Special sequences for those searching

Aside

Apparently, some people want the MASPERGERS*<->MLARGESPER* sequence back after I removed it following a period of dabbling in existentialist philosophy, which is a torture I wish only on those peers performing grave offenses against something I cherished. In any case, here they are:

AATGGCAAGC CCTGAAAGAG GAGAACGTTC GTAG

Keep the fact that you cannot just dump it into a standard DNA translation engine and expect to see the pattern in mind. You have to translate it biologically, meaning that you start at the ATG and end and the TAR. Translated forwards and assuming a 100% translation by those constraints (and ignoring things like friction and potential jamming), you will get MASPERGERS*. Translated backwards, you will get MLARGESPER*, which is very close to an anagram. Finding out that no one else had done this example was almost unbelievable (and you may see the initial posts at WrongPlanet, the other WP, as a vanished signature).

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Return to Biochemistry

Ach! Vae mihi! I was commissioned to construct a paper model of G. gallus catalase last year q3 and forgot about working on it until now! It is time to launch the almighty UGene with the alignment between the PDB of the cow catalase and the sequence (i.e. non-graphical) of the chicken catalase.

A brief look at the PDB entries reveals that the vertebrate with the most entries is the cow, B. taurus. There are some human models as well, but the ones available are erythrocyte catalase while the cow models are liver catalases, just like the ones used during the first laboratory assignment in AP Biology.

[If only Chimera was a bit more stable and had a better alignment interface. Ah well, UGene has a perfectly good one. Also, keep in mind the fact that I am using only B. taurus and G. gallus and H. sapiens sequences when I say anything is conserved.]

The initial 41 or so residues seem a bit less conserved. 1TGU reflects this with a somewhat chaotic arrangement with an unusual amount of coil. This is just sequence A, so it may be incorrect. Enabling sequence D and taking a cursory look at only the ribbons (without atoms), reveals that the initial helix is probably necessary for proper assembly of the enzyme. The loosest interval at the moment (to be verified against conservation later)  seems to be (16,22), although 16 and 17 would have to have fairly high helix propensities. What I previously thought was a practically non-essential coil seems to be the place where chain C binds to chain A, and hydrogen bond inference indicated that the two chains were bound relatively tightly through the interval (24,38). Perhaps, this simply indicates that the choice of amino acids for this component is less strict and easily adaptable. I doubt the heme-binding sites will be as loose.

Next, I compare the results to the alignments. I thought I must have deleted something, because the initial alanine in the PDB as seen in Chimera sequence viewer was absent. It probably matters less, because the residue itself is not visible. In any case, the crazy mix of colors that provided the bases [sic, pun not intended] for the conjecture above stops as early as about 21 (by now shifted to match the Chimera sequence numerically). In addition, the relatively conserved initial sequence seems to terminate at 14, which is quite close to 16 and probably explains the necessity of that particular sequence. For this purpose, similar amino acids were also considered, i.e. d-e, n-q, g-a, and the others. I see few differences until 40, in which there is serine (hydrophilic) in B. taurus but isoleucine and valine in the chicken and human catalases respectively. I will note this oddity when I reach the 156th residue. Perhaps, the serine is only a, “spacer,” of sorts.

Euh, 156 is aspartate in the chicken, cow, and human sequences. This will be a good excuse to take a break from dull, “high,” school for a nice 0240 of Berg, Tymoczko, and Stryer.

The next major difference seems to occur at 290, with isoleucine, arginine, and threonine for the cow, chicken, and human sequences respectively. Most coincidentally, it is on the outer surface of the protein and selecting everything within a nanometer yields only the sequences from and to the rest of the protein. In this case anything without too much reactivity should work. Replacing this residue with histidine would make an interesting study.

The next irregularity is the presence of an extra sequence TK prior to the TK found in the mammals of the group, yielding a sequence of TKTK on the interval (299,302) relative to the corrected G. gallus sequence. Mammalian TK is located next to the barrel. I will have to make sure this is not a human or computer error later. Burying a duplicate inside an already-tight location seems more than a little harmful.

Following that, there is a rather sudden appearance of less conserved residues (411,426). It seems to be another one of the surface regions because showing within a radius of 2 nm still provides the sequence clear access to the surface. My random conjecture is that it forms a hinge of some kind, but it is probably wrong because of its placement.

With that, the initial examination of catalase is finished. Tomorrow (or rather, later today), I will be preparing a general view of the critical components and focus on the most conserved intervals, because those are the most likely, “moving parts.”

Many thanks to another member (A real-life doctor with similar interests and models of proteins!) who revived my interest in this specific component of biochemistry. Sic tyrannidem nvmerorvm terminatvr.

Happy 2012!

With a mere, “tick,” 2011 ended. What comes next?

