The geometrical route presents an accurate and adaptable framework by which molecular dynamics simulations can be used to estimate the binding free energies of biomolecules. Past efforts have implemented the geometrical route to precisely calculate binding free energies of transmembrane helices and ligand-protein complexes in strong agreement with experimental values. In this work, the geometrical route is adapted for peripheral membrane-binding proteins. We chose Bacillus thuringiensis phosphatidylinositol-specific phospholipase C (PLC) as our model system and measure its binding free energy with a homogenous palmitoyl-oleoylphosphatidylcholine (POPC) lipid membrane in silico. Utilizing NAMD Colvars, a series of restraints are applied to the orientational and positional degrees of freedom of the system to extract their free energy contributions to the binding phenomenon. We thoroughly sample the binding process utilizing enhanced sampling techniques such as well-tempered metadynamics and extended adaptive biasing force. Consequently, we have validated our method by comparing our final free energy results with previous in vitro experiments of PLC binding to POPC vesicles. Ultimately, we aim to build upon this framework by adapting it to more complex peripheral membrane-binding proteins which may interact with non-homogenous lipid environments.
Gee et al. (Sun,) studied this question.