Figure 1.
Ensemble workflow of computational procedure.
Table 1.
The CDRs and identified paratope residues of 6B4 [16].
Figure 2.
A, model of 6B4-ScFv via Homology modeling, where the heavy chain (iceblue), light chain (cyan) and (Gly4Ser)3 linker (yellow) were shown in transparent newcartoon representation, and the six complementarity determining regions (CDRs) (mauve), i.e. CDR H1, H2, H3, L1, L2 and L3, were marked; B, conformation of the 339th complex of 6B4 bound to GPIbα subunit (orange); C, structural superposition of 6B4/GPIbα and A1-GPIbα complex (PDB code 1SQ0), where A1 is shown in transparent lime and 6B4 in prunosus; D, the back side view of C.
Table 2.
Hydrophobic and polar interactions from docking analysis.
Figure 3.
Conformation of the 339th complex after the first (A) and second (B) equilibration.
GPIbα (cyan) and 6B4 (iceblue) are shown in transparent newcartoon representation. All ten bonds were numbered with the index listed in Table 3. The 5th, 4th and 9th bonds express the three salt bridges, others are H-bonds.
Table 3.
Summary of survival ratios, rupture times and involved residues of hydrogen bonds and salt bridges obtained from free and steered simulations.
Figure 4.
Time courses of interatomic distances of six representative bonds in binding site of 6B4/GPIbα complex.
The interatomic distances of six representative bonds were plotted against simulation time, where the interatomic distances were from the oxygen atoms of acidic residues and their respective partners, the nitrogen atoms of basic residues, for three salt bridges, 5th (A), 4th (B) and 9th (C) bonds, or from doners to their respective acceptors for three hydrogen bonds, 16th (D), 10th (E) and 1st (F) bonds. The salt bridges and hydrogen bonds were simulated with the initial conformation I (Fig. 3 A) and II (Fig. 3 B), respectively. The gray dashed line expresses the distance cut-off of 0.35 nm beyond which the bonds breaks, and the blue, green and red lines exhibit the variation of interatomic distances (nm) of a bond against simulation time (ns) for thrice-repeat independent free MD simulations, respectively. The thermal stabilizations of the 4th and 10th bonds (B and E) seemed to be higher than those of the 5th and 16th bonds but lower than those of the 9th and 1st bonds. Remarkable difference in the thrice-repeat independent simulations showed a random behavior of intermolecular interactions.
Figure 5.
Variation of interatomic distance versus steered simulation time.
The interatomic distances of the six representative bonds under stretching were plotted against simulation time, where all descriptions for line types, bonds and their lengths are same as in Figure 4. These time courses of interatomic distances showed that, the 5th and 16th bonds were very quickly ruptured (A and D), in comparison with others, in which the 9th and 1st bonds would maintain more long time (C and F) than 4th and 10th bonds (B and E).
Figure 6.
Residues involved in H-bonds and salt bridges of top 8 HBSI values.
Red, significantly disrupted binding when mutated; orange, mutagenesis data are unavailable; green, no obvious effect was observed when mutated. A, surf representation of GPIbα; B, surf representation of 6B4.
Table 4.
Hydrogen bonds and salt bridges with higher stabilization in Top 8.
Table 5.
The false discovery rate, sensitivity and specificity of three different positive criterions.