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

Structure and mechanism of the γ-secretase intramembrane protease complex

(2022) Michael S. Wolfe et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2022) Apurba Bhattarai et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A thermodynamic investigation of amyloid precursor protein processing by human γ-secretase

(2022) Xiaoli Lu et al.   Communications Biology

Familial Alzheimer’s disease mutations in amyloid protein precursor alter proteolysis by γ-secretase to increase amyloid β-peptides of >45 residues

(2021) Sujan Devkota et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Gaussian accelerated molecular dynamics: Principles and applications

(2021) Jinan Wang et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

The dynamics of γ-secretase and its substrates

(2020) Manuel Hitzenberger et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

CHARMM-GUI supports the Amber force fields

(2020) Jumin Lee et al.   JOURNAL OF CHEMICAL PHYSICS

The substrate repertoire of γ-secretase/presenilin

(2020) Gökhan Güner et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Mechanisms of γ-Secretase Activation and Substrate Processing

(2020) Apurba Bhattarai et al.   ACS Central Science

How Mutations Perturb γ-Secretase Active Site Studied by Free Energy Simulations

(2020) Shu-Yu Chen et al.   ACS Chemical Neuroscience

A computer-simulated mechanism of familial Alzheimer’s disease: Mutations enhance thermal dynamics and favor looser substrate-binding to γ-secretase

(2020) Budheswar Dehury et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structural basis of γ-secretase inhibition and modulation by small molecule drugs

(2020) Guanghui Yang et al.   CELL

Recognition of the amyloid precursor protein by human γ-secretase

(2019) Rui Zhou et al.   SCIENCE

γ-Secretase Studied by Atomistic Molecular Dynamics Simulations: Global Dynamics, Enzyme Activation, Water Distribution and Lipid Binding

(2019) Manuel Hitzenberger et al.   Frontiers in Chemistry

Structure and Function of the γ-Secretase Complex

(2019) Michael S. Wolfe   BIOCHEMISTRY

Aβ43‐producing PS 1 FAD mutants cause altered substrate interactions and respond to γ‐secretase modulation

(2019) Johannes Trambauer et al.   EMBO REPORTS

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans

(2018) Jumin Lee et al.   Journal of Chemical Theory and Computation

Structural basis of Notch recognition by human γ-secretase

(2018) Guanghui Yang et al.   NATURE

Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach

(2017) Rodrigo Aguayo-Ortiz et al.   Chemical Science

Generation and deposition of Aβ43 by the virtually inactive presenilin‐1 L435F mutant contradicts the presenilin loss‐of‐function hypothesis of Alzheimer's disease

(2016) Benedikt Kretner et al.   EMBO Molecular Medicine

The amyloid hypothesis of Alzheimer's disease at 25 years

(2016) Dennis J Selkoe et al.   EMBO Molecular Medicine

Loss of stability and hydrophobicity of presenilin 1 mutations causing Alzheimer's disease

(2016) Arun Kumar Somavarapu et al.   JOURNAL OF NEUROCHEMISTRY

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

The dynamic mechanism of presenilin-1 function: Sensitive gate dynamics and loop unplugging control protein access

(2016) Arun Kumar Somavarapu et al.   NEUROBIOLOGY OF DISEASE

Familial Alzheimer’s Disease Mutations in Presenilin Generate Amyloidogenic Aβ Peptide Seeds

(2016) Sarah Veugelen et al.   NEURON

The amyloid-beta forming tripeptide cleavage mechanism of γ-secretase

(2016) David M Bolduc et al.   eLife

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

(2015) Yinglong Miao et al.   Journal of Chemical Theory and Computation

Molecular dynamics simulation study reveals potential substrate entry path into γ-secretase/presenilin-1

(2015) Ren Kong et al.   JOURNAL OF STRUCTURAL BIOLOGY

An atomic structure of human γ-secretase

(2015) Xiao-chen Bai et al.   NATURE

Structural basis of human γ-secretase assembly

(2015) Linfeng Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sampling the conformational space of the catalytic subunit of human γ-secretase

(2015) Xiao-chen Bai et al.   eLife

Alzheimer Presenilin-1 Mutations Dramatically Reduce Trimming of Long Amyloid β-Peptides (Aβ) by γ-Secretase to Increase 42-to-40-Residue Aβ

(2014) Marty A. Fernandez et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

(2014) Yinglong Miao et al.   Journal of Chemical Theory and Computation

CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations

(2014) Emilia L. Wu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

γ-Secretase Modulators and Presenilin 1 Mutants Act Differently on Presenilin/γ-Secretase Function to Cleave Aβ42 and Aβ43

(2013) Masayasu Okochi et al.   Cell Reports

The Genetics of Alzheimer Disease

(2013) R. E. Tanzi   Cold Spring Harbor Perspectives in Medicine

The Amyloid State of Proteins in Human Diseases

(2012) David Eisenberg et al.   CELL

The mechanism of γ-Secretase dysfunction in familial Alzheimer disease

(2012) Lucía Chávez-Gutiérrez et al.   EMBO JOURNAL

Dissociation between the Processivity and Total Activity of γ-Secretase: Implications for the Mechanism of Alzheimer's Disease-Causing Presenilin Mutations

(2011) Omar Quintero-Monzon et al.   BIOCHEMISTRY

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

A Presenilin-1 Mutation Identified in Familial Alzheimer Disease with Cotton Wool Plaques Causes a Nearly Complete Loss of γ-Secretase Activity

(2010) Elizabeth A. Heilig et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

 -Secretase: Successive Tripeptide and Tetrapeptide Release from the Transmembrane Domain of  -Carboxyl Terminal Fragment

(2009) M. Takami et al.   JOURNAL OF NEUROSCIENCE

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY