Proteopedia - User contributions [en]

Molecular Playground/OmpG

2014-12-18T03:51:11Z

Monifa Fahie:

==Outer Membrane Protein G==
<Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'/>

Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores as stochastic sensors for single molecule detection. The applications of biosensors range from fundamental research, clinical diagnosis and even advances in homeland security. PCR (Polymerase chain reaction) and ELISA (Enzyme- linked immunosorbent assay) are current sensitive detection methods. However, these methods are time consuming and require laborious effort, where results are provided hours or days later. For this reason alternate approaches are mounting in demands that are rapid in detection time, highly sensitive and reliable.

Conventional nanopore sensing is achieved by monitoring the passage of ionic current through a pore containing natural or engineered recognition sites. Analyte detection is visualized as a change (most commonly as a current blockage) in the ionic current. We will tailor and fine tune monomeric protein, Outer membrane protein G (OmpG) for detecting large analytes.

This <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'>monomeric porin</scene> has seven flexible loops in which we can attach ligands or insert peptide sequences. Utilizing the flexibility of loop 6, which is the longest and most flexible, we will append ligands and peptide sequences so that our target analytes to bind to OmpG. <scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'>Location of ligand</scene>
<scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

==Structural Features of OmpG==

OmpG is a 14-stranded beta-barrel and in contrast to most porins, appears to function as a monomer.[1] The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the passive transport of large oligosaccharides.[1] OmpG adopts two main conformations: open and closed which is termed gating.

[[Image:Open and closed OmpG.jpg|left|thumb|]]

At neutral pH the porin is mainly in an open conformation, with periodic closures. However at a more acidic pH the closed conformation is becomes dominant. This fluctuation between open and closed is a result of OmpG's flexible loop 6 (highlighted in red), which folds across the channel blocking the pore opening. The rearrangement of loop 6 appears to be triggered by a pair of histidine residues, which repel each other at acidic pH, resulting in the breakage of neighbouring H-bonds and a lengthening of loop 6 from 10 to 17 residues[2,3]. <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

[2IWW]
[http://en.wikipedia.org/wiki/Outer_membrane_protein_G].

The loop environment of OmpG carries a net negative charge. This highly negative character may be implicated in the gating behavior of OmpG. If we can gain a deeper understanding of the individual loop behavior in the overall gating, we could use this knowledge to tune it for specific detection of a wide variety of target analytes.

[[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]]

==Current OmpG Projects in the Chen Lab==

Engineering loop 6 to detect large protein analytes

Investigating the effect of loop charge on the gating behavior of OmpG

==Additional Resources==

Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]
For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]

==References==

[1] Chen M, Li Q-H and Bayley, H (2008) "Orientation of the monomeric porin OmpG in planar lipid bilayers." ChemBioChem 9(18):3029-36

[2] Chen M, Khalid S, Sansom M and Bayley H (2008) "Outer membrane protein G: engineering a quiet pore for biosensing." Proc Natl Acad Sci U S A 105: 6272-6277

[3] Damaghi M, Bippes C, et al. (2010) "pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG." J Mol Biol 397(4):878-82.

File:Open and closed OmpG.jpg

2014-12-18T03:46:57Z

Monifa Fahie:

Molecular Playground/OmpG

2014-12-18T03:38:38Z

Monifa Fahie:

==Outer Membrane Protein G==
<Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'/>

Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores as stochastic sensors for single molecule detection. The applications of biosensors range from fundamental research, clinical diagnosis and even advances in homeland security. PCR (Polymerase chain reaction) and ELISA (Enzyme- linked immunosorbent assay) are current sensitive detection methods. However, these methods are time consuming and require laborious effort, where results are provided hours or days later. For this reason alternate approaches are mounting in demands that are rapid in detection time, highly sensitive and reliable.

Conventional nanopore sensing is achieved by monitoring the passage of ionic current through a pore containing natural or engineered recognition sites. Analyte detection is visualized as a change (most commonly as a current blockage) in the ionic current. We will tailor and fine tune monomeric protein, Outer membrane protein G (OmpG) for detecting large analytes.

