Time courses of interatomic distances of six representative bonds in binding site of 6B4/GPIbα complex.

<p>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, 5^th (A), 4^th (B) and 9^th (C) bonds, or from doners to their respective acceptors for three hydrogen bonds, 16^th (D), 10^th (E) and 1^st (F) bonds. The salt bridges and hydrogen bonds were simulated with the initial conformation I (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042263#pone-0042263-g003" target="_blank">Fig. 3 A</a>) and II (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042263#pone-0042263-g003" target="_blank">Fig. 3 B</a>), 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 4^th and 10^th bonds (B and E) seemed to be higher than those of the 5^th and 16^th bonds but lower than those of the 9^th and 1^st bonds. Remarkable difference in the thrice-repeat independent simulations showed a random behavior of intermolecular interactions.