Proteopedia - User contributions [en]

Molecular playground/beta 2 microglobulin

2011-12-07T18:05:53Z

Nick Borotto:

{{STRUCTURE_2f8o| PDB=2f8o | SIZE=400| SCENE='Molecular_playground/beta_2_microglobulin/Real_start_molecule/1'/ |right|CAPTION=Human beta-2 microglobulin, [[2f8o]] }}

Banner: Beta-2 microglobulin is a 12 kDa protein sub-unit of the class I major histocompatibility complex, and in dialysis patients, it forms amyloid fibrils in a condition known as dialysis-related amyloidosis (DRA).

DRA is a complication of dialysis treatment in which these fibrils build up in joints causing pain and often eventually necessitating joint replacement. beta-2-microglobulin can self-assemble into amyloid fibrils under physiological conditions in vitro when copper is present.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. Dimer formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, copper binding causes structural changes throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

<scene name='Molecular_playground/beta_2_microglobulin/Real_start_molecule/1'>TextToBeDisplayed</scene>

==3D structures of β-2 microglobulin==

[[Beta-2 microglobulin]]

==Additional Resources==
For additional information, see: [[Metabolic Disorders]]
<br />

Molecular playground/beta 2 microglobulin

2011-12-07T18:05:02Z

Nick Borotto:

{{STRUCTURE_2f8o| PDB=2f8o | SIZE=400| SCENE='Molecular_playground/beta_2_microglobulin/Real_start_molecule/1'/ |right|CAPTION=Human beta-2 microglobulin, [[2f8o]] }}

Banner: Beta-2 microglobulin is a 12 kDa protein sub-unit of the class I major histocompatibility complex, and in dialysis patients, it forms amyloid fibrils in a condition known as dialysis-related amyloidosis (DRA).

DRA is a complication of dialysis treatment in which these fibrils build up in joints causing pain and often eventually necessitating joint replacement. beta-2-microglobulin can self-assemble into amyloid fibrils under physiological conditions in vitro when copper is present.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. Dimer formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, copper binding causes structural changes throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

==3D structures of β-2 microglobulin==

[[Beta-2 microglobulin]]

==Additional Resources==
For additional information, see: [[Metabolic Disorders]]
<br />

User:Nick Borotto/Sandboxerika

2011-04-27T02:35:49Z

Nick Borotto: New page: Alginate monomers One of the CBI Molecules being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface P...

[[Image:mandg.jpg|frame|Alginate monomers]]

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].

Alginate is a natural, linear, organic polymer isolated from bacteria and algae. It has been shown to be biocompatible (non-toxic to human cells) and has thus found numerous applications as a thickener in food processing and biomaterial for tissue engineering. Owing to its unique physical properties, alginate hydrogels have been used as a scaffold material for building artificial organs, as a dressing for ulcerous wounds and as a vector for the targeted delivery of anti-cancer drugs.

[[Image:PFOB-Alginate Swatch Wet small.jpg|frame|left|Alginate hydrogel on gauze swatch]]

Alginate is composed of a random sequence of mannuronic acid (M) and guluronic acid (G). Exposure to divalent cations (e.g. calcium, barium, etc.) causes the guluronic acid residues to chemically cross-link, and the ensuing entanglements cause the alginate solution to form a hydrogel. Alginate can vary widely in length, monomeric sequence and G/M ratio depending on the source and native climate. The ratio of G/M in the chain influences the strength of alginate hydrogels and can be tuned by combining alginate obtained from different organisms and locations. The rotating molecule to the right is an example of a short chain of sodium alginate.

