Water Networks Repopulate Protein-Ligand Interfaces with Temperature.

Area of Science:

• Structural Biology
• Biochemistry
• Drug Discovery

Background:

• High-resolution crystal structures are vital for understanding protein-ligand interactions, often emphasizing the role of water networks.
• Traditional cryogenic temperature methods for structure determination may yield precise but biologically inaccurate insights due to altered water networks.

Purpose of the Study:

• To investigate the impact of temperature on water networks within protein structures.
• To determine how temperature-induced water network changes affect protein conformations and ligand binding interfaces.
• To explore the utility of room-temperature structural data in drug discovery, particularly for targets like Hsp90α.

Main Methods:

• Collected matched room-temperature and cryogenic datasets for the biomedical target heat shock protein 90 alpha (Hsp90α).
• Analyzed changes in water networks and their influence on protein conformations at the ligand binding interface.
• Introduced Flipper conformational barcodes to identify temperature-sensitive regions in electron density maps.

Main Results:

• Identified significant changes in water networks between room-temperature and cryogenic datasets of Hsp90α.
• Observed that water repositioning with temperature alters protein ensembles and influences ligand interactions.
• Flipper conformational barcodes revealed that temperature-responsive states correlate with ligand-responsive regions, capturing unique binding signatures lost upon cryo-cooling.

Conclusions:

• Room-temperature structural data provides biologically relevant insights into protein-ligand interactions, including dynamic water networks.
• Temperature-sensitive protein conformations and water networks are critical for understanding binding signatures.
• Findings have implications for discovering selective Hsp90 ligands and highlight the broader utility of hidden protein and water conformations in drug discovery.