Mechanism of Tripeptide Trimming of Amyloid β-Peptide 49 by γ-Secretase

Bhattarai, Apurba; Devkota, Sujan; Do, Hung Nguyen; Wang, Jinan; Bhattarai, Sanjay; Wolfe, Michael S.; Miao, Yinglong

doi:10.1021/jacs.1c10533

Mechanism of Tripeptide Trimming of Amyloid β-Peptide 49 by γ-Secretase

Journal Article · 04 April 2022 · Journal of the American Chemical Society

DOI:https://doi.org/10.1021/jacs.1c10533· OSTI ID:1982051

Bhattarai, Apurba; Devkota, Sujan; Do, Hung Nguyen; ; Bhattarai, Sanjay; ;

Not provided.

Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC02-05CH11231

OSTI ID:: 1982051

Journal Information:: Journal of the American Chemical Society, Vol. 144, Issue 14; ISSN 0002-7863

Publisher:: American Chemical Society (ACS)

Country of Publication:: United States

Language:: English

References (44)

Current understanding of Alzheimer’s disease diagnosis and treatment Weller, Jason; Budson, Andrew F1000Research, Vol. 7 https://doi.org/10.12688/f1000research.14506.1	journal	July 2018
Successive cleavage of β-amyloid precursor protein by γ-secretase Funamoto, Satoru; Tagami, Shinji; Okochi, Masayasu Seminars in Cell & Developmental Biology, Vol. 105 https://doi.org/10.1016/j.semcdb.2020.04.002	journal	September 2020
Proteomic Profiling of γ-Secretase Substrates and Mapping of Substrate Requirements Hemming, Matthew L.; Elias, Joshua E.; Gygi, Steven P. PLoS Biology, Vol. 6, Issue 10 https://doi.org/10.1371/journal.pbio.0060257	journal	October 2008
The substrate repertoire of γ-secretase/presenilin Güner, Gökhan; Lichtenthaler, Stefan F. Seminars in Cell & Developmental Biology, Vol. 105 https://doi.org/10.1016/j.semcdb.2020.05.019	journal	September 2020
Distinct Intramembrane Cleavage of the β-Amyloid Precursor Protein Family Resembling γ-Secretase-like Cleavage of Notch Gu, Yongjun; Misonou, Hiroaki; Sato, Toru Journal of Biological Chemistry, Vol. 276, Issue 38 https://doi.org/10.1074/jbc.C100357200	journal	September 2001
Longer Forms of Amyloid Protein: Implications for the Mechanism of Intramembrane Cleavage by -Secretase Qi-Takahara, Y. Journal of Neuroscience, Vol. 25, Issue 2 https://doi.org/10.1523/JNEUROSCI.1575-04.2005	journal	January 2005
-Secretase: Successive Tripeptide and Tetrapeptide Release from the Transmembrane Domain of -Carboxyl Terminal Fragment Takami, M.; Nagashima, Y.; Sano, Y. Journal of Neuroscience, Vol. 29, Issue 41 https://doi.org/10.1523/JNEUROSCI.2362-09.2009	journal	October 2009
The amyloid hypothesis of Alzheimer's disease at 25 years Selkoe, Dennis J.; Hardy, John EMBO Molecular Medicine, Vol. 8, Issue 6 https://doi.org/10.15252/emmm.201606210	journal	March 2016
The Genetics of Alzheimer Disease Tanzi, R. E. Cold Spring Harbor Perspectives in Medicine, Vol. 2, Issue 10 https://doi.org/10.1101/cshperspect.a006296	journal	July 2012
The amyloid-beta forming tripeptide cleavage mechanism of γ-secretase Bolduc, David M.; Montagna, Daniel R.; Seghers, Matthew C. eLife, Vol. 5 https://doi.org/10.7554/eLife.17578	journal	August 2016
Structural basis of Notch recognition by human γ-secretase Yang, Guanghui; Zhou, Rui; Zhou, Qiang Nature, Vol. 565, Issue 7738 https://doi.org/10.1038/s41586-018-0813-8	journal	December 2018
Recognition of the amyloid precursor protein by human γ-secretase Zhou, Rui; Yang, Guanghui; Guo, Xuefei Science, Vol. 363, Issue 6428 https://doi.org/10.1126/science.aaw0930	journal	January 2019
Structural Modeling of γ-Secretase Aβ_n Complex Formation and Substrate Processing Hitzenberger, M.; Zacharias, M. ACS Chemical Neuroscience, Vol. 10, Issue 3 https://doi.org/10.1021/acschemneuro.8b00725	journal	January 2019
Modulating Hinge Flexibility in the APP Transmembrane Domain Alters γ-Secretase Cleavage Götz, Alexander; Mylonas, Nadine; Högel, Philipp Biophysical Journal, Vol. 116, Issue 11 https://doi.org/10.1016/j.bpj.2019.04.030	journal	June 2019
Molecular dynamics of C99-bound γ-secretase reveal two binding modes with distinct compactness, stability, and active-site retention: implications for Aβ production Dehury, Budheswar; Tang, Ning; Kepp, Kasper P. Biochemical Journal, Vol. 476, Issue 7 https://doi.org/10.1042/BCJ20190023	journal	April 2019
