Ation, or no less than a pointer towards how this ought to be performed. Authors’ response: We’re happy to see that Reviewer appreciated the scale with the problem that the object of this study has set for theoretical calculations. We thank the reviewer for his quite beneficial comments. We agreed and have taken into account all of them with the single exception from the 1 that had been marked as an error by the Reviewer. We still believe that we’ve got employed a right criterion for the salt bridges in our analysis. Figure 1a and b, the necessity of which has been questioned by the Reviewer inside the comment (34), show how our final model fits in the EM density. Inside the revised manuscript we provide some hints on how the functional consequences from our model could possibly beShalaeva et al. Biology Direct (2015) 10:Page 26 ofvalidated by mutating the acidic residues of Apaf-1. Obviously, we hope to determine a well-resolved crystal and or cryo-EM structure from the cytochrome cApaf-1 complicated inside the near future.Extra 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 inside the WD domains of Apaf-1 homologs. More file 2: The PatchDock’ model structure right after energy minimization. This is the structure obtained soon after manual editing of PatchDock-predicted model and power minimization. The PatchDock’ model shows essentially the most number of salt bridges involving functionally relevant cytochrome c residues and remained stable during molecular dynamics simulations. Additional file 3: Original EM-fitted model structure [PDB:3J2T] [25] immediately after power minimization. Additional file 4: The ClusPro-predicted model structure just after power minimization. Extra file 5: The PatchDock-predicted model structure after power minimization. Further file six: The very first ZDOCK-predicted model structure soon after energy minimization. More file 7: The second ZDOCK-predicted model structure right after energy minimization. Abbreviations Apaf-1: Apoptotic protease activating issue 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, as well as wrote the initial draft of your manuscript, DVD performed the sequence analysis of cytochrome c, MYG performed the sequence evaluation of Apaf-1 and contributed for the writing the manuscript, AYM developed the study, interpreted the information, and wrote the final version from the manuscript. All authors study, Altafur Biological Activity edited and approved the final manuscript. Acknowledgements The authors are grateful to Prof. V.P. Skulachev for drawing their interest to the potential essential role from the residues of Apaf-1 inside the formation of an apoptosome. The study on the authors was supported in portion by the Osnabrueck Cyclohexanecarboxylic acid supplier University, Germany plus a fellowship in the German Academic Exchange Service (DNS), grants from the Russian Science Foundation (1440592, AYM, molecular modeling of apoptosome formation, and 1400029, DVD, AYM, phylogenomic analysis of cytochrome c), by the Improvement Plan with the Lomonosov Moscow State University, Russia (access to the supercomputer facility), and by the Intramural Investigation Plan of t.
