Ation, or no less than a pointer towards how this should be performed. Authors’ response: We are satisfied to determine that Reviewer appreciated the scale of your trouble that the object of this study has set for theoretical calculations. We thank the reviewer for his very beneficial comments. We agreed and have taken into account all of them with the single exception with the one that had been marked as an error by the Reviewer. We nevertheless think that we have employed a proper criterion for the salt bridges in our evaluation. Figure 1a and b, the necessity of which has been questioned by the Reviewer within the comment (34), show how our final model fits inside the EM density. Within the revised manuscript we present some hints on how the functional consequences from our model may well beShalaeva et al. Biology Direct (2015) 10:Page 26 ofvalidated by mutating the acidic residues of Apaf-1. Of course, we hope to find out a well-resolved crystal and or cryo-EM structure from the cytochrome cApaf-1 complicated within the close to future.Further filesAdditional file 1: Figures S1 and S2. Figure S1. Backbone coordinates RMSD heat maps for WD domains of Apaf-1 in complex with cytochrome c in the course of MD simulation. Figure S2. Conservation of negatively charged residues in the WD domains of Apaf-1 homologs. More file two: The PatchDock’ model structure soon after power minimization. That is the structure obtained soon after manual editing of PatchDock-predicted model and power minimization. The PatchDock’ model shows the most variety of salt bridges involving functionally relevant cytochrome c residues and remained steady in the course of molecular dynamics simulations. Extra file three: Original EM-fitted model structure [PDB:3J2T] [25] following energy minimization. Added file 4: The ClusPro-predicted model structure immediately after energy minimization. Further file five: The PatchDock-predicted model structure immediately after power minimization. Further file six: The initial ZDOCK-predicted model structure following power minimization. Extra file 7: The second ZDOCK-predicted model structure following energy minimization. Abbreviations Apaf-1: Apoptotic protease activating aspect 1; CARD: Caspase activation and recruitment domain; Cryo-EM: Cryo-electron microscopy; And so on.: Electron-transfer chain; MD: Molecular dynamics; NBD: Nucleotide-binding domain; ROS: Reactive oxygen species. Competing interests The authors declare that they’ve no competing interests. Authors’ contributions DNS performed molecular modeling and MD Allosteric pka Inhibitors medchemexpress simulations, analyzed the data, also as wrote the very first draft on the manuscript, DVD performed the sequence Ferrous bisglycinate supplier evaluation of cytochrome c, MYG performed the sequence analysis of Apaf-1 and contributed towards the writing the manuscript, AYM made the study, interpreted the data, and wrote the final version on the manuscript. All authors read, edited and approved the final manuscript. Acknowledgements The authors are grateful to Prof. V.P. Skulachev for drawing their consideration for the prospective essential role with the residues of Apaf-1 within the formation of an apoptosome. The investigation in the authors was supported in portion by the Osnabrueck University, Germany plus a fellowship in the German Academic Exchange Service (DNS), grants in the Russian Science Foundation (1440592, AYM, molecular modeling of apoptosome formation, and 1400029, DVD, AYM, phylogenomic analysis of cytochrome c), by the Improvement Plan on the Lomonosov Moscow State University, Russia (access towards the supercomputer facility), and by the Intramural Research System of t.