Proteopedia - User contributions [en]

Molecular Playground/Streptavidin

2014-11-19T18:12:20Z

Katrina Rieger:

== The Use of Streptavidin/Biotin Complex to Functionalize Materials ==

Streptavidin is a protein best known for its ability to bind to biotin creating the strongest non-covalent interaction in nature.

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].

<StructureSection load='1MEP' size='350' side='right' caption='Structure of Streptavidin (PDB entry [[Ŏ1MEP]])' scene=''>

In the [http://www.umas.edu/schiffman Schiffman Lab], we fabricate many types of soft materials including electrospun nanofibers, hydrogels, and nanoparticles. In order to tailor each material for wound management and health care applications, it is necessary to functionalize each material with polymers, enzymes, growth factors or antibiotics. To attach such molecules, we attach streptavidin to our material and take advantage of the streptavidin/biotin bond to add agents such as biotinylated antibodies. Biotin can attach to any of the four subunits of streptavidin. The <scene name='56/567309/F/1'>disappearance</scene> of biotin in the complex shows where biotin can bind to streptavidin. The <scene name='56/567309/Residues_binding/1'>tryptophan residues</scene> comprise part of the biotin-binding site of the streptavidin molecule.

In addition to using Streptavidin for attaching antibiotics, we have also start to use Streptavidin to attach Quantum Dots to materials as new sensing devices. These devices should be utilized to determine the presence of specific markers for a variety of applications including the medical field and water purification.

</StructureSection>

Molecular Playground/Streptavidin

2014-11-19T18:11:34Z

Katrina Rieger:

== The Use of Streptavidin/Biotin Complex to Functionalize Materials ==

Streptavidin is a protein best known for its ability to bind to biotin creating the strongest non-covalent interaction in nature.

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].

<StructureSection load='1MEP' size='350' side='right' caption='Structure of Streptavidin (PDB entry [[Ŏ1MEP]])' scene=''>

In the [http://www.umas.edu/schiffman Schiffman Lab], we fabricate many types of soft materials including electrospun nanofibers, hydrogels, and nanoparticles. In order to tailor each material for wound management and health care applications, it is necessary to functionalize each material with polymers, enzymes, growth factors or antibiotics. To attach such molecules, we attach streptavidin to our material and take advantage of the streptavidin/biotin bond to add agents such as biotinylated antibodies. Biotin can attach to any of the four subunits of streptavidin. The <scene name='56/567309/F/1'>disappearance</scene> of biotin in the complex shows where biotin can bind to streptavidin. The <scene name='56/567309/Residues_binding/1'>tryptophan residues</scene> comprise part of the biotin-binding site of the streptavidin molecule.
</StructureSection>

In addition to using Streptavidin for attaching antibiotics, we have also start to use Streptavidin to attach Quantum Dots to materials as new sensing devices. These devices should be utilized to determine the presence of specific markers for a variety of applications including the medical field and water purification.

Molecular Playground/Streptavidin

2014-11-19T18:10:53Z

Katrina Rieger:

== The Use of Streptavidin/Biotin Complex to Functionalize Materials ==

Streptavidin is a protein best known for its ability to bind to biotin creating the strongest non-covalent interaction in nature.

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].

<StructureSection load='1MEP' size='350' side='right' caption='Structure of Streptavidin (PDB entry [[Ŏ1MEP]])' scene=''>

In the [http://www.umas.edu/schiffman Schiffman Lab], we fabricate many types of soft materials including electrospun nanofibers, hydrogels, and nanoparticles. In order to tailor each material for wound management and health care applications, it is necessary to functionalize each material with polymers, enzymes, growth factors or antibiotics. To attach such molecules, we attach streptavidin to our material and take advantage of the streptavidin/biotin bond to add agents such as biotinylated antibodies. Biotin can attach to any of the four subunits of streptavidin. The <scene name='56/567309/F/1'>disappearance</scene> of biotin in the complex shows where biotin can bind to streptavidin. The <scene name='56/567309/Residues_binding/1'>tryptophan residues</scene> comprise part of the biotin-binding site of the streptavidin molecule.
</StructureSection>

== Other uses in lab ==

In addition to using Streptavidin for attaching antibiotics, we have also start to use Streptavidin to attach Quantum Dots to materials as new sensing devices. These devices should be utilized to determine the presence of specific markers for a variety of applications including the medical field and water purification.

Molecular Playground/Streptavidin

2014-11-19T18:10:00Z

Katrina Rieger:

== The Use of Streptavidin/Biotin Complex to Functionalize Materials ==

Streptavidin is a protein best known for its ability to bind to biotin creating the strongest non-covalent interaction in nature.

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].

