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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].
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].
 
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[[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.]]
<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])' />
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== Introduction ==
== Introduction ==


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[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''] (H<sub>2</sub>ase) 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.
[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''] (H<sub>2</sub>ase) 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 in the maturation of [NiFe]-[http://en.wikipedia.org/wiki/Hydrogenase ''H<sub>2</sub>ase''] 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 ''H<sub>2</sub>ase'']<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>.  
 
Accessory proteins HypABCDEF and UreIEFGH facilitate the maturation of [NiFe]-[http://en.wikipedia.org/wiki/Hydrogenase ''H<sub>2</sub>ase''] 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 ''H<sub>2</sub>ase'']<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>.  




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<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])' />
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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 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])<ref>PMID:19621959</ref>.  The monomeric structure shows an alpha/beta lobe containing the N- and C-termini well separated from the zinc binding lobe (Fig. 1).  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 similating the internal pH of H. pylori under acid shock or at neutral pH conditions<ref name="bob"/>.  Whereas the Ni(II) site is 6-coordinate N/O under both pH conditions, the Zn(II) coordination changes from Cys<sub>4</sub> at neutral pH to Cys<sub>2</sub>His<sub>2</sub> at acidic pH with nickel-bound<ref name="bob"/> (Fig. 2).  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<ref name="bob"/>.


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 Cys<sub>4</sub> at neutral pH to Cys<sub>2</sub>His<sub>2</sub> 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 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<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 ==


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== Research Interests ==


[[Image:HypA-pH-Ni-Change.png|150 px|thumb|Fig. 2: Diagram of Ni- and pH-dependent structural changes to Zn(II) site of ''Hp''HypA (adapted figure<ref name="bob"/>)]]
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 ''H<sub>2</sub>ase''] 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.
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 ''H<sub>2</sub>ase''] 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.


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Heidi Hu
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