Proteopedia - User contributions [en]

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-19T23:50:13Z

Zhe Zhang:

== How native structure is preserved in gas phase ==
{{STRUCTURE_2pea| PDB=2pea | SCENE= }}

This page is going to talk about a gas phase or mass spectrum idea about this. From the perspective of solution phase, we can know the salt bridges stay between E51-R54, R54-D58, E18-K29, D21-K29 and K27-D52. And there is one opinion that most protein when electrosprayed into gas phase from its native solution, the structure features will retain mostly. And electron based dissociation method, like ECD or ETD, can break the protein back bonds instead of disrupting its structure.

Once we have one electron based dissociation pattern of ubiquitin, which in real world does not either break any salt bridge above. For reference, ubiquitin's sequence is below:

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

From this particular sequence, there are 11 D and Es as well as 11 R and Ks. Imagine how many possibile salt bridge patterns if all those residues formed randomly. Based on the electron dissociation data, we can eliminate those pattern inside which salt bridges are broken. so, we can get the number of possible or reasonable patterns. Here it is, only 1 percent of the millions of possibilities go into the team of "preserving the salt bridge". This result also supports the statement that protein can stay native when ESIed into gas phase which is so important aspect for analyst who works on mass spectrometry.

This discussion utilized JAVA by algorithm of premutation and combination. Premutation and combination generate the random pattern which is passed into the mass spectrom result to tell how much salt bridge breaking it happens.All the ideas, coding and running program are acchieved in Nov. 2012 by Zhe Zhang in Richard W. Vachet's lab. For further information or detail, please contact zhez@chem.umass.edu.
</StructureSection>.

To see the ubiquitin PDB of 2jzz please click <scene name='Molecular_Playground/Ubiquitin_salt_bridge_discussion/Ubiquitin_basic/3'>ubiquitin</scene>.

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-19T23:49:43Z

Zhe Zhang:

== How native structure is preserved in gas phase ==
{{STRUCTURE_2pea| PDB=2pea | SCENE= }}

This page is going to talk about a gas phase or mass spectrum idea about this. From the perspective of solution phase, we can know the salt bridges stay between E51-R54, R54-D58, E18-K29, D21-K29 and K27-D52. And there is one opinion that most protein when electrosprayed into gas phase from its native solution, the structure features will retain mostly. And electron based dissociation method, like ECD or ETD, can break the protein back bonds instead of disrupting its structure.

Once we have one electron based dissociation pattern of ubiquitin, which in real world does not either break any salt bridge above. For reference, ubiquitin's sequence is below:

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

From this particular sequence, there are 11 D and Es as well as 11 R and Ks. Imagine how many possibile salt bridge patterns if all those residues formed randomly. Based on the electron dissociation data, we can eliminate those pattern inside which salt bridges are broken. so, we can get the number of possible or reasonable patterns. Here it is, only 1 percent of the millions of possibilities go into the team of "preserving the salt bridge". This result also supports the statement that protein can stay native when ESIed into gas phase which is so important aspect for analyst who works on mass spectrometry.

This discussion utilized JAVA by algorithm of premutation and combination. Premutation and combination generate the random pattern which is passed into the mass spectrom result to tell how much salt bridge breaking it happens.All the ideas, coding and running program are acchieved in Nov. 2012 by Zhe Zhang in Richard W. Vachet's lab. For further information or detail, please contact zhez@chem.umass.edu.
</StructureSection>
To see the ubiquitin PDB of 2jzz please click <scene name='Molecular_Playground/Ubiquitin_salt_bridge_discussion/Ubiquitin_basic/3'>ubiquitin</scene>

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-19T23:48:27Z

Zhe Zhang:

== How native structure is preserved in gas phase ==
{{STRUCTURE_2pea| PDB=2pea | SCENE= }}

This page is going to talk about a gas phase or mass spectrum idea about this. From the perspective of solution phase, we can know the salt bridges stay between E51-R54, R54-D58, E18-K29, D21-K29 and K27-D52. And there is one opinion that most protein when electrosprayed into gas phase from its native solution, the structure features will retain mostly. And electron based dissociation method, like ECD or ETD, can break the protein back bonds instead of disrupting its structure.

