Proteopedia - User contributions [en]

Sandbox3

2009-05-22T04:06:31Z

Amit Shavit: /* Extra Credit Submissions */

'''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]])

Juna Jovani - Carbonic Anhydrase ([[Sandbox1029]])

Amit Shavit - Cytochrome P450 2C8 ([[Sandbox1111]])

===Help Editing===

Hint: Ctl-click or right-click on links below and select "Open Link in New Window"

[[http://www.proteopedia.org/wiki/index.php/Help:EditingProteopedia Help page]]

[[http://meta.wikimedia.org/wiki/Cheatsheet Wikimedia cheat sheet]]

[[http://en.wikipedia.org/wiki/How_to_edit General help with Wiki editing]], plus more [[http://en.wikipedia.org/wiki/Help:Wikitext_examples Wiki Text examples]]

Some of the above are for help editing Wikipedia pages, but the syntax is mostly the same. Proteopedia ADDS protein stuff to the WikiMedia markup language, which powers both WEB sites.

Sandbox1111

2009-05-22T04:04:12Z

Amit Shavit: /* Structure */

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

==Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8==

'''By Amit Shavit''', 5/21/09

{{STRUCTURE_3cin | PDB=1pq2 | SCENE= }}

==Protein==

CYP2C8 is one of the principal hepatic drug-metabolizing enzymes that oxidizes therapeutic drugs such as taxol and cerivastatin and endobiotics such as retinoic acid and arachidonic acid. This protein has relatively large active site volume [go to Structure section and choose the green link to portray the active sites]. CYP2C8 crystallized as a symmetric dimer and is observed in solution. Furthermore, mass spectrometry confirmed the association of palmitic acid with the enzyme. This novel finding identifies a peripheral binding site in P450s that may contribute to drug-drug interactions in P450 metabolism. Perhaps an implement of Kerpolla's ingenious BiFC could provide a better understanding and monitoring of these drug-drug interactions.

==Structure==

This protein is a dimer. The two subunits of the dimer are visually distinguishable by their different color schemes. Moreover this protein is mostly composed of <scene name='Sandbox1111/Alpha/3'>Alpha Helices</scene>, as shown in blue. While it's initially hard to tell, there are several <scene name='Sandbox1111/Beta/1'>Beta Sheets</scene>, as shown in purple. Furthermore, as most proteins contain a hydrophobic core, this protein indeed contains many <scene name='Sandbox1111/Hydrophobic_red/1'>Hydrophobic interactions</scene>, as shown in red, and relatively fewer <scene name='Sandbox1111/Polar_bonds/1'>Polar bonds</scene>, as shown in dark green. Lastly, the protein's <scene name='Sandbox1111/Active_sites/1'>Active Sites</scene> are shown in brown.

==Reference==

Schoch GA, Yano JK, Wester MR, Griffin KJ, Stout CD, Johnson EF Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site. J Biol Chem. 2004 Mar 5;279(10):9497-503. Epub 2003 Dec 15. PMID:14676196

Sandbox1111

2009-05-22T04:00:06Z

Amit Shavit: /* Structure */

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

==Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8==

'''By Amit Shavit''', 5/21/09

{{STRUCTURE_3cin | PDB=1pq2 | SCENE= }}

==Protein==

CYP2C8 is one of the principal hepatic drug-metabolizing enzymes that oxidizes therapeutic drugs such as taxol and cerivastatin and endobiotics such as retinoic acid and arachidonic acid. This protein has relatively large active site volume [go to Structure section and choose the green link to portray the active sites]. CYP2C8 crystallized as a symmetric dimer and is observed in solution. Furthermore, mass spectrometry confirmed the association of palmitic acid with the enzyme. This novel finding identifies a peripheral binding site in P450s that may contribute to drug-drug interactions in P450 metabolism. Perhaps an implement of Kerpolla's ingenious BiFC could provide a better understanding and monitoring of these drug-drug interactions.

