An update of the chemiosmotic theory as suggested by possible proton currents inside the coupling membrane

Understanding how biological systems convert and store energy is a primary purpose of basic research. However, despite Mitchell's chemiosmotic theory, we are far from the complete description of basic processes such as oxidative phosphorylation (OXPHOS) and photosynthesis. After more than half a century, the chemiosmotic theory may need updating, thanks to the latest structural data on respiratory chain complexes. In particular, up-to date technologies, such as those using fluorescence indicators following proton displacements, have shown that proton translocation is lateral rather than transversal with respect to the coupling membrane. Furthermore, the definition of the physical species involved in the transfer (proton, hydroxonium ion or proton currents) is still an unresolved issue, even though the latest acquisitions support the idea that protonic currents, difficult to measure, are involved. Moreover, FoF1-ATP synthase ubiquitous motor enzyme has the peculiarity (unlike most enzymes) of affecting the thermodynamic equilibrium of ATP synthesis. It seems that the concept of diffusion of the proton charge expressed more than two centuries ago by Theodor von Grotthuss is to be taken into consideration to resolve these issues. All these uncertainties remind us that also in biology it is necessary to consider the Heisenberg indeterminacy principle, which sets limits to analytical questions.

As you will see from the reviewer's comments below, there are a number of criticisms that prevent us from accepting your manuscript at this stage. The reviewer suggest, however, that a revised version could be acceptable, if you are able to address their concerns. If you think that you can deal satisfactorily with the reviewer's suggestions, we would be pleased to consider a revised manuscript.
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The Open Biology Team mailto: openbiology@royalsociety.org Reviewer's Comments to Author(s): The submitted manuscript deals with an interesting area of energy transduction and its coupling in biological system. In general, this subject would be interesting for a wide group of readers. Partially, consideration and critical analysis of P. Mitchell theory is certainly very appreciated. However, at the present form the manuscript does not satisfy the aim it has been created for. Instead of comprehensive and detailed analysis the authors made a strong but strange suggestion that the P. Mitchell has to be rejected because non-mitochondrial phosphorylation had been found. This conclusion does not really matter to the theory because the main aspect of chemoosmatic theory is a COUPLING MEMBRANE. The general phenomenon is the local energetic barriers near the membrane which create a new possible ability of local coupling. However, this aspect just modifies but does not reject the theory. It needs to be considered and described properly. The text is filled up with many cites of reviews and researches but for a reader it looks like nonsystemic. There is no real idea what is a new hypothesis on coupling which is postulated in the title. Extra-mitochondrial phosphorylation is not a new hypothesis of coupling. Possibly, authors need to discuss a parallel existence of proton leakage and transport in the channel. Explain the role of local processes for the coupling. And it will be development but not rejection of Mitchell theory. It will make an appropriate level of knowledge for the readers. Additionally, the figures in the manuscript are too schematic and could be improved. If the main aim is to discover the mechanism of coupling at least one figure must contain many details and indications of the process. Thus, the illustrative materials have to be essentially improved. For minor but essential remarks. In line 236 in the phrase "..transversal or permeability diffusion coefficients…" the word "diffusion" must be omitted. The references are prepared in inaccurate manner. In particular, in line 800 ref.# 117 is formed as a mistake.
Author's Response to Decision Letter for (RSOB-18-0221.R0) As you will see from the reviewer's comments below, there are a number of criticisms that prevent us from accepting your manuscript at this stage. The reviewer suggests, however, that a revised version could be acceptable, if you are able to address their concerns. If you think that you can deal satisfactorily with the reviewer's suggestions, we would be pleased to consider a revised manuscript.
--> We thank the Editor and the Referee for their considerations and suggestion. In the revised version, have addressed all the issues raised by the Referee. All the changes made in the text are marked in blue.<--Reviewer's Comments to Author(s): The submitted manuscript deals with an interesting area of energy transduction and its coupling in biological system. In general, this subject would be interesting for a wide group of readers. Partially, consideration and critical analysis of P. Mitchell theory is certainly very appreciated. However, at the present form the manuscript does not satisfy the aim it has been created for. Instead of comprehensive and detailed analysis the authors made a strong but strange suggestion that the P. Mitchell has to be rejected because non-mitochondrial phosphorylation had been found. This conclusion does not really matter to the theory because the main aspect of chemoosmatic theory is a COUPLING MEMBRANE. The general phenomenon is the local energetic barriers near the membrane which create a new possible ability of local coupling. However, this aspect just modifies but does not reject the theory. It needs to be considered and described properly.
--> We agree with the Reviewer that the main aspect of chemio-osmotic theory is a coupling membrane. In the revised manuscript, we have eliminated the suggestion that the existence of a non-mitochondrial phosphorylation allows to reject the P. Mitchell theory, focusing our attention to the possible local coupling. For the same reason, we have also changed the title of the manuscript in: "AN UPDATE OF THE CHEMIOSMOTIC THEORY AS SUGGESTED BY POSSIBLE PROTON CURRENTS INSIDE THE COUPLING MEMBRANE" <-- The text is filled up with many cites of reviews and researches but for a reader it looks like nonsystemic.
--> We thank for this suggestion. In the revised manuscript, we have checked the references list and their citation in the text. <--There is no real idea what is a new hypothesis on coupling which is postulated in the title. Extramitochondrial phosphorylation is not a new hypothesis of coupling. Possibly, authors need to discuss a parallel existence of proton leakage and transport in the channel. Explain the role of local processes for the coupling. And it will be development but not rejection of Mitchell theory. It will make an appropriate level of knowledge for the readers.
--> We agree with the Reviewer. Indeed, the extra-mitochondrial phosphorylation was cited to justify the idea of proton currents occurring inside the Coupling Membrane instead of across it: considering that the extra-mitochondrial phosphorylation takes place outside the plasmamembrane, free protons could not accumulate there. Therefore, in the revised version, to highlight the crucial existence of proton currents inner the membrane we proposed the following new title : "AN UPDATE OF THE CHEMIOSMOTIC THEORY AS SUGGESTED BY POSSIBLE PROTON CURRENTS INSIDE THE COUPLING MEMBRANE". <--Additionally, the figures in the manuscript are too schematic and could be improved. If the main aim is to discover the mechanism of coupling at least one figure must contain many details and indications of the process. Thus, the illustrative materials have to be essentially improved.
--> We apologize for the poor quality of the images. In the revised version, the three figures were changed, adding more details and indications. <--For minor but essential remarks. In line 236 in the phrase "..transversal or permeability diffusion coefficients…" the word "diffusion" must be omitted.
--> We thank to Reviewer for this suggestion. The word "diffusion" was eliminated in the revised version <-- The references are prepared in inaccurate manner. In particular, in line 800 ref.# 117 is formed as a mistake.
--> We apologize for inaccuracy in the references. In the revised version, we have checked and correct the references list. ß

