NMR observable-based structure refinement of DAP12-NKG2C activating immunoreceptor complex in explicit membranes

Area of Science:

• Structural Biology
• Biophysics
• Computational Chemistry

Background:

• Nuclear Magnetic Resonance (NMR) observables, like NOE-based distance restraints, are vital for membrane protein structure determination.
• Challenges in membrane protein NMR studies can lead to limited restraints, causing ambiguity in side chain interactions.

Purpose of the Study:

• To investigate the energetic optimality of side-chain interactions in the DAP12-NKG2C immunoreceptor transmembrane helix complex.
• To refine the published solution NMR structure using molecular dynamics simulations in explicit membrane environments.

Main Methods:

• Utilized published distance restraints from NMR data.
• Performed molecular dynamics (MD) simulations in explicit micelle and bilayer environments.
• Refined membrane protein structures based on simulation results.

Main Results:

• Refined structures maintained global similarity to the published NMR structure.
• A stable network of salt bridges and hydrogen bonds formed among key interfacial residues.
• Aspartic acid side chains were shielded from the hydrophobic membrane core, aligning with experimental observations.
• Simulations revealed consistent short-range interactions between the complex and lipid/detergent molecules.

Conclusions:

• Molecular dynamics simulations in explicit membrane systems effectively refine NMR-derived membrane protein structures.
• The refined structures provide a more energetically favorable arrangement of interfacial residues.
• This approach enhances the characterization of critical side chain interactions in membrane proteins.