==Structure==

This protein is mostly composed of <scene name='Sandbox1111/Alpha/3'>Alpha Helices</scene>, as shown in blue. While it's initially hard to tell, there are several <scene name='Sandbox1111/Beta/1'>Beta Sheets</scene>, as shown in purple.

<scene name='Sandbox1111/Alpha/3'>Alpha Helices</scene> are portrayed in blue

<scene name='Sandbox1111/Hydrophobic_red/1'>Hydrophobic interactions</scene> in red

<scene name='Sandbox1111/Polar_bonds/1'>Polar bonds</scene> in dark green

<scene name='Sandbox1111/Active_sites/1'>Active Sites</scene> are shown in brown

==Reference==

Schoch GA, Yano JK, Wester MR, Griffin KJ, Stout CD, Johnson EF Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site. J Biol Chem. 2004 Mar 5;279(10):9497-503. Epub 2003 Dec 15. PMID:14676196

Sandbox1111

2009-05-22T03:59:00Z

Amit Shavit: /* Protein */

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

==Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8==

'''By Amit Shavit''', 5/21/09

{{STRUCTURE_3cin | PDB=1pq2 | SCENE= }}

==Protein==

CYP2C8 is one of the principal hepatic drug-metabolizing enzymes that oxidizes therapeutic drugs such as taxol and cerivastatin and endobiotics such as retinoic acid and arachidonic acid. This protein has relatively large active site volume [go to Structure section and choose the green link to portray the active sites]. CYP2C8 crystallized as a symmetric dimer and is observed in solution. Furthermore, mass spectrometry confirmed the association of palmitic acid with the enzyme. This novel finding identifies a peripheral binding site in P450s that may contribute to drug-drug interactions in P450 metabolism. Perhaps an implement of Kerpolla's ingenious BiFC could provide a better understanding and monitoring of these drug-drug interactions.

==Structure==

<scene name='Sandbox1111/Beta/1'>Beta Sheet</scene> are portrayed in purple.

<scene name='Sandbox1111/Alpha/3'>Alpha Helices</scene> are portrayed in blue

<scene name='Sandbox1111/Hydrophobic_red/1'>Hydrophobic interactions</scene> in red

<scene name='Sandbox1111/Polar_bonds/1'>Polar bonds</scene> in dark green

<scene name='Sandbox1111/Active_sites/1'>Active Sites</scene> are shown in brown

==Reference==

Schoch GA, Yano JK, Wester MR, Griffin KJ, Stout CD, Johnson EF Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site. J Biol Chem. 2004 Mar 5;279(10):9497-503. Epub 2003 Dec 15. PMID:14676196

Sandbox1111

2009-05-22T03:52:18Z

Amit Shavit: /* Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8 */

Sandbox1111

2009-05-22T03:51:43Z

Amit Shavit: /* Protein */

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

==Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8==

'''By Amit Shavit'''

{{STRUCTURE_3cin | PDB=1pq2 | SCENE= }}

==Protein==

==Structure==

<scene name='Sandbox1111/Beta/1'>Beta Sheet</scene> are portrayed in purple.

<scene name='Sandbox1111/Alpha/3'>Alpha Helices</scene> are portrayed in blue

<scene name='Sandbox1111/Hydrophobic_red/1'>Hydrophobic interactions</scene> in red

<scene name='Sandbox1111/Polar_bonds/1'>Polar bonds</scene> in dark green

<scene name='Sandbox1111/Active_sites/1'>Active Sites</scene> are shown in brown

==Reference==

Schoch GA, Yano JK, Wester MR, Griffin KJ, Stout CD, Johnson EF Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site. J Biol Chem. 2004 Mar 5;279(10):9497-503. Epub 2003 Dec 15. PMID:14676196

Sandbox1111

2009-05-22T03:51:05Z

Amit Shavit: /* Structure */

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

==Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8==

'''By Amit Shavit'''

{{STRUCTURE_3cin | PDB=1pq2 | SCENE= }}

==Protein==

<scene name='Sandbox1111/Active_sites/1'>Active Sites</scene> are shown in brown

==Structure==

<scene name='Sandbox1111/Beta/1'>Beta Sheet</scene> are portrayed in purple.

