OptZyme: Computational Enzyme Redesign Using Transition State Analogues

Matthew J. Grisewood, Nathanael P. Gifford, Robert J. Pantazes, Ye Li, Patrick C. Cirino, Michael J. Janik, Costas D. Maranas

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

OptZyme is a new computational procedure for designing improved enzymatic activity (i.e., kcat or kcat/KM) with a novel substrate. The key concept is to use transition state analogue compounds, which are known for many reactions, as proxies for the typically unknown transition state structures. Mutations that minimize the interaction energy of the enzyme with its transition state analogue, rather than with its substrate, are identified that lower the transition state formation energy barrier. Using Escherichia coli β-glucuronidase as a benchmark system, we confirm that KM correlates (R2 = 0.960) with the computed interaction energy between the enzyme and the para-nitrophenyl- β, D-glucuronide substrate, kcat/KM correlates (R2 = 0.864) with the interaction energy of the transition state analogue, 1,5-glucarolactone, and kcat correlates (R2 = 0.854) with a weighted combination of interaction energies with the substrate and transition state analogue. OptZyme is subsequently used to identify mutants with improved KM, kcat, and kcat/KM for a new substrate, para-nitrophenyl- β, D-galactoside. Differences between the three libraries reveal structural differences that underpin improving KM, kcat, or kcat/KM. Mutants predicted to enhance the activity for para-nitrophenyl- β, D-galactoside directly or indirectly create hydrogen bonds with the altered sugar ring conformation or its substituents, namely H162S, L361G, W549R, and N550S.

Original languageEnglish (US)
Article numbere75358
JournalPloS one
Volume8
Issue number10
DOIs
StatePublished - Oct 7 2013

Fingerprint

Galactosides
energy
Substrates
Enzymes
enzymes
galactosides
Benchmarking
Glucuronidase
Glucuronides
Proxy
Libraries
Hydrogen
mutants
Escherichia coli
Energy barriers
Mutation
Sugars
hydrogen
Conformations
Hydrogen bonds

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Grisewood, Matthew J. ; Gifford, Nathanael P. ; Pantazes, Robert J. ; Li, Ye ; Cirino, Patrick C. ; Janik, Michael J. ; Maranas, Costas D. / OptZyme : Computational Enzyme Redesign Using Transition State Analogues. In: PloS one. 2013 ; Vol. 8, No. 10.
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OptZyme : Computational Enzyme Redesign Using Transition State Analogues. / Grisewood, Matthew J.; Gifford, Nathanael P.; Pantazes, Robert J.; Li, Ye; Cirino, Patrick C.; Janik, Michael J.; Maranas, Costas D.

In: PloS one, Vol. 8, No. 10, e75358, 07.10.2013.

Research output: Contribution to journalArticle

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T2 - Computational Enzyme Redesign Using Transition State Analogues

AU - Grisewood, Matthew J.

AU - Gifford, Nathanael P.

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Grisewood MJ, Gifford NP, Pantazes RJ, Li Y, Cirino PC, Janik MJ et al. OptZyme: Computational Enzyme Redesign Using Transition State Analogues. PloS one. 2013 Oct 7;8(10). e75358. https://doi.org/10.1371/journal.pone.0075358