Va et al. Biology Direct (2015) ten:Web 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, could be Trequinsin supplier connected 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 because they have been 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 used a 10 cut-off for coulombic interactions and 14 cut-off for all long-distance interactions with combination of PME in addition to a switch function for the direct-space portion. 29) The story about “..angle involving the C atoms..” is greater left out. It weakens the story. There’s no sensible justification for this that I can believe of that does not automatically goes together with the wash in MD. Authors’ response: We would rather leave this aspect in since the cooperativity of the complicated salt bridges, which can be determined not by the exact nature from 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 starts with “..As already noted..” may be deleted. Here also. We would rather hold it because it is actually a reference to prior work. 31) If lysines boost (evolutionary) in the a single side in the binding interface, then what about the negative charges at the other side Authors’ response: We now address this point in the second component of the’Sequence analysis’ section and inside the Discussion section of your revised manuscript. 32) The discussion is too much a repeat on the preceding, and not adequate a discussion. Authors’ response: In 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 find out how properly the electrostatic potentials about the two proteins thatare docked fit, or how well things cancel out, or one thing like that. After all, nature wants items to be neutral. Authors’ response: We have modified Fig. 3 (Fig. four inside the revised manuscript) to illustrate the electrostatic complementarity. 34) Is Fig. 4 actually necessary Authors’ response: Figure 4 is now the Figure 1 on the revised manuscript. It’s a comparison with the PatchDock’ model (this work) with all the previously published model structure by Yuan et al. [PDB:3J2T] [25]. Both Ethyl glucuronide Metabolic Enzyme/Protease models are fitted into experimental cryo-EM density map [24]. We believe that this figure is useful, because it illustrates that the proposed PatchDock’ model matches the cryo-EM data. 35) Figures eight and 9 nicely indicate the sequence patterns, but there is a lot distraction that they practically make it tougher as an alternative to easier to determine items. Authors’ response: We utilised the Sequence Logo representation [89], a well known tool for illustrating numerous alignments of large numbers of sequences, for these figures (Figs. 9 and ten inside the revised manuscript). Inside a such presentation, the statistical significance in every position is cseen. Inside the revised manuscript, we also add a various alignment with the WD domains as Extra file 1: Figure S2. In summary, I believe this is a easy study that primarily got complicated by the enormous size in the complicated at hand. I indicated one error that ought to be fixed. I would adore to determine how their final model fits in the EM density, and I miss a little the experimental valid.
