Proteopedia - User contributions [en]

User:David Solfiell/sandbox 1

2011-12-07T17:49:07Z

David Solfiell: New page: {{STRUCTURE_1xtc| PDB=1xtc | SIZE=500| SCENE=Cholera_toxin/Cv/1 |right|CAPTION=Cholera toxin 1xtc }} Cholera toxin (CTX) from the bacterium ''Vibrio cholerae'' is an oligomeric...

{{STRUCTURE_1xtc| PDB=1xtc | SIZE=500| SCENE=Cholera_toxin/Cv/1 |right|CAPTION=Cholera toxin [[1xtc]] }}

[[Cholera toxin]] (CTX) from the bacterium ''Vibrio cholerae'' is an oligomeric complex of an enzymatic subunit (chain A) and 5 copies of chain B which bind to the cell surface. The enzymatic subunit has a globular domain (CTA1) and a long helical domain (CTA2). Once the CTX binds to the cell surface, it is internalized, and its CTA1 domain binds to ADP-ribosylation factor 6 (Arf6) enabling its catalytic activity. The images at the left and at the right correspond to the crystal structure of cholera toxin ([[1xtc]]).

{{TOC limit|limit=2}}

== 3D Structures of Cholera toxin ==

''Updated November 2011''

=== CTX ===

[[1xtc]] - CTX

=== CTX A subunit ===

[[2a5d]], [[2a5g]] – CTX A subunit+hArf6+GTP – human 
[[2a5f]] - CTX A subunit+hArf6+GTP+NAD 
[[1s5b]], [[1s5c]], [[1s5d]], [[1s5e]], [[1s5f]] - CTX A subunit (mutant)

=== CTX B subunits ===

[[1fgb]] - CTX B subunits 
[[1g8z]] , [[1chp]], [[1chq]] - CTX B subunits (mutant) 
[[1rcv]], [[1rd9]], [[1rdp]], [[1rf2]], [[1pzi]], [[1pzj]], [[1pzk]], [[1efi]], [[1eef]], [[1djr]], [[1eei]] – CTX B subunits+ galactoside derivatives 
[[1llr]], [[1jqy]], [[1jr0]], [[1fd7]], [[1md2]] - CTX B subunits+BMSC derivatives 
[[1eef]] - CTX B subunits+PEPG 
[[3chb]], [[2chb]] - CTX B subunits+pentasaccharide 
[[1ct1]] - CTX B subunits (mutant)+pentasaccharide 
[[3efx]] – CTX B/heat-labile enterotoxin B chain 
[[1tet]] – CTX peptide 3+FAB light and heavy chains - mouse

[[Category:Topic Page]]

Molecular Playground/Targeting Peptide

2010-05-05T19:47:58Z

David Solfiell:

<applet scene='Molecular_Playground/Targeting_Peptide/Dark_background_cartoon/2' load='1l5g' size='300' frame='true' align='right' caption='The RGD peptide is a popular peptide targeting motif used in experimental, nanoscale drug delivery vehicles (such as liposomes, micelles, dendrimers, nanoparticles, etc.) The RGD peptide binds specifically with cell adhesion molecules on the cell surface. Upregulation/overexpression of cell surface markers (such as this integrin) on certain kinds of cancer cells leads to selective accumulation of nanomaterial drug carriers within cancerous tissues, and targeted delivery of their payloads (drugs, contrast agents for imaging, etc.). Shown is the cyclic analogue of the RGD peptide complexed with alpha 5 Integrin.' />

== Targeted Drug Delivery ==

Drugs are exogenous compounds administered to organisms to generate therapeutic effects. However, drugs exhibit complex and, often, unintended side effects. Targeted drug delivery systems can ameliorate the problem of drug toxicity by concentrating drugs exclusively at sites of their intended activity. Furthermore, targeted drug vehicles can deliver molecules (DNA/RNA) with known therapeutic value, but which, by themselves, are incapable of reaching tissues and cells in their therapeutic form. Aided by the vast knowledge of biological systems made available over the last fifty years by discoveries in the fields of Molecular Biology, Genomics, Biochemistry, and Physiology, advances in Materials Science hold great promise in bringing about a pharmacological revolution.

