Proteopedia - User contributions [en]

CBI Molecules

2015-01-06T17:52:31Z

Mallory Gordon:

These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].
Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.

UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.

Fall 2014: CBI Molecules are due 12/3/14 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished, and then as "New 2014" or "Revised 2014". For those editing an existing CBI Molecule, start by making a copy of that entry (leaving the original intact) so that it retains the full author list of all authors that contributed (or include credits and a link to the original page and authors if it does not).
Follow the instructions at the bottom of this page.

==Molecules==
'''** Designates CBI Molecules Featured on [http://www.umass.edu/cbi/ CBI website]'''

[http://chamberslab.com/wp/ Chambers Lab]

: '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano

[http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab]

: '''[[Molecular Playground/ClyA]]''', Monifa Fahie, Bib Yang '''Revised 2014'''
: '''[[Molecular Playground/OmpG]]''', Christina Chisholm, Monifa Fahie, Bib Yang '''Revised 2014'''

[http://openwetware.org/wiki/Chien Chien Lab]

: '''[[Molecular Playground/ClpP]]''', Lisa Hernandez, Rob Vass '''New 2014'''
: '''[[Molecular Playground/Homo-dimeric RcdA]]''', Kamal K. Joshi
: **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau '''Best CBI Molecule 2011'''
: '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu

Farkas Lab
: '''[[Molecular Playground/CLOCK:BMAL1 heterodimer complex]]''', Hui-Hsien Lin, Joseph Hardie, Michael Mingroni '''New 2014'''

Forbes Lab

: '''[[Molecular Playground/CheR]]''', Miaomin Zhang
: '''[[Molecular Playground/RBP]]''', Jan Panteli
: '''[[Molecular Playground/TRAIL]]''', Charley Swofford

[http://www.biochem.umass.edu/garman/index.html Garman Lab]

: '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon
: '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli

[http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]

: '''[[Molecular_Playground/DnaK]]''', Joseph Tilitsky, New 2014
: '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy '''Best Overall CBI Molecule 2010'''
: '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez
: **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani '''Best CBI Molecule 2012'''

[http://people.chem.umass.edu/jhardy/ Hardy Lab]

: '''[[Molecular Playground/Executioner Caspase-7]]''', Derek MacPherson, Maureen E. Hill
: '''[[Molecular Playground/Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao
: '''[[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay
: '''[[Molecular Playground/Caspase-7 Dynamics]]'''
: '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber
: '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez
: '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls
: '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz

Hebert Lab

: '''[[Molecular_Playground/Hsp70-Hsp90]]''', Jill Graham "Revised 2014"
: '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben
: '''[[Molecular Playground/Saposin C]]''', Abla Tannous
: '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd

[http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]

: '''[[Molecular_Playground/Pcr H]]''', Fabian Romano, Carolina Morell-Pérez, Yuzhou Tang

[http://people.chem.umass.edu/mholden/ Holden Lab]

: '''[[Molecular Playground/Protective Antigen]]''', Jing Huang

[http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]
: '''[[Molecular Playground/Hemoglobin-Haptoglobin Complex]]''', Ololade Fatunmbi, Chibueze Egeruoh '''***New Fall 2014***'''
: '''[http://proteopedia.org/wiki/index.php/Chengfeng_Ren Molecular Playground/Inteferon]'''[Revised], Chengfeng Ren
: ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski
: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita
: '''[[Molecular Playground/Antithrombin-Heparin]]''', Yunlong Zhao

[http://people.chem.umass.edu/knapplab/?q=knappchem/index.html/ Knapp Lab]
: '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas '''Best CBI Molecule Proteopedia Page 2010''' '''***New Fall 2014***'''
: '''[[Molecular Playground/FIH]]''', Vanessa Chaplin, Cornelius Taabazuing, Breanne Holmes, John Hangasky

[http://people.chem.umass.edu/mmaroney/ Maroney Lab]

: '''[[Molecular Playground/UreE]]''', Priyanka Basak, '''New 2014'''
: '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr
: '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu, Carolyn Carr, Hsin-Ting (Tiffany )Huang, '''Revised 2014'''
: '''[[Molecular Playground/HypA]]''', Heidi Hu

[http://www.chem.umass.edu/~cmartin/ Martin Lab]

: **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia '''Best CBI Molecule 2011'''
: '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia
: '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan

