Sunday, June 30, 2013

My biggest contribution to the field of biochemistry

LinkedIn has a feature by which one can endorse other people for different fields. Periodically the system prompts me to vote yea-or-nay on a bunch of endorsements, and conversely I get regular updates as to what others have endorsed me.  It's always nice to get a vote of confidence, but sometimes I find myself wondering what it really means.

Some of these are pretty easy.  I'd definitely say I have experience in bioinformatics.  Drug discovery is a field which I have trod quite a bit, though I certainly wouldn't see myself leading a whole program. But others make me pause, because I can kind of see myself in the space but definitely don't see myself as an expert.

A case in point is biochemistry. I took two semesters at Delaware and had decent grades - but that was over two decades ago. I know my way around a biochemical pathway database, but please don't ask me to compute a Scatchard plot.  My publication record has a smattering of biochemistry related pubs, though in each case I organized the sequencing or maybe a little bit more (in the case of the protease ACE2, I first spotted it in the stream of EST data), but that's all pretty minor.  But there is one case where I think I made a somewhat, though not much, larger contribution to the biochemical literature, by finding what had been lost.

It's a story I should have told long ago, and it's a bit strange I haven't.  But, there was another key player in this story, and when I offered to shine a blogical spotlight on the individual they demurred, and that took a bit of the fun out of the story.  Later, I broached an idea based on it to someone who was looking for a collaborative project, but that never went anywhere.  Last week I saw a tweet somewhat related, and that by a mysterious mechanism has finally spurred me to write.

What started this tale is an article in Nature describing further work on a family of enzymes which proofread charged tRNAs and remove the amino acid moiety from those which have been charged incorrectly.  This is fascinating on multiple levels.  First, I'm always fascinated by information transfer in biological systems and their error rates.  Second, and the subject of the paper, was the whole question of how a second enzyme (i.e. other than the tRNA synthetase) recognized the pairing of amino acid and tRNA.  The Nature paper explored the structural elements of these proofreading enzymes, building off earlier work which showed the existence of the activity.  I was curious to see what EC number these enzymes were classified under, and discovered that not only was there no EC number for them but this activity appeared to be not annotated in any protein database either.  A whole fascinating family of enzymes, and the electronic database world was unaware of the activity's existence!  Indeed, I checked the orphan enzyme database, which lists reported enzyme activities which do not have known protein sequences assigned to them, and sure enough this activity wasn't known there either!

Now, an embarrassing bit.  My memory is that I discovered this during the final days of Codon.  But, the next stage didn't occur until the end of the year, so I apparently sat on my finding for about 7 months.  or is my memory failing me?  Either is a good shot.

In any case, I finally got around to submitting an update request to TrEMBL/SwissProt, which read

"[uuw] UniProtKB/TrEMBL Q8TPA0 entry update request"

This protein, and indeed the whole family of similar proteins, have been shown to be enzymes which edit misacylated tRNAs

Natural homolog of tRNA synthetase editing domain rescues conditional lethality caused by mistranslation.
Chong YE, Yang XL, Schimmel P.
J Biol Chem. 2008 Oct 31;283(44):30073-8. Epub 2008 Aug 22.
PMID: 1872350

Distinct domains of tRNA synthetase recognize the same base pair.
Beebe K, Mock M, Merriman E, Schimmel P.
Nature. 2008 Jan 3;451(7174):90-3.
PMID: 18172502

While the impending Christmas holidays slowed things down a bit, the curator who took on this task (the one who wishes to remain out of the spotlight) not only annotated the entry I noted, but all the other known members of the family.  Plus at least two other families of potential tRNA editing enzymes.  Plus the tRNA editing capability of some tRNA synthetases.  Wow!  I suppose you could say I played a catalytic role, triggering a cascade of valuable improvements to trEMBL!

The episode also made me wonder if there are other examples of this, other cases of various groups doing a lot of detailed work on a protein family but that work never leaping into the protein databases.  I can imagine trying to mine through figures in papers for proteins, BLASTing them against databases, and flagging for further study multiple alignments which tie together a bunch of proteins which do not have a common functional annotation.  Perhaps my previous case was the one example, but quite likely not.  Of course, nearly all of those figures with be images, and so one would need to OCR the alignments and that could prove fun, though getting perfect OCR wouldn't be strictly necessary given the sensitivity of BLAST.  This was the project I proposed once to a former colleague, but neither of us pushed it off the ground (actually, I found in my email that I had noted it in correspondence with an individual who was looking for project ideas).

So, that's what I would nominate as my significant, contribution to biochemistry: I spurred a slightly shy but extraordinary diligent individual to add a bunch of overlooked information to the protein databases.  I'm still unsure if I'd endorse myself for biochemistry, though I won't object to people doing so.


Anonymous said...

I'll be more impressed by your biochemistry skills if you can derive an Eadie-Hofstee plot. :)

Brian Krueger said...

Usually I find myself saying, "You don't know me, how the hell can you say I'm any good at that."