Molecular Playground banner: A short, linear chain of sodium alginate.
<applet size='[450,338]' frame='true' align='right'
caption='Sodium Alginate (24,000 Da)' scene='User:David_Griffin/Sandbox_1/Alginate_24000da/1'/>

User:Nick Borotto/sandbox

2010-11-09T17:33:28Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
<caption='β-2 Microglobulin'>
Banner: Beta-2 microglobulin is a 12 kDa protein sub-unit of the class I major histocompatibility complex, and in dialysis patients, it forms amyloid fibrils in a condition known as dialysis-related amyloidosis (DRA).
alkfa;jf;akjf;a;fkj;ajf

<scene name='User:Nick_Borotto/sandbox/Blah_blah/1'>example 1</scene>

CBI Molecules

2010-11-09T00:30:12Z

Nick Borotto:

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 (which is alphabetical by CBI research mentor); follow the instructions below the list.

Bhatia Lab
: '''[[Molecular Playground/Alginate]]''', David Griffin

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

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

Forbes Lab

: '''[[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

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

: '''[[Molecular Playground/Caspase-7 Dynamics]]''', Daniel Seeman

: '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber

: '''[[Molecular Playground/Caspase-6]]''', Elih Velazquez

: '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls

Hebert Lab

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

Kaltashov Lab

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

Knapp lab

:'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin
:: Best CBI Molecule Proteopedia Page 2010

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

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

: '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia

[http://robertsgroup.ecs.umass.edu/ Roberts Lab]

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

: '''[[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

Schnarr Lab

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

Thayumanavan Lab

: '''[[Molecular Playground/Lysozime ]]''', 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

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

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

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

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]

Instructions:

'''Congratulations to the prize-winning CBI molecules noted above! These also provide great examples to follow. Another prize for best CBI Molecules page and/or scene will be awarded in spring 2011!'''

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.

CBI Molecules

2010-11-09T00:29:12Z

Nick Borotto:

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 (which is alphabetical by CBI research mentor); follow the instructions below the list.

Bhatia Lab
: '''[[Molecular Playground/Alginate]]''', David Griffin

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

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

Forbes Lab

: '''[[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

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

: '''[[Molecular Playground/Caspase-7 Dynamics]]''', Daniel Seeman

: '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber

: '''[[Molecular Playground/Caspase-6]]''', Elih Velazquez

: '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls

Hebert Lab

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

Kaltashov Lab

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

Knapp lab

:'''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin
:: Best CBI Molecule Proteopedia Page 2010

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

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

: '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia

[http://robertsgroup.ecs.umass.edu/ Roberts Lab]

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

: '''[[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

Schnarr Lab

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

Thayumanavan Lab

: '''[[Molecular Playground/Lysozime ]]''', 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

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

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

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

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]

Instructions:

'''Congratulations to the prize-winning CBI molecules noted above! These also provide great examples to follow. Another prize for best CBI Molecules page and/or scene will be awarded in spring 2011!'''

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.

User:Nick Borotto/sandbox

2010-11-09T00:18:06Z

Nick Borotto:

User:Nick Borotto/sandbox

2010-11-08T23:56:00Z

Nick Borotto:

User:Nick Borotto/sandbox

2010-11-08T23:55:12Z

Nick Borotto: New page: <applet size='[450,338]' frame='true' align='right' <caption='β-2 Microglobulin'>

Molecular playground/beta 2 microglobulin

2010-05-12T17:42:41Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
<caption='β-2 Microglobulin' scene='User:Nick_Borotto/Sandbox_1/Basic_view/4'/>
Banner: Beta-2 microglobulin is a 12 kDa protein sub-unit of the class I major histocompatibility complex, and in dialysis patients, it forms amyloid fibrils in a condition known as dialysis-related amyloidosis (DRA).

DRA is a complication of dialysis treatment in which these fibrils build up in joints causing pain and often eventually necessitating joint replacement. beta-2-microglobulin can self-assemble into amyloid fibrils under physiological conditions in vitro when copper is present.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. Dimer formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, copper binding causes structural changes throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-05-02T02:33:02Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
<caption='β-2 Microglobulin' scene='User:Nick_Borotto/Sandbox_1/Basic_view/4'/>
Banner: Beta-2 microglobulin is a 12 kDa protein sub-unit of the class I major histocompatibility complex, and in dialysis patients, it forms amyloid fibrils in a condition known as dialysis-related amyloidosis (DRA).

