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

Hitzenberger, Manuel; Zacharias, Martin

doi:10.1101/500488

Cited by 6 publications

(7 citation statements)

References 72 publications

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“…To make sure that the substrate remains in a conformation that is cleavable during the sampling, a transition state‐like geometry (Singh et al , ) at the interface between the cleavage (C99‐V46 and C99‐I47) and the active site (PSEN‐D257 and PSEN‐D385) was stabilized by the use of appropriate harmonic restraints with weak force constants (for details, cf. to the previous study; Hitzenberger & Zacharias, ). The complex of GSEC‐I242E and GSEC‐Aβ49 was placed in a bilayer of 301 POPC molecules and solvated in a 0.15 M KCl solution containing 53,829 water molecules.…”

Section: Methodssupporting

confidence: 67%

“…The NCT‐I242E mutant molecular dynamics (MD) simulation conducted for this study was based on a 3000‐ns‐long simulation of the APP‐derived substrate Aβ49 in complex with WT (human) GSEC, part of a computational study of GSEC‐Aβn complexes (Hitzenberger & Zacharias, ). The structures were based on PDB entries 5FN2 (Bai et al , ) (GSEC) and 2LP1 (Barrett et al , ) (APP C99 ).…”

Section: Methodsmentioning

confidence: 99%

“…The implicit lipid slab was centered around the mean center of mass (COM) of the explicit bilayer in the simulation. The (internal) permittivity of the protein was assumed to be ε = 1.0 and the salt concentration was set to 0.15 M. In order to estimate the influence of the I242E mutation to ΔΔG bind , 1,500 frames of the simulation generated for this study were compared to the same amount of frames of the previously performed WT GSEC‐Aβ49 simulation (Hitzenberger & Zacharias, ). Due to the large system sizes and the enormous computational effort involved in estimating changes of entropy upon binding, only PBSA‐intrinsic solvation entropies have been considered.…”

Section: Methodsmentioning

confidence: 99%

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Extracellular interface between APP and Nicastrin regulates Aβ length and response to γ‐secretase modulators

et al. 2019

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γ‐Secretase complexes ( GSEC s) are multimeric membrane proteases involved in a variety of physiological processes and linked to Alzheimer's disease ( AD ). Presenilin ( PSEN , catalytic subunit), Nicastrin ( NCT ), Presenilin Enhancer 2 ( PEN ‐2), and Anterior Pharynx Defective 1 ( APH 1) are the essential subunits of GSEC s. Mutations in PSEN and the Amyloid Precursor Protein ( APP ) cause early‐onset AD . GSEC s successively cut APP to generate amyloid‐β (Aβ) peptides of various lengths. AD ‐causing mutations destabilize GSEC ‐ APP /Aβ n interactions and thus enhance the production of longer Aβs, which elicit neurotoxic events underlying pathogenesis. Here, we investigated the molecular strategies that anchor GSEC and APP /Aβ n during the sequential proteolysis. Our studies reveal that a direct interaction between NCT ectodomain and APP C99 influences the stability of GSEC ‐Aβn assemblies and thereby modulates Aβ length. The data suggest a potential link between single‐nucleotide variants in NCSTN and AD risk. Furthermore, our work indicates that an extracellular interface between the protease ( NCT , PSEN ) and the substrate ( APP ) represents the target for compounds ( GSM s) modulating Aβ length. Our findings may guide future rationale‐based drug discovery efforts.

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Section: Methodssupporting

confidence: 67%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Extracellular interface between APP and Nicastrin regulates Aβ length and response to γ‐secretase modulators

et al. 2019

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“…Cryo‐electron microscopy (cryo‐EM) experiences a revolution in terms of sample control and resolution 101,102 . With the advent of cryo‐electron microscopy structures of γ‐secretase, 47,77–80,103 many computational simulation studies were undertaken to understand the mechanism of the protein and the function of drugs directed toward it 14,81,84,86–88,104–111 …”

