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From the Cover
BIOLOGICAL SCIENCES / BIOPHYSICS
A dry ligand-binding cavity in a solvated protein

Johan Qvist^*, Monika Davidovic^*, Donald Hamelberg, and Bertil Halle^*,

*Center for Molecular Protein Science, Department of Biophysical Chemistry, Lund University, SE-22100 Lund, Sweden; and Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093-0365

Edited by Brian W. Matthews, University of Oregon, Eugene, OR, and approved January 31, 2008 (received for review October 16, 2007)

Ligands usually bind to proteins by displacing water from the binding site. The affinity and kinetics of binding therefore depend on the hydration characteristics of the site. Here, we show that the extreme case of a completely dehydrated free binding site is realized for the large nonpolar binding cavity in bovine β-lactoglobulin. Because spatially delocalized water molecules may escape detection by x-ray diffraction, we use water ¹⁷O and ²H magnetic relaxation dispersion (MRD), ¹³C NMR spectroscopy, molecular dynamics simulations, and free energy calculations to establish the absence of water from the binding cavity. Whereas carbon nanotubes of the same diameter are filled by a hydrogen-bonded water chain, the MRD data show that the binding pore in the apo protein is either empty or contains water molecules with subnanosecond residence times. However, the latter possibility is ruled out by the computed hydration free energies, so we conclude that the 315 ų binding pore is completely empty. The apo protein is thus poised for efficient binding of fatty acids and other nonpolar ligands. The qualitatively different hydration of the β-lactoglobulin pore and carbon nanotubes is caused by subtle differences in water–wall interactions and water entropy.

β-lactoglobulin | free energy simulation | hydrophobic hydration | magnetic relaxation dispersion

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/cgi/content/full/0709844105/DCSupplemental.

To whom correspondence should be addressed. E-mail: bertil.halle{at}bpc.lu.se

© 2008 by The National Academy of Sciences of the USA

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