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Research Article
Hydrophilicity of cavities in proteins
Article first published online: 7 DEC 1998
DOI: 10.1002/(SICI)1097-0134(199604)24:4<433::AID-PROT3>3.0.CO;2-F
Copyright © 1996 Wiley-Liss, Inc.
Issue
1097-0134/asset/cover.gif?v=1&s=d817e79b67ba6cacf8bdcce1a819c04de300a7e3 "Proteins: Structure, Function, and Bioinformatics")
Proteins: Structure, Function, and Bioinformatics
Volume 24, Issue 4, pages 433–438, April 1996
Additional Information
How to Cite
Zhang, L. and Hermans, J. (1996), Hydrophilicity of cavities in proteins. Proteins, 24: 433–438. doi: 10.1002/(SICI)1097-0134(199604)24:4<433::AID-PROT3>3.0.CO;2-F
Publication History
- Issue published online: 7 DEC 1998
- Article first published online: 7 DEC 1998
- Manuscript Accepted: 27 OCT 1995
- Manuscript Received: 11 AUG 1995
Funded by
- National Science Foundation. Grant Numbers: MCB-9314854, BIR-9123574
- NIH Division of Research Resources. Grant Number: RR08102
- Abstract
- References
- Cited By
Keywords:
- structure refinement;
- buried water;
- free energy calculation;
- molecular dynamics simulation
Abstract
Water molecules inside cavities in proteins constitute integral parts of the structure. We have sought a quantitative measure of the hydrophilicity of the cavities by calculating energies and free energies of introducing a water molecule into these cavities. A threshold value of the water-protein interaction energy at −12 kcal/mol was found to be able to distinguish hydrated from empty cavities. It follows that buried waters have entropy comparable to that of liquid water or ice. A simple consistent picture of the energetics of the buried waters provided by this study enabled us to address the reliability of buried waters assigned in experiments.