Interactive Interface for Graph-Based Analyses of Dynamic H-Bond Networks: Application to Spike Protein S

Area of Science:

• Biophysics
• Structural Biology
• Computational Biology

Background:

• Dynamic hydrogen-bond networks are crucial for protein conformational changes.
• Analyzing these networks in large macromolecular complexes requires efficient computational methods.

Purpose of the Study:

• To present a novel, efficient interface for analyzing dynamical hydrogen-bond networks in biomolecules and macromolecular complexes.
• To incorporate hydrophobic interaction analyses for a comprehensive understanding of protein dynamics.

Main Methods:

• Development of a standalone, efficient software interface.
• Application of the interface to analyze the dynamics of the SARS-CoV-2 spike protein ectodomain.

Main Results:

• Identification of numerous local clusters of dynamic hydrogen bonds within the SARS-CoV-2 spike protein.
• Discovery of persistently sampled hydrogen bonds and a limited number of such clusters in the receptor binding domain, indicating structural plasticity.

Conclusions:

• The developed interface is effective for dissecting protein dynamics and hydrogen-bond networks.
• The findings provide insights into the structural plasticity of the SARS-CoV-2 spike protein.