Table 1. Protein orientational states and protein unfolding behavior of Aβ42 in PC/CHO bilayers.
The protein orientational states and unfolding % of Aβ42 in the I and II systems before (I (initial) or II (initial)) and after 1000 ns-CG or after 200 ns-UA MD simulations are shown. For the 1000 ns-CG simulation (I-rep* or II-rep*), the unfolding % was calculated after the CG-to-UA reverse mapping. For the 200 ns-UA simulation, (I-rep*-* or II-rep*-*), the unfolding % was based on the last 50 ns of the simulation with the average and the standard error of the mean given. Average unfolding % across all 4 replicates in CG (I (avg)-CG or II (avg)-CG) or 8 replicates in UA (I (avg)-UA or II (avg)-UA) and the standard error of the mean are also presented. * represents replicate number 0–3.
| System | Simulation conditions |
Protein orientational statea |
Unfolding %c D1-N27 (non-LID) |
Unfolding %c K28-A42 (LID) |
Unfolding %c D1-A42 |
|---|---|---|---|---|---|
| I (initial) | 0 | Inserted | 51.9 | 26.7 | 42.9 |
| I-rep0 | 1000 ns-CG | Deep inserted | 40.7 | 26.7 | 35.7 |
| I-rep0-0 | 200 ns-UA | Deep inserted-Ca | 53.2 ± 1.4 | 47.1 ± 0.3 | 51.0 ± 0.3 |
| I-rep0-1 | 200 ns-UA | Deep inserted-Ca | 32.4 ± 0.8 | 48.4 ± 0.7 | 38.1 ± 0.7 |
| I-rep1 | 1000 ns-CG | Deep inserted | 63.0 | 26.7 | 50.0 |
| I-rep1-0 | 200 ns-UA | Deep inserted | 63.9 ± 0.9 | 55.5 ± 1.5 | 60.9 ± 1.5 |
| I-rep1-1 | 200 ns-UA | Deep inserted | 73.3 ± 1.2 | 61.5 ± 0.9 | 69.1 ± 0.9 |
| I-rep2 | 1000 ns-CG | Deep inserted | 59.3 | 20.0 | 45.2 |
| I-rep2-0 | 200 ns-UA | Deep inserted | 66.8 ± 1.0 | 39.6 ± 0.3 | 57.1 ± 0.3 |
| I-rep2-1 | 200 ns-UA | Deep inserted-Pb | 57.4 ± 0.7 | 28.0 ± 0.5 | 46.9 ± 0.5 |
| I-rep3 | 1000 ns-CG | Deep inserted | 48.1 | 40.0 | 45.2 |
| I-rep3-0 | 200 ns-UA | Deep inserted | 44.4 ± 0.7 | 41.9 ± 0.8 | 43.5 ± 0.8 |
| I-rep3-1 | 200 ns-UA | Deep inserted | 42.3 ± 1.3 | 68.1 ± 1.3 | 51.5 ± 1.3 |
| I (avg)-CG | 1000 ns-CG | Deep inserted | 52.8 ± 5.1 | 28.3 ± 4.2 | 44.0 ± 2.6 |
| I (avg)-UA | 200 ns-UA | Deep inserted | 54.2 ± 4.9 | 48.8 ± 4.5 | 52.3 ± 3.5 |
| II (initial) | 0 | Inserted | 40.7 | 60.0 | 47.6 |
| II-rep0 | 1000 ns-CG | Deep surface | 85.2 | 100 | 90.5 |
| II-rep0-0 | 200 ns-UA | Deep surface | 59.0 ± 0.6 | 99.3 ± 0.5 | 73.4 ± 0.5 |
| II-rep0-1 | 200 ns-UA | Deep surface | 69.5 ± 1.0 | 98.8 ± 0.7 | 80.1 ± 0.9 |
| II-rep1 | 1000 ns-CG | Deep surface | 44.4 | 100 | 64.3 |
| II-rep1-0 | 200 ns-UA | Deep surface | 41.6 ± 0.6 | 63.3 ± 2.3 | 49.3 ± 1.2 |
| II-rep1-1 | 200 ns-UA | Deep surface | 36.9 ± 0.7 | 52.5 ± 1.9 | 42.5 ± 1.1 |
| II-rep2 | 1000 ns-CG | Deep surface | 63.0 | 100 | 76.2 |
| II-rep2-0 | 200 ns-UA | Deep surface | 62.6 ± 0.9 | 89.3 ± 0.9 | 72.1 ± 0.9 |
| II-rep2-1 | 200 ns-UA | Deep surface | 57.9 ± 1.3 | 100.0 ± 0.1 | 72.9 ± 0.8 |
| II-rep3 | 1000 ns-CG | Deep surface | 48.1 | 66.7 | 54.8 |
| II-rep3-0 | 200 ns-UA | Deep surface | 62.9 ± 0.1 | 55.0 ± 0.5 | 60.1 ± 0.3 |
| II-rep3-1 | 200 ns-UA | Deep surface | 53.3 ± 0.4 | 65.7 ± 1.1 | 57.7 ± 0.6 |
| II (avg)-CG | 1000 ns-CG | Deep surface | 60.2 ± 9.2 | 91.7 ± 8.3 | 71.4 ± 8.5 |
| II (avg)-UA | 200 ns-UA | Deep surface | 55.4 ± 3.9 | 78.0 ± 7.4 | 63.5 ± 4.7 |
Protein orientational substate of Aβ42 with K28 hydrogen-bonded with CHO polar group.
Protein orientational substate of Aβ42 with K28 hydrogen-bonded with PC polar group.
Unfolding % was based on the % of residues in the non-hydrogen-bonded SC structures in the LID (27 residues total), the non-LID (15 residues total) or the whole chain (42 residues total).