Mapping the Structural and Dynamic Determinants of pH-sensitive Heparin Binding to Granulocyte Macrophage-colony Stimulating Factor

GMCSF is an immunomodulatory cytokine that is harnessed as a therapeutic. GMCSF is also known to interact with other clinically important molecules, such as heparin, suggesting endogenous and administered GMCSF has potential to interfere with orthogonal treatment outcomes. Thus, molecular level characterization of GMCSF and its interactions with other biologically active compounds is critical to understanding these mechanisms and predicting clinical outcomes. Here we dissect the molecular motions and structural contributions that facilitate the GMCSF-heparin interaction, that was previously shown to be pH-dependent, using NMR spectroscopy, SPR, and molecular docking. We find that GMCSF and heparin binding is related to a change in flexibility reflected in the dynamic profile of GMCSF at acidic pH. The molecular motions driving this interaction largely occur on the ms-us timescale. Interestingly, we find that GMCSF and heparin binding is not only pH-dependent but is also heparin chain length dependent. We propose a mechanism where a positive binding pocket that is not fully solvent accessible at neutral pH becomes more accessible at acidic pH, allowing heparin to dock with the protein.