UCSF-Chimera/C3/Structure-Analysis/English
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Slide Number 1
Title Slide |
Welcome to this tutorial on Structure Analysis |
Slide Number 2
Learning Objectives |
In this tutorial, we will learn to,
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Slide Number 3
Pre-requisites |
To follow this tutorial you should be familiar with,
If not, for relevant tutorials, please visit our website. |
Slide Number 4
System Requirement |
Here I am using
Chimera version 1.10.2 Mozilla firefox browser 42.0 And a working Internet connection.
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Double-click on the Chimera icon on the desktop. | Here I have opened a Chimera window. |
Open Command line using Favorites menu.
Type Open 3w7f |
Using command line open a structure of Squalene Synthase.
It is a Transferace enzyme with a pdb code 3w7f. On the command line, type Open space 3w7f Press Enter |
Open Presets menu, scroll down and click on Interactive1. | A model of the enzyme is displayed on the panel.
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Type
delete:.a Press enter |
The protein is displayed as two copies.
To delete one of the copies , type
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Type
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To delete solvent molecules from the structure, type
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Cursor on the ligand.
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In this structure, the ligand is farnesyl thiopyrophosphate.
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Type
rlabel ligand press enter |
Label the ligand residues using commands.
Type, rlabel space ligand press enter |
Cursor on the panel | There are two farnesyl thiopyrophosphate:
that is, FPS for short in this structure.
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Drag the mouse to rotate.
Scroll the center mouse wheel to zoom. |
Rotate the structure and zoom-in. |
Cursor on the structure.
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There are several side chains that can donate hydrogen bonds to phosphate oxygens of FPS.
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Hover the cursor on the structure. | Locate Serine 21 residue.
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Cursor on the strucrure.
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To measure the distance.
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While Pressing the CTRL key, click on the side chain oxygen of Serine 21.
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While Pressing the CTRL key, click on the side chain oxygen of Serine 21.
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While pressing CTRL and Shift keys simultaneously;
double-click on the nearest phosphate oxygen. |
While pressing CTRL and Shift keys simultaneously;
double-click on the nearest phosphate oxygen of FPS.
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Click Show Distance in the resulting context menu. | Select Show Distance from the context menu.
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Cursor on the panel. | Observe the panel,
The distance between two atoms is displayed.
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While pressing CTRL and Shift keys simultaneously;
double-click on oxygen of Tyrosine 248 |
Similarly, measure distance between side-chain oxygen of Tyrosine and the same phosphate oxygen of FPS.
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Cursor on the panel. | The distances seem consistent with hydrogen bonds. |
Slide Number 5
Hydrogen Bond Distances |
Hydrogen bonds with donor and acceptor distances of 2.2 to 2.5 Angstroms are classified as strong.
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Click on Select menu, click on Residue, then FPS. | Now, select the ligand using Select menu.
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Scroll down the Tools menu >> Structure Analysis >> FindHbond. | The easy way to find hydrogen bonds formed by FPS is to use Find Hydrogen bond feature from Tools menu.
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H-Bond Parameters dialog opens. | A H-Bond Parameters dialog opens.
Fix the line width to 3.0 for a thicker line. |
Click ON: Label H-bond with distance.
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Click on the check box against:
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Click on OK button. | Click on OK button. |
Cursor on hydrogen bond.
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Observe the panel.
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Click on Favorites >> Reply log. | Details of the bonds can viewed on the Reply log.
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A Reply log dialog box opens.
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Information about each hydrogen bond is given here.
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Type,
~hbond
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If you want to remove the hydrogen bonds from the structure;
The Tilda symbol followed by hbond
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Click on Tools menu >> Findclashes/contacts. | There is another feature in the Tools menu under Structure Analysis option, it is Findclashes/contacts.
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Slide Number 6
Clashes and Contacts |
Clashes are unfavorable interactions where atoms are too close together.
Contacts are all direct interactions: polar and non-polar, favorable and unfavorable (including clashes)
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Cursor on the panel.
Choose FPS from Residue sub-menu.
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Let us identify contacts of the FPS residues with all other atoms.
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Point to the number. | It shows 48 atoms designated.
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Click the radio button against “all other atoms”. | Click on the radio button against “all other atoms”. |
Set the Clash/Contact Parameters to the default contact.
Click on contact button. |
Set the Clash/Contact Parameters to default contact. |
Set the Treatment of Clash/Contact Atoms to:
Select Draw pseudo-bonds If endpoint atom hidden, show endpoint residue Write information to reply log
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Under Treatment of Clash/Contact Atoms.
Click on the following check boxes.
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Click on Apply option. | Click on OK button.
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Favorites menu >> Reply Log.
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Open the Reply Log.
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Cursor on Reply log. | Close the dialog box. |
Cursor on the panel. | Now lets display some clashes.
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On the command line type :
Press enter. |
On the command line type :
Press enter. |
Press CTRL key and click on the panel. | Clear the selection. |
While pressing the CTRL key click on any atom or bond in Tyr 248.
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Now select Tyrosine 248 residue.
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Cursor on the panel. | Now we will rotate the side-chain Tyrosine 248 interactively and check for Clashes.
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On the command line type
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Display residues within 4 Angstroms of Tyrosine 248.
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Select Fine Clashes/Contacts option from the Tools menu. | To display the clashes, select FindClashes/Contacts option from the Tools menu. |
n the Find Clashes dialog box, click on Designate. | In the dialog box, click on Designate.
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Click on Clash button.
Set the Treatment of Clash/Contact Atoms to Draw pseudobonds.
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Set the Clash/Contact Parameters to Clash.
Select Draw pseudobonds If end point atom hidden And set the Frequency of Checking to Continuously. |
Click on minimize button. | Hide the dialog box. |
While pressing ctrl key, double-click on the bond that is attached to the ribbon.
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To rotate the side-chain of Tyrosine 248 interactively;
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Rotate the bond by dragging the pointer on the dial.
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A Build structure dialog opens.
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Cursor on Find clashes dialog box.
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Observe the panel.
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Click the entry under Bond to show a menu.
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To revert bond back to the original position:
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Close the dialog. | Close the dialog box. |
Select Try 248.
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We can compare all the rotamers of Tyrosine 248 using the option in the tools menu.
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Click OK button.
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Click on OK button.
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Click on the line in the dialog. | Another dialog opens.
Click on the lines in the dialog box to display the rotamer.
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Cursor on the panel. | We can also detect Clash and hydrogen bonds for the rotamers. |
Click on Columns >> Add>> Clashes>> Click on OK | Click on Columns ,then Add. Select Clashes.
Click on OK in the dialog box. |
Click on Columns >> Add>> Clashes>> Click on OK. | Now to add Hydrogen Bonds:
Click on Columns, scroll down to Add, and select hydrogen bonds. Click on OK in the hydrogen bonds dialog box. |
Click on the dialog. | Observe the dialog, two new columns are added.
Now each rotamer forms several Clashes but no hydrogen bonds. Try finding rotamers by rotating bonds in a different residue . |
Slide Number 7
Summary |
Let's summarize.
In this tutorial we have learnt to
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Slide Number 8
Assignment |
For the assignment,
Open a structure of Squalene Synthase, pdb code 3w7f .
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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 on line 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. |