Proteopedia - User contributions [en]

Molecular Playground/Pcr H

2014-12-03T19:33:11Z

Yuzhou Tang:

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]
----

<Structure load='PcrH_monomer.pdb' size='370' frame='true' align='right' caption='Pseudomonas aeruginosa PcrH monomer'/>

== PcrH ==

=== Introduction ===

''Pseudomonas aeruginosa'' is a bacterium widely found in the environment, nonetheless is capable of infecting patients with a weak immune system. ''P. aeruginosa'' has been linked to more than 65% of cases of human infections that exhibit great resistance to antibiotics; moreover, is the predominant cause of mortality in cystic fibrosis patients. As many Gram-negative pathogens, ''P. aeruginosa'' is armed with a sophisticated Type III Secretion System (T3SS) used to inject toxic proteins into human host cells. T3SS has been shown to have an important role in disease and pathogenicity of this bacterium. The T3SS is structured like a syringe that protrudes from the bacterial membrane towards the target cell membrane.[[Image:TypeIIIsecre.png|370px|right|thumb| Model of'' P. aeruginosa'' Type III secretion system. PcrH remains in the bacterial cytoplasm bound to PopB and PopD to keep them soluble and competent for secretion.]] Within this system, two secreted proteins called PopB and PopD are found to insert into the target cell membrane and form a proteinaceous structure called the translocon that will connect with the syringe to serve as a gateway for the toxic proteins into the target cell cytoplasm.<ref name="fabian">PMID: 21770428</ref> Substantial genetic and biochemical data indicate the translocon is composed by two T3S proteins, in the case of ''Pseudomonas'' ''aeruginosa'', the translocators protein are PopB and PopD<ref name="fabian" />. While they are in the bacterial cytoplasm they need to be maintained in a state competent for secretion and also not toxic for the bacterial cell, the system achieves this by employing a Type II chaperone called PcrH. '''PrcH''' is a small (18.4 kDa) non-secreted bacterial co-chaperone that binds uniquely to these translocator proteins.

=== PcrH Structure ===

PcrH's characteristic fold is composed of Tetratricopeptide Repeats (TPR repeats). TPR repeats consist of a 34 amino-acid sequence motif that folds into two antiparallel alpha-helices that serve as interaction modules and multi-protein complex mediators.<ref name="dimer">PMID: 23974025</ref> In this case, PcrH from ''Pseudomonas aeruginosa'' consist of three <scene name='Molecular_Playground/Pcr_H/Tprs_2/2'>Tpr-like motifs</scene>. The first Tpr motif is represented in red, the second in green and the third in cyan color, also an additional alpha-helix is represented in blue. This fold is also present in Eukaryotic co-chaperons such as HOP(Heat shock protein Organizing Protein).

PcrH dimerization has been reported to be required for stability of PcrH in the absence of the cargo but not their function. But their dimerization interface is controversial. In the solved structure of PcrH, it showed a dimer with <scene name='44/447152/Pcrh_dimer/1'>back-to-back PcrH monomer</scene> (each monomer is labeled in green and blue) <ref name="pcrh">PMID: 20385547</ref>. The interaction only seems to happen at Y95, L98 and M99 (labeled in yellow) between helix 4 in the neighboring monomers. However, Tomalka et al <ref name="dimer" />showed by mutagenesis that the dimer should be head-to-head where monomers interact via two N terminal helices (TPR1). This result resembles the solved structure of <scene name='44/447152/Sycd_dimer/1'>SycD dimer</scene> <ref>PMID: 18054956 </ref>which is the chaperone of translocators in Yersinia and shares 59.3% identity with PcrH. (each monomer is labeled in green and blue, mutation in residue A61 and L65 labeled in yellow has been shown to disrupt dimerization)

=== PcrH bound to PopB/D ===

PcrH crystal structure has also been solved <scene name='Molecular_Playground/Pcr_H/Pcrh_active_site/1'>when bound to a synthetic peptide </scene> carrying a homologous sequence that is present in these two translocators.<ref>PMID: 24297169</ref> <ref name="pcrh" /> PcrH has a <scene name='Molecular_Playground/Pcr_H/Concavecharge/1'>charged concave cleft</scene> (Histidine and Arginine residues shown in yellow) where it binds to a <scene name='Molecular_Playground/Pcr_H/Motif_chainb/1'>sequence motif</scene> (VXLXXP) present in both PopB and PopD (9 residue peptide (rainbow) shown bound to Chain A). The VXLXXP sequence motif binding is displayed as three hydrophobic pockets in the concave side of the TPR domain receive three hydrophobic residues within the CBM present in the synthetic peptide. This interaction keeps them in a metastable non oligomeric state in the cytosol, thus protecting them from degradation and aggregation. It is also believed that PcrH has an active role in delivering PopB and PopD to the basal body of the T3S system, where an ATPse unfolds and secretes the translocators PopB and PopD.

Given its key role in molecular pathogenesis PcrH is a potential target for drug design.

==References==
<references />

Molecular Playground/Pcr H

2014-12-03T17:31:32Z

Yuzhou Tang:

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]
----

<Structure load='PcrH_monomer.pdb' size='370' frame='true' align='right' caption='Pseudomonas aeruginosa PcrH monomer'/>

== PcrH ==

=== Introduction ===

''Pseudomonas aeruginosa'' is a bacterium widely found in the environment, nonetheless is capable of infecting patients with a weak immune system. ''P. aeruginosa'' has been linked to more than 65% of cases of human infections that exhibit great resistance to antibiotics; moreover, is the predominant cause of mortality in cystic fibrosis patients. As many Gram-negative pathogens, ''P. aeruginosa'' is armed with a sophisticated Type III Secretion System (T3SS) used to inject toxic proteins into human host cells. T3SS has been shown to have an important role in disease and pathogenicity of this bacterium. The T3SS is structured like a syringe that protrudes from the bacterial membrane towards the target cell membrane.[[Image:TypeIIIsecre.png|370px|right|thumb| Model of'' P. aeruginosa'' Type III secretion system. PcrH remains in the bacterial cytoplasm bound to PopB and PopD to keep them soluble and competent for secretion.]] Within this system, two secreted proteins called PopB and PopD are found to insert into the target cell membrane and form a proteinaceous structure called the translocon that will connect with the syringe to serve as a gateway for the toxic proteins into the target cell cytoplasm.<ref>PMID: 21770428</ref> Substantial genetic and biochemical data indicate the translocon is composed by two T3S proteins, in the case of ''Pseudomonas'' ''aeruginosa'', the translocators protein are PopB and PopD.<ref>PMID: 21770428</ref> While they are in the bacterial cytoplasm they need to be maintained in a state competent for secretion and also not toxic for the bacterial cell, the system achieves this by employing a Type II chaperone called PcrH. '''PrcH''' is a small (18.4 kDa) non-secreted bacterial co-chaperone that binds uniquely to these translocator proteins.

