Red to experimental information, predictions of pKa values within a couple of seconds. For the Apaf-1 and cytochrome c, PROPKA predicted the lysine residues to be protonated (positively charged) whereas residues of aspartate and glutamate to be deprotonated (negatively charged). Naturally, this can be not always the case in proteins, and for buried, functionally relevant amino acid residues deviations from this rule were described [96]. Nevertheless, provided that the residues that had been implied inside the formation of salt bridges in between cytochrome c and Apaf-1 have been exclusively surface positioned, these trivial assumptions on their protonation states appear to become reasonable. The pairs of neighboring acidic residues around the surface of Apaf-1 could, in principle, share a proton even in spite of their surface place. Having said that, inside the presence of a positively charged lysine residue (see Figs. two and three) even partial protonation of these carboxyl groups is really unlikely 4ebp1 Inhibitors Related Products simply because of simple electrostatic factors. Query two. Referring to “dynamic nature” of interactions which can be observed in MD simulations, it will be interesting to analyze Fig. five when it comes to major states (long-living interactions) current amongst corresponding residues. Authors’ response: We thank the reviewer for this comment. Indeed, the essential function of the interactions described is their dynamic nature; none from the contacts observed was long-living. Alternatively, every single distinct get in touch with was lost then regained at picoseconds. The only exceptions had been salt bridges among residues Lys25 and Asp941 at the same time as Lys8 and Asp1147, which could possibly be maintained for as much as ten ns, see Fig. five. In the revised manuscript, we’ve got updated Fig. five to include things like the graph for distance between Lys86 and Asp1064, and have rescaled the Y axis (distances) to better illustrate the mobility of residues. To provide additional details concerning the dynamic properties ofthe salt bridges, we’ve added a brand new Table three in to the revised manuscript. Additionally, we plotted the distances among proton donor and acceptor atoms of interacting residues against one another for every single with the three steady bifurcated bridges (see the new Fig. six). Question three. The binding of cytochrome C to WD domains on the apoptotic activating aspect Apaf-1 is generalizedhypothesized inside the discussion onto the potential role of WD domains in “transmitting mechanical signals rather than their purely structural role”. This idea need to be explained and formulated in additional clear way. Authors’ response: We’ve got expanded the respective section on the Discussion.Reviewer’s report four: Prof. Gerrit Vriend, Centre for Molecular and Biomolecular Informatics, Radboud University Health-related Centre, Nijmegen, The NetherlandsReviewer 4: I am not familiar with cytochrome c at all and Zinc Protoporphyrin site poorly read-in on apoptosis, which, I guess, disqualifies me a bit as a referee. But I’ll do my finest. 1) As a bioinformatician, I normally get worried when I read that protein structures got `improved’ by molecular dynamics. MD is a nice method, but our YASARA experiences [85] created clear that MD normally drives structure models away from the accurate minimum. Authors’ response: We completely agree with the notion that MD simulations could possibly drive structures away in the true power minima. For that reason, in our article, we initially obtained energy minimized model structures and only then made use of MD simulations to tackle the dynamics of a number of them. Within the revised version we’ve got replaced `improved’ with a more.
