extrinsic component of cytoplasmic side of plasma membrane/anchored component of the cytoplasmic side of the plasma membrane

[ValWood]

I’m struggling with the terms:

GO:0031234
extrinsic component of cytoplasmic side of plasma membrane The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.

and GO:0098753 anchored component of the cytoplasmic side of the plasma membrane The component of the plasma membrane consisting of gene products and protein complexes with covalently attached hydrophobic anchors products that penetrate only the cytoplasmic side of the membrane.

I guess that GO:0031234 means that a phosphorylated residue (or similar) inserts into the plasma membrane, rather than a transmembrane domain?

1. Aren’t people more likely to call GO:0031234 “anchored” than GO:0098753 ?
2. Sometimes we know a protein is cytoplasmic side and attached to the membrane but we cannot differentiate between these 2 options However the common parent is “plasma membrane part” (we want to say it is plasma membrane, cytoplasmic side, peripherally attached)

(at present cytoplasmic plasma membrane attached gene products seem to be split arbitrarily between these 2 terms)

[krchristie]

It seems to me that the "extrinsic component" term is talking about things that are bound to something on the cytoplasmic side of the PM, but not inserted into the membrane themselves, while the "anchored component" term requires that there be an anchor (I think of things like farnysyl or geranylgeranyl) attached to the protein that is inserted into the membrane.

Usage wise though, it seems that it might often be hard to know which one is correct if all you have is a localization experiment.

[ValWood]

OK I see what you mean. "loosely bound to its cytoplasmic surface" seems ambiguous. I have used these 2 for both. I think I need to move GO:0031234 to GO:0098753

So, do you think GO:0031234 is for if a protein is membrane associated via another protein ? There needs to be some means of attachment presumably? I haven't annotated these to plasma membrane, (this would involve a whole bunch of cortical stuff like actin, myosin, lots of kinases (I have these as cell cortex).

[pgaudet]

Hi,

We could clarify these terms. I think in GO 'anchored' means lipid-anchored, but this is not necessary the only way

http://what-when-how.com/molecular-biology/membrane-anchors-molecular-biology/

According to the 'extrinsic' definition, is not anchored at all ("The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.") Therefore the child 'heterotrimeric G protein complex should be anchored instead of extrinsic:

[bmeldal]

I remember looking at these, too, a while ago. I thought anchors are all sorts of PTMs and non-protein molecules (lipids, sugars...) that are anchored in the membrane while the protein binds this anchor on the outside of the membrane.

[pgaudet]

See #23880

Hopefully this addresses the issue?

[pgaudet]

In fact this is a different set of terms - reopening