Lipid-binding surfaces of membrane proteins: evidence from evolutionary and structural analysis

Area of Science:

• Biochemistry
• Structural Biology
• Evolutionary Biology

Background:

• Membrane proteins operate within the lipid bilayer, and specific lipid-protein interactions are known to influence their function.
• Lipid molecules can act as co-factors, playing vital roles in membrane protein activity.

Purpose of the Study:

• To investigate the evolutionary selection pressures on lipid-binding sites in membrane proteins.
• To identify residues involved in lipid binding through structural analysis.

Main Methods:

• Posterior probability analysis of synonymous vs. nonsynonymous substitution ratios (ω-ratio) to assess evolutionary selection.
• Geometric analysis of membrane protein structures to pinpoint residues interacting with co-crystallized lipids.
• Statistical mechanical modeling to understand lipid-protein interactions.

Main Results:

• Residues in cholesterol-binding sites of β(2)-adrenergic receptor and Na(+)-K(+)-ATPase show strong conservation, leading to an expanded cholesterol consensus motif for GPCRs.
• Aromatic stacking and interhelical hydrogen bonds are key for protein-cholesterol interactions.
• Strong purifying selection pressure observed at cardiolipin and phosphatidylglycerol binding sites.
• Lipopolysaccharide (LPS) binding to a less stable β-strand in FhuA stabilizes it against the lipid environment.

Conclusions:

• Specific lipid binding is a general mechanism for stabilizing membrane proteins, especially β-barrel proteins.
• Residues at specific lipid-binding sites frequently undergo strong purifying selection, highlighting their functional importance.