A membrane protein which is "immersed completely inside the bilayer" (as you said it) would not be so beneficial to the cell, because it will not be accessible to the cytoplasm (inside the cell) nor to the extracellular environment. There won't be a strong-enough evolutionary pressure to preserve its existence, so I would have to guess that there are very few if none of those types of membrane proteins at all. The basic function of membrane proteins is to transduce extracellular signals into the cell interior, and to be able to do that function, it must be accessible to the cell's exterior environment, i.e., part of it must protrude outside the cell membrane, and another part of it should also do the same with respect to the cell's interior, or "touch bases" with another membrane proteins that does. Cela a-t-il du sens?

Dear Vicente.

Oui, Je crois que ce terme a un sens [ If I am not wrong ].

I am trying to construct a dimer structure of GPCR and I think no experimental crystal structures for GPCR dimers are available. Docking results provide me where any of the monomer in the complex is immersed in the layer. I am aware that it is hard to validate the docking predicted structure without a crystal form, but i thought I would lay the first stone to predict a most valid structure computationally.

Thank you

I think the truncatrd receptors concept might help you.

Dear Mohammad

Thank you.

How this truncation concept is involved here? Any reference

As far as I have searched, this truncation is something like shortening of AAs or deletion of some loops. How could I relate it in my case?

Hi Rahul,

All GPCRs have extracellular N-terminus and 2 extracellular loops, and intracellular C-terminus plus 3 intracellular loops. Nevertheless, the 7 transmembrane helices are not exactly perpendicular to the bilayer, as you can check in the known crystal structures. There is no GPCR which is completely immersed into the bilayer, also GPCR with the "transmembrane" helices oriented parallel to the bilayer does not exist at all. The homo- and hetero-dimerization of GPCRs are also well-known, with several published examples. Although the crystal structure for such natural dimer does not exist yet, any dimer structure, computational or experimental, must fulfill the above mentioned requirements. A close enough to a dimer structure eventually exist - the original determination of rhodopsin can give you a clue as it is extremely densly packed in rod outer segment membrane.

Best: Karoly

Thank you Dr. Liliom