Marina Y161 55 |BEST|

Marina Y161 55 |BEST|

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The four selected proteins were employed in an in silico activity study, in NpH2O [35] at several temperatures. The results were compared to those of the equivalent proteins from P. hydrogeniphila, as well as to TtCA, which is more studied. Protein stability was evaluated by producing the conformational and secondary structures of each protein, using the default parameters provided by NpH2O. Stereochemical quality of the stereochemistries of amino acids and the compositions of secondary structures were then evaluated. A 3D homology structure model was then built for each protein using Modeller [36], as well as stereochemically sorted and deposited in the PDB [37]. 8 thermodynamic characteristics were then evaluated, in the NpH2O environment, which were selected based on literature [38] and previous studies of P. hydrogeniphila and T. thermophilus HB8. The selected characteristics were: free energy change of hydration (ΔH2O), free energy change of hydroxynonanoic acid bond (ΔHoxn), free energy change of C-O bond (ΔHooxn), free energy change of CO2 formation (ΔGco2), free energy change of H2O formation (ΔGh2), free energy change of C tail to bulk water (ΔHbulk), the free energy change of O-H...O bonds (ΔGo), and the entropic change of surface hydration (ΔSh).

The theoretical stability of the -CAs was also calculated, as an indicator of thermostability. The conformation of the proteins was then predicted using molecular dynamics simulations at constant pressure and temperature. The simulation involved the solvent-solvent interactions in the catalytic center via the water molecules, which were replaced by dummy residues or by retained water molecules. An integrative approach was then applied to the CA proteins, involving both force fields and solvation models to obtain theoretical stability models for -CAs and for comparison purposes, -TtCAs. d2c66b5586