Cited Article: Hummer, G. Water conduction through the hydrophobic channel of a carbon nanotube
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Title:
Dewetting transitions in protein cavities
Authors:
Young, T; Hua, L; Huang, XH; Abel, R; Friesner, R; Berne, BJ
Author Full Names:
Young, Tom; Hua, Lan; Huang, Xuhui; Abel, Robert; Friesner, Richard; Berne, B. J.
Source:
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 78 (8): 1856-1869 JUN 2010
Language:
English
Document Type:
Article
Author Keywords:
hydrophobic enclosure; surface hydrophobicity; narrowness measure; molecular dynamics; holo-and apo-protein active site
KeyWords Plus:
RETINOL-BINDING-PROTEIN; HUMAN SERUM-ALBUMIN; LIGAND-BINDING; MOLECULAR-DYNAMICS; HYDROPHOBIC ENCLOSURE; CRYSTAL-STRUCTURES; FATTY-ACIDS; WATER; RESOLUTION; SIMULATION
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.
Reprint Address:
Berne, BJ, San Jose State Univ, Dept Chem, San Jose, CA 95192 USA.
Research Institution addresses:
[Young, Tom] San Jose State Univ, Dept Chem, San Jose, CA 95192 USA; [Young, Tom; Hua, Lan; Huang, Xuhui; Abel, Robert; Friesner, Richard; Berne, B. J.] Columbia Univ, Dept Chem, New York, NY 10027 USA
E-mail Address:
simpleliquid@gmail.com; bb8@columbia.edu
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Cited Reference Count:
43
Times Cited:
0
Publisher:
WILEY-LISS; DIV JOHN WILEY & SONS INC, 111 RIVER ST, HOBOKEN, NJ 07030 USA
Subject Category:
Biochemistry & Molecular Biology; Biophysics
ISSN:
0887-3585
DOI:
10.1002/prot.22699
IDS Number:
597ON
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