Jmol-Application/C4/3D-Models-of-Enzymes/English-timed - Revision history

PoojaMoolya at 09:59, 28 October 2020

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PoojaMoolya at 13:05, 28 March 2017

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Sandhya.np14 at 09:28, 17 June 2016

2016-06-17T09:28:22Z

Sandhya.np14 at 05:08, 16 June 2016

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Sandhya.np14 at 10:55, 2 June 2016

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Sandhya.np14 at 11:49, 11 February 2016

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Sandhya.np14 at 11:49, 14 September 2015

2015-09-14T11:49:40Z

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PoojaMoolya: Created page with "{| border=1 || '''Time''' || '''Narration''' |- ||00:01 ||Hello everyone. Welcome to this tutorial on '''3D Models of Enzymes in Jmol '''. |- ||00:08 || In this tutorial,..."

2015-03-10T05:24:40Z

Created page with "{| border=1 || '''Time''' || '''Narration''' |- ||00:01 ||Hello everyone. Welcome to this tutorial on '''3D Models of Enzymes in Jmol '''. |- ||00:08 || In this tutorial,..."

New page

{| border=1
|| '''Time'''
|| '''Narration'''

|-
||00:01
||Hello everyone. Welcome to this tutorial on '''3D Models of Enzymes in Jmol '''.

|-
||00:08
|| In this tutorial, we will learn to Load structure of '''Human Pancreatic Hexokinase''' on '''Jmol panel'''.

|-
||00:16
||Modify the display of secondary structure .

|-
||00:20
||Highlight amino acid residues at the active site.

|-
||00:25
|| Highlight substrate and cofactors of the enzyme.

|-
||00:30
|| And view '''Ramachandran plot''' for protein

|-
||00:35
|| To follow this tutorial you should have Knowledge of basic biochemistry.

|-
||00:41
||And familiar with basic operations from '''Jmol Application window'''.

|-
||00:46
||Please view the tutorial '''Proteins and Macromolecules''' in the Jmol Application series.

|-
||00:53
||It is available at the following link.

|-
||00:57
||To record this tutorial I am using, '''Ubuntu''' Operating System version 12.04 .

|-
||01:05
||'''Jmol''' version 12.2.2.

|-
||01:08
|| '''Java''' version 7. and '''Mozilla Firefox browser''' 22.0

|-
||01:16
||Open the Jmol window and load the structure of '''hexokinase''' enzyme.

|-
||01:22
||I am connected to '''internet''', so I will load the structure directly from the '''PDB website'''.

|-
||01:28
|| To do so, Open the '''File''' menu, scroll down and click on '''Get PDB''' option.

|-
||01:37
||An Input dialogue box appears on the screen. Type the four letter '''PDB code''' for '''hexokinase''', that is '''3IDH''' in the text box.

|-
||01:50
||This code was obtained from the '''Protein Data Bank''' website.

|-
||01:55
|| If you do not have a working Internet connection: Open the existing '''pdb''' file using '''open a file''' icon on the tool bar.

|-
||02:06
|| Click on '''OK''' button.

|-
||02:09
|| 3D Structure of '''hexokinase''' also known as '''glucokinase''' opens on the screen.

|-
||02:16
|| Open the console window using the '''File''' menu.

|-
||02:21
||As shown on the Console, The structure on the panel is for '''Human Pancreatic Glucokinase''' along with substrate '''Glucose'''.

|-
||02:31
||Close the Console.

|-
||02:34
||On the panel we have the ball and stick model of '''hexokinase'''.
|-
||02:40
||Remove the '''water molecules''' from the '''protein model''' on the panel.

|-
||02:44
||This process is explained in detail in the Jmol tutorial '''Proteins and macromolecules'''.

|-
||02:53
||About '''hexokinase''' Enzyme.

|-
||02:56
|| '''Hexokinase''' is a monomeric protein of 465 amino acids.

|-
||03:02
|| It has two '''domains''', a large '''domain''' and a small '''domain'''.