=== PcrH Structure ===

PcrH's characteristic fold is composed of Tetratricopeptide Repeats (TPR repeats). TPR repeats consist of a 34 amino-acid sequence motif that folds into two antiparallel alpha-helices that serve as interaction modules and multi-protein complex mediators.<ref name="dimer">PMID: 23974025</ref> In this case, PcrH from ''Pseudomonas aeruginosa'' consist of three <scene name='Molecular_Playground/Pcr_H/Tprs_2/2'>Tpr-like motifs</scene>. The first Tpr motif is represented in red, the second in green and the third in cyan color, also an additional alpha-helix is represented in blue. This fold is also present in Eukaryotic co-chaperons such as HOP(Heat shock protein Organizing Protein).

PcrH dimerization has been reported to be required for stability of PcrH in the absence of the cargo but not their function. But their dimerization interface is controversial. In the solved structure of PcrH, it showed a dimer with <scene name='44/447152/Pcrh_dimer/1'>back-to-back PcrH monomer</scene> (each monomer is labeled in green and blue) <ref name="pcrh">PMID: 20385547</ref>. The interaction only seems to happen at Y95, L98 and M99 (labeled in yellow) between helix 4 in the neighboring monomers. However, Tomalka et al <ref name="dimer" />showed by mutagenesis that the dimer should be head-to-head where monomers interact via two N terminal helices (TPR1). This result resembles the solved structure of <scene name='44/447152/Sycd_dimer/1'>SycD dimer</scene> <ref>PMID: 18054956 </ref>which is the chaperone of translocators in Yersinia and shares 59.3% identity with PcrH. (each monomer is labeled in green and blue, mutation in residue A61 and L65 labeled in yellow has been shown to disrupt dimerization)

=== PcrH bound to PopB/D ===

PcrH crystal structure has also been solved <scene name='Molecular_Playground/Pcr_H/Pcrh_active_site/1'>when bound to a synthetic peptide </scene> carrying a homologous sequence that is present in these two translocators.<ref>PMID: 24297169</ref> <ref name="pcrh" /> PcrH has a <scene name='Molecular_Playground/Pcr_H/Concavecharge/1'>charged concave cleft</scene> (Histidine and Arginine residues shown in yellow) where it binds to a <scene name='Molecular_Playground/Pcr_H/Motif_chainb/1'>sequence motif</scene> (VXLXXP) present in both PopB and PopD (9 residue peptide (rainbow) shown bound to Chain A). The VXLXXP sequence motif binding is displayed as three hydrophobic pockets in the concave side of the TPR domain receive three hydrophobic residues within the CBM present in the synthetic peptide. This interaction keeps them in a metastable non oligomeric state in the cytosol, thus protecting them from degradation and aggregation. It is also believed that PcrH has an active role in delivering PopB and PopD to the basal body of the T3S system, where an ATPse unfolds and secretes the translocators PopB and PopD.

Given its key role in molecular pathogenesis PcrH is a potential target for drug design.

==References==
<references />

CBI Molecules

2014-12-03T17:19:33Z

Yuzhou Tang:

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 2014: CBI Molecules are due 12/3/14 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished, and then as "New 2014" or "Revised 2014". For those editing an existing CBI Molecule, start by making a copy of that entry (leaving the original intact) so that it retains the full author list of all authors that contributed (or include credits and a link to the original page and authors if it does not).
Follow the instructions at the bottom of this page.

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

[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]

: '''[[Molecular Playground/ClyA]]''', Bib Yang
: '''[[Molecular Playground/OmpG]]''', Christina Chisholm

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

: '''[[Molecular Playground/Homo-dimeric RcdA]]''', Kamal K. Joshi
: **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau '''Best CBI Molecule 2011'''
: '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu

Farkas Lab
: '''[[Molecular Playground/CLOCK:BMAL1 heterodimer complex]]''', Hui-Hsien Lin, Joseph Hardie, Michael Mingroni '''New 2014'''

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]

: '''[[Molecular_Playground/DnaK]]''', Joseph Tilitsky, New 2014
: '''[[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
: **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani '''Best CBI Molecule 2012'''

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

: '''[[Molecular Playground/Executioner Caspase-7]]''', Derek MacPherson, Maureen E. Hill
: '''[[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/Hsp70-Hsp90]]''', Jill Graham
: '''[[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, Carolina Morell-Pérez, Yuzhou Tang

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

: '''[[Molecular Playground/Protective Antigen]]''', Jing Huang

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

: '''[http://proteopedia.org/wiki/index.php/Chengfeng_Ren Molecular Playground/Inteferon]'''[Revised], Chengfeng Ren
: ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski
: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita
: '''[[Molecular Playground/Antithrombin-Heparin]]''', Yunlong Zhao

Knapp lab

: '''[[Molecular Playground/FIH]]''', Vanessa Chaplin, Cornelius Taabazuing, Breanne Holmes, John Hangasky
: '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas '''Best CBI Molecule Proteopedia Page 2010'''

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

: '''[[Molecular Playground/UreE]]''', Priyanka Basak, '''New 2014'''
: '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr
: '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu, Carolyn Carr, Hsin-Ting (Tiffany )Huang, '''Revised 2014'''
: '''[[Molecular Playground/HypA]]''', Heidi Hu

