Difference between revisions of "SUIT protocol library"

Revision as of 23:15, 17 July 2018

high-resolution terminology - matching measurements at high-resolution

SUIT protocol library

Description

The Substrate-uncoupler-inhibitor titration (SUIT) protocol library contains a sequential list of SUIT protocols (D01, D02, ..) 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: MitoPedia: SUIT

List of SUIT protocol D-numbers

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: @@
 {{MitoPedia
 |abbr=SUITs
-|description=The '''Substrate-uncoupler-inhibitor titration (SUIT) protocol library''' contains classes of [[SUIT|SUIT protocols]] with coupling and substrate control defined for [[mitochondrial preparations]].
+|description=The '''Substrate-uncoupler-inhibitor titration (SUIT) protocol library''' contains a sequential list of SUIT protocols (D01, D02, ..) 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]]
 }}
-{{MitoPedia concepts
+__TOC__
-|mitopedia concept=MiP concept, SUIT concept
-}}
+== List of SUIT protocol D-numbers ==
-{{MitoPedia methods}}
-{{MitoPedia O2k and high-resolution respirometry}}
+:::# [[D01_1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd]]
-{{MitoPedia topics}}
+:::# [[D02_1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd]]
-'''''This page is in preparation''''' (intern wiki: [http://intern.oroboros.at/index.php/Category:Library_of_SUIT_protocols])
+:::# [[D03_ce1;1Dig;1PM;2D;2c;3U;4G;5S;6Oct;7Rot;8Gp;9Ama;10AsTm;11Azd]]
+:::# [[D04_ce1;1Dig;1PM;2D;2c;3U;4G;5S;6Rot;7Gp;8Ama;9AsTm;10Azd]]
+:::# [[D05_1D;2M;3Oct;3c;4M;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd]]
+:::# [[D06_1D;2M;3Oct;3c;4M;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd]]
+:::# [[D07_ce1;1Dig;1D;2M;3Oct;3c;4M;5P;6G;7S;8Gp;9U;10Rot;11Ama;12AsTm;13Azd]]
+:::#
+:::# [[D09_ce1;ce2Omy;ce3U;ce4Rot;ce5Ama]]
+:::# [[D10_1PM;2D;3U;4S;5Rot]]
+:::# [[D11_1OctM;2D;3P;4S;5U;6Rot]]
+:::# [[D12_ce1;ce2P;ce3Omy;ce4U;ce5Rot;ce6Ama]]
+:::# [[D13_ce1;ce2P;ce3Omy;ce4U;ce5Glc;ce6M;ce7Rot;ce8S;1Dig;1U;1c;2Ama;3AsTm;4Azd]]
+:::# [[D14_1PM;2D;2c;3G;4S;4D;5U;6Rot;7Ama;8AsTm;9Azd]]
+:::# [[SUIT-9 O2 mt D15]]
+:::# [[SUIT-9 O2 pce D16]]
+:::# [[D17_ce1;ce2P;ce3Omy;ce4U;ce5Rot;ce6S;ce7Ama]]
+:::# [[SUIT-9 AmR mt D18]]
+:::# [[SUIT-9 AmR pce D19]]
-__TOC__
 == Strategy ==
-:::# Select a [[#Pathway control states |pathway control state]].
-:::# Select a [[#Control patterns |control pattern]].
 :::# [[#Define pathway states |Define substrates and inhibitors]] for each pathway state.
 :::# [[#Define coupling states |Define coupling states]].
@@ Line 68: / Line 83: @@
-== SUIT library ==
+== Examples of SUIT protocols ==
 === N; NS; S diametral ===
@@ Line 111: / Line 126: @@
 ::::* [[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}}