The glycocalyx is a sugar-rich layer located at the luminal part of the endothelial cells. It is involved in key metabolic processes and its malfunction is related to several diseases. To understand the function of the glycocalyx, a molecular level characterization is necessary. In this article, we present large-scale molecular-dynamics simulations that provide a comprehensive description of the structure and dynamics of the glycocalyx. We introduce the most detailed, to-date, all-atom glycocalyx model, composed of lipid bilayer, proteoglycan dimers, and heparan sulfate chains with realistic sequences. Our results reveal the folding of proteoglycan ectodomain and the extended conformation of heparan sulfate chains. Furthermore, we study the glycocalyx response under shear flow and its role as a flypaper for binding fibroblast growth factors (FGFs), which are involved in diverse functions related to cellular differentiation, including angiogenesis, morphogenesis, and wound healing. The simulations show that the glycocalyx increases the effective concentration of FGFs, leading to FGF oligomerization, and acts as a lever to transfer mechanical stimulus into the cytoplasmic side of endothelial cells. © 2014 by the Biophysical Society.