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

: **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia '''Best CBI Molecule 2011'''
: '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia
: '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan

[http://www.peytonlab.org/ Peyton Lab]
: '''[[Molecular Playground/IntegrinBeta1]]''', Lauren Jansen, Lauren Barney, Elizabeth Brooks, Alyssa Schwartz ***'''NEW FALL 2014''''***
: '''[[Molecular Playground/MMP14]]''', Lauren Jansen
: '''[[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

[http://http://www.umass.edu/schiffman/ Schiffman Lab]
: '''[[Molecular Playground/Streptavidin]]''', Katrina Rieger

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

Tew Lab

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

Thayumanavan Lab
: '''[[Interleukin-1 beta]]''', Huan He
: '''[[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 Lab]

: '''[[Molecular Playground/Bacterial Chemotaxis Complex]]''', Elizabeth R. Haglin, Maryam Kashefi
: '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin
: '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones
: '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li

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

: ''[[Molecular Playground/Human Serum Albumin]]''', Mahalia Serrano
: '''[[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
: '''[[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/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey, Schnarr lab
: '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey, Schnarr lab
: '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad, Schnarr lab

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

: '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffi, Bhatia Lab
: '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer, Bhatia Lab

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

: '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab

: '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab

==Instructions==

'''The goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''

Fall 2014: Complete steps 1-3 before the CBI Molecule Workshop on 11/19; bring your computer to the CBI Molecule Workshop in ISB 321. You will be able to start work on your CBI Molecule at the workshop. You should plan to stay and finish your molecule after the workshop (or as soon as possible) while the instructions and ideas are fresh in your mind.

A successful CBI Molecule is an interesting, nontechnical description of a molecule related to your group's research. It should tell an interesting story with few words and many green scenes. Green scenes should be clear and attractive illustrations that tell your story. It's great if you can end with a brief statement about how it relates to your group's research goals.

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

2. Read through the rest of the instructions, do the tutorials below, and look at any existing CBI Molecules from your research group. Talk with other CBI students in your research group and decide how you will collaborate to make an improved CBI Molecule related to your group's research. Develop ideas for the scenes that each of you will make.

3. Get started working in Proteopedia. 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. Explore the HELP links below to learn how to make 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).

'''Complete the above steps before the CBI Molecule Workshop.'''

4. When editing an existing CBI Molecule, leave the original intact and make a copy that you will edit so that it retains the full author list of all authors that contributed. You are encouraged to collaborate on the CBI Molecules, but everyone will need to log in as themself and create a green scene to get credit for their work and to appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.

5. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished, and then "new 2014" or "revised 2014". Minimize text; tell your story with green scenes!

6. When your CBI Molecule is complete, send Lynmarie an email to nominate a cool scene/clever caption you would like to feature at the Molecular Playground (include a link to your CBI Molecule, name of the green scene, and caption).

==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/Pcr H

2014-12-03T17:15:52Z

Yuzhou Tang:

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]
----

<Structure load='PcrH_monomer.pdb' size='370' frame='true' align='right' caption='Pseudomonas aeruginosa PcrH monomer'/>

== PcrH ==

=== Introduction ===

''Pseudomonas aeruginosa'' is a bacterium widely found in the environment, nonetheless is capable of infecting patients with a weak immune system. ''P. aeruginosa'' has been linked to more than 65% of cases of human infections that exhibit great resistance to antibiotics; moreover, is the predominant cause of mortality in cystic fibrosis patients. As many Gram-negative pathogens, ''P. aeruginosa'' is armed with a sophisticated Type III Secretion System (T3SS) used to inject toxic proteins into human host cells. T3SS has been shown to have an important role in disease and pathogenicity of this bacterium. The T3SS is structured like a syringe that protrudes from the bacterial membrane towards the target cell membrane.[[Image:TypeIIIsecre.png|370px|right|thumb| Model of'' P. aeruginosa'' Type III secretion system. PcrH remains in the bacterial cytoplasm bound to PopB and PopD to keep them soluble and competent for secretion.]] Within this system, two secreted proteins called PopB and PopD are found to insert into the target cell membrane and form a proteinaceous structure called the translocon that will connect with the syringe to serve as a gateway for the toxic proteins into the target cell cytoplasm.<ref>PMID: 21770428</ref> Substantial genetic and biochemical data indicate the translocon is composed by two T3S proteins, in the case of ''Pseudomonas'' ''aeruginosa'', the translocators protein are PopB and PopD.<ref>PMID: 21770428</ref> While they are in the bacterial cytoplasm they need to be maintained in a state competent for secretion and also not toxic for the bacterial cell, the system achieves this by employing a Type II chaperone called PcrH. '''PrcH''' is a small (18.4 kDa) non-secreted bacterial co-chaperone that binds uniquely to these translocator proteins.

=== PcrH Structure ===

PcrH's characteristic fold is composed of Tetratricopeptide Repeats (TPR repeats). TPR repeats consist of a 34 amino-acid sequence motif that folds into two antiparallel alpha-helices that serve as interaction modules and multi-protein complex mediators.<ref>PMID: 23974025</ref> In this case, PcrH from ''Pseudomonas aeruginosa'' consist of three <scene name='Molecular_Playground/Pcr_H/Tprs_2/2'>Tpr-like motifs</scene>. The first Tpr motif is represented in red, the second in green and the third in cyan color, also an additional alpha-helix is represented in blue. This fold is also present in Eukaryotic co-chaperons such as HOP(Heat shock protein Organizing Protein).

