UCSF-Chimera/C3/Superimposing-and-Morphing/English-timed

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