Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 103, Issue 52, Pages 19749-19753Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0609442104
Keywords
hydration; protein folding; water
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Funding
- NIGMS NIH HHS [GM021967, R01 GM021967] Funding Source: Medline
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The extent to which water is present within apolar cavities in proteins remains unclear. in the case of interleukin-1 beta (IL-1 beta), four independent structures solved by x-ray crystallography indicate that water is not present in the central apolar cavity. In contrast, results from NMR spectroscopy suggest that water has high occupancy within the cavity but is positionally disordered, making it undetectable by standard crystallographic methods. A theoretically based crystallographic-phase refinement technique also suggested that there was the equivalent of two fully occupied water molecules within the apolar cavity. To resolve these discrepancies we sought to obtain an experimentally phased electron density map that was free of possible bias caused by mathematical modeling of the protein or the solvent. By combining native diffraction data with multiple wavelength anomalous data from a platinum derivative, accurate phases were obtained. Using these experimental phases, we estimate that occupancy of the apolar cavity in IL-1 beta by solvent is close or equal to zero. Polar cavities in the protein that contain ordered solvent molecules serve as internal controls.
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