This <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'>monomeric porin</scene> has seven flexible loops in which we can attach ligands or insert peptide sequences. Utilizing the flexibility of loop 6, which is the longest and most flexible, we will append ligands and peptide sequences so that our target analytes to bind to OmpG. <scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'>Location of ligand</scene>
<scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

==Structural Features of OmpG==

OmpG is a 14-stranded beta-barrel and in contrast to most porins, appears to function as a monomer.[1] The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the passive transport of large oligosaccharides.[1] OmpG adopts two main conformations: open and closed.

[[Image:OmpG_opening_and_closing.gif|left|thumb|]]

At neutral pH the porin is mainly in an open conformation, with periodic closures. However at a more acidic pH the closed conformation is becomes dominant. This fluctuation between open and closed is a result of OmpG's flexible loop 6 (highlighted in red), which folds across the channel blocking the pore opening. The rearrangement of loop 6 appears to be triggered by a pair of histidine residues, which repel each other at acidic pH, resulting in the breakage of neighbouring H-bonds and a lengthening of loop 6 from 10 to 17 residues[2,3]. <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

[2IWW]
[http://en.wikipedia.org/wiki/Outer_membrane_protein_G].

The loop environment of OmpG carries a net negative charge. This highly negative character may be implicated in the gating behavior of OmpG. If we can gain a deeper understanding of OmpG gating, we could use this knowledge to tune it for specific detection of a wide variety of target analytes.

[[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]]

==Current OmpG Projects in the Chen Lab==

Engineering loop 6 to detect large protein analytes

Investigating the effect of loop charge on the gating behavior of OmpG

==Additional Resources==

Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]
For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]

==References==

[1] Chen M, Li Q-H and Bayley, H (2008) "Orientation of the monomeric porin OmpG in planar lipid bilayers." ChemBioChem 9(18):3029-36

[2] Chen M, Khalid S, Sansom M and Bayley H (2008) "Outer membrane protein G: engineering a quiet pore for biosensing." Proc Natl Acad Sci U S A 105: 6272-6277

[3] Damaghi M, Bippes C, et al. (2010) "pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG." J Mol Biol 397(4):878-82.

Molecular Playground/OmpG

2014-12-18T03:14:12Z

Monifa Fahie:

==Outer Membrane Protein G==
<Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'/>

Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores to be used as stochastic sensors, for single molecule detection. The applications of biosensors range from fundamental research, clinical diagnosis, and even advances in homeland security. PCR (Polymerase chain reaction) and ELISA (Enzyme- linked immunosorbent assay) are current sensitive detection methods. However, these methods are time consuming and require laborious effort, where results are provided hours or days later. For this reason alternate approaches are mounting in demands that are rapid in detection time, highly sensitive and reliable.

Through stochastic sensing, we utilize the passage of ionic current through a protein pore containing engineered recognition sites, allowing for monitoring of analytes present. We propose the use of monomeric protein Outer membrane protein G (OmpG) will allow us to tailor and fine tune properties of this pore in detection of analytes.

This <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'>monomeric porin</scene> has features that can be customized as a sensor component, using protein engineering we can develop this protein to be a successful biosensor. Utilizing the flexibility of an extracellular loop, we will append a ligand to help detect our target analyte. <scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'>Location of ligand</scene>
<scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

==Structural Features of OmpG==

OmpG is a 14-stranded beta-barrel and in contrast to most porins, appears to function as a monomer.[1] The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the passive transport of larger oligosaccharides.[1] OmpG adopts two conformations: open and closed. At neutral pH the porin displays an open conformation. However at a more acidic pH the closed conformation is adopted. This closed conformation is a result of OmpG's flexible extracellular loop 6, which folds across the channel blocking the pore opening. The rearrangement of loop 6 appears to be triggered by a pair of histidine residues, which repel each another at acidic pH, resulting in the breakage of neighbouring H-bonds and a lengthening of loop 6 from 10 to 17 residues[2,3]. <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

[2IWW]
[http://en.wikipedia.org/wiki/Outer_membrane_protein_G].

The loop environment of OmpG carries a net negative charge. This highly negative character may be implicated in the gating behavior of OmpG. If we can gain a deeper understanding of OmpG gating, we could could use this knowledge to tune it for specific detection of target analytes.

