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 related to not salt bridges per se but to “longer variety ion pairs” (as defined by Nussinov and co-workers, see [50, 51]). We were not keen on such weak interactions since they have been unlikely to contribute to triggering a major rearrangement from the WD-7 domain of Apaf-1 upon the binding of cytochrome c. As for electrostatics interactions generally, for MD simulations we used a ten 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 involving the C atoms..” is better 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 in the complex salt bridges, that is determined not by the precise nature with the lysine residue, but by the neighboring position on the two aspartate residues, might be essential for triggering the rearrangement of Apaf-1.. 30) Any sentence that starts with “..As already noted..” could be deleted. Right here also. We would rather keep it since it is usually a reference to prior operate. 31) If lysines improve (evolutionary) at the 1 side from the binding interface, then what regarding the adverse charges in the other side Authors’ response: We now address this point within the second part of the’Sequence analysis’ section and in the Discussion section on the revised manuscript. 32) The discussion is too much a repeat from the earlier, and not sufficient a discussion. Authors’ response: In the revised manuscript, we Ristomycin Protocol deleted the repeats (a minimum of, some) and have substantially expanded the Discussion. 33) In Fig. three I’d have loved to determine how effectively the electrostatic potentials about the two proteins thatare docked fit, or how effectively issues cancel out, or anything like that. After all, nature desires things to be neutral. Authors’ response: We have modified Fig. three (Fig. 4 inside the revised manuscript) to illustrate the electrostatic complementarity. 34) Is Fig. 4 genuinely necessary Authors’ response: Figure four is now the Figure 1 of your revised manuscript. It’s a comparison in the PatchDock’ model (this perform) with all the previously published model structure by Yuan et al. [PDB:3J2T] [25]. Each models are fitted into experimental cryo-EM density map [24]. We believe that this figure is useful, since it Thiodicarb Autophagy illustrates that the proposed PatchDock’ model matches the cryo-EM information. 35) Figures 8 and 9 nicely indicate the sequence patterns, but there’s a lot distraction that they almost make it tougher as opposed to less difficult to determine issues. Authors’ response: We employed the Sequence Logo representation [89], a popular tool for illustrating numerous alignments of huge numbers of sequences, for these figures (Figs. 9 and ten in the revised manuscript). In a such presentation, the statistical significance in each and every position is cseen. Within the revised manuscript, we also add a several alignment from the WD domains as Added file 1: Figure S2. In summary, I believe this can be a very simple study that primarily got complicated by the huge size in the complex at hand. I indicated a single error that really should be fixed. I would really like to see how their final model fits in the EM density, and I miss a little the experimental valid.