Once we have one electron based dissociation pattern of ubiquitin, which in real world does not either break any salt bridge above. For reference, ubiquitin's sequence is below:

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

From this particular sequence, there are 11 D and Es as well as 11 R and Ks. Imagine how many possibile salt bridge patterns if all those residues formed randomly. Based on the electron dissociation data, we can eliminate those pattern inside which salt bridges are broken. so, we can get the number of possible or reasonable patterns. Here it is, only 1 percent of the millions of possibilities go into the team of "preserving the salt bridge". This result also supports the statement that protein can stay native when ESIed into gas phase which is so important aspect for analyst who works on mass spectrometry.

This discussion utilized JAVA by algorithm of premutation and combination. Premutation and combination generate the random pattern which is passed into the mass spectrom result to tell how much salt bridge breaking it happens.All the ideas, coding and running program are acchieved in Nov. 2012 by Zhe Zhang in Richard W. Vachet's lab. For further information or detail, please contact zhez@chem.umass.edu.
</StructureSection>
<scene name='Molecular_Playground/Ubiquitin_salt_bridge_discussion/Ubiquitin_basic/3'>TextToBeDisplayed</scene>

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-17T19:54:59Z

Zhe Zhang:

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-17T19:53:17Z

Zhe Zhang:

== How native structure is preserved in gas phase ==
{{STRUCTURE_2pea| PDB=2pea | SCENE= }}

This page is going to talk about a gas phase or mass spectrum idea about this. From the perspective of solution phase, we can know the salt bridges stay between E51-R54, R54-D58, E18-K29, D21-K29 and K27-D52. And there is one opinion that most protein when electrosprayed into gas phase from its native solution, the structure features will retain mostly. And electron based dissociation method, like ECD or ETD, can break the protein back bonds instead of disrupting its structure.

Once we have one electron based dissociation pattern of ubiquitin, which in real world does not either break any salt bridge above. For reference, ubiquitin's sequence is below:

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

From this particular sequence, there are 11 D and Es as well as 11 R and Ks. Imagine how many possibile salt bridge patterns if all those residues formed randomly. Based on the electron dissociation data, we can eliminate those pattern inside which salt bridges are broken. so, we can get the number of possible or reasonable patterns. Here it is, only 1 percent of the millions of possibilities go into the team of "preserving the salt bridge". This result also supports the statement that protein can stay native when ESIed into gas phase which is so important aspect for analyst who works on mass spectrometry.

This discussion facilitates JAVA by algorithm of premutation and combination. Premutation and combination generate the random pattern which is passed into the mass spectrom result to tell how much salt bridge breaking it happens.All the ideas, coding and running program are acchieved in Nov. 2012 by Zhe Zhang in Richard W. Vachet's lab. For further information or detail, please contact zhez@chem.umass.edu.
</StructureSection>

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-17T19:52:59Z

Zhe Zhang:

== How native structure is preserved in gas phase ==
{{STRUCTURE_2pea| PDB=2pea | SCENE= }}

This page is going to talk about a gas phase or mass spectrum idea about this. From the perspective of solution phase, we can know the salt bridges stay between E51-R54, R54-D58, E18-K29, D21-K29 and K27-D52. And there is one opinion that most protein when electrosprayed into gas phase from its native solution, the structure features will retain mostly. And electron based dissociation method, like ECD or ETD, can break the protein back bonds instead of disrupting its structure.

