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Difference between revisions of "MitoEAGLE preprint 2017-09-21"

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{{MITOEAGLE}}
{{MITOEAGLE}}
{{Publication
{{Publication
|title=MitoEAGLE preprint 2018-02-06(21) The protonmotive force and respiratory control. - http://www.mitoeagle.org/index.php/MitoEAGLE_preprint_2017-09-21.
|title=MitoEAGLE preprint 2018-02-18(21) The protonmotive force and respiratory control.
|info=<big></big> [[File:PDF.jpg|120px|link=http://www.mitoeagle.org/images/5/5b/MitoEAGLE_preprint_2017-09-21.pdf |Bioblast pdf]] - » [http://www.mitoeagle.org/index.php/File:MitoEAGLE_preprint_2017-09-21.pdf Versions] -- '''Next step » [[MitoEAGLE preprint 2018-02-08]]'''
|info=<big></big> [[File:PDF.jpg|120px|link=http://www.mitoeagle.org/images/5/5b/MitoEAGLE_preprint_2017-09-21.pdf |Bioblast pdf]] - » [http://www.mitoeagle.org/index.php/File:MitoEAGLE_preprint_2017-09-21.pdf Versions]
|authors='''''Corresponding author:''''', Gnaiger E, '''''Contributing co-authors:''''', Ahn B, Alves MG, Amati F, Aral C, Arandarcikaite O, Asander Frostner E, Bailey DM, Bastos Sant'Anna Silva AC, Battino M, Beard DA, Ben-Shachar D, Bishop D, Breton S, Brown GC, Brown RA, Buettner GR, Calabria E, Cardoso LHD, Carvalho E, Casado Pinna M, Cervinkova Z, Chang SC, Chicco AJ, Chinopoulos C, Coen PM, Collins JL, Crisostomo L, Davis MS, Dias T, Distefano G, Doerrier C, Drahota Z, Duchen MR, Ehinger J, Elmer E, Endlicher R, Fell DA, Ferko M, Ferreira JCB, Filipovska A, Fisar Z, Fisher J, Garcia-Roves PM, Garcia-Souza LF, Genova ML, Gonzalo H, Goodpaster BH, Gorr TA, Grefte S, Han J, Harrison DK, Hellgren KT, Hernansanz P, Holland O, Hoppel CL, Houstek J, Hunger M, Iglesias-Gonzalez J, Irving BA, Iyer S, Jackson CB, Jansen-Duerr P, Jespersen NR, Jha RK, Kaambre T, Kane DA, Kappler L, Karabatsiakis A, Keijer J, Keppner G, Komlodi T, Kopitar-Jerala N, Krako Jakovljevic N, Kuang J, Kucera O, Labieniec-Watala M, Lai N, Laner V, Larsen TS, Lee HK, Lemieux H, Lerfall J, Lucchinetti E, MacMillan-Crow LA, Makrecka-Kuka M, Meszaros AT, Michalak S, Moisoi N, Molina AJA, Montaigne D, Moore AL, Mracek T, Muntane J, Muntean DM, Murray AJ, Nedergaard J, Nemec M, Newsom S, Nozickova K, O'Gorman D, Oliveira PF, Oliveira PJ, Orynbayeva Z, Pak YK, Palmeira CM, Patel HH, Pecina P, Pereira da Silva Grilo da Silva F, Pesta D, Petit PX, Pichaud N, Pirkmajer S, Porter RK, Pranger F, Prochownik EV, Puurand M, Radenkovic F, Reboredo P, Renner-Sattler K, Robinson MM, Rohlena J, Roesland GV, Rossiter HB, Rybacka-Mossakowska J, Salvadego D, Scatena R, Schartner M, Scheibye-Knudsen M, Schilling JM, Schlattner U, Schoenfeld P, Scott GR, Shabalina IG, Shevchuk I, Siewiera K, Singer D, Sobotka O, Spinazzi M, Stankova P, Stier A, Stocker R, Sumbalova Z, Suravajhala P, Tanaka M, Tandler B, Tepp K, Tomar