Background:

Hydrophobic pockets often play a decisive part in the mechanisms underlying the selectivity of enzymes. Yet, the interactions between hydrophobic substrates and the highly dynamic hydrophobic surfaces of these catalytic motifs are still poorly understood, making a control of selectivity by rational design exceedingly difficult. The project deals with the role of hydrophobic pockets in the catalytic mechanism of a membrane-bound monooxygenase.

Structure elucidation of membrane enzymes used to be exceedingly difficult, which was a considerable challenge for their enzyme engineering. The advent of CryEM and de novo structure prediction methods greatly facilitated structure-based enzyme engineering approaches. Bacterial alkane monooxygenase (AlkB) catalyzes the terminal hydroxylation of alkanes. The Kourist group showed a 6-fold activity increase of an AlkB-based whole-cell biocatalysts in the synthesis of precursor of the biobased monomer Tulipalin A.

Aims / Hypotheses:

The project aims to characterize AlkB in a cell-free system in order to investigate the effect of amino acid substitutions in the hydrophobic active-site cavities, and to analyze the molecular basis of a side-reactivity of the enzyme. Furthermore, the influence of peripheral amino acids on catalysis is investigated. The evolutionary emergency of the acceptance of different substrates such as alkanes and aromates will be analyzed by ancestral sequence reconstruction.

Method:

- Phylogeny and ancestor reconstruction

- Kinetic investigation of membrane-enzymes

- Collaboration with Oostenbrink will focus on MD simulations of membrane-enzymes. The feasibility of mechanistic modeling will be tested.

- In the long term, we plan to develop a methodology to characterize fitness landscapes of these enzymes by coupling of high-throughput screens and deep sequencing of libraries.

Where to apply:

https://www.circularbioengineering.at/

 

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