DRA is a complication of dialysis treatment in which these fibrils build up in joints causing pain and often eventually necessitating joint replacement. ?-2-microglobulin can self-assemble into amyloid fibrils under physiological conditions in vitro when copper is present.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. Dimer formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, copper binding causes structural changes throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T20:59:43Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
<caption='β-2 Microglobulin' scene='User:Nick_Borotto/Sandbox_1/Basic_view/4'/>
Banner: Beta-2 microglobulin the protein associated with the formation of amyloid fibrils in DRA, a kidney disease.

β-2 Microglobulin is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T20:57:33Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
<caption='β-2 Microglobulin' scene='User:Nick_Borotto/Sandbox_1/Basic_view/4'/>
Beta-2 microglobulin the protein associated with the formation of amyloid fibrils in DRA, a kidney disease.

β-2 Microglobulin is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

CBI Molecules

2010-04-30T20:48:48Z

Nick Borotto:

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]]''', Rohan Patil, [http://robertsgroup.ecs.umass.edu/ Roberts Research Group]

'''[[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]]''', 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

'''[[Molecular Playground/Alginate]]''', 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

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

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

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.

CBI Molecules

2010-04-30T20:47:03Z

Nick Borotto:

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]]''', Rohan Patil, [http://robertsgroup.ecs.umass.edu/ Roberts Research Group]

'''[[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]]''', 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

'''[[Molecular Playground/Alginate]]''', 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

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

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

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.

User:Nick Borotto/Sandbox 1

2010-04-30T20:43:56Z

Nick Borotto: User:Nick Borotto/Sandbox 1 moved to Molecular playground/beta 2 microglobulin: Finished and ready for publication

#REDIRECT [[Molecular playground/beta 2 microglobulin]]

Molecular playground/beta 2 microglobulin

2010-04-30T20:43:56Z

Nick Borotto: User:Nick Borotto/Sandbox 1 moved to Molecular playground/beta 2 microglobulin: Finished and ready for publication

<applet size='[450,338]' frame='true' align='right'
<caption='β-2 Microglobulin' scene='User:Nick_Borotto/Sandbox_1/Basic_view/4'/>

β-2 Microglobulin is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T16:05:08Z

Nick Borotto:

Molecular playground/beta 2 microglobulin

2010-04-30T16:00:47Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
<caption='β-2 Microglobulin' scene='User:Nick_Borotto/Sandbox_1/Basic_view/4'>

β-2 Microglobulin is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T16:00:13Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
<caption='β-2 Microglobulin' scene='User:Nick_Borotto/Sandbox_1/Basic_view/4'>
β-2 Microglobulin is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:59:20Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
<caption='β-2 Microglobulin' scene='User:Nick_Borotto/Sandbox_1/Basic_view/4' scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:58:04Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
<caption='β-2 Microglobulin' scene='User:Nick_Borotto/Sandbox_1/Basic_view/4'
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:56:51Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'>

<caption='β-2 Microglobulin' scene='User:Nick_Borotto/Sandbox_1/Basic_view/4'>

<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:55:56Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'>
<caption='β-2 Microglobulin' scene='User:Nick_Borotto/Sandbox_1/Basic_view/4'>

<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:55:17Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
<caption='β-2 Microglobulin' scene='User:Nick_Borotto/Sandbox_1/Basic_view/4'>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:53:41Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
<SCENE='User:Nick_Borotto/Sandbox_1/Basic_view/4'>
<caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:52:42Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
<SCENE=User:Nick_Borotto/Sandbox_1/Basic_view/4>
<caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:52:00Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
SCENE=User:Nick_Borotto/Sandbox_1/Basic_view/4
<caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:49:07Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
{{STRUCTURE_2f8o| PDB=2f8o | SCENE=User:Nick_Borotto/Sandbox_1/Basic_view/4 }}
<caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:46:54Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
{{STRUCTURE_User:Nick_Borotto| PDB=2f8o | SCENE=User:Nick_Borotto/Sandbox_1/Basic_view/4 }}
<caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:43:10Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
{{STRUCTURE_2f8o| PDB=2f8o | SCENE=2f8o/Sandbox_1/Basic_view/4 }}
<caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:41:34Z

