Is actually meant with this If all 4 models had already the maximal possible variety of salt bridges, then they have to all four be rather related, and MD optimization wouldn’t accomplish substantially further. As documented within the manuscript (Table 1 and Further files), the three structures that were obtained by diverse docking software tools were very distinct. They provided diverse salt bridges and also the numbers of salt bridges were unique. In addition, within the case in the PatchDock’ structure the amount of salt bridges improved dramatically soon after energy minimization (Table 1). The Reviewer is quite right that application from the MD routine did not enhance the number of salt bridges any further. 20) “..manual adjustment yielded..” usually worries me a bit and may well have to have a bit far more justification. 21) “.. Hence, throughout manual editing, we adjusted the position of this loop in all model structures to provide salt bridge partners..” how was this done MB-0223 Autophagy Authors’ response: For the duration of manual editing and additional evaluation of model structures we applied the presence of salt bridges like functionally vital (as shown by experiments) residues because the principal criteria. Hence, during manual editing we’ve adjusted the amino acid positions, if such an adjustment yielded a new salt bridge and didn’t call for important disturbance with the structure. In one case, we succeeded to slightly tilt the whole molecule of cytochrome c, supplying salt bridge partners for the four functionally most significant lysine residues (the PatchDock’ structure). The distinction between the model structures, as offered by unique docking routines, might be, to some extent, particular towards the interaction studied. Certainly, the modest globule of cytochrome c is virtually evenly and densely Pentagastrin Cancer covered by 18 lysine residues; pretty much 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 while our model structure could be a non-unique option because it issues the orientation of cytochrome c, this model structure enabled the identification of the 3 acidic duplets of Apaf-1 that, on one particular hand, are involved in complicated, bifurcated bonds with the lysine residues of cytochrome c and, on the other hand, show a distinct evolutionary pattern, appearing only within Chordata, concomitantly together with the appearance from 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. 4 and 10), we believe that these acidic pairs could bind cytochrome c, hence triggering the apoptosome formation. 22) “..and in each of these models, lysine residues of cytochrome c formed quite a few salt bridges..” how numerous lysines did this, all of them Quantify, please. Authors’ response: A list of all lysine-involving salt bridges for every model, calculated just before and right after power minimization, is presented in Table 1. 23) “.. Notably, the ClusPro model changed insignificantly after energy minimization, while the manually edited PatchDock’ model gained 6 new salt bridges..” this possibly could be the outcome of a single docking server working with EMMD along with the other not, or both using various force fields, one of that is related to yours Authors’ response: The ClusPro server utilised a MD method together with the CHARMM force field, same as we employed inside the MD simulations, so the consistency of energy minimization outcomes was expected. The oth.
