GS-SMD - MD&mut

1γ-Secretase Mode

all

membrane part

presenilin

2Substrate

Peptide substrate selection (* - suggested cutting point):

Sequence for threading to substrate structure:Please use A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*

Final sequence for simulation (min. 15 aa, max 33 aa) is highlighted:

Please use only one star

Substrate must be longer than 14 aminoacids

3SMD

SMD:

SMD residues list:

SMD velocity [m/s]:

0.01

0.5

SMD k [kcal/mol/Å²]:

0.1

10.0

SMD x [Å]:

-10

+10

SMD y [Å]:

-10

+10

SMD z [Å]:

-10

+10

Default SMD input

Center

Fullscreen

Background

Color:

Representation:

4γ-Secretase Mutations

Please use numbers, A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y, coma and space

Nicastrin (chain A), residues 34-700 Nicastrin (chain A), residues 664-700

Presenilin-1 (chain B), residues 73-298, 374-467

Aph1-A (chain C), residues 2-244

PEN-2 (chain D), residues 2-101

EXAMPLE:

Familiar Alzheimer Disease (chain B): E280A, G384A, A434C

Default Mutations

5Dynamics

Total length [ns]:

5

25

Number of frames:

10

200

Membrane thickness [Å]:

20

40

Number of tasks to run:

1

4

Molecular dynamics & mutations

Please use numbers, A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y, coma and space

EXAMPLE: