Structure of APP-C99_1-99and Implications for Role of Extra-Membrane Domains in Function and Oligomerization

Abstract

The 99 amino acid C-terminal fragment of Amyloid Precursor Protein APP-C99 (C99) is cleaved by γ-secretase to form Aβ peptide, which plays a critical role in the etiology of Alzheimer's Disease (AD). The structure of C99 consists of a single transmembrane domain flanked by intra and intercellular domains. While the structure of the transmembrane domain has been well characterized, little is known about the structure of the flanking domains and their role in C99 processing by γ-secretase. To gain insight into the structure of full-length C99, REMD simulations were performed for monomeric C99 in model membranes of varying thickness. We find equilibrium ensembles of C99 from simulation agree with experimentally-inferred residue insertion depths and protein backbone chemical shifts. In thin membranes, the transmembrane domain structure is correlated with extra-membrane structural states. Mean and variance of the transmembrane and G 37 G 38 hinge angles are found to increase with thinning membrane. The Nterminus of C99 forms β-strands that may seed aggregation of Aβ on the membrane surface, promoting amyloid formation. The N-terminus, which forms α-helices that interact with the nicastrin domain of γ-secretase. The C-terminus of C99 becomes more α-helical as the membrane thickens, forming structures that may be suitable for binding by cytoplasmic proteins, while Cterminal residues essential to cytotoxic function become α-helical as the membrane thins. The heterogeneous but discrete extra-membrane domain states analyzed here open the path to new investigations of the role of C99 structure and membrane in amyloidogenesis.All rights reserved. No reuse allowed without permission.

Understanding familial Alzheimer's disease: The fit‐stay‐trim mechanism of γ‐secretase

“…The FIST model also explains in a simple way why the amount of long and short Aβ depends on membrane thickness (which favors the more compact precise cleavage) 105,119 and protein‐conformation‐dependent drug binding 120 . In an important study, Winkler et al showed that membrane thickness directly reduces the production of longer Aβ 42/43 by pathogenic mutations 121 According to the FIST model, fAD PS1 mutations impair the stability and hydrophobic packing of the enzyme in the membrane, that is, fAD mutations shift the two‐state equilibrium toward the open state (looser squeezing by the “fist”), thus producing less stable enzyme–substrate complexes, less activity, earlier release, imprecise cleavage, and relatively more of the longer Aβ 60,88,89,114 .…”

Molecular dynamics of C99-bound γ-secretase reveal two binding modes with distinct compactness, stability, and active-site retention: implications for Aβ production

“…The initial full-length C99 structure was obtained from a recent study [14]. The structure of C99 is sensitive to membrane lipid composition, and thus we used the structure of fragment 23−55 sampled by Dominguez et al (2016) [40], which is in agreement with the experimental data.…”

“…During the last decade, various computational and experimental studies have explored the transmembrane domain (C99-TMD) structure and dynamics of C99 [12][13][14][15]. Some studies have identified specific residues of the extra-membrane segment of C99 that may affect Aβ production, and some of these may change upon mutations leading to AD [16][17][18].…”

“…protein folding [36][37][38]. More importantly, atomicresolution dynamics are not achievable in any other way than from MD and thus MD has been instrumental in understanding proteins within realistic membrane environments [13,14,39,40].…”

Ion channel formation by N-terminally truncated Aβ (4–42): relevance for the pathogenesis of Alzheimer's disease

“…The post translationally modified peptides also include different N-and C-terminally truncated Aβ species that have been identified in animal models and AD patients [5,6] and are likely generated by a number of Aβ-degrading enzymes among them neprilysin, insulin degrading-and endothelin converting-enzymes, plasmin and matrix metalloproteases [7,8]. In this sense, biochemical and mass spectrometry analyses have revealed the presence of a variety of C-terminally truncated Aβ species in human brain interstitial fluid (ISF) and cerebrospinal fluid (CSF), among them Aβ 1-16 , Aβ 1-30 , Aβ 1-34 , and Aβ 1-37 [9][10][11][12] likely representing the proteolytic action of local resident enzymes.…”