Table 5. Hydrogen-Bond occupancies analysis from the results of MD simulations for the peptide-PKA interactions for shorter chain peptides derived from Kemptide (WT).
| WT | RRASLG | RASLG | LRRASL | |||||
| Peptide-PKA atoms.a | Occupancy(%).b | Distance (Å).c | Occupancy(%).b | Distance (Å).c | Occupancy(%).b | Distance (Å).c | Occupancy(%).b | Distance (Å).c |
| Arg18-NE - Glu127-OE1 | 96.10 | 3.38±0.11 | 100 | 2.87±0.15 | 99.60 | 2.88±0.17 | ||
| Arg18-NE - Glu127-OE2 | 99.00 | 2.99±0.13 | 97.70 | 3.13±0.20 | 96.01 | 3.08±0.22 | ||
| Arg18-NE - Tyr330-OH | 68.00 | 3.50±0.17 | 67.96 | 3.51±0.20 | 69.96 | 3.50±0.20 | ||
| Arg18-NH1 - Thr51-O | 99.70 | 2.97±0.10 | 99.60 | 2.94±0.19 | 95.31 | 3.07±0.26 | ||
| Arg18-NH2 - ATP-O3′ | 100 | 2.98±0.13 | 99.90 | 3.00±0.14 | 100 | 3.00±0.14 | ||
| Arg18-NH2 - Glu127-OE1 | 39.00 | 3.28±0.62 | 22.55 | 3.78±0.27 | 18.96 | 3.85±0.31 | ||
| Arg18-NH2 - Glu127-OE2 | 34.20 | 3.04±0.25 | 100 | 2.71±0.12 | 100 | 2.76±0.14 | ||
| Arg18-NH2 - Thr51-O | 19.10 | 3.18±0.32 | 93.51 | 3.16±0.26 | 87.62 | 3.26±0.51 | ||
| Arg19-N - Glu170-OE2 | 85.50 | 2.83±0.11 | 100 | 2.77±0.10 | 100 | 2.66±0.08 | 100 | 2.80±0.11 |
| Arg19-NE - Glu170-OE1 | 75.00 | 3.50±0.13 | 81.54 | 3.46±0.14 | 75.35 | 3.51±0.14 | 67.27 | 3.53±0.13 |
| Arg19-NE - Glu170-OE2 | 98.30 | 2.73±0.09 | 100 | 2.75±0.09 | 100 | 2.72±0.09 | 100 | 2.71±0.08 |
| Arg19-NH1 - Glu203-OE2 | 87.10 | 2.81±0.21 | 97.21 | 2.81±0.27 | 98.40 | 2.81±0.23 | 87.33 | 3.00±0.70 |
| Arg19-NH1 - Glu230-OE1 | 88.00 | 2.76±0.12 | 100 | 2.78±0.12 | 99.90 | 2.82±0.16 | 100 | 2.78±0.03 |
| Arg19-NH1 - Glu230-OE2 | 79.80 | 3.42±0.23 | 82.04 | 3.39±0.23 | 82.04 | 3.37±0.25 | 78.44 | 3.40±0.25 |
| Arg19-NH2 - Glu170-OE1 | 97.20 | 2.74±0.10 | 100 | 2.74±0.10 | 100 | 2.73±0.10 | 100 | 2.75±0.11 |
| Arg19-NH2 - Glu170-OE2 | 89.20 | 3.41±0.15 | 85.73 | 3.43±0.15 | 81.64 | 3.47±0.15 | 93.71 | 3.37±0.14 |
| Arg19-NH2 - Glu230-OE1 | 98.00 | 3.19±0.12 | 98.90 | 3.15±0.19 | 99.40 | 3.10±0.20 | 99.60 | 3.10±0.19 |
| Arg19-NH2 - Glu230-OE2 | 96.80 | 3.07±0.10 | 92.91 | 3.14±0.28 | 94.01 | 3.11±0.27 | 91.02 | 3.19±0.27 |
| Ser21-N - ATP-O1G | 98.80 | 3.11±0.19 | 22.26 | 2.96±0.15 | 99.70 | 2.98±0.17 | 95.31 | 2.98±0.16 |
| Ser21-O - Ser53-OG | 66.40 | 2.77±0.14 | 99.50 | 2.74±0.15 | 97.50 | 2.89±0.24 | 94.31 | 3.03±0.30 |
| Ser21-OG - Asp166-OD1 | 100 | 2.72±0.17 | 99.60 | 2.78±0.21 | 99.60 | 2.95±0.22 | 98.80 | 3.06±0.21 |
| Ser21-OG - ATP-O3G | 66.00 | 3.44±0.33 | 63.67 | 5.58±0.35 | 90.62 | 3.05±0.34 | 98.20 | 2.86±0.23 |
| Ser21-OG - Lys168-NZ | 96.20 | 2.87±0.14 | 95.41 | 2.87±0.13 | 89.92 | 2.89±0.15 | 89.02 | 2.98±0.20 |
| Leu22-N - Gly200-O | 63.70 | 2.93±0.17 | 99.90 | 2.91±0.16 | 99.90 | 2.94±0.15 | 99.50 | 3.05±0.19 |
a
Peptide-PKA heavy atoms that form a HB (Notations of atoms refer to the name of atoms from the CHARMM force field). The listed donor and acceptor pairs satisfy the criteria for the HB over 50% of time during the whole MD simulation (distance between heavy atoms <3.5 Å, values higher than 3.5 are included only for comparison).
b
The occupancies reflect the % of the time that the HB exists with respect to the whole time.
c
The averaged distance ± standard deviation between hydrogen-acceptor and hydrogen-donor heavy atoms during the time that the HB is formed.