Difference between revisions of "SUIT protocol library"
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{{MitoPedia O2k and high-resolution respirometry}} | {{MitoPedia O2k and high-resolution respirometry}} | ||
{{MitoPedia topics}} | {{MitoPedia topics}} | ||
'''''This page is in preparation''''' (intern wiki: [http:// | '''''This page is in preparation''''' (intern wiki: [http://intern.oroboros.at/index.php/Category:Library_of_SUIT_protocols]) | ||
__TOC__ | __TOC__ | ||
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:::# Select a [[#Pathway control states |pathway control state]]. | :::# Select a [[#Pathway control states |pathway control state]]. | ||
:::# Select a [[#Control patterns |control pattern]]. | :::# Select a [[#Control patterns |control pattern]]. | ||
:::# [[#Define | :::# [[#Define pathway states |Define substrates and inhibitors]] for each pathway state. | ||
:::# [[#Define coupling states |Define coupling states]]. | :::# [[#Define coupling states |Define coupling states]]. | ||
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=== Define | === Define pathway states === | ||
:::: [[ | :::: [[Pathway control state]]s are defined for many substrate-inhibitor combinations in SUIT protocols, particularly: ([[N-pathway control state]], [[S-pathway control state]], [[NS-pathway control state]]). Titrations may performed in a single step, or in multiple steps for sequential analyis of different pathway control states. | ||
:::* | :::* N: PM, GM, PGM, M, .. | ||
:::* | :::* S: S(Rot), S, SM, .. | ||
:::* | :::* NS: PS, GS, PMS, GMS, PGMS, .. | ||
:::* CIV: AsTM | :::* CIV: AsTM | ||
:::* | :::* F: Oct, Pal, ... | ||
:::* | :::* Gp | ||
Β | |||
=== Define coupling states === | === Define coupling states === | ||
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== SUIT library == | == SUIT library == | ||
=== CI + CI<small>&</small>II + CII diametral | === N; NS; S diametral === | ||
Β | |||
:::: Old nomenclature: CI + CI<small>&</small>II + CII diametral | |||
:::: Respiratory states: N<sub>''L''</sub> -> N<sub>''P''</sub> -> NS<sub>''P''</sub> -> NS<sub>''E''</sub> -> S<sub>''E''</sub> -> ROX | |||
:::: | ::::* '''GM;D;S;U;Rot''' ''Innsbruck-Copenhagen protocol'': GM;D;c;S;U;Rot ::Cyt ''c'': added after ADP; cyt ''c'' added after S; ADP conc: _ _; ROX: Ama ([[Boushel 2007 Diabetologia]]) | ||
::::* ''' | ::::* '''PMG;D;S;U;Rot''' ''Brain protocol'': PGM;D;c;S;U;Rot::ADP conc: in mouse brain homogenate a final conc. of 2 mM ADP in the NS-[[OXPHOS]] state (NS<sub>''P''</sub>) is saturating ([[Sumbalova 2011 Abstract Bordeaux]]); [[ROX]]: Mna&Ama; Myx | ||
=== N; N; NS; S diamteral === | |||
:::: Old nomenclature: CI + CI + CI<small>&</small>II + CII diamteral | |||
::::* '''GM | ::::* '''GM;D;P;S;U;Rot''' ''Innsbruck-Liege protocol 1'': GM;D;c;P;S;U;Rot::[[Cytochrome c]]: early addition of ''c'' ensures comparability of all states in case of any ''c'' effect. | ||
::::* '''PM | ::::* '''PM;D;G;S;U;Rot''' ''Innsbruck-Liege protocol 2'': PM;D;c;G;S;U;Rot Β | ||
=== | === F; FN; FNS; S diametral === | ||
:::: Respiratory states: | :::: Old nomenclature: FAO + CI + CI<small>&</small>II + CII diametral | ||
:::: Respiratory states: F<sub>''L''</sub> -> F<sub>''P''</sub> -> FN<sub>''P''</sub> -> FNS<sub>''P''</sub> -> FNS<sub>''E''</sub> -> S''E''</sub> -> ROX | |||
::::* '''OctM | ::::* '''OctM;D;G;S;U;Rot''' ''Innsbruck training protocol'': OctM;D;G;c;S;U;Rot::[[Pesta 2012 Methods Mol Biol]], [[Pesta 2011 Am J Physiol Regul Integr Comp Physiol]] | ||
:::: Respiratory states: | :::: Respiratory states: F<sub>''L''</sub> -> F<sub>''P''</sub> -> FN<sub>''P''</sub> -> FNS<sub>''P''</sub> -> S<sub>''P''</sub> -> S<sub>''L''</sub> -> S<sub>''E''</sub> -> ROX | ||
::::* '''OctM | ::::* '''OctM;D;G;S;Rot;Omy;U''' ''Greenland-Monte Rosa protocol'': OctM;D;G;S;Rot;Omy;U;c::[[Cytochrome c|Cyt ''c'']]: added after U. 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 | ||
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:::* [[MitoPedia: Terms and abbreviations]] | :::* [[MitoPedia: Terms and abbreviations]] | ||
::::* [[Doerrier 2018 Methods Mol Biol]] | |||
::::* [[Gnaiger_2014_MitoPathways]] | ::::* [[Gnaiger_2014_MitoPathways]] | ||
::::* [[Gnaiger_2009_Int J Biochem Cell Biol]] | ::::* [[Gnaiger_2009_Int J Biochem Cell Biol]] | ||
::::* [[Pesta 2012 Methods Mol Biol]] | ::::* [[Pesta 2012 Methods Mol Biol]] | ||
::::* [[Pesta 2011 Am J Physiol Regul Integr Comp Physiol]] | ::::* [[Pesta 2011 Am J Physiol Regul Integr Comp Physiol]] | ||
Revision as of 22:06, 17 July 2018
Description
The Substrate-uncoupler-inhibitor titration (SUIT) protocol library contains classes of SUIT protocols with coupling and substrate control defined for mitochondrial preparations.
