Pharyngula

This last week in Biochemistry

It’s been quite busy last week. Despite the Neurobiology class didn’t meet that week, my other classes kept my hands full. I blame it on two exams and a paper due during the week of Homecoming.

Since I don’t have any new thoughts on Neurobiology, let’s see what can be dug up from my Biochemistry class. For the lab, I wrote my paper of Desulforedoxen. Its job is reducing sulfates. You can look it up at JMol using “1DHG” as the code.

I found this protein very interesting. In class, we had learned about the driving forces for tertiary structure in proteins: H-bonding, hydrophobic/Vanderwal’s, salt bridges, and disulfide bonds between Cystine residues. Upon examining Desulforedoxen, I learned that Cystines were capable of more than just S-S bonding. With four Cystines clustered nearby each other in the tertiary structure, an iron atom sits tetrahedrally bonded to the four sulfurs. While I bet it is a major player in tertiary structure, it just reeks of active site. Since the transition metal, and its neighboring sulfurs, have ‘D’ orbitals, this looks like it’s capable of something that can’t easily be performed in a test tube.

I’ll be a lot of you already know that this can happen in proteins. For me, it was learning it by observation instead of in lecture, that was fun. Moments like that have made it well worth it to go into biology. It’s also cool how such lesser-used amino acids have more than one purpose that they can serve in cells.

Note: the article I read about this protein said that it had iron bonded to the sulfur. When I looked it up in JMol, it was instead bonded to mercury. Weird. An abstract of the article I used can be found here. Anyways, just washing my hands so I don’t fall victim to the inconsistencies-lynch-mob. Have a nice day.

Comments

  1. #1 Sili
    September 30, 2007

    Since this is sorta my subject, I’ll venture a guess without reading the paper.

    Metalloproteins as the one you describe can be notoriously difficult to characterise because the coordination bonds are far more labile than the covalent backbone of the protein. So in many cases the metal ‘disappears’ in crystallisation – or a completely different metal is taken up from the growth solution.

    In this case, though, I think the mercury has been added deliberately. Firstly because the Hg-S is very strong (organic sulphur compounds – now known as thiols – were originally dubbed mercaptanes because they trapped mercury – GO ZEISE!) so it’s more likely to stay in place during crystallisation. Secondly mercury because of its higher atomic number is far far better at scattering X-rays than in iron (scattering crosssection goes as Z^2), so doing the datacollection on the Hg derivative is relatively easier (smaller crystal – growing big ones is hard; weaker X-ray source – lab vs. synchrotron).

  2. #2 sailor
    September 30, 2007

    Thanks for the post Mark, I know almost nothing about chemistry and way less about biochemistry, so it was at least entertaining to go and find out what things like active site and D orbitals were. I found out, but I am not sure I am much wiser.

  3. #3 Greg
    September 30, 2007

    Interesting post. The protein in the body contains iron. A common thing to do when trying to study metalloproteins is to exchange the natural metal ion for other metals. This can help in obtaining suitable crystals for x-ray analysis. Thus, the structure you found containing mercury.

  4. #4 skw
    September 30, 2007

    Admittedly, I haven’t yet attempted to grow protein crystals, so take this with a grain of salt. I’m fairly sure that the benefit of using mercury over iron in the crystallography has less to do with growing the crystals, as previous comments have said, and more to do with phasing the diffraction data. Typically when you are phasing with methods like multiple isomorphous replacement (MIR), you use atoms much heavier than iron, like mercury. In other words, it has less to do with data collection and more to do with data analysis.

  5. #5 Pete
    September 30, 2007

    that’s a nice site you linked to.
    btw, it’s “desulforedoxin”, not “-en”.

  6. #6 sailor
    September 30, 2007

    that’s a nice site you linked to.
    btw, it’s “desulforedoxin”, not “-en”.

    Thanks Pete that makes it much easier to look up on Google!

  7. #7 Dave Eaton
    October 1, 2007

    Nice post.

    I know only a little biochem, but did graduate work in organometallic chemistry. One of the things that I find compelling about this sort of subject is the amount of subtlety encoded into exactly how the metal center is held, just so, first so that only suitable substrates are able to reach the site, and second, how the energy levels can be fine-tuned by this very special coordination environment.

    Oh, and don’t worry about being perfect. At your stage in life, your job is to learn a huge amount of stuff, and some of that learning will come at the hands of acerbic assholes correcting you. C’est la vie. Do your best, don’t talk out of your ass, but don’t be afraid to risk looking foolish. It is a part of learning.

  8. #8 Walter
    October 1, 2007

    Small nitpick:

    Desulforedoxin is a redox protein isolated from sulfate-reducing bacteria, but I don’t think it’s directly involved in sulfate reduction except possibly as a link in the electron chain between donor and acceptor. There is a very specific and highly conserved dissimilatory sulfate reduction pathway in SRB species that allows the cell to respire sulfate. This pathway in itself is biochemically interesting because sulfate is the only terminal electron acceptor that has to be activated by ATP before it can be reduced. In fact, stoichiometrically in Desulfovibrio species, the ATP produced by substrate-level phosphorylation during oxidation of 2 mol lactate to acetate exactly equals the ATP consumed in activating sulfate (i.e. delta[ATP] = 0), which was the first indication that these species must establish maintain a chemiosmotic gradient for energy production.

  9. #9 Frieda
    October 1, 2007

    Enjoyed your post.

    I just want to make a small but important correction to the link to “Jmol” in your post. The link goes to *FirstGlance in Jmol*, an application that uses Jmol as its molecular rendering engine. Jmol itself is an open source, Java molecular viewer, and is used in many other cool contexts, as you can see from the Jmol wiki page, Websites Using Jmol.

    Anyway, good for you for using FGiJ to investigate the protein you learned about in class, and for finding/posting an inconsistency that generated some informative and interesting comments!

  10. #10 Sili
    October 1, 2007

    Good point, skw.

    It shows that I’ve never done anything but small molecule work. I’m used to just plugging the data into direct methods and a Patterson search. The difficulty for me has always been to find and model counterions and solvent. Boring stuff.

  11. #11 Reginald Selkirk
    October 1, 2007

    I looked up the paper associated with the X-ray structure under discussion; Archer, Carvalho, Teixeira, Moura, Rusnak & Romao (1999) Protein Science 8: 1536-1545. From the abstract:

    The simplicity of the active center in Dx and the possibility of replacing the iron by other metals make this protein an attractive case for the crystallographic analysis of metal-substituted derivatives… Metal replacement experiments were carried out by reconstituting the apoprotein with In3+, Ga3+, Cd2+, Hg2+, and Ni2+ salts…

    So in this case, the metal substitution was not for crystallographic phasing, but was a topic of structural and biochemical study in itself. The iron-containing structure was already available, and was used to solve the structures containing other metals via difference maps for the isomorphous structures and molecular replacement for the nonisomorphous structures.

    The iron-containing structure is available as PDB code 1DXG. It is associated with Archer, et.al (1995) J. Mol. Biol. 251:690-702. The original structure was solved with SIRAS phasing (single isomorphous replacement with anomalous scattering). The 1995 paper reported both iron-containing and indium-containing structures, and the isomorphous difference between the two metals was used to locate the metal sites, with phasing then based on both the isomorphous differences and the anomalous scattering of the metals. They did this on a copper rotating anode; at a synchrotron they could have gotten much more phasing power out of the anomalous scattering.

  12. #12 murat
    December 4, 2007

    Vatan gazetesi yazar? Ha?met Babao?lu’yla ili?kisini noktalayan Ay?e Özy?lmazel, gönlünü Okan Bayülgen’e kapt?rd?.

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