|-
||03:07
|| The '''active-site''' for this '''enzyme''' is located in the '''cleft''' between the two domains.
|-
||03:14
|| Active-site for '''hexokinase''' has 3 amino acid residues: '''Aspergine''' at 204, '''Aspergine''' at position 231 and '''Glutamic acid''' at 256.

|-
||03:30
||'''Alpha-D-Glucose''' is the substrate for this enzyme.

|-
||03:34
||Now let us go back to the Jmol panel.
|-
||03:38
||We can select and highlight the components of enzymes like : Substrate, Cofactors or Amino acid residues at the active site.
|-
|| 03:49
||To select a particular component Open the pop-up menu using the right click.

|-
||03:55
|Scroll down to '''Select''' option.

|-
||03:57
||From the sub-menu, '''Proteins''', select '''By Residue name'''.

|-
||04:04
||We have individual amino acid residues listed here.

|-
||04:10
||Click on the name of the amino acid to select it.

|-
||04:14
||Also amino acids are grouped under headings like: '''Polar''', '''Non-polar''', '''Basic''', '''Acidic''', '''Uncharged''' etc.
|-
||04:26
||Listed in the '''Hetero''' menu, are the metal ion '''potassium''' and '''substrate glucose'''.
|-
||04:34
||We can modify the display of enzyme to easily locate the substrate binding site.`
|-
||04:41
||Let us change the display and color of the atoms of the protein.
|-
||04:46
||Open the pop-up menu, go to '''Select''', and scroll down to '''Protein''' option. Click on '''All'''.
|-
||04:55
||Open the pop-up menu again, scroll down to '''Style''', then to '''Scheme'''.
And click on '''Sticks''' option.
|-
||05:05
||Now we have on the panel the protein in '''sticks''' display

|-
||05:11
|Now to change the color, open the pop-up menu again, go to '''Color''', '''Atoms''', and click on '''Blue''' option.
|-
||05:23
||We have on the screen the model of '''hexokinase''' in blue color and in sticks display
|-
||05:30
||Observe the substrate, '''Alfa-D-Glucose''' in ball and stick display in the cleft.
|-
||05:38
||To highlight the substrate, open the pop-up menu, go to '''Select''', then '''Hetero''' and click on '''GLC-ALFA-D-GLUCOSE'''.
|-
||05:52
||Open the pop-up menu again , scroll down to '''Style''', '''Scheme''' and click on '''Sticks''' option.

|-
||06:00
||To change the color, Open the pop-up menu again, go down to '''Color''', '''Atoms''' and click on '''White''' option.
|-
||06:12
||On panel is the model of '''hexokinase''' with position of the substrate clearly highlighted.
|-
||06:20
||We can change the color of the amino acids at the active site to highlight them.

|-
||06:26
||To do so, we have to type commands in the '''Console''' window.

|-
||06:32
||As mentioned earlier the amino acids involved at the active-site are '''Aspergine''' at position 204,

'''Aspergine''' at position 231 and '''Glutamic acid''' at 256.
|-
||06:50
|| Open the console window using '''File menu'''. Click on '''Console'''.

|-
||06:57
||I am using '''Kmag''' Screen magnifier to magnify the console window.

|-
||07:03
||At the $ prompt type: '''select within square brackets Asn for aspergine close the bracket, 204 i.e the position semicolon color atoms orange'''.

|-
||07:25
||Press enter.

|-
||07:27
||Observe that the atoms of '''aspargine''' residue now in orange color.
|-
||07:33
||Press up arrow button on the key board and edit the command.

|-
||07:39
||Edit the amino acid position to 231 and color of atoms to red.
|-
||07:48
||Press Enter
|-
||07:51
||Press up arrow key and again and edit name of amino acid to GLU, that is '''glutamic acid''' and position to 256

|-
||08:06
||Color of atoms to green and Press Enter .
|-
||08:13
|| We have on the panel a 3D model of '''hexokinase''' with substrate and the active site highlighted.
|-
||08:23
||Also highlighted in the model is the '''potassium''' atom shown here in purple color.
|-
||08:30
||We can also show '''ramachandran plots''' for a particular protein in jmol.
|-
||08:36
||On the console, at the $ prompt type '''plot ramachandran'''

|-
||08:45
||Press Enter .
|-
||08:47
||On the screen we have a '''ramachandran plot''' for '''hexokinase'''.
|-
||08:54
||Try to load different enzymes using '''pdb files''' from the database.