D, Towheed A, Tretter L, Trivigno C, Tronstad KJ, Trougakos IP, Tyrrell DJ, Urban T, Velika B, Vendelin M, Vercesi AE, Victor VM, Villena JA, Wagner BA, Ward ML, Watala C, Wei YH, Wieckowski MR, Wohlwend M, Wolff J, Wuest RCI, Zaugg K, Zaugg M, Zorzano A, '''''Supporting co-authors:''''', Bakker BM, Bernardi P, Boetker HE, Borsheim E, Borutaite V, Bouitbir J, Calbet JA, Calzia E, Chaurasia B, Clementi E, Coker RH, Collin A, Das AM, De Palma C, Dubouchaud H, Durham WJ, Dyrstad SE, Engin AB, Fornaro M, Gan Z, Garlid KD, Garten A, Genova ML, Gourlay CW, Granata C, Haas CB, Haavik J, Haendeler J, Hand SC, Hepple RT, Hickey AJ, Hoel F, Jang DH, Kainulainen H, Khamoui AV, Klingenspor M, Koopman WJH, Kowaltowski AJ, Krajcova A, Lane N, Lenaz G, Malik A, Markova M, Mazat JP, Menze MA, Methner A, Neuzil J, Oliveira MT, Pallotta ML, Parajuli N, Pettersen IKN, Porter C, Pulinilkunnil T, Ropelle ER, Salin K, Sandi C, Sazanov LA, Silber AM, Skolik R, Smenes BT, Soares FAA, Sokolova I, Sonkar VK, Swerdlow RH, Szabo I, Trifunovic A, Thyfault JP, Valentine JM, Vieyra A, Votion DM, Williams C, Zischka H
|year=2017
|journal=MitoEAGLE preprint
|abstract=Clarity of concept and consistency of nomenclature are key trademarks of a research field. These trademarks facilitate effective transdisciplinary communication, education, and ultimately further discovery. As the knowledge base and importance of mitochondrial physiology to human health expand, the necessity for harmonizing nomenclature concerning mitochondrial respiratory states and rates has become increasingly apparent. Peter Mitchell’s chemiosmotic theory establishes the links between electric and chemical components of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theory and nomenclature for mitochondrial physiology and bioenergetics. Herein, we follow IUPAC guidelines on general terms of physical chemistry, extended by considerations on open systems and irreversible thermodynamics. The protonmotive force is not a vector force as defined in physics. This conflict is resolved by the generalized formulation of isomorphic, compartmental forces in energy transformations. We align the nomenclature and symbols of classical bioenergetics with a concept-driven constructive terminology to express the meaning of each quantity clearly and consistently. Uniform standards for evaluation of respiratory states and rates will ultimately support the development of databases of mitochondrial respiratory function in species, tissues, and cells studied under diverse physiological and experimental conditions. In this position statement, in the frame of COST Action MitoEAGLE, we endeavour to provide a balanced view on mitochondrial respiratory control, a fundamentally updated presentation of the concept of the protonmotive force, and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes.
 