<StructureSection load='1MEP' size='350' side='right' caption='Structure of Streptavidin (PDB entry [[Ŏ1MEP]])' scene=''>

In the [http://www.umas.edu/schiffman Schiffman Lab], we fabricate many types of soft materials including electrospun nanofibers, hydrogels, and nanoparticles. In order to tailor each material for wound management and health care applications, it is necessary to functionalize each material with polymers, enzymes, growth factors or antibiotics. To attach such molecules, we attach streptavidin to our material and take advantage of the streptavidin/biotin bond to add agents such as biotinylated antibodies. Biotin can attach to any of the four subunits of streptavidin. The <scene name='56/567309/F/1'>disappearance</scene> of biotin in the complex shows where biotin can bind to streptavidin. The
<scene name='56/567309/Residues_binding/1'>tryptophan residues</scene> comprise part of the biotin-binding site of the streptavidin molecule.
</StructureSection>

== Other uses in lab ==

In addition to using Streptavidin for attaching antibiotics, we have also start to use Streptavidin to attach Quantum Dots to materials as new sensing devices. These devices should be utilized to determine the presence of specific markers for a variety of applications including the medical field and water purification.

Molecular Playground/Streptavidin

2014-11-19T17:53:15Z

Katrina Rieger:

== The Use of Streptavidin/Biotin Complex to Functionalize Materials ==

Streptavidin is a protein best known for its ability to bind to biotin creating the strongest non-covalent interaction in nature.

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].

<StructureSection load='1MEP' size='350' side='right' caption='Structure of Streptavidin (PDB entry [[Ŏ1MEP]])' scene=''>

In the [http://www.umas.edu/schiffman Schiffman Lab], we fabricate many types of soft materials including electrospun nanofibers, hydrogels, and nanoparticles. In order to tailor each material for wound management and health care applications, it is necessary to functionalize each material with polymers, enzymes, growth factors or antibiotics. To attach such molecules, we attach streptavidin to our material and take advantage of the streptavidin/biotin bond to add agents such as biotinylated antibodies. Biotin can attach to any of the four subunits of streptavidin. The <scene name='56/567309/F/1'>disappearance</scene> of biotin in the complex shows where biotin can bind to streptavidin.
</StructureSection>

== Other uses in lab ==

In addition to using Streptavidin for attaching antibiotics, we have also start to use Streptavidin to attach Quantum Dots to materials as new sensing devices. These devices should be utilized to determine the presence of specific markers for a variety of applications including the medical field and water purification.

KatrinaRieger/Sandbox 2

2014-11-19T17:32:16Z

Katrina Rieger:

==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 '''KatrinaRieger/Sandbox 2'''. 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 ==

== Headline text ==
In the Schiffman Lab [http://www.umass.edu Schiffman]

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/>

KatrinaRieger/Sandbox 2

2014-11-19T17:28:56Z

Katrina Rieger: 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 '''KatrinaRieger/Sandbox 2'''. 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/>

CBI Molecules

2013-11-05T19:19:40Z

Katrina Rieger:

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 2013: CBI Molecules are due 12/4/13 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 2013" or "Revised 2013". For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not).

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

Bhatia Lab

: '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin

: '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin

: '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer

[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]

: New Fall 2012!! '''[[Molecular Playground/OmpG]]''', Christina Chisholm

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

: **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau
:: Best CBI Molecule 2011

: '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu

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]

: '''[[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
(compare this to the previous version above to see what's new)

: **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani
:: Best CBI Molecule 2012

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

: New Fall 2012!! ''' [[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

: New Fall 2012!! '''[[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]

: Updated Fall 2012!! '''[[Molecular_Playground/Pcr H]]''', Fabian Romano, Carolina Morell-Pérez

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

: New Fall 2012!! '''[[Molecular Playground/Protective Antigen]]''', Jing Huang

[http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]

: Updated Fall 2012!! ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski

: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita

Knapp lab

: Updated Fall 2012!! '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas
:: Best CBI Molecule Proteopedia Page 2010

: '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky

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

: '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr
: Updated Fall 2013!! '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu, Carolyn Carr
: '''[[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/C-Raf]]''', Thuy Nguyen
: '''[[Molecular Playground/FAK]]''', Dannielle Ryman
: New Fall 2013! '''[[Molecular Playground/MMP14]]''', Lauren Jansen

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

: '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson

: '''[[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]
:New Fall 2013! '''[[Molecular Playground/Streptavidin]]''', Katrina Rieger

[https://elements.chem.umass.edu/schnarrlab/ Schnarr Lab]

: New Fall 2012!! '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey

: '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey

: '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad

[http://www.biochem.umass.edu/faculty/danny-j-schnell Schnell Lab]
: New Fall 2012!! '''[[Molecular Playground/Tic40]]''', Mine Canakci

Tew Lab

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

Thayumanavan Lab

: '''[[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

Thayumanavan & Vachet Labs

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

[http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs

: New Fall 2012!! '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin

: '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones

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

: '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li

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

: '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto
:: Best CBI Molecule Jmol scenes 2010

: '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou

:'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne

: New Fall 2012!! '''[[Molecular Playground/Ubiquitin salt bridge discussion]]''', Zhe Zhang

Other Molecules of interest

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

Other Laboratories

: '''[[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 2013: Complete steps 1-2 by 10/18, and bring your computer to the CBI Molecule Workshop on Wed 10/23 in ISB 321.