<scene name='Sandbox1111/Alpha/3'>Alpha Helices</scene> are portrayed in blue

<scene name='Sandbox1111/Hydrophobic_red/1'>Hydrophobic interactions</scene> in red

<scene name='Sandbox1111/Polar_bonds/1'>Polar bonds</scene> in dark green

<scene name='Sandbox1111/Active_sites/1'>Active Sites</scene> are shown in brown

==Reference==

Schoch GA, Yano JK, Wester MR, Griffin KJ, Stout CD, Johnson EF Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site. J Biol Chem. 2004 Mar 5;279(10):9497-503. Epub 2003 Dec 15. PMID:14676196

Sandbox1111

2009-05-22T03:50:51Z

Amit Shavit: /* Protein */

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

==Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8==

'''By Amit Shavit'''

{{STRUCTURE_3cin | PDB=1pq2 | SCENE= }}

==Protein==

<scene name='Sandbox1111/Active_sites/1'>Active Sites</scene> are shown in brown

==Structure==

<scene name='Sandbox1111/Beta/1'>Beta Sheet</scene> are portrayed in purple.

<scene name='Sandbox1111/Alpha/3'>Alpha Helices</scene> are portrayed in blue

<scene name='Sandbox1111/Hydrophobic_red/1'>Hydrophobic interactions</scene> in red

<scene name='Sandbox1111/Polar_bonds/1'>Polar bonds</scene> in dark green

==Reference==

Schoch GA, Yano JK, Wester MR, Griffin KJ, Stout CD, Johnson EF Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site. J Biol Chem. 2004 Mar 5;279(10):9497-503. Epub 2003 Dec 15. PMID:14676196

Sandbox1111

2009-05-22T03:48:20Z

Amit Shavit: /* Reference */

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

==Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8==

'''By Amit Shavit'''

{{STRUCTURE_3cin | PDB=1pq2 | SCENE= }}

==Protein==

==Structure==

<scene name='Sandbox1111/Beta/1'>Beta Sheet</scene> are portrayed in purple.

<scene name='Sandbox1111/Alpha/3'>Alpha Helices</scene> are portrayed in blue

<scene name='Sandbox1111/Hydrophobic_red/1'>Hydrophobic interactions</scene> in red

<scene name='Sandbox1111/Polar_bonds/1'>Polar bonds</scene> in dark green

==Reference==

Schoch GA, Yano JK, Wester MR, Griffin KJ, Stout CD, Johnson EF Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site. J Biol Chem. 2004 Mar 5;279(10):9497-503. Epub 2003 Dec 15. PMID:14676196

Sandbox1111

2009-05-22T03:48:11Z

Amit Shavit: /* Structure */

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

==Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8==

'''By Amit Shavit'''

{{STRUCTURE_3cin | PDB=1pq2 | SCENE= }}

==Protein==

==Structure==

<scene name='Sandbox1111/Beta/1'>Beta Sheet</scene> are portrayed in purple.

<scene name='Sandbox1111/Alpha/3'>Alpha Helices</scene> are portrayed in blue

<scene name='Sandbox1111/Hydrophobic_red/1'>Hydrophobic interactions</scene> in red

<scene name='Sandbox1111/Polar_bonds/1'>Polar bonds</scene> in dark green

==Reference==

Schoch GA, Yano JK, Wester MR, Griffin KJ, Stout CD, Johnson EF Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site. J Biol Chem. 2004 Mar 5;279(10):9497-503. Epub 2003 Dec 15. PMID:14676196

<scene name='Sandbox1111/Beta/1'>Beta Sheet</scene> are portrayed in purple.

