Title: Computational design of enzyme selectivity

Presenter: Prof. Hein J. Wijma

University: Groningen Biomolecular sciences and Biotechnology institute, University of Groningen

Time: 9:00-10:00, SEP 18, 2016

Venue: Room F421, Institute of Microbiology, Chinese Academy of Sciences

Abstract: Computational enzyme design holds great promise for providing new biocatalysts. Methodology development is currently crucial. In computational protein design, it is often hard to obtain enzyme variants that bind the substrate in the intended orientation (Blomberg et al., 2013). To address this problem, we developed the CASCO method (Catalytic Selectivity by Computation, Wijma et al., 2015). Key features of this method are the design of mutations that favor binding of the substrate in a predefined orientation, the introduction of steric hindrance to prevent unwanted substrate binding modes, and ranking of designs by high-throughput molecular dynamics simulations. Specifically, all the designed enzyme variants (> 3000) were screened by MD simulation for their ability to bind the substrate selectively in the desired orientation. This could be done in a limited time-frame (weeks instead of years), after developing an optimized MD protocol (Wijma et al., 2014). Using this strategy we obtained highly stereoselective mutants of limonene epoxide hydrolase after experimental screening of only 37 variants. The results indicate that computational methods can replace a substantial amount of laboratory work when developing enantioselective enzymes.

References

Blomberg, R. Kries, H., Pinkas, D.M., Mittl, P.R.E., Grütter, M.G., Privett, H.K., Mayo, S.L., Hilvert, D., Nature, 503, 418-421, 2013.

Wijma, H.J., Floor, R.J., Bjelic, S., Marrink, S.J., Baker, D., Janssen, D.B. Angew. Chem. Int. Ed. 54, 3726-3730, 2015.

Wijma, H.J., Marrink, S.J., Janssen, D.B., J. Chem. Inf. Model. 54, 2079-2092, 2014