Table 2 Analysis of hydrogen bonding between polar moieties in nisin and the lipid II head group.
From: Docking and molecular dynamics simulations of the ternary complex nisin2:lipid II
Atom | Trajectory | ||||||
|---|---|---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | 6 | ||
Occupancy of interaction with pyrophosphate (%) | |||||||
Nisin 1 | Ile1 HT1 | 5 | 22 | 23 | 0 | 0 | 0 |
Ile1 HT2 | 4 | 25 | 25 | 0 | 0 | 0 | |
Ile1 HT3 | 4 | 22 | 24 | 0 | 0 | 0 | |
Dhb2 NH | 4 | 2 | 17 | 0 | 0 | 0 | |
Ala3 NH | 2 | 0 | 22 | 0 | 0 | 75 | |
Cys7 NH | 2 | 1 | 22 | 7 | 8 | 0 | |
Abu8 NH | 94 | 18 | 87 | 24 | 86 | 99 | |
Nisin 2 | Lys12 HZ1 | 0 | 0 | 0 | 37 | 30 | 60 |
Lys12 HZ2 | 0 | 0 | 0 | 26 | 28 | 16 | |
Lys12 HZ3 | 0 | 0 | 0 | 28 | 26 | 15 | |
Asn20 HD21 | 0 | 19 | 0 | 0 | 0 | 0 | |
Lys22 NH | 18 | 0 | 0 | 0 | 0 | 0 | |
Occupancy of interaction with disaccharide (%) | |||||||
Nisin 2 | Ile1 HT1 | 15 | 0 | 4 | 7 | 1 | 3 |
Ile1 HT2 | 15 | 0 | 2 | 9 | 1 | 4 | |
Ile1 HT3 | 14 | 0 | 2 | 11 | 1 | 4 | |
Cys11 O | 0 | 20 | 0 | 0 | 0 | 0 | |
Lys12 HZ1 | 0 | 42 | 0 | 0 | 0 | 3 | |
Lys12 HZ2 | 0 | 35 | 0 | 0 | 0 | 6 | |
Lys12 HZ3 | 0 | 29 | 0 | 0 | 0 | 3 | |
Asn20 HN | 38 | 0 | 0 | 0 | 0 | 0 | |
Asn20 HD22 | 0 | 34 | 0 | 0 | 0 | 0 | |
Occupancy of interaction with pentapeptide (%) | |||||||
Nisin 2 | Ile1 HT1 | 34 | 64 | 50 | 24 | 30 | 7 |
Ile1 HT2 | 29 | 37 | 59 | 48 | 27 | 6 | |
Ile1 HT3 | 30 | 69 | 49 | 28 | 29 | 10 | |
Dhb2 HN | 1 | 16 | 25 | 93 | 0 | 0 | |
Asn20 OD1 | 0 | 25 | 0 | 0 | 0 | 0 | |
Asn20 HD21 | 16 | 0 | 0 | 0 | 0 | 0 | |
Met21 HN | 75 | 0 | 0 | 0 | 0 | 0 | |
