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Buried waters and internal cavities in monomeric proteins
M A Williams1, J M Goodfellow, J M Thornton
1Department of Biochemistry and Molecular Biology, University College London, United Kingdom.
Protein Science : a Publication of the Protein Society
|August 1, 1994
Summary
Buried water molecules are frequently found in protein cavities, with nearly half forming clusters. Cavity size and hydrogen bonding potential influence water occupancy, impacting protein stability.
Area of Science:
- Structural Biology
- Biophysics
- Computational Biology
Background:
- Proteins contain internal cavities and buried water molecules that influence their structure and function.
- Understanding the distribution and interactions of these water molecules is crucial for protein dynamics and stability.
Purpose of the Study:
- To analyze the characteristics and occupancy of buried water molecules and internal cavities in a diverse set of protein structures.
- To investigate the relationship between cavity properties, water molecule interactions, and protein stability.
Main Methods:
- Analysis of 75 high-resolution, nonhomologous, monomeric protein structures.
- Utilized a novel program, PRO_ACT, to identify and characterize protein internal cavities.
- Quantified hydrogen bonds between water molecules and protein residues.
Main Results:
- Nearly half of buried water molecules exist in clusters (pairs or larger).
- Approximately 90% of water molecules are associated with large protein cavities.
- Cavity volume correlates with protein molecular weight and is independent of structural class.
- Larger, elongated cavities are more common than globular ones; empty cavities outnumber hydrated ones.
- Water occupancy increases with cavity size and available hydrogen bond partners, stabilizing the state by ~0.6 kcal/mol per partner.
Conclusions:
- Internal protein cavities are significant reservoirs for buried water molecules.
- Cavity characteristics and hydrogen bonding networks are key determinants of water molecule localization and stability within proteins.
- These findings provide insights into protein hydration, stability, and internal dynamics.