Structural basis for ApoE4-induced Alzheimer's disease

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Alzheimer's disease (AD) is the 6th leading cause of death in the USA and there are no effective treatments. Moreover, the prevalence of this age-related neurodegenerative disease is likely to increase as the US population ages. Therefore, there is a great need to understand AD and develop therapeutics. ApoE is an appealing target because this lipid transporter is one of the strongest genetic risk factors for AD. ApoE3 is the most common isoform and is considered neutral. Carriers of ApoE4 are up to 15-fold more likely to develop AD, while ApoE2 appears to be protective against AD. Subsequent experiments have confirmed that ApoE4 plays a causal role in AD. However, the mechanism coupling ApoE and AD remains unclear. Strikingly, ApoE4 and ApoE2 each differ from ApoE3 by a single substitution (C112R in ApoE4 and R158C in ApoE2). Neither substitution occurs in a functional site, suggesting they indirectly impact function by altering the protein's conformational preferences. However, characterizing these structural differences remains challenging. Partial crystal structures of the different isoforms are essentially identical and the rest of the protein has largely defied structural characterization because ApoE's role in lipid transport requires it to be partially disordered and prone to oligomerization. This proposal aims to uncover the structural determinants of ApoE-induced neurotoxicity by building and analyzing atomically-detailed Markov state models (MSMs) of neurotoxic and non-toxic variants. The primary focus will be on monomeric, lipid-free ApoE as it is the relevant species for many functional processes, lipid-free ApoE is believed to be the neurotoxic species, and the fluctuations of the monomer are expected to reveal structures whose populations are enhanced/suppressed by binding partners. In Aim 1, new adaptive sampling algorithms will be developed to address the extreme conformational heterogeneity of disordered regions. Then these algorithms will be applied to understand the gross structural properties of representative ApoE variants, such as the extent of domain opening. Computational predictions will be tested with single molecule Förster resonance energy transfer (smFRET) experiments performed with our collaborators. In Aim 2, the allosteric mechanism that couples distant regions of ApoE will be dissected, employing tools once again designed to account for disorder. Resulting insight into the structural differences between neurotoxic and non-toxic isoforms will provide a foundation for the design of new variants to test our models. We will also design `structure correctors' that stabilize non-toxic conformations, providing leads for the future design of drugs that combat AD.