Abbreviation: SUITs
Reference: MitoPedia: SUIT
MitoPedia concepts:
MiP concept,
SUIT concept
This page is in preparation (intern wiki: [1])
Strategy
- Select a pathway control state.
- Select a control pattern.
- Define substrates and inhibitors for each pathway state.
- Define coupling states.
Definition of states
Experimental conditions
- Temp
- O2
- Medium
- Oxygen level
- ADP kinetics
- Substrate kinetics
O2k configuration
- Amp: Amplex Red, TMRM, Ca Green, ...
- Pot
- Spectrophotometry
Define pathway states
- Pathway control states are defined for many substrate-inhibitor combinations in SUIT protocols, particularly: (N-pathway control state, S-pathway control state, NS-pathway control state). Titrations may performed in a single step, or in multiple steps for sequential analyis of different pathway control states.
- N: PM, GM, PGM, M, ..
- S: S(Rot), S, SM, ..
- NS: PS, GS, PMS, GMS, PGMS, ..
- CIV: AsTM
- F: Oct, Pal, ...
- Gp
Define coupling states
- The coupling control states require a complementary definition of an ET-pathway competent state.
- L, P, E (Uncouplers, U: FCCP, CCCP, DNP)
Define residual oxygen consumption
- ROX: Rot&Ama, Rot&Mna&Ama, Myx, Cn, Az, ..
Categories of SUIT protocols
SUIT protocol patterns
SUIT library
N; NS; S diametral
- Old nomenclature: CI + CI&II + CII diametral
- Respiratory states: NL -> NP -> NSP -> NSE -> SE -> ROX
- GM;D;S;U;Rot Innsbruck-Copenhagen protocol: GM;D;c;S;U;Rot ::Cyt c: added after ADP; cyt c added after S; ADP conc: _ _; ROX: Ama (Boushel 2007 Diabetologia)
- PMG;D;S;U;Rot Brain protocol: PGM;D;c;S;U;Rot::ADP conc: in mouse brain homogenate a final conc. of 2 mM ADP in the NS-OXPHOS state (NSP) is saturating (Sumbalova 2011 Abstract Bordeaux); ROX: Mna&Ama; Myx
N; N; NS; S diamteral
- Old nomenclature: CI + CI + CI&II + CII diamteral
- GM;D;P;S;U;Rot Innsbruck-Liege protocol 1: GM;D;c;P;S;U;Rot::Cytochrome c: early addition of c ensures comparability of all states in case of any c effect.
- Old nomenclature: CI + CI + CI&II + CII diamteral
- PM;D;G;S;U;Rot Innsbruck-Liege protocol 2: PM;D;c;G;S;U;Rot
F; FN; FNS; S diametral
- Old nomenclature: FAO + CI + CI&II + CII diametral
- Respiratory states: FL -> FP -> FNP -> FNSP -> FNSE -> SE -> ROX
- OctM;D;G;S;U;Rot Innsbruck training protocol: OctM;D;G;c;S;U;Rot::Pesta 2012 Methods Mol Biol, Pesta 2011 Am J Physiol Regul Integr Comp Physiol
- Respiratory states: FL -> FP -> FNP -> FNSP -> SP -> SL -> SE -> ROX
- OctM;D;G;S;Rot;Omy;U Greenland-Monte Rosa protocol: OctM;D;G;S;Rot;Omy;U;c::Cyt c: added after U. 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