Difference between revisions of "Categories of SUIT protocols"
From Bioblast
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== Categorization of SUIT protocols: substrate types == | == Categorization of SUIT protocols: substrate types == | ||
There are many ways to define groups of SUIT protocols. Since the complexity of SUIT protocols is primarily determined by the large number of possible [[substrate state]]s, and to a lesser extent by the smaller number of possible [[coupling state]]s, a relevant type of categories of SUIT protocols | There are many ways to define groups of SUIT protocols. Since the complexity of SUIT protocols is primarily determined by the large number of possible [[substrate state]]s, and to a lesser extent by the smaller number of possible [[coupling state]]s, a relevant type of categories of SUIT protocols considers the substrate types involved. | ||
At the present stage of development of the 'library of SUIT protocols' as part of the [[MitoFit Quality Control System]], five substrate types are considered: | At the present stage of development of the 'library of SUIT protocols' as part of the [[MitoFit Quality Control System]], five substrate types are considered: | ||
* On the pathway level of converging NADH- and FADH<sub>2</sub>-linked dehydrogenases, including the TCA cycle and beta-oxidation: | * On the pathway level of converging NADH- and FADH<sub>2</sub>-linked dehydrogenases, including the TCA cycle and beta-oxidation: | ||
:'''N:''' NADH-linked substrates (CI-linked) | :'''N:''' [[NADH]]-linked substrates (CI-linked) | ||
:'''F:''' FADH<sub>2</sub>-linked substrates (FAO) | :'''F:''' [[FADH2 |FADH<sub>2</sub>]]-linked substrates (FAO) | ||
* On the pathway level of electron transfer complexes converging at the Q-junction: | * On the pathway level of electron transfer complexes converging at the Q-junction: | ||
:'''S:''' [[Succinate]] (CII-linked) | :'''S:''' [[Succinate]] (CII-linked) | ||
:'''Gp:''' Glycerophosphate (CGpDH-linked) | :'''Gp:''' [[Glycerophosphate]] (CGpDH-linked) | ||
* On the single step level of cytochrome ''c'' oxidase (CIV), the terminal step in the aerobic electron transfer system: | * On the single step level of cytochrome ''c'' oxidase (CIV), the terminal step in the aerobic electron transfer system: | ||
:'''Tm:''' Artificial electron transfer susbstrate TMPD (Tm) maintained in a reduced state by ascorbate (As) and reducing cytochrome ''c'' as the substrate of CIV. | :'''Tm:''' Artificial electron transfer susbstrate [[TMPD]] (Tm) maintained in a reduced state by [[ascorbate]] (As) and reducing cytochrome ''c'' as the substrate of [[CIV]]. | ||
== SUITp Catg: single substrate type == | == SUITp-Catg: single substrate type == | ||
# N | # N | ||
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== SUITp- | == SUITp-Catg: multiple substrate types with NS == | ||
=== NFSGpTm === | === NFSGpTm === | ||
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== SUITp- | == SUITp-Catg: multiple substrate types with N (without S) == | ||
=== NF === | === NF === | ||
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== SUITp- | == SUITp-Catg: multiple substrate types without N == | ||
: | : F and S without N are problematic substrate states due to accumulation of Oxa or Acetyl-CoA. Therefore, addition of malate alone (M without P or G) is not considered as substrate type N. However, high mt-malic enzyme activity requires a change of this concept, when M alone represents an ETS ccompetent substrate state. Low concentration of M may be used to support FAO, whereas a higher concentration of M may be required for N-linked respiratory capacity to override FAO capacity; this needs corresponding kinetic analyses ([[SUIT test protocols]]). | ||
=== FS === | === FS === | ||
Revision as of 19:06, 31 January 2016
- high-resolution terminology - matching measurements at high-resolution
Categories of SUIT protocols
Description
Categories of SUIT protocols group SUIT protocols according to all substrate types involved in a protocol, independent of titrations of inhibitors which block the oxidation of the substrates present.
Abbreviation: SUITp-Catg
Categorization of SUIT protocols: substrate types
There are many ways to define groups of SUIT protocols. Since the complexity of SUIT protocols is primarily determined by the large number of possible substrate states, and to a lesser extent by the smaller number of possible coupling states, a relevant type of categories of SUIT protocols considers the substrate types involved.
At the present stage of development of the 'library of SUIT protocols' as part of the MitoFit Quality Control System, five substrate types are considered:
- On the pathway level of converging NADH- and FADH2-linked dehydrogenases, including the TCA cycle and beta-oxidation:
- On the pathway level of electron transfer complexes converging at the Q-junction:
- S: Succinate (CII-linked)
- Gp: Glycerophosphate (CGpDH-linked)
- On the single step level of cytochrome c oxidase (CIV), the terminal step in the aerobic electron transfer system:
- Tm: Artificial electron transfer susbstrate TMPD (Tm) maintained in a reduced state by ascorbate (As) and reducing cytochrome c as the substrate of CIV.
SUITp-Catg: single substrate type
- N
- F
- S
- Gp
- Tm
SUITp-Catg: multiple substrate types with NS
NFSGpTm
Tm can always be included or excluded at the end of a SUIT protocol. To simplify the categorization, Tm is not considered in this system of SUIT protocols.
NS
NFS
NSGp
NFSGp
SUITp-Catg: multiple substrate types with N (without S)
NF
NGp
NFGp
SUITp-Catg: multiple substrate types without N
- F and S without N are problematic substrate states due to accumulation of Oxa or Acetyl-CoA. Therefore, addition of malate alone (M without P or G) is not considered as substrate type N. However, high mt-malic enzyme activity requires a change of this concept, when M alone represents an ETS ccompetent substrate state. Low concentration of M may be used to support FAO, whereas a higher concentration of M may be required for N-linked respiratory capacity to override FAO capacity; this needs corresponding kinetic analyses (SUIT test protocols).
