SUIT protocol library: Difference between revisions

Latest revision as of 15:01, 8 June 2020

high-resolution terminology - matching measurements at high-resolution

SUIT protocol library

Description

[[Description::The Substrate-uncoupler-inhibitor titration (SUIT) protocol library contains a sequential list of SUIT protocols (D001, D002, ..) with links to the specific SUIT pages. Classes of SUIT protocols are explained with coupling and substrate control defined for mitochondrial preparations.]]

Abbreviation: SUITs

Reference: [[Info::MitoPedia: SUIT]]

List of SUIT numbers

SUIT code
SUIT-001
SUIT-002
SUIT-003
SUIT-004
SUIT-005
SUIT-006
SUIT-007
SUIT-008
SUIT-010
SUIT-011
SUIT-012
SUIT-013
SUIT-014
SUIT-015
SUIT-016
SUIT-017
SUIT-018
SUIT-019
SUIT-020
SUIT-021
SUIT-022
SUIT-024
SUIT-025
SUIT-027
SUIT-031

List of SUIT protocols with D-numbers

SUIT code	SUIT technical name
SUIT-001 O2 ce-pce D003	D003_ce1;1Dig;1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd
SUIT-001 O2 ce-pce D004	D004_ce1;1Dig;1PM;2D;2c;3U;4G;5S;(6Oct);7Rot;8Gp;9Ama;10AsTm;11Azd
SUIT-001 O2 mt D001	D001_mt;1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd
SUIT-001 O2 pfi D002	D002_pfi;1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd
SUIT-002 O2 ce-pce D007	D007_ce1;1Dig;1D;2M;3Oct;3c;4M;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd
SUIT-002 O2 ce-pce D007a	D007a_ce1;1Dig;1D;2M;3Oct;3c;4M;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd
SUIT-002 O2 mt D005	D005_mt;1D;2M;3Oct;3c;4M;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd
SUIT-002 O2 pfi D006	D006_pfi;1D;2M.1;3Oct;3c;4M2;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd
SUIT-003 AmR ce D017	D017_ce1;ce2P;ce3Omy;ce4U;ce5Rot;ce6S;ce7Ama
SUIT-003 AmR ce D058	D058_ce1;ce1SOD;ce1HRP;ce1AmR;ce2Omy;ce3U;ce4Rot;ce5Ama
SUIT-003 AmR ce D059	D059_ce1;ce1H2O;ce1MiR05;ce1DMSO;ce2Omy;ce3U;ce4Rot;ce5Ama
SUIT-003 O2 ce D009	D009_ce1;ce2Omy;ce3U;ce4Ama