[http://www.peytonlab.org/ Peyton Lab]
: '''[[Molecular Playground/IntegrinBeta1]]''', Lauren Jansen, Lauren Barney, Elizabeth Brooks, Alyssa Schwartz ***'''NEW FALL 2014''''***
: '''[[Molecular Playground/MMP14]]''', Lauren Jansen
: '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen
: '''[[Molecular Playground/FAK]]''', Dannielle Ryman

[http://roberts.openwetware.org/ Roberts Lab]

: '''[[Molecular Playground/Taxol]]''', Elizabeth Cummings, Rohan Patil, Sarah Wilson ***'''Revised Fall 2014'''***
: '''[[Molecular Playground/Insulin]]''', Whitney Stoppel

[http://www.umass.edu/rotellogroup/ Rotello Lab]

: '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino
: '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang
: '''[[Molecular playground/Chymotrypsin]]''', Brad
: '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell

[http://http://www.umass.edu/schiffman/ Schiffman Lab]
: '''[[Molecular Playground/Streptavidin]]''', Katrina Rieger

[http://www.biochem.umass.edu/faculty/danny-j-schnell Schnell Lab]
: '''[[Molecular Playground/Tic40]]''', Mine Canakci

Tew Lab

: '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde, Coralie Backlund

Thayumanavan Lab
: '''[[Interleukin-1 beta]]''', Huan He
: '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez
: '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura
: '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi
: '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy
: '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado
: '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang
: ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo
: '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko
: '''[[Molecular Playground/MMP9]]''', Jiaming Zhuang, Mallory Gordon '''Revised 2014'''

Thayumanavan & Vachet Labs

: '''[[Molecular Playground/Trypsin]]''', Gladys Murage

[http://people.chem.umass.edu/thompson/index.html Thompson Lab]

: '''[[Molecular Playground/Bacterial Chemotaxis Complex]]''', Elizabeth R. Haglin, Maryam Kashefi '''"Revised 2014"'''
: '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin
: '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones
: '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li

[http://www.chem.umass.edu/~vachet/index.html Vachet Lab]

: '''[[Molecular Playground/Human Serum Albumin]]''', Mahalia Serrano ''*Revised 2014*''
: '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto, Tyler Marcinko ***'''Revised Fall 2014'''*** '''Best CBI Molecule Jmol scenes 2010'''
: '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou
:'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne
: '''[[Molecular Playground/Ubiquitin salt bridge discussion]]''', Zhe Zhang

Vierling Lab

: '''[[Molecular Playground/sHSP]]''', Keith Ballard '''New 2014'''

Other Molecules of interest

: '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]

Other Laboratories

:'''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey, Schnarr lab
: '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey, Schnarr lab
: '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad, Schnarr lab

: '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang, Weis lab

: '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffi, Bhatia Lab
: '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer, Bhatia Lab

: '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]

: '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab

: '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab

==Instructions==

'''The goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''

Fall 2014: Complete steps 1-3 before the CBI Molecule Workshop on 11/19; bring your computer to the CBI Molecule Workshop in ISB 321. You will be able to start work on your CBI Molecule at the workshop. You should plan to stay and finish your molecule after the workshop (or as soon as possible) while the instructions and ideas are fresh in your mind.

A successful CBI Molecule is an interesting, nontechnical description of a molecule related to your group's research. It should tell an interesting story with few words and many green scenes. Green scenes should be clear and attractive illustrations that tell your story. It's great if you can end with a brief statement about how it relates to your group's research goals.

1. If you don't already have one, request a Proteopedia account and log in.

2. Read through the rest of the instructions, do the tutorials below, and look at any existing CBI Molecules from your research group. Talk with other CBI students in your research group and decide how you will collaborate to make an improved CBI Molecule related to your group's research. Develop ideas for the scenes that each of you will make.

3. Get started working in Proteopedia. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. Explore the HELP links below to learn how to make a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made).

'''Complete the above steps before the CBI Molecule Workshop.'''

4. When editing an existing CBI Molecule, leave the original intact and make a copy that you will edit so that it retains the full author list of all authors that contributed. You are encouraged to collaborate on the CBI Molecules, but everyone will need to log in as themself and create a green scene to get credit for their work and to appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.

5. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished, and then "new 2014" or "revised 2014". Minimize text; tell your story with green scenes!

6. When your CBI Molecule is complete, send Lynmarie an email to nominate a cool scene/clever caption you would like to feature at the Molecular Playground (include a link to your CBI Molecule, name of the green scene, and caption).

