Salt Bridge Builder: Using Residue Distances to Predict Salt Bridge Formation

Area of Science:

• Protein engineering
• Computational biology
• Biophysics

Background:

• Salt bridges are crucial for protein stability and interactions.
• Existing tools focus on removing salt bridges, not creating them.
• Systematic methods for engineering new salt bridges are limited.

Purpose of the Study:

• Introduce Salt Bridge Builder (SBB), a software for engineering interprotein salt bridges.
• Validate the stabilizing role of salt bridges at protein interfaces.
• Develop an efficient algorithm for predicting salt bridge formation.

Main Methods:

• Utilized residue distance heuristics from structural data.
• Analyzed the SKEMPI v2 database for mutation effects.
• Benchmarked six residue distance metrics, selecting side-chain centroid distance (SCCD).
• Applied SBB to kinesin-5 and microtubule interactions.
• Employed molecular dynamics simulations and principal component analysis.

Main Results:

• SBB identifies candidate sites for novel interprotein salt bridges.
• Disrupting salt bridges significantly reduces binding free energy.
• SCCD offers optimal predictive performance and computational efficiency.
• Kinesin-5 shows enrichment in potential salt bridge sites at the microtubule interface.
• Local microenvironments influence engineered salt bridge stability.

Conclusions:

• Residue-distance-based salt bridge engineering is a viable protein engineering strategy.
• SBB provides a foundation for predicting engineered salt bridge stability.
• Future SBB extensions will incorporate microenvironment-aware stability prediction.