Automated Design of Efficient and Functionally Diverse Enzyme Repertoires

Mol Cell. 2018 Oct 4;72(1):178-186.e5. doi: 10.1016/j.molcel.2018.08.033. Epub 2018 Sep 27.

Abstract

Substantial improvements in enzyme activity demand multiple mutations at spatially proximal positions in the active site. Such mutations, however, often exhibit unpredictable epistatic (non-additive) effects on activity. Here we describe FuncLib, an automated method for designing multipoint mutations at enzyme active sites using phylogenetic analysis and Rosetta design calculations. We applied FuncLib to two unrelated enzymes, a phosphotriesterase and an acetyl-CoA synthetase. All designs were active, and most showed activity profiles that significantly differed from the wild-type and from one another. Several dozen designs with only 3-6 active-site mutations exhibited 10- to 4,000-fold higher efficiencies with a range of alternative substrates, including hydrolysis of the toxic organophosphate nerve agents soman and cyclosarin and synthesis of butyryl-CoA. FuncLib is implemented as a web server (http://FuncLib.weizmann.ac.il); it circumvents iterative, high-throughput experimental screens and opens the way to designing highly efficient and diverse catalytic repertoires.

Keywords: FuncLib; PROSS; Rosetta; enzyme design; enzyme repertoires; epistatic mutations; nerve agents.

Publication types

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

MeSH terms

  • Acyl Coenzyme A / biosynthesis
  • Acyl Coenzyme A / chemistry
  • Catalysis
  • Catalytic Domain*
  • Coenzyme A Ligases / chemistry*
  • Coenzyme A Ligases / genetics
  • Kinetics
  • Mutation
  • Organophosphorus Compounds / chemistry
  • Phosphoric Triester Hydrolases / chemistry*
  • Phosphoric Triester Hydrolases / genetics
  • Phylogeny
  • Protein Engineering*
  • Software
  • Substrate Specificity

Substances

  • Acyl Coenzyme A
  • Organophosphorus Compounds
  • butyryl-coenzyme A
  • Phosphoric Triester Hydrolases
  • Coenzyme A Ligases
  • acetate-CoA ligase (ADP-forming)
  • cyclohexyl methylphosphonofluoridate