Aggregation Mechanism of Alzheimer’s Amyloid β-Peptide Mediated by α-Strand/α-Sheet Structure
Abstract
:1. Introduction
2. Results
2.1. Occurrence of α-Strand Structure in Region 24–26
2.2. Transition of Dihedrals
2.3. Effect of Mutation on Occurrence of α-Strand Structure in Region 24–26
2.4. PDB Search for α-Strand Structure with VGS Sequence
3. Discussion
4. Materials and Methods
4.1. Structures of Human Aβ1–42 and Mutants
4.2. Molecular Dynamics Simulation
4.3. Computation of Dihedral Angles
4.4. PDB Search for α-Strand Structure
Author Contributions
Funding
Conflicts of Interest
References
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Simulated System | PDB, Type | Counter Ion | Temperature | pH | MD Run |
---|---|---|---|---|---|
1 | 1IYT, WT | 3 Na+ | 310 K | NpH | 50 ns |
2 | 1Z0Q, WT | 3 Na+ | 310 K | NpH | 50 ns |
3 | 2NAO, WT | 3 Na+ | 310 K | NpH | 50 ns |
4 | 1IYT, WT | 3 Na+ | 498 K | NpH | 50 ns |
5 | 1Z0Q, WT | 3 Na+ | 498 K | NpH | 50 ns |
6 | 2NAO, WT | 3 Na+ | 498 K | NpH | 50 ns |
7 | 1IYT, WT | 6 Cl− | 310 K | LpH | 50 ns |
8 | 1Z0Q, WT | 6 Cl− | 310 K | LpH | 50 ns |
9 | 2NAO, WT | 6 Cl− | 310 K | LpH | 50 ns |
10 | 1IYT, WT | 6 Cl− | 498 K | LpH | 50 ns |
11 | 1Z0Q, WT | 6 Cl− | 498 K | LpH | 50 ns |
12 | 2NAO, WT | 6 Cl− | 498 K | LpH | 50 ns |
13 | 1IYT, Mutant (A2T) | 3 Na+ | 498 K | NpH | 50 ns |
14 | 1Z0Q, Mutant (A2T) | 3 Na+ | 498 K | NpH | 50 ns |
15 | 2NAO, Mutant (A2T) | 3 Na+ | 498 K | NpH | 50 ns |
16 | 1IYT, Mutant (D7N) | 2 Na+ | 498 K | NpH | 50 ns |
17 | 1Z0Q, Mutant (D7N) | 2 Na+ | 498 K | NpH | 50 ns |
18 | 2NAO, Mutant (D7N) | 2 Na+ | 498 K | NpH | 50 ns |
19 | 1IYT, Mutant (E22G) | 2 Na+ | 310 K | NpH | 50 ns |
20 | 1Z0Q, Mutant (E22G) | 2 Na+ | 310 K | NpH | 50 ns |
21 | 2NAO, Mutant (E22G) | 2 Na+ | 310 K | NpH | 50 ns |
22 | 1IYT, Mutant (E22G) | 2 Na+ | 498 K | NpH | 50 ns |
23 | 1Z0Q, Mutant (E22G) | 2 Na+ | 498 K | NpH | 50 ns |
24 | 2NAO, Mutant (E22G) | 2 Na+ | 498 K | NpH | 50 ns |
25 | 1IYT, Mutant (E22Q) | 2 Na+ | 310 K | NpH | 50 ns |
26 | 1Z0Q, Mutant (E22Q) | 2 Na+ | 310 K | NpH | 50 ns |
27 | 2NAO, Mutant (E22Q) | 2 Na+ | 310 K | NpH | 50 ns |
28 | 1IYT, Mutant (E22Q) | 2 Na+ | 498 K | NpH | 50 ns |
29 | 1Z0Q, Mutant (E22Q) | 2 Na+ | 498 K | NpH | 50 ns |
30 | 2NAO, Mutant (E22Q) | 2 Na+ | 498 K | NpH | 50 ns |
31 | 1IYT, Mutant (D23N) | 2 Na+ | 498 K | NpH | 50 ns |
32 | 1Z0Q, Mutant (D23N) | 2 Na+ | 498 K | NpH | 50 ns |
33 | 2NAO, Mutant (D23N) | 2 Na+ | 498 K | NpH | 50 ns |
34 | 1IYT, Mutant (G25P) | 3 Na+ | 310 K | NpH | 50 ns |
35 | 1Z0Q, Mutant (G25P) | 3 Na+ | 310 K | NpH | 50 ns |
36 | 2NAO, Mutant (G25P) | 3 Na+ | 310 K | NpH | 50 ns |
37 | 1IYT, Mutant (G25P) | 3 Na+ | 498 K | NpH | 50 ns |
38 | 1Z0Q, Mutant (G25P) | 3 Na+ | 498 K | NpH | 50 ns |
39 | 2NAO, Mutant (G25P) | 3 Na+ | 498 K | NpH | 50 ns |
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Balupuri, A.; Choi, K.-E.; Kang, N.S. Aggregation Mechanism of Alzheimer’s Amyloid β-Peptide Mediated by α-Strand/α-Sheet Structure. Int. J. Mol. Sci. 2020, 21, 1094. https://doi.org/10.3390/ijms21031094
Balupuri A, Choi K-E, Kang NS. Aggregation Mechanism of Alzheimer’s Amyloid β-Peptide Mediated by α-Strand/α-Sheet Structure. International Journal of Molecular Sciences. 2020; 21(3):1094. https://doi.org/10.3390/ijms21031094
Chicago/Turabian StyleBalupuri, Anand, Kwang-Eun Choi, and Nam Sook Kang. 2020. "Aggregation Mechanism of Alzheimer’s Amyloid β-Peptide Mediated by α-Strand/α-Sheet Structure" International Journal of Molecular Sciences 21, no. 3: 1094. https://doi.org/10.3390/ijms21031094