Ed's Big Plans

Last week, Liz, Aron, Andrew, Brendan and I sat down to discuss the beta-trefoil project. It was a good chance for me to understand the methods used and the kinds of results we are interested in for my own TIM Barrel project.

Continuing on with the structural repeat problem, I’ll today be writing a short FSA parser that can handle DSSP or DSS output– simply, a very primitive machine will be used to imitate a human’s visual inspection of repeated secondary structural elements in given proteins. This is in line with the work I did manually staring at structures to get a grasp of how to look at protein models, and also in line with the objective to automate much of this work. Prior to that step, I reduced the probability of doing redundant work by using BLASTCLUST and selecting only a few known structures in each cluster to inspect… a sequence based alignment for each cluster will inform me of where my manually detected repeat boundaries map to the remaining sequences.

Oddity: If you BLASTCLUST all the “FULL” (not “SEED”) sets of TIM Barrel sequences for the entire fold from PFAM along with the sequences of known TIM Barrel fold structures of SCOP, you’ll find that cluster fifteen (as of today) has these elements:

1YBE_A A6U5X9 A6WV52 Q2KDT0 Q2YNV6 Q6G0X7 Q6G5H6 Q8UIS9 Q8YEP2 Q92S49 Q98D24 A1UUA2

In the above listing, 1YBE:A (PDB code) is the sole known PDB structure, while the remainder are putative TIM Barrels (uniprot codes) as determined by the HMM model from PFAM.

The enzyme 1YBE looks like this…

It’s an oddity because of the number of alpha-helices inserted within what is usually a hydrophobic beta barrel– the red pieces of ribbon should form a hollow cylinder, but it’s split apart for 1YBE and accommodates a bunch of cyan helices. Labeled in white are helices that break with the beta-alpha repeating secondary structural element (SSE) pattern by occurring before the first repeat. Labeled in green are breaks between beta-alpha SSE patterns.

Reference

Seetharaman, J., Swaminathan, S., Crystal Structure of a Nicotinate phosphoribosyltransferase [To be Published]

Link: University of Waterloo iGem 2009 Team Page

The team’s off to the 2009 iGem conference in Boston soon (not me though due to prior engagements). Our wiki was finally finished about a week ago– the wiki is a required objective that iGem teams must produce.

As luck would have it — through all the hustle and bustle of daily busy, I still managed to contribute to the original draft and to the final summary for the poster version of our presentation.

Our wiki pages this year are something to be proud of. It is a stark improvement over last year’s work and the team effort shows through in the varied though unified writing styles and diagrams. The modeling team worked especially well– I’m impressed with the amount of team work just looking through the discussions we had on the Google Group.

There’s a presentation practice today– I wish I could go, but the construction in and around the university is becoming prohibitive… The construction should stop some time around the first snowfall.

Future: Andre has some plans for the modeling team in iGem for the coming year… and I have some interesting ideas for what this team can do in the long run.

Detour: I was just thinking today that there are three really odd Chinese characters that I wanted to show you. Each of these glyphs are mapped to both spoken Cantonese and Mandarin words but are not generally compatible with everyday speech. For instance, the second word listed below is replaced by the informal “ah(r)3″ sound that Cantonese speakers make at the end of sentences on occasion (varies with situation, personality).

• 嗎 0x55CE: Audible Question Mark “ma3″
• 了 0x4E86: Audible Exclamation Mark “lew5″
• 的 0×7684: Reverse of “of” in English “di(k)6″

The hex code is the position that each character occupies in the big giant unicode table of glyphs for Chinese characters– the integers correspond to relative intonations. These intonations are equally as important as vowel sounds. I really want to learn how to encode human pronunciations using International Phoenetic Alphabet (IPA), but that would be a project for a later day…

Update: In spoken Cantonese, the first word [from the above list] is often replaced by the sound “gwa3″, and the third word may be replaced by “gò3″.

