DOMAIN-LIGAND BINDING FREE ENERGY CALCULATIONS ON PDC109, A TWO-DOMAIN PROTEIN

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. PDC109 is a 10.6 kDa modular protein containing two fibronectin type II (Fn2) repeats joined by a flexible linker. It plays a major role in bull sperm binding to the oviductal epithelium through its interactions with the sperm cell membrane. These interactions stimulate the efflux of phosphorylcholine (PhC), the soluble head group of the sperm cell membrane lipids, resulting in the specific binding to the PDC109 domains. Long timescale molecular dynamics simulation on PDC109 suggests that PhC binding is correlated with domain-domain interactions. We propose to estimate PhC binding affinity by calculating a potential of mean force (PMF) as a function of distance between binding sites of each domain and the ligand using the adaptive biasing force (ABF) method. The free energy profiles will be calculated on the individual domains and on the intact PDC109. This study will improve interpretation of reported experimental results for the interaction between PDC109 and phospholipid membranes and provide insight into roles of domain-domain interactions on ligand binding in related systems.