PcrH dimerization has been reported to be required for stability of PcrH in the absence of the cargo but not their function. But their dimerization interface is controversial. In the solved structure of PcrH, it showed a dimer with <scene name='44/447152/Pcrh_dimer/1'>back-to-back PcrH monomer</scene> (each monomer is labeled in green and blue). The interaction only seems to happen at Y95, L98 and M99 (labeled in yellow) between helix 4 in the neighboring monomers. However, Tomalka et al showed by mutagenesis that the dimer should be head-to-head where monomers interact via two N terminal helices (TPR1). This result resembles the solved structure of <scene name='44/447152/Sycd_dimer/1'>SycD dimer</scene> which is the chaperone of translocators in Yersinia and shares 59.3% identity with PcrH. (each monomer is labeled in green and blue, mutation in residue A61 and L65 labeled in yellow has been shown to disrupt dimerization)

=== PcrH bound to PopB/D ===

PcrH crystal structure has also been solved <scene name='Molecular_Playground/Pcr_H/Pcrh_active_site/1'>when bound to a synthetic peptide </scene> carrying a homologous sequence that is present in these translocator proteins.<ref>PMID: 24297169</ref><ref>PMID: 20385547</ref> PcrH has a <scene name='Molecular_Playground/Pcr_H/Concavecharge/1'>charged concave cleft</scene> (Histidine and Arginine residues shown in yellow) where it binds to a <scene name='Molecular_Playground/Pcr_H/Motif_chainb/1'>sequence motif</scene> (VXLXXP) present in both PopB and PopD (9 residue peptide (rainbow) shown bound to Chain A). The VXLXXP sequence motif binding is displayed as three hydrophobic pockets in the concave side of the TPR domain receive three hydrophobic residues within the CBM present in the synthetic peptide. This interaction keeps them in a metastable non oligomeric state in the cytosol, thus protecting them from degradation and aggregation. It is also believed that PcrH has an active role in delivering PopB and PopD to the basal body of the T3S system, where an ATPse unfolds and secretes the translocators PopB and PopD.

Given its key role in molecular pathogenesis PcrH is a potential target for drug design.

==References==
<references />

Molecular Playground/Pcr H

2014-12-03T17:02:59Z

Yuzhou Tang:

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]
----

<Structure load='PcrH_monomer.pdb' size='370' frame='true' align='right' caption='Pseudomonas aeruginosa PcrH monomer'/>

== PcrH ==

=== Introduction ===

''Pseudomonas aeruginosa'' is a bacterium widely found in the environment, nonetheless is capable of infecting patients with a weak immune system. ''P. aeruginosa'' has been linked to more than 65% of cases of human infections that exhibit great resistance to antibiotics; moreover, is the predominant cause of mortality in cystic fibrosis patients. As many Gram-negative pathogens, ''P. aeruginosa'' is armed with a sophisticated Type III Secretion System (T3SS) used to inject toxic proteins into human host cells. T3SS has been shown to have an important role in disease and pathogenicity of this bacterium. The T3SS is structured like a syringe that protrudes from the bacterial membrane towards the target cell membrane.[[Image:TypeIIIsecre.png|370px|right|thumb| Model of'' P. aeruginosa'' Type III secretion system. PcrH remains in the bacterial cytoplasm bound to PopB and PopD to keep them soluble and competent for secretion.]] Within this system, two secreted proteins called PopB and PopD are found to insert into the target cell membrane and form a proteinaceous structure called the translocon that will connect with the syringe to serve as a gateway for the toxic proteins into the target cell cytoplasm.<ref>PMID: 21770428</ref> Substantial genetic and biochemical data indicate the translocon is composed by two T3S proteins, in the case of ''Pseudomonas'' ''aeruginosa'', the translocators protein are PopB and PopD.<ref>PMID: 21770428</ref> While they are in the bacterial cytoplasm they need to be maintained in a state competent for secretion and also not toxic for the bacterial cell, the system achieves this by employing a Type II chaperone called PcrH. '''PrcH''' is a small (18.4 kDa) non-secreted bacterial co-chaperone that binds uniquely to these translocator proteins.

=== PcrH Structure ===

PcrH's characteristic fold is composed of Tetratricopeptide Repeats (TPR repeats). TPR repeats consist of a 34 amino-acid sequence motif that folds into two antiparallel alpha-helices that serve as interaction modules and multi-protein complex mediators.<ref>PMID: 23974025</ref> In this case, PcrH from ''Pseudomonas aeruginosa'' consist of three <scene name='Molecular_Playground/Pcr_H/Tprs_2/2'>Tpr-like motifs</scene>. The first Tpr motif is represented in red, the second in green and the third in cyan color, also an additional alpha-helix is represented in blue. This fold is also present in Eukaryotic co-chaperons such as HOP(Heat shock protein Organizing Protein).

PcrH dimerization has been reported to be required for stability of PcrH in the absence of the cargo but not their function. But their dimerization interface is controversial. In the solved structure of PcrH, it showed a dimer with <scene name='44/447152/Pcrh_dimer/1'>back-to-back PcrH monomer</scene> (each monomer is labeled in green and blue). The interaction only seems to happen at Y95, L98 and M99 (labeled in yellow) between helix 4 in the neighboring monomers. However, Tomalka et al showed by mutagenesis that the dimer should be head-to-head where monomers interact via two N terminal helices (TPR1). This result resembles the solved structure of SycD dimer which is the chaperone of translocators in Yersinia and shares 59.3% identity with PcrH. (each monomer is labeled in green and magenta, mutation in residue A61 and L65 labeled in yellow has been shown to disrupt dimerization)

=== PcrH bound to PopB/D ===

PcrH crystal structure has also been solved <scene name='Molecular_Playground/Pcr_H/Pcrh_active_site/1'>when bound to a synthetic peptide </scene> carrying a homologous sequence that is present in these translocator proteins.<ref>PMID: 24297169</ref><ref>PMID: 20385547</ref> PcrH has a <scene name='Molecular_Playground/Pcr_H/Concavecharge/1'>charged concave cleft</scene> (Histidine and Arginine residues shown in yellow) where it binds to a <scene name='Molecular_Playground/Pcr_H/Motif_chainb/1'>sequence motif</scene> (VXLXXP) present in both PopB and PopD (9 residue peptide (rainbow) shown bound to Chain A). The VXLXXP sequence motif binding is displayed as three hydrophobic pockets in the concave side of the TPR domain receive three hydrophobic residues within the CBM present in the synthetic peptide. This interaction keeps them in a metastable non oligomeric state in the cytosol, thus protecting them from degradation and aggregation. It is also believed that PcrH has an active role in delivering PopB and PopD to the basal body of the T3S system, where an ATPse unfolds and secretes the translocators PopB and PopD.

