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 and even longer’ talked about by the Reviewer, might be related not to salt bridges per se but to “longer variety ion pairs” (as defined by Nussinov and co-workers, see [50, 51]). We weren’t interested in such weak interactions considering that they have been unlikely to contribute to triggering a significant rearrangement of the WD-7 domain of Carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone In Vivo 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 combination of PME along with a switch function for the direct-space element. 29) The story about “..angle among the C atoms..” is improved left out. It weakens the story. There’s no sensible justification for this that I can assume of that does not automatically goes together with the wash in MD. Authors’ response: We would rather leave this part in since the cooperativity in the complicated salt bridges, which can be determined not by the exact nature in the lysine residue, but by the neighboring position of the two aspartate residues, could be vital for triggering the rearrangement of Apaf-1.. 30) Any sentence that begins with “..As 4-Hydroxychalcone site currently noted..” can be deleted. Here too. We would rather hold it because it can be a reference to prior perform. 31) If lysines enhance (evolutionary) at the one side in the binding interface, then what in regards to the unfavorable charges at the other side Authors’ response: We now address this point within the second element of the’Sequence analysis’ section and within the Discussion section in the revised manuscript. 32) The discussion is a lot of a repeat on the previous, and not adequate a discussion. Authors’ response: Inside the revised manuscript, we deleted the repeats (at the very least, some) and have substantially expanded the Discussion. 33) In Fig. three I’d have loved to find out how properly the electrostatic potentials about the two proteins thatare docked match, or how effectively items cancel out, or something like that. Soon after all, nature wants issues to become neutral. Authors’ response: We have modified Fig. three (Fig. 4 within the revised manuscript) to illustrate the electrostatic complementarity. 34) Is Fig. four genuinely required Authors’ response: Figure 4 is now the Figure 1 of your revised manuscript. It can be a comparison from the PatchDock’ model (this perform) 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 think that this figure is helpful, because 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 so much distraction that they practically make it harder rather than simpler to find out things. Authors’ response: We employed the Sequence Logo representation [89], a well-liked tool for illustrating multiple alignments of substantial numbers of sequences, for these figures (Figs. 9 and ten inside the revised manuscript). Within a such presentation, the statistical significance in every single position is cseen. Inside the revised manuscript, we also add a a number of alignment with the WD domains as Extra file 1: Figure S2. In summary, I feel this can be a uncomplicated study that mostly got difficult by the massive size from the complicated at hand. I indicated 1 error that should be fixed. I’d appreciate to see how their final model fits inside the EM density, and I miss a little the experimental valid.
