Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 78, Issue 8, Pages 1856-1869Publisher
WILEY-BLACKWELL
DOI: 10.1002/prot.22699
Keywords
hydrophobic enclosure; surface hydrophobicity; narrowness measure; molecular dynamics; holo-and apo-protein active site
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Funding
- NIH [52018, GM 43340]
- NSF
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM043340] Funding Source: NIH RePORTER
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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.
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