Difference between revisions of "UCSF-Chimera/C3/Structure-Analysis/English-timed"
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| − | | | Now to add Hydrogen bonds: Click on '''Columns''', scroll down to '''Add, and select hydrogen bonds.''' | + | | | Now to add Hydrogen bonds: Click on '''Columns''', scroll down to '''Add''', and select '''hydrogen bonds.''' |
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Revision as of 16:24, 27 February 2018
| Time | Narration |
| 00:01 | Welcome to this tutorial on Structure Analysis. |
| 00:05 | In this tutorial, we will learn to : Measure distance between atoms in the structure.Show Hydrogen bonds, Identify non-polar interactions. |
| 00:16 | And rotate bonds in the residues to get different rotamers |
| 00:21 | To follow this tutorial you should be familiar with Chimera Interface. If not, for relevant tutorials, please visit our website. |
| 00:30 | Here I am using Ubuntu OS version. 14.04 ,Chimera version 1.10.2 , Mozilla firefox browser 42.0 , And a working Internet connection. |
| 00:46 | Here I have opened a Chimera window. |
| 00:49 | Using command line, open a structure of Squalene Synthase. It is a Transferace enzyme with a pdb code 3w7f. |
| 01:00 | On the command line, typen Open space 3w7f Press Enter. |
| 01:09 | A model of the enzyme is displayed on the panel. |
| 01:12 | Change the display to Interactive 1, using Presets menu. |
| 01:18 | The protein is displayed as two copies. |
| 01:21 | To delete one of the copies, type delete colon dot a Press Enter. |
| 01:29 | To delete solvent molecules from the structure, type delete solventPress Enter. |
| 01:37 | In this structure, the ligand is farnesyl thiopyrophosphate. |
| 01:43 | Label the ligand residues using commands. Type, rlabel space ligand Press Enter. |
| 01:53 | There are two farnesyl thiopyrophosphate: that is, FPS for short in this structure. |
| 02:01 | The structures are shown in sticks display. |
| 02:05 | Rotate the structure and zoom-in. |
| 02:08 | There are several side chains that can donate hydrogen bonds to phosphate oxygens of FPS. |
| 02:15 | Place the cursor over the atoms in the side-chain residues. |
| 02:21 | Locate Serine 21 residue. |
| 02:23 | Now, lets measure the distance between oxygen of Serine 21: and nearest phosphate oxygen of FPS. |
| 02:32 | To measure the distance, select oxygen of Serine 21 residue. |
| 02:37 | While pressing the CTRL key, click on the side chain oxygen of Serine 21. |
| 02:43 | While pressing CTRL and Shift keys simultaneously, double-click on the nearest phosphate oxygen of FPS. |
| 02:52 | Select Show Distance from the context menu. |
| 02:56 | Observe the panel. The distance between two atoms is displayed. Clear selection. |
| 03:04 | Similarly, measure distance between side-chain oxygen of Tyrosine and the same phosphate oxygen of FPS. |
| 03:15 | The distances seem consistent with hydrogen bonds. |
| 03:20 | Hydrogen bonds with donor and acceptor distances of 2.2 to 2.5 Angstroms are classified as strong. 2.5 to 3.2 as moderate. 3.2 to 4.0 as weak. |
| 03:36 | Now, select the ligand using Select menu. |
| 03:40 | Scroll down to residue option, click on FPS from the sub-menu. |
| 03:46 | The easy way to find hydrogen bonds formed by FPS is to use Find Hydrogen bond feature from Tools menu. |
| 03:55 | Click on FindHbond in the Structure Analysis option. |
| 04:01 | A H-Bond Parameters dialog opens. |
| 04:05 | Fix the color of the hydrogen bond by clicking on the colored box. |
| 04:09 | Fix the line width to 3.0 for a thicker line. |
| 04:13 | Click on the check box against Label Hydrogen bond with distance. |
| 04:21 | Click on Only find H-bonds with at least one end selected. |
| 04:26 | And click on Write information to reply log. |
| 04:31 | Click on OK button. |
| 04:33 | Observe the panel. Hydrogen bonds are shown as pseudo-bonds of specified color and line width. |
| 04:42 | Details of the bonds can viewed on the Reply log. |
| 04:45 | Open Reply log using Favorites menu. |
| 04:49 | Information about each hydrogen bond is given here. |
| 04:53 | Close the dialog box. |
| 04:55 | If you want to remove the hydrogen bonds from the structure,On the command line type: The Tilda symbol followed by hbond Press Enter. |
| 05:07 | There is another feature in the Tools menu under Structure Analysis option. |
| 05:13 | It is Findclashes/contacts. A dialog box opens. |
| 05:19 | This feature identifies non-polar interactions such as Clashes and Contacts. |
| 05:26 | Clashes are unfavorable interactions where atoms are too close together. |
