Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways

Area of Science:

• Biophysics
• Computational Biology
• Structural Biology

Background:

• T4 lysozyme L99A mutant is a model for small-molecule protein binding.
• Ligand entry/exit pathways and protein conformational changes remain unclear.

Purpose of the Study:

• To investigate benzene exit pathways from T4 lysozyme's binding site.
• To characterize protein conformational changes during ligand unbinding.

Main Methods:

• Weighted ensemble (WE) molecular dynamics simulations were used to enhance sampling of unbinding events.
• Simulations modeled benzene exit from the T4 lysozyme binding cavity.

Main Results:

• Four distinct pathways for benzene exit were identified.
• Benzene unbinding utilizes transient tunnels formed by protein structural fluctuations.
• Protein conformational changes involving alpha-helices and side chains facilitate ligand escape.

Conclusions:

• Benzene unbinding from T4 lysozyme is a heterogeneous process involving multiple pathways.
• Intrinsic protein dynamics contribute to the formation of ligand exit routes.
• Provides semiquantitative characterization of pathway heterogeneity in small-molecule protein binding.