Searching Pathogen Protein Sequences For Immune System Related Motifs

Question

[Andrew]

Hi

I have a couple of thousand protein sequences from pathogens that I want to search for proteins that could potentially interact with the immune system (ie virulence factors). One way I thought I could do this was to search the proteins for motifs / domains related to the immune system. My knowledge of the immune system is minimal… I was wondering if there were any resources that implement this kind of search already, or if not, one that might list domains or motifs that would be of interest to me. This publication lists some of the kind of domains I would be looking for http://www.ncbi.nlm.nih.gov/pubmed/18031241 (like I said I am not familiar with immune biology so I’m not sure how full a picture looking at just these domains would give me.) I can retrieve motifs / domains by searching Prosite, but a systematic way to do this without relying on searching through the site annotations would be preferable.

Any help appreciated! Cheers

Answer 1

[Neilfws]

There is certainly a resource of domains: PFAM and the tool to search sequences for them - HMMER.

I think you need to define your research question more tightly. Pathogens - which ones? Bacteria, viruses, fungi? You're not searching for "motifs / domains related to the immune system" - you want domains which interact with or are recognised by the immune system. Perhaps choosing a couple of examples from the reference that you gave, searching PFAM to see if it contains those domains then using HMMER to search your sequences for those domains is a good way into the problem.

[Andrew]

Sorry, to clarify i am looking at orfs from a single fungal pathogen genome. Also, yes your right, I am looking for domains that interact with or are recognised by the immune system. As a starting point I had thought about using PFAM/HMMER combo in this way, using examples from the reference I gave, but since I have minimum background knowledge on the immune system i wasn't sure how comprehensive a coverage this would give me. It certainly seems like a good starting point though. Cheers!

Answer 2

[Niallhaslam]

SLiMSearch described here: NAR, allows you to look for predefined motifs, using the webinterface you can restrict the motif matches to those with specific GO terms (e.g. immune related). SLiMFinder which looks for novel motifs in a set of proteins has a new (relatively untested I should add) webservice available here. Its only recently been installed so no promises. Alternatively the code for slimsearch and slimfinder is available here for use as part of a pipeline. The ELM database and MiniMotif Miner databases have information on short protein motifs that have been identified. MiniMotif Miner contains some predictions as well. ELM has a webservice, though it will only have eukaryotic motifs.

The MEME suite also allows the identification and subsequent searching of identified motifs and is available here. It is also available for download from the same link.

pFam as mentioned is a very comprehensive database of domains. The other one worth mentioning is InterPro which is like a meta-domain database.

From the question its not clear what exactly you want to do. Do you need a list of proteins involved in the immune system? Gene Ontology terms and UniProt annotation would be a good starting point for this.

(disclaimer - I've worked on some of the above mentioned tools)

Answer 3

[Larry_Parnell]

Something to try to complement your approach is to search for predicted regions of high antigenicity. Such sites would also interact with the immune system albeit in another way - eliciting antibody production. One such tool for these predictions is EpiC. There are others.

[Andrew]

Thanks, I think that would compliment what I am trying to do quite nicely. EpiC looks interesting, and its something I will look at once I have a more refined group of proteins to examine, but it doesn't currently accept batch submissions. I will have a look at some of the other tools that make similar predictions.

[Larry_Parnell]

Write to the developer/manager of the tool. Perhaps there is a way that you can analyze your proteins in batch.

[Niallhaslam]

Hi, I'm the developer. Whilst there isn't a batch service, it is built using webservices and DAS. So any of the specific tools you want to run are all available as independent resources. If you click on the help tab the names of all the services are listed there. You can also find them on the das registry and biocatalogue. My mail is [e-mail] if you have any questions.

Answer 4

[Larry_Parnell]

Still other tools can predict amino acid residues residing on the surface, thus available to interact with other proteins or molecules. Perhaps a combined approach to look for surface residues comprising or within a conserved motif, as Neil (+1) suggests with Pfam/HMMER and as Nial (+1) offers, would produce what you need. Such surface predictions can be gleaned from protein secondary/tertiary prediction tools.