Directed Evolution's Influence on Rapid Density Fluctuations Illustrates How Protein Dynamics Can Become Coupled to Chemistry

Joseph W. Schafer, Steven D. Schwartz

Research output: Contribution to journalArticle

Abstract

Protein engineering is a growing field with a variety of experimental techniques available for altering protein function. However, creating an enzyme de novo is still in its infancy, so far yielding enzymes of modest catalytic efficiency. In this study, a system of artificial retro-aldolase enzymes found to have chemistry coupled to protein dynamics was examined. The original design was created computationally, and this protein was then subjected to directed evolution to improve the initial low catalytic efficiency. We found that this re-engineering of the enzyme resulted in rapid density fluctuations throughout the enzyme being reshaped via alterations in the hydrogen bonding network. This work also led to the discovery of a second important motion which aids in the release of an intermediate product. These results provide compelling evidence that to engineer efficient protein catalysts, fast protein dynamics need to be considered in the design.

Original languageEnglish (US)
Pages (from-to)8476-8484
Number of pages9
JournalACS Catalysis
Volume10
Issue number15
DOIs
StatePublished - Aug 7 2020

Keywords

  • directed evolution
  • hydrogen bonding network
  • Markov chain Monte Carlo
  • protein dynamics
  • QMMM simulation
  • transition path sampling

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)

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