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PACMANS: A bioinformatically informed algorithm to predict, design, and disrupt protease-on-protease hydrolysis.

Meghan C Ferrall-Fairbanks1, Zachary T Barry1, Maurizio Affer1

  • 1Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia.

Protein Science : a Publication of the Protein Society
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Summary

Protease-on-protease degradation was investigated using the novel PACMANS algorithm. This tool accurately predicts cleavage sites, enabling experimental validation of protease interactions.

Keywords:
MMPsbioinformaticscathepsinshydrolysismutagenesispredictionproteasesproteolysis

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Area of Science:

  • Biochemistry
  • Proteomics
  • Bioinformatics

Background:

  • Proteases are enzymes that break down proteins.
  • Emerging evidence shows proteases can degrade other proteases, impacting biological systems.
  • Cathepsin S hydrolysis of cathepsin K exemplifies this protease-on-protease interaction.

Purpose of the Study:

  • To develop and validate an in silico tool for predicting protease-on-protease cleavage sites.
  • To explore protease interactions beyond known substrate-enzyme relationships.

Main Methods:

  • Developed PACMANS (Protease-Ase Cleavage from MEROPS ANalyzed Specificities) algorithm.
  • Utilized a sliding-window approach scoring amino acid sequences against the MEROPS database.
  • Validated predictions using site-directed mutagenesis of cathepsin K.

Main Results:

  • PACMANS identified L253 and V171 as cathepsin S cleavage sites on cathepsin K.
  • Mutations L253A and L253V in cathepsin K significantly reduced hydrolysis by cathepsin S.
  • PACMANS predictions were confirmed for interfamilial interactions involving MMP-2 and MMP-9.

Conclusions:

  • PACMANS is a validated, unbiased tool for predicting protease cleavage sites on other proteases.
  • The algorithm can be applied to various protease pairs and non-protease substrates.
  • This tool advances the study of complex protease regulatory networks.