Excessive osteoclast activity underlies many bone diseases such as osteoporosis, periodontitis, rheumatoid arthritis and Paget’s disease. Bone resorption requires degradation of organic bone matrix, whose main component is type I collagen. To degrade bone matrix, osteoclasts secrete cathepsin K (CtsK), a potent collagenase that functions optimally under acidic pH. CtsK-null mice display severe osteopetrotic phenotype despite normal differentiation of osteoclasts, which strongly supports the essential role of CtsK in bone resorption. A highly positively charged protein, CtsK is known to bind negatively charged glycosaminoglycans, among which it binds heparan sulfate (HS) most avidly. Widely distributed at the cell surface and in the extracellular matrix, it is conceivable that the high-affinity interaction between CtsK and HS plays a role in CtsK biology. However, how HS regulates the biological functions of CtsK remains completely unknown. The persistence of this critical knowledge gap prevents us from gaining a more complete understanding of CtsK biology, and likely also from fulfilling the therapeutic potential of targeting CtsK. Our central hypothesis is that heparan sulfate regulates the activity and localization of CtsK, and that CtsK activity can be manipulated by targeting its HS-binding site. Guided by strong preliminary data generated in the lab, our hypothesis will be tested by pursuing the following three specific aims. Aim 1: Determine the structural details of CtsK-HS interaction. We will employ complementary biophysical/biochemical methods including X-ray crystallography, small-angle X-ray scattering and HS oligosaccharide microarray to understand the structural basis of CtsK-HS interaction. Aim 2: Determine the biological roles of CtsK-HS interaction. By utilizing a newly generated knock-in mouse strain bearing an HS-binding deficient CtsK (CtsK∆HS), we will try to understand the physiological consequence of disrupted CtsK-HS interaction. Aim 3: Inhibition of CtsK with structurally defined HS oligosaccharides. We will examine the antiresorptive activity of CtsK-binding HS oligosaccharides in a number of murine models of bone remodeling. By investigating CtsK-HS interaction using a combination of in vitro and in vivo methods, our contribution will be significant because we will identify multiple mechanisms by which HS regulates the biological functions of CtsK. Without this critical knowledge, our understanding of CtsK biology will never be complete. The outcome of our investigation could also help design novel ways of manipulating the activity of this highly important protease. In particular, because HS possesses the unique property of selectively inhibiting the collagenase activity of CtsK without compromising its normal peptidase activity, our investigation might help develop an ideal CtsK inhibitor for treating many bone diseases.