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

Title Slide

Learning Objectives

• Superimpose and compare different structures of the same protein.
• Morph conformations and create a trajectory.

Pre-requisites

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System Requirement

• Ubuntu OS version. 14.04
• Chimera version 1.10.2
• Mozilla firefox browser 42.0
• And a working Internet connection.

Now let us prepare this structure for superimposing.

Using the command line delete one of the chains.

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

Press Enter.

press enter.

• to remove solvent molecules from the structure
• I will select the command “del solvent”.

Press Enter.

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

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

The new structure is in blue color.

Structural alignment

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

Scroll down to Add to favorites/Tool bar option.

A Preferences dialog box opens.

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

Command line

Model Panel

Side View

MatchMaker

Match-Align

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

Select tools according to your requirement.

Click on the Toolbar placement button.

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.

Close the window.

And click on Close to close the dialog box.

A MatchMaker dialog box opens.

Press OK button.

For now, let us continue with the default settings.

Press OK button.

The two structures are superimposed on each other.

Except for a small part which is non-superimposable.

The amino acid number 53 to amino acid number 57.

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

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

Click on Match-Align tool from the tool bar.

A dialog box opens.

To select the chains, click on their pdb Ids.

Cursor on the sequence alignment dialog box.

A sequence alignment dialog box opens.

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

Click on light orange boxes to select.

Select this part using the cursor.

Choose any color from the sub-menu.

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.

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

Now this part is highlighted.

Clear the selection and close the dialog box.

Morphing

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

Start the morphing tool from the Tools menu.

Click on Tools menu scroll down to Structure Comparison.

Click on Morph conformations option.

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

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.

• a morph trajectory from ligand
• bound to the structure to empty structure
• and then back.

The dialog box appears on the screen.

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

Observe the panel.

Pause the movie and close the MD movie dialog box.

Summary

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.

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.

Acknowledgement

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