Molecular Modeling Protocol

Transcription

1 Molecular Modeling of an unknown protein 1. Register for your own SWISS-MODEL Workspace at Follow the Login link in the upper right hand corner. Bring your password to lab (you will be able to access your if necessary). 2. Open the SPDBV_4.1.0_OSX folder on the desktop and double click Swiss-PDBViewer (formerly called DeepView) to launch Swiss-PDB Viewer. 3. Cancel the dialog box if it automatically opens. 4. In Prefs: Swiss/Model, make sure your SWISS-MODEL Workspace address is included. Click SwissModel: Load Raw Sequence from Amino Acids to load the Unknown Protein.txt file from the Desktop. You should be looking at a red, blue, white and yellow stick model on a black background. *What secondary structure do you see? Why? 5. On startup, Swiss-PDB Viewer opens two windows, the display or graphics window, which is labeled with the name of the PDB file (and the window size in pixels), and the Control Panel (on the right if the Control Panel does not appear, use the command Wind: Control Panel to display it). The Control Panel lists the amino-acids residues and other contents of the PDB file. You use the Control Panel to select residues, establish the content of the display, label residues, and color them. Above the graphics window is the Tool Bar. You use the graphics window and the buttons on the Tool Bar to view, manipulate, and measure the model. You must click on a window to make it active. 6. Display additional windows: Wind: Alignment The narrow Align window appears below the graphics window, showing the amino-acid sequence of the protein in one-letter abbreviations. You use this window when comparing sequences of two or more proteins. Select: All The color of residues listed in the Control Panel changes from black to red (and in the Sequence Alignment window, from white to purple). The new color means that a residue is currently selected. Some Swiss-PDB Viewer commands affect only the selected residues. Wind: Ramachandran Plot The Ramachandran Plot window appears in the upper left. You can use this window to judge the quality of a model, by finding residues whose conformational angles lie outside allowed ranges. You can also display and change conformational angles in the model. Each dot (actually, a tiny cross or square) on the diagram gives the phi and psi angles of one residue in the protein. Because all residues are selected, all are represented in the window. 1

2 Wind: Layer Info The small Layer Info table appears at the upper right. This table provides control of multiple protein models, allowing you to choose which models are visible, which models can move, and which models have certain features on display. 7. On the Tool Bar, below the first square button on the left (Zoom and Center), are two symbols, a globe and a little dog-eared piece of paper (document icon). Click the document icon to see the.txt file of the protein currently on display. Later, you will be able to display PDB file information, as well. Close the Align, Ramachandran Plot, and Layer Info windows. 8. Center the model by clicking the first button on the left of the tool bar, Zoom and Center (or press = on the keyboard). Control the movement of the model by clicking through the next three buttons. 9. Turn on stereo display by clicking Prefs: Stereo Display. The Allow Real Time Stereo Display box should be checked and Use Side by Side Stereo should be selected. Set the Rotation angle to for cross-eyed viewing and set the Stereo Separation to 180 pixels. Adjust if you need more or less space between the pictures. Click OK. Switch between stereo display and normal display by clicking on command (apple key), t. 10. Click anywhere on the Control Panel window to make it active. First, simply scroll down to the bottom of the list to see how many amino-acid residues the protein contains. * How many amino acids are present in the model? 11. In Control Panel, select all of the amino acids by clicking on one of them and then pressing command a. 12. Select SwissModel: Submit Template Search Request against ExPDB for Current Layer to find a modeling template. 13. Supply your password when asked. 14. Retrieve the results from your by clicking the direct link. 15. Results for possible templates will be displayed under Interpro. Click on the first option. *Which protein did you pick? How do you think this template was identified? 16. Click on the name. 17. In the new window, to the left, under Overview select Structures. 18. Chose 1kwg. 2

3 *What is the name of this protein? *What organism is the template from? Does this make sense given the nature of the organism the unknown protein is from? 19. Click Download PDB file and save the file 1kwg. 20. Load this template file into Swiss-PDB Viewer clicking File: Open PDB File. 21. Make sure the Alignment window is open. 22. Click Fit: Magic Fit then Fit: Iterative Magic Fit. 23. Click Fit: Generate Structural Alignment. 24. Click Save: Project (all layers) to file name proj_bgal. Close all of the layers. 25. Return to your SWISS-MODEL Workspace online. In the drop down menu, select Modeling: Project Mode, choose the project that you just saved with Swiss-PDB Viewer and submit it to your SWISS-MODEL workspace. 26. When results appear (this will take some time), download the model as a Swiss-PDB Viewer Project. 27. Open the newly received project file with Download: DeepView Project. In it, you will find your final homology model and the template, superimposed as they were during the work by SwissModel. 28. Your model is displayed as a ribbon colored by confidence factor, a measure of how well the model fits the template. When the template and target are strongly homologous, the ribbon is typically uniformly colored. *Are your template and target strongly homologous? 29. Show the Alignment window. *Where is the strongest and weakest sequence identity? 3