I am very grateful to NIH Chemistry-Biology Interface (CBI) Training Program, whose funding has made this work possible.

[http://www.umass.edu/cbi/ Chemistry-Biology Interface Program at The University of Massachusetts, Amherst]
[http://www.umass.edu/rotellogroup/ Rotello Group Website]

[[Image:DavesNanoparticle.jpg|thumb|left|Schematic representation of a 2 nm Au nanoparticle delivery vehicle, functioanlized with an RGD peptide (image by David Solfiell)]]

Molecular Playground/Targeting Peptide

2010-05-05T19:44:22Z

David Solfiell:

<applet scene='Molecular_Playground/Targeting_Peptide/Dark_background_cartoon/2' load='1l5g' size='300' frame='true' align='right' caption='The RGD peptide is a popular peptide targeting motif used in experimental, nanoscale drug delivery vehicles (such as liposomes, micelles, dendrimers, nanoparticles, etc.) The RGD peptide binds specifically with cell adhesion molecules on the cell surface. Upregulation/overexpression of cell surface markers (such as this integrin) on certain kinds of cancer cells leads to selective accumulation of nanomaterial drug carriers within cancerous tissues, and targeted delivery of their payloads (drugs, contrast agents for imaging, etc.). Shown is the cyclic analogue of the RGD peptide complexed with alpha 5 Integrin.' />

== Targeted Drug Delivery ==

Drugs are exogenous compounds administered to organisms to generate therapeutic effects. However, drugs exhibit complex and, often, unintended side effects. Targeted drug delivery systems can ameliorate the problem of drug toxicity by concentrating drugs exclusively at sites of their intended activity. Furthermore, targeted drug vehicles can deliver molecules (DNA/RNA) with known therapeutic value, but which, by themselves, are incapable of reaching tissues and cells in their therapeutic form. Aided by the vast knowledge of biological systems made available over the last fifty years by discoveries in the fields of Molecular Biology, Genomics, Biochemistry, and Physiology, advances in Materials Science hold great promise in bringing about a pharmacological revolution.

[http://www.umass.edu/cbi/ Chemistry-Biology Interface Program at The University of Massachusetts, Amherst]
[http://www.umass.edu/rotellogroup/ Rotello Group Website]

[[Image:DavesNanoparticle.jpg|thumb|left|Schematic representation of a 2 nm Au nanoparticle delivery vehicle, functioanlized with an RGD peptide (image by David Solfiell)]]

Molecular Playground/Targeting Peptide

2010-05-05T19:37:50Z

David Solfiell:

<applet scene='Molecular_Playground/Targeting_Peptide/Dark_background_cartoon/2' load='1l5g' size='300' frame='true' align='right' caption='The RGD peptide is a popular peptide targeting motif used in experimental, nanoscale drug delivery vehicles (such as liposomes, micelles, dendrimers, nanoparticles, etc.) The RGD peptide binds specifically with cell adhesion molecules on the cell surface. Upregulation/overexpression of cell surface markers (such as this integrin) on certain kinds of cancer cells leads to selective accumulation of nanomaterial drug carriers within cancerous tissues, and targeted delivery of their payloads (drugs, contrast agents for imaging, etc.). Shown is the cyclic analogue of the RGD peptide complexed with alpha 5 Integrin.' />

== Targeted Drug Delivery ==

Drugs are exogenous compounds administered to organisms to generate therapeutic effects. However, drugs exhibit complex and, often, unintended side effects. Targeted drug delivery systems can ameliorate the problem of drug toxicity by concentrating drugs exclusively at sites of their intended activity. Furthermore, targeted drug vehicles can deliver molecules (DNA/RNA) with known therapeutic value, but which, by themselves, are incapable of reaching tissues and cells in their therapeutic form. Aided by the vast knowledge of biological systems made available over the last fifty years by discoveries in the fields of Molecular Biology, Genomics, Biochemistry, and Physiology, advances in Materials Science hold great promise in bringing about a pharmacological revolution.