<scene name='Sandbox1111/Alpha/3'>Alpha Helices</scene> are portrayed in blue

<scene name='Sandbox1111/Hydrophobic_red/1'>Hydrophobic interactions</scene> in red

<scene name='Sandbox1111/Polar_bonds/1'>Polar bonds</scene> in dark green

Sandbox1111

2009-05-22T03:48:02Z

Amit Shavit: /* Reference */

Sandbox1111

2009-05-22T03:47:49Z

Amit Shavit: /* Structure */

Sandbox1111

2009-05-22T03:47:37Z

Amit Shavit: /* Protein */

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

==Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8==

'''By Amit Shavit'''

{{STRUCTURE_3cin | PDB=1pq2 | SCENE= }}

==Protein==

=Structure=

=Reference=

Schoch GA, Yano JK, Wester MR, Griffin KJ, Stout CD, Johnson EF Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site. J Biol Chem. 2004 Mar 5;279(10):9497-503. Epub 2003 Dec 15. PMID:14676196

<scene name='Sandbox1111/Beta/1'>Beta Sheet</scene> are portrayed in purple.

<scene name='Sandbox1111/Alpha/3'>Alpha Helices</scene> are portrayed in blue

<scene name='Sandbox1111/Hydrophobic_red/1'>Hydrophobic interactions</scene> in red

<scene name='Sandbox1111/Polar_bonds/1'>Polar bonds</scene> in dark green

Sandbox1111

2009-05-22T03:47:05Z

Amit Shavit: /* Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8 */

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

==Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8==

'''By Amit Shavit'''

{{STRUCTURE_3cin | PDB=1pq2 | SCENE= }}

=Protein=

=Structure=

=Reference=

Schoch GA, Yano JK, Wester MR, Griffin KJ, Stout CD, Johnson EF Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site. J Biol Chem. 2004 Mar 5;279(10):9497-503. Epub 2003 Dec 15. PMID:14676196

<scene name='Sandbox1111/Beta/1'>Beta Sheet</scene> are portrayed in purple.

<scene name='Sandbox1111/Alpha/3'>Alpha Helices</scene> are portrayed in blue

<scene name='Sandbox1111/Hydrophobic_red/1'>Hydrophobic interactions</scene> in red

<scene name='Sandbox1111/Polar_bonds/1'>Polar bonds</scene> in dark green

Sandbox1111

2009-05-22T03:42:22Z

Amit Shavit: /* Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8 */

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

==Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8==

'''By Amit Shavit'''

{{STRUCTURE_3cin | PDB=1pq2 | SCENE= }}

<scene name='Sandbox1111/Beta/1'>Beta Sheet</scene> are portrayed in purple.

<scene name='Sandbox1111/Alpha/3'>Alpha Helices</scene> are portrayed in blue

<scene name='Sandbox1111/Hydrophobic_red/1'>Hydrophobic interactions</scene> in red

<scene name='Sandbox1111/Polar_bonds/1'>Polar bonds</scene> in dark green

Sandbox1111

2009-05-22T03:39:43Z

Amit Shavit:

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

==Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8==

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

{{STRUCTURE_3cin | PDB=1pq2 | SCENE= }}

<scene name='Sandbox1111/Beta/1'>Beta Sheet</scene> are portrayed in purple.

<scene name='Sandbox1111/Alpha/3'>Alpha Helices</scene> are portrayed in blue

<scene name='Sandbox1111/Hydrophobic_red/1'>Hydrophobic interactions</scene> in red

<scene name='Sandbox1111/Polar_bonds/1'>Polar bonds</scene> in dark green

Sandbox1111

2009-05-22T03:20:33Z

Amit Shavit: New page: ==NMR STRUCTURE OF LAC REPRESSOR HP62-DNA COMPLEX== '''This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!''' This is a place...

==NMR STRUCTURE OF LAC REPRESSOR HP62-DNA COMPLEX==

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

This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

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

{{STRUCTURE_3cin | PDB=1cjg | SCENE= }}