Membrane Dynamics of γ-Secretase Provides a Molecular Basis for β-Amyloid Binding and Processing Somavarapu, Arun Kumar; Kepp, Kasper P. ACS Chemical Neuroscience, Vol. 8, Issue 11 https://doi.org/10.1021/acschemneuro.7b00208	journal	August 2017
Increased H-Bond Stability Relates to Altered ε-Cleavage Efficiency and Aβ Levels in the I45T Familial Alzheimer’s Disease Mutant of APP Götz, Alexander; Högel, Philipp; Silber, Mara Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-41766-1	journal	March 2019
γ-Secretase Studied by Atomistic Molecular Dynamics Simulations: Global Dynamics, Enzyme Activation, Water Distribution and Lipid Binding Hitzenberger, Manuel; Zacharias, Martin Frontiers in Chemistry, Vol. 6 https://doi.org/10.3389/fchem.2018.00640	journal	January 2019
Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach Aguayo-Ortiz, Rodrigo; Chávez-García, Cecilia; Straub, John E. Chemical Science, Vol. 8, Issue 8 https://doi.org/10.1039/C7SC00980A	journal	January 2017
Allosteric Modulation of Intact γ-Secretase Structural Dynamics Lee, Ji Young; Feng, Zhiwei; Xie, Xiang-Qun Biophysical Journal, Vol. 113, Issue 12 https://doi.org/10.1016/j.bpj.2017.10.012	journal	December 2017
Mapping the Binding Site of BMS-708163 on γ-Secretase with Cleavable Photoprobes Gertsik, Natalya; am Ende, Christopher W.; Geoghegan, Kieran F. Cell Chemical Biology, Vol. 24, Issue 1 https://doi.org/10.1016/j.chembiol.2016.12.006	journal	January 2017
Extracellular interface between APP and Nicastrin regulates Aβ length and response to γ‐secretase modulators Petit, Dieter; Hitzenberger, Manuel; Lismont, Sam The EMBO Journal, Vol. 38, Issue 12 https://doi.org/10.15252/embj.2019101494	journal	May 2019
Uncovering the Binding Mode of γ -Secretase Inhibitors Hitzenberger, Manuel; Zacharias, Martin ACS Chemical Neuroscience, Vol. 10, Issue 8 https://doi.org/10.1021/acschemneuro.9b00272	journal	June 2019
A computer-simulated mechanism of familial Alzheimer’s disease: Mutations enhance thermal dynamics and favor looser substrate-binding to γ-secretase Dehury, Budheswar; Somavarapu, Arun K.; Kepp, Kasper P. Journal of Structural Biology, Vol. 212, Issue 3 https://doi.org/10.1016/j.jsb.2020.107648	journal	December 2020
Side-by-side comparison of Notch- and C83 binding to γ-secretase in a complete membrane model at physiological temperature Dehury, Budheswar; Tang, Ning; Mehra, Rukmankesh RSC Advances, Vol. 10, Issue 52 https://doi.org/10.1039/D0RA04683C	journal	January 2020
How Mutations Perturb γ-Secretase Active Site Studied by Free Energy Simulations Chen, Shu-Yu; Zacharias, Martin ACS Chemical Neuroscience, Vol. 11, Issue 20 https://doi.org/10.1021/acschemneuro.0c00440	journal	September 2020
Protein Predictive Modeling and Simulation of Mutations of Presenilin-1 Familial Alzheimer’s Disease on the Orthosteric Site Soto-Ospina, Alejandro; Araque Marín, Pedronel; Bedoya, Gabriel Frontiers in Molecular Biosciences, Vol. 8 https://doi.org/10.3389/fmolb.2021.649990	journal	June 2021
The Role of Cholesterol in Amyloidogenic Substrate Binding to the γ-Secretase Complex Orzeł, Urszula; Jakowiecki, Jakub; Młynarczyk, Krzysztof Biomolecules, Vol. 11, Issue 7 https://doi.org/10.3390/biom11070935	journal	June 2021
Mechanisms of γ-Secretase Activation and Substrate Processing Bhattarai, Apurba; Devkota, Sujan; Bhattarai, Sanjay ACS Central Science, Vol. 6, Issue 6 https://doi.org/10.1021/acscentsci.0c00296	journal	June 2020
Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation Miao, Yinglong; Feher, Victoria A.; McCammon, J. Andrew Journal of Chemical Theory and Computation, Vol. 11, Issue 8 https://doi.org/10.1021/acs.jctc.5b00436	journal	July 2015
Familial Alzheimer’s disease mutations in amyloid protein precursor alter proteolysis by γ-secretase to increase amyloid β-peptides of ≥45 residues Devkota, Sujan; Williams, Todd D.; Wolfe, Michael S. Journal of Biological Chemistry, Vol. 296 https://doi.org/10.1016/j.jbc.2021.100281	journal	January 2021
Intramembrane Proteolysis of β-Amyloid Precursor Protein by γ-Secretase Is an Unusually Slow Process Kamp, Frits; Winkler, Edith; Trambauer, Johannes Biophysical Journal, Vol. 108, Issue 5 https://doi.org/10.1016/j.bpj.2014.12.045	journal	March 2015
Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding Wang, Jinan; Miao, Yinglong The Journal of Chemical Physics, Vol. 153, Issue 15 https://doi.org/10.1063/5.0021399	journal	October 2020
Role of Electrostatic Interactions in Binding of Peptides and Intrinsically Disordered Proteins to Their Folded Targets. 1. NMR and MD Characterization of the Complex between the c-Crk N-SH3 Domain and the Peptide Sos Xue, Yi; Yuwen, Tairan; Zhu, Fangqiang Biochemistry, Vol. 53, Issue 41 https://doi.org/10.1021/bi500904f	journal	October 2014
Presenilin 1 is linked with γ-secretase activity in the detergent solubilized state Li, Yue-Ming; Lai, Ming-Tain; Xu, Min Proceedings of the National Academy of Sciences, Vol. 97, Issue 11 https://doi.org/10.1073/pnas.110126897	journal	May 2000
Mutations in amyloid precursor protein affect its interactions with presenilin/γ-secretase Herl, Lauren; Thomas, Anne V.; Lill, Christina M. Molecular and Cellular Neuroscience, Vol. 41, Issue 2 https://doi.org/10.1016/j.mcn.2009.02.008	journal	June 2009
Mechanism of the cleavage specificity of Alzheimer’s disease γ-secretase identified by phenylalanine-scanning mutagenesis of the transmembrane domain of the amyloid precursor protein Lichtenthaler, Stefan F.; Wang, Rong; Grimm, Heike Proceedings of the National Academy of Sciences, Vol. 96, Issue 6 https://doi.org/10.1073/pnas.96.6.3053	journal	March 1999
Autosomal-dominant Alzheimer's disease mutations at the same codon of amyloid precursor protein differentially alter Aβ production Suárez-Calvet, Marc; Belbin, Olivia; Pera, Marta Journal of Neurochemistry, Vol. 128, Issue 2 https://doi.org/10.1111/jnc.12466	journal	October 2013
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data Roe, Daniel R.; Cheatham, Thomas E. Journal of Chemical Theory and Computation, Vol. 9, Issue 7 https://doi.org/10.1021/ct400341p	journal	June 2013
Advancing research diagnostic criteria for Alzheimer's disease: the IWG-2 criteria Dubois, Bruno; Feldman, Howard H.; Jacova, Claudia The Lancet Neurology, Vol. 13, Issue 6 https://doi.org/10.1016/S1474-4422(14)70090-0	journal	June 2014
Dissociation between the Processivity and Total Activity of γ-Secretase: Implications for the Mechanism of Alzheimer's Disease-Causing Presenilin Mutations Quintero-Monzon, Omar; Martin, Morgan M.; Fernandez, Marty A. Biochemistry, Vol. 50, Issue 42 https://doi.org/10.1021/bi2007146	journal	September 2011
Alzheimer Presenilin-1 Mutations Dramatically Reduce Trimming of Long Amyloid β-Peptides (Aβ) by γ-Secretase to Increase 42-to-40-Residue Aβ Fernandez, Marty A.; Klutkowski, Julia A.; Freret, Taylor Journal of Biological Chemistry, Vol. 289, Issue 45 https://doi.org/10.1074/jbc.M114.581165	journal	November 2014
Structural basis of γ-secretase inhibition and modulation by small molecule drugs Yang, Guanghui; Zhou, Rui; Guo, Xuefei Cell, Vol. 184, Issue 2 https://doi.org/10.1016/j.cell.2020.11.049	journal	January 2021
APP717 missense mutation affects the ratio of amyloid beta protein species (A beta 1-42/43 and a beta 1-40) in familial Alzheimer's disease brain Tamaoka, A.; Odaka, A.; Ishibashi, Y. Journal of Biological Chemistry, Vol. 269, Issue 52 https://doi.org/10.1016/S0021-9258(20)30050-8	journal	December 1994

Similar Records

Effects of presenilin-1 familial Alzheimer’s disease mutations on γ-secretase activation for cleavage of amyloid precursor protein

Journal Article · 2023 · Communications Biology · OSTI ID:2422941

Do, Hung N.; Devkota, Sujan; Bhattarai, Apurba; +2 more

CD147 is a regulatory subunit of the gamma-secretase complex inAlzheimer's disease amyloid beta-peptide production

Journal Article · 2005 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:861515

Zhou, Shuxia; Zhou, Hua; Walian, Peter J; +1 more

Ferrous iron formation following the co-aggregation of ferric iron and the Alzheimer's disease peptide β-amyloid (1–42)

Journal Article · 2014 · Journal of the Royal Society Interface · OSTI ID:1625586

Everett, J.; Céspedes, E.; Shelford, L. R.; +7 more

Related Subjects

Chemistry

Mechanism of Tripeptide Trimming of Amyloid β-Peptide 49 by γ-Secretase

Citation Formats

References (44)

Similar Records

Related Subjects