![air-water interface hydrophobic amino acids air-water interface hydrophobic amino acids](http://www.whatislife.com/reader/selfassembly/Image120.gif)
Hydrophobicity is frequently visualized by a hydrophobic to non-hydrophobic color gradient based on experimentally based classification of amino acid properties ( Eisenberg et al., 1984).Īssessment of major determinants for protein-protein interactions typically requires a combination of the aforementioned color schemes. Electrostatic potential maps highlight protein surfaces based on the Boltzmann equation, representing a gradient from negative to positive potential. CPK coloring highlights atoms per type and allows distinguishing between different elements in a protein ( Corey and Pauling, 1953 Koltun, 1965). Widely used highlighting schemes include CPK coloring and highlighting according to electrostatic potential or hydrophobicity gradient. Adequate highlighting of protein surfaces in structural models allows identification of specificity determinants. Specificity of protein-protein interactions is determined by matching of complementary functional groups with those of the opposite surface ( Chothia and Janin, 1975 Eaton et al., 1995).
![air-water interface hydrophobic amino acids air-water interface hydrophobic amino acids](https://els-jbs-prod-cdn.jbs.elsevierhealth.com/cms/attachment/b7e1d434-60d9-4a75-ae41-1b4080c341bf/gr1_lrg.gif)
Protein-protein interactions underlie all processes in the cell.
#Air water interface hydrophobic amino acids software#
We provide YRB highlighting in form of a script that runs using the software PyMOL. 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. The charged oxygens of glutamate and aspartate are highlighted red and the charged nitrogens of arginine and lysine are highlighted blue. YRB highlighting visualizes hydrophobicity by highlighting all carbon atoms that are not bound to nitrogen and oxygen atoms. Here, we propose a highlighting scheme, YRB, which highlights both hydrophobicity and charge in protein structures. Matching of hydrophobic contacts and charged groups on both sites of the interface are crucial to ensure specificity. The composition of protein surfaces determines both affinity and specificity of protein-protein interactions. Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands.van Belzen, Tania Morán Luengo and Stefan G.