[http://www.umass.edu/rotellogroup/ Rotello Group Website]

[[Image:DavesNanoparticle.jpg|thumb|left|Schematic representation of a 2 nm Au nanoparticle delivery vehicle, functioanlized with an RGD peptide (image by David Solfiell)]]

Molecular Playground/Targeting Peptide

2010-05-05T19:36:04Z

David Solfiell: /* Targeted Drug Delivery */

<applet scene='Molecular_Playground/Targeting_Peptide/Dark_background_cartoon/2' load='1l5g' size='300' frame='true' align='right' caption='The RGD peptide is a popular peptide targeting motif used in experimental, nanoscale drug delivery vehicles (such as liposomes, micelles, dendrimers, nanoparticles, etc.) The RGD peptide binds specifically with cell adhesion molecules on the cell surface. Upregulation/overexpression of cell surface markers such as this integrin on certain kinds of cancer cells leads to selective accumulation of nanomaterial drug carriers within cancerous tissues, and targeted delivery of their payloads (drugs, contrast agents for imaging, etc.). Shown is the cyclic analogue of the RGD peptide complexed with alpha 5 Integrin.' />

== Targeted Drug Delivery ==

Drugs are exogenous compounds administered to organisms to generate therapeutic effects. However, drugs exhibit complex and, often, unintended side effects. Targeted drug delivery systems can ameliorate the problem of drug toxicity by concentrating drugs exclusively at sites of their intended activity. Furthermore, targeted drug vehicles can deliver molecules (DNA/RNA) with known therapeutic value, but which, by themselves, are incapable of reaching tissues and cells in their therapeutic form. Aided by the vast knowledge of biological systems made available over the last fifty years by discoveries in the fields of Molecular Biology, Genomics, Biochemistry, and Physiology, advances in Materials Science hold great promise in bringing about a pharmacological revolution.

[http://www.umass.edu/rotellogroup/ Rotello Group Website]

[[Image:DavesNanoparticle.jpg|thumb|left|Schematic representation of a 2 nm Au nanoparticle delivery vehicle, functioanlized with an RGD peptide (image by David Solfiell)]]

Molecular Playground/Targeting Peptide

2010-05-05T19:33:45Z

David Solfiell:

<applet scene='Molecular_Playground/Targeting_Peptide/Dark_background_cartoon/2' load='1l5g' size='300' frame='true' align='right' caption='The RGD peptide is a popular peptide targeting motif used in experimental, nanoscale drug delivery vehicles (such as liposomes, micelles, dendrimers, nanoparticles, etc.) The RGD peptide binds specifically with cell adhesion molecules on the cell surface. Upregulation/overexpression of cell surface markers such as this integrin on certain kinds of cancer cells leads to selective accumulation of nanomaterial drug carriers within cancerous tissues, and targeted delivery of their payloads (drugs, contrast agents for imaging, etc.). Shown is the cyclic analogue of the RGD peptide complexed with alpha 5 Integrin.' />

== Targeted Drug Delivery ==

Drugs are exogenous compounds administered to organisms to generate therapeutic effects. However, drugs exhibit complex and, often, unintended side effects. Targeted drug delivery systems can ameliorate the problem of drug toxicity by concentrating drugs exclusively at sites of their intended activity. Furthermore, targeted drug vehicles can deliver molecules with known therapeutic value, but which, by themselves (DNA/RNA), are incapable of reaching the tissues and cells in their therapeutic form. Aided by the vast knowledge of biological systems made available by Molecular Biology, Genomics, Biochemistry, and Physiology, advances in Materials Science hold great promise in bringing about a pharmacological revolution.

