Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein...

Area of Science:

• Structural Biology
• Computational Biology
• Biophysics

Background:

• Positively charged electrostatic patches on protein surfaces often indicate nucleic acid binding sites.
• However, many proteins lacking nucleic acid interactions also exhibit significant positive surface patches.
• These patches can correlate with other protein family-specific functional characteristics.

Purpose of the Study:

• To introduce PatchFinderPlus (PFplus), a web-based tool for identifying and visualizing continuous electrostatic positive patches on protein surfaces.
• To provide a resource for researchers to analyze protein surface electrostatics beyond known nucleic acid binding interfaces.

Main Methods:

• Utilizes user-provided Protein Data Bank (PDB) codes or coordinate files.
• Computes continuum electrostatics potential for protein surfaces.
• Extracts the largest continuous positive electrostatic patch for each protein chain.

Main Results:

• PFplus successfully identifies and displays positive electrostatic patches on protein surfaces.
• The tool outputs a list of residues comprising the largest positive patch in PDB format.
• Visualizations of the largest positive patch are provided using Jmol with color coding.

Conclusions:

• PFplus is a valuable tool for exploring electrostatic properties of protein surfaces.
• It facilitates the discovery of potential functional sites and interactions not solely related to nucleic acid binding.
• The tool aids in understanding diverse protein functions through surface electrostatics analysis.