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

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.