Proteopedia - User contributions [en]

Sandbox1313

2009-05-19T18:51:54Z

Mark Omobono:

'''This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!'''

{{STRUCTURE_1bbw| PDB=1bbw | SCENE=Sandbox1313/Defaultscene/1 }}==Lysyl-tRNA Synthase==

Shown here is PDB number 1bbu, lysyl-tRNA Synthase shown here complexed with the lysine substrate. It consists of both <scene name='Sandbox1313/Alpha_and_beta_strands/1'>alpha helices and beta sheets</scene> (the latter in sheets and a barrel). Below is pictured the exact same synthase complexed with it's residue of interest, lysine.

<applet load='1bbu' size='250' color='white' frame='true' align='left' caption='Lysine-bound lysyl-tRNA synthase' name='1bbu'/>

In the active site, the bound lysine participates in multiple hydrogen bonding interactions to stay complexed to the synthase protein as it moves into position to build the tRNA in the ribosome. Specifically,
<scene name='Sandbox1313/Hydrogen_bonding_partners/1'>these residues</scene> trigger a complex conformational change that completely changes the shape of part of the synthase. These changes involve <scene name='Sandbox1313/These_two_loops/1'>these two loops</scene> and some <scene name='Sandbox1313/Other_pieces/2'>other pieces</scene> of the molecule. This conformational change effectively closes the active site when bound to lysine.

Sandbox1313

2009-05-13T17:36:25Z

Mark Omobono:

{{STRUCTURE_1bbw| PDB=1bbw | SCENE=Sandbox1313/Defaultscene/1 }}==Lysyl-tRNA Synthase==

Shown here is PDB number 1bbu, lysyl-tRNA Synthase shown here complexed with the lysine substrate. It consists of both <scene name='Sandbox1313/Alpha_and_beta_strands/1'>alpha helices and beta sheets</scene> (the latter in sheets and a barrel). Below is pictured the exact same synthase complexed with it's residue of interest, lysine.

<applet load='1bbu' size='250' color='white' frame='true' align='left' caption='Lysine-bound lysyl-tRNA synthase' name='1bbu'/>

In the active site, the bound lysine participates in multiple hydrogen bonding interactions to stay complexed to the synthase protein as it moves into position to build the tRNA in the ribosome. Specifically,
<scene name='Sandbox1313/Hydrogen_bonding_partners/1'>these residues</scene> trigger a complex conformational change that completely changes the shape of part of the synthase. These changes involve <scene name='Sandbox1313/These_two_loops/1'>these two loops</scene> and some <scene name='Sandbox1313/Other_pieces/2'>other pieces</scene> of the molecule. This conformational change effectively closes the active site when bound to lysine.

Sandbox3

2009-05-13T05:39:34Z

Mark Omobono:

'''This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!'''

L Thompson 3/1/09
:Start by finding a protein with a known structure that interests you (see assignment sheet instructions). Determine whether anyone else in the class has already started a sandbox page for your protein (see list below). If so, join their page. If not, start a new sandbox page (you can use any unused ones listed below, or search for available numbers) and add a link to your page to our class list below (use editing button above (Ab) or follow my model).

Copy the message at the top into your sandbox page to "reserve" this sandbox for this course (others can still edit it but there is a way to go back -- not sure how yet).

Give "credit" for all your entries: add your name (like mine above) and also the source of anything that you got from another source.

Look for the pdb id for your protein in the Protein Data Bank. I looked for the earliest GFP structure I could find in the protein data bank and found 1ema, then followed the directions below to pull up a rotating GFP on this page.

Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.

{{STRUCTURE_1ema | PDB=1ema | SCENE= }}

Wow -- you can start exploring your structure now!

Task#1 (Due Wed 3/4 in the workshop). Describe the overall structure of your protein in words and make a "greenlink" illustration to go along with your description. Use the scene authoring tools and watch video 7 for instructions.
Example: (L Thompson)
The <scene name='Sandbox3/Secondary_structure/1'>overall structure</scene> of green fluorescent protein is an 11-stranded beta barrel (yellow) surrounding a central helix (pink). The chromophore is part of the central helix. Information from [[1ema]].

Task#2 – Find a view that shows an amphipathic element along the surface of the protein (alpha helix or beta strand or sheet -- not just a single residue). Make a green link of this view and describe it in words (ie explain colors etc). Always include your name in case others decide to join this page.