SUIT-003 O2 ce D012	D012_ce1;ce1P;ce2Omy;ce3U;ce4Rot;ce5Ama
SUIT-003 O2 ce D028	D028_ce1;ce2Omy;ce3U;ce4Rot;ce5S;ce6Ama
SUIT-003 O2 ce D037	D037_ce1;ce1Glc;(ce2Omy);ce3U;ce4Ama
SUIT-003 O2 ce D038	D038_ce1;(ce2Omy);ce3U;ce3Glc;ce3'U;ce4Ama
SUIT-003 O2 ce D039	D039_ce1;(ce2Omy);ce3U;ce4Rot;ce5Ama
SUIT-003 O2 ce D050	D050_ce1;ce1Snv;(ce2Omy);ce3U;ce4Rot;ce5Ama
SUIT-003 O2 ce D060	D060_ce1;(ce2Omy);ce3U;ce4Rot;ce5Snv;ce6Mnanv;ce7Ama
SUIT-003 O2 ce D061	D061_ce1;(ce2Omy);ce3U;ce4Rot;ce5DMSO;ce6DMSO;ce7Ama
SUIT-003 O2 ce D062	D062_ce1;ce1DMSO;(ce2Omy);ce3U;ce4Rot;ce5Ama
SUIT-003 O2 ce-pce D013	D013_ce1;ce1P;ce2Omy;ce3U;ce3Glc;ce3M;ce4Rot;ce5S;1Dig;1U;1c;2Ama;3AsTm;4Azd
SUIT-003 O2 ce-pce D018	D018_ce1;ce1P;ce2Omy;ce3U;ce3Glc;ce4Rot;ce5S;1Dig;1c;2Ama;3AsTm;4Azd
SUIT-003 O2 ce-pce D020	D020_ce1;ce1P;ce2Omy;ce3U;ce4Rot;ce5S;1Dig;1c;2Ama;3AsTm;4Azd
SUIT-003 pH ce D067	D067_ce1;ce1Glc;ce2Omy;ce3DG;ce4Ama
SUIT-004 O2 pfi D010	D010_1PM;2D;2c;3U;4S;5Rot;6Ama;7AsTm;8Azd
SUIT-005 O2 pfi D011	D011_1OctM;2D;2c;3P;4S;5U;6Rot;7Ama;8AsTm;9Azd
SUIT-006 AmR mt D048	D048_1PM;2D;3Omy;4U;5Ama
SUIT-006 Fluo mt D034	D034_1PM;2D;3Omy;4U;5Ama
SUIT-006 MgG ce-pce D085	D085_ce1;1Dig;1PM;2D;3Cat;4U;5Ama
SUIT-006 MgG mt D055	D055_1PM;2D;3Cat;4U;5Ama
SUIT-006 O2 ce-pce D029	D029_ce1;1Dig;1PM;2D;2c;3Omy;4U;5Ama
SUIT-006 O2 mt D022	D022_1SRot;2D;2c;(3Omy);4U;5Ama
SUIT-006 O2 mt D047	D047_1PM;2D;2c;3Omy;4U;5Ama
SUIT-006 Q ce-pce D073	D073_ce1;1Dig;1Q2;1Rot;1S;2D;(3Omy);4U;5Anox;6Ama.png
SUIT-006 Q mt D071	D071_mt;1Q2;1Rot;1S;2D;(3Omy);4U;5Anox;6Ama.png
SUIT-007 O2 ce-pce D030	D030_ce1;1Dig;1G;2D;2c;3M;4U;5Ama
SUIT-008 O2 ce-pce D025	D025_ce1;1Dig;1PM;2D;2c;3G;4S;5U;6Rot;7Ama;8AsTm;9Azd
SUIT-008 O2 mt D026	D026_1PM;2D;2c;3G;4S;4D;5U;6Rot;7Ama;8AsTm;9Azd
SUIT-008 O2 pfi D014	D014_1PM;2D;2c;3G;4S;4D;5U;6Rot;7Ama;8AsTm;9Azd
SUIT-009 AmR ce-pce D019	D019_ce1;1Dig;1S;2D;3P;4Rot;5Ama
SUIT-009 AmR mt D021	D021_1S;2D;3P;4Rot;5Ama
