A Benzene-Mapping Approach for Uncovering Cryptic Pockets in Membrane-Bound Proteins

Area of Science:

• Computational biology
• Structural biology
• Biophysics

Background:

• Molecular dynamics (MD) simulations with solvent probes can identify cryptic pockets missed by experimental methods.
• Benzene is used as a small organic probe to explore these pockets on membrane-embedded proteins.

Purpose of the Study:

• To implement and validate a computational method using benzene as a probe to explore cryptic pockets on membrane-embedded proteins.
• To apply this method to the dengue virus (DENV) envelope (E) protein complex.

Main Methods:

• Utilized CHARMM force field within GROMACS for MD simulations.
• Employed modified nonbonded parameters and repulsive potentials between lipids and benzene.
• Performed solvent mapping on membrane-embedded DENV E protein complex and compared with soluble E protein ectodomain.

Main Results:

• Consistently revealed a known cryptic pocket on the DENV E protein that binds n-octyl-β-d-glucoside detergent.
• Benzene addition enhanced pocket flexibility and hydrophobic exposure at a key functional interface.
• Identified a novel, potentially druggable pocket on the membrane-associated E protein.

Conclusions:

• The benzene probe MD simulation method effectively reveals cryptic pockets on membrane-embedded viral proteins.
• This approach can identify novel targets for antiviral drug development against DENV.
• The method provides insights into protein dynamics and potential drug interactions.