[http://www.umass.edu/rotellogroup/ Rotello Group Website]

[[Image:DavesNanoparticle.jpg|thumb|left|Schematic representation of a 2 nm Au nanoparticle delivery vehicle, functioanlized with an RGD peptide (image by David Solfiell)]]

Molecular Playground/Targeting Peptide

2010-05-05T18:31:55Z

David Solfiell:

File:DavesNanoparticle.jpg

2010-05-05T18:30:45Z

David Solfiell:

== Summary ==
Schematic representation of a 2 nm Au nanoparticle delivery vehicle, functioanlized with an RGD peptide (image by David Solfiell)
== Licensing ==
{{self|cc-by-sa-3.0}}

Molecular Playground/Targeting Peptide

2010-05-05T18:28:35Z

David Solfiell:

Molecular Playground/Targeting Peptide

2010-05-05T18:25:36Z

David Solfiell:

Molecular Playground/Targeting Peptide

2010-05-05T18:24:53Z

David Solfiell:

File:DavesNanoparticle.jpg

2010-05-05T18:22:20Z

David Solfiell: Schematic representation of a 2 nm Au nanoparticle delivery vehicle, functioanlized with an RGD peptide

== Summary ==
Schematic representation of a 2 nm Au nanoparticle delivery vehicle, functioanlized with an RGD peptide
== Licensing ==
{{self|cc-by-sa-3.0}}

Molecular Playground/Targeting Peptide

2010-05-05T18:11:41Z

David Solfiell:

Molecular Playground/Targeting Peptide

2010-05-05T18:07:55Z

David Solfiell:

Molecular Playground/Targeting Peptide

2010-05-05T18:02:40Z

David Solfiell:

Molecular Playground/Targeting Peptide

2010-05-05T17:32:42Z

David Solfiell:

Molecular Playground/Targeting Peptide

2010-05-05T17:30:57Z

David Solfiell:

Molecular Playground/Targeting Peptide

2010-05-05T17:30:25Z

David Solfiell:

Molecular Playground/Targeting Peptide

2010-05-05T17:17:19Z

David Solfiell: New page: <applet scene='Molecular_Playground/David's_temporary_page/Temp_scene/1' load='1l5g' size='300' frame='true' align='right' caption='The RGD peptide is a popular peptide targeting motif use...

CBI Molecules

2010-05-05T17:15:00Z

David Solfiell:

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]. Follow the links below to read nontechnical descriptions in Proteopedia.

UMass CBI Members, add your molecules to the list; follow the instructions below the list.

'''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', [http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] laboratories

'''[[6-deoxyerythronolide B synthase (DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Schnarr lab (Tsung-Yi Lin)

'''[[Molecular Playground/Lysozime ]]''', Daniella Gonzalez, Thayumanavan Research Group

'''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura, Thayumanavan Research group

'''[[Molecular Playground/TRAIL]]''', Charley Swofford

'''[[Molecular Playground/Taxol]]''', [http://robertsgroup.ecs.umass.edu/ Roberts Research Group] (Rohan Patil)

'''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon, [http://www.biochem.umass.edu/garman/index.html Garman Research Group]

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

'''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Rotello lab (Daniel Moyano-Marino)

'''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Thai lab (Krishna Reddy Raghupathi)

'''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Thai lab (Rami Rajasekar Reddy)

'''[[Molecular_Playground/ERMan1]]''', Johan Sunryd

'''[[Molecular Playground/Insulin]]''', [http://robertsgroup.ecs.umass.edu/ Roberts Research Group] (Whitney Stoppel)

'''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia ([http://www.chem.umass.edu/~cmartin/ Martin] lab)

'''[[Molecular Playground/Human PPCA]]''', Nilima Kolli ([http://www.biochem.umass.edu/garman/index.html Garman Lab])

