. 2022 May 20;121(12):2330–2344. doi: 10.1016/j.bpj.2022.05.023

Table 2.

Conducted simulations in the study

	^aApo (5FN2)	^aApo (6IYC)	Notch1_S3	C99_ε49	C99_ε49,V44G
Protonation	D385^H	D385^H	D257^H,D385^H	D257^H,D385^H	D257^H,D385^H
Atom #	284,455	292,134	300,408	293,748	293,739

	C99_ε49,I45G	C99_ε49,GG	^bC99_ε48-1	^bC99_ε48-2	Aβ49_ζ46

Protonation	D257^H,D385^H	D385^H	D385^H	D385^H	D257^H,D385^H
Atom #	293,736	293,727	301,518	294,453	293,523

	Aβ46_γ43	Aβ43_γ40	Aβ40_γ37	Aβ40_γ37,G33I	Aβ40_γ37,K28A

Protonation	D257^H,D385^H	D257^H,D385^H	D257^H,D385^H	D257^H,D385^H	D257^H,D385^H
Atom #	287,745	259,525	305,198	305,210	305,255

Each system is simulated for 600 ns twice with the same initial structure but different randomly generated initial velocity.

Three simulations of the each apo-form γ-secretase with initial structures taken from PDB 5FN2 and PDB 6IYC are performed with the D385-protonated PS1.

Only one trajectory with D385-protonated PS1 was simulated and analyzed in each of the C99_ε48-bound γ-secretase complexes.