Ation, or no less than a pointer towards how this ought to be performed. Authors’ response: We are delighted to determine that Reviewer appreciated the scale of your difficulty that the object of this study has set for theoretical calculations. We thank the reviewer for his very useful comments. We agreed and have taken into account all of them using the single exception from the a single that had been marked as an error by the Reviewer. We nevertheless believe that we have employed a appropriate criterion for the salt bridges in our evaluation. Figure 1a and b, the necessity of which has been questioned by the Reviewer inside the comment (34), show how our final model fits within the EM density. Within the revised manuscript we offer some hints on how the functional consequences from our model may beShalaeva et al. Biology Direct (2015) ten:Web page 26 ofvalidated by mutating the acidic (-)-Cedrene medchemexpress residues of Apaf-1. Naturally, we hope to see a well-resolved crystal and or cryo-EM structure of the cytochrome cApaf-1 complex in 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 during MD simulation. Figure S2. Conservation of negatively charged residues within the WD domains of Apaf-1 homologs. More file two: The PatchDock’ model structure following energy minimization. This is the structure obtained just after manual editing of PatchDock-predicted model and energy minimization. The PatchDock’ model shows by far the most quantity of salt bridges involving functionally relevant cytochrome c residues and remained steady during molecular dynamics simulations. More file 3: Original EM-fitted model structure [PDB:3J2T] [25] following energy minimization. Extra file 4: The ClusPro-predicted model structure after energy minimization. More file five: The PatchDock-predicted model structure right after power minimization. More file 6: The initial ZDOCK-predicted model structure right after power minimization. Additional file 7: The second ZDOCK-predicted model structure right after energy minimization. Abbreviations Apaf-1: Apoptotic protease activating factor 1; CARD: Caspase activation and recruitment domain; Cryo-EM: Cryo-electron microscopy; And so forth.: 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 very first draft on the manuscript, DVD performed the sequence evaluation of cytochrome c, MYG performed the sequence evaluation of Apaf-1 and N-(3-Hydroxytetradecanoyl)-DL-homoserine lactone MedChemExpress contributed for the writing the manuscript, AYM designed the study, interpreted the data, and wrote the final version on the manuscript. All authors study, edited and authorized the final manuscript. Acknowledgements The authors are grateful to Prof. V.P. Skulachev for drawing their interest for the possible essential function on the residues of Apaf-1 inside the formation of an apoptosome. The research of your authors was supported in element by the Osnabrueck University, Germany as well as 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 Program from the Lomonosov Moscow State University, Russia (access for the supercomputer facility), and by the Intramural Study System of t.
