Basis for substrate recognition and distinction by matrix metalloproteinases.

Area of Science:

• Biochemistry
• Structural Biology
• Bioinformatics

Background:

• Genomic and structural data offer opportunities for in silico structure-function analysis.
• Limited experimental datasets exist for benchmarking protein function predictions.
• Predicting functional similarity among proteins remains challenging.

Purpose of the Study:

• To quantify structure-function relationships in the matrix metalloproteinase (MMP) family.
• To establish a measure of functional similarity based on cleavage efficiencies.
• To identify residues responsible for substrate specificity in MMPs.

Main Methods:

• Comparing cleavage efficiencies of three MMP phylogenetic branches against a large set of phage peptide substrates.
• Utilizing observed second-order rate constants [k(obs)] as a measure of functional distance.
• Correlating functional distances with phylogenetic distance and sequence identity of residues around the catalytic groove.

Main Results:

• Functional distances among MMPs correlate directly with their phylogenetic distance.
• MMP substrate preference strongly correlates with the sequence identity of 50-57 discontinuous residues surrounding the catalytic groove.
• These residues were identified as specificity-determining positions (SDPs) crucial for MMP functional expansion.

Conclusions:

• SDPs dictate MMP substrate specificity and proteolytic function evolution.
• Modifying a few key SDPs can globally alter an MMP's substrate preference.
• This highlights the potential for rational redesign of MMP cleavage specificity.