Learning to Use PyMOL (includes instructions for PS #2)
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1 Learning to Use PyMOL (includes instructions for PS #2) To begin, download the saved PyMOL session file, 4kyz.pse from the Chem 391 Assignments web page: The file should be saved to your disk. If you are working on a lab PC, save the file to the Downloads folder. 1. Double-click on the 4kyz.pse icon. Should that fail to open the file in PyMOL, open the software by double-clicking on its icon, and then opening 4kyz.pse by selecting Open under the File menu. The name of the file is based on its protein data bank ID. It is a computer-designed protein with no designed function. (Note you can download the raw 4kyz coordinate file at 2. Note the window is divided into three sectons: (1) a large black Viewer display, (2) above that a command line entry space and message window, and (3) a Control area to the right with a series of buttons and lists etc. that help control what s in the display window. Also there is a standard set of menus at the top of the screen. 3. After noting all that, set the software to 1-button or 3-button viewing mode under the Mouse menu (as appropriate), and turn virtual trackball to the unchecked condition (my preference). The mouse now has the following functions (also abbreviated at the lower right of the window). A. Clicking on background 3-Button Mode 1-Button Mode Rotate Left button Click/drag Translate (move x, y) Middle button Option-Click Zoom (move z) Right button Control-Click B. Clicking on atom 3-Button Mode 1-Button Mode Select group Left button Click/drag Center view on atom Middle button Option-Click ID atom Right button Control-Click Go ahead play with it. If the molecule becomes hopelessly lost, you can recover it by right-clicking (control-clicking in 1 button mode) on the display window and then left-clicking on zoom from the menu of options that appears.
2 4. I have prepared a series of selections for this exercise. They are listed at the right of the window in the control area: Note that all and 4kyz have no parentheses. all refers to all open structural models, and there is only one structural model here 4kyz. The parenthetical selections are subsets of atoms within 4kyz. To start, let s play with 4kyz. Four menu buttons appear to its right: A/S/H/L/C. A=action S=show H=hide L=label C=color b. Click on H, and hide the lines. Then click on S and show sticks. Then click on H and hide sticks. Repeat the S and H with spheres and with cartoon. Different views of the protein will be helpful in different circumstances. a. Click on C button and play with coloring schemes. You can color chain/chainbows to obtain a meaningful variant of the current scheme, which is by element. There are 4 copies of the 4kyz protein in this file. You can also color by ss (secondary structure) or. c. To view a single protein chain from among the four, click on H next to all, and hide everything. Then, next to (achain), show cartoon under S. You may also wish to zoom in on it (under the A button next to (achain). You can see it as sticks as well (H and S as above). These are different views of one protein chain. d. Ultimately, we will be looking only at a single αβ motif in the A chain. To view the motif alone, click on H next to all, and hide everything. Then, next to (abmotif), show cartoon under S. Note that some problem set questions (for PS #2) related to 4kyz.pse follow on the next page. I recommend closing PyMOL and starting again from the file afresh. There s a PyMOL basics document that gives you a broader look at some basic PyMOL commands that may help as you go forward.
3 Problem Set #2 Questions 1. What is the secondary structure composition of the αβmotif? Which elements are first on the chain and last? Is the sheet parallel or antiparallel If you need to refresh the view, in the control window, go to the H button next to all and select everything. Then select the S button next to (abmotif) and select cartoon. You can visualize the peptide from N-terminus to C-terminus by Coloring by chain and chainbows. The N- terminus is blue and the C-terminus is red. 2. Sketch an H-bond between side chains on the surface of the alpha helix that might help stabilize the protein structure. Identify the two residues that participate and the distance between the donor and acceptor atoms. (Note: only sketch side chains.) Recolor the abmotif by element (choose your favorite scheme). Show sticks and Show cartoon. This hybrid view is sometimes easiest to interpret. You can zoom under the Action menu, or center a residue in the display window by middle clicking on it. Look at polar side chains on the helix surface. You will have to ID the residues by Label residues. It may be useful to Hide label after you have made identifications. Alternately, you can identify a residue by right clicking on it (or control-click in one-button mode). You should see something like the following appear: This is the atom identifier. It indicates that I have clicked on the 4kyz model the A chain Glu35 and the α-carbon (CA). 3. Sketch an H-bond network between 3 side chains on the surface of the beta sheet that might help stabilize the protein structure. Identify the three residues that participate and the distance between the donor and acceptor atoms (2 H-bonds). Repeat your actions for question #2, now looking at the β sheet region of the abmotif. 4. Residues 6-10 constitute a type II β-turn, which typically has a Gly residue at the position occupied by residue Gly14. To see why, mutate residue 14 to an alanine. First, zoom on turn in the Action menu. To mutate residue 14 to Ala31, select Mutagenesis under the Wizard menu. In the control panel to the right of the display window, you should see a bar menu that reads No Mutation. Left click on that bar and select ( ALA). Now click on any atom in residue 14 in the display window. The methyl side chain will appear. Now select Apply and Done in the control window. Where does the methyl group cause a steric conflict? Using the Measurement Wizard measure the distance between clashing atoms (they can be identified by right clicking). When done, click Done. 5. Proline is rarely found in the middle of the helix. To show why not, mutate residue 34 to proline. Sketch, and then measure the inappropriate contacts made by proline. To mutate residue 34 to 34, select Mutagenesis under the Wizard menu. In the control panel to the right of the display window, you should see a bar menu that reads No Mutation. Left click on that bar and select ( PRO). Now click on any atom in residue 34 in the display window. Both Asn and Pro side chains will now overlap. Points of steric conflict between the proline side chain and other atoms in the model will appear as red disks. Identify the atom and residue in conflict with proline at position 34. How does that atom normally interact with residue 34?