A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). 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 and look at any existing CBI Molecules from your research group. Talk with other Chalk Talk students in your research group and think about how you can make a new or improved CBI Molecule related to your group's research. Develop ideas for the scenes you wish to show. You will work learn how to make scenes during the workshop.

3. Get started working in Proteopedia by using the links at [[Help:Contents]]. 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. 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).

4. For those editing an existing CBI Molecule, start from that entry 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 do some editing of the molecule so that they each 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 2013" or "revised 2013".

==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.

CBI Molecules

2013-11-05T19:17:01Z

Katrina Rieger:

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 2013: CBI Molecules are due 12/4/13 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 2013" or "Revised 2013". For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not).

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

Bhatia Lab

: '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin

: '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin

: '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer

[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]

: New Fall 2012!! '''[[Molecular Playground/OmpG]]''', Christina Chisholm

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

: **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau
:: Best CBI Molecule 2011

: '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu

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]

: '''[[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
(compare this to the previous version above to see what's new)

: **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani
:: Best CBI Molecule 2012

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

: New Fall 2012!! ''' [[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

: New Fall 2012!! '''[[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]

: Updated Fall 2012!! '''[[Molecular_Playground/Pcr H]]''', Fabian Romano, Carolina Morell-Pérez

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

: New Fall 2012!! '''[[Molecular Playground/Protective Antigen]]''', Jing Huang

[http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]

: Updated Fall 2012!! ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski

: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita

Knapp lab

: Updated Fall 2012!! '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas
:: Best CBI Molecule Proteopedia Page 2010

: '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky

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

: '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr
: Updated Fall 2013!! '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu, Carolyn Carr
: '''[[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/C-Raf]]''', Thuy Nguyen
: '''[[Molecular Playground/FAK]]''', Dannielle Ryman
: New Fall 2013! '''[[Molecular Playground/MMP14]]''', Lauren Jansen

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

: '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson

: '''[[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

[https://elements.chem.umass.edu/schnarrlab/ Schnarr Lab]

: New Fall 2012!! '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey

: '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey

: '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad

[http://www.biochem.umass.edu/faculty/danny-j-schnell Schnell Lab]
: New Fall 2012!! '''[[Molecular Playground/Tic40]]''', Mine Canakci

Schiffman Lab
:New Fall 2013! '''[[Molecular Playground/Streptavidin]]''', Katrina Rieger

Tew Lab

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

Thayumanavan Lab

: '''[[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

Thayumanavan & Vachet Labs

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

[http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs

: New Fall 2012!! '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin

: '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones

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

: '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li

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

: '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto
:: Best CBI Molecule Jmol scenes 2010

: '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou

:'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne

: New Fall 2012!! '''[[Molecular Playground/Ubiquitin salt bridge discussion]]''', Zhe Zhang

Other Molecules of interest

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

Other Laboratories

: '''[[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 2013: Complete steps 1-2 by 10/18, and bring your computer to the CBI Molecule Workshop on Wed 10/23 in ISB 321.

A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). 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 and look at any existing CBI Molecules from your research group. Talk with other Chalk Talk students in your research group and think about how you can make a new or improved CBI Molecule related to your group's research. Develop ideas for the scenes you wish to show. You will work learn how to make scenes during the workshop.

3. Get started working in Proteopedia by using the links at [[Help:Contents]]. 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. 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).

4. For those editing an existing CBI Molecule, start from that entry 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 do some editing of the molecule so that they each 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 2013" or "revised 2013".

==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/Streptavidin

2013-11-05T19:13:56Z

Katrina Rieger:

== The Use of Streptavidin/Biotin Complex to Functionalize Materials ==

Streptavidin is a protein best known for its ability to bind to biotin creating the strongest non-covalent interaction in nature.

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].

