BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics

Area of Science:

• Biophysics
• Structural Biology
• Computational Biology

Background:

• Atomic Force Microscopy (AFM) is crucial for visualizing biomolecular structures at high resolution.
• Interpreting complex AFM data, especially for dynamic processes, can be challenging.

Purpose of the Study:

• To develop a standalone software, BioAFMviewer, for simulating AFM graphics from biomolecular structures.
• To aid researchers in interpreting biomolecular AFM experimental results.

Main Methods:

• The software visualizes Protein Data Bank (PDB) files and simulates AFM scanning with variable resolution and tip shapes.
• It integrates molecular structure visualization with synchronized AFM graphics generation.
• The software can process molecular dynamics simulations to create AFM movies.

Main Results:

• BioAFMviewer successfully transforms biomolecular structures into realistic AFM graphical representations.
• Simulated AFM graphics generated by the software were validated against high-speed AFM observations of proteins.
• The software demonstrated the ability to produce AFM movies from conformational motion data.

Conclusions:

• BioAFMviewer provides a valuable platform for interpreting biomolecular AFM experiments.
• The software bridges the gap between structural/dynamical data and experimental AFM observations.
• It enhances the understanding of protein dynamics and functional transitions through simulated AFM movies.