'''Note''': Subscript ‘§’ indicates throughout the text those parts, where ''potential differences'' provide a mathematically correct but physicochemically incomplete description and should be replaced by ''stoichiometric potential differences'' ([[Gnaiger 1993 Pure Appl Chem |Gnaiger 1993b]]). A unified concept on vectorial motive transformations and scalar chemical reactions will be derived elsewhere (Gnaiger, in prep.). Appreciation of the fundamental distinction between ''differences of potential'' versus ''differences of stoichiometric potential'' may be considered a key to critically evaluate the arguments presented in Section 3 on the protonmotive force. Since this discussion appears to be presently beyond the scope of a MitoEAGLE position statement, Section 3 will be removed from the [[MitoEAGLE preprint 2018-02-08 |'''next version''']] and final manuscript. This section should become a topic of discussion within [[WG1 MitoEAGLE protocols, terminology, documentation |Working Group 1]] of the MitoEAGLE consortium, following a primary peer-reviewed publication of the concept of stoichiometric potential differences.


:::: '''Published''': » Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. doi:10.26124/bec:2020-0001.v1. - [[BEC_2020.1_doi10.26124bec2020-0001.v1 |»Bioblast link«]]


|authors=MitoEAGLE
|year=2018
|journal=MitoEAGLE
|abstract='''Note''': Subscript ‘§’ indicates throughout the text those parts, where ''potential differences'' provide a mathematically correct but physicochemically incomplete description and should be replaced by ''stoichiometric potential differences'' ([[Gnaiger 1993 Pure Appl Chem |Gnaiger 1993b]]). A unified concept on vectorial motive transformations and scalar chemical reactions will be derived elsewhere (Gnaiger, in prep.). Appreciation of the fundamental distinction between ''differences of potential'' versus ''differences of stoichiometric potential'' may be considered a key to critically evaluate the arguments presented in Section 3 on the protonmotive force. Since this discussion appears to be presently beyond the scope of a MitoEAGLE position statement, Section 3 is removed from the next version and [[Gnaiger 2019 MitoFit Preprint Arch |'''final manuscript''']]. This section should become a topic of discussion within [[WG1 MitoEAGLE protocols, terminology, documentation |Working Group 1]] of the MitoEAGLE consortium, following a primary peer-reviewed publication of the concept of stoichiometric potential differences.
|keywords=Mitochondrial respiratory control, coupling control, mitochondrial preparations, protonmotive force, chemiosmotic theory, oxidative phosphorylation, OXPHOS, efficiency, electron transfer, ET; proton leak, LEAK, residual oxygen consumption, ROX, State 2, State 3, State 4, normalization, flow, flux
|keywords=Mitochondrial respiratory control, coupling control, mitochondrial preparations, protonmotive force, chemiosmotic theory, oxidative phosphorylation, OXPHOS, efficiency, electron transfer, ET; proton leak, LEAK, residual oxygen consumption, ROX, State 2, State 3, State 4, normalization, flow, flux
|editor=[[Gnaiger E]]
}}
}}
[[File:OXPHOS system.png|right|400px|thumb|Fig. 1. The oxidative phosphorylation (OXPHOS) system. Electron transfer pathways (A) are coupled to the phosphorylation pathway (B).]]
{{MitoEAGLE preprint 1 Phases}}


[[File:Coupling in OXPHOS.png|right|400px|thumb|Fig. 2. The proton circuit and coupling in oxidative phosphorylation (OXPHOS). Modified after [[Gnaiger_2014_MitoPathways#Chapter_1._Real-time_OXPHOS_analysis |Gnaiger 2014 MitoPathways]].]]
[[File:Coupling in OXPHOS.png|right|400px|thumb|Fig. 2. The proton circuit and coupling in oxidative phosphorylation (OXPHOS). Modified after [[Gnaiger_2014_MitoPathways#Chapter_1._Real-time_OXPHOS_analysis |Gnaiger 2014 MitoPathways]].]]


[[Gentle_Science#Preprints_for_Gentle_Science |'''Preprints for Gentle Science''']]
[[Gentle_Science#Preprints_for_Gentle_Science |'''Preprints for Gentle Science''']]
:::: Citation:
:::: MitoEAGLE preprint 2017-09-21(Version 21). The protonmotive force and respiratory control. - http://www.mitoeagle.org/index.php/MitoEAGLE_preprint_2017-09-21
'''Authors'''
:::: '''Contributing co-authors''': ''Confirming to have read the final manuscript, possibly to have made additions or suggestions for improvement, and to agree to implement the recommendations into future manuscripts, presentations and teaching materials. (alphabetical, to be extended)''
:::: '''Supporting co-authors''': ''Confirming to have read the final manuscript, and to agree to implement the recommendations into future manuscripts, presentations and teaching materials. (alphabetical, to be extended)''
'''Discussion'''
::::» [[Talk:MitoEAGLE preprint 2017-09-21]]
::::» [[Talk:The protonmotive force and respiratory control| Phase 1]]
'''Concept''': [[COST Action MitoEAGLE |COST Action MitoEAGLE]]
::::* Phase 1: [[The protonmotive force and respiratory control |44 versions until 2017-09-18]]
::::* '''Phase 2 (2017-09-21 ongoing): MitoEAGLE preprint''' - with updates on route to let the final publication fly. Feedback, suggestions, and confirmation from co-authors.
::::* Phase 3: [[MiP2017/MitoEAGLE Hradec Kralove CZ]] - Discussion of manuscript submission for journal publication. Contact the editor(s) of our finally targeted journal(s), to obtain a first opinion if submission to this journal will be adequate. Cell Metabolism and BBA have been mentioned as possible preferences.
::::* Phase 4: Manuscript submission to a preprint server, such as [[BioRxiv]] and a peer-reviewed open access journal that is indexed by ''The Web of Science'' and ''PubMed''.