[[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]]

==Current OmpG Projects in the Chen Lab==

Engineering loop 6 to detect large protein analytes

Investigating the effect of loop charge on the gating behavior of OmpG

==Additional Resources==

Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]
For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]

==References==

[1] Chen M, Li Q-H and Bayley, H (2008) "Orientation of the monomeric porin OmpG in planar lipid bilayers." ChemBioChem 9(18):3029-36

[2] Chen M, Khalid S, Sansom M and Bayley H (2008) "Outer membrane protein G: engineering a quiet pore for biosensing." Proc Natl Acad Sci U S A 105: 6272-6277

[3] Damaghi M, Bippes C, et al. (2010) "pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG." J Mol Biol 397(4):878-82.

Molecular Playground/OmpG

2014-12-06T20:44:40Z

Monifa Fahie:

<Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'>
===Outer Membrane Protein G===
<StructureSection load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'>

Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores to be used as stochastic sensors, for single molecule detection. The applications of biosensors range from fundamental research, clinical diagnosis, and even advances in homeland security. PCR (Polymerase chain reaction) and ELISA (Enzyme- linked immunosorbent assay) are current sensitive detection methods. However, these methods are time consuming and require laborious effort, where results are provided hours or days later. For this reason alternate approaches are mounting in demands that are rapid in detection time, highly sensitive and reliable.

Through stochastic sensing, we utilize the passage of ionic current through a protein pore containing engineered recognition sites, allowing for monitoring of analytes present. We propose the use of monomeric protein Outer membrane protein G (OmpG) will allow us to tailor and fine tune properties of this pore in detection of analytes.

This <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'>monomeric porin</scene> has features that can be customized as a sensor component, using protein engineering we can develop this protein to be a successful biosensor. Utilizing the flexibility of an extracellular loop, we will append a ligand to help detect our target analyte. <scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'>Location of ligand</scene>
<scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

==Structural Features of OmpG==
OmpG is a 14-stranded beta-barrel and in contrast to most porins, appears to function as a monomer.[1] The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the passive transport of larger oligosaccharides.[1] OmpG adopts two conformations: open and closed. At neutral pH the porin displays an open conformation. However at a more acidic pH the closed conformation is adopted. This closed conformation is a result of OmpG's flexible extracellular loop 6, which folds across the channel blocking the pore opening. The rearrangement of loop 6 appears to be triggered by a pair of histidine residues, which repel each another at acidic pH, resulting in the breakage of neighbouring H-bonds and a lengthening of loop 6 from 10 to 17 residues[2,3]. <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

[[Image:OmpG Conformation.png|thumb|]]
[2IWW]
[http://en.wikipedia.org/wiki/Outer_membrane_protein_G].

The loop environment of OmpG carries a net negative charge. This highly negative character may be implicated in the gating behavior of OmpG. If we can gain a deeper understanding of OmpG gating, we could could use this knowledge to tune it for specific detection of target analytes.

[[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]]

==Current OmpG Projects in the Chen Lab==
Engineering loop 6 to detect large protein analytes
Investigating the effect of loop charge on the gating behavior of OmpG

==Additional Resources==
Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]
For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]


==References==

[1] Chen M, Li Q-H and Bayley, H (2008) "Orientation of the monomeric porin OmpG in planar lipid bilayers." ChemBioChem 9(18):3029-36

[2] Chen M, Khalid S, Sansom M and Bayley H (2008) "Outer membrane protein G: engineering a quiet pore for biosensing." Proc Natl Acad Sci U S A 105: 6272-6277

[3] Damaghi M, Bippes C, et al. (2010) "pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG." J Mol Biol 397(4):878-82.

</StructureSection>

Molecular Playground/ClyA

2014-12-06T16:03:26Z

Monifa Fahie:

<Structure load='1QOY' size='350' frame='true' align='right' caption='Please select a link from the left to display desired ClyA form' scene='Insert optional scene name here' />
==Introduction==

Pore-forming toxins (PFTs) are virulence factors secreted by pathogenic organisms. These are proteins that form transmembrane channels on target cell membranes. They cause cell death by making the cell membrane permeable, leading to osmotic imbalance and lysis. There are two classes of PFTs based on their secondary structure, alpha-PFTs and beta-PFTs. Cytolysin A (ClyA) is an alpha-PFT and is secreted by ''Salmonella'', ''Shigella'' and ''E. coli'' strains.