Once we have one electron based dissociation pattern of ubiquitin, which in real world does not either break any salt bridge above. For reference, ubiquitin's sequence is below:

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

From this particular sequence, there are 11 D and Es as well as 11 R and Ks. Imagine how many possibile salt bridge patterns if all those residues formed randomly. Based on the electron dissociation data, we can eliminate those pattern inside which salt bridges are broken. so, we can get the number of possible or reasonable patterns. Here it is, only 1 percent of the millions of possibilities go into the team of "preserving the salt bridge". This result also supports the statement that protein can stay native when ESIed into gas phase which is so important aspect for analyst who works on mass spectrometry.

This discussion facilitates JAVA by algorithm of premutation and combination. Premutation and combination generate the random pattern which is passed into the mass spectrom result to tell how much salt bridge breaking it happens.All the ideas, coding and running program are acchieved in Nov. 2012 by Zhe Zhang in Richard W. Vachet's lab. For further information or detail, please contact zhez@chem.umass.edu.
</StructureSection>

{{STRUCTURE_2pea| PDB=2pea | SCENE= }}

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-17T19:52:21Z

Zhe Zhang:

== How native structure is preserved in gas phase ==
<StructureSection load='2jzz' size='350' side='right' caption='Structure of ubiquitin (PDB entry [[2jzz]])' scene=''>

This page is going to talk about a gas phase or mass spectrum idea about this. From the perspective of solution phase, we can know the salt bridges stay between E51-R54, R54-D58, E18-K29, D21-K29 and K27-D52. And there is one opinion that most protein when electrosprayed into gas phase from its native solution, the structure features will retain mostly. And electron based dissociation method, like ECD or ETD, can break the protein back bonds instead of disrupting its structure.

Once we have one electron based dissociation pattern of ubiquitin, which in real world does not either break any salt bridge above. For reference, ubiquitin's sequence is below:

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

From this particular sequence, there are 11 D and Es as well as 11 R and Ks. Imagine how many possibile salt bridge patterns if all those residues formed randomly. Based on the electron dissociation data, we can eliminate those pattern inside which salt bridges are broken. so, we can get the number of possible or reasonable patterns. Here it is, only 1 percent of the millions of possibilities go into the team of "preserving the salt bridge". This result also supports the statement that protein can stay native when ESIed into gas phase which is so important aspect for analyst who works on mass spectrometry.

This discussion facilitates JAVA by algorithm of premutation and combination. Premutation and combination generate the random pattern which is passed into the mass spectrom result to tell how much salt bridge breaking it happens.All the ideas, coding and running program are acchieved in Nov. 2012 by Zhe Zhang in Richard W. Vachet's lab. For further information or detail, please contact zhez@chem.umass.edu.
</StructureSection>

[[Image:2pea.png|left|200px]]

{{STRUCTURE_2pea| PDB=2pea | SCENE= }}

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-17T19:43:55Z

Zhe Zhang:

== How native structure is preserved in gas phase ==
<StructureSection load='2jzz' size='350' side='right' caption='Structure of ubiquitin (PDB entry [[2jzz]])' scene=''>

This page is going to talk about a gas phase or mass spectrum idea about this. From the perspective of solution phase, we can know the salt bridges stay between E51-R54, R54-D58, E18-K29, D21-K29 and K27-D52. And there is one opinion that most protein when electrosprayed into gas phase from its native solution, the structure features will retain mostly. And electron based dissociation method, like ECD or ETD, can break the protein back bonds instead of disrupting its structure.

Once we have one electron based dissociation pattern of ubiquitin, which in real world does not either break any salt bridge above. For reference, ubiquitin's sequence is below:

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

From this particular sequence, there are 11 D and Es as well as 11 R and Ks. Imagine how many possibile salt bridge patterns if all those residues formed randomly. Based on the electron dissociation data, we can eliminate those pattern inside which salt bridges are broken. so, we can get the number of possible or reasonable patterns. Here it is, only 1 percent of the millions of possibilities go into the team of "preserving the salt bridge". This result also supports the statement that protein can stay native when ESIed into gas phase which is so important aspect for analyst who works on mass spectrometry.