| 05:33 | Contacts are all direct interactions: polar and non-polar, favorable and unfavorable (including clashes) |
| 05:43 | Let us identify contacts of the FPS residues with all other atoms. |
| 05:48 | Select FPS residue using Select menu. |
| 05:52 | Click on Designate in the Find Clashes/Contacts dialog box. |
| 05:58 | It shows 48 atoms designated. |
| 06:02 | Click on the radio button against “All other atoms”. |
| 06:06 | Set the Clash/Contact Parameters to default Contact. |
| 06:11 | Under Treatment of Clash/Contact Atoms, click on the following check boxes. Select Draw pseudo-bonds If endpoint atom hidden And Write information to reply log |
| 06:27 | Click on OK button. Observe the panel. |
| 06:32 | All the contacts of FPS residues are shown. |
| 06:37 | Open the Reply Log. . Atom-atom contacts are listed here. |
| 06:44 | Close the dialog box. |
| 06:46 | Now let's display some clashes. |
| 06:49 | Let us focus on the residue Tyrosine 248. |
| 06:54 | On the command line type: focus space colon 248 Press Enter. |
| 07:03 | Clear the selection. |
| 07:06 | Now select Tyrosine 248 residue. |
| 07:10 | While pressing the CTRL key, click on any atom in Tyrosine 248. |
| 07:15 | Press up arrow key on the keyboard to select the entire molecule. |
| 07:20 | Now we will rotate the side-chain Tyrosine 248 interactively and check for Clashes. |
| 07:27 | Display residues within 4 Angstroms of Tyrosine 248. |
| 07:32 | On the command line type display, disp space colon 248 space z less than four. (disp :248 z<4) Press Enter. |
| 07:45 | To display the clashes, select FindClashes/Contacts option from the Tools menu. |
| 07:53 | click on Designate. |
| 07:55 | Click the button against “All other atoms”. |
| 07:59 | Set the Clash/Contact Parameters to Clash. . The Treatment of Clash/Contact Atoms to Select , Draw pseudobonds , If end point atom hidden |
| 08:11 | And set the Frequency of Checking to Continuously. |
| 08:15 | Hide the dialog box. |
| 08:18 | To rotate the side-chain of Tyrosine 248 interactively; |
| 08:22 | While pressing CTRL key, double-click on the bond that is attached to the ribbon. |
| 08:29 | Choose rotate bond option from the context menu. |
| 08:33 | A Build structure dialog opens. |
| 08:36 | Rotate the bond by dragging the pointer on the dial. |
| 08:41 | Alternatively, click on the black arrowheads to edit the angle values. |
| 08:47 | Observe the panel. As the side-chain moves, new pseudo-bonds are formed or disappear. |
| 08:55 | To revert bond back to the original position: Click the entry under Bond. Choose Revert. |
| 09:03 | Again click on the bond then Deactivate to make the bond no longer rotate-able. |
| 09:09 | Close the dialog box. |
| 09:11 | We can compare all the rotamers of Tyrosine 248 using the option in the Tools menu. |
| 09:18 | First select Tryrosine 248. |
| 09:22 | Click on Tools menu, scroll down to Structure editing. |
| 09:26 | Click on Rotamers option. |
| 09:29 | In the Rotamer dialog box, select Dunbrack from the rotamer library. |
| 09:36 | Click on OK button. |
| 09:38 | The rotamers are shown as wire representation on the panel. |
| 09:43 | Another dialog opens. Click on the lines in the dialog box to display the rotamer. Observe the panel. |
| 09:52 | We can also detect Clash and hydrogen bonds for the rotamers. |
| 09:58 | Click on Columns ,then Add. Select Clashes. |
| 10:03 | Click on OK in the dialog box. |
| 10:06 | Now to add Hydrogen bonds: Click on Columns, scroll down to Add, and select hydrogen bonds. |
| 10:15 | Click on OK in the Hydrogen bonds dialog box. |
| 10:19 | Observe the dialog, two new columns are added. |
| 10:24 | Now each rotamer forms several Clashes but no hydrogen bonds. |
| 10:30 | Try finding rotamers by rotating bonds in a different residue. |
| 10:35 | Let's summarize. In this tutorial we have learnt to- Measure distance between atoms in the structure . |
| 10:43 | Show Hydrogen bonds Identify non-polar interactions |
| 10:48 | Rotate bonds in the residues to find clashes and contacts. And compare different rotamers. |
| 10:56 | For the assignment, Open a structure of Squalene Synthase, pdb code 3w7f . |
| 11:03 | Rotate bonds in Tyrosine 41, residue to determine Clashes and Contacts. And compare the rotamers. |
| 11:11 | The video at the following link summarizes the Spoken Tutorial project. Please download and watch it. |
| 11:17 | 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. |
| 11:27 | Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. More information on this Mission is available at the link shown |
| 11:37 | This is Snehalatha from IIT Bombay signing off. Thank you for joining. |