<StructureSection load='1MEP' size='350' side='right' caption='Structure of Streptavidin (PDB entry [[Ŏ1MEP]])' scene=''>

In the Schiffman lab, we fabricate many types of soft materials including electrospun nanofibers, hydrogels, and nanoparticles. In order to tailor each material for wound management and health care applications, it is necessary to functionalize each material with polymers, enzymes, growth factors or antibiotics. To attach such molecules, we attach streptavidin to our material and take advantage of the streptavidin/biotin bond to add agents such as biotinylated antibodies. Biotin can attach to any of the four subunits of streptavidin. The <scene name='56/567309/F/1'>disappearance</scene> of biotin in the complex shows where biotin can bind to streptavidin.
</StructureSection>

Molecular Playground/Streptavidin

2013-11-05T19:13:01Z

Katrina Rieger:

== The Use of Streptavidin/Biotin Complex to Functionalize Materials ==

Streptavidin is a protein best known for its ability to bind to biotin creating the strongest non-covalent interaction in nature.

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].

<StructureSection load='1MEP' size='350' side='right' caption='Structure of Streptavidin (PDB entry [[Ŏ1MEP]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.
In the Schiffman lab, we fabricate many types of soft materials including electrospun nanofibers, hydrogels, and nanoparticles. In order to tailor each material for wound management and health care applications, it is necessary to functionalize each material with polymers, enzymes, growth factors or antibiotics. To attach such molecules, we attach streptavidin to our material and take advantage of the streptavidin/biotin bond to add agents such as biotinylated antibodies. Biotin can attach to any of the four subunits of streptavidin. The <scene name='56/567309/F/1'>disappearance</scene> of biotin in the complex shows where biotin can bind to streptavidin.
</StructureSection>

Molecular Playground/Streptavidin

2013-11-05T18:33:47Z

Katrina Rieger:

Molecular Playground/Streptavidin

2013-11-05T16:51:54Z

Katrina Rieger: /* The Use of Streptavidin to Functionalize Materials */

== The Use of Streptavidin to Functionalize Materials ==

Streptavidin is a protein best known for its ability to bind to biotin creating the strongest non-covalent interaction in nature.

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].

<StructureSection load='1MEP' size='350' side='right' caption='Structure of Streptavidin (PDB entry [[Ŏ1MEP]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

<scene name='56/567309/Biotin_attachment/1'>TextToBeDisplayed</scene>

</StructureSection>
<scene name='56/567309/Protein_1/1'>Biotin</scene>

<scene name='56/567309/F/1'>TextToBeDisplayed</scene>

Molecular Playground/Streptavidin

2013-11-05T16:48:56Z

Katrina Rieger:

== The Use of Streptavidin to Functionalize Materials ==

Streptavidin is a protein best known for its ability to bind to biotin creating the strongest non-covalent interaction in nature.

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].

<StructureSection load='1MEP' size='350' side='right' caption='Structure of Streptavidin (PDB entry [[1MEP]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

<scene name='56/567309/Biotin_attachment/1'>TextToBeDisplayed</scene>

</StructureSection>
<scene name='56/567309/Protein_1/1'>Biotin</scene>

Molecular Playground/Streptavidin

2013-11-05T14:54:06Z

Katrina Rieger:

== The Use of Streptavidin to Functionalize Materials ==

Streptavidin is a protein best known for its ability to bind to biotin creating the strongest non-covalent interaction in nature.

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].

<StructureSection load='1MEP' size='350' side='right' caption='Structure of Streptavidin (PDB entry [[1MEP]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

<scene name='56/567309/Biotin_attachment/1'>TextToBeDisplayed</scene>

</StructureSection>

Molecular Playground/Streptavidin

2013-11-05T14:26:29Z

Katrina Rieger:

== The Use of Streptavidin to Functionalize Materials ==

Streptavidin is a protein best known for its ability to bind to biotin creating the strongest non-covalent interaction in nature.

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].

<StructureSection load='1MEP' size='350' side='right' caption='Structure of Streptavidin (PDB entry [[1MEP]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

</StructureSection>

Molecular Playground/Streptavidin

2013-11-05T13:58:15Z

Katrina Rieger:

== Your Heading Here (The Use of Streptavidin to Functionalize Materials) ==

Streptavidin is a protein best known for its ability to bind to biotin creating the strongest non-covalent interaction in nature.

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].

<StructureSection load='1MEP' size='350' side='right' caption='Structure of Streptavidin (PDB entry [[1MEP]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

</StructureSection>

Molecular Playground/Streptavidin

2013-11-05T13:35:24Z

Katrina Rieger: New page: == Your Heading Here (maybe something like 'Structure') == Streptavidin is a protein best known for its ability to bind to biotin creating the strongest non-covalent interaction in nature...

== Your Heading Here (maybe something like 'Structure') ==

Streptavidin is a protein best known for its ability to bind to biotin creating the strongest non-covalent interaction in nature.

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].

<StructureSection load='1MEP' size='350' side='right' caption='Structure of Streptavidin (PDB entry [[1MEP]])' scene=''>
Anything in this section will appear adjacent to the 3D structure and will be scrollable.

</StructureSection>