==Links to HELP pages==
Overview at [[Help:Contents ]]

See also [[Help:Getting_Started_in_Proteopedia]]

Videos showing how to use Proteopedia:
[[Proteopedia:Video_Guide]]
(Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)

[[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]
gives succinct step by step instructions on how to create a molecular scene.

A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.
[http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]

[[Proteopedia:Guidelines for Ethical Writing]].
Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.

For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.

Molecular Playground/MMP9

2014-12-11T01:04:38Z

Mallory Gordon: New page: <Structure load='1gkc' size='400' frame='true' align='right' caption='MMP9' scene='Insert optional scene name here' /> MMP9 is a member of ''' matrix metalloproteinases''' (MMPs) which ar...

<Structure load='1gkc' size='400' frame='true' align='right' caption='MMP9' scene='Insert optional scene name here' />

MMP9 is a member of ''' matrix metalloproteinases''' (MMPs) which are zinc-dependent endopeptidases. It has been found to associate with many types of cancers and investigated as a potential drug target. Various of <scene name='User:Jiaming_Zhuang/Sandbox_2/Ligand/1'>inhibitors</scene> have been designed to bind to the <scene name='User:Jiaming_Zhuang/Sandbox_2/Domain1/1'>catalytic domain</scene> and inhibit the activity of MMP9.

ProMMP9 has a propeptide domain with a zinc ligating "cysteine switch" at the <scene name='40/400553/Pro_cat_motif/4'>active site</scene>, rendering the enzyme inactive until the propeptide is cleaved.

----
Reference:
Siân Rowsell, Paul Hawtin,Claire A. Minshull, Holly Jepson, Sarah M.V. Brockbank,Derek G. Barratt, Anthony M. Slater, William L. McPheat, David Waterson, Adriano M. Henney, Richard A. Pauptit Crystal Structure of Human MMP9 in Complex with a Reverse Hydroxamate Inhibitor, Volume 319, Issue 1, 24 May 2002, Pages 173–181
----

User:Jiaming Zhuang

2014-12-11T01:03:39Z

Mallory Gordon:

*[[Molecular Playground/MMP9]]

User:Jiaming Zhuang/Sandbox 2

2014-12-11T00:58:40Z

Mallory Gordon:

User:Jiaming Zhuang/Sandbox 2

2014-12-11T00:47:23Z

Mallory Gordon:

<Structure load='1gkc' size='400' frame='true' align='right' caption='MMP9' scene='Insert optional scene name here' />

MMP9 is a member of ''' matrix metalloproteinases''' (MMPs) which are zinc-dependent endopeptidases. It has been found to associate with many types of cancers and investigated as a potential drug target. Various of <scene name='User:Jiaming_Zhuang/Sandbox_2/Ligand/1'>inhibitors</scene> have been designed to bind to the <scene name='User:Jiaming_Zhuang/Sandbox_2/Domain1/1'>catalytic domain</scene> and inhibit the activity of MMP9.

This is the <scene name='40/400553/Pro_cat_motif/4'>active site</scene> of the protein.

----
Reference:
Siân Rowsell, Paul Hawtin,Claire A. Minshull, Holly Jepson, Sarah M.V. Brockbank,Derek G. Barratt, Anthony M. Slater, William L. McPheat, David Waterson, Adriano M. Henney, Richard A. Pauptit Crystal Structure of Human MMP9 in Complex with a Reverse Hydroxamate Inhibitor, Volume 319, Issue 1, 24 May 2002, Pages 173–181
----

User:Mallory Gordon/Sandbox

2014-12-11T00:45:26Z

Mallory Gordon:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1L6J' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Mallory Gordon/Sandbox'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is the <scene name='40/400553/Pro_cat_motif/4'>active site</scene> of the protein.

[[Image:1L6J_Zn_residues.png | thumb |right|280px| ProMMP9 (from PDB entry 1L6J) with propeptide conserved sequence (purple) including "cysteine switch" (blue), and catalytic zinc conserved binding motif (orange)]]

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Jiaming Zhuang/Sandbox 2

2014-12-11T00:30:15Z

Mallory Gordon:

<Structure load='1gkc' size='400' frame='true' align='right' caption='MMP9' scene='Insert optional scene name here' />

MMP9 is a member of ''' matrix metalloproteinases''' (MMPs) which are zinc-dependent endopeptidases. It has been found to associate with many types of cancers and investigated as a potential drug target. Various of <scene name='User:Jiaming_Zhuang/Sandbox_2/Ligand/1'>inhibitors</scene> have been designed to bind to the <scene name='User:Jiaming_Zhuang/Sandbox_2/Domain1/1'>catalytic domain</scene> and inhibit the activity of MMP9.

