Ure of its conclusions, the general image is pretty compelling and will probably withstand the scrutiny of further experimental studies. Triggering and guiding the follow-up verification experiments, even though potentially refuting a few of the conjectures within the operate of Shalaeva et al., might be thought of among the crucial impacts of this publication Authors’ response: We thank the reviewer for these intriguing comments, and agree that evolutionary studies played the key part in establishing significance of Sudan IV Protocol predicted interactions. How the cytochrome c dependent apoptotic mechanism may have emerged is an intriguing question indeed. In organisms with cytochrome c-independent apoptosome formation, Apaf-1 molecules are prevented from oligomerization by getting bound to some cellular partners and getting released only in response to an apoptotic signal, see [11] for any Polyinosinic-polycytidylic acid Activator critique. Most likely, cytochrome c got involved in certainly one of such apoptotic cascades just by possibility, supplying an added effective hyperlink involving mitochondrial damage and apoptosis. On one particular hand, the tiny size of cytochrome c and its place within the intermembrane space lead to its prompt look inside the cytoplasm following mitochondrial harm. Alternatively, the lysine residues of cytochrome c, which evolved already within bacteria to facilitate the interactions inside respiratory chains [14], could complement a number of surface acidic residues on the WD domains of Apaf-1; these residues are normally typical for WD domains [17, 19, 90, 91], which, apparently, also emerged within bacteria [92]. Nature could just choose for a binding mode for cytochrome cReviewers’ comments We thank the reviewers for their useful comments and valuable ideas that helped us increase the manuscript.Reviewer’s report 1: Prof. Andrei L. Osterman, Sanford-Burnham Medical Investigation Institute, La Jolla, California 92037, USAReviewer 1: The manuscript by D. Shalaeva et al. “Modeling of interaction between cytochrome c and Apaf-1: bifurcated salt bridges underlying apoptosome assembly” is addressing an intriguing and fundamentally vital issue. How the two seemingly unrelated proteins with distinct evolutionary history, molecular functions and compartmentalization recognize one another and type a unique molecular machine of cellular self-distraction The importance of this recognition and assembly is really obvious thinking about devastating prospective consequences of imprecision, the untimely cell death or even much more harmful immortality (as in malignant transformation). Remarkably, although various experimental research in this subject area provided wealthy and diverse information, none of them proposed a sufficiently detailed mechanistic model. Furthermore to apparent experimental difficulties, this is also due to the general tendency of such (or any other) studies to concentrate on one particular particular technology, which normally falls quick of supplying sufficient resolution to effectively address such aShalaeva et al. Biology Direct (2015) ten:Page 19 ofthat would cause the activation of Apaf-1. Additional choice would just have increased the specificity of interaction involving cytochrome c and Apaf-1. Within the revised manuscript, we discuss in extra detail the evolutionary implications from our study, as well as the potential verification experiments.Reviewer’s report 2: Prof. Narayanaswamy Srinivasan, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, IndiaAuthors’ response: The application that we made use of for calc.