This discussion facilitates JAVA by algorithm of premutation and combination. Premutation and combination generate the random pattern which is passed into the mass spectrom result to tell how much salt bridge breaking it happens.All the ideas, coding and running program are acchieved in Nov. 2012 by Zhe Zhang in Richard W. Vachet's lab. For further information or detail, please contact zhez@chem.umass.edu.
</StructureSection>

<scene name='Sandbox_myoglobin/Water/2'>ubiquitin</scene>

CBI Molecules

2012-12-17T19:37:34Z

Zhe Zhang:

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 2012: CBI Molecules are due 12/12/12 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished. 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 -- I may be able to request additions to the author list).

==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]

: '''[[Molecular_Playground/Pcr H]]''', Fabian Romano

[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]

: New Fall 2012!! '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr
: '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu
: New Fall 2012!! '''[[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

Peyton Lab
: '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen
: '''[[Molecular Playground/FAK]]''', Dannielle Ryman

[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

: '''[[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==

'''Congratulations to the prize-winning CBI molecules noted above! The new 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 2012: Complete steps 1-3 by 10/10/12, in preparation for the CBI Molecule Workshop.

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

2. 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).

3. Get together with the other Chalk Talk students in your research group and decide which molecule you will improve or create. Develop ideas for the scenes you wish to show. You will work on these during the workshop with our help, and then finish them on your own.

You are encouraged to collaborate on this year's 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.

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.

4. 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.

==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.

Ubiquitin salt bridge discussion

2012-12-17T19:36:09Z

Zhe Zhang: Ubiquitin salt bridge discussion moved to Molecular Playground/Ubiquitin salt bridge discussion: Make public

#REDIRECT [[Molecular Playground/Ubiquitin salt bridge discussion]]

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-17T19:36:09Z

Zhe Zhang: Ubiquitin salt bridge discussion moved to Molecular Playground/Ubiquitin salt bridge discussion: Make public

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-17T19:18:00Z

Zhe Zhang:

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-17T19:16:20Z

Zhe Zhang:

== How native structure is preserved in gas phase ==
<StructureSection load='2jzz' size='350' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[2jzz]])' scene=''>
<applet size='[450,338]' frame='true' align='left'
caption='Ubiquitin (PDB ID: [http://www.pdb.org/pdb/explore/explore.do?structureId=2JZZ 2JZZ] )' scene='User:Joanne_Lau/sandbox_3/Clpx_hexamer_morph/8' />
This page is going to talk about a gas phase or mass spectrum idea about this. From the perspective of solution phase, we can know the salt bridges stay between E51-R54, R54-D58, E18-K29, D21-K29 and K27-D52. And there is one opinion that most protein when electrosprayed into gas phase from its native solution, the structure features will retain mostly. And electron based dissociation method, like ECD or ETD, can break the protein back bonds instead of disrupting its structure.

Once we have one electron based dissociation pattern of ubiquitin, which in real world does not either break any salt bridge above. For reference, ubiquitin's sequence is below:

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

From this particular sequence, there are 11 D and Es as well as 11 R and Ks. Imagine how many possibile salt bridge patterns if all those residues formed randomly. Based on the electron dissociation data, we can eliminate those pattern inside which salt bridges are broken. so, we can get the number of possible or reasonable patterns. Here it is, only 1 percent of the millions of possibilities go into the team of "preserving the salt bridge". This result also supports the statement that protein can stay native when ESIed into gas phase which is so important aspect for analyst who works on mass spectrometry.

