IMPROvER: the Integral Membrane Protein Stability Selector

Area of Science:

• Biochemistry and structural biology
• Computational biology and bioinformatics
• Membrane protein research

Background:

• Structure determination of membrane proteins is essential for understanding their function.
• Identifying stabilizing variants is a common prerequisite for successful membrane protein structure determination.
• Existing methods for variant selection can be inefficient and labor-intensive.

Purpose of the Study:

• To develop a general-purpose computational tool for selecting stabilizing variants of membrane proteins.
• To improve the efficiency and reduce the workload associated with identifying suitable variants for structure determination.
• To provide a rational approach for variant selection using multiple independent strategies.

Main Methods:

• Development of the Integral Membrane Protein Stability Selector (IMPROvER) computational pipeline.
• Integration of three independent variant selection approaches: deep-sequence, model-based, and data-driven.
• In silico validation using known stability data and in vitro testing with multiple membrane protein targets.

Main Results:

• IMPROvER successfully identified stabilizing variants for membrane protein targets.
• Individual selection approaches showed success rates better than random chance.
• Combining the three approaches and focusing on top-ranked sites yielded a fourfold improvement over random selection.
• The tool demonstrated effectiveness across membrane proteins with varying numbers of transmembrane helices.

Conclusions:

• IMPROvER is the first general-purpose tool for selecting stabilizing variants of α-helical membrane proteins.
• The computational pipeline offers a rational and efficient approach to variant selection for structure determination.
• The tool's ability to integrate diverse data sources enhances its applicability and success rate.
• IMPROvER is accessible online, facilitating its use in the broader scientific community.