association/physical/direct

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Lukasz?luisa to explain

Reported by: orchard

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• summary: affinity/physical/direct --> association/physical/direct

Original comment by: orchard

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Logged In: YES user_id=719654 Originator: NO

ok.. pasted from my notes prepared for Lyon meeting:

Interaction types:

(a) when two proteins are demonstrated to interact in a setup where there is no doubt they are covalently bound (ie comparing the results of reducing/nonreducing sds-page experiments) interaction is classified as 'covalent'

(b) when two proteins are demonstrated to interact in a setup where there is no doubt they contact each other (eg co-IP, gel filtration, native page, X-Ray structure determination or any other experiment where purified proteins are used) interaction is classified as 'direct'

(c) when two, or more proteins are demonstrated to be present in the same complex (ie gel filtration, native page, etc) the interaction is classified as 'physical'

(d) when two, or more proteins are demonstrated to copurify on an affinity column (His tag, GST or like) or co-immunoprecipitate the interaction is to be classified as 'physical'

NOTE: (b) vs (c): distinguishing between these can become quite complicated when dealing with structures. Currently, we enter these in a way that ensures 'direct' is used only in cases when every pair-wise interaction within the list of participants is, at least once, direct within the structure. This boils down to:

- homooligomers -> always direct

• heterodimers -> always direct
• other heterooligomers -> either direct or physical depending on the details of the structure

- homo/heterooligomers with a non-protein part forming a bridge between protein chains -> physical

(c) vd (d): after polling about a dozen of people of mostly experimental background all but one was strongly in favour of making a clear disctinction between (c) & (d) at the level of interaction type. Opinion about the exact name to use for (d) did vary but my overall impression is the need is there and it should be accomodatad as soon as possible by creating the additional term to be used in (d) case, ie when, say, five proteins (A,B,C,D,E,F) demonstrated to copurify on an affinity column (say A is his-tagged, the column is actually a nickel column of some sort). The prep is well characterized so the presence of molecules other than A,C,D,E,F can be safely excluded. Pairwise interactions A-B, A-C, A-D & A-E are physical; the experiment, when performed correctly, demonstrates that any of these pairs are within some physicalcomplex. Any other pairwise interaction (say B-C) does not have to be physical at all as B and C can constitute pats of distinct physical complexes (say A-B-D is one of them, A-C is the other; this knowledge would come later on from additional experiments; unfortunately we have to describe this one particular experiment we're dealing with at the moment in order to enter it into a database. Possible names to use suggested by various people range through 'putative complex', 'possible complex', 'putative association', 'physical association'.

[NOTE: the consensus after Lyon meeting seems to be the terms to use for (c) and (d) are, respectively, 'physical assembly' and 'assembly']

lukasz

Original comment by: lukasz99

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Logged In: YES user_id=653048 Originator: NO

the rule for remapping the interaction when we will have the new terms all physical interaction that is not binary and detected by coIP or pull down become a 'assembly' correct?

luisa

Original comment by: luisa_montecchi

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Logged In: YES user_id=719654 Originator: NO

yes.. I would guess so... unless others will start to pick on more experimental techniques - coIP & affinity pulldowns seems to be the most obvious cases.

lukasz

Original comment by: lukasz99

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Logged In: YES user_id=653048 Originator: NO

association MI:0914 physical association MI:0915

Original comment by: luisa_montecchi

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• status: open --> closed

Original comment by: luisa_montecchi