TY - JOUR
T1 - A script to highlight hydrophobicity and charge on protein surfaces
AU - Hagemans, Dominique
AU - van Belzen, Ianthe A.E.M.
AU - Luengo, Tania Morán
AU - Rüdiger, Stefan G.D.
N1 - Publisher Copyright:
© 2015 Hagemans, van Belzen, Morán Luengo and Rüdiger.
PY - 2015/10/13
Y1 - 2015/10/13
N2 - 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. Here, we propose a highlighting scheme, YRB, which 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.
AB - 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. Here, we propose a highlighting scheme, YRB, which 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.
KW - Amino acid properties
KW - Charge pairs
KW - Protein-protein interaction
KW - PyMOL
KW - Surface hydrophobicity
UR - http://www.scopus.com/inward/record.url?scp=85003924504&partnerID=8YFLogxK
U2 - 10.3389/fmolb.2015.00056
DO - 10.3389/fmolb.2015.00056
M3 - Article
AN - SCOPUS:85003924504
SN - 2296-889X
VL - 2
JO - Frontiers in Molecular Biosciences
JF - Frontiers in Molecular Biosciences
IS - OCT
M1 - 56
ER -