SUIT-009 O2 ce-pce D016	D016_ce1;1Dig;1S;2D;3P;4Rot;5Ama
SUIT-009 O2 mt D015	D015_1S;2D;3P;4Rot;5Ama
SUIT-010 O2 ce-pce D008	D008_ce1;ce2Rot;ce3S;ce4D;1Dig;1c
SUIT-011 O2 pfi D024	D024_1GM;2D;2c;3S;4U;5Rot;6Ama
SUIT-012 O2 ce-pce D052	D052_ce1;1Dig;1PM;2D;2c;3G;4U;5Ama
SUIT-012 O2 mt D027	D027_1PM;2D;2c;3G;4U;5Ama
SUIT-013 AmR ce D023	D023_ce1
SUIT-014 O2 pfi D042	D042_1GM;2D;2c;3P;4S;5U;6Rot;7Ama
SUIT-015 O2 pti D043	D043_1OctM;2D;2c;3G;4P;5S;6U;7Rot;8Ama
SUIT-016 O2 pfi D044	D044_1OctM;2D;3G;4S;5Rot;6Omy;7U;8Ama
SUIT-017 O2 mt D046	D046_1OctM;2D;2c;3G;3c;4S;5U;6Rot;7Ama
SUIT-017 O2 pfi D049	D049_1OctM;2D;2c;3G;4S;5U;6Rot;7Ama
SUIT-018 AmR ce-pce D068	D068_ce1;1Dig;1GMS;2D;3Ama
SUIT-018 AmR mt D031	D031_mt;1GMS;2D;3Ama
SUIT-018 AmR mt D040	D040_mt;1GMS;2D;3Ama
SUIT-018 AmR mt D041	D041_mt;1GMS;2D;3Ama
SUIT-018 O2 mt D054	D054_mt;1GMS;2D;2c;3Ama
SUIT-019 O2 pfi D045	D045_1PalM;2D;2c;3Oct;4P;5G;6U;7S;8Rot;9Ama
SUIT-020 Fluo mt D033	D033_1PM;2D;3G;4S;5Rot;6Omy;7U;8Ama
SUIT-020 O2 mt D032	D032_1PM;2D;2c;3G;4S;5Rot;6Omy;7U;8Ama
SUIT-021 Fluo mt D036	D036_1GM;2D;3S;4Rot;5Omy;6U;7Ama
SUIT-021 O2 mt D035	D035_1GM;2D;2c;3S;4Rot;5Omy;6U;7Ama
SUIT-022 O2 ce D051	D051_ce1;ce2KCN;ce3SHAM
SUIT-023 O2 ce D053	D053_ce1;ce2SHAM;ce3KCN
SUIT-024 O2 ce-pce D056	D056_ce1;1Dig;1PM;2T;2D;3Omy;4Ama
SUIT-025 O2 mt D057	D057_1D;2M;3Oct;3c;4M;5P;6G;7S;8Rot;9Ama
SUIT-026 AmR ce-pce D087	D087_ce1;1Dig;1S;2Rot;3D;4Ama
SUIT-026 AmR mt D064	D064_1S;2Rot;3D;4Ama
SUIT-026 AmR mt D077	D077_1S;2Rot;3D;4Ama
SUIT-026 O2 ce-pce D088	D088_ce1;1Dig;1S;2Rot;3D;3c;4Ama
SUIT-026 O2 mt D063	D063_1S;2Rot;3D;3c;4Ama
SUIT-027 O2 ce-pce D065	D065_ce1;1Dig;1M;2D;3M;4P;5G
SUIT-029 O2 mt D066	D066_mt;1PM;2T;2D;2c;3Omy;4U;5G;6S;6U;7Rot;8Ama
SUIT-031 O2 ce-pce D079	D079_ce1;1Dig;1PM;2D;2c;3S;4Rot;5U;6Ama
SUIT-031 O2 mt D075	D075_1mt;1PM;2D;2c;3S;4Rot;5U;6Ama
SUIT-031 Q ce-pce D074	D074_ce1;1Dig;1Q2;1PM;2D;3S;4Rot;5U;6Anoxia;7Ama
SUIT-031 Q mt D072	D072_mt;1Q2;1PM;2D;3S;4Rot;5U;6Anox;7Ama

