ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins.

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Protein interface stability is crucial for protein dynamics and unfolding.
• Identifying less stable protein interfaces aids in understanding protein dynamics and guiding stabilization of proteins with non-two-state unfolding.
• Current methods lack specific tools for identifying inherently unstable protein interfaces.

Purpose of the Study:

• To introduce ProteinLIPs, a web server for detecting and visualizing protein interfaces characterized by high polarity and low packing density (LIPs).
• To analyze the distinct characteristics of the sequence segment (mLIP) and contacting residues (cLIP) within LIPs.
• To demonstrate the utility of ProteinLIPs in guiding the engineering of non-two-state proteins.

Main Methods:

• Development of the ProteinLIPs web server, which scans monomeric and oligomeric proteins.
• Graphical sequence profiling and interactive 3D visualization of detected LIPs.
• Statistical analysis of 53 protein domains from 10 superfamilies to characterize mLIPs and cLIPs.

Main Results:

• ProteinLIPs successfully identifies LIPs, composed of mLIPs (conserved, unstable, polar) and cLIPs (stable, less conserved, apolar).
• cLIPs are enriched in small-molecule binding sites, suggesting a role in ligand interaction facilitated by mLIP instability.
• The analysis revealed distinct properties for mLIPs and cLIPs, contributing to understanding protein interface stability.

Conclusions:

• ProteinLIPs is a valuable tool for automated identification and visualization of LIPs.
• LIPs are preferential targets for thermostabilization in engineering non-two-state proteins.
• The findings advance the understanding of protein dynamics and rational protein design.