Va et al. Biology Direct (2015) ten:Page 25 oflength is “washing out” the differences within the population of salt bridges. The `cutoff of 8-12A or perhaps longer’ mentioned by the Reviewer, might be related to not salt bridges per se but to “longer range ion pairs” (as defined by Nussinov and co-workers, see [50, 51]). We were not considering such weak interactions given that they had been unlikely to contribute to triggering a major rearrangement with the WD-7 domain of Apaf-1 upon the binding of cytochrome c. As for electrostatics interactions generally, for MD simulations we made use of a ten cut-off for coulombic interactions and 14 cut-off for all long-distance interactions with mixture of PME along with a switch function for the direct-space portion. 29) The story about “..angle among the C atoms..” is far better left out. It weakens the story. There’s no sensible justification for this that I can assume of that doesn’t automatically goes using the wash in MD. Authors’ response: We would rather leave this component in because the cooperativity in the complicated salt bridges, which is determined not by the exact nature of the lysine residue, but by the neighboring position in the two aspartate residues, might be essential for triggering the rearrangement of Apaf-1.. 30) Any sentence that begins with “..As currently noted..” could be deleted. Here also. We would rather hold it as it is actually a reference to prior operate. 31) If lysines increase (evolutionary) in the one side from the binding interface, then what regarding the adverse charges at the other side Authors’ response: We now address this point in the second component of the’Sequence analysis’ section and in the Discussion section of your revised manuscript. 32) The discussion is too much a repeat on the preceding, and not enough a discussion. Authors’ response: In the revised manuscript, we deleted the repeats (no less than, some) and have substantially expanded the Discussion. 33) In Fig. three I’d have loved to find out how effectively the electrostatic potentials about the two proteins thatare docked match, or how nicely items cancel out, or something like that. Right after all, nature wants factors to become neutral. Authors’ response: We’ve got modified Fig. three (Fig. 4 within the revised manuscript) to illustrate the electrostatic complementarity. 34) Is Fig. 4 definitely required Authors’ response: Figure four is now the Figure 1 of the revised manuscript. It truly is a comparison with the PatchDock’ model (this operate) with the previously published model structure by Yuan et al. [PDB:3J2T] [25]. Each models are fitted into experimental cryo-EM density map [24]. We consider that this figure is beneficial, as it illustrates that the proposed PatchDock’ model matches the cryo-EM information. 35) Figures 8 and 9 nicely indicate the sequence patterns, but there is a lot distraction that they virtually make it tougher as opposed to less complicated to see items. Authors’ response: We applied the Sequence Logo representation [89], a common tool for illustrating multiple alignments of significant numbers of sequences, for these figures (Figs. 9 and 10 inside the revised manuscript). In a such presentation, the statistical significance in each position is cseen. In the revised manuscript, we also add a numerous Spadin Purity & Documentation alignment on the WD domains as More file 1: Figure S2. In summary, I believe this is a easy study that mostly got complex by the enormous size from the complicated at hand. I indicated one error that ought to be fixed. I would adore to view how their final model fits in the EM density, and I miss a bit the experimental valid.
