications.
Eleanor’s paper ‘The role of protein dynamics in the evolution of new enzyme function’, published in Nature Chemical Biology examines a ‘molecular fossil record’ that was recently obtained during the laboratory evolution of a phosphotriesterase from Pseudomonas diminuta to an arylesterase. This results of this work establish that changes to the conformational landscapes of proteins are an essential aspect of molecular evolution and that change in function can be achieved through enrichment of preexisting conformational sub-states.
Blair and Hafna’s paper ‘The methanogenic redox cofactor F420 is widely synthesized by aerobic soil bacteria.’ in The ISME Journal, presents work in which the genes encoding F420 biosynthesis enzymes are detected in a wide range of bacterial and archaea species, and are disproportionally abundant in aerated soils. The data suggest that although the Fo precursor to F420 originated in methanogens, F420 itself was first synthesized in an ancestral actinobacterium.
Camilla, Ben, Joe and Colin, in collaboration with the Cockburn lab at John Curtin School of Medical Research, released a pre-print version of their paper ‘Multivalency drives the neutralizing activity of antibodies against the Plasmodium falciparum circumsporozoite protein.’ in bioRxiv. In this work, we analysed the binding of the Plasmodium-neutralizing 2A10 antibody to the Plasmodium falciparum circumsporozoite protein.
In Thanavit, Blair, Brendon and Colin’s paper ‘The redox cofactor F420 protects mycobacteria from diverse antimicrobial compounds and mediates a reductive detoxification system’ in Applied Environmental Microbiology, we explored our hypothesis that F420 enhances persistence by serving as a cofactor in antimicrobial-detoxifying enzymes. This was work done in collaboration with CSIRO.
Nick, Galen and Colin contributed to ‘Molecular basis for the behavioral effects of the odorant degrading enzyme Esterase 6’ in Scientific Reports. This work presents a model in which esterase 6 acts as a direct odorant degrading enzyme for many bioactive food esters, but not cis-vaccenyl acetate.