FEEDBACK:
Great start -- I enjoyed your cool representations of your proteins!
Please complete Task #2 if you haven't already (I fixed the wording above, which was not clear on the assignment page).

Ideas for improvements:
Does your overview of the structure convey the secondary elements? (ie 5 alpha helices and 2 beta strands)
I see problems with greek letters on the JMol, so best to write out alpha and beta.
Be sure you include your reference to your source.
Be sure you have your name on the list below.

==='''Chem490a Sandbox pages:'''Student projects:===

Jamal Salah & Vishwa Shah- deoxyhemoglobin ([[sandbox4]])

Elli Schmidt - HRas p21 ([[sandbox5]])

Abraham Khorasani - Potassium channel (streptomyces lividans) [[sandbox7]]

Marissa McGarry - ([[sandbox8]])

Tami Allen - Human Beta-Secretase ([[sandbox9]])

Brendan Jones - Myosin 2 motor domain ([[sandbox10]])

K Sniffen - ?? ([[sandbox11]])

Bejan Hakimi & Brendan Walker- GLYCOGEN SYNTHASE KINASE 3 BETA ([[sandbox28]])

Elaine Foun - Porin ([[sandbox12]])

Prof Martin - T7 RNA polymerase ([[sandbox20]])

Ankit Patel- 1bcr ([[sandbox314]])

Minal Patel- Mitochondrial Creatine Kinase([[sandbox26]])

Meenal Datta - Bacteriorhodopsin([[sandbox27]])

David Mortenson - Fe-only hydrogenase ([[sandbox23]])

Quoc Hung Pham - Human Serum Albumin ([[sandbox13]])

Kevin Chen- Trypsin([[sandbox21]])

Tinuke Adeyemi & Niva Ran- Glucokinase ([[sandbox22]])

Lori Mathis - acetylcholinesterase ([[sandbox29]])

Amit Shavit & Nikola Finneran - human Beta secretase complexed with inhibitor ([[sandbox16]])

Zachariah Blegen - Subtilisin ([[sandbox15]])

Josef Johann Polak the Third -- Beta-2-Glycoprotein-I ([[Sandbox109]])

Mark A. Omobono - Lipase ([[Sandbox313]])

Jonathan Rayla- Prion Protein ([[Sandbox_50]])

Adam Nelson - Phosphoglucose Isomerase ([[Sandbox 55]])

Juna Jovani - Macrophage Elastase ([[Sandbox315]])

Sophia Murray - aquaporin ([[Sandbox17]])

Chris Baker - lac permease ([[Sandbox18]])

==Extra Credit Submissions==

Mark Omobono - lysyl-tRNA synthase (ligand-less and complexed)- ([[Sandbox1313]])

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Sandbox1313

2009-05-12T22:49:44Z

Mark Omobono:

{{STRUCTURE_1bbw| PDB=1bbw | SCENE= }}==Lysyl-tRNA Synthase==

Shown here is PDB number 1bbu, lysyl-tRNA Synthase shown here complexed with the lysine substrate. It consists of both <scene name='Sandbox1313/Alpha_and_beta_strands/1'>alpha helices and beta sheets</scene> (the latter in sheets and a barrel). Below is pictured the exact same synthase complexed with it's residue of interest, lysine.

<applet load='1bbu' size='250' color='white' frame='true' align='left' caption='Lysine-bound lysyl-tRNA synthase' name='1bbu'/>

In the active site, the bound lysine participates in multiple hydrogen bonding interactions to stay complexed to the synthase protein as it moves into position to build the tRNA in the ribosome. Specifically,
<scene name='Sandbox1313/Hydrogen_bonding_partners/1'>these residues</scene> trigger a complex conformational change that completely changes the shape of part of the synthase. These changes involve <scene name='Sandbox1313/These_two_loops/1'>these two loops</scene> and some <scene name='Sandbox1313/Other_pieces/2'>other pieces</scene> of the molecule. This conformational change effectively closes the active site when bound to lysine.

Sandbox1313

2009-05-12T22:48:37Z

Mark Omobono:

{{STRUCTURE_1bbw| PDB=1bbw | SCENE= }}

==Lysyl-tRNA Synthase==
Shown here is PDB number 1bbu, lysyl-tRNA Synthase shown here complexed with the lysine substrate. It consists of both <scene name='Sandbox1313/Alpha_and_beta_strands/1'>alpha helices and beta sheets</scene> (the latter in sheets and a barrel). Below is pictured the exact same synthase complexed with it's residue of interest, lysine.