'''[[Molecular Playground/Alginate]]''', Bhatia Research Group (David Griffin)

'''[[Molecular Playground/Glutamate Receptor]]''', [http://chamberslab.com/wp/ Chambers Lab] (Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano)

'''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado (Thai Lab)

'''[[Molecular Playground/FIH]]''', Knapp Lab, (Cornelius Taabazuing, Breanne Holmes, John Hangasky)

'''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Thai lab (Jiaming Zhuang)

'''[[Molecular Playground/Pancreatic Lipase]]''', [http://www.umass.edu/rotellogroup/ Rotello lab] (Rui Tang)

'''[[Molecular Playground/Trypsin]]''', Thai-Vachet lab (Murage, Gladys)

'''[[Molecular playground/beta 2 microglobulin]]''', Vachet lab (Nick)

''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Thai lab (Jing Guo)

'''[[Molecular playground/Chymotrypsin]]''', Rotello lab (Brad)

'''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab] (Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy)

'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Knapp lab (Cristina Martin)

'''[[Molecular Playground/Glutathione Reductase]]''', Thai Lab (Reuben Chacko)

'''[[Molecular Playground/Velaglucerase]]''', Adriana Kita, Kaltashov Lab

'''[[Molecular Playground/Caspase-7 Dynamics]]''', Hardy Lab (Daniel Seeman)

'''[[Molecular Playground/Caspase-9 Regulation]]''', Hardy Lab (Kristen Huber)

'''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Hardy Lab[http://people.chem.umass.edu/jhardy/] (Samantha Nicholls)

'''[[Molecular Playground/Targeting Peptide]]''', Rotello Lab (David Solfiell)

Instructions:

'''We plan to award a prize for the best CBI Molecules page and/or scene!'''

Choose a molecule that is part of your research project.

1. If you don't already have one, request a Proteopedia account and log in. If you are new to Proteopedia, click Help in the navigation box on the left to get started.

2. Make yourself a sandbox page in which you will develop your CBI Molecule scene and description (Enter "User:your name/sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. See example [[User:Lynmarie K Thompson/Sandbox 1]]).

3. Follow the format of the sample CBI molecule page [[Molecular Playground/Bacterial Chemotaxis Receptors]]. Easiest way to do this is to copy this page (in editing mode), paste it into your sandbox page, keep the first paragraph about CBI molecules, and then edit to describe and display your molecule. Your goal is to make this an interesting, nontechnical description of the molecule. If multiple people in one group work on the same molecule, you can each make different scenes for the same CBI molecule and each describe them on the same proteopedia page. Talk with each other about your plans so you are not duplicating efforts.

4. Create an attractive scene for your molecule: use the scene authoring tools in the edit mode to create the view you like, then copy the wiki text into your window.

5. Follow instructions at [[Molecular Playground/Procedures]] as well. But don't "capture the state script for your scene"; that will be done for you (see #7). With your chosen Jmol scene for the Molecular Playground, specify a "banner", which will be projected with the molecule on the Molecular Playground. This should be a short, one-line headline for your scene that includes the name of the molecule and what is important about the scene or the molecule. Remember to design this for the general public, including non-scientists. My example is: "Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment."

6. When you are happy with your sandbox page, make yourself a permanent Proteopedia page, which will be editable by others. Enter "Molecular Playground/your molecule" (omit quotes) in the search box, then follow the instructions to create a new page with this title. Copy the content of your sandbox to this new page.

7. When you have finished the final version of your page and scene, edit this CBI Molecules page to add a listing and link for your molecule, following the "Bacterial chemotaxis receptors" example above. Please list your lab group, with your name in parentheses. That way more than one name can be associated with a Molecular Playground page (if there are several students on the Molecular Playground page, please indicate your scene with your initials). It would be great to link the lab names to web pages too. Once this link is there, your scene is considered done, and someone will capture the state script for display on the Molecular Playground.