eMap: A Web Application for Identifying and Visualizing Electron or Hole Hopping Pathways in Proteins

Area of Science:

• Biophysics
• Computational Biology
• Structural Biology

Background:

• Understanding electron and hole transfer in proteins is crucial for various biological processes.
• Existing models often require detailed input or lack comprehensive visualization capabilities.
• Protein-mediated charge transport influences functions from photosynthesis to DNA repair.

Purpose of the Study:

• To introduce eMap 1.0, a novel web-based platform for identifying and visualizing protein electron/hole transfer pathways.
• To provide a user-friendly interface for analyzing charge transport in proteins using crystal structures.
• To offer a tool that complements existing pathway models with enhanced visualization and automated moiety detection.

Main Methods:

• eMap utilizes a coarse-grained model based on the Pathways model, employing effective decay parameters for protein-mediated tunneling.
• It automatically detects electron transfer active (ETA) moieties, including aromatic amino acid residues and cofactor fragments.
• Users can specify electron/hole sources and targets, with the software identifying shortest pathways ranked by effective length.

Main Results:

• The platform successfully identifies and visualizes electron or hole transfer pathways within protein structures.
• Pathways are presented in both 2D graph format and 3D visualizations using standard protein visualization tools.
• eMap 1.0 provides a comprehensive interface for exploring charge transport routes.

Conclusions:

• eMap 1.0 offers a powerful and accessible tool for researchers studying biological charge transport.
• The platform facilitates the analysis of electron/hole transfer mechanisms by integrating structural data with pathway modeling.
• This tool enhances the understanding of protein function by providing insights into charge transfer dynamics.