Given its key role in molecular pathogenesis PcrH is a potential target for drug design.

==References==
<references />

Molecular Playground/Pcr H

2014-12-03T16:24:52Z

Yuzhou Tang:

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]
----

<Structure load='PcrH_monomer.pdb' size='370' frame='true' align='right' caption='Pseudomonas aeruginosa PcrH monomer'/>

== PcrH ==

=== Introduction ===

''Pseudomonas aeruginosa'' is a bacterium widely found in the environment, nonetheless is capable of infecting patients with a weak immune system. ''P. aeruginosa'' has been linked to more than 65% of cases of human infections that exhibit great resistance to antibiotics; moreover, is the predominant cause of mortality in cystic fibrosis patients. As many Gram-negative pathogens, ''P. aeruginosa'' is armed with a sophisticated Type III Secretion System (T3SS) used to inject toxic proteins into human host cells. T3SS has been shown to have an important role in disease and pathogenicity of this bacterium. The T3SS is structured like a syringe that protrudes from the bacterial membrane towards the target cell membrane.[[Image:TypeIIIsecre.png|370px|right|thumb| Model of'' P. aeruginosa'' Type III secretion system. PcrH remains in the bacterial cytoplasm bound to PopB and PopD to keep them soluble and competent for secretion.]] Within this system, two secreted proteins called PopB and PopD are found to insert into the target cell membrane and form a proteinaceous structure called the translocon that will connect with the syringe to serve as a gateway for the toxic proteins into the target cell cytoplasm.<ref>PMID: 21770428</ref> Substantial genetic and biochemical data indicate the translocon is composed by two T3S proteins, in the case of ''Pseudomonas'' ''aeruginosa'', the translocators protein are PopB and PopD.<ref>PMID: 21770428</ref> While they are in the bacterial cytoplasm they need to be maintained in a state competent for secretion and also not toxic for the bacterial cell, the system achieves this by employing a Type II chaperone called PcrH. '''PrcH''' is a small (18.4 kDa) non-secreted bacterial co-chaperone that binds uniquely to these translocator proteins.

=== PcrH Structure ===

PcrH's characteristic fold is composed of Tetratricopeptide Repeats (TPR repeats). TPR repeats consist of a 34 amino-acid sequence motif that folds into two antiparallel alpha-helices that serve as interaction modules and multi-protein complex mediators.<ref>PMID: 23974025</ref> In this case, PcrH from ''Pseudomonas aeruginosa'' consist of three <scene name='Molecular_Playground/Pcr_H/Tprs_2/2'>Tpr-like motifs</scene>. The first Tpr motif is represented in red, the second in green and the third in cyan color, also an additional alpha-helix is represented in blue. This fold is also present in Eukaryotic co-chaperons such as HOP(Heat shock protein Organizing Protein).

PcrH dimerization has been reported to be required for stability of PcrH in the absence of the cargo but not their function. But their dimerization interface is controversial. In the solved structure of PcrH, it showed a dimer with back-to-back PcrH monomer (each monomer is labeled in green and magenta). The interaction only seems to happen at Y95, L98 and M99 (labeled in yellow) between helix 4 in the neighboring monomers. However, Tomalka et al showed by mutagenesis that the dimer should be head-to-head where monomers interact via two N terminal helices (TPR1). This result resembles the solved structure of SycD dimer which is the chaperone of translocators in Yersinia and shares 59.3% identity with PcrH. (each monomer is labeled in green and magenta, mutation in residue A61 and L65 labeled in yellow has been shown to disrupt dimerization)

=== PcrH bound to PopB/D ===

PcrH crystal structure has also been solved <scene name='Molecular_Playground/Pcr_H/Pcrh_active_site/1'>when bound to a synthetic peptide </scene> carrying a homologous sequence that is present in these translocator proteins.<ref>PMID: 24297169</ref><ref>PMID: 20385547</ref> PcrH has a <scene name='Molecular_Playground/Pcr_H/Concavecharge/1'>charged concave cleft</scene> (Histidine and Arginine residues shown in yellow) where it binds to a <scene name='Molecular_Playground/Pcr_H/Motif_chainb/1'>sequence motif</scene> (VXLXXP) present in both PopB and PopD (9 residue peptide (rainbow) shown bound to Chain A). The VXLXXP sequence motif binding is displayed as three hydrophobic pockets in the concave side of the TPR domain receive three hydrophobic residues within the CBM present in the synthetic peptide. This interaction keeps them in a metastable non oligomeric state in the cytosol, thus protecting them from degradation and aggregation. It is also believed that PcrH has an active role in delivering PopB and PopD to the basal body of the T3S system, where an ATPse unfolds and secretes the translocators PopB and PopD.

Given its key role in molecular pathogenesis PcrH is a potential target for drug design.

==References==
<references />

Molecular Playground/Pcr H

2014-12-03T16:20:05Z

Yuzhou Tang:

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]
----
'
<Structure load='PcrH_monomer.pdb' size='370' frame='true' align='right' caption=' ''Pseudomonas aeruginosa'' PcrH monomer '/>

