Difference between revisions of "SUIT protocol library"

Revision as of 22:06, 17 July 2018

high-resolution terminology - matching measurements at high-resolution

SUIT protocol library

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)

Coupling states:

Define residual oxygen consumption

ROX: Rot&Ama, Rot&Mna&Ama, Myx, Cn, Az, ..

Categories of SUIT protocols

» Categories of SUIT protocols

» Talk:SUIT protocol library

SUIT protocol patterns

» SUIT protocol pattern

SUIT library

N; NS; S diametral

Old nomenclature: CI + CI&II + CII diametral

Respiratory states: N_L -> N_P -> NS_P -> NS_E -> S_E -> 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_P) 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.

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: F_L -> F_P -> FN_P -> FNS_P -> FNS_E -> 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: F_L -> F_P -> FN_P -> FNS_P -> S_P -> S_L -> S_E -> 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

References and notes

@@ Line 10: / Line 10: @@
 {{MitoPedia O2k and high-resolution respirometry}}
 {{MitoPedia topics}}
-'''''This page is in preparation''''' (intern wiki: [http://www.intern.oroboros.at/index.php/Protocol_development])
+'''''This page is in preparation''''' (intern wiki: [http://intern.oroboros.at/index.php/Category:Library_of_SUIT_protocols])
 __TOC__
@@ Line 17: / Line 17: @@
 :::# Select a [[#Pathway control states |pathway control state]].
 :::# Select a [[#Control patterns |control pattern]].
-:::# [[#Define substrates |Define substrates]] for each pathway state.
+:::# [[#Define pathway states |Define substrates and inhibitors]] for each pathway state.
 :::# [[#Define coupling states |Define coupling states]].
@@ Line 37: / Line 37: @@
-=== Define substrates ===
+=== Define pathway states ===
-:::: [[Substrate control state]]s are defined for each pathway control state ([[Complex I-linked substrate state |CI-linked]], [[Complex II-linked substrate state |CII-linked]], [[Complex I&II-linked substrate state |CI<small>&</small>II-linked]]) is defined by a specific substrate or substrate combination. These substrates may be added in a single step, or in multiple steps for analyis of the effect of different substrate combinations within a pathway control state.
+:::: [[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.
-:::* CI: PM, GM, PGM, M, ..
+:::* N: PM, GM, PGM, M, ..
-:::* CII: S(Rot), S, SM, ..
+:::* S: S(Rot), S, SM, ..
-:::* CI<small>&</small>II: PS, GS, PMS, GMS, PGMS, ..
+:::* NS: PS, GS, PMS, GMS, PGMS, ..
 :::* CIV: AsTM
-:::* FAO: Oct, Pal, ...
+:::* F: Oct, Pal, ...
-:::* CGpDH:
+:::* Gp
-:::* c
 === Define coupling states ===
@@ Line 69: / Line 69: @@
 == SUIT library ==
- ''Work in progress''
-:::» [[MitoPedia: SUIT]]
-=== CI + CI<small>&</small>II + CII diametral ===
+=== N; NS; S diametral ===
+:::: 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
-:::: Respiratory states: CI<sub>''L''</sub> -> CI<sub>''P''</sub> -> CI<small>&</small>II<sub>''P''</sub> -> CI<small>&</small>II<sub>''E''</sub> -> CII<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]])
-::::* '''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
-::::* '''PMG+D+S+U+Rot''' ''Brain protocol'': PMG+D+c+S+U+Rot::ADP conc: in mouse brain homogenate a final conc. of 2 mM ADP in the [[OXPHOS]] state (CI<small>&</small>II) is saturating ([[Sumbalova 2011 Abstract Bordeaux]]); [[ROX]]: Mna&Ama; Myx
+=== N; N; NS; S diamteral ===
-=== CI + CI + CI<small>&</small>II + CII diamteral ===
+:::: Old nomenclature: CI + CI + CI<small>&</small>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.
+::::* '''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+D+G+S+U+Rot''' ''Innsbruck-Liege protocol 2'': PM+D+c+G+S+U+Rot
+::::* '''PM;D;G;S;U;Rot''' ''Innsbruck-Liege protocol 2'': PM;D;c;G;S;U;Rot
-=== FAO + CI + CI<small>&</small>II + CII diametral ===
+=== F; FN; FNS; S diametral ===
-:::: Respiratory states: FAO<sub>''L''</sub> -> FAO<sub>''P''</sub> -> CI<small>&</small>FAO<sub>''P''</sub> -> CI<small>&</small>II<small>&</small>FAO<sub>''P''</sub> -> CI<small>&</small>II<small>&</small>FAO<sub>''E''</sub> -> CII<sub>''E''</sub> -> ROX
+:::: 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+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]]
+::::* '''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: FAO<sub>''L''</sub> -> FAO<sub>''P''</sub> -> CI<small>&</small>FAO<sub>''P''</sub> -> CI<small>&</small>II<small>&</small>FAO<sub>''P''</sub> -> CII<sub>''P''</sub> -> CII<sub>''L''</sub> -> CII<sub>''E''</sub> -> ROX
+:::: 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+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
+::::* '''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
@@ Line 104: / Line 106: @@
 :::* [[MitoPedia: Terms and abbreviations]]
+::::* [[Doerrier 2018 Methods Mol Biol]]
 ::::* [[Gnaiger_2014_MitoPathways]]
 ::::* [[Gnaiger_2009_Int J Biochem Cell Biol]]
 ::::* [[Pesta 2012 Methods Mol Biol]]
 ::::* [[Pesta 2011 Am J Physiol Regul Integr Comp Physiol]]
-::::* [[Sumbalova 2011 Abstract Bordeaux]]