|-
||09:00
||Change the display of secondary structure
|-
||09:04
||Lets summarize, In this tutorial we learnt to, Load structure of Human Pancreatic Hexokinase using PDB code.

|-
||09:14
|| Modify the display of secondary structure.

|-
||09:17
|| Highlight amino acid residues at the active site.
|-
||09:21
||* Highlight substrate and cofactors of the enzyme.

|-
||09:25
||And View '''ramachandran''' plot for proteins.
|-
||09:30
||As an Assignment: Load the dot pdb file of enzyme '''Lysozyme''' on Jmol panel.

|-
||09:38
|| Highlight the substrate bound to the enzyme.

|-
||09:42
|| Highlight the amino acids at the active site.

|-
||09:46
||Hint: Get the '''pdb''' file of '''Lysozyme''' from '''PDB database'''.

|-
||09:52
||Watch the video available at this URL.

|-
||09:56
||It summarizes the Spoken Tutorial project.

|-
||10:00
||If you do not have a good bandwidth, you can download and watch it.

|-
||10:04
|| The Spoken Tutorial Project Team:

|-
||10:07
||Conducts workshops and distributes certificates.

|-
||10:10
||For more details, please write to us.
|-
||10:14
|| Spoken Tutorial Project is a part of the Talk to a Teacher project.

|-
||10:19
||It is supported by the National Mission on Education through ICT, MHRD, Government of India.

|-
||10:25
||More information on this Mission is available at this link

|-
||10:30
||This is '''Snehalatha''' from '''IIT Bombay''' signing off. Thank you for joining.
|-
|}

@@ Line 69: / Line 69: @@
 |-
 ||01:37
-||An '''Input''' dialogue-box appears on the screen. Type the four letter '''PDB code''' for '''hexokinase''',  that is, '''3IDH'''  in the text-box.
+||An '''Input''' dialog-box appears on the screen. Type the four letter '''PDB code''' for '''hexokinase''',  that is, '''3IDH'''  in the text-box.
 |-

@@ Line 138: / Line 138: @@
 |-
 ||03:38
-||We can select and highlight the components  of  enzymes like :  '''Substrate, Cofactors''' or '''Amino acid residues''' at the active site.
+||We can select and highlight the components  of  enzymes like '''Substrate, Cofactors''' or '''Amino acid residues''' at the active site.
 |-
 || 03:49

@@ Line 9: / Line 9: @@
 |-
 ||00:08
-|| In this tutorial, we will learn to:   * '''Load''' structure of '''Human Pancreatic Hexokinase''' on '''Jmol panel'''
+|| In this tutorial, we will learn to:  * '''Load''' structure of '''Human Pancreatic Hexokinase''' on '''Jmol panel'''
 |-
@@ Line 25: / Line 25: @@
 |-
 ||00:30
-||* And, view '''Ramachandran plot''' for protein.
+||* And, view '''Ramachandran plot''' for '''protein'''.
 |-