== PcrH ==

=== Introduction ===

''Pseudomonas aeruginosa'' is a bacterium widely found in the environment, nonetheless is capable of infecting patients with a weak immune system. ''P. aeruginosa'' has been linked to more than 65% of cases of human infections that exhibit great resistance to antibiotics; moreover, is the predominant cause of mortality in cystic fibrosis patients. As many Gram-negative pathogens, ''P. aeruginosa'' is armed with a sophisticated Type III Secretion System (T3SS) used to inject toxic proteins into human host cells. T3SS has been shown to have an important role in disease and pathogenicity of this bacterium. The T3SS is structured like a syringe that protrudes from the bacterial membrane towards the target cell membrane.[[Image:TypeIIIsecre.png|370px|right|thumb| Model of'' P. aeruginosa'' Type III secretion system. PcrH remains in the bacterial cytoplasm bound to PopB and PopD to keep them soluble and competent for secretion.]] Within this system, two secreted proteins called PopB and PopD are found to insert into the target cell membrane and form a proteinaceous structure called the translocon that will connect with the syringe to serve as a gateway for the toxic proteins into the target cell cytoplasm.<ref>PMID: 21770428</ref> Substantial genetic and biochemical data indicate the translocon is composed by two T3S proteins, in the case of ''Pseudomonas'' ''aeruginosa'', the translocators protein are PopB and PopD.<ref>PMID: 21770428</ref> While they are in the bacterial cytoplasm they need to be maintained in a state competent for secretion and also not toxic for the bacterial cell, the system achieves this by employing a Type II chaperone called PcrH. '''PrcH''' is a small (18.4 kDa) non-secreted bacterial co-chaperone that binds uniquely to these translocator proteins.

=== PcrH Structure ===

PcrH's characteristic fold is composed of Tetratricopeptide Repeats (TPR repeats). TPR repeats consist of a 34 amino-acid sequence motif that folds into two antiparallel alpha-helices that serve as interaction modules and multi-protein complex mediators.<ref>PMID: 23974025</ref> In this case, PcrH from ''Pseudomonas aeruginosa'' consist of three <scene name='Molecular_Playground/Pcr_H/Tprs_2/2'>Tpr-like motifs</scene>. The first Tpr motif is represented in red, the second in green and the third in cyan color, also an additional alpha-helix is represented in blue. This fold is also present in Eukaryotic co-chaperons such as HOP(Heat shock protein Organizing Protein).

PcrH dimerization has been reported to be required for stability of PcrH in the absence of the cargo but not their function. But their dimerization interface is controversial. In the solved structure of PcrH, it showed a dimer with back-to-back PcrH monomer (each monomer is labeled in green and magenta). The interaction only seems to happen at Y95, L98 and M99 (labeled in yellow) between helix 4 in the neighboring monomers. However, Tomalka et al showed by mutagenesis that the dimer should be head-to-head where monomers interact via two N terminal helices (TPR1). This result resembles the solved structure of SycD dimer which is the chaperone of translocators in Yersinia and shares 59.3% identity with PcrH. (each monomer is labeled in green and magenta, mutation in residue A61 and L65 labeled in yellow has been shown to disrupt dimerization)

=== PcrH bound to PopB/D ===

PcrH crystal structure has also been solved <scene name='Molecular_Playground/Pcr_H/Pcrh_active_site/1'>when bound to a synthetic peptide </scene> carrying a homologous sequence that is present in these translocator proteins.<ref>PMID: 24297169</ref><ref>PMID: 20385547</ref> PcrH has a <scene name='Molecular_Playground/Pcr_H/Concavecharge/1'>charged concave cleft</scene> (Histidine and Arginine residues shown in yellow) where it binds to a <scene name='Molecular_Playground/Pcr_H/Motif_chainb/1'>sequence motif</scene> (VXLXXP) present in both PopB and PopD (9 residue peptide (rainbow) shown bound to Chain A). The VXLXXP sequence motif binding is displayed as three hydrophobic pockets in the concave side of the TPR domain receive three hydrophobic residues within the CBM present in the synthetic peptide. This interaction keeps them in a metastable non oligomeric state in the cytosol, thus protecting them from degradation and aggregation. It is also believed that PcrH has an active role in delivering PopB and PopD to the basal body of the T3S system, where an ATPse unfolds and secretes the translocators PopB and PopD.

Given its key role in molecular pathogenesis PcrH is a potential target for drug design.

==References==
<references />

Molecular Playground/Pcr H

2014-12-03T16:18:22Z

Yuzhou Tang:

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]
----
'
<Structure load='PcrH_monomer.pdb' size='370' frame='true' align='right' caption='''Pseudomonas aeruginosa'' PcrH monomer'/>

== PcrH ==

=== Introduction ===

''Pseudomonas aeruginosa'' is a bacterium widely found in the environment, nonetheless is capable of infecting patients with a weak immune system. ''P. aeruginosa'' has been linked to more than 65% of cases of human infections that exhibit great resistance to antibiotics; moreover, is the predominant cause of mortality in cystic fibrosis patients. As many Gram-negative pathogens, ''P. aeruginosa'' is armed with a sophisticated Type III Secretion System (T3SS) used to inject toxic proteins into human host cells. T3SS has been shown to have an important role in disease and pathogenicity of this bacterium. The T3SS is structured like a syringe that protrudes from the bacterial membrane towards the target cell membrane.[[Image:TypeIIIsecre.png|370px|right|thumb| Model of'' P. aeruginosa'' Type III secretion system. PcrH remains in the bacterial cytoplasm bound to PopB and PopD to keep them soluble and competent for secretion.]] Within this system, two secreted proteins called PopB and PopD are found to insert into the target cell membrane and form a proteinaceous structure called the translocon that will connect with the syringe to serve as a gateway for the toxic proteins into the target cell cytoplasm.<ref>PMID: 21770428</ref> Substantial genetic and biochemical data indicate the translocon is composed by two T3S proteins, in the case of ''Pseudomonas'' ''aeruginosa'', the translocators protein are PopB and PopD.<ref>PMID: 21770428</ref> While they are in the bacterial cytoplasm they need to be maintained in a state competent for secretion and also not toxic for the bacterial cell, the system achieves this by employing a Type II chaperone called PcrH. '''PrcH''' is a small (18.4 kDa) non-secreted bacterial co-chaperone that binds uniquely to these translocator proteins.

