Homodimerization Protects the Amyloid Precursor Protein C99 Fragment from Cleavage by γ-Secretase

Winkler, Edith; Julius, Ayse; Steiner, Harald; Langosch, Dieter

doi:10.1021/acs.biochem.5b00986

Cited by 43 publications

(41 citation statements)

References 30 publications

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“…(1) Mutations that (de)stabilize the GSEC-Aβ n complex, situated at the interface between Another topic often discussed in the context of APP processing is APP homodimerization. [50][51][52] Our study strongly disfavors the proteolytic cleavage of APP homodimers, as the binding model suggests that there is not enough space at the active site cavity to accommodate such dimers.…”

Section: Discussionmentioning

confidence: 88%

“…Another topic controversially discussed in the context of APP processing is APP homodimerization. [51][52][53] Our study strongly disfavors the proteolytic cleavage of APP homodimers, as the binding model suggests that there is not enough space at the active site cavity to accom- Table 6: Overview over the simulations that have been conducted in the course of this investigation. "GSEC" indicates if the TMDs of GSEC were present in the simulation box, while ECD indicates the presence (or absence) of the NCT ECD.…”

Section: Discussionmentioning

confidence: 99%

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Structural Modeling of γ-Secretase Aβ_n Complex Formation and Substrate Processing

Hitzenberger

Zacharias

2018

Preprint

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The human intra-membrane aspartyl protease γ-secretase (GSEC) cleaves single-span transmembrane helices including the C-terminal fragment of the amyloid precursor protein (APP). This substrate is cleaved at an initial -site followed by successive processing (trimming) events mostly in steps of three amino acids. GSEC is responsible for the formation of N-terminal APP amyloid-β (Aβ) peptides of different length (e.g. Aβ 42 ) that can form aggregates involved in neuro-degenerative diseases. The molecular mechanism of GSEC-APP substrate recognition is a key for understanding how different peptide products are formed and could help in designing inhibitors. Based on the known structure of apo GSEC and a cleavable APP fragment we have generated putative structural models of the initial binding in three different possible modes using extensive Molecular Dynamics (MD) simulations. The binding mode with the substrate helix located in a cleft between the transmembrane helices 2 and 3 of the presenilin subunit was identified as a most likely binding mode. Based on this arrangement the processing steps were investigated using restraint MD simulations to pull the scissile bond (for each processing step) into a transition like (cleavable) state. It allowed us to analyze in detail the motions and energetic contributions of participating residues. The structural model agrees qualitatively well with the influence of many substitutions and substrate mutations in GSEC. It can also explain effects of inhibitors, cross-linking and spectroscopic data on GSEC substrate binding and can serve as working model for the future planning of structural and biochemical studies.

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Section: Discussionmentioning

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Structural Modeling of γ-Secretase Aβ_n Complex Formation and Substrate Processing

Hitzenberger

Zacharias

2018

Preprint

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“…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 depend on a number of factors including peptide sequence (9-13) and lipid composition of the membrane environment (14,15). However, recent studies have questioned the role (16) and importance (17,18) of homodimerization in the processing of full-length C99 by γ-secretase. Regardless of whether C99 homodimer is a natural substrate for γ-secretase, its ready formation both in vitro and in vivo raises the question, what is the functional role of the dimer?…”

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confidence: 99%

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

Domı́nguez

Foster

Straub

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

116

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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...

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“…Very recent results indicate that the PTB2 rather than the WW domain is important for the nuclear localization of Fe65 (Koistinen et al, 2017). Secretase cleavage is influenced by various aspects like APP cellular localization (Haass et al, 2012), APP dimerization (Winkler et al, 2015) and APP and Fe65 phosphorylation (Bukhari et al, 2016). Due to the tight and extended interaction involving 2/3 of the AICD (Radzimanowski et al, 2008c) and co-localization studies (von Rotz et al, 2004), we favor co-migration without degradation of the AICD.…”

Section: Discussionmentioning

confidence: 99%

Fe65-PTB2 Dimerization Mimics Fe65-APP Interaction

Feilen

Haubrich

Strecker

et al. 2017

Front. Mol. Neurosci.

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Physiological function and pathology of the Alzheimer’s disease causing amyloid precursor protein (APP) are correlated with its cytosolic adaptor Fe65 encompassing a WW and two phosphotyrosine-binding domains (PTBs). The C-terminal Fe65-PTB2 binds a large portion of the APP intracellular domain (AICD) including the GYENPTY internalization sequence fingerprint. AICD binding to Fe65-PTB2 opens an intra-molecular interaction causing a structural change and altering Fe65 activity. Here we show that in the absence of the AICD, Fe65-PTB2 forms a homodimer in solution and determine its crystal structure at 2.6 Å resolution. Dimerization involves the unwinding of a C-terminal α-helix that mimics binding of the AICD internalization sequence, thus shielding the hydrophobic binding pocket. Specific dimer formation is validated by nuclear magnetic resonance (NMR) techniques and cell-based analyses reveal that Fe65-PTB2 together with the WW domain are necessary and sufficient for dimerization. Together, our data demonstrate that Fe65 dimerizes via its APP interaction site, suggesting that besides intra- also intermolecular interactions between Fe65 molecules contribute to homeostatic regulation of APP mediated signaling.

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Homodimerization Protects the Amyloid Precursor Protein C99 Fragment from Cleavage by γ-Secretase

Cited by 43 publications

References 30 publications

Structural Modeling of γ-Secretase Aβ_n Complex Formation and Substrate Processing

Structural Modeling of γ-Secretase Aβ_n Complex Formation and Substrate Processing

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

Fe65-PTB2 Dimerization Mimics Fe65-APP Interaction

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Homodimerization Protects the Amyloid Precursor Protein C99 Fragment from Cleavage by γ-Secretase

Cited by 43 publications

References 30 publications

Structural Modeling of γ-Secretase Aβn Complex Formation and Substrate Processing

Structural Modeling of γ-Secretase Aβn Complex Formation and Substrate Processing

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

Fe65-PTB2 Dimerization Mimics Fe65-APP Interaction

Contact Info

Product

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Structural Modeling of γ-Secretase Aβ_n Complex Formation and Substrate Processing

Structural Modeling of γ-Secretase Aβ_n Complex Formation and Substrate Processing