Strategy

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

Examples of SUIT protocols

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

MitoPedia concepts: MiP concept, SUIT concept

@@ Line 1: / Line 1: @@
-== CI ==
+{{MitoPedia
+|abbr=SUITs
+|description=The '''Substrate-uncoupler-inhibitor titration (SUIT) protocol library''' contains a sequential list of SUIT protocols (D001, D002, ..) with links to the specific SUIT pages. Classes of [[SUIT|SUIT protocols]] are explained with coupling and substrate control defined for [[mitochondrial preparations]].
+|info=[[MitoPedia: SUIT]]
+}}
+__TOC__
-== CII ==
+== List of SUIT numbers ==
-== CI+CII ==
+{{#ask:[[MitoPedia concept::MiP concept]] [[MitoPedia concept::SUIT protocol]]
+| mainlabel=SUIT code
+| format=broadtable
+| limit=5000
+| order=ascending
+}}
+== List of SUIT protocols with D-numbers ==
+{{#ask:[[MitoPedia concept::SUIT protocol]] [[MitoPedia concept::Find]]
+| ?Has SUIT number=SUIT technical name
+| mainlabel=SUIT code
+| format=broadtable
+| limit=5000
+| order=ascending
+}}
-== CI - CI+CII - CII ==
+== Strategy ==
+:::# [[#Define pathway states |Define substrates and inhibitors]] for each pathway state.
+:::# [[#Define coupling states |Define coupling states]].
-=== GM+D+S+F+Rot ===
-# GM+D+c+S+F+Rot: [[Cytochrome_c|cyt c]] added after ADP ([[Boushel 2007 Diabetologia]])
+== Definition of states ==
-# GM+D+S+c+F+Rot: cyt c added after S
-* ADP conc:
+=== Experimental conditions ===
-* ROX: Ama ([[Boushel 2007 Diabetologia]])
+:::* Temp
+:::* O2
+:::* Medium
+:::* Oxygen level
+:::* ADP kinetics
+:::* Substrate kinetics
-=== GM+D+P+S+F+Rot ===
+=== O2k configuration ===
+:::* Amp: Amplex Red, TMRM, Ca Green, ...
+:::* Pot
+:::* Spectrophotometry
-# ''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
+=== Define pathway states ===
-* [[Cytochrome c|''Cyt c'']]: early addition of ''c'' ensures comparability of all states in case of any ''c'' effect
+:::: [[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.
-* ([[Gnaiger_2007_MitoPathways]])
-=== PM+D+G+S+F+Rot ===
+:::* N: PM, GM, PGM, M, ..
+:::* S: S(Rot), S, SM, ..
+:::* NS: PS, GS, PMS, GMS, PGMS, ..
+:::* CIV: AsTM
+:::* F: Oct, Pal, ...
+:::* Gp
-# ''Innsbruck protocol 2'': PM+D+c+G+S+F+Rot
-* Respiratory states: CI(L) - CI(P) - CI+II(P) - CI+II(E) - CII(E)  - ROX
+=== Define coupling states ===
-* ([[Gnaiger_2007_MitoPathways]])
+:::: The [[coupling-control state]]s require a complementary definition of an [[ET-pathway competent state]].
+:::* ''L'', ''P'', ''E'' ([[Uncoupler]]s, U: FCCP, CCCP, DNP)
+Coupling states: [[Image:L.jpg|link=LEAK respiration|LEAK]] [[Image:P.jpg|link=OXPHOS capacity|OXPHOS]] [[Image:E.jpg|link=ET capacity|ET capacity]]
-=== PMG+D+S+F+Rot ===
-# PMG+D+c+S+F+Rot
+=== Define residual oxygen consumption ===
+:::* ROX: Rot&Ama, Rot&Mna&Ama, Myx, Cn, Az, ..
+[[Image:ROX.jpg|link=Residual oxygen consumption|ROX]]
-* Respiratory states: CI(L) - CI(P) - CI+II(P) - CI+II(E) - CII(E)
-* ADP conc: in mouse brain homogenate a final conc. of 2 mM ADP in the [[OXPHOS]] state (CI+CII) is saturating ([[Sumbalova_2011_Abstract]])
+== Categories of SUIT protocols  ==
-* [[ROX]]: Mna+Ama; Myx ([[Gnaiger_2009_IJBCB]])
+:::» [[Categories of SUIT protocols]]
+:::» [[Talk:SUIT protocol library]]
-== ETF + CI ==
+== SUIT protocol patterns ==
+:::» [[SUIT protocol pattern]]
-== ETF + CI + CII ==
+== Examples of SUIT protocols ==
-== CIV ==
+=== 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
-== ADP kinetics ==
+::::* '''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]])
-== cytochrome c ==
+::::* '''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
-== ROX ==
+=== N; N; NS; S diamteral ===
-== Abbreviations ==
+:::: 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.
-* [[List_of_respiratory_states]]
+::::* '''PM;D;G;S;U;Rot''' ''Innsbruck-Liege protocol 2'': PM;D;c;G;S;U;Rot
-* [[List_of_terms_and_abbreviations]]
+=== F; FN; FNS; S diametral ===
+:::: 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]]
+:::: 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
+== References and notes ==
+:::* [[MitoPedia: Respiratory states]]
+:::* [[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]]
+{{MitoPedia concepts
+|mitopedia concept=MiP concept, SUIT concept
+}}
+{{MitoPedia methods}}
+{{MitoPedia O2k and high-resolution respirometry}}
+{{MitoPedia topics}}