Difference between revisions of "UCSF-Chimera/C3/Superimposing-and-Morphing/English-timed"
From Script | Spoken-Tutorial
Sandhya.np14 (Talk | contribs) |
Sandhya.np14 (Talk | contribs) |
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|05:13 | |05:13 | ||
− | | The structures are mostly similar except for the loop at residues 52-54. | + | | The structures are mostly similar except for the '''loop''' at '''residues 52-54'''. |
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|05:45 | |05:45 | ||
− | | This corresponds to the | + | | This corresponds to the non-superimposable part of the structure. |
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|05:50 | |05:50 | ||
− | | You can change the color of this | + | | You can change the color of this non-superimposing parts using '''Actions''' menu. |
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| 06:10 | | 06:10 | ||
− | | Now, let me demonstrate how to morph '''conformations''' and create a trajectory. | + | | Now, let me demonstrate how to morph '''conformations''' and create a '''trajectory'''. |
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|06:15 | |06:15 | ||
− | | | + | | Morphing involves calculating a series of intermediate structures between the original input structures. |
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|06:23 | |06:23 | ||
− | | The series of intermediate structures created can be saved as '''Molecular Dynamics Movie | + | | The series of intermediate structures created can be saved as '''Molecular Dynamics Movie,''' in short,''' MD Movie.''' |
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|06:37 | |06:37 | ||
− | | Click on '''Tools menu scroll down to Structure Comparison | + | | Click on '''Tools''' menu, scroll down to '''Structure Comparison'''. |
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|06:42 | |06:42 | ||
− | | ''' | + | | Click on '''Morph conformations '''option. |
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|06:52 | |06:52 | ||
− | | In the resulting list of the models dialog box | + | | In the resulting list of the models dialog box, double click on model number zero, that is, '''3w7f''' to add to the conformations. |
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|07:03 | |07:03 | ||
− | | Next click on model number 1 that is '''2zco'''. | + | | Next, click on model number 1, that is, '''2zco'''. |
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|07:16 | |07:16 | ||
− | | This sequence corresponds to | + | | This sequence corresponds to a morph '''trajectory''' from '''ligand''', bound to the structure to empty structure and then back. |
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|07:34 | |07:34 | ||
− | | After a few seconds a''' MD Movie''' is created. | + | | After a few seconds, a''' MD Movie''' is created. |
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|07:42 | |07:42 | ||
− | | The dialog box has buttons to play or pause the movie. | + | | The dialog box has buttons to '''play''' or '''pause''' the movie. |
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|08:02 | |08:02 | ||
− | | Now let's summarize what we have learnt. | + | | Now, let's summarize what we have learnt. |
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|08:05 | |08:05 | ||
− | | In this tutorial we have learnt to | + | | In this tutorial, we have learnt to: '''superimpose '''and compare different structures of the same protein, |
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|08:12 | |08:12 | ||
− | | | + | | morph '''conformations''' and create a '''trajectory''', |
|- | |- | ||
|08:16 | |08:16 | ||
− | | | + | | '''save''' the trajectory as '''Molecular Dynamics Movie.''' |
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|08:20 | |08:20 | ||
− | | For the assignment, | + | | For the assignment, open the structures of '''GTP binding '''proteins with the '''PDB code''': '''1TAG''' and '''1TND''' |
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|08:31 | |08:31 | ||
− | | Superimpose the structures using '''MatchMaker''' tool. | + | | '''Superimpose''' the structures using '''MatchMaker''' tool. |
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|08:48 | |08:48 | ||
− | | The '''Spoken Tutorial Project''' | + | | 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 | | 08:57 | ||
− | | '''Spoken Tutorial | + | | '''Spoken Tutorial''' project is funded by '''NMEICT, MHRD''', Government of India. More information on this mission is available at the '''link''' shown. |
|- | |- | ||
|09:09 | |09:09 | ||
− | | This is '''Snehalatha''' from '''IIT Bombay''' signing off. Thank you for joining. | + | | This is '''Snehalatha''' from '''IIT Bombay''', signing off. Thank you for joining. |
|} | |} |
Latest revision as of 13:50, 28 June 2018
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. |