  <big>'''Section 2: Oxidative phosphorylation and coupling states in mitochondrial preparations'''</big>
  <big>'''Section 2: Oxidative phosphorylation and coupling states in mitochondrial preparations'''</big>
[[File:Uncoupling.png|400px|thumb|Fig. 3. Mechanisms of respiratory uncoupling.]]
[[File:OXPHOS compartments.png|400px|thumb|Fig. 7. Four-compartmental model of oxidative phosphorylation with respiratory states (ET, OXPHOS, LEAK) and corresponding rates (''E, P, L''). Modified from Gnaiger (2014).]]
[[File:Table Coupling states.png|400px]] [[File:Table Coupling terms.png|400px]] [[File:Table Chance states.png|400px]]


  <big>'''Section 3: The protonmotive force and proton flux'''</big>
  <big>'''Section 3: The protonmotive force and proton flux'''</big>
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[[File:Table Power, exergy, force, flux, advancement.png|400px]]
[[File:Table Power, exergy, force, flux, advancement.png|400px]]


 
{{Keywords: Force and membrane potential}}
<big>'''Section 4: Normalization: fluxes and flows'''</big>
{{Keywords: pH}}
 
[[File:Rate.png|left|400px|thumb|Fig. 9. Different meanings of rate may lead to confusion, if the normalization is not sufficiently specified.]]
 
[[File:Mt-recovery.png|right|400px|thumb|Fig. 10. Mitochondrial recovery, ''Y<sub>mtE</sub>'', in preparation of isolated mitochondria.]]
 
 
[[File:Table Sample concentrations and normalization of flux.png|left|400px|thumb|]]
 
[[File:Flow in structure-function analysis.png|right|400px|thumb|Fig. 11. Structure-function analysis of performance of an object ''X'' (an organism, organ or tissue, or a cell). O<sub>2</sub> flow, ''I''<sub>''X'',O2</sub>, is the product of performance per functional element (element function, mitochondria-specific flux), element density (mitochondrial density, ''D<sub>mtE</sub>''), and size of the object ''X'' (mass ''M<sub>X</sub>'').]]
 
[[File:Table Sample types.png|400px]]


{{Labeling
{{Labeling
|area=Respiration, mt-Awareness
|additional= MitoEAGLEPublication
|preparations=Permeabilized cells, Permeabilized tissue, Homogenate, Isolated mitochondria
|enzymes=Marker enzyme
|topics=Coupling efficiency;uncoupling, Flux control, mt-Membrane potential, Uncoupler
|couplingstates=LEAK, OXPHOS, ET
|pathways=ROX
}}
}}

Latest revision as of 11:48, 23 May 2020


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COST Action CA15203 (2016-2021): MitoEAGLE
Evolution-Age-Gender-Lifestyle-Environment: mitochondrial fitness mapping


MitoEAGLE preprint 2017-09-21


Publications in the MiPMap
MitoEAGLE preprint 2018-02-18(21) The protonmotive force and respiratory control.

» Bioblast pdf - » Versions

Published: » Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. doi:10.26124/bec:2020-0001.v1. - »Bioblast link«

MitoEAGLE (2018) MitoEAGLE

Abstract: Note: Subscript ‘§’ indicates throughout the text those parts, where potential differences provide a mathematically correct but physicochemically incomplete description and should be replaced by stoichiometric potential differences (Gnaiger 1993b). A unified concept on vectorial motive transformations and scalar chemical reactions will be derived elsewhere (Gnaiger, in prep.). Appreciation of the fundamental distinction between differences of potential versus differences of stoichiometric potential may be considered a key to critically evaluate the arguments presented in Section 3 on the protonmotive force. Since this discussion appears to be presently beyond the scope of a MitoEAGLE position statement, Section 3 is removed from the next version and final manuscript. This section should become a topic of discussion within Working Group 1 of the MitoEAGLE consortium, following a primary peer-reviewed publication of the concept of stoichiometric potential differences. Keywords: Mitochondrial respiratory control, coupling control, mitochondrial preparations, protonmotive force, chemiosmotic theory, oxidative phosphorylation, OXPHOS, efficiency, electron transfer, ET; proton leak, LEAK, residual oxygen consumption, ROX, State 2, State 3, State 4, normalization, flow, flux


