Ation, or no less than a pointer towards how this must be accomplished. Authors’ response: We are content to view that Reviewer appreciated the scale of your issue 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 together with the single exception in the 1 that had been marked as an error by the Reviewer. We still believe that we’ve got used a appropriate criterion for the salt bridges in our analysis. 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. Inside the Pamoic acid disodium Formula revised manuscript we supply 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. Naturally, we hope to find out a well-resolved crystal and or cryo-EM structure in the cytochrome cApaf-1 complex in 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 for the duration of MD simulation. Figure S2. Conservation of negatively charged residues inside the WD domains of Apaf-1 homologs. Additional file two: The PatchDock’ model structure just after power minimization. This is the structure obtained following manual editing of PatchDock-predicted model and energy minimization. The PatchDock’ model shows the most quantity of salt bridges involving functionally relevant cytochrome c residues and remained steady for the duration of molecular dynamics simulations. Further file 3: Original EM-fitted model structure [PDB:3J2T] [25] after power minimization. Additional file 4: The ClusPro-predicted model structure right after energy minimization. Additional file 5: The PatchDock-predicted model structure immediately after power minimization. Extra file 6: The initial ZDOCK-predicted model structure following power minimization. Extra file 7: The second ZDOCK-predicted model structure immediately 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, too as wrote the first draft on the manuscript, DVD performed the sequence analysis of cytochrome c, MYG performed the sequence evaluation of Apaf-1 and contributed towards the writing the manuscript, AYM created the study, interpreted the information, and wrote the final version of the manuscript. All authors read, edited and authorized the final manuscript. Acknowledgements The authors are grateful to Prof. V.P. Skulachev for drawing their focus for the potential key part with the residues of Apaf-1 within the formation of an apoptosome. The study with the authors was supported in aspect by the Osnabrueck University, Germany and also a fellowship from 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 Development Plan of the Lomonosov Moscow State University, Russia (access to the supercomputer facility), and by the Intramural Study System of t.