This discussion facilitates JAVA by algorithm of premutation and combination. Premutation and combination generate the random pattern which is passed into the mass spectrom result to tell how much salt bridge breaking it happens.All the ideas, coding and running program are acchieved in Nov. 2012 by Zhe Zhang in Richard W. Vachet's lab. For further information or detail, please contact zhez@chem.umass.edu.
</StructureSection>

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-17T19:15:08Z

Zhe Zhang:

== How native structure is preserved in gas phase ==
<StructureSection load='2jzz' size='350' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[2jzz]])' scene=''>
<applet size='[450,338]' frame='true' align='left'
caption='Hexameric ClpX (PDB ID: [http://www.pdb.org/pdb/explore/explore.do?structureId=3HWS 3HWS] and [http://www.pdb.org/pdb/explore/explore.do?structureId=3HTE 3HTE])' scene='User:Joanne_Lau/sandbox_3/Clpx_hexamer_morph/8' />
This page is going to talk about a gas phase or mass spectrum idea about this. From the perspective of solution phase, we can know the salt bridges stay between E51-R54, R54-D58, E18-K29, D21-K29 and K27-D52. And there is one opinion that most protein when electrosprayed into gas phase from its native solution, the structure features will retain mostly. And electron based dissociation method, like ECD or ETD, can break the protein back bonds instead of disrupting its structure.

Once we have one electron based dissociation pattern of ubiquitin, which in real world does not either break any salt bridge above. For reference, ubiquitin's sequence is below:

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

From this particular sequence, there are 11 D and Es as well as 11 R and Ks. Imagine how many possibile salt bridge patterns if all those residues formed randomly. Based on the electron dissociation data, we can eliminate those pattern inside which salt bridges are broken. so, we can get the number of possible or reasonable patterns. Here it is, only 1 percent of the millions of possibilities go into the team of "preserving the salt bridge". This result also supports the statement that protein can stay native when ESIed into gas phase which is so important aspect for analyst who works on mass spectrometry.

This discussion facilitates JAVA by algorithm of premutation and combination. Premutation and combination generate the random pattern which is passed into the mass spectrom result to tell how much salt bridge breaking it happens.All the ideas, coding and running program are acchieved in Nov. 2012 by Zhe Zhang in Richard W. Vachet's lab. For further information or detail, please contact zhez@chem.umass.edu.
</StructureSection>

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-11T22:53:13Z

Zhe Zhang:

== How native structure is preserved in gas phase ==
<StructureSection load='2jzz' size='350' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[2jzz]])' scene=''>
This page is going to talk about a gas phase or mass spectrum idea about this. From the perspective of solution phase, we can know the salt bridges stay between E51-R54, R54-D58, E18-K29, D21-K29 and K27-D52. And there is one opinion that most protein when electrosprayed into gas phase from its native solution, the structure features will retain mostly. And electron based dissociation method, like ECD or ETD, can break the protein back bonds instead of disrupting its structure.

Once we have one electron based dissociation pattern of ubiquitin, which in real world does not either break any salt bridge above. For reference, ubiquitin's sequence is below:

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

From this particular sequence, there are 11 D and Es as well as 11 R and Ks. Imagine how many possibile salt bridge patterns if all those residues formed randomly. Based on the electron dissociation data, we can eliminate those pattern inside which salt bridges are broken. so, we can get the number of possible or reasonable patterns. Here it is, only 1 percent of the millions of possibilities go into the team of "preserving the salt bridge". This result also supports the statement that protein can stay native when ESIed into gas phase which is so important aspect for analyst who works on mass spectrometry.

This discussion facilitates JAVA by algorithm of premutation and combination. Premutation and combination generate the random pattern which is passed into the mass spectrom result to tell how much salt bridge breaking it happens.All the ideas, coding and running program are acchieved in Nov. 2012 by Zhe Zhang in Richard W. Vachet's lab. For further information or detail, please contact zhez@chem.umass.edu.
</StructureSection>

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-11T22:51:02Z

Zhe Zhang:

== how native structure is preserved in gas phase ==
<StructureSection load='2jzz' size='350' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[2jzz]])' scene=''>
This page is going to talk about a gas phase or mass spectrum idea about this. From the perspective of solution phase, we can know the salt bridges stay between E51-R54, R54-D58, E18-K29, D21-K29 and K27-D52. And there is one opinion that most protein when electrosprayed into gas phase from its native solution, the structure features will retain mostly. And electron based dissociation method, like ECD or ETD, can break the protein back bonds instead of disrupting its structure.

