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Decoding the Functional Evolution of an Intramembrane Protease Superfamily by Statistical Coupling Analysis.

Ljubica Mihaljević1, Siniša Urban1

  • 1Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA.

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|August 16, 2020
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Summary

Statistical coupling analysis (SCA) identified functional amino acid sectors in membrane enzymes like rhomboid proteases. Grafting these sectors can engineer enzyme specificity and catalytic efficiency.

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Ras-converting enzyme-1gamma-secretasemembrane protein evolutionpresenilinproteolysissite-2 proteasestatistical coupling analysis

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Area of Science:

  • Biochemistry
  • Evolutionary Biology
  • Membrane Protein Function

Background:

  • Understanding enzyme evolution in cellular membranes is challenging.
  • Rhomboid proteases are widely distributed membrane proteins with poorly understood evolutionary mechanisms.

Purpose of the Study:

  • To investigate the applicability of statistical coupling analysis (SCA) for identifying functional amino acid sectors in rhomboid proteases.
  • To explore how these sectors contribute to substrate specificity and catalytic efficiency.

Main Methods:

  • Applied statistical coupling analysis (SCA) to rhomboid protease sequences.
  • Identified coevolving residue networks forming distinct functional sectors.
  • Performed 'sector grafting' by altering residues in a recipient rhomboid protease.

Main Results:

  • SCA revealed two distinct coevolving sectors in rhomboid proteases.
  • Sector 1 controls substrate specificity and is dynamically distributed.
  • Sector 2 maintains catalytic site and protein fold, predicting pseudoprotease evolution.
  • Modifying Sector 1 residues successfully transferred substrate specificity and catalytic efficiency between rhomboid proteases.

Conclusions:

  • SCA is a powerful tool for dissecting functional evolution in membrane proteins.
  • The sector grafting approach enables efficient engineering of enzyme properties.
  • Findings provide insights into the evolution of membrane enzymes and offer a strategy for enzyme design.