=== PcrH Structure ===

PcrH's characteristic fold is composed of Tetratricopeptide Repeats (TPR repeats). TPR repeats consist of a 34 amino-acid sequence motif that folds into two antiparallel alpha-helices that serve as interaction modules and multi-protein complex mediators.<ref>PMID: 23974025</ref> In this case, PcrH from ''Pseudomonas aeruginosa'' consist of three <scene name='Molecular_Playground/Pcr_H/Tprs_2/2'>Tpr-like motifs</scene>. The first Tpr motif is represented in red, the second in green and the third in cyan color, also an additional alpha-helix is represented in blue. This fold is also present in Eukaryotic co-chaperons such as HOP(Heat shock protein Organizing Protein).

PcrH dimerization has been reported to be required for stability of PcrH in the absence of the cargo but not their function. But their dimerization interface is controversial. In the solved structure of PcrH, it showed a dimer with back-to-back PcrH monomer (each monomer is labeled in green and magenta). The interaction only seems to happen at Y95, L98 and M99 (labeled in yellow) between helix 4 in the neighboring monomers. However, Tomalka et al showed by mutagenesis that the dimer should be head-to-head where monomers interact via two N terminal helices (TPR1). This result resembles the solved structure of SycD dimer which is the chaperone of translocators in Yersinia and shares 59.3% identity with PcrH. (each monomer is labeled in green and magenta, mutation in residue A61 and L65 labeled in yellow has been shown to disrupt dimerization)

=== PcrH bound to PopB/D ===

PcrH crystal structure has also been solved <scene name='Molecular_Playground/Pcr_H/Pcrh_active_site/1'>when bound to a synthetic peptide </scene> carrying a homologous sequence that is present in these translocator proteins.<ref>PMID: 24297169</ref><ref>PMID: 20385547</ref> PcrH has a <scene name='Molecular_Playground/Pcr_H/Concavecharge/1'>charged concave cleft</scene> (Histidine and Arginine residues shown in yellow) where it binds to a <scene name='Molecular_Playground/Pcr_H/Motif_chainb/1'>sequence motif</scene> (VXLXXP) present in both PopB and PopD (9 residue peptide (rainbow) shown bound to Chain A). The VXLXXP sequence motif binding is displayed as three hydrophobic pockets in the concave side of the TPR domain receive three hydrophobic residues within the CBM present in the synthetic peptide. This interaction keeps them in a metastable non oligomeric state in the cytosol, thus protecting them from degradation and aggregation. It is also believed that PcrH has an active role in delivering PopB and PopD to the basal body of the T3S system, where an ATPse unfolds and secretes the translocators PopB and PopD.

Given its key role in molecular pathogenesis PcrH is a potential target for drug design.

==References==
<references />

File:PcrH dimer.pdb

2014-12-03T16:02:18Z

Yuzhou Tang:

Molecular Playground/Pcr H

2014-12-03T15:51:08Z

Yuzhou Tang:

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]
----

<Structure load='2xcc' size='350' frame='true' align='right' caption='''Pseudomonas aeruginosa'' PcrH crystal structure' scene='Molecular_Playground/PcrH/Pcrhblackback/1' />

== PcrH ==

=== Introduction ===

''Pseudomonas aeruginosa'' is a bacterium widely found in the environment, nonetheless is capable of infecting patients with a weak immune system. ''P. aeruginosa'' has been linked to more than 65% of cases of human infections that exhibit great resistance to antibiotics; moreover, is the predominant cause of mortality in cystic fibrosis patients. As many Gram-negative pathogens, ''P. aeruginosa'' is armed with a sophisticated Type III Secretion System (T3SS) used to inject toxic proteins into human host cells. T3SS has been shown to have an important role in disease and pathogenicity of this bacterium. The T3SS is structured like a syringe that protrudes from the bacterial membrane towards the target cell membrane.[[Image:TypeIIIsecre.png|370px|right|thumb| Model of'' P. aeruginosa'' Type III secretion system. PcrH remains in the bacterial cytoplasm bound to PopB and PopD to keep them soluble and competent for secretion.]] Within this system, two secreted proteins called PopB and PopD are found to insert into the target cell membrane and form a proteinaceous structure called the translocon that will connect with the syringe to serve as a gateway for the toxic proteins into the target cell cytoplasm.<ref>PMID: 21770428</ref> Substantial genetic and biochemical data indicate the translocon is composed by two T3S proteins, in the case of ''Pseudomonas'' ''aeruginosa'', the translocators protein are PopB and PopD.<ref>PMID: 21770428</ref> While they are in the bacterial cytoplasm they need to be maintained in a state competent for secretion and also not toxic for the bacterial cell, the system achieves this by employing a Type II chaperone called PcrH. '''PrcH''' is a small (18.4 kDa) non-secreted bacterial co-chaperone that binds uniquely to these translocator proteins.

=== PcrH Structure ===

PcrH's characteristic fold is composed of Tetratricopeptide Repeats (TPR repeats). TPR repeats consist of a 34 amino-acid sequence motif that folds into two antiparallel alpha-helices that serve as interaction modules and multi-protein complex mediators.<ref>PMID: 23974025</ref> In this case, PcrH from ''Pseudomonas aeruginosa'' consist of three <scene name='Molecular_Playground/Pcr_H/Tprs_2/2'>Tpr-like motifs</scene>. The first Tpr motif is represented in red, the second in green and the third in cyan color, also an additional alpha-helix is represented in blue. This fold is also present in Eukaryotic co-chaperons such as HOP(Heat shock protein Organizing Protein).