c) Introduction Yes
Is the length of the paper justified? Yes

Comments to the Author
The revised version of the manuscript is improved in general according to the reviewers' comments. Unfortunately, some technical errors still exist in the text (for example, on Page 7 line 29, missed space). Nevertheless, it seems to be in general appropriate for presentation to a common reader. Certainly, many aspects of membrane bioenergetics still remain unclear and they are the points of the discussion. Not all of them included into the review. However, the point of view represented in the submitted manuscript is a general point of possible discussion and it seems to be a background of further development of the coupling theory.

13-Mar-2019
Dear Dr Morelli We are pleased to inform you that your manuscript RSOB-18-0221.R1 entitled "AN UPDATE OF THE CHEMIOSMOTIC THEORY AS SUGGESTED BY POSSIBLE PROTON CURRENTS INSIDE THE COUPLING MEMBRANE" has been accepted by the Editor for publication in Open Biology.
The referee does not recommend any further changes that need to be made. However, we would like to request that the authors carry out a final proof-read of the manuscript and upload the final files for publication.
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Online supplementary material will also carry the title and description provided during submission, so please ensure these are accurate and informative. Note that the Royal Society will not edit or typeset supplementary material and it will be hosted as provided. Please ensure that the supplementary material includes the paper details (authors, title, journal name, article DOI Referee: Comments to the Author(s) The revised version of the manuscript is improved in general according to the reviewers' comments. Unfortunately, some technical errors still exist in the text (for example, on Page 7 line 29, missed space). Nevertheless, it seems to be in general appropriate for presentation to a common reader. Certainly, many aspects of membrane bioenergetics still remain unclear and they are the points of the discussion. Not all of them included into the review. However, the point of view represented in the submitted manuscript is a general point of possible discussion and it seems to be a background of further development of the coupling theory.
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