<applet load='1bbu' size='250' color='white' frame='true' align='left' caption='Lysine-bound lysyl-tRNA synthase' name='1bbu'/>

In the active site, the bound lysine participates in multiple hydrogen bonding interactions to stay complexed to the synthase protein as it moves into position to build the tRNA in the ribosome. Specifically,
<scene name='Sandbox1313/Hydrogen_bonding_partners/1'>these residues</scene> trigger a complex conformational change that completely changes the shape of part of the synthase. These changes involve <scene name='Sandbox1313/These_two_loops/1'>these two loops</scene> and some <scene name='Sandbox1313/Other_pieces/2'>other pieces</scene> of the molecule. This conformational change effectively closes the active site when bound to lysine.

Sandbox1313

2009-05-12T22:46:26Z

Mark Omobono: /* Lysyl-tRNA Synthase */

{{STRUCTURE_1bbw | PDB=1bbw | SCENE= }}
{{STRUCTURE_1bbw| PDB=1bbw | SCENE= }}

==Lysyl-tRNA Synthase==
Shown here is PDB number 1bbu, lysyl-tRNA Synthase shown here complexed with the lysine substrate. It consists of both <scene name='Sandbox1313/Alpha_and_beta_strands/1'>alpha helices and beta sheets</scene> (the latter in sheets and a barrel). Below is pictured the exact same synthase complexed with it's residue of interest, lysine.

<applet load='1bbu' size='250' color='white' frame='true' align='left' caption='Lysine-bound lysyl-tRNA synthase' name='1bbu'/>

In the active site, the bound lysine participates in multiple hydrogen bonding interactions to stay complexed to the synthase protein as it moves into position to build the tRNA in the ribosome. Specifically,
<scene name='Sandbox1313/Hydrogen_bonding_partners/1'>these residues</scene> trigger a complex conformational change that completely changes the shape of part of the synthase. These changes involve <scene name='Sandbox1313/These_two_loops/1'>these two loops</scene> and some <scene name='Sandbox1313/Other_pieces/1'>other pieces</scene> of the molecule. This conformational change effectively closes the active site when bound to lysine.

Sandbox1313

2009-05-12T22:32:41Z

Mark Omobono: /* Lysyl-tRNA Synthase */

{{STRUCTURE_1bbw | PDB=1bbw | SCENE= }}
==Lysyl-tRNA Synthase==
Shown here is PDB number 1bbu, lysyl-tRNA Synthase shown here complexed with the lysine substrate. It consists of both <scene name='Sandbox1313/Alpha_and_beta_strands/1'>alpha helices and beta sheets</scene> (the latter in sheets and a barrel). Below is pictured the exact same synthase complexed with it's residue of interest, lysine.

<applet load='1bbu' size='400' color='white' frame='true' align='left' caption='Lysine-bound lysyl-tRNA synthase' />
As you can see in the "active site", the lysine participates in multiple hydrogen bonding interactions to stay complexed to the synthase protein as it moves into position to build the tRNA in the ribosome. Specifically,
<scene name='Sandbox1313/Hydrogen_bonding_partners/1'>these residues</scene> trigger a complex conformational change that completely changes the synthase. These changes involve "these two loops" and some "other pieces" of the molecule. This conformational change effecively closes the active site when bound to lysine.

Sandbox1313

2009-05-12T21:52:28Z

Mark Omobono: New page: ==Lysyl-tRNA Synthase== Shown here is PDB number 1bbu, lysyl-tRNA Synthase shown here complexed with the lysine substrate. It consists of both "α-helices" and "β-strands" (the latter in ...

==Lysyl-tRNA Synthase==
Shown here is PDB number 1bbu, lysyl-tRNA Synthase shown here complexed with the lysine substrate. It consists of both "α-helices" and "β-strands" (the latter in sheets and a barrel).

As you can see in the "active site", the lysine participates in multiple "hydrogen bonding interactions" to stay complexed to the synthase protein as it moves into position to build the tRNA in the ribosome.

It is also worth mentioning that when the lysine enters the complex, a small number of "residues" trigger a

{{STRUCTURE_1bbw | PDB=1bbw | SCENE= }}