PcrH dimerization has been reported to be required for stability of PcrH in the absence of the cargo but not their function. But their dimerization interface is controversial. In the solved structure of PcrH, it showed a dimer with back-to-back PcrH monomer (each monomer is labeled in green and magenta). The interaction only seems to happen at Y95, L98 and M99 (labeled in yellow) between helix 4 in the neighboring monomers. However, Tomalka et al showed by mutagenesis that the dimer should be head-to-head where monomers interact via two N terminal helices (TPR1). This result resembles the solved structure of SycD dimer which is the chaperone of translocators in Yersinia and shares 59.3% identity with PcrH. (each monomer is labeled in green and magenta, mutation in residue A61 and L65 labeled in yellow has been shown to disrupt dimerization)

=== PcrH bound to PopB/D ===

PcrH crystal structure has also been solved <scene name='Molecular_Playground/Pcr_H/Pcrh_active_site/1'>when bound to a synthetic peptide </scene> carrying a homologous sequence that is present in these translocator proteins.<ref>PMID: 24297169</ref><ref>PMID: 20385547</ref> PcrH has a <scene name='Molecular_Playground/Pcr_H/Concavecharge/1'>charged concave cleft</scene> (Histidine and Arginine residues shown in yellow) where it binds to a <scene name='Molecular_Playground/Pcr_H/Motif_chainb/1'>sequence motif</scene> (VXLXXP) present in both PopB and PopD (9 residue peptide (rainbow) shown bound to Chain A). The VXLXXP sequence motif binding is displayed as three hydrophobic pockets in the concave side of the TPR domain receive three hydrophobic residues within the CBM present in the synthetic peptide. This interaction keeps them in a metastable non oligomeric state in the cytosol, thus protecting them from degradation and aggregation. It is also believed that PcrH has an active role in delivering PopB and PopD to the basal body of the T3S system, where an ATPse unfolds and secretes the translocators PopB and PopD.

Given its key role in molecular pathogenesis PcrH is a potential target for drug design.

==References==
<references />

File:PcrH monomer.pdb

2014-12-03T15:32:35Z

Yuzhou Tang:

Molecular Playground/Pcr H

2014-12-03T15:22:37Z

Yuzhou Tang:

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]
----

<Structure load='2xcc' size='350' frame='true' align='right' caption='''Pseudomonas aeruginosa'' PcrH crystal structure' scene='Molecular_Playground/PcrH/Pcrhblackback/1' />

== PcrH ==

=== Introduction ===

''Pseudomonas aeruginosa'' is a bacterium widely found in the environment, nonetheless is capable of infecting patients with a weak immune system. ''P. aeruginosa'' has been linked to more than 65% of cases of human infections that exhibit great resistance to antibiotics; moreover, is the predominant cause of mortality in cystic fibrosis patients. As many Gram-negative pathogens, ''P. aeruginosa'' is armed with a sophisticated Type III Secretion System (T3SS) used to inject toxic proteins into human host cells. T3SS has been shown to have an important role in disease and pathogenicity of this bacterium. The T3SS is structured like a syringe that protrudes from the bacterial membrane towards the target cell membrane.[[Image:TypeIIIsecre.png|370px|right|thumb| Model of'' P. aeruginosa'' Type III secretion system. PcrH remains in the bacterial cytoplasm bound to PopB and PopD to keep them soluble and competent for secretion.]] Within this system, two secreted proteins called PopB and PopD are found to insert into the target cell membrane and form a proteinaceous structure called the translocon that will connect with the syringe to serve as a gateway for the toxic proteins into the target cell cytoplasm.<ref>PMID: 21770428</ref> Substantial genetic and biochemical data indicate the translocon is composed by two T3S proteins, in the case of ''Pseudomonas'' ''aeruginosa'', the translocators protein are PopB and PopD.<ref>PMID: 21770428</ref> While they are in the bacterial cytoplasm they need to be maintained in a state competent for secretion and also not toxic for the bacterial cell, the system achieves this by employing a Type II chaperone called PcrH. '''PrcH''' (Dimer structure shown in Blue/Green) is a small (18.4 kDa) non-secreted bacterial co-chaperone that binds uniquely to these translocator proteins.

=== PcrH Structure ===

PcrH's characteristic fold is composed of Tetratricopeptide Repeats (TPR repeats). TPR repeats consist of a 34 amino-acid sequence motif that folds into two antiparallel alpha-helices that serve as interaction modules and multi-protein complex mediators.<ref>PMID: 23974025</ref> In this case, PcrH from ''Pseudomonas aeruginosa'' consist of three <scene name='Molecular_Playground/Pcr_H/Tprs_2/2'>Tpr-like motifs</scene>. The first Tpr motif is represented in red, the second in green and the third in cyan color, also an additional alpha-helix is represented in blue. This fold is also present in Eukaryotic co-chaperons such as HOP(Heat shock protein Organizing Protein).

PcrH dimerization has been reported to be required for stability of PcrH in the absence of the cargo but not their function. But their dimerization interface is controversial. In the solved structure of PcrH, it showed a dimer with back-to-back PcrH monomer (each monomer is labeled in green and magenta). The interaction only seems to happen at Y95, L98 and M99 (labeled in yellow) between helix 4 in the neighboring monomers. However, Tomalka et al showed by mutagenesis that the dimer should be head-to-head where monomers interact via two N terminal helices (TPR1). This result resembles the solved structure of SycD dimer which is the chaperone of translocators in Yersinia and shares 59.3% identity with PcrH. (each monomer is labeled in green and magenta, mutation in residue A61 and L65 labeled in yellow has been shown to disrupt dimerization)

=== PcrH bound to PopB/D ===

PcrH crystal structure has also been solved <scene name='Molecular_Playground/Pcr_H/Pcrh_active_site/1'>when bound to a synthetic peptide </scene> carrying a homologous sequence that is present in these translocator proteins.<ref>PMID: 24297169</ref><ref>PMID: 20385547</ref> PcrH has a <scene name='Molecular_Playground/Pcr_H/Concavecharge/1'>charged concave cleft</scene> (Histidine and Arginine residues shown in yellow) where it binds to a <scene name='Molecular_Playground/Pcr_H/Motif_chainb/1'>sequence motif</scene> (VXLXXP) present in both PopB and PopD (9 residue peptide (rainbow) shown bound to Chain A). The VXLXXP sequence motif binding is displayed as three hydrophobic pockets in the concave side of the TPR domain receive three hydrophobic residues within the CBM present in the synthetic peptide. This interaction keeps them in a metastable non oligomeric state in the cytosol, thus protecting them from degradation and aggregation. It is also believed that PcrH has an active role in delivering PopB and PopD to the basal body of the T3S system, where an ATPse unfolds and secretes the translocators PopB and PopD.

Given its key role in molecular pathogenesis PcrH is a potential target for drug design.

==References==
<references />