Difference between revisions of "SUIT protocol library"

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Substrate-uncoupler-inhibitor titration (SUIT) protocols

Classes of SUIT protocols with coupling and substrate control defined for mitochondrial preparations

Strategy

Select a pathway control state.
Select a control pattern.
#Define substrates for each pathway state.
#Define coupling states.

Definition of states

Define substrates

Substrate control states are defined for each pathway control state (CI-linked, CII-linked, CI&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.

CI: PM, GM, PGM, M, ..
CII: S(Rot), S, SM, ..
CI&II: PS, GS, PMS, GMS, PGMS, ..
CIV: AsTM
FAO: Oct, Pal, ...
CGPDH:
c

Define coupling states

The coupling control states require a complementary definition of an ETS-competent substrate state.

L, P, E

Coupling states:

Define residual oxygen consumption

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

Pathway control states

Single pathway control states

CI
CII
CI&CII
CIV
FAO
CGPDH

Multiple pathway control states

A. CI-CII-CIV

CI + CII
CI + CII + CIV
CI + CI&CII + CII
CI + CI&CII + CII + CIV

B. FAO-CI-CII-CIV

FAO + CI + CII
FAO + CI + CII + CIV
FAO + CI + CI&CII + CII
FAO + CI + CI&CII + CII + CIV

C. CGPDH-CI-CII-CIV

CGPDH + CI
CGPDH + CI + CII
CGPDH + CI + CII + CIV
CGPDH + CI + CI&CII + CII
CGPDH + CI + CI&CII + CII + CIV
CI + CGPDH + ...
CI + CI&CII + CGPDH + ...
CI&CII + CGPDH + ...

D. FAO-CGPDH-CI-CII-CIV

FAO + CGPDH + CI + ...
CGPDH + FAO + CI + ...
CI + FAO + CGPDH + ...
CI + CGPDH + FAO + ...
...

Control patterns

Linear

Linear coupling control: at a single substrate state (classical State 3 -> State 4, or P -> L_T).
Linear substrate control: at a single coupling state (unusual).
Monodirectional linear coupling control: L_N -> P_D -> E_F
Bidirectional linear coupling control: L_N -> P_D -> L_Omy -> E_F

@@ Line 3: / Line 3: @@
 <big><big>'''[[Substrate-uncoupler-inhibitor titration]] (SUIT) protocols</big>
-Classes of SUIT protocols with coupling and substrate control'''</big>
+Classes of SUIT protocols with coupling and substrate control defined for [[mitochondrial preparations]]'''</big>
 __TOC__
-== Structure ==
+== Strategy ==
-# Select a [[#Pathway control states |pathway control state]]
+# Select a [[#Pathway control states |pathway control state]].
-# Define substrates for each pathway state
+# Select a [[#Control patterns |control pattern]].
+# [[#Define substrates]] for each pathway state.
+# [[#Define coupling states]].
 == Definition of states ==
 === Define substrates ===
+[[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&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.
 * CI: PM, GM, PGM, M, ..
 * CII: S(Rot), S, SM, ..
@@ Line 23: / Line 27: @@
 === Define coupling states ===
+The [[coupling control state]]s require a complementary definition of an [[ETS-competent substrate state]].
 * ''L'', ''P'', ''E''
+Coupling states: [[Image:L.jpg|link=LEAK respiration|LEAK]] [[Image:P.jpg|link=OXPHOS capacity|OXPHOS]] [[Image:E.jpg|link=ETS capacity|ETS]]
 === Define residual oxygen consumption ===
 * ROX: Rot&Ama, Rot&Mna&Ama, Cn, Az, ..
+[[Image:ROX.jpg|link=Residual oxygen consumption|ROX]]