Is really meant with this If all four models had already the maximal probable variety of salt bridges, then they have to all 4 be rather similar, and MD optimization would not achieve considerably added. As documented within the manuscript (Table 1 and Further files), the 3 structures that had been obtained by distinct docking computer software tools have been really distinct. They supplied unique salt bridges as well as the numbers of salt bridges had been distinct. Additionally, within the case of the PatchDock’ structure the number of salt bridges improved drastically just after power minimization (Table 1). The Reviewer is really suitable that application of your MD routine didn’t enhance the number of salt bridges any further. 20) “..manual adjustment yielded..” normally worries me a bit and may have to have a bit additional justification. 21) “.. Consequently, for the duration of manual editing, we adjusted the position of this loop in all model structures to supply salt bridge partners..” how was this accomplished Authors’ response: In the course of manual editing and further evaluation of model structures we applied the presence of salt bridges like functionally essential (as shown by experiments) residues because the main criteria. Thus, during manual editing we’ve adjusted the amino acid positions, if such an adjustment yielded a brand new salt bridge and didn’t require significant disturbance from the structure. In one particular case, we succeeded to slightly tilt the whole molecule of cytochrome c, giving salt bridge partners for the four functionally most significant lysine residues (the PatchDock’ structure). The difference in between the model structures, as supplied by distinct docking routines, could be, to some extent, precise for the interaction studied. Certainly, the compact globule of cytochrome c is practically evenly and densely covered by 18 lysine residues; practically each and every of them can potentially make a salt bridge with acidic residue (s) of a WD domain. In the revised manuscript, we explicitly state that despite the fact that our model structure could be a non-unique resolution since it issues the orientation of cytochrome c, this model structure enabled the identification with the three acidic duplets of Apaf-1 that, on one particular hand, are involved in complex, bifurcated bonds with the lysine residues of cytochrome c and, alternatively, show a distinct evolutionary pattern, 2-Cyanopyrimidine Autophagy appearing only inside Chordata, concomitantly with the look with the cytochrome c-dependent apoptotic pathway.Shalaeva et al. Biology Direct (2015) 10:Page 24 ofSince only 3 acidic duplets of Apaf-1 are within a position to interact with cytochrome c (see Figs. four and 10), we think that these acidic pairs may well bind cytochrome c, hence triggering the apoptosome formation. 22) “..and in every single of those models, lysine residues of cytochrome c formed quite a few salt bridges..” how a lot of lysines did this, all of them Quantify, please. Authors’ response: A list of all CL 316243 site lysine-involving salt bridges for each and every model, calculated before and just after power minimization, is presented in Table 1. 23) “.. Notably, the ClusPro model changed insignificantly immediately after energy minimization, while the manually edited PatchDock’ model gained six new salt bridges..” this likely may be the outcome of 1 docking server working with EMMD along with the other not, or both making use of distinct force fields, certainly one of which can be equivalent to yours Authors’ response: The ClusPro server utilized a MD method together with the CHARMM force field, exact same as we applied within the MD simulations, so the consistency of energy minimization results was expected. The oth.
