Do You Know Any Outer Membrane Protein Which Do Not Have A Beta-Barrel Structure?

Question

[Marcinmagnus]

Do you know any outer membrane protein which do not have a beta-barrel structure?

[Bio_X2Y]

Hi, I think the question is OK for here - protein structures still fall on the computational side of the fence :)

[Michael]

Keep this question open please!

[Eric Normandeau]

Hi. I just feel that a slightly different phrasing would have made the question already much more relevant and interesting to this forum. Maybe something like: 'How would you proceed to find known outer membrane proteins that do not have a beta-barrel structure?' Cheers :)

[Neilfws]

Best way to solve this problem is (intelligently) searching the PDB - definitely a bioinformatics question.

[Eric Normandeau]

Hi MarcinMagnus. This forum is about bioinformatics, the application of computer methods to help solve biology analysis problems. Your question seems to be purely biology oriented. You should try to ask it on a biology forum. Cheers.

[Marcinmagnus]

Exactly! I was not obvious to me how to do it. I try to develop a bioinfo tool to do some subcellular localization prediction and I need information on some kind of untypical proteins. It is quite hard to find it.

Answer 1

[Pawel Szczesny]

Majority of OMPs are indeed beta-barrels, but there are (very few) examples of helical proteins as well. See for example this entry in Orientations of Proteins in Membranes Database.

Solving structures of membrane proteins is not that easy, so I'd say we haven't sampled structural variability of membrane proteome yet.

[Marcinmagnus]

Thanks, nice.. it is exactly what I wanted to see :-)

Answer 2

[Bosco Ho]

If you want to just have an eyeball, I recently created an image gallery for a pretty comprehensive bunch of structures of membrane proteins.

[Khader Shameer]

Bosco, welcome to BioStar !

Answer 3

[Neilfws]

You can address this question using the advanced search interface at the Protein Data Bank. As the PDB has an API, I imagine there's also a programmatic solution.

You might get started as follows:

1. Select secondary structure content as a query and specify a minimum of 1 alpha helix
2. Click "add search criteria"
3. Select cell component browser (GO), search for "outer membrane" and add the appropriate GO term, e.g. cell outer membrane GO ID:9279
4. Submit query

The parameters described above return about 204 results. Many of these are predominantly beta-barrel. The query can be refined by specifying minimum/maximum number or percentage content of alpha-helix and beta sheet. Specifying minimum 50% alpha-helix, for example, currently returns 27 results.

[Pawel Szczesny]

Neil, none of the proteins from the latter query (27) has a helical region integral to the membrane. There are variations of TolC channel (of which integral to the membrane is a beta-barrel part), misannotated proteins (few are anchored to the membrane, not integral to the membrane) or protein fragments. To show the level of shallowness of GO annotations in PDB let me point you to stannin, which is one of the classic alpha-helical proteins in outer-membrane (albeit not that spectacular), which since 2005 doesn't have GO annotation of "integral to outer membrane".

[Neilfws]

Interesting - yes, I had that impression from a brief inspection. So is there a GO (or other term) that specifies integral to membrane, rather than associated?

[Pawel Szczesny]

Yes, there is: "integral to cell outer membrane" - GO ID:45203. But only 11 structures in PDB have that level of detail in annotation.

[Neilfws]

Still, the query in principle is a good approach, even if the database annotation leaves something to be desired :-)

Answer 4

[Keith Callenberg]

The Stephen White lab keeps a constantly updated tab on membrane proteins of known structure on this page.

Apparently the answer is yes, there are at least 3. If you go down to the Transmembrane Proteins: Alpha-Helical > Outer Membrane Proteins section you will see these 3:

1. Wza translocon for capsular polysaccharides: Escherichia coli, 2.25 Å
2. Porin B monomer: Corynebacterium glutamicum (expressed in Escherichia coli), 1.82 Å
3. Type IV outer membrane secretion complex: Escherichia coli, 2.60 Å

This link brings you to that section of the page.

Answer 5

[Pierre Lindenbaum]

See also TMPad

The TransMembrane Protein Helix-Packing Database (TMPad) is an integrated repository of experimentally determined structural folds derived from helix-helix interactions in alpha-helical membrane proteins.