Aggregation of proteins of known sequence is linked to a variety of neurodegenerative disorders. Familial mutations in the Amyloid Precursor Protein (APP), from which the amyloid ? (A?) protein is derived, have been linked with the early onset of Alzheimer's disease (AD). After fifteen years of fundamental research using computer simulations guided by experiments to identify the factors that determine in vitro aggregation of A?, the stage is now set to address questions of utmost relevance to AD. They arise in the context of how heterogeneous membrane environments, cholesterol, and downstream interactions with cofactors affect the cleavage of APP, the production of A?, and subsequent interactions of A? oligomers and receptors mediating their toxic effects. We are uniquely poised to use computational models to answer these questions and drive advances in critical areas of AD research. In this computational and theoretical research proposal, augmented by synergistic experimental research collaborations, we address fundamental biophysical questions with substantial practical implications articulated in three specific aims. (1) Developing a quantitative understanding of how membrane lipid composition and structural heterogeneity impacts the partitioning of APP and secretases critical to the processing of APP in the genesis A?. (2) Elucidating the crucial role cholesterol plays in determining the extent of amyloidogenic cleavage in the differential processing of APP. (3) Characterizing at the molecular-level the conformational transitions and interactions involved in the binding of A? monomer and oligomers to cellular prion protein (PrPC), implicated in a plausible mechanism of A? cytotoxicity. The proposed coordinated studies will lead to a fundamental molecular-level understanding of the network of interactions that are essential to the biogenesis of A? protein and its role as a pathogenic agent in AD. Through the development of novel computational models and identification of new concepts, the expected outcomes could change the landscape for the use of simulations and theory not only in the AD field but also in the general study of membrane- protein interactions.!
Alzheimer's disease (AD), which accounts for nearly 50% of all cases of senile dementia, is the third leading cause of death in the elderly population of the United States, and is presently incurable. The proposed computational studies and experimental collaborations will explore the structure and function of the transmembrane domains of Amyloid Precursor Protein (APP) and key secretases involved in its proteolytic processing to produce amyloid ? (A?) protein, as well as interactions of A? with cellular prion protein (PrPC) implicated in a putative mechanism of A? cytotoxicity. Our results will elucidate the role of familial AD mutations and environmental conditions, including cholesterol levels, in the processing of APP and the onset of AD, providing new insights valuable to the future development of preventive or early stage therapeutics.
|Pantelopulos, George A; Straub, John E (2018) Regimes of Complex Lipid Bilayer Phases Induced by Cholesterol Concentration in MD Simulation. Biophys J 115:2167-2178|
|Pantelopulos, George A; Straub, John E; Thirumalai, D et al. (2018) Structure of APP-C991-99 and implications for role of extra-membrane domains in function and oligomerization. Biochim Biophys Acta Biomembr :|
|Xu, Fangda; Bandara, Asanga; Akiyama, Hisashi et al. (2018) Membrane-wrapped nanoparticles probe divergent roles of GM3 and phosphatidylserine in lipid-mediated viral entry pathways. Proc Natl Acad Sci U S A 115:E9041-E9050|
|Bove-Fenderson, Erin; Urano, Ryo; Straub, John E et al. (2017) Cellular prion protein targets amyloid-? fibril ends via its C-terminal domain to prevent elongation. J Biol Chem 292:16858-16871|
|Pantelopulos, George A; Nagai, Tetsuro; Bandara, Asanga et al. (2017) Critical size dependence of domain formation observed in coarse-grained simulations of bilayers composed of ternary lipid mixtures. J Chem Phys 147:095101|
|Bandara, Asanga; Panahi, Afra; Pantelopulos, George A et al. (2017) Exploring the structure and stability of cholesterol dimer formation in multicomponent lipid bilayers. J Comput Chem 38:1479-1488|
|Aguayo-Ortiz, Rodrigo; Chávez-García, Cecilia; Straub, John E et al. (2017) Characterizing the structural ensemble of ?-secretase using a multiscale molecular dynamics approach. Chem Sci 8:5576-5584|
|Panahi, Afra; Bandara, Asanga; Pantelopulos, George A et al. (2016) Specific Binding of Cholesterol to C99 Domain of Amyloid Precursor Protein Depends Critically on Charge State of Protein. J Phys Chem Lett 7:3535-41|
|Dominguez, Laura; Foster, Leigh; Straub, John E et al. (2016) Impact of membrane lipid composition on the structure and stability of the transmembrane domain of amyloid precursor protein. Proc Natl Acad Sci U S A 113:E5281-7|
|Viswanath, Shruthi; Dominguez, Laura; Foster, Leigh S et al. (2015) Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization. Proteins 83:2170-85|