Structure and computation-guided yeast surface display for the evolution of TIMP-based matrix metalloproteinase inhibitors

Alireza Shoari, Ghazaleh Khalili-Tanha, Mathew A. Coban, Evette S. Radisky

Research output: Contribution to journalShort surveypeer-review

Abstract

The study of protein-protein interactions (PPIs) and the engineering of protein-based inhibitors often employ two distinct strategies. One approach leverages the power of combinatorial libraries, displaying large ensembles of mutant proteins, for example, on the yeast cell surface, to select binders. Another approach harnesses computational modeling, sifting through an astronomically large number of protein sequences and attempting to predict the impact of mutations on PPI binding energy. Individually, each approach has inherent limitations, but when combined, they generate superior outcomes across diverse protein engineering endeavors. This synergistic integration of approaches aids in identifying novel binders and inhibitors, fine-tuning specificity and affinity for known binding partners, and detailed mapping of binding epitopes. It can also provide insight into the specificity profiles of varied PPIs. Here, we outline strategies for directing the evolution of tissue inhibitors of metalloproteinases (TIMPs), which act as natural inhibitors of matrix metalloproteinases (MMPs). We highlight examples wherein design of combinatorial TIMP libraries using structural and computational insights and screening these libraries of variants using yeast surface display (YSD), has successfully optimized for MMP binding and selectivity, and conferred insight into the PPIs involved.

Original languageEnglish (US)
Article number1321956
JournalFrontiers in Molecular Biosciences
Volume10
DOIs
StatePublished - 2023

Keywords

  • directed evolution
  • matrix metalloproteinase
  • protein engineering
  • tissue inhibitor of metalloproteinases
  • yeast surface display

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)

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