Abstract Aberrant lipoprotein metabolism is a hallmark of obesity that affects >40% of Americans. Obesity and its com- plications, including type-2 diabetes (T2D), cardiovascular, amyloid and severe viral diseases, are the leading causes of premature death. The ultimate goal of this research is to help diagnose and treat these disorders. This project addresses critical unresolved questions in the lipoprotein functionality in obesity. High-, low- and very low- density lipoproteins (HDL, LDL and VLDL) are diverse nanoparticles comprised of lipids and apolipoproteins that direct lipid metabolism in plasma. This process is extremely complex and many details are unknown. Our current focus is on the interactions of lipoproteins and proteins with heparan sulfate (HS), which can trigger both cardio- vascular and amyloid diseases. We will determine the molecular mechanisms of apolipoprotein-HS interactions and altered lipoprotein functionality in obesity. Our powerful approach, which integrates a wide array of biochem- ical, biophysical and computational tools, enabled us to postulate compelling new hypotheses that will be tested in three complementary specific aims. Aim 1 will determine how lipoprotein functionality changes in obesity be- fore and after treatment. Lipoproteins from healthy and morbidly obese subjects will be isolated based on the heparin binding affinity, and their biochemical and functional properties will be determined. Our new hypothesis supported by strong pilot studies will be tested: small particles formed upon action of lipoprotein lipase on circu- lating VLDL provide novel biomarkers of obesity and readouts for treatment. Aim 2 will define the biochemical and functional details of serum amyloid A (SAA) transfer from HDL to LDL in obesity. Our pilot studies indicate that transfer of this small protein induces pro-atherogenic changes in LDL, and suggest two hypotheses that will be tested: i) new mechanistic links between obesity, elevated SAA and atherosclerosis, and ii) novel beneficial role of SAA as a lipid scavenger in obesity. Aim 3 will determine how HS and heparin affect SAA misfolding in amyloid A (AA) amyloidosis, a life-threatening complication of obesity and chronic inflammation. SAA binding to HS is a therapeutic target in AA amyloidosis but molecular details are lacking. Our pilot studies suggest that: i) SAA binding to HS initiates an extracellular pathway of amyloid deposition; ii) periodic anionic arrays in HS bind to stacks of basic residues in amyloid and stabilize amyloid nuclei. To test these intriguing new ideas, we will combine biochemical, biophysical, hydrogen-deuterium exchange mass spectrometry, and computational meth- ods with atomic structures of SAA in crystals and fibrils. Outcome: this research will identify new mechanistic links between obesity and atherosclerosis; verify the hypothetical vital role of SAA as a lipid scavenger; clarify its misfolding pathway in amyloid; and help develop new diagnost...