Questions.jpg


Click to expand or collaps
» Manuscript phases and versions

Manuscript phases and versions - an open-access apporach

COST Action MitoEAGLE
This manuscript on ‘Mitochondrial respiratory states and rates’ is a position statement in the frame of COST Action CA15203 MitoEAGLE. The list of coauthors evolved beyond phase 1 in the bottom-up spirit of COST.
The global MitoEAGLE network made it possible to collaborate with a large number of coauthors to reach consensus on the present manuscript. Nevertheless, we do not consider scientific progress to be supported by ‘declaration’ statements (other than on ethical or political issues). Our manuscript aims at providing arguments for further debate rather than pushing opinions. We hope to initiate a much broader process of discussion and want to raise the awareness on the importance of a consistent terminology for reporting of scientific data in the field of bioenergetics, mitochondrial physiology and pathology. Quality of research requires quality of communication. Some established researchers in the field may not want to re-consider the use of jargon which has become established despite deficiencies of accuracy and meaning. In the long run, superior standards will become accepted. We hope to contribute to this evolutionary process, with an emphasis on harmonization rather than standardization.
  • Phase 1: The protonmotive force and respiratory control
» The protonmotive force and respiratory control - Discussion
» MitoEAGLE preprint 2017-09-21 - Discussion
  • Phase 2: Mitochondrial respiratory states and rates: Building blocks of mitochondrial physiology Part 1
» MitoEAGLE Task Group States and rates - Discussion
  • Phase 4: Journal submission
  • Target: CELL METABOLISM, aiming at indexing by The Web of Science and PubMed.
Coauthors
  • 2017-09-21 Version 01: 105 coauthors
  • 2017-10-15 Version 10: 131 coauthors
  • 2018-01-18 Version 20: 168 coauthors
  • 2018-02-26 Version 30: 225 coauthors
  • 2018-08-20 Version 40: 350 coauthors - EBEC Poster
  • 2018-10-17 Version 44: 426 coauthors - MiPschool Tromso-Bergen 2018
  • 2018-12-12 Version 50: 517 coauthors - Submission to the preprint server bioRxiv not successful
  • 2019-02-12 Preprint version 1: 530 coauthors
  • 2019-03-15 Preprint version 2: 533 coauthors
  • 2019-04-24 Preprint version 3: 533 coauthors
  • 2019-05-20 Preprint version 4: 542 coauthors
  • 2019-07-24 Preprint version 5: 612 coauthors
  • 2019-08-30 Preprint version 6: 622 coauthors - Preprint publication doi:10.26124/mitofit:190001.v6
  • BEC 2020.1. - Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. doi:10.26124/bec:2020-0001.v1. - »Bioblast link«


Fig. 2. The proton circuit and coupling in oxidative phosphorylation (OXPHOS). Modified after Gnaiger 2014 MitoPathways.

Preprints for Gentle Science

Section 2: Oxidative phosphorylation and coupling states in mitochondrial preparations
Section 3: The protonmotive force and proton flux
Table Protonmotive force matrix.png
Fig. 8. Three formats of the protonmotive unit (A) and protonmotive force (B).
Table Physical constants.png

Table Power, exergy, force, flux, advancement.png


Questions.jpg


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Bioblast links: Force and membrane potential - >>>>>>> - Click on [Expand] or [Collapse] - >>>>>>>
Fundamental relationships
» Force
» Affinity
» Flux
» Advancement
» Advancement per volume
» Stoichiometric number
mt-Membrane potential and protonmotive force
» Protonmotive force
» Mitochondrial membrane potential
» Chemical potential
» Faraday constant
» Format
» Uncoupler
O2k-Potentiometry
» O2k-Catalogue: O2k-TPP+ ISE-Module
» O2k-Manual: MiPNet15.03 O2k-MultiSensor-ISE
» TPP - O2k-Procedures: Tetraphenylphosphonium
» Specifications: MiPNet15.08 TPP electrode
» Poster
» Unspecific binding of TPP+
» TPP+ inhibitory effect
O2k-Fluorometry
» O2k-Catalogue: O2k-FluoRespirometer
» O2k-Manual: MiPNet22.11 O2k-FluoRespirometer manual
» Safranin - O2k-Procedures: MiPNet20.13 Safranin mt-membranepotential / Safranin
» TMRM - O2k-Procedures: TMRM
O2k-Publications
» O2k-Publications: mt-Membrane potential
» O2k-Publications: Coupling efficiency;uncoupling



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