  1. Organization: temporal: Goals for the entire year will be planned on a quarter-to-quarter basis, and a hierarchical process priority algorithm will be implemented for work and tasks to be done.
  2. Organization: spatial: All items, papers, and supplies will be catalogued [sic] and identified with unique identification numbers signifying the time, place, mood, and memory of each item catalogued [sic].
  3. Language: constructed: The language will be completed and will have a potential lexicon larger than 850 words with all grammatical rules completed.
  4. ASD: social: No one can notice my condition for the initial two minutes and I can maintain eye contact for more than 300ms without triggering a fear response.
  5. ASD: stereotypies: All stereotypies will be converted into subtler and less noticeable forms that still provide equivalent satisfaction, if such is possible.
  6. ASD: special interests: All short-term special interests will be catalogued [sic] and placed within a secure store for future reference.
  7. ASD: prosody: I will be able to stress syllables properly and automatically and use contractions where appropriate.
  8. ASD: formal(/academic) diagnosis: I will have my contract by the end of 201201.
  9. Mathematics: applied: I will be able to calculate the day of the week in a few seconds when requested.
  10. Chemistry: pure: I will memorize the atomic masses, electronegativities, electron configurations, atomic radii, and first ionization energies in a non-sequential format.
  11. Special interest: toxicology: I will know 120 common poisons (including household products that may get switched), their toxicities and their antidotes.
  12. Special interest: conworld: I will complete the questionnaire for all factions and even their provinces or regions.
  13. Special interest: biochemistry (!!!): I will know the propensity data for all amino acids along with their monomeric weights and formulae.
  14. Academic: university: I will enroll in a university with a good program without too many students that still balances my skills.
  15. Special interest: linguistics: I will finally memorize the Latin grammar tables and be able to recall any entry with no difficulty.
  16. Special interest: optics: I will have a set of mounted lenses for my weak but dominant eye.
  17. Special interest: philosophy: I will complete 40 pages on the fields of philosophy and my beliefs about them.
  18. Academic: rules: I will memorize the infractions and their punishments and establish some sense of order at school.
  19. Special interest: cryptography: I will develop a cipher based on the unique properties of my constructed language such that no one without sufficient knowledge of the language and its irregularities can decipher my words.
  20. I will come up with better attempts at New Year’s resolutions.

Creating Art

My creative drive (defined as the drive to create, rather than the ability to produce art), becomes unusually active when I am stressed or bored. Currently, it is the latter, and it is irritating, because I cannot stand colors at the moment (leading to Saturation -90). After seeing an excellent webcomic, I noticed that I want to do so as well, but know that I would have neither enough subjects to discuss nor the ability to draw good pictures (especially because Saturation 0, the value a vast majority of readers use, will make the colors seem excessively saturated). This time, the drive affects visual art more than auditory art, so music theory is out of the question. Maybe I should just produce a protein model, because no one else cares about the colors as long as the physical structure is available.

Protein Modeling I

I finally got around to crafting a basic model. This one is of a monomer of 4-oxalocrotonate tautomerase. Here is a picture of it:

See the beauty of this monomer of a hexameric enzyme! See it fail at functioning!

Now if that does not make a professor laugh, I really have no idea what will. Of course, when I end up making people laugh, it is always unintentional because bringing up the obvious seems humorous. On the other hand, when I make a pun I personally think is funny, no one understands. Must all the, “humor,” these days involve something blatantly truthful or something blatantly obscene?

Ach, I am getting too impatient. Therefore, I will green-light Project: Ortingeni (from now on, stylized as Ortingenia) and commence my personal ConWorld!

Catalase Construction II

Now that I have verified my project with my teacher, I can get started. I decided to construct the model of Gallus gallus, or chicken, liver catalase. Although the PDB seems to have plenty of structures for other species, the humble chicken, which is absent, is significant because of the fact that chicken liver was used for a catalase experiment. Because I plan to build a moderately functioning model (out of paper, no less), I will be testing out smaller, less complicated enzymes. Anything done for Knowledge! can eventually be excused.

After alignment and checking, the structures are similar enough that the average non-interested lay person would not notice if I simply built bovine liver catalase. However, the alignment and verification are very interesting components, and that is why I must do them. As with any project, there will be no cheating.

Catalase Construction I

I have been commissioned to construct a paper model of catalase. Just for an extra challenge, I decided against copying the existing PDB and began aligning the chicken catalase (which brings back memories of the liver experiment). As it turns out, the two are similar enough to not require much SP, so the next step will be making forms for confirming this commission. Apparently, most NT students do not care much for learning about the molecules but are fascinated by the models. My teacher requested something grand that would shock the students into loving the curriculum. Therefore, I will have to complete this by the end of Thanksgiving, or finals will dominate the students’ minds and distract them from the molecular component of biology that I love discussing. If only all people were also AS and did not care much for the non-verbal cues and shared the special interest…