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Dewetting transitions in protein cavities
Author(s) -
Young Tom,
Hua Lan,
Huang Xuhui,
Abel Robert,
Friesner Richard,
Berne B. J.
Publication year - 2010
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.22699
Subject(s) - dewetting , solvation , chemistry , protein data bank (rcsb pdb) , molecular dynamics , affinities , protein structure , protein folding , biophysics , hydrophobic effect , plasma protein binding , crystallography , chemical physics , nanotechnology , computational chemistry , stereochemistry , biochemistry , biology , materials science , solvent , thin film
Abstract In a previous analysis of the solvation of protein active sites, a drying transition was observed in the narrow hydrophobic binding cavity of Cox‐2. With the use of a crude metric that often seems able to discriminate those protein cavities that dry from those that do not, we made an extensive search of the PDB, and identified five other proteins that, in molecular dynamics simulations, undergo drying transitions in their active sites. Because such cavities need not desolvate before binding hydrophobic ligands they often exhibit very large binding affinities. This article gives evidence that drying in protein cavities is not unique to Cox‐2. Proteins 2010. © 2010 Wiley‐Liss, Inc.