Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering

We recently introduced ENCoM, an elastic network atomic contact model, as the first coarse-grained normal mode analysis method that accounts for the nature of amino acids and can predict the effect of mutations on thermostability based on changes vibrational entropy. In this proof-of-concept article, we use pairs of mesophile and thermophile homolog proteins with identical structures to determine if a measure of vibrational entropy based on normal mode analysis can discriminate thermophile from mesophile proteins. We observe that in around 60% of cases, thermophile proteins are more rigid at equivalent temperatures than their mesophile counterpart and this difference can guide the design of proteins to increase their thermostability through series of mutations. We observe that mutations separating thermophile proteins from their mesophile orthologs contribute independently to a decrease in vibrational entropy and discuss the application and implications of this methodology to protein engineering.     

Distribution of microorganisms in the oil-polluted ground of vadose and saturation zones

The ground polluted with oil products was analyzed at a depth of 0.5–7.8 m (loamy soil), 11.5–13.0 m (gravelstone), 13.0–15.0 m (siltstone). It was shown that the distribution of oil products and microorganisms in the ground over the profile depends on the hydrogeological properties of the rock (porosity, hydraulic conductivity). The number of aerobic heterotrophic microorganisms varied from 10⁶–10⁷ CFU/g, the fraction of hydrocarbon-oxidizing ones increased with depth from 30 to 85%. The number of anaerobic microorganisms was comparable to the number of aerobic ones. The number of psychrotrophs and psychrophiles increases with depth; in the lower horizon these organisms prevail over the number of mesophiles.     

How do thermophilic proteins resist aggregation?

Aggregation is an ancient threat that must be overcome by proteins from all organisms to maintain their native functional states. This is essential for the maintenance of metabolic flux and viability of their cellular machineries. Here, we compare the aggregation-resistance strategies adapted by the thermophilic proteins and their mesophilic homologs using a dataset of 373 protein families. Like their mesophilic homologs, the thermophilic protein sequences also contain potential aggregation prone regions (APRs), capable of forming cross-β motif and amyloid-like fibrils. Tetrapeptide and hexapeptide amyloid-like fibril forming sequence patterns and experimentally proven amyloid-like fibril forming peptide sequences were also detected in the thermophilic proteins. Both the thermophilic and the mesophilic proteins use similar strategies to resist aggregation. However, the thermophilic proteins show superior utilization of these strategies. The thermophilic protein monomers show greater ability to "stow away" the APRs in the hydrophobic cores to protect them from solvent exposure. The thermophilic proteins are also better at gatekeeping the APRs by surrounding them with charged residues (Asp, Glu, Lys, and Arg) and Pro to a greater extent. While thermophilic and mesophilic proteins in our dataset are highly homologous and show strong overall sequence conservation, the APRs are not conserved between the homologs. These findings indicate that evolution is working to avoid amyloidogenic regions in proteins. Our results are also consistent with the observation that thermophilic cells often accumulate small molecule osmolytes capable of stabilizing their proteins and other macromolecules. This study has important implications for rational design and formulation of therapeutic proteins and antibodies.     

Growth of Mesophilic Methanotrophs at Low Temperatures

The optimal growth of mesophilic methanotrophic bacteria (collection strains of the genera Methylocystis, Methylomonas, Methylosinus, and Methylobacter) occurred within temperature ranges of 31–34°C and 23–25°C. None of the 12 strains studied were able to grow at 1.5 or 4°C. Representatives of six methanotrophic species (strains Mcs. echinoides2, Mm. methanica12, Mb. bovis89, Mcs. pyriformis14, Mb. chroococcum90, and Mb. vinelandii87) could grow at 10°C (with a low specific growth rate). The results obtained suggest that some mesophilic methane-oxidizing bacteria display psychrotolerant (psychrotrophic) but not psychrophilic properties. In general, the Rosso model, which describes bacterial growth rate as a function of temperature, fits the experimental data well, although, for most methanotrophs, with symmetrical approximations for the optimal temperature.