Impact of membrane lipid composition on the structure and stability of the transmembrane domain of amyloid precursor protein

Abstract

Cleavage of the amyloid precursor protein (APP) by γ-secretase is a crucial first step in the evolution of Alzheimer's disease. To discover the cleavage mechanism, it is urgent to predict the structures of APP monomers and dimers in varying membrane environments. We determined the structures of the C99 23−55 monomer and homodimer as a function of membrane lipid composition using a multiscale simulation approach that blends atomistic and coarsegrained models. We demonstrate that the C99 23−55 homodimer structures form a heterogeneous ensemble with multiple conformational states, each stabilized by characteristic interpeptide interactions. The relative probabilities of each conformational state are sensitive to the membrane environment, leading to substantial variation in homodimer peptide structure as a function of membrane lipid composition or the presence of an anionic lipid environment. In contrast, the helicity of the transmembrane domain of monomeric C99 1−55 is relatively insensitive to the membrane lipid composition, in agreement with experimental observations. The dimer structures of human EphA2 receptor depend on the lipid environment, which we show is linked to the location of the structural motifs in the dimer interface, thereby establishing that both sequence and membrane composition modulate the complete energy landscape of membrane-bound proteins. As a by-product of our work, we explain the discrepancy in structures predicted for C99 congener homodimers in membrane and micelle environments. Our study provides insight into the observed dependence of C99 protein cleavage by γ-secretase, critical to the formation of amyloid-β protein, on membrane thickness and lipid composition.nderstanding the structural and thermodynamic properties of transmembrane (TM) helical dimers is of fundamental importance to molecular biology. It is known that the association of "bitopic" proteins, having single pass TM helical domains, is essential to immunoreceptors and protein kinases that play critical roles in cellular function. Computational and experimental studies have provided insight into the role of sequence-specific interactions stabilizing helix dimerization (1, 2). Examples include the heptad repeat motif responsible for the stability of coiled-coils in GCN4 phospholamban (3) and the M2 proton channel (4), the role of the GxxxG motif in stabilizing TM helix-helix association in systems including the glycophorin A (GpA) homodimer (5, 6), found in the human erythrocyte membrane, and GxxxG and heptad repeat motifs, which play a role in stabilizing homodimers of APP-C99 (C99), the 99-aa C-terminal fragment of the amyloid precursor protein (APP) (7,8).The amyloid β (Aβ) peptide aggregation pathway, known to be crucial to the evolution of Alzheimer's disease (AD), begins with the cleavage of C99 by γ-secretase leading to the formation of a number of isoforms of Aβ. The formation of homodimers of C99 has been proposed to be critical to the mechanism by which C99 is cleaved by γ-secretase, a process that is known to dep...

Structure of APP-C991–99 and implications for role of extra-membrane domains in function and oligomerization

“…Heterogeneous but discrete structural states observed in the C99 C- and N-terminal extra-membrane regions of C99 are found to be unique to the specific membrane condition. This observation supports past work on C99 congeners in lipid bilayers[25–27] in which the specific lipid composition, membrane thickness, and membrane curvature were observed to impact C99 monomer and dimer structure. We observe the TMD and G 37 G 38 hinge angle means and variances to increase as the membrane thins.…”

“…al. [27] Onto this fragment, residues 1-22 and 56-99 were built using dihedral angles predicted via the TALOS+,[70] using the Cα, Cβ, C, N, and H chemical shifts reported for C99 in LMPG micelles. [30] To remove clashes and effectively move the C-Helix close to the membrane surface, the ψ angle of H 14 , located in the disordered loop of the N-teminus (see Figure 1), was adjusted to 180° and the φ angle of Q 82 was adjusted to 180°.…”

“…[25] It is likely that magnitude of fluctuations in the hinge may enhance Aβ 42 and Aβ 43 production. [8] Additionally, simulation studies have revealed[20,26,27] that the GG hinge is an important structural feature for C99 dimers, with the angle of the hinge varying for several distinct dimerization motifs. It has further been noted that the membrane thickness can preferentially stabilize and environmentally select specific C99 dimer strucutres.…”

“…[19,20,27] We employed replica-exchange molecular dynamics (REMD)[68] to sample hundreds of nanoseconds of C99 dynamics at physiological temperatures in 30, 35, and 40 Å-thick membranes modeled using the GBSW implicit solvation method. [69]…”

Biocompatible and blood–brain barrier permeable carbon dots for inhibition of Aβ fibrillation and toxicity, and BACE1 activity

“…To obtain more details about the Aβ fibrillation by C-Dots, molecular dynamics simulations with the Martini coarse-grained force field 26 were performed to study the interaction between C-Dots and Aβ monomers, which has been a valuable tool for the study of Aβ peptides. 27–29 In this study, the surface of C-Dots has a high oxygen content, 24 which indicates high hydrophilicity. In order to see the role of the hydrophilic surface, C-Dot models with both hydrophilic and hydrophobic C-Dots were constructed.…”