Va et al. Biology Direct (2015) ten:Web page 25 oflength is “washing out” the variations inside the population of salt bridges. The `cutoff of 8-12A or perhaps longer’ pointed out by the Reviewer, may be associated 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 considering the fact that they were unlikely to contribute to triggering a major rearrangement in the WD-7 domain of Apaf-1 upon the binding of cytochrome c. As for electrostatics interactions generally, for MD simulations we utilised a 10 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 part. 29) The story about “..angle amongst the C atoms..” is far better left out. It weakens the story. There isn’t any 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 portion in because the cooperativity in the complicated salt bridges, which is determined not by the exact nature on the lysine residue, but by the neighboring position with the two aspartate residues, might be critical for triggering the rearrangement of Apaf-1.. 30) Any sentence that begins with “..As currently noted..” can be deleted. Here also. We would rather maintain it because it is actually a reference to prior operate. 31) If lysines boost (evolutionary) in the a single side with the binding interface, then what in regards to the adverse charges at the other side Authors’ response: We now address this point within the second portion of the’Sequence analysis’ section and inside the Discussion section of your Acetamide Metabolic Enzyme/Protease revised manuscript. 32) The discussion is too much a repeat on the prior, and not adequate a discussion. Authors’ response: In the revised manuscript, we deleted the repeats (at the least, some) and have substantially expanded the Discussion. 33) In Fig. three I would have loved to determine how well the electrostatic potentials about the two proteins thatare docked match, or how effectively items cancel out, or anything like that. Right after all, nature desires factors to become neutral. Authors’ response: We’ve modified Fig. 3 (Fig. four within the revised manuscript) to illustrate the electrostatic complementarity. 34) Is Fig. four actually necessary Authors’ response: Figure four is now the Figure 1 of the revised manuscript. It is a comparison with the PatchDock’ model (this perform) together 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 feel that this figure is valuable, as 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 so much distraction that they pretty much make it harder instead of a lot easier to determine points. Authors’ response: We utilized the Sequence Logo representation [89], a well known tool for illustrating various alignments of substantial 1-Methylguanidine hydrochloride Cancer numbers of sequences, for these figures (Figs. 9 and ten within the revised manuscript). Within a such presentation, the statistical significance in every single position is cseen. In the revised manuscript, we also add a various alignment of the WD domains as Extra file 1: Figure S2. In summary, I think this is a uncomplicated study that mostly got complicated by the enormous size in the complicated at hand. I indicated 1 error that should be fixed. I would like to see how their final model fits within the EM density, and I miss a little the experimental valid.
