An Energy Optimization Strategy Based on the Perfect Conformation of Prolyl Endopeptidase for Improving Catalytic Efficiency

Xiaolin Li, Yalong Cong, Mingzhe Ma, Zhi Neng You, Bei Gao, John Z.H. Zhang, Lujia Zhang

Research output: Contribution to journalArticle

Abstract

Prolyl endopeptidases (PEPs) hydrolyze proteins to yield bioactive peptides and are effective in the treatment of celiac disease. However, the catalytic efficiency of PEPs still has the potential to be improved, which could further strengthen their industrial and therapeutic applications. Herein, a novel rational design strategy based on a "near-attack conformation" of the catalytic state of PEP was adopted. Constrained dynamic simulations were applied, followed by the virtual screening of potentially favorable mutants according to their binding free energy. We redesigned Sphaerobacter thermophiles PEP with high-temperature activity/stability, a wide range of pH stabilities, and high proline specificity. As a result, the kcat value of two PEP mutants (I462W and Q560Y) increased by 208.2 and 150.1%, respectively, and the kcat/KM increased by 32.7 and 6.3%, respectively. These data revealed that the PEP mutants had improved catalytic efficiency and that our strategy can be applied for enzyme engineering.

Original languageEnglish (US)
Pages (from-to)5129-5137
Number of pages9
JournalJournal of Agricultural and Food Chemistry
Volume68
Issue number18
DOIs
StatePublished - May 6 2020

Keywords

  • catalytic efficiency
  • molecular dynamics simulations
  • prolyl endopeptidase
  • protein engineering
  • site-directed mutagenesis

ASJC Scopus subject areas

  • Chemistry(all)
  • Agricultural and Biological Sciences(all)

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