I would suggest taking the amino acid sequenced of some FNIP domain proteins and get a predicted crystal structure using I-TASSER (it's free)

http://zhanglab.ccmb.med.umich.edu/I-TASSER/

then use I-TASSER or DALI (also free) 

http://ekhidna.biocenter.helsinki.fi/dali_server/

to compare the predicted .pdb structure to all known crystal structures, we recently had a Dicty protein (AprA) that had no significant amino acid sequence to any mammalian protein and using the above tools found a similar human protein...

cheers

Richard Gomer
Professor
TAMU Biology
ILSB    MS 3474
301 Old Main Drive
College Station, TX  77843-3474
979 458 5745


________________________________________
From: DICTY [[log in to unmask]] on behalf of Richard Sucgang PhD [[log in to unmask]]
Sent: Thursday, October 31, 2013 11:07 AM
To: [log in to unmask]
Subject: Re: [DICTY] FNIP motif

Hi, Ricardo,

I don't think we have a specific function for the FNIP domain since for the longest time it is considered to be a Dicty-specific protein domain, and occurs in repetitive forms, too. It is found in all sorts of proteins, but I do think protein-protein interaction is best guess at the moment.

But reevaluating FNIP is probably due, now with better comparative genomics in place. FNIP domains are found in most amoebozoa, definitely in Acanthamoeba, but most notably, in a few genes in Mimivirus, the giant viruses that infect free living amoebae.

We still won't get an immediate view to their role, but the ubiquity within that domain of life suggests a pretty generic function (i.e., homotypic protein interaction) but the primordial module was lost in early divergence from other eukaryotes.

R

On Oct 31, 2013, at 6:21 AM, Ricardo Escalante <[log in to unmask]> wrote:

> Hi all,
> Does anyone have a clue about the function of the Dicty-specific domain FNIP? Could it be the equivalent of other  protein-protein interaction domains like coilded-coil or leucine rich? I found that FNIP is frequently associated with Zinc finger B-box domain, which is commonly associated with other protein-protein interaction domains in E3-ubiquitin ligases in other organisms.
>
> Thank you very much
> Best
> Ricardo
>
>
>
>
>
> Ricardo Escalante, PhD.
> Instituto de Investigaciones Biomédicas Alberto Sols
> Arturo Duperier 4
> 28029-Madrid
> Spain
> [log in to unmask]
> lab web: http://www2.iib.uam.es/rescalante_lab/Sitio_web/Escalante_Lab.html
>
>
>