4 30. On the Control Panel, click on the top left corner and select unknown. Uncheck the box next to visible. Select 1kwg (the T. thermophilus model) and make sure that the box next to visible is checked. 31. Click and drag, starting on the first residue (methionine) near the top of the window and finishing at TYR6 (this will include amino acids at position 1-6). All of these group names from should turn red and are now selected. Press return on the keyboard. Zoom and center. *What type of secondary structure are you viewing? 32. Repeat with residues Glu14 through Ala26. *What type of secondary structure are you viewing? *Generally, where do these elements of secondary structure fall on the Ramachandran plot (Phi and Psi angles)? Is this what you expect? Feel free to consult your textbook or the internet. 33. Select residues 1-6 again. Notice also that a checkmark has appeared in the show column next to the selected residues, indicating that they are on display. There are checks also in the side column, which means that side chains are shown. A side chain is shown only if the rest of the residue is shown, so you only see the side chains of displayed residues in the graphics window. 34. Click the check in the side column next to MET1, to hide the side chain. Click the same space again to replace the check and display the MET1 sidechain. Try the same thing in the show, label, surface (little circle of dots), and ribn columns. Surface displays a dotted van der Waals surface for the group. Ribn (ribbon) draws a smooth-stranded cartoon of the selected backbone. *What element does the yellow color represent? *Is there a second residue within positions 1-6 that contains this same element? If so, which residue is it (be general)? 4

5 35. Now, click on the small s next to GLY597 and press enter. *What type of secondary structure did you just display? 36. Press the command key and select the s next to THR605 and press enter. You can display the names of the side chains by clicking the plus sign above the labl coumn. *Are these two secondary structures parallel or anti-parallel? 37. Find and display all potential hydrogen bonds in the molecule, including those involving side chains and hetero groups with Tools: Compute H Bonds. Swiss-PDB Viewer displays hydrogen bonds as green dashed lines. 38. To see only the alpha-helical regions of β-galactosidase with hydrogen bonds shown, choose Select: Secondary Structure: Helices return. Turn off all side chains. Look around to confirm that the segments shown are helical. Confirm that most of the hydrogen bonds are from the carbonyl oxygen of residue n to the amide nitrogen of residue n + 4. Notice the Control Panel: only the residues in helices are red. This allows you to take further action on the selected groups, such as coloring them, as you will see in the next section. 39. Repeat with strands (beta-pleated sheets) and coils. *Describe H-bonds that are found in random coil regions. Use the Measuring Tool (1.5 Å symbol in the toolbar) to assist in your description. 40. Display: Show H Bonds You will find that this command has a checkmark to its left, which means it is turned on. By selecting it, you turn it off, and remove the hydrogen bonds from the display. 41. Notice the other Select menu commands. Can you select and display only the residues whose side chains carry positive charge (basic residues)? Can you select and display only the histidine residues and their side chains? (Look at the submenu that pops up when you choose Select: Group Kind.) *How many histidines are present in β-galactosidase? 5

6 42. The Layers Info window provides information about the display. Select Wind: Layers Info. Note the SelGrp heading at the top of the far right column. This column shows the number of groups currently selected. Again select the basic residues, and notice the number selected under the SelGrp heading. Now select acidic residues. Compare the number of acidic and basic residues in 1kwg and the unknown protein. Compare the number of polar and non-polar residues. Put away the Layers Info window by clicking on its close box, the small square in its upper left corner. * Would you expect the pi of β-galactosidase to be acidic, basic or neutral? *Is the molecule predominately polar or non-polar? 43. T. thermophilus β-galactosidase contains a metal-binding site (it is not clear if the metal binding is Zn 2+ or Fe 2+ ). The four residues that are involved in this metal-binding cluster are Cys106, Cys150, Cys152 and Cys155. In the control panel, press command and select these four cysteines. Press return and Zoom and center. 44. In the alignment window, the four selected Cysteines are displayed. *Do these four cysteines align with cysteines in the unknown protein? 45. In the alignment window, press control and select these four residues. In the control panel, the four residues will be red. In order to display these residues, check the box next to visible. Center and zoom. *Which four residues in the unknown protein are being displayed? *Do these four residues overlay perfectly with the four residues in T. thermophilus? *Would you expect these four cysteines to be able to bind a Zn 2+ or Fe 2+ ion? Why? 6

7 46. Switch back to the 1kwg (T. thermophilus model) view. You are now going to find the active site. 47. In T. thermophilus β-galactosidase the galactose-binding site and putative catalytic residues are PHE350, GLU141, GLU312, PHE181 and TRP182. Display these residues only on the model and identify the aligned residues on the unknown protein. *Do these residues align with the same residues in the unknown molecule? *Which residues did you identify? 7