<Structure load='1L6J' size='350' frame='true' align='right' caption='MMP-9 (from PDB entry 1L6J)' scene='scene 1' />

----
Reference:
Siân Rowsell, Paul Hawtin,Claire A. Minshull, Holly Jepson, Sarah M.V. Brockbank,Derek G. Barratt, Anthony M. Slater, William L. McPheat, David Waterson, Adriano M. Henney, Richard A. Pauptit Crystal Structure of Human MMP9 in Complex with a Reverse Hydroxamate Inhibitor, Volume 319, Issue 1, 24 May 2002, Pages 173–181
----

User:Mallory Gordon/Sandbox

2014-12-10T23:02:40Z

Mallory Gordon:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1L6J' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Mallory Gordon/Sandbox'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

[[Image:1L6J_pro_and_act.png | thumb]]

[[Image:1L6J_Zn_residues.png | thumb | ProMMP9 (from PDB entry 1L6J) with propeptide conserved sequence (purple) including "cysteine switch" (blue), and catalytic zinc conserved binding motif (orange)]]

[[Image:1L6J_Zn_residues.png | thumb |right|280px| ProMMP9 (from PDB entry 1L6J) with propeptide conserved sequence (purple) including "cysteine switch" (blue), and catalytic zinc conserved binding motif (orange)]]

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Mallory Gordon/Sandbox

2014-12-10T22:57:37Z

Mallory Gordon:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1L6J' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Mallory Gordon/Sandbox'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

[[Image:1L6J_pro_and_act.png | thumb]]

[[Image:1L6J_Zn_residues.png | thumb | ProMMP9 (from PDB entry 1L6J) with propeptide conserved sequence (purple) including "cysteine switch" (blue), and catalytic zinc conserved binding motif (orange)]]

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Mallory Gordon/Sandbox

2014-12-10T22:45:38Z

Mallory Gordon:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1L6J' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Mallory Gordon/Sandbox'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

[[Image:1L6J_pro_and_act.png | thumb]]

[[Image:1L6J_Zn_residues.png | thumb]]

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

File:1L6J Zn residues.png

2014-12-10T22:45:07Z

Mallory Gordon:

User:Mallory Gordon/Sandbox

2014-12-10T22:37:12Z

Mallory Gordon:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1L6J' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Mallory Gordon/Sandbox'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

[[Image:1L6J_pro_and_act.png | thumb]]

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Mallory Gordon/Sandbox

2014-12-10T22:27:42Z

Mallory Gordon:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Mallory Gordon/Sandbox'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

<Structure load='1L6j' size='350' frame='true' align='right' caption='MMP-9, PDB 1L6J' scene='Insert optional scene name here' />

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Mallory Gordon/Sandbox

2014-12-10T22:25:07Z

Mallory Gordon: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Mallory Gordon/Sandbox'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==
[[Image:1L6J pro and act.png]]

<Structure load='1L6j' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

File:3iap.pdb

2014-11-19T17:41:52Z

Mallory Gordon:

Molecular Playground/Beta-galactosidase

2014-11-19T17:40:48Z

Mallory Gordon:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

'''β-Galactosidase''' is a hydrolase enzyme that catalyzes the hydrolysis of beta- galactosidase into monosaccharides (carbon/energy source). Is encoded by the ''lacZ'' gene of the ''lac'' operon in E.coli. It is a large 120 kDa, >1000 amino acids) protein that forms a tetramer.

It is commonly used as a reporter molecule in genetics and molecular biology. Usually, experiments are designed so that the β-Galactosidase concentration in the cell is a readout for some aspect of a system being studied. When the β-Galactosidase cleaves the substrate o-nitrophenyl-b-D-galactopyraniside (ONPG), o-nitrophenol is released. This compound has a yellow color, and absorbs 420 nm light. To measure β-Galactosidase activity the accumulation of yellow color (increase 420 nm absorbance)/minute is monitored.

{{STRUCTURE_3iap | PDB=3iap | SCENE= }}

<scene name='Judy_Ventura/Sandbox1/All_protein/1'>All Molecule</scene>

<scene name='Judy_Ventura/Sandbox1/4_subunits/1'>Subunits</scene>

==3D structures of beta-galactosidase==

[[Beta-galactosidase]]

Mallory Gordon/Sandbox1

2014-11-19T17:34:20Z

Mallory Gordon: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='3iap' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='3iap' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Mallory Gordon/Sandbox1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>