4 Problem Set #2 Chem 391 Due in class on 9/15/16 Name 1. What is the secondary structure composition of the αβmotif? Which elements are first on the chain and last? Is the sheet parallel or antiparallel? 2. Sketch an H-bond between side chains on the surface of the alpha helix that might help stabilize the protein structure. Identify the two residues that participate and the distance between the donor and acceptor atoms. (Note: only sketch side chains.) 3. Sketch an H-bond network between 3 side chains on the surface of the beta sheet that might help stabilize the protein structure. Identify the three residues that participate and the distance between the donor and acceptor atoms (2 H-bonds) 4. Residues 6-10 constitute a type II β-turn, which typically has a Gly residue at the position occupied by residue Gly14. Why won t a side chain fit there? 5. Proline is rarely found in the middle of the helix. To show why not, mutate residue 34 to proline. Sketch, and then measure the inappropriate contacts made by proline. Why is proline a poor choice for a central residue in an alpha helix?
5 6. The following are the Ramachandran plots for alanine (left) and aminoisobutyric acid (Aib; right), an α-amino acid with two methyl groups on the α carbon atom. H 3 C CH 3 +H 3 N CO 2 - Consider a helix-forming peptide that substitutes an alanine residue with Aib. Would Aib shift the equilibrium between random coil and helix towards helix or towards coil? Suggest enthalpic and/or entropic rationales as appropriate. 7. Use a ph line to estimate the isoelectric point of the following peptides: a. CHARGED b. ACIDIFIER
6 8. An MS/MS sequencing project is being conducted. A tryptic digest of the protein is performed, and from the primary MS spectrum of these peptides a peak with m/z ratio of is selected. Following CID fragmentation, the peaks (corresponding to B & Y fragments) are observed at the following m/z ratios: 132.2, 147.1, 231.3, 250.3, 334.5, What is the sequence of the peptide with m/z ratio of 240.8? Show your reasoning. (See: for a helpful fact checker) 9. The membrane that envelopes cells is composed largely of phospholipids, containing hydrocarbons tails typically methylene or methane groups in length. Proteins are embedded in the membrane, and that portion of the peptide chain that crosses the membrane is always found in either alpha-helical or beta sheet conformation. Provide a thermodynamic explanation for that observation (use words like entropy and enthalpy to make me smile).
7 10. There is a strong interest in developing stable α-helices that could act as peptide inhibitors of cellular processes. The Horne lab has recently published on helix stabilization via cross-linking of residues in an alpha helix of the villin headpiece (VPH; Haney et al., 2016; link on web page in assignments page). Figure 1 shows the structures of five relevant constructs: 1 The native protein 3a, b Protein with alkyne/azide before (a) and after (b) crosslinking. 4a, b Protein with before (a) and after (b) crosslinking with an oxime. The following CD spectra are obtained. a. Based on the CD spectra of the five variants, which appears to stabilize the helix best? Explain briefly. b. In Table 1, the thermodynamic values for helix formation are given. By these standards, which is the most stably folded variant of VPH? Is the stabilization relative to the wild-type (1) for enthalpic or entropic reasons? How might you explain that observation? 11. For every rule I give you, there s an exception. The following amide is protonated on the nitrogen, not the oxygen. Furthermore it hydrolyzes rapidly with a half-life in minutes instead of years as for the typical peptide bond. Provide an explanation for this odd behavior. Feel free to check out Komarav et al. (2015) JACS 137, 926. They solved the crystal structure of the little beasty.
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