PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability

J Chem Inf Model. 2023 Nov 27;63(22):6964-6971. doi: 10.1021/acs.jcim.3c01490. Epub 2023 Nov 7.

Abstract

The electrostatic properties of proteins arise from the number and distribution of polar and charged residues. Electrostatic interactions in proteins play a critical role in numerous processes such as molecular recognition, protein solubility, viscosity, and antibody developability. Thus, characterizing and quantifying electrostatic properties of a protein are prerequisites for understanding these processes. Here, we present PEP-Patch, a tool to visualize and quantify the electrostatic potential on the protein surface in terms of surface patches, denoting separated areas of the surface with a common physical property. We highlight its applicability to elucidate protease substrate specificity and antibody-antigen recognition and predict heparin column retention times of antibodies as an indicator of pharmacokinetics.

MeSH terms

  • Antibodies*
  • Proteins* / chemistry
  • Solubility
  • Static Electricity
  • Viscosity

Substances

  • Proteins
  • Antibodies