Modifying the catalytic preference of alpha-amylase toward n-alkanes for bioremediation purposes using in silico strategies

Abstract

Since the beginning of oil exploration, whole ecosystems have been affected by accidents and bad practices involving petroleum compounds. In this sense, bioremediation stands out as the cheapest and most eco-friendly alternatives to reverse the damage done in oil-impacted areas. However, more efforts must be made to engineer enzymes that could be used in the bioremediation process. Interestingly, a recent work described that α-amylase, one of the most evolutionary conserved enzymes, was able to promiscuously degrade n-alkanes, a class of molecules abundant in the petroleum admixture. Considering that α-amylase is expressed in almost all known organisms, and employed in numerous biotechnological processes, using it can be a great leap toward more efficient applications of enzyme or microorganism-consortia bioremediation approaches. In this work, we employed a strict computational approach to design new α-amylase mutants with potentially enhanced catalytic efficiency toward n-alkanes. Using in silico techniques, such as molecular docking, molecular dynamics, metadynamics, and residue–residue interaction networks, we generated mutants potentially more efficient for degrading n-alkanes, L183Y, and N314A. Our results indicate that the new mutants have an increased binding rate for tetradecane, the longest n-alkane previously tested, which can reside in the catalytic center for more extended periods. Additionally, molecular dynamics and network analysis showed that the new mutations have no negative impact on protein structure than the WT. Our results aid in solidifying this enzyme as one more tool in the petroleum bioremediation toolbox.

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