Could it be a member of a coiled coil at some point in its lifetime, as a part of its function in regulating position or activity of this receptor? Does the helix have sequence similarity to other coiled coils? see https://www.uniprot.org/help/coiled for a primer on the topic.
Looks fun! Emily. On Sun, Mar 4, 2018 at 5:01 PM, Cheng Zhang <chengzh1...@gmail.com> wrote: > Hi Michael, > > Thanks for the information. > > It is amphipathic. It follows a transmembrane helical domain of a cell > surface receptor and adopts an orientation parallel to the membrane. So it > may be associated with the membrane. I am just wondering if such > leucine-repeat motif is special among all amphipathic, membrane-associated > helical structures. In other words, any other possible functional roles > than just membrane association? > > Best, > > Cheng > > > On Sat, Mar 3, 2018 at 10:23 PM, R. Michael Garavito <rmgarav...@gmail.com > > wrote: > >> Dear Cheng, >> >> Chris and Ruud have provided you with the typical interpretation of such >> a motif, but you have forgotten to give the CCP4 community the context of >> this leucine-repeat helix. Is it amphipathic? Does the protein also have >> transmembrane helices (as suggested by the figure provided) which would >> provide the membrane anchoring? >> >> Look up structurally similar membrane proteins (not necessarily >> homologous by sequence), such as proteins which have a monotonic-like >> membrane interaction, but that also have a transmembrane helix (monoamine >> oxidase or some mammalian cyt P450s). If your protein is monotopic, look >> at that class of membrane proteins (squalene cyclase, fatty acid hydrolase, >> cyclooxygenase, etc.). One structurally undescribed motif is a “reentrant >> membrane helix.” In other words, look at context before assigning >> function. >> >> Good luck and hope this helps, >> >> Michael >> >> ****************************************************************** >> >> *R. Michael Garavito, Ph.D.* >> >> *Professor of Biochemistry & Molecular Biology* >> >> *513 Biochemistry Bldg. * >> >> *Michigan State University * >> >> *East Lansing, MI 48824-1319* >> >> *Office:* *(517) 355-9724 <(517)%20355-9724> Lab: (517) 353-9125 >> <(517)%20353-9125>* >> >> *FAX: (517) 353-9334 <(517)%20353-9334> Email: >> rmgarav...@gmail.com <garav...@gmail.com>* >> >> ****************************************************************** >> >> >> >> On Mar 3, 2018, at 3:51 PM, Cheng Zhang <chengzh1...@gmail.com >> <chengzh1...@gmail.com>> wrote: >> >> Hi all, >> >> We recently got a structure of a transmembrane protein. There is a helix >> that is parallel to the membrane. The function of this helix is not known >> and we are trying to make some hypothesis. A unique feature is that there >> are repeated leucine residues on this helix facing the lipids. I am >> wondering if anyone has seen a similar pattern and could suggest possible >> function, e.g. membrane anchoring? >> >> Thanks! >> >> Best, >> >> Cheng >> >> <LeuRHelix.jpg> >> >> >> -- >> --------------------- >> Cheng Zhang >> >> >> > > > -- > --------------------- > Cheng Zhang > -- "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell "I'm not afraid of storms for I'm learning to sail my ship." - Louisa May Alcott
