UCSC BME 205 Fall 2006

Intro to Bioinformatics
Paper Assignment 1

(Last Update: 15:21 PDT 18 October 2006 )

Play with model kit. Due Fri 14 Oct 2006 (noon).

This assignment will ask you to build some models with your Darling Model kit, then make a few observations. Please turn in clear descriptions of what you did and what observations you made. Assume that the person grading the assignment will not have the "prompt questions" in front of them, so that your answers can be a stand-alone document—you will be graded on the clarity of your writeup as well as the correctness of your observations.

Submit the file as a PDF file using the "submit" command. The class locker is "bme206-kk.f06" and the assignment is "darling". There are scanners in most of the ITS computer labs (not in Baskin 105, but next door in Baskin 109), if you want to convert something hand-drawn into a digital image. See http://ic.ucsc.edu/labs/hardware.shtml for a list of which ITS labs have which equipment. You can also you ChemDraw or similar software (see http://ic.ucsc.edu/labs/software.shtml for what software is in the instructional computing labs).

Note: we will only be accepting PDF files, *not* Microsoft word files. Because this assignment requires some pictures, plain text will not be adequate. Note: Acrobat is supposedly available in all Mac and PC labs run by Instructional Computing, so PDF should be fairly easy to produce. The Acrobat Distiller is also available on School of Engineering SUN Sparc computers (as "distill"), but not on the Linux machines or solopteron (run distill on "sundance", "moondance", or "apache" from an SoE account).

  1. Build a protein backbone, at least 6 (and preferably 9) amino acids long, following the instructions I wrote. Make sure you get the chirality right---this is determined by which of the two available bond positions on C-alpha is used for the hydrogen and which is used for the sidechain. The CORN mnemonic (CO-R-N clockwise around the alpha carbon when looking at the alpha hydrogen) helps get chirality right. Fold the backbone into an alpha helix, remembering that there should be a hydrogen bond between Oi and Ni+4. Remember that the peptide plane with Oi has Ni+1. Some things to check: do all the attachment points for side chains point out of the helix? Is the helix fairly rigid? Have you got the twist going the right way (if you hold the helix axis vertically, the backbone should be slanted like the middle line of a Z)?

    Measure the distances between C-alpha atoms separated by 1, 2, 3, ... The scale of the Darling models is about 2 inches (or 5cm) to an Angstrom. (Turn in the table of distances in Angstroms between the centers of C-alpha atoms.)

    Add a C-beta carbon to each C-alpha, and measure the distances for C-beta atoms separated by 1, 2, 3, ... (Turn in the table of distances in Angstroms between the centers of C-beta atoms.)

  2. Make a proline residue and add it to the C-terminal end of the helix. Note how the lack of a hydrogen on the backbone nitrogen prevents the proline from participating in the hydrogen bonds that stabilize the helix. Try putting the proline at the N-terminal end of the helix. Are there problems with the H-bond at this end? Can the helix extend back before the proline? How far back can it extend? (That is can the proline be the first, second, third, ... position in an alpha helix?) I am not looking for a distance here, but a count of the number of residues. That is, if proline is residue "i", can i-1 be part of the helix, i-2, ... ?

    Try converting the peptide of the proline from trans to cis conformation. There are two ways to do this: taking apart the peptide plane and twisting the omega angle from 180o to 0o, or changing which carbon you think of as Calpha and which as Cdelta, changing which one the carbonyl carbon bonds to. The first method is probably closer to what happens with a cis-trans-isomerase, but the second is a lot easier to do with the models.

  3. Remove the proline, and add a serine side chain to the C-alpha before the first residue of the helix (remember that "first" means N-terminal). Make a hydrogen bond between the O of the OH group and the HN of third residue of the helix. This is a common N-cap motif for helices. Try the same cap with a threonine instead of a serine (also fairly common).
  4. Undo your helix H-bonds and split your protein backbone into two chains. Align the chains as parallel beta strands, and arrange the H bonds correctly. Which Hbonds are formed? Measure and report the distance between the closest C-beta atoms from one strand to the other. What is the distance from one C-beta to the next one along the strand? To the C-beta that is two away on the strand?
  5. Now rearrange the strands to be anti-parallel. Again, which H-bonds are formed, and what is the distance between the closest C-beta atoms?
  6. Join the two anti-parallel strands with an aspartic acid (D) or asparagine (N) followed by a glycine. If you want, you can also make the two residues on either side be lysine (K), so that you have the sequence KDGK or KNGK. This sequence makes a tight bend about 41% of the time, XXK[DN]GXX forms a hairpin about 36% of the time. (In past years, I suggested XPDG, which produces a tight bend about 45% of the time, but XXXPDGXX only forms a hairpin about 2% of the time.) Note that the K[DN]GK turn is going to be a type I' turn (See http://www.cryst.bbk.ac.uk/PPS95/course/6_super_sec/super1.html by j.cooper for an explanation of type I' and II' turns.

    Come up with a pattern of hydrogen bonds that holds this hairpin together. Hand in a sketch of the Hbonds. Make sure that you take into consideration that the atoms are actually space-filling—many of the conformations obtainable with the models correspond to physically impossible ones.

    Also, make sure that the lysine side chains are both on the same side of the hairpin.

  7. Build a pair of complementary DNA bases and find the Hbonds. Note that the Hbonds may not come straight out from the double-bonded oxygen (as in the proteins) but may be at closer to a 120 degree angle. For the pair of bases you chose, make a sketch of the structure showing the Hbonds, and indicate the angles for carbon-donor-acceptor (CDA) and donor-acceptor-carbon (DAC). Note: the nitrogen (or whatever the hydrogen is covalently bound to) is the donor of the hydrogen for the hydrogen bond, and the oxygen (or whatever electronegative atom is not covalently bonded to the hydrogen) is the acceptor.

    The CDA angle has its vertex at the donor atom, one ray to the acceptor, and the other ray to the carbon that the donor is covalently bonded to (there may be multiple such carbons, and so multiple CDA angles). Similarly the DAC angle has its vertex at the acceptor, and the rays to the donor and to a carbon covalently bonded to the acceptor.

    Note: no one outside the Karplus lab uses the CDA and DAC angles, preferring to work with angles around the hydrogen atom.



    Things learned to improve assignment next time

    Still some confusion about the beta hairpin. Emphasize in class (or somewhere) the need to have 2 H-bonds to stabilize a pair of beta strands. Perhaps provide a pointer to a structure in PDB that has a hairpin that they can copy the structure from???

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    Questions about page content should be directed to

    Kevin Karplus
    Biomolecular Engineering
    University of California, Santa Cruz
    Santa Cruz, CA 95064
    USA
    karplus@soe.ucsc.edu
    1-831-459-4250