The dynamics of γ-secretase and its substrates
Abbreviations
AA
amino acid
Aβ
amyloid-β
ACE
acetyl
AICD
amyloid intracellular domain
APH1
anterior-pharynx-defective-1
APP
amyloid-β precursor protein
CG
coarse-grained
COM
center of mass
cryo-EM
cryo-electron microscopy
DAPT
N-[N-(3,5-Difluorophenacyl)-L-alanyl]-S-phenylglycrine t-Butyl Ester
DHPC
di-hexaonyl phosphatidylcholine
DMPC
di-myristoyl phosphatidylcholine
DPC
dodecyl phosphocholine
ECD
extracellular domain, ectodomain
E-S complex
enzyme-substrate complex
FAD
familial Alzheimer’s disease
GSEC
γ-secretase
H-bonds
hydrogen bonds
ICD
intracellular domain
ITGB1
integrin β1
LMPC
lyso-myristoyl phosphatidylcholin
LMPG
lyso-myristoyl phosphatidylglycerol
LRT
linear response theory
MD
molecular dynamics
MMPBSA
molecular mechanics Poisson-Boltzmann surface area
MSF
mean square fluctuation
NCT
nicastrin
NICD
NOTCH intracellular domain
NME
N-methyl
PA
phosphatidic acid
PCA
principal component analysis
PE
phosphoethanolamine
PEN2
presenilin enhancer 2
PMF
potential of mean force
POPC
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
PS
presenilin
RMSD
root-mean square deviation
S2P
site-2 protease
SASA
solvent accessible surface area
SPP
signal peptide peptidase
TFE
2.2,2-trifluoroethanol
TM
transmembrane
TMD
transmembrane domain
TSA
transition-state analogue
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Current affiliation: Leibniz Supercomputing Centre, Garching.
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