@@ Line 9: / Line 9: @@
 |-
 ||00:08
-|| In this tutorial, we will learn to:   * '''Load''' '''structure''' of '''Human Pancreatic Hexokinase''' on '''Jmol panel'''.
+|| In this tutorial, we will learn to:   * '''Load''' structure of '''Human Pancreatic Hexokinase''' on '''Jmol panel'''
 |-
 ||00:16
-||* Modify the display of secondary structure .
+||* Modify the display of secondary structure
 |-
@@ Line 25: / Line 25: @@
 |-
 ||00:30
-||* And view '''Ramachandran plot''' for protein.
+||* And, view '''Ramachandran plot''' for protein.
 |-
@@ Line 53: / Line 53: @@
 |-
 ||01:08
-||* '''Java''' version '''7'''. and * '''Mozilla Firefox browser''' '''22.0'''.
+||* '''Java''' version '''7''' and * '''Mozilla Firefox browser''' '''22.0'''.
 |-
@@ Line 85: / Line 85: @@
 |-
 ||02:09
-|| '''3D''' structure of  '''hexokinase''' also known as '''glucokinase''' opens on the screen.
+|| 3D structure of  '''hexokinase''' also known as '''glucokinase''' opens on the screen.
 |-
@@ Line 108: / Line 108: @@
 |-
 ||02:44
-||This process is explained in detail in the  Jmol tutorial '''Proteins and macromolecules'''.
+||This process is explained in detail, in the  Jmol tutorial '''Proteins and macromolecules'''.
 |-
@@ Line 120: / Line 120: @@
 |-
 ||03:02
-|| It has two '''domains''', a large '''domain''' and a small '''domain'''.
+|| It has two '''domains''', a large domain and a small domain.
 |-
@@ Line 127: / Line 127: @@
 |-
 ||03:14
-|| Active-site  for '''hexokinase''' has 3 amino acid residues:  '''Aspergine''' at '''204''',  '''Aspergine''' at position '''231''' and  '''Glutamic acid''' at '''256'''.
+|| Active-site  for '''hexokinase''' has 3 '''amino acid residue'''s:  '''Aspergine''' at '''204''',  '''Aspergine''' at position '''231''' and  '''Glutamic acid''' at '''256'''.
 |-
@@ Line 153: / Line 153: @@
 |-
 ||04:04
-||We have individual amino acid residues listed here.
+||We have individual '''amino acid residue'''s listed here.
 |-
@@ Line 183: / Line 183: @@
 |-
 ||05:11
-|Now, to change the color- open the pop-up menu again, go to '''Color''', '''Atoms''' and click on '''Blue''' option.
+|Now, to change the color- open the pop-up menu again, go to '''Color''' >> '''Atoms''' and click on '''Blue''' option.
 |-
 ||05:23
@@ Line 195: / Line 195: @@
 |-
 ||05:52
-||Open the pop-up menu again, scroll down to '''Style''', '''Scheme''' and  click on '''Sticks''' option.
+||Open the pop-up menu again, scroll down to '''Style''' >> '''Scheme''' and  click on '''Sticks''' option.
 |-
 ||06:00
-||To change the color- open the pop-up menu again, go down to '''Color''', '''Atoms''' and click on '''White''' option.
+||To change the color- open the pop-up menu again, go down to '''Color''' >> '''Atoms''' and click on '''White''' option.
 |-
 ||06:12
-||On panel is the model of '''hexokinase''' with position of the '''substrate''' clearly highlighted.
+||On the panel is the model of '''hexokinase''' with position of the '''substrate''' clearly highlighted.
 |-
 ||06:20
@@ Line 224: / Line 224: @@
 |-
 ||07:03
-||At the $ (dollar) prompt, type: '''"select"''' within square brackets '''"Asn"''' for aspergine close the bracket, '''"204"''' i.e the position '''semicolon''' '''"color atoms orange"'''.
+||At the $ (dollar) prompt, type: '''"select"''' within square brackets '''"Asn"''' for aspergine close the bracket, '''"204"''' i.e the position semicolon '''"color atoms orange"'''.
 |-
@@ Line 249: / Line 249: @@
 |-
 ||08:06
-||Color of atoms to green and press '''Enter'''.
+||and,color of atoms to green and press '''Enter'''.
 |-
 ||08:13
@@ Line 278: / Line 278: @@
 |-
 ||09:04
-||Let's summarize. In this tutorial we learnt to: * '''Load''' structure of '''Human Pancreatic Hexokinase''' using PDB code.
+||Let's summarize. In this tutorial, we learnt to: * '''Load''' structure of '''Human Pancreatic Hexokinase''' using PDB code.
 |-
@@ Line 293: / Line 293: @@
 |-
 ||09:25
-||And view '''ramachandran''' plot for  proteins.
+||And, view '''ramachandran''' plot for  proteins.
 |-
 ||09:30