Ation, or no less than a pointer towards how this ought to be performed. Authors’ response: We are content to see that Reviewer appreciated the scale with the trouble that the object of this study has set for theoretical calculations. We thank the reviewer for his incredibly helpful comments. We agreed and have taken into account all of them together with the single exception from the one particular that had been marked as an error by the Reviewer. We still believe that we have employed a suitable criterion for the salt bridges in our analysis. Figure 1a and b, the necessity of which has been questioned by the Reviewer in the comment (34), show how our final model fits in the EM density. Within the revised manuscript we give some hints on how the functional consequences from our model could beShalaeva et al. Biology Direct (2015) 10:Page 26 ofvalidated by mutating the acidic residues of Apaf-1. Of course, we hope to see a well-resolved crystal and or cryo-EM structure in the cytochrome cApaf-1 complicated within the near future.More filesAdditional file 1: Figures S1 and S2. Figure S1. Backbone coordinates RMSD heat maps for WD domains of Apaf-1 in complicated with cytochrome c through MD simulation. Figure S2. Conservation of negatively charged residues in the WD domains of Apaf-1 homologs. Added file two: The PatchDock’ model structure after energy minimization. That is the structure obtained just after manual editing of PatchDock-predicted model and energy minimization. The PatchDock’ model shows by far the most number of salt bridges involving functionally relevant cytochrome c residues and remained steady throughout molecular dynamics simulations. More file 3: Original EM-fitted model structure [PDB:3J2T] [25] right after energy minimization. More file 4: The ClusPro-predicted model structure after power minimization. Additional file 5: The PatchDock-predicted model structure after energy minimization. Added file six: The first ZDOCK-predicted model structure right after power minimization. Extra file 7: The second ZDOCK-predicted model structure soon after energy minimization. Abbreviations Apaf-1: Apoptotic protease activating element 1; CARD: Caspase activation and recruitment domain; Cryo-EM: Cryo-electron microscopy; Etc.: Electron-transfer chain; MD: Molecular dynamics; NBD: Nucleotide-binding domain; ROS: Reactive oxygen species. Competing interests The authors declare that they have no competing interests. Authors’ contributions DNS performed molecular modeling and MD simulations, analyzed the data, at the same time as wrote the initial draft from the manuscript, DVD performed the sequence analysis of cytochrome c, MYG performed the sequence evaluation of Apaf-1 and contributed to the writing the manuscript, AYM created the study, interpreted the information, and wrote the final version on the manuscript. All authors study, edited and approved the final manuscript. Acknowledgements The authors are grateful to Prof. V.P. Skulachev for drawing their Etiocholanolone Formula attention towards the possible crucial role with the residues of Apaf-1 within the formation of an apoptosome. The analysis from the authors was supported in element by the Osnabrueck University, Germany and also 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 Development Program from the SKI-178 Immunology/Inflammation Lomonosov Moscow State University, Russia (access towards the supercomputer facility), and by the Intramural Research System of t.