Nick Borotto:

Molecular playground/beta 2 microglobulin

2010-04-30T15:38:24Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
{{STRUCTURE_User:Nick_Borotto| User:Nick_Borotto | SCENE=User:Nick_Borotto/Sandbox_1/Basic_view/4 }}
<caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:36:43Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
{{STRUCTURE_User:Nick_Borotto| User:Nick_Borotto | SCENE=Sandbox_1/Basic_view/4 }}
<caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:34:11Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
{{STRUCTURE_'User:Nick_Borotto| 'User:Nick_Borotto | SCENE=Sandbox_1/Basic_view/4 }}
<caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:33:03Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
{{STRUCTURE_User:Nick_Borotto| Nick_Borotto | SCENE=Sandbox_1/Basic_view/4 }}
<caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:31:37Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
{{STRUCTURE_Nick_Borotto| Nick_Borotto | SCENE=Sandbox_1/Basic_view/4 }}
<caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:26:19Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
{{scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'}}
<caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T15:23:42Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>
caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T05:19:40Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'

caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/4'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/4'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T05:16:15Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'

caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/4'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/3'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/3'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/3'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T04:55:39Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'

caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/3'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/2'>Dimer</scene>. This structures formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/2'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/2'>planes</scene>. These planes interact in an antiparallel fashion forming the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T04:46:53Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'

caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/3'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/2'>Dimer</scene>. This dimer formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/2'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_interface/1'>planes</scene>. These planes interact in an antiparallel fashion to form the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T04:25:37Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'

caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/3'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/2'>Dimer</scene>. This dimer formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/2'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new planes. These planes interact in an antiparallel fashion to form the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T04:12:50Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'

caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/3'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/2'>Dimer</scene>. This dimer formation is initiated when copper binds near the <scene name='User:Nick_Borotto/Sandbox_1/Metal_coordination_site/1'>N-terminus</scene>, this binding causes structural shifts throughout the protein, creating two new planes. These planes interact in an antiparallel fashion to form the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T04:02:52Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'

caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/3'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

Fibril assembly begins with the formation of a <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/1'>Dimer</scene>. This dimer formation is initiated when copper binds near the N-terminus, this binding causes structural shifts throughout the protein, creating two new planes. These planes interact in an antiparallel fashion to form the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T03:57:22Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'

caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/3'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

The proposed mechanism for <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/1'>Dimer</scene> formation is that the copper binds near the N-terminus of the protein, this binding causes structural shifts throughout, creating two new planes. These planes interact in an antiparallel fashion to form the dimer.

Molecular playground/beta 2 microglobulin

2010-04-30T03:52:49Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'

caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/3'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

The proposed mechanism for <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/1'>Dimer</scene> formation is that the copper binds near the N-terminal of the protein, this binding causes structural shifts throughout the protein creating two new planes that interact favorably.

Molecular playground/beta 2 microglobulin

2010-04-30T03:52:21Z

Nick Borotto:

<applet size='[450,338]' frame='true' align='right'

caption='β-2 Microglobulin' scene='Basic_view'/>
<scene name='User:Nick_Borotto/Sandbox_1/Basic_view/3'>β-2 Microglobulin</scene> is a 12kd protein that self-assembles into amyloid fibrils in the presence of copper. This reaction is considered a likely cause for dialysis related amyloidosis; a disease where these fibrils build up in joints causing pain and eventually necessitating joint replacement.

The proposed mechanism for <scene name='User:Nick_Borotto/Sandbox_1/Proposed_dimer_structure/1'>Dimer</scene>
formation is that the copper binds near the N-terminal of the protein, this binding causes structural shifts throughout the protein creating two new planes that interact favorably.

File:Dimer.pdb

2010-04-30T03:30:44Z

Nick Borotto:

Proposed Dimer structure of B2m