==About this Structure==
<scene name='57/571278/Clya_monomer/2'>ClyA monomer in its inactive form</scene>

[[1QOY]] is a 34 kDa monomer from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli''] (''E. coli''). It is a pore-forming toxin (PFT) comprised of four alpha helicies, a smaller fifth alpha helix, and a beta tongue. The N-terminus and the C-terminus are highlighted. ClyA has been shown to form pores through a non-classical assembly pathway, excreted in oligomeric form in outer-membrane vesicles (OMV) as pre-pores. Only until ClyA reaches the target host membrane does it form the dodecameric PFT with hemolytic activity, possessing the ability to lyse the host cell.

<scene name='57/571278/Clya_protomer/1'>ClyA protomer</scene>

The protomer of ClyA reveals slight differences between the monomer and protomer (from the dodecameric oligomer). The major conformational changes between the monomer and the protomer are the positions of the N-terminal helix and the beta-tongue. As ClyA oligomerizes and forms a pore, the N-terminal helix swings to the opposite side of the molecule while the beta-tongue changes its conformation and turns into an alpha-helix that interacts with the lipid bilayer.

<scene name='57/571278/Clya_oligomer/1'>The oligomeric form of ClyA</scene>

Its crystal structure, [[2WCD]], reveals a dodecamer. Larger [http://pubs.acs.org/doi/abs/10.1021/ja4053398 pores] have been isolated, as well. A few research endeavors involving ClyA include using [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2839435/ ClyA as part of cancer therapy], as well as a [http://www.nature.com/ncomms/2013/130912/ncomms3415/full/ncomms3415.html DNA delivery vehicle].

==Research on ClyA at UMass Amherst==
The [http://www.chem.umass.edu/~chenlab/index.HTML, Chen Lab] recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] non-classical assembly. We use a technique commonly used for nanopore sensing called electrophysiology, which allows us to measure the ionic current through the ClyA nanopore.

Current ClyA projects focus on 3 main areas:

ClyA non-classical assembly and attack

ClyA engineered for cancer therapy

Studies of [http://en.wikipedia.org/wiki/Electro-osmosis, electro-osmosis] using ClyA nanopore

==References==

1. Wallace, a J. et al. E. coli hemolysin E (HlyE, ClyA, SheA): X-ray crystal structure of the toxin and observation of membrane pores by electron microscopy. Cell 100, 265–76 (2000).

2. Atkins, a et al. Structure-function relationships of a novel bacterial toxin, hemolysin E. The role of alpha G. J. Biol. Chem. 275, 41150–5 (2000).

3. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. & Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–30 (2009).

4. Fahie, M. et al. A non-classical assembly pathway of Escherichia coli pore-forming toxin cytolysin A. J. Biol. Chem. 288, 31042–51 (2013).

Molecular Playground/ClyA

2014-12-06T16:02:46Z

Monifa Fahie:

<Structure load='1QOY' size='350' frame='true' align='right' caption='Please select a link from the left to display desired ClyA form' scene='Insert optional scene name here' />
==Introduction==

Pore-forming toxins (PFTs) are virulence factors secreted by pathogenic organisms. These are proteins that form transmembrane channels on target cell membranes. They cause cell death by making the cell membrane permeable, leading to osmotic imbalance and lysis. There are two classes of PFTs based on their secondary structure, alpha-PFTs and beta-PFTs. Cytolysin A (ClyA) is an alpha-PFT and is secreted by ''Salmonella'', ''Shigella'' and ''E. coli'' strains.

==About this Structure==
<scene name='57/571278/Clya_monomer/2'>ClyA monomer in its inactive form</scene>

[[1QOY]] is a 34 kDa monomer from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli''] (''E. coli''). It is a pore-forming toxin (PFT) comprised of four alpha helicies, a smaller fifth alpha helix, and a beta tongue. The N-terminus and the C-terminus are highlighted. ClyA has been shown to form pores through a non-classical assembly pathway, excreted in oligomeric form in outer-membrane vesicles (OMV) as pre-pores. Only until ClyA reaches the target host membrane does it form the dodecameric PFT with hemolytic activity, possessing the ability to lyse the host cell.

