Proteopedia - User contributions [en]

CBI Molecules

2012-12-13T04:02:37Z

Heidi Hu:

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://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]

: '''[[Molecular Playground/[[Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao

: ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay

: '''[[Molecular Playground/Caspase-7 Dynamics]]'''

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

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

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

: '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz

Hebert Lab

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

: ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski

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

Knapp lab

:'''[[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 ]

: '''[[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

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

: '''[[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

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.

Molecular Playground/HypA

2012-12-13T04:01:49Z

Heidi Hu: New page: ---- 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 disp...

----

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].
 
<applet load='3A44' size='[450,438]' frame='true' align='right'
caption='Structures of HypA (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=2kdx 2KDX]), (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=3A43 3A43]), and (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=3A44 3A44])' />
 
== Introduction ==

[http://en.wikipedia.org/wiki/Helicobacter_pylori ''Helicobacter pylori''] is a pathogenic bacterium that colonizes the human gastric mucosa, which can cause peptic ulcers and has been linked to stomach cancers.<ref>PMID:9146793</ref> [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori''] requires the activity of nickel-dependent enzymes, [NiFe]-[http://en.wikipedia.org/wiki/Hydrogenase ''Hydrogenase''] (H2ase) and [http://en.wikipedia.org/wiki/Urease ''urease''], to survive in the acidic environment of the stomach.<ref>PMID:2050411</ref><ref>PMID:8063376</ref><ref>PMID:12459589</ref> Thus nickel is an important nutrient for H. pylori.

Accessory proteins HypABCDEF and UreIEFGH facilitate the maturation of [NiFe]-[http://en.wikipedia.org/wiki/Hydrogenase ''H2ase''] and [http://en.wikipedia.org/wiki/Urease ''urease''] respectively<ref>PMID:9252185</ref>. HypA is a nickel metallochaperone normally associated with the maturation of [NiFe]-[http://en.wikipedia.org/wiki/Hydrogenase ''H2ase'']<ref name="NiTraff">PMID:22970729</ref>. In H. pylori, however, it is also require for the full activy of urease, despite the presence of the urease-specific Ni-chaperone, UreE<ref>PMID:11123699</ref>.

== HypA ==

 

The [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori'']HypA (''Hp''HypA) is a 13.2kDa Ni-chaperone with both a nickel binding site and and structural zinc site. Zn(II) is coordinated by two CXXC motif each with a flanking histidine, whereas the Ni(II) is known to bind to the N-terminus MHE motif<ref name="bob">PMID:20662514</ref>. The ''Hp''HypA protein has also been characterized as a monomer and a homodimer. The <scene name='Heidi_Hu/Sandbox_2/Hphypa/2'>N-terminal modified monomeric structure</scene> (N-terminal tag colored in red) has been solved by NMR (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=2KDX 2KDX])<ref>PMID:19621959</ref>. The monomeric structure shows an <scene name='Heidi_Hu/Sandbox_2/Hphypa_2nd_structure/1'>alpha/beta lobe</scene> containing the N- and C-termini well separated from the <scene name='Heidi_Hu/Sandbox_2/Hphypa_2nd_structure/2'>zinc binding lobe</scene>. The homodimeric ''Hp''HypA has been characterized by NMR to have the similar overall structure with discrepancies to the metal binding sites<ref name="bob"/>. The metal sites in ''Hp''HypA have been characterized by [http://en.wikipedia.org/wiki/X-ray_absorption_spectroscopy ''X-ray absorption spectroscopy''] (XAS) at pH 6.3 and 7.2 to similate the internal pH of [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori''] under acid shock or at neutral pH conditions<ref name="bob"/> respectively. While the Ni(II) site is 6-coordinate N/O under both pH conditions, the Zn(II) coordination changes from Cys4 at neutral pH to Cys2His2 at acidic pH with nickel-bound<ref name="bob"/> (Fig. 1). Changes to the coordination of structural Zinc site in response to pH has been hypothesized to be linked to changes in HypA conformations and protein interaction partners<ref name="bob"/>.
[[Image:HypA-pH-Ni-Change.png|200 px|thumb|Fig. 1: Diagram of Ni- and pH-dependent structural changes to Zn(II) site of ''Hp''HypA (adapted figure<ref name="bob"/>)]]

The crystal structure of <scene name='Heidi_Hu/Sandbox_2/Hypa_monomer/1'>monomeric</scene> (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=3A43 3A43]) and <scene name='Heidi_Hu/Sandbox_2/Dimeric_hypa/1'>homodimeric</scene> (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=3A44 3A44]) HypA from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis ''Thermococcus kodakarensis''] has been solved<ref>PMID:19769985</ref>. The HypA homodimer from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis ''T. kodakarensis''] shows a switch dimer, where one beta strand of each alpha/beta lobe comes from the opposite subunit. Additionally, each <scene name='Heidi_Hu/Sandbox_2/Dimeric_zinc_site/1'>Zn(II) site</scene> is coordinated by CXXC motifs from a different subunit. These observations were consistent with the [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori''] homodimeric HypA NMR data<ref name="bob"/>.

