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

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press enter.
 
press enter.
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Next,  
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Next, to remove '''solvent '''molecules from the structure;
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*to remove '''solvent '''molecules from the structure
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I will select the command “'''del solvent'''”.
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*I will select the command “'''del solvent'''”.
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Press '''Enter'''.
 
Press '''Enter'''.

Latest revision as of 17:04, 1 July 2016

Visual Cue
Narration
Slide Number 1

Title Slide

Welcome to this tutorial on Superimposing and Morphing
Slide Number 2

Learning Objectives

In this tutorial, we will learn to
  • Superimpose and compare different structures of the same protein.
  • Morph conformations and create a trajectory.
Slide Number 3

Pre-requisites


spoken-tutorial.org

To follow this tutorial you should be familiar with, Chimera Interface.


If not, for relevant tutorials, please visit our website.

Slide Number 4

System Requirement

Here I am using
  • Ubuntu OS version. 14.04
  • Chimera version 1.10.2
  • Mozilla firefox browser 42.0
  • And a working Internet connection.
Double-click on the Chimera Here I have opened a Chimera window.
Click on the file 3w7f from the side panel. From the graphic access interface, click on the file 3w7f.
Cursor on the panel. The structure of Squalin Synthase opens on the screen.


Now let us prepare this structure for superimposing.

Cursor on the panel. It contains two copies of the same protein.


Using the command line delete one of the chains.

Click on the small back triangle at the end of the command line. I will recall the command by clicking on the command history.
Scroll down the command history dialog box.


Select the command “delete:.a” press enter.

From the command history dialog box, select the command “delete:.a”


Press Enter.

Select the command “del solvent” from command history.

press enter.

Next, to remove solvent molecules from the structure;

I will select the command “del solvent”.

Press Enter.

Cursor on the panel. This structure is bound to the substrate analog Farnesyl thiopyrophosphate. FPS in short.


We will superimpose two similar proteins to compare their secondary structures.


For this we will fetch a structure of the same enzyme without substrate.

On the command line type “open 2zco” press enter. On the command line type “open 2zco” press enter.


The new structure is in blue color.

Cursor on the panel. Now these two structures are ready to be superimposed.
Slide Number 5

Structural alignment

Superimposition or Structural alignment is a tool to compare two or more protein structures.


The alignment is based on their shape and three-dimensional conformation.

Cursor on the panel. Before we start superimposing, let us place some icons in the tool bar.
Click on Favorites menu >>Add to favorites. Click on Favorites menu.


Scroll down to Add to favorites/Tool bar option.


A Preferences dialog box opens.

Cursor on preferences dialog box.


Under the heading “Settings”, under the “On Tool bar” column, check th boxes for:


Command line

Model Panel

Side View

MatchMaker

Match-Align

From the Category drop-down, select Tools.


Under the heading “Settings”, check boxes under “On Tool bar” column.


Check boxes for,

  • Command line
  • Model Panel
  • Side View


Scroll down and click on,

  • MatchMaker
  • and Match-Align


Cursor on the panel. You can customize your own tool bar.


Select tools according to your requirement.

Cursor pointing tool bar.


Click on the Toolbar placement button.

Observe the panel.

Icons have been added to the Tool bar on top of the panel.


To change the position of the tool bar, click on the Toolbar placement button.


And select the option from the drop-down menu.

Click on Save button.

Close the window.

When you finish adding all icons to the tool bar, click on Save button.


And click on Close to close the dialog box.

Hold the mouse button and drag on the panel. The structures are now in different positions.
Cursor on the panel. Now let us superimpose the structures using MatchMaker function.
Click on MatchMaker tool on the Tool bar. Click on MatchMaker tool on the Tool bar.


A MatchMaker dialog box opens.

Cursor on MatchMaker dialog box.


Press OK button.

Click on 3w7f as Reference structure.


For now, let us continue with the default settings.


Press OK button.

Cursor on the panel. Observe the panel.

The two structures are superimposed on each other.