Once we have one electron based dissociation pattern of ubiquitin, which in real world does not either break any salt bridge above. For reference, ubiquitin's sequence is below:

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

From this particular sequence, there are 11 D and Es as well as 11 R and Ks. Imagine how many possibile salt bridge patterns if all those residues formed randomly. Based on the electron dissociation data, we can eliminate those pattern inside which salt bridges are broken. so, we can get the number of possible or reasonable patterns. Here it is, only 1 percent of the millions of possibilities go into the team of "preserving the salt bridge". This result also supports the statement that protein can stay native when ESIed into gas phase which is so important aspect for analyst who works on mass spectrometry.

This discussion facilitates JAVA by algorithm of premutation and combination. Premutation and combination generate the random pattern which is passed into the mass spectrom result to tell how much salt bridge breaking it happens.All the ideas, coding and running program are acchieved in Nov. 2012 by Zhe Zhang in Richard W. Vachet's lab. For further information or detail, please contact zhez@chem.umass.edu.
</StructureSection>

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-11T22:48:12Z

Zhe Zhang:

== how native structure is preserved in gas phase ==
<StructureSection load='2jzz' size='350' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[2jzz]])' scene=''>
This page is going to talk about a gas phase or mass spectrum idea about this. From the perspective of solution phase, we can know the salt bridges stay between E51-R54, R54-D58, E18-K29, D21-K29 and K27-D52. And there is one opinion that most protein when electrosprayed into gas phase from its native solution, the structure features will retain mostly. And electron based dissociation method, like ECD or ETD, can break the protein back bonds instead of disrupting its structure.

Once we have one electron based dissociation pattern of ubiquitin, which in real world does not either break any salt bridge above. The sequence is below:

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

From this particular sequence, there are 11 D and Es as well as 11 R and Ks. Imagine how many possibile salt bridge patterns if all those residues formed randomly. Based on the electron dissociation data, we can eliminate those pattern inside which salt bridges are broken. so, we can get the number of possible patterns. Here it is, only 1 percent of the millions of possibilities go into the team of "preserving the salt bridge". This result also supports the statement that protein can stay native when ESIed into gas phase which is so important aspect for analyst who works on mass spectrometry.

This discussion facilitates JAVA by algorithm of premutation and combination. Premutation and combination generate the random pattern which is passed into the mass spectrom result to tell how much salt bridge breaking it happens.All the idea, coding and running program are acchieved in Nov. 2012 by Zhe Zhang in Vachet W. Richard's lab. For further information or detail, please contact zhez@chem.umass.edu.
</StructureSection>

Molecular Playground/Ubiquitin salt bridge discussion

2012-12-11T22:23:45Z

Zhe Zhang: New page: == Your Heading Here (maybe something like 'Structure') == <StructureSection load='2jzz' size='350' side='right' caption='Structure of HMG-CoA reductase (PDB entry 2jzz)' scene=''> Thi...

== Your Heading Here (maybe something like 'Structure') ==
<StructureSection load='2jzz' size='350' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[2jzz]])' scene=''>
This page is going to talk about a gas phase or mass spectrum idea about this. From the perspective of solution phase, we can know the salt bridges stay between E51-R54, R54-D58, E18-K29, D21-K29 and K27-D52. And there is one opinion that most protein when electrosprayed into gas phase from its native solution, the structure features will retain mostly. And electron based dissociation method, like ECD or ETD, can break the protein back bonds instead of disrupting its structure.

Once we have one electron based dissociation pattern of ubiquitin, which in real world does not either break any salt bridge above. The sequence is below:

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

From this particular sequence, there are 11 D and Es as well as 11 R and Ks.
</StructureSection>