Published October 16, 2021
| Version V.1
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Exploring the interaction of a curcumin azobioisostere with Abeta42 dimers using replica exchange molecular dynamics simulations
Authors/Creators
- 1. Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
- 2. Department of Nutrition, Food Science and Gastronomy, Fac-ulty of Pharmacy and Food Sciences, Institute of Theoretical and Computational Chemistry and Institute of Biomedicine, Campus Torribera, University of Barcelona, Santa Coloma de Gramenet 08921, Spain
Description
Structural data and parameters relative to the evaluation of the interaction of an anti aggregating azobioisostere compound with the full-length Aβ42 peptide by replica-exchange molecular dynamics (REMD) simulations. Two different force fields (Amber and CHARMM) were used to simulate the azobioisostere-Abeta42 (AZ-Ab42) complex in a monomeric and dimeric assembly.
A brief description of the shared output data is reported below:
1. Amber and CHARMM-adapted parameters for the simulated azobioisostere (AZ) compound.
2. Modified version of the CHARMM36m FF - (CHARMM36mW)
3. Starting (equilibrated) structures (first 5 T-replicas) for REMD on each of the following three systems (PDB):
- Amber: AZ-Ab42 (monomeric ensemble): Repl.0 (315.0 K), Repl.1 (316.7 K), Repl.2 (318.4 K), Repl.3 (320.1 K), Repl.4 (321.8 K)
- Amber: AZ-Ab42 (dimeric ensemble): Repl.0 (315.0 K), Repl.1 (316.0 K), Repl.2 (317.0 K), Repl.3 (318.0 K), Repl.4 (319.1 K)
- CHARMM: AZ-Ab42 (dimeric ensemble): Repl.0 (315.0 K), Repl.1 (316.0 K), Repl.2 (317.0 K), Repl.3 (318.0 K), Repl.4 (319.1 K)
4. Most populated clusters for the three simulated systems (PDB):
- Amber AZ-Ab42 (monomeric ensemble): 7 clusters (Cl.0: 12.4%, Cl.1: 10.1%, Cl.2: 9.8%, Cl.3: 5.4%, Cl.4: 3.7%, Cl.5: 3.6%, Cl.6: 2.0%)
- Amber AZ-Ab42 (dimeric ensemble): 5 clusters (Cl.0: 7.1%, Cl.1: 4.3%, Cl.2: 3.5%, Cl.3: 3.2%, Cl.4: 2.4%)
- CHARMM: AZ-Ab42 (dimeric ensemble): 3 clusters (Cl.0: 4.7%, Cl.1: 4.6%, Cl.2: 2.5%)