The response to selection in Glycoside Hydrolase Family 13 structures: A comparative quantitative genetics approach

Area of Science:

• Biochemistry
• Structural Biology
• Bioinformatics

Background:

• Glycoside Hydrolase Family 13 (GH13) proteins are crucial for starch hydrolysis and industrial applications.
• Bioengineering efforts have focused on enhancing GH13 catalytic functions for industrial settings.

Purpose of the Study:

• To introduce a computational framework for analyzing the response to selection in GH13 protein structures.
• To identify key residues that can be modified to improve protein properties, specifically thermodynamic stability.

Main Methods:

• Phylogenetic analysis and simulated dynamic information were integrated into the framework.
• Protein structural analysis was performed to assess selection pressures on the TIM-barrel fold.
• Fitness was defined as inferred thermodynamic stability to rank important residues.

Main Results:

• The conserved TIM-barrel fold within GH13 proteins is under purifying selection and not directly selectable.
• A method was developed to rank residues based on their inferred response to selection.
• Specific residues (112Y, 122K, 124D, 125W, 126P) in a Geobacillus thermoleovorans α-amylase were identified as candidates for stability enhancement.

Conclusions:

• The developed framework is effective for analyzing protein structure evolution and identifying targets for bioengineering.
• The study demonstrates the feasibility of applying this framework to other protein families and fitness landscapes.
• Identified residues offer potential for improving the stability of α-amylase for biotechnological applications.