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Disordered water within a hydrophobic protein cavity visualized by x-ray crystallography
B Yu1, M Blaber, A M Gronenborn
1Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA.
Summary
Researchers mapped water molecules within human interleukin 1beta
Area of Science:
- Structural Biology
- Biophysics
- Computational Biology
Background:
- Interleukin 1beta (IL-1β) is a key inflammatory cytokine.
- Hydrophobic cavities within proteins can influence function.
- Water molecules in protein cavities are challenging to visualize with X-ray crystallography.
Purpose of the Study:
- To quantitatively map water molecules in the hydrophobic cavity of human interleukin 1beta.
- To overcome limitations of high-resolution X-ray crystallography for visualizing internal water.
Main Methods:
- Quantitative analysis of low-resolution X-ray diffraction data from a single crystal.
- Iterative density modification and phasing of diffraction data.
- Restrained refinement using atomic models and resolution-dependent damping to avoid overfitting.
- XPLOR refinement for atomic modeling of water distribution.
Main Results:
- The hydrophobic cavity can accommodate up to four water molecules.
- A refined solvent difference map indicated approximately two water molecules in the cavity.
- A water dimer was observed in the central cavity about 70% of the time.
- Constricted channels connecting to the cavity were occupied by single water molecules (40% and 10% occupancy).
Conclusions:
- Low-resolution X-ray diffraction data can effectively map internal protein water invisible to high-resolution methods.
- The hydrophobic cavity of IL-1β contains a dynamic water population, including a dimer and molecules in connecting channels.
- Understanding internal water structure provides insights into protein dynamics and function.