Section: Molecular Simulations Of γ‐Secretasementioning

confidence: 99%

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

Mehra

Kepp

2021

WIREs Comput Mol Sci

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Understanding Alzheimer's disease is a central challenge of the 21st century, as the disease affects tens of millions of people and kills a million people each year, with current drugs having modest effect. This article reviews how computational science integrating new cryo‐electron microscopy structures and biochemical and clinical data has led to a causative model of familial Alzheimer's disease (fAD). The model's basis is open and compact conformational states of the membrane protease γ‐secretase, controlled by transmembrane helix “fingers” that hold the substrate either tightly or loosely. The two states are in thermal equilibrium and lead to different amounts of long and short Aβ peptides, explaining the much‐debated Aβ42/Aβ40 ratio. Pathogenic mutations shift the equilibrium toward the open state by reducing the stability and hydrophobic packing of the enzyme‐substrate complex, which increases toxic Aβ42 and other longer peptide forms compared with Aβ40. In contrast, drugs that selectively target longer, pathogenic Aβ peptides should preferentially stabilize the compact state to reverse this tendency. The model may explain how inherited mutations cause fAD and provides a molecular roadmap for the development of γ‐secretase modulators, one of the most promising causative treatment strategies in current Alzheimer research. In summary, we showcase the power of modern multiscale computational science in integrating biochemical, protein‐structural, and clinical data to elucidate complex disease mechanisms. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Data Science > Chemoinformatics

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“…However, artificial structural constraints were included that could affect the enzyme-substrate interactions. Molecular dynamics (MD) simulations have proven useful in understanding the structural dynamics of γ-secretase, notably the enzyme-substrate interactions (13)(14)(15)(16)(17). Recently, we computationally restored the wildtype (WT) enzyme-substrate co-structure and applied all-atom simulations using the Gaussian accelerated molecular dynamics (GaMD) method to build the first dynamic model of γ-secretase activation (18).…”

Section: Introductionmentioning

confidence: 99%

Mechanism of Tripeptide Trimming by γ-Secretase

Bhattarai

Devkota

Nguyen

et al. 2021

Preprint

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The membrane-embedded γ-secretase complex processively cleaves within the transmembrane domain of amyloid precursor protein (APP) to produce 37-to-43-residue amyloid β-peptides (Aβ) of Alzheimer’s disease (AD). Despite its importance in pathogenesis, the mechanism of processive proteolysis by γ-secretase remains poorly understood. Here, mass spectrometry and western blotting were used to quantify the efficiency of the first tripeptide trimming step (Aβ49→Aβ46) of wildtype (WT) and familial AD (FAD) mutant APP substrate. In comparison to WT APP, the efficiency of this first trimming step was slightly higher for the I45F, A42T and V46F APP FAD mutants, but substantially diminished for the I45T and T48P mutants. In parallel with biochemical experiments, all-atom simulations using a novel Peptide Gaussian accelerated molecular dynamics (Pep-GaMD) method were applied to investigate tripeptide trimming of Aβ49 by γ-secretase. The starting structure was active γ-secretase bound to Aβ49 and APP intracellular domain (AICD), as generated from our previous study that captured activation of γ-secretase for the initial endoproteolytic cleavage of APP (Bhattarai et al., ACS Cent Sci, 2020, 6:969-983). Pep-GaMD simulations captured remarkable structural rearrangements of both the enzyme and substrate, in which hydrogen-bonded catalytic aspartates and water became poised for tripeptide trimming of Aβ49 to Aβ46. These structural changes required a positively charged N-terminus of endoproteolytic coproduct AICD, which could dissociate during conformational rearrangements of the protease and Aβ49. The simulation findings were highly consistent with biochemical experimental data. Taken together, our complementary biochemical experiments and Pep-GaMD simulations have enabled elucidation of the mechanism of tripeptide trimming by γ-secretase.Significance statementProduction of amyloid β-peptide (Aβ) of Alzheimer’s disease (AD) from its precursor protein requires a series of proteolytic events carried out by the membrane-embedded γ-secretase complex. Mutations in the substrate and enzyme that produce Aβ cause hereditary AD and these mutations affect tripeptide trimming of initially formed long Aβ peptides by γ-secretase. Little is known about the structural mechanism of this trimming process. Here we have developed a molecular dynamics model for the first step of trimming (Aβ49 to Aβ46) by γ-secretase. Conformational changes in the enzyme-substrate complex to set up this trimming step require the presence of N-terminally charged endoproteolytic cleavage co-product. Computational effects of AD-causing mutations in Aβ49 on the trimming process were validated through biochemical experiments.

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

Cited by 6 publications

References 72 publications

Extracellular interface between APP and Nicastrin regulates Aβ length and response to γ‐secretase modulators

Extracellular interface between APP and Nicastrin regulates Aβ length and response to γ‐secretase modulators

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

Mechanism of Tripeptide Trimming by γ-Secretase

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