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The anthropogenic toxic compound 1,2,3-trichloropropane is poorly degradable by natural enzymes. We have previously constructed the haloalkane dehalogenase DhaA31 by focused directed evolution ( Pavlova, M. et al. Nat. Chem. Biol. 2009 , 5 , 727 - 733 ), which is 32 times more active than the wild-type enzyme and is currently the most active variant known against that substrate. Recent evidence has shown that the structural basis responsible for the higher activity of DhaA31 was poorly understood. Here we have undertaken a comprehensive computational study of the main steps involved in the biocatalytic hydrolysis of 1,2,3-trichloropropane to decipher the structural basis for such enhancements. Using molecular dynamics and quantum mechanics approaches we have surveyed (i) the substrate binding, (ii) the formation of the reactive complex, (iii) the chemical step, and (iv) the release of the products. We showed that the binding of the substrate and its transport through the molecular tunnel to the active site is a relatively fast process. The cleavage of the carbon-halogen bond was previously identified as the rate-limiting step in the wild-type. Here we demonstrate that this step was enhanced in DhaA31 due to a significantly higher number of reactive configurations of the substrate and a decrease of the energy barrier to the S N 2 reaction. C176Y and V245F were identified as the key mutations responsible for most of those improvements. The release of the alcohol product was found to be the rate-limiting step in DhaA31 primarily due to the C176Y mutation. Mutational dissection of DhaA31 and kinetic analysis of the intermediate mutants confirmed the theoretical observations. Overall, our comprehensive computational approach has unveiled mechanistic details of the catalytic cycle which will enable a balanced design of more efficient enzymes. This approach is applicable to deepen the biochemical knowledge of a large number of other systems and may contribute to robust strategies in the development of new biocatalysts.

The catalytic space of the P450 monooxygenase CYP153AM.aq was opened from a terminal (ω‐) fatty acid hydroxylase to a catalyst capable of performing ω‐hydroxylation of dodecylamine, which is a potent inhibitor for the wild‐type enzyme. A simple screening method named Rapid‐flow Analysis of Product Peaks (RAPP) was established and applied to measure saturation libraries directly from a 96‐deepwell plate in 36 seconds per sample. The obtained variants are less inhibited by the amine, although concurrently show less affinity towards the acid. Molecular modelling and molecular dynamics simulations showed significant effects of the mutations on the substrate tunnel architectures. [ABSTRACT FROM AUTHOR]

• Enzymes are increasingly used in technological applications but often require prior optimization. • Computational tools save time and effort in protein engineering endeavours. • Web-based tools make computational enzyme design accessible to a broad user community. • The recent enzyme engineering web-tools are described and classified by engineering purpose. Enzymes are in high demand for very diverse biotechnological applications. However, natural biocatalysts often need to be engineered for fine-tuning their properties towards the end applications, such as the activity, selectivity, stability to temperature or co-solvents, and solubility. Computational methods are increasingly used in this task, providing predictions that narrow down the space of possible mutations significantly and can enormously reduce the experimental burden. Many computational tools are available as web-based platforms, making them accessible to non-expert users. These platforms are typically user-friendly, contain walk-throughs, and do not require deep expertise and installations. Here we describe some of the most recent outstanding web-tools for enzyme engineering and formulate future perspectives in this field. [ABSTRACT FROM AUTHOR]

The catalytic space of the P450 monooxygenase CYP153AM.aq was opened from a terminal (ω‐) fatty acid hydroxylase to a catalyst capable of performing ω‐hydroxylation of dodecylamine, which is a potent inhibitor for the wild‐type enzyme. A simple screening method named Rapid‐flow Analysis of Product Peaks (RAPP) was established and applied to measure saturation libraries directly from a 96‐deepwell plate in 36 seconds per sample. The obtained variants are less inhibited by the amine, although concurrently show less affinity towards the acid. Molecular modelling and molecular dynamics simulations showed significant effects of the mutations on the substrate tunnel architectures. [ABSTRACT FROM AUTHOR]