Difference between revisions of "UCSF-Chimera/C3/Superimposing-and-Morphing/English-timed"

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| This structure is bound to the substrate analog '''Farnesyl thiopyrophosphate'''. '''FPS''' in short.
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| This structure is bound to the '''substrate analog Farnesyl thiopyrophosphate''', '''FPS''' in short.
  
 
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|For this we will fetch a structure of the same enzyme without substrate.
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|For this, we will fetch a structure of the same enzyme without substrate.
  
 
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| On the '''command line''' type “'''open 2zco'''” press enter.
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| On the '''command line''', type: “'''open 2zco'''”, press '''Enter'''.
  
 
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| Now these two structures are ready to be '''superimposed'''.
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| Now, these two structures are ready to be superimposed.
  
 
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| '''Superimposition or Structural alignment''' is a tool to compare two or more '''protein''' structures.
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| '''Superimposition''' or '''Structural alignment''' is a tool to compare two or more '''protein''' structures.
  
 
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|The alignment is based on their shape and three-dimensional conformation.
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|The alignment is based on their shape and three-dimensional '''conformation'''.
  
 
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| Before we start '''superimposing''', let us place some icons in the tool bar.  
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| Before we start superimposing, let us place some '''icon'''s in the tool bar.  
  
 
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| Click on '''Favorites menu.'''
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| Click on '''Favorites''' menu.
  
 
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|'''Scroll down to Add to favorites/Tool bar '''option.
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|Scroll down to '''Add to favorites/Tool bar '''option.
  
 
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| Check boxes for, '''Command line''' , '''Model Panel''' , '''Side View'''.
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| Check boxes for '''Command line''' , '''Model Panel''' , '''Side View'''.
  
 
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| Scroll down and click on, '''MatchMaker '''  and '''Match-Align'''
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| Scroll down and click on '''MatchMaker '''  and '''Match-Align'''.
  
 
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|Select tools according to your requirement.
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|Select '''tool'''s according to your requirement.
  
 
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| Observe the panel.  
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| Observe the '''panel'''.  
  
 
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| Now let us '''superimpose''' the structures using '''MatchMaker''' function.
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| Now, let us '''superimpose''' the structures using '''MatchMaker''' function.
  
 
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|For now, let us continue with the default settings. Press '''OK''' button.  
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|For now, let us continue with the '''default setting'''s. Press '''OK''' button.  
  
 
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|The two structures are '''superimposed''' on each other.
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|The two structures are superimposed on each other.
  
 
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| The two structures are almost completely '''superimposable''' with each other.
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| The two structures are almost completely superimposable with each other
  
 
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|Except for a small part which is '''non-superimposable'''.
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|except for a small part which is non-superimposable.
  
 
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| The fragment involved in this '''non-superimposable''' part starts from : The '''amino acid''' number 53 to '''amino acid''' number 57.
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| The fragment involved in this non-superimposable part starts from the '''amino acid''' number 53 to '''amino acid''' number 57.
  
 
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| To select the chains, click on their '''pdb Ids'''.
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| To select the '''chain'''s, click on their '''pdb Ids'''.
  
 
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| In this box the '''amino acid '''pairs used in the final fit, are shown with light orange boxes.
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| In this box, the '''amino acid '''pairs used in the final fit, are shown with light orange boxes.
  
 
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Revision as of 12:43, 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.

Contributors and Content Editors

Devraj, Jyotisolanki, Sandhya.np14

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