UCSF-Chimera/C3/Superimposing-and-Morphing/English-timed
From Script | Spoken-Tutorial
| Time | Narration |
| 00:01 | Welcome to this tutorial on Superimposing and Morphing. |
| 00:06 | In this tutorial, we will learn to: superimpose and compare different structures of the same protein, |
| 00:13 | morph conformations and create a trajectory. |
| 00:17 | To follow this tutorial, you should be familiar with Chimera interface. |
| 00:22 | If not, for relevant tutorials, please visit our website. |
| 00:27 | Here I am using :Ubuntu OS version 14.04, Chimera version 1.10.2 , Mozilla firefox browser 42.0 and a working internet connection. |
| 00:43 | Here, I have opened a Chimera window. |
| 00:46 | From the graphic access interface, click on the file 3w7f. |
| 00:53 | The structure of Squalin Synthase opens on the screen. |
| 00:57 | Now, let us prepare this structure for superimposing. |
| 01:01 | It contains two copies of the same protein. |
| 01:05 | Using the command line, delete one of the chains. |
| 01:09 | I will recall the command by clicking on the command history. |
| 01:14 | From the command history dialog box, select the command “delete:.a”. |
| 01:20 | Press Enter. |
| 01:22 | Next, to remove solvent molecules from the structure, I will select the command “del solvent”. Press Enter. |
| 01:32 | This structure is bound to the substrate analog Farnesyl thiopyrophosphate, FPS in short. |
| 01:40 | We will superimpose two similar proteins to compare their secondary structures. |
| 01:46 | For this, we will fetch a structure of the same enzyme without substrate. |
| 01:52 | On the command line, type: “open 2zco”, press Enter. |
| 02:02 | The new structure is in blue color. |
| 02:05 | Now, these two structures are ready to be superimposed. |
| 02:10 | Superimposition or Structural alignment is a tool to compare two or more protein structures. |
| 02:18 | The alignment is based on their shape and three-dimensional conformation. |
| 02:24 | Before we start superimposing, let us place some icons in the tool bar. |
| 02:30 | Click on Favorites menu. |
| 02:32 | Scroll down to Add to favorites/Tool bar option. |
| 02:37 | A Preferences dialog box opens. |
| 02:40 | From the Category drop-down, select Tools. |
| 02:44 | Under the heading “Settings”, check boxes under “On Tool bar” column. |
| 02:53 | Check boxes for Command line , Model Panel , Side View. |
| 02:59 | Scroll down and click on MatchMaker and Match-Align. |
| 03:05 | You can customize your own tool bar. |
| 03:08 | Select tools according to your requirement. |
| 03:12 | Observe the panel. |
| 03:14 | Icons have been added to the Tool bar on top of the panel. |
| 03:19 | To change the position of the tool bar, click on the Toolbar placement button. |
| 03:25 | And select the option from the drop-down menu. |
| 03:29 | When you finish adding all icons to the tool bar, click on Save button. |
| 03:35 | And click on Close to close the dialog box. |
| 03:39 | The structures are now in different positions. |
| 03:43 | Now, let us superimpose the structures using MatchMaker function. |
| 03:48 | Click on MatchMaker tool on the Tool bar. |
| 03:53 | A MatchMaker dialog box opens. |
| 03:56 | Click on 3w7f as Reference structure. |
| 04:01 | For now, let us continue with the default settings. Press OK button. |
| 04:07 | Observe the panel. |
| 04:09 | The two structures are superimposed on each other. |
| 04:13 | The two structures are almost completely superimposable with each other |
| 04:19 | except for a small part which is non-superimposable. |
| 04:23 | The fragment involved in this non-superimposable part starts from the amino acid number 53 to amino acid number 57. |
| 04:34 | The MatchMaker generates a sequence alignment using residue types and secondary structure. |
| 04:40 | And then fits the sequence-aligned residues in 3D. |
| 04:44 | Let us now check the Match-Align tool. |
| 04:48 | Click on Match-Align tool from the tool bar. A dialog box opens. |
| 04:55 | To select the chains, click on their pdb Ids. |
| 04:59 | Click on OK button. |
| 05:03 | A sequence alignment dialog box opens. |
| 05:05 | In this box, the amino acid pairs used in the final fit, are shown with light orange boxes. |
| 05:13 | The structures are mostly similar except for the loop at residues 52-54. |
| 05:21 | Place the cursor over the corresponding one letter code. |
| 05:25 | The residues from 52 to 54 are shifted due to the presence of gaps in the sequence. |
| 05:33 | Select this part using the cursor. |
| 05:38 | Observe the panel. |
| 05:41 | The part of the sequence selected is highlighted. |
| 05:45 | This corresponds to the non-superimposable part of the structure. |
| 05:50 | You can change the color of this non-superimposing parts using Actions menu. |
| 05:55 | Click on Actions menu. |
| 05:57 | Scroll down to Color, click on orange-red option. |
| 06:02 | Now this part is highlighted. |
| 06:05 | Clear the selection and close the dialog box. |
| 06:10 | Now, let me demonstrate how to morph conformations and create a trajectory. |
| 06:15 | Morphing involves calculating a series of intermediate structures between the original input structures. |
| 06:23 | The series of intermediate structures created can be saved as Molecular Dynamics Movie, in short, MD Movie. |
| 06:32 | Back to the panel. |
| 06:34 | Start the morphing tool from the Tools menu. |
| 06:37 | Click on Tools menu, scroll down to Structure Comparison. |
| 06:42 | Click on Morph conformations option. |
| 06:46 | A Morph conformations dialog box opens. |
| 06:50 | Click on Add. |
| 06:52 | In the resulting list of the models dialog box, double click on model number zero, that is, 3w7f to add to the conformations. |
| 07:03 | Next, click on model number 1, that is, 2zco. |
| 07:10 | Then again click on 3w7f, that is model number zero. |
| 07:16 | This sequence corresponds to a morph trajectory from ligand, bound to the structure to empty structure and then back. |
| 07:26 | Close the model list dialog. |
| 07:29 | Click on Create in the Morph conformations dialog box. |
| 07:34 | After a few seconds, a MD Movie is created. |
| 07:39 | The dialog box appears on the screen. |
| 07:42 | The dialog box has buttons to play or pause the movie. |
| 07:46 | Click on the arrow button to play. |
| 07:50 | Observe the panel. |
| 07:52 | The morphing of conformations is being played as a movie. |
| 07:57 | Pause the movie and close the MD movie dialog box. |
| 08:02 | Now, let's summarize what we have learnt. |
| 08:05 | In this tutorial, we have learnt to: superimpose and compare different structures of the same protein, |
| 08:12 | morph conformations and create a trajectory, |
| 08:16 | save the trajectory as Molecular Dynamics Movie. |
| 08:20 | For the assignment, open the structures of GTP binding proteins with the PDB code: 1TAG and 1TND |
| 08:31 | Superimpose the structures using MatchMaker tool. |
| 08:34 | Using Sequence Alignment tool, find out the regions that are non-identical. |
| 08:41 | The video at the following link summarizes the Spoken Tutorial project. Please download and watch it. |
| 08:48 | The Spoken Tutorial Project team conducts workshops and gives certificates for those who pass an online test. For more details, please write to us. |
| 08:57 | Spoken Tutorial project is funded by NMEICT, MHRD, Government of India. More information on this mission is available at the link shown. |
| 09:09 | This is Snehalatha from IIT Bombay, signing off. Thank you for joining. |
