Monday, January 09, 2012

Monday's Molecule #155

We're going to talk about the evolution of this molecule in my class tomorrow. It's a good examples for illustrating some basic principles of molecular evolution.

You need to identify the exact molecule, including the species. Here's a hint: ANKSKGIVWN.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The winner is Dima Klenchin who was the first to identify the molecule as cytochrome c from tuna (Thunnus alalunga). The figure is from the PDB file 3CYT. This PDB file supercedes 1CYT which was reportedly from another species of tuna.

Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody


  1. Cytochrome c

  2. Cytochrome C, in species Katsuwonus pelamis (skipjack tuna).

    Not a graduate student, just playing along :)

  3. I knew immediately what it is except, of course, the species. However, giving a partial sequence is like giving away the whole thing, from A to Z. Two seconds of googling is all it takes. Cytochrome C from tuna (Thunnus thynnus).

    Can we have the little puzzles back? :-)

  4. Its obviously a cytochrome c.
    Your partial sequence is conserved in many fishes including the Pacific lamprey, the large yellow croaker, the tuna Thunnus alalunga (albacore)and Bonito (Katsuo). Since crystal structures are available for the latter two, either could be your molecule.

  5. Google told me that it's the small heme protein Cytochrome c, this particular one being found in tuna...maybe?

  6. Cytochrome c.

    Multiple answers possible on the species portion of the quiz.

    Google search had an easy time providing an initial lead.

    Swiss-prot sequence matches:
    Lampetra tridentata
    Katsuwonus pelamis
    However, since there is apparently a structure solved, Lampetra is out.

    Species with sequence matches at RCSB:

    Thunnus thynnus (northern bluefin tuna)
    RCSB entries 1LFM, 1I54, 1I55

    Thunnus alalunga (albacore tuna)
    RCSB entries 5CYT (supercedes 4CYT), 3CYT (supercedes 1CYT)

    Katsuwonus pelamis (bonito, skipjack tuna)
    RCSB entry 1CYC

  7. It is a heme-bound monomeric cytochrome c from Thunnus alalunga (Albacore tuna). The gold atom is iron, of course.

  8. Larry- The hint made it too easy. I figured out myself that it was cytochrome after determining that the central molecule was heme, and that the protein was not myoglobin (which at first looked promising). Searching Google with the partial aa sequence gives you the answer on the fourth hit - and your post gets two of the first three hits! -Matt

  9. Larry-

    It is cytochrome C from the large yellow croaker, Larimichthys crocea.

  10. I'm going with:

    Ferrocytochrome c from Katsuwonus pelamis (1CYC)

    Thunnus alalunga is also a 100% match over the 10aa you gave, but 3CYT is complexed with Protoporphyrin IX, not heme and no sulfur atoms are visible (to me at least) in the structure you've shown. No other ferrocytochrome c structure has a 100% match over those particular 10aa.

  11. Larry, but Rumraket got it right almost an hour an a half earlier than I did. The skipjack tuna has the same partial sequence (PDB ID 1CYC):


  12. Dima said,

    ... Rumraket got it right almost an hour an a half earlier than I did

    You can't win if you use a pseudonym.

  13. It's okay, I'm not a graduate student anyway and I'm from Denmark so we'll probably never meet, I just like following your blog. For some reason, learning about science, biochemistry and evolution is more effective when it's explained how people who lie and obfuscate intentionally, are wrong.