Software

YRB script to highlight hydrophobicity and charge in protein structures (Pymol)

The composition of protein surfaces determines both affinity and specificity of protein-protein interactions. Matching of hydrophobic contacts and charged groups on both sites of the interface are crucial to ensure specificity. The YRB scheme highlights both hydrophobicity and charge in protein structures. YRB highlighting visualizes hydrophobicity by highlighting all carbon atoms that are not bound to nitrogen and oxygen atoms. The charged oxygens of glutamate and aspartate are highlighted red and the charged nitrogens of arginine and lysine are highlighted blue. For a set of representative examples, we demonstrate that YRB highlighting intuitively visualizes segments on protein surfaces that contribute to specificity in protein-protein interfaces, including Hsp90/co-chaperone complexes, the SNARE complex and a transmembrane domain. We provide YRB highlighting in form of a script that runs using the software PyMOL. Link to article

Instructions            Script

“This paper provides a new color scheme for protein surface representations in the popular molecular graphics program PyMol. The authors created a script that colors amino acid residues so that hydrophobicity and charge are emphasized. This scheme is more intuitive than the usual method of coloring surface residues using electrostatic potential. This script will make it easier to highlight residues important for protein-protein interactions or protein-ligand interactions when teaching about protein structure.  ” Link