I finally found a solution for the port forwarding issue I was having with Sun VirtualBox (i.e. NAT provided a weird one-way mapping from which Tin (host) couldn’t dial into TinUbuntu (guest)…) — as far as I understand, this solution is guest operating system neutral but must be configured for each guest handled by a particular installation of Sun VirtualBox. That means that if you’re crazy like me and plan to put your virtual harddrives on USB sticks, you’d probably do just as well to put in a makefile that will do your configurations for you too. So here’s the solution, also saved in my wiki for extra truthiness!

Thanks to Evan and his “justwerks software” blog.

The following commands were issued…

cd /Applications/VirtualBox.app/Contents/MacOS

$VBoxManage setextradata "TinUbuntu"\
     "VBoxInternal/Devices/pcnet/0/LUN#0/Config/guesthttp/Protocol" TCP

$VBoxManage setextradata "TinUbuntu"\
     "VBoxInternal/Devices/pcnet/0/LUN#0/Config/guesthttp/GuestPort" 22

$VBoxManage setextradata "TinUbuntu"\
     "VBoxInternal/Devices/pcnet/0/LUN#0/Config/guesthttp/HostPort" 2222

Which causes TinUbuntu TCP:22 to be forwarded to Tin TCP:2222.

In future, I should remove these rules and re-add them replacing “guesthttp” with my own name for this rule– In his blog, Evan has used a series of names: “guesthttp”, “guestssh” and “guestsql”– In reality, these are actually very good, unambiguous names that I’ll probably end up borrowing.

The one thing I should really dig around for is the meaning of “LUN#0″– it looks like something that’s important– the remaining virtual-directory-like objects in the configuration string look less daunting– “pcnet/0″ is likely referring to the first virtual network adaptor connected to TinUbuntu.

Brief: Phew! Pointing two URLs to the same doc root apparently can give search engines gas. I’ve thus changed my apache httpd.conf by specifying 301 redirects instead!

#####
<VirtualHost *>
        ServerName tin.blogdns.com
        #DocumentRoot /Volumes/SnO2 ### OLD BEHAVIOUR
        RewriteEngine on
        RewriteRule ^/(.*) http://eddiema.ca/$1 [L,R=301]
</VirtualHost>
#####

Excellent… In case you’re lost, the old behaviour made it so that going to tin.blogdns.com would just forward the content from the server without changing the URL; now the URL is correctly rewritten and content is served first hand from eddiema.ca instead.

Again with the TIM Barrel pictures! Here’s some text about it from my notes…

1a5m (A Urease) is a really interesting protein– it consists of three subunits. Each subunit consists of three unique domains: a very squashed TIM Barrel, an alpha-alpha-alpha-beta-beta domain and a beta-beta-alpha-beta-beta domain. I’m not yet sure what to call little broken alpha helices that have less than two complete turns. The TIM Barrel (though exceedingly asymmetrical) will still be accounted for in the data to be analyzed. The TIM Barrel (566 amino acids) is the alpha subunit of each symmetrical subunit. The remaining two domains are the alpha and beta subunit though PDB is not clear which is which: they each weigh in at 100 and 101 amino acids. 1a5m is part of several solved urease structures in the PDB– the collection: {1A5K, 1A5L, 1A5M, 1A5N, 1A5O} are solved by Pearson et al. (1998).

References
Matthew A. Pearson, Ruth A. Schaller, Linda Overbye Michel, P. Andrew Karplus, and, Robert P. Hausinger (1998). Chemical Rescue of Klebsiella aerogenes Urease Variants Lacking the Carbamylated-Lysine Nickel Ligand. Biochemistry. 37(17):6214-20.

Squishy squishy shapes– the giant pink object in the next picture is actually three such TIM Barrels, each of which belongs to one of the three subunits.

Each of the three subunits are shown separately below…

Aesthetically pleasing– these images were captured from the JMol output available from RCSB PDB.