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Difference between revisions of "SUIT protocol library"

From Bioblast
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'''''This page is in preparation'''''
'''''This page is in preparation'''''


== CI ==
= Classes of protocols with coupling and substrate control =


== CII ==
== Linear ==


== CI+CII ==
# '''Linear coupling control''': at a single substrate state (classical State 3 -> State 4).
# '''Linear substrate control''': at a single coupling state (unusual).
# '''Monodirectional linear coupling control''': ''L''<sub>N</sub> -> ''P''<sub>D</sub> -> ''E''<sub>F</sub>
# '''Bidirectional linear coupling control''': ''L''<sub>N</sub> -> ''P''<sub>D</sub> -> ''L''<sub>Omy</sub> -> ''E''<sub>F</sub>


* CI
* CII
* CI+CII
* CIV
* ETF
* GPDH




== CI - CI+CII - CII ==
== Orthogonal ==


=== GM+D+S+F+Rot ===
# '''Orthogonal coupling -> substrate control''' (mono- or bidirectional)
# '''Orthogonal substrate -> coupling control''' (mono- or bidirectional)


#''' ''Innsbruck-Copenhagen protocol'': GM+D+c+S+F+Rot:'''
#''' GM+D+S+c+F+Rot:'''


* Cyt c: added after ADP ([[Boushel 2007 Diabetologia]]); cyt c added after S
== Diametral ==
* ADP conc:
* ROX: Ama ([[Boushel 2007 Diabetologia]])


=== GM+D+P+S+F+Rot ===
# '''Diametral coupling -> substrate ->> control''' (mono- or bidirectional)
# '''Diametral substrate -> coupling ->> control''' (mono- or bidirectional)


# '''''Innsbruck protocol 1'': GM+D+c+P+S+F+Rot:'''


* Respiratory states: CI(L) - CI(P) - CI+II(P) - CI+II(E) - CII(E)  - ROX
=== CI -> CI+CII -> CII ===
* [[Cytochrome c|''Cyt c'']]: early addition of ''c'' ensures comparability of all states in case of any ''c'' effect
* ([[Gnaiger_2007_MitoPathways]])


=== PM+D+G+S+F+Rot ===
Respiratory states: CI<sub>L</sub> -> CI<sub>P</sub> -> CI+II<sub>P</sub> -> CI+II<sub>E</sub> -> CII<sub>E</sub> -> ROX


# '''''Innsbruck protocol 2'': PM+D+c+G+S+F+Rot '''
* '''GM+D+S+F+Rot''' ''Innsbruck-Copenhagen protocol'': GM+D+c+S+F+Rot  
::Cyt c: added after ADP; cyt c added after S; ADP conc: _ _; ROX: Ama ([[Boushel 2007 Diabetologia]])


* Respiratory states: CI(L) - CI(P) - CI+II(P) - CI+II(E) - CII(E) - ROX
* '''PMG+D+S+F+Rot''' ''Brain protocol'': PMG+D+c+S+F+Rot
* ([[Gnaiger_2007_MitoPathways]])
::ADP conc: in mouse brain homogenate a final conc. of 2 mM ADP in the [[OXPHOS]] state (CI+CII) is saturating ([[Sumbalova 2011 Abstract Bordeaux]]); [[ROX]]: Mna+Ama; Myx


=== PMG+D+S+F+Rot ===


# '''PMG+D+c+S+F+Rot'''
=== CI -> CI -> CI+CII -> CII ===


* Respiratory states: CI(L) - CI(P) - CI+II(P) - CI+II(E) - CII(E)
* '''GM+D+P+S+F+Rot''' ''Innsbruck-Liege protocol 1'': GM+D+c+P+S+F+Rot
::[[Cytochrome c]]: early addition of ''c'' ensures comparability of all states in case of any ''c'' effect.


* ADP conc: in mouse brain homogenate a final conc. of 2 mM ADP in the [[OXPHOS]] state (CI+CII) is saturating ([[Sumbalova_2011_Abstract]])
* '''PM+D+G+S+F+Rot''' ''Innsbruck-Liege protocol 2'': PM+D+c+G+S+F+Rot
* [[ROX]]: Mna+Ama; Myx ([[Gnaiger_2009_IJBCB]])


== ETF - CI ==


=== ETF -> CI -> CI+CII -> CII ===
Respiratory states: ETF<sub>L</sub> -> ETF<sub>P</sub> -> CI<sub>P</sub> -> CI+II<sub>P</sub> -> CI+II<sub>E</sub> -> CII<sub>E</sub> -> ROX


== ETF - CI+CII ==
* '''OctM+D+G+S+F+Rot''' ''Innsbruck training protocol'': OctM+D+G+c+S+F+Rot
::[[Pesta 2012 Methods Mol Biol]], [[Pesta 2011 Am J Physiol Regul Integr Comp Physiol]]


== ETF - CI - CI+CII - CII==
Respiratory states: ETF<sub>L</sub> -> ETF<sub>P</sub> -> CI<sub>P</sub> -> CI+II<sub>P</sub> -> CII<sub>P</sub> -> CII<sub>L</sub> -> CII<sub>E</sub> -> ROX


