Understanding epistatic networks in the B1 β-lactamases through coevolutionary statistical modeling and deep...

Area of Science:

• Biochemistry and Molecular Biology
• Evolutionary Biology
• Structural Biology

Background:

• Protein families evolve sequence divergence while maintaining structure and function.
• Epistatic networks of intramolecular interactions can alleviate deleterious mutations during evolution.
• Comprehensive analysis of epistatic networks across protein families is limited.

Purpose of the Study:

• To conduct a family-wide analysis of epistatic networks in B1 metallo-β-lactamases.
• To combine experimental and computational methods to quantify epistasis.
• To identify the structural and functional roles of epistatic residues.

Main Methods:

• Deep mutational scanning (DMS) on NDM-1 and VIM-2 homologs.
• In silico DMS using Direct Coupling Analysis (DCA) on 100 homologs.
• Comparative analysis of experimental and computational data.

Main Results:

• Approximately one-third of equivalent mutations are epistatic in DMS experiments.
• Direct Coupling Analysis (DCA) indicates significant differences in tolerated mutations across the family.
• Strongest epistasis is observed in regions with intermediate residue burial, balancing packing and freedom.
• Entrenched residues show distinct behaviors, suggesting complex epistatic networks.

Conclusions:

• Epistasis is prevalent in protein family evolution and can be quantified.
• Intermediate residue burial is crucial for forming epistatic networks.
• Entrenched residues are key components of complex epistatic networks that stabilize protein function.