Comments on: Structure prediction without structure – visual inspection of BLAST results

By: Ana Rojas

Ana Rojas — Sun, 08 Feb 2009 10:39:04 +0000

Hi Pawel!
Nice post. Definitely to get insights into real biology experimental sicence data shouldn´t be ruled out, but for sure they shouldn´t be considered as standard of truth.
Keep on going.

By: Brad Chapman

Brad Chapman — Sat, 07 Feb 2009 22:32:07 +0000

Pawel; Awesome. Thanks for the pointer; it was great to be able to sanity check against your by eye findings. I put together an automated script inspired by this with an alternative visualization of conserved regions. The post on the code is here. Marcin -- wow, and here I thought you were joking. It turns out you are a master at deconstructing alignment figures. I will be certain to keep all my top secret pictures extra blurry from now on.

By: Andrew Perry

Andrew Perry — Fri, 06 Feb 2009 23:50:13 +0000

Reading the first part of this post, I thought you were about to announce a ‘paradigm busting’ finding of an integral inner membrane beta-barrel protein ! Then again, after the structure of Wza was revealed (apparently a helical integral outer membrane protein), I guess a beta-barrel in the inner membrane couldn’t be entirely ruled out. For instance … some of the smaller 8-stranded barrels often don’t show much ion passage – maybe a non-pore forming one could exist in the inner membrane without causing too much havoc ?

Despite that, there is no known protein import machinery specialized for beta-barrel insertion into the inner membrane, so it seems unlikely (based on what we know, the transmembrane strands wouldn’t be hydrophobic enough for SecYEG dependent integration into the membrane, and spontaneous insertion can happen in vitro but is too slow for bacteria).

Anyhow, nice post – it’s a good example of how useful the interplay of sequence analysis and wet-lab experiments can work as ‘sanity checks’ on experimental results that may otherwise be taken as gospel.

By: Marcin Cieslik

Marcin Cieslik — Fri, 06 Feb 2009 01:59:02 +0000

(assuming I have been given only the image)
My first thought was to:
- screen alignment vis software and find this color code
- decode colors to residue groups
- based on the length of the non-loop fragments and their amphipaticity decide if they are more likely alpha-helices or beta-strands
- I would reconstruct each site in the PSSM by sampling the residues from the groups which make up the columns according to the number of residues in the MSA which are of this group and some general alpha-helix or beta-strand propensities
- if this would not work I would further try to refine the PSSMs for different organisms (e.g. bacteria, archea etc. and using their amino acid frequencies) and/or specific protein types.

If I didn’t know the color-coding… hmmm… The number of possible 7?8?-color reduced alphabets from the 20 amino acids is enormous, but on the other hand most of them should be so lousy that no psi-blast queries would pop-up. My idea would be to break this task down to a) breaking the alphabet b) finding the protein with probably more then one reduced alphabet being blasted. Still this is an alignment so it has to be somehow optimal given some substitution matrix and insertion/deletion model. I would try to find the alphabet which maximises the likelihood of producing the alignment given commonly used substitution matrices. Honestly I don’t know how to sample/converge alphabets. Probably I would start by trying to _really_ understand how joint alignment/phylogeny given evolution model: http://www.biomath.ucla.edu/msuchard/bali-phy/Redelings_and_Suchard_2005.pdf and how to estimate Q-matrices from alignment/phylogeny using MCMC. (lost the reference for this one will fix it)

By: Pawel Szczesny

Pawel Szczesny — Thu, 05 Feb 2009 08:01:18 +0000

Brad, of course I can share it: it's this protein. Marcin, assuming that you make no assumption on color codes (if you can guess the code, it's trivial), how would you proceed?

By: Marcin Cieslik

Marcin Cieslik — Wed, 04 Feb 2009 23:36:58 +0000

Brad you could reverse-engineer the PSSM from this low-res image. No Ids are hush-hush enough;)

By: Brad Chapman

Brad Chapman — Wed, 04 Feb 2009 23:15:51 +0000

Pawel;
This is great and inspired a bit of coding on my part to calculate and display conservation across a protein based on BLAST results. When I am putting together a post with the code, it would be great to have a graph of your protein displayed here. Is the protein ID hush-hush, or can you share it? If not yet, I can use a favorite gene. Thanks,

Brad