#''''' Greenland-Monte Rosa protocol'': OctM+D+G+S+Rot+Omy+F'''
* '''OctM+D+G+S+Rot+Omy+F''' ''Greenland-Monte Rosa protocol'': OctM+D+G+S+Rot+Omy+F+c
::[[Cytochrome c|Cyt ''c'']]: added after F. The absence of a significant ''c''-effect shows the integrity of the outer mitochondrial membrane after fibre preparation and also shows the preservation of integrity over a 90-100 min incubation in the O2k ([[MiR05]]); Oxygen: oxygen limitation of flux was preventd by maintaining oxygen levels in the respirometer above air saturation ([[Pesta 2012 Methods Mol Biol]]); [[ROX]]: Mna+Ama


* Respiratory states: ETF(L) - ETF(P) - CI(P) - CI+II(P) - CII(P) - CII(L) - CII(E) - ROX
* [[Cytochrome c|Cyt c]]: added after F. The absence of a significant c-effect shows the integrity of the outer mitochondrial membrane after fibre preparation and also shows the preservation of integrity over a 90-100 min incubation in the O2k ([[MiR06]]).
* Oxygen: oxygen limitation of flux was preventd by maintaining oxygen levels in the respirometer above air saturation ([[Pesta 2012 Methods Mol. Biol.]])
* [[ROX]]: Mna+Ama
* ([[Gnaiger_2007_MitoPathways]])
== CIV ==




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== Cytochrome c ==
== Cytochrome c ==


[[#CI - CI+CII - CII|CI - CI+CII - CII]]
[[#CI -> CI+CII -> CII|CI -> CI+CII -> CII]]
 
[[#ETF -> CI -> CI+CII -> CII|ETF -> CI -> CI+CII -> CII]]
 


[[#ETF - CI - CI+CII - CII|ETF - CI - CI+CII - CII]]


== ROX ==
== ROX ==


== Abbreviations ==
 
== References and Notes ==


* [[List_of_respiratory_states]]
* [[List_of_respiratory_states]]
* [[List_of_terms_and_abbreviations]]
* [[List_of_terms_and_abbreviations]]
* [[Gnaiger_2007_MitoPathways]]
* [[Gnaiger_2009_Int J Biochem Cell Biol]]
* [[Boushel 2007 Diabetologia]]
* [[Pesta 2012 Methods Mol Biol]]
* [[Pesta 2011 Am J Physiol Regul Integr Comp Physiol]]
* [[Sumbalova 2011 Abstract Bordeaux]]

Revision as of 08:17, 22 November 2011

This page is in preparation

Classes of protocols with coupling and substrate control

Linear

  1. Linear coupling control: at a single substrate state (classical State 3 -> State 4).
  2. Linear substrate control: at a single coupling state (unusual).
  3. Monodirectional linear coupling control: LN -> PD -> EF
  4. Bidirectional linear coupling control: LN -> PD -> LOmy -> EF
  • CI
  • CII
  • CI+CII
  • CIV
  • ETF
  • GPDH


Orthogonal

  1. Orthogonal coupling -> substrate control (mono- or bidirectional)
  2. Orthogonal substrate -> coupling control (mono- or bidirectional)


Diametral

  1. Diametral coupling -> substrate ->> control (mono- or bidirectional)
  2. Diametral substrate -> coupling ->> control (mono- or bidirectional)


CI -> CI+CII -> CII

Respiratory states: CIL -> CIP -> CI+IIP -> CI+IIE -> CIIE -> ROX

  • GM+D+S+F+Rot Innsbruck-Copenhagen protocol: GM+D+c+S+F+Rot
Cyt c: added after ADP; cyt c added after S; ADP conc: _ _; ROX: Ama (Boushel 2007 Diabetologia)
  • PMG+D+S+F+Rot Brain protocol: PMG+D+c+S+F+Rot
ADP conc: in mouse brain homogenate a final conc. of 2 mM ADP in the OXPHOS state (CI+CII) is saturating (Sumbalova 2011 Abstract Bordeaux); ROX: Mna+Ama; Myx


CI -> CI -> CI+CII -> CII

  • GM+D+P+S+F+Rot Innsbruck-Liege protocol 1: GM+D+c+P+S+F+Rot
Cytochrome c: early addition of c ensures comparability of all states in case of any c effect.
  • PM+D+G+S+F+Rot Innsbruck-Liege protocol 2: PM+D+c+G+S+F+Rot


ETF -> CI -> CI+CII -> CII

Respiratory states: ETFL -> ETFP -> CIP -> CI+IIP -> CI+IIE -> CIIE -> ROX

  • OctM+D+G+S+F+Rot Innsbruck training protocol: OctM+D+G+c+S+F+Rot
Pesta 2012 Methods Mol Biol, Pesta 2011 Am J Physiol Regul Integr Comp Physiol

Respiratory states: ETFL -> ETFP -> CIP -> CI+IIP -> CIIP -> CIIL -> CIIE -> ROX

  • OctM+D+G+S+Rot+Omy+F Greenland-Monte Rosa protocol: OctM+D+G+S+Rot+Omy+F+c
Cyt c: added after F. The absence of a significant c-effect shows the integrity of the outer mitochondrial membrane after fibre preparation and also shows the preservation of integrity over a 90-100 min incubation in the O2k (MiR05); Oxygen: oxygen limitation of flux was preventd by maintaining oxygen levels in the respirometer above air saturation (Pesta 2012 Methods Mol Biol); ROX: Mna+Ama


ADP kinetics

Cytochrome c

CI -> CI+CII -> CII

ETF -> CI -> CI+CII -> CII


ROX

References and Notes

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