Conserved buried water molecules enable the β-trefoil architecture

Area of Science:

• Structural biology
• Biochemistry
• Protein science

Background:

• Beta-trefoil proteins are a common structural motif.
• The role of internal water molecules in protein stability is not fully understood.

Purpose of the Study:

• To identify and characterize buried water molecules within beta-trefoil protein structures.
• To investigate the structural and functional significance of conserved buried waters in this protein family.

Main Methods:

• Computational analysis of high-resolution crystal structures from structural databases.
• Classification of buried waters based on conservation across beta-trefoil folds.
• Analysis of water molecule structural properties, including hydrogen bonding and B-factors.

Main Results:

• Three water molecules were identified as conserved across all beta-trefoil folds.
• These conserved waters occupy small cavities and exhibit low positional uncertainty.
• They form ideal hydrogen bonds with main chain groups and bridge different beta-strands.
• These waters orient conserved hydrophobic side chains, contributing to core packing.

Conclusions:

• Buried water molecules are fundamental structural components of the beta-trefoil fold.
• Conserved buried waters play a critical role in protein folding nucleus formation and thermostability.
• The threefold symmetry of the beta-trefoil fold is surprisingly mediated by these internal water molecules.