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Enzymes for energy. Structural computational analysis, substrate association and product dissociation from the thermophilic esterase of Alicyclobacillus acidocaldarius: Implications in biodiesel production

Whiteley, Chris G., Lee, Duu-Jong
Journal of Molecular Catalysis. B, Enzymatic 2013 v.97 pp. 156-168
Alicyclobacillus acidocaldarius, alcohols, binding sites, biodiesel, catalysts, catalytic activity, dissociation, energy, enzyme substrates, esterases, fatty acid esters, fatty acids, hydrogen bonding, molecular dynamics, solubility, solvents, temperature, thermodynamics
Enzymes, as natural catalysts, are prime players in the search for the new efficient environmentally friendly production of biofuels. The different permutations of the many variables, such as source, selectivity, stability and structure of substrates and enzyme, immobilization and/or life-time of the catalyst, temperature and time of the reaction and solvent constituency, polarity and quantity make the use of enzymes for this purpose a daunting task. An esterase is a unique family of enzymes that can either esterify a fatty acid in a non-polar solvent containing a stoichiometric amount of short-chain alcohol or hydrolyse an ester into the corresponding acid and alcohol. Even though tolerance of the esterase to such solvents increases the solubility of the substrates and assists in the recovery of product final product yield is controlled provided a specific amount of water is also present influencing the enzyme–substrate equilibrium and the lipid–water interface – an area that is occupied by the esterase. Knowing the composition of the solvent medium needed for esterase activity is complicated by knowledge of the structure of the binding pocket, substrate entry into the enzyme active channel, the flexibility of the enzyme itself, unwanted hydrolytic reactions and total changes in the thermodynamic footprint between substrate and enzyme. This article explores a computational structural analysis of an esterase investigating the substrate–enzyme binding site and uses simple simulations and molecular dynamics to address the mechanism(s) and pathways that products – fatty acid esters (biodiesel) – dissociate from the enzyme. Two simulations in hexane:MeOH (9:1) and water as well as hydrogen bond interactions of the substrate/product with the enzyme, RMSD and B-factor calculations and the presence of water molecules in enzyme active binding pocket dictate which entry or exit pathway is preferable.