Va et al. Biology Direct (2015) 10:Web page 25 oflength is “washing out” the variations within the population of salt bridges. The `cutoff of 8-12A or perhaps longer’ mentioned by the Reviewer, might be associated not to salt bridges per se but to “longer range ion pairs” (as defined by Nussinov and co-workers, see [50, 51]). We weren’t considering such weak interactions due to the fact they were unlikely to contribute to triggering a significant 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 combination of PME and a switch function for the direct-space component. 29) The story about “..angle in between the C atoms..” is much better left out. It weakens the story. There’s no sensible justification for this that I can assume of that does not automatically goes using the wash in MD. Authors’ response: We would rather leave this component in since the cooperativity of your complicated salt bridges, which is determined not by the exact nature of the lysine residue, but by the neighboring position from the two aspartate residues, may be significant for triggering the rearrangement of Apaf-1.. 30) Any sentence that begins with “..As already noted..” can be deleted. Here too. We would rather keep it since it is often a reference to prior operate. 31) If lysines boost (evolutionary) in the a single side of your binding interface, then what about the negative charges in the other side Authors’ response: We now address this point within the second aspect of the’Sequence analysis’ section and within the L-Azidonorleucine Technical Information Discussion section from the revised manuscript. 32) The discussion is too much a repeat of your prior, and not enough a discussion. Authors’ response: Inside the revised manuscript, we deleted the repeats (a minimum of, some) and have substantially expanded the Discussion. 33) In Fig. 3 I would have loved to see how properly the electrostatic potentials about the two proteins thatare docked fit, or how effectively factors Ninhydrin site cancel out, or something like that. Immediately after all, nature wants factors to become neutral. Authors’ response: We’ve modified Fig. 3 (Fig. 4 inside the revised manuscript) to illustrate the electrostatic complementarity. 34) Is Fig. 4 truly necessary Authors’ response: Figure 4 is now the Figure 1 on the revised manuscript. It can be a comparison on the PatchDock’ model (this operate) together with the previously published model structure by Yuan et al. [PDB:3J2T] [25]. Both models are fitted into experimental cryo-EM density map [24]. We feel that this figure is beneficial, since it illustrates that the proposed PatchDock’ model matches the cryo-EM information. 35) Figures eight and 9 nicely indicate the sequence patterns, but there’s a lot distraction that they almost make it tougher in lieu of much easier to find out things. Authors’ response: We employed the Sequence Logo representation [89], a well-known tool for illustrating numerous alignments of huge numbers of sequences, for these figures (Figs. 9 and 10 in the revised manuscript). In a such presentation, the statistical significance in each and every position is cseen. Inside the revised manuscript, we also add a various alignment from the WD domains as Extra file 1: Figure S2. In summary, I believe this is a uncomplicated study that mainly got difficult by the huge size from the complex at hand. I indicated a single error that ought to be fixed. I would enjoy to view how their final model fits in the EM density, and I miss a bit the experimental valid.