== Research Interests ==

The Ni- and pH-dependent changes in the [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori''] HypA structural zinc site suggests multiple conformations of this protein. Thus HypA is likely interfacing between the maturation of [NiFe]-[http://en.wikipedia.org/wiki/Hydrogenase ''H2ase''] and/or [http://en.wikipedia.org/wiki/Urease ''urease''] in [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori''] in a pH-dependent manner, as it is required for the full activation of both of these nickel enzymes. The [http://people.chem.umass.edu/mmaroney/ Maroney Lab] at the University of Massachusetts Amherst is interested in characterizing the conformational changes in HypA and its interaction partners under neutral and acid shock conditions.

== References ==

<references/>

== Also See ==

[[2kdx]] 
[[3a43]] 
[[3a44]]

CBI Molecules

2012-12-13T04:00:49Z

Heidi Hu:

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://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]

: '''[[Molecular Playground/[[Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao

: ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay

: '''[[Molecular Playground/Caspase-7 Dynamics]]'''

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

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

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

: '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz

Hebert Lab

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

: ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski

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

Knapp lab

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

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

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

: '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr
: '''[[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 ]

: '''[[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

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

: '''[[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

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.

2012-12-12T22:00:50Z

Heidi Hu:

----

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].

[[Image:2KDX N to C.png|150 px|thumb|Fig. 1: Structure of monomeric H. pylori HypA (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=2kdx 2KDX]), colored from N- to C-terminus from blue to red.]]

 
== Introduction ==

 
[http://en.wikipedia.org/wiki/Helicobacter_pylori ''Helicobacter pylori''] is a pathogenic bacterium that colonizes the human gastric mucosa, which can cause peptic ulcers and has been linked to stomach cancers.<ref>PMID:9146793</ref> [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori''] requires the activity of nickel-dependent enzymes, [NiFe]Hydrogenase and urease, to survive in the acidic environment of the stomach.<ref>PMID:2050411</ref><ref>PMID:8063376</ref><ref>PMID:12459589</ref> Thus nickel is an important nutrient for H. pylori.

Accessory proteins HypABCDEF and UreIEFGH facilitate in the maturation of [NiFe]hydrogenase and urease respectively. HypA is a nickel metallochaperone normally associated with the maturation of [NiFe]hydrogenase. In H. pylori, however, it is also require for the full activy of urease, despite the presence of the urease-specific Ni-chaperone, UreE.

== HypA ==

<applet load='3A44' size='[400,388]' frame='true' align='left'
caption='NMR structure of monomeric H. pylori HypA (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=3A44 3A44])' />
 
The [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori'']HypA (''Hp''HypA) is a 13.2kDa Ni-chaperone with both a nickel binding site and and structural zinc site. Zn(II) is coordinated by two CXXCXH motifs in HypA, whereas the Ni(II) is known to bind to the N-terminus with His2 as a known ligand. The ''Hp''HypA protein has also been characterized as a monomer or a homodimer. The N-terminal modified monomeric structure has been solved by NMR (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=2KDX 2KDX]). The monomeric structure shows an alpha/beta lobe containing the N- and C-termini well separated from the zinc binding lobe. The homodimeric ''Hp''HypA has been characterized by NMR to have the similar overall structure with exception to the metal binding sites. The metal sites in ''Hp''HypA have been characterized by X-ray absorption spectroscopy (XAS) at pH 6.3 and 7.2 similating the internal pH of H. pylori under acid shock or at neutral pH conditions. Whereas the Ni(II) site is 6-coordinate N/O under both pH conditions, the Zn(II) coordination changes from Cys4 at neutral pH to Cys2His2 at acidic pH with nickel-bound. Changes in the coordination of structural Zinc site in response to pH has been hypothesized to be linked to altered HypA structures and protein interaction partners.

The crystal structure of monomeric (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=3A43 3A43]) and homodimeric (PDB ID: [http://www.rcsb.org/pdb/explore/explore.do?structureId=3A44 3A44]) HypA from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis ''Thermococcus kodakarensis''] has been solved. The HypA homodimer from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis ''T. kodakarensis''] shows a switch dimer, where one beta strand of each alpha/beta lobe comes from the opposite subunit. Additionally, each Zn(II) site is coordinated by CXXC motifs from a different subunit. These observations were consistent with the [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori''] homodimeric HypA NMR data.

 

== Research Interests ==

 
The Ni- and pH-dependent changes in the [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori''] HypA structural zinc site suggests multiple conformations of this protein. Thus HypA is likely interfacing between the maturation of [NiFe]hydrogenase and/or urease in [http://en.wikipedia.org/wiki/Helicobacter_pylori ''H. pylori''] in a pH-dependent manner, as it is required for the full activation of both of these nickel enzymes. The [http://people.chem.umass.edu/mmaroney/ Maroney Lab] at the University of Massachusetts Amherst is interested in characterizing the conformational changes in HypA and its interaction partners under neutral and acid shock conditions.

== References ==

<references/>

== Also See ==

[[2hh7]]