Cursor on the panel. The two structures are almost completely superimposable with each other.


Except for a small part which is non-superimposable.

Cursor on amino acids 53 and 57. The fragment involved in this non-superimposable part starts from :


The amino acid number 53 to amino acid number 57.

Cursor on the panel. The MatchMaker generates a sequence alignment using residue types and secondary structure.


And then fits the sequence-aligned residues in 3D.

Click on Match-Align tool.


Click on the pdb Id of both the chains to select them.

Let us now check the Match-Align tool.


Click on Match-Align tool from the tool bar.

A dialog box opens.


To select the chains, click on their pdb Ids.

Click on OK button.


Cursor on the sequence alignment dialog box.

Click on OK button.

A sequence alignment dialog box opens.


In this box the amino acid pairs used in the final fit, are shown with light orange boxes.

Cursor on the sequence alignment dialog box. The structures are mostly similar except for the loop at residues 52-54.
Hover the cursor over one letter code. Place the cursor over the corresponding one letter code.
Cursor on the sequence alignment dialog box.


Click on light orange boxes to select.

The residues from 52 to 54 are shifted due to the presence of gaps in the sequence.


Select this part using the cursor.

Click on Actions menu, Scroll down to Color.


Choose any color from the sub-menu.

Observe the panel.

The part of the sequence selected is highlighted.


This corresponds to the non-superimposable part of the structure.


You can change the color of this non-superimposing parts using Actions menu.

Click on Actions menu, scroll down to Color, click on orange-red option. Click on Actions menu.

Scroll down to Color, click on orange-red option.


Now this part is highlighted.


Clear the selection and close the dialog box.

Cursor on the panel. Now, let me demonstrate how to morph conformations and create a trajectory.
Slide Number 6

Morphing

Morphing involves calculating a series of intermediate structures between the original input structures.


The series of intermediate structures created can be saved as Molecular Dynamics Movie.- in short MD Movie.

Click on Tools menu >> Structure Comparison >> Morph conformations. Back to the panel.

Start the morphing tool from the Tools menu.

Click on Tools menu scroll down to Structure Comparison.

Click on Morph conformations option.

Cursor on the Morph conformations dialog box. A Morph conformations dialog box opens.
Click on Add button.


In Model dialog, double click on model number 0 and model number 1.

Click on Add.


In the resulting list of the models dialog box;

  • double click on model number zero, that is 3w7f to add to the conformations.


Next click on model number 1 that is 2zco.

Then again click on 3w7f, that is model number zero.

Cursor on the Morph conformations dialog box.


This sequence corresponds to
  • a morph trajectory from ligand
  • bound to the structure to empty structure
  • and then back.
Click on x button. Close the model list dialog.
Click on Create in the Morph conformations dialog. Click on Create in the Morph conformations dialog box.
Cursor on the dialog box. After a few seconds a MD Movie is created.


The dialog box appears on the screen.


The dialog box has buttons to play or pause the movie.

Click on arrow button. Click on the arrow button to play.


Observe the panel.

Cursor on the panel. The morphing of conformations is being played as a movie.

Pause the movie and close the MD movie dialog box.

Slide Number 7

Summary

Now let's summarize what we have learnt.


In this tutorial we have learnt to,

  • Superimpose and compare different structures of the same protein.
  • Morph conformations and create a trajectory.
  • Save the trajectory as Molecular Dynamics Movie.
Slide Number 8

Assignment

For the assignment,
  • Open the structures of GTP binding proteins with the PDB code: 1TAG and 1TND
  • Superimpose the structures using MatchMaker tool.
  • Using Sequence Alignment tool, find out the regions that are non-identical.
Slide Number 9

Acknowledgement

The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

Slide Number 10 The Spoken Tutorial Project Team
  • conducts workshops and
  • gives certificates for those who pass an online test.

For more details, please write to us.

Slide number 11 Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this Mission is available at the link shown

This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Nancyvarkey, Snehalathak

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