Kinetic Characterization of 100 Glycoside Hydrolase Mutants Enables the Discovery of Structural Features Correlated with Kinetic Constants

PLoS One. 2016 Jan 27;11(1):e0147596. doi: 10.1371/journal.pone.0147596. eCollection 2016.

Abstract

The use of computational modeling algorithms to guide the design of novel enzyme catalysts is a rapidly growing field. Force-field based methods have now been used to engineer both enzyme specificity and activity. However, the proportion of designed mutants with the intended function is often less than ten percent. One potential reason for this is that current force-field based approaches are trained on indirect measures of function rather than direct correlation to experimentally-determined functional effects of mutations. We hypothesize that this is partially due to the lack of data sets for which a large panel of enzyme variants has been produced, purified, and kinetically characterized. Here we report the kcat and KM values of 100 purified mutants of a glycoside hydrolase enzyme. We demonstrate the utility of this data set by using machine learning to train a new algorithm that enables prediction of each kinetic parameter based on readily-modeled structural features. The generated dataset and analyses carried out in this study not only provide insight into how this enzyme functions, they also provide a clear path forward for the improvement of computational enzyme redesign algorithms.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computer Simulation*
  • Glycoside Hydrolases / genetics
  • Glycoside Hydrolases / metabolism*
  • Humans
  • Kinetics
  • Models, Molecular*
  • Mutation
  • Protein Conformation
  • Structure-Activity Relationship

Substances

  • Glycoside Hydrolases

Grants and funding

This work was supported by Army Research Office #201121557 and National Science Foundation #1254205 (IT) and Alfred P. Sloan Foundation #BR2014-012 and University of California Davis Startup Funds (JBS).