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Table 3 Summary of survival ratios, rupture time and involved residues of hydrogen bonds detected from free and steered MD simulations

From: Computer prediction of paratope on antithrombotic antibody 10B12 and epitope on platelet glycoprotein VI via molecular dynamics simulation

Bond GPVI 10B12 Survival ratio Rupture time
No. Residue Atom Residue Atom I II ω I (ns) II (ns) α
1 ARG46 NH2 ASP98 OD1 0.39 ± 0.04 0.94 ± 0.01 0.94 1.20 ± 0.31 2.18 ± 0.81 0.75
2 LYS41 NZ GLU102 OE2 0.79 ± 0.08   0.79 2.88 ± 1.08 0.14 ± 0.11 1.00
3 ARG38 NH2 GLU1 OE1 0.42 ± 0.30 0.66 ± 0.14 0.66 0.69 ± 0.80 1.71 ± 0.50 0.59
4 TYR47 OH GLU1 OE2 0.09 ± 0.04 0.65 ± 0.15 0.65   1.48 ± 0.23 0.51
5 ARG166 NH2 GLU102 OE1   0.56 ± 0.04 0.56   0.44 ± 0.23 0.15
6 ARG46 NH2 ASP111 OD2   0.54 ± 0.29 0.54   2.41 ± 0.71 0.83
7 ARG166 NH1 GLU102 OE2   0.54 ± 0.06 0.54   0.36 ± 0.29 0.12
8 LYS59 NZ ASP107 OD2   0.53 ± 0.27 0.53   0.44 ± 0.25 0.15
9 ARG46 NH1 ASP98 OD1 0.50 ± 0.13   0.50 2.48 ± 0.53   0.86
10 LYS59 NZ ASP108 OD1 0.33 ± 0.10 0.48 ± 0.38 0.48 0.56 ± 0.30 0.30 ± 0.27 0.19
11 SER44 OG GLU102 OE2 0.45 ± 0.11   0.45 1.28 ± 0.98 0.05 ± 0.09 0.44
12 ARG38 NH1 GLU1 OE2 0.44 ± 0.21 0.45 ± 0.09 0.45 0.72 ± 0.80 1.50 ± 0.49 0.52
13 ARG46 NE GLU102 OE1 0.40 ± 0.08   0.40 1.54 ± 0.10 0.02 ± 0.04 0.53
14 SER44 OG GLU102 OE1 0.40 ± 0.10   0.40 1.52 ± 0.35 0.01 ± 0.01 0.53
15 LYS59 NZ ASP108 OD2 0.39 ± 0.08 0.36 ± 0.40 0.39 0.44 ± 0.31   0.15
16 ARG166 NH2 GLU102 OE2   0.30 ± 0.01 0.30   0.61 ± 0.24 0.21
17 LYS59 NZ ASP107 OD1   0.29 ± 0.30 0.29    
18 ARG46 NH2 ASP98 OD2 0.27 ± 0.03 . 0.27 1.18 ± 0.92   0.41
19 ARG38 NH2 GLU1 OE2 0.25 ± 0.17 0.21 ± 0.16 0.25 0.56 ± 0.71 0.07 ± 0.07 0.19
20 ARG166 NH1 GLU102 OE1   0.23 ± 0.02 0.23   0.63 ± 0.27 0.22
21 ARG46 NH1 ASP111 OD2   0.23 ± 0.13 0.23   0.71 ± 0.35 0.24
22 SER43 OG GLU102 OE1 0.22 ± 0.20   0.22    
23 TYR32 OH ASP167 OD2 0.17 ± 0.35   0.17    
24 ARG38 NH1 GLU1 OE1 0.11 ± 0.08 0.12 ± 0.10 0.12 0.57 ± 0.71   0.20
25 TYR47 OH GLU1 OE1 0.01 ± 0.01 0.09 ± 0.12 0.09   0.09 ± 0.08 0.03
  1. The heading I and II denote two different equilibrated complex conformation of 10B12 bound to GPVI, and the values (Column 8 and 11) of express the thermal and mechanical stabilities of the bonds detected from free and steered MD simulations thrice with two different equilibrated conformations (see “Methods” section). The superscript numbers on residues (Column 2 and 4) designate the positions of their respective involved residues in sequences of GPVI and 10b12 with serial numbering, the donor- and acceptor-atoms (Column 5) on paratope residues (Column 4) together with their respectively partners (Column 3) on epitope residues (Column 2) contribute to bonds in binding site. All bonds, which were derived from thrice independent free and steered MD simulations with equilibrated conformation I and II, respectively, were designated by nonzero values (mean ± SD) of survival ratios and rupture times of bonds
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