Pswms For Rna Binding Proteins

Question

[Anima Mundi]

Hello,

could you please suggest me a PSWMs database for RNA binding proteins? I am interested in particular in DEAD-boxes.

[Michael Schubert]

for rpsblast or HMMER? have you looked at PFAM, CDD, etc.?

[Anima Mundi]

Thanks, I would like to use the MEME Suite (is the first time I deal with RNA binding proteins in silico, and I have a pipeline ready for TFs that I could mostly reuse). I am in search of binding site (RNA matrices or alignments), PFAM and CDD seem to provide proteins alignments.

[joangibert14]

Hi! I know I'm super late but, did you accomplished your task? I am quite new using MEME but I would like to do the same with some sequences that I have...Any advice would be great! Thanks

[Anima Mundi]

Hi, at that time I did not have that much success (but cannot remember details!). I guess things might have changed a bit in 6.3 years. If the sequences you have are putative binding sites, then all you need to do is to generate a PSWM (or a few, e.g. using MEME), then use some other tool (e.g. FIMO) to scan a database of interest for motif occurrence. If instead your sequences are the target of your motif hunt then you will have to find either ready-to-go PSWMs or sequences of putative binding sites (e.g. from literature).

[joangibert14]

Great! I will try with FIMO. Thanks!!

[Michael Schubert]

Ok, so you're searching matrices for sequence motifs where proteins bind, not the proteins themselves. That makes sense ;)

Answer 1

[Qdjm]

The only two databases that I know about are RBPDB and AREsite. RBPDB is for all sequence-specific RNA-binding proteins in metazoa and AREsite focuses on those that bind AU-rich elements.

RBPDB may contain some data on DEAD-box protein but this seems unlikely. Is there evidence that DEAD-box protein binding is sequence specific?

[Qdjm]

The dogma is that because dsRNA is generally in an A-form helix, that the major groove is too deep and narrow for dsRNA binding proteins to recognize base identity; unless there are deformations in the RNA helix like unmatched bases. My guess is that they won't show a strong sequence preference (if they do, that would be exciting). Maybe try a sequence and structure motif finding algorithm like CMfinder or RNApromo.

[Anima Mundi]

Well, to tell the truth I am not sure. I could multi-align recognized sequences in order to underline possible conservations. I have left behind this topic but I will be glad to test the databases suggested.