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

Substrate recruitment of γ‐secretase and mechanism of clinical presenilin mutations revealed by photoaffinity mapping

(2016) Akio Fukumori et al.   EMBO JOURNAL

Conformational Changes in Transmembrane Domain 4 of Presenilin 1 Are Associated with Altered Amyloid-  42 Production

(2016) A. Tominaga et al.   JOURNAL OF NEUROSCIENCE

Nicastrin guards Alzheimer’s gate

(2016) Siniša Urban   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the transmembrane domain of human nicastrin-a component of γ-secretase

(2016) Yan Li et al.   Scientific Reports

CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field

(2015) Yifei Qi et al.   Journal of Chemical Theory and Computation

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

Cooperative Roles of Hydrophilic Loop 1 and the C-Terminus of Presenilin 1 in the Substrate-Gating Mechanism of  -Secretase

(2015) S. Takagi-Niidome et al.   JOURNAL OF NEUROSCIENCE

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

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

The topology of pen-2, a γ-secretase subunit, revisited: evidence for a reentrant loop and a single pass transmembrane domain

(2015) Xulun Zhang et al.   Molecular Neurodegeneration

An atomic structure of human γ-secretase

(2015) Xiao-chen Bai et al.   NATURE

Nicastrin functions to sterically hinder γ-secretase–substrate interactions driven by substrate transmembrane domain

(2015) David M. Bolduc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cleavage of amyloid precursor protein by an archaeal presenilin homologue PSH

(2015) Shangyu Dang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The dynamic conformational landscape of  -secretase

(2014) N. Elad et al.   JOURNAL OF CELL SCIENCE

g_mmpbsa—A GROMACS Tool for High-Throughput MM-PBSA Calculations

(2014) Rashmi Kumari et al.   Journal of Chemical Information and Modeling

CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations

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

Three-dimensional structure of human γ-secretase

(2014) Peilong Lu et al.   NATURE

Structure of nicastrin unveils secrets of  -secretase

(2014) D. M. Bolduc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal structure of the γ-secretase component nicastrin

(2014) Tian Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the Active Site Protonation State in Aspartic Proteases: Implications for Drug Design

(2013) Fredy Sussman et al.   CURRENT PHARMACEUTICAL DESIGN

Structural Biology of Presenilins and Signal Peptide Peptidases

(2013) Taisuke Tomita et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

(2013) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

Structural Interactions between Inhibitor and Substrate Docking Sites Give Insight into Mechanisms of Human PS1 Complexes

(2013) Yi Li et al.   STRUCTURE

Bendix: intuitive helix geometry analysis and abstraction

(2012) A. C. E. Dahl et al.   BIOINFORMATICS

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Structure of a presenilin family intramembrane aspartate protease

(2012) Xiaochun Li et al.   NATURE

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

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

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Novel Research Horizons for Presenilins and γ-Secretases in Cell Biology and Disease

(2010) Bart De Strooper et al.   Annual Review of Cell and Developmental Biology

Functional Analysis of the Transmembrane Domains of Presenilin 1

(2010) Naoto Watanabe et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

WIWS: a protein structure bioinformatics Web service collection

(2010) M. L. Hekkelman et al.   NUCLEIC ACIDS RESEARCH

Polarizable Water Model for the Coarse-Grained MARTINI Force Field

(2010) Semen O. Yesylevskyy et al.   PLoS Computational Biology

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

(2009) Xavier Periole et al.   Journal of Chemical Theory and Computation

Alzheimer's disease

(2009) Lennart Mucke   NATURE

How intramembrane proteases bury hydrolytic reactions in the membrane

(2009) Elinor Erez et al.   NATURE

Glu332in the Nicastrin Ectodomain Is Essential for γ-Secretase Complex Maturation but Not for Its Activity

(2008) Lucía Chávez-Gutiérrez et al.   JOURNAL OF BIOLOGICAL CHEMISTRY