<scene name='57/571278/Clya_protomer/1'>ClyA protomer</scene>

The protomer of ClyA reveals slight differences between the monomer and protomer (from the dodecameric oligomer). The major conformational changes between the monomer and the protomer are the positions of the N-terminal helix and the beta-tongue. As ClyA oligomerizes and forms a pore, the N-terminal helix swings to the opposite side of the molecule while the beta-tongue changes its conformation and turns into an alpha-helix that interacts with the lipid bilayer.

<scene name='57/571278/Clya_oligomer/1'>The oligomeric form of ClyA</scene>

Its crystal structure, [[2WCD]], reveals a dodecamer. Larger [http://pubs.acs.org/doi/abs/10.1021/ja4053398 pores] have been isolated, as well. A few research endeavors involving ClyA include using [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2839435/ ClyA as part of cancer therapy], as well as a [http://www.nature.com/ncomms/2013/130912/ncomms3415/full/ncomms3415.html DNA delivery vehicle].

==Research on ClyA at UMass Amherst==
The [http://www.chem.umass.edu/~chenlab/index.HTML, Chen Lab] recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] non-classical assembly. We use a technique commonly used for nanopore sensing called electrophysiology, which allows us to measure the ionic current through the ClyA nanopore.

Current ClyA projects focus on 3 main areas:
ClyA non-classical assembly and attack

ClyA engineered for cancer therapy

Studies of [http://en.wikipedia.org/wiki/Electro-osmosis, electro-osmosis] using ClyA nanopore

==References==

1. Wallace, a J. et al. E. coli hemolysin E (HlyE, ClyA, SheA): X-ray crystal structure of the toxin and observation of membrane pores by electron microscopy. Cell 100, 265–76 (2000).

2. Atkins, a et al. Structure-function relationships of a novel bacterial toxin, hemolysin E. The role of alpha G. J. Biol. Chem. 275, 41150–5 (2000).

3. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. & Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–30 (2009).

4. Fahie, M. et al. A non-classical assembly pathway of Escherichia coli pore-forming toxin cytolysin A. J. Biol. Chem. 288, 31042–51 (2013).

Molecular Playground/OmpG

2014-12-06T15:37:52Z

Monifa Fahie:

<Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'>
==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='3rec' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''>
===Outer Membrane Protein G===
Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores to be used as stochastic sensors, for single molecule detection. The applications of biosensors range from fundamental research, clinical diagnosis, and even advances in homeland security. PCR (Polymerase chain reaction) and ELISA (Enzyme- linked immunosorbent assay) are current sensitive detection methods. However, these methods are time consuming and require laborious effort, where results are provided hours or days later. For this reason alternate approaches are mounting in demands that are rapid in detection time, highly sensitive and reliable.

Through stochastic sensing, we utilize the passage of ionic current through a protein pore containing engineered recognition sites, allowing for monitoring of analytes present. We propose the use of monomeric protein Outer membrane protein G (OmpG) will allow us to tailor and fine tune properties of this pore in detection of analytes.

This <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'>monomeric porin</scene> has features that can be customized as a sensor component, using protein engineering we can develop this protein to be a successful biosensor. Utilizing the flexibility of an extracellular loop, we will append a ligand to help detect our target analyte. <scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'>Location of ligand</scene>
<scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

==Structural Features of OmpG==
OmpG is a 14-stranded beta-barrel and in contrast to most porins, appears to function as a monomer.[1] The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the passive transport of larger oligosaccharides.[1] OmpG adopts two conformations: open and closed. At neutral pH the porin displays an open conformation. However at a more acidic pH the closed conformation is adopted. This closed conformation is a result of OmpG's flexible extracellular loop 6, which folds across the channel blocking the pore opening. The rearrangement of loop 6 appears to be triggered by a pair of histidine residues, which repel each another at acidic pH, resulting in the breakage of neighbouring H-bonds and a lengthening of loop 6 from 10 to 17 residues[2,3]. <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

[[Image:OmpG Conformation.png|thumb|]]
[2IWW]
[http://en.wikipedia.org/wiki/Outer_membrane_protein_G].

The loop environment of OmpG carries a net negative charge. This highly negative character may be implicated in the gating behavior of OmpG. If we can gain a deeper understanding of OmpG gating, we could could use this knowledge to tune it for specific detection of target analytes.

[[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]]

==Current OmpG Projects in the Chen Lab==
Engineering loop 6 to detect large protein analytes
Investigating the effect of loop charge on the gating behavior of OmpG

==Additional Resources==
Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]
For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]


==References==

[1] Chen M, Li Q-H and Bayley, H (2008) "Orientation of the monomeric porin OmpG in planar lipid bilayers." ChemBioChem 9(18):3029-36

[2] Chen M, Khalid S, Sansom M and Bayley H (2008) "Outer membrane protein G: engineering a quiet pore for biosensing." Proc Natl Acad Sci U S A 105: 6272-6277

[3] Damaghi M, Bippes C, et al. (2010) "pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG." J Mol Biol 397(4):878-82.
</StructureSection>
===Outer Membrane Protein G===
Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores to be used as stochastic sensors, for single molecule detection. The applications of biosensors range from fundamental research, clinical diagnosis, and even advances in homeland security. PCR (Polymerase chain reaction) and ELISA (Enzyme- linked immunosorbent assay) are current sensitive detection methods. However, these methods are time consuming and require laborious effort, where results are provided hours or days later. For this reason alternate approaches are mounting in demands that are rapid in detection time, highly sensitive and reliable.

Through stochastic sensing, we utilize the passage of ionic current through a protein pore containing engineered recognition sites, allowing for monitoring of analytes present. We propose the use of monomeric protein Outer membrane protein G (OmpG) will allow us to tailor and fine tune properties of this pore in detection of analytes.

This <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'>monomeric porin</scene> has features that can be customized as a sensor component, using protein engineering we can develop this protein to be a successful biosensor. Utilizing the flexibility of an extracellular loop, we will append a ligand to help detect our target analyte. <scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'>Location of ligand</scene>
<scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

==Structural Features of OmpG==
OmpG is a 14-stranded beta-barrel and in contrast to most porins, appears to function as a monomer.[1] The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the passive transport of larger oligosaccharides.[1] OmpG adopts two conformations: open and closed. At neutral pH the porin displays an open conformation. However at a more acidic pH the closed conformation is adopted. This closed conformation is a result of OmpG's flexible extracellular loop 6, which folds across the channel blocking the pore opening. The rearrangement of loop 6 appears to be triggered by a pair of histidine residues, which repel one another at acidic pH, resulting in the breakage of neighbouring H-bonds and a lengthening of loop 6 from 10 to 17 residues[2,3]. <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

[[Image:OmpG Conformation.png|thumb|]]
[2IWW]
[http://en.wikipedia.org/wiki/Outer_membrane_protein_G].

==Additional Resources==
Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]
For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]


==References==

[1] Chen M, Li Q-H and Bayley, H (2008) "Orientation of the monomeric porin OmpG in planar lipid bilayers." ChemBioChem 9(18):3029-36

[2] Chen M, Khalid S, Sansom M and Bayley H (2008) "Outer membrane protein G: engineering a quiet pore for biosensing." Proc Natl Acad Sci U S A 105: 6272-6277

[3] Damaghi M, Bippes C, et al. (2010) "pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG." J Mol Biol 397(4):878-82.

</StructureSection>OmpG is a member of [[CBI Molecules]] being studied in the [http://www.chem.umass.edu/~chenlab/ Chen Lab] 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].

===Outer Membrane Protein G===
Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores to be used as stochastic sensors, for single molecule detection. The applications of biosensors range from fundamental research, clinical diagnosis, and even advances in homeland security. PCR (Polymerase chain reaction) and ELISA (Enzyme- linked immunosorbent assay) are current sensitive detection methods. However, these methods are time consuming and require laborious effort, where results are provided hours or days later. For this reason alternate approaches are mounting in demands that are rapid in detection time, highly sensitive and reliable.

Through stochastic sensing, we utilize the passage of ionic current through a protein pore containing engineered recognition sites, allowing for monitoring of analytes present. We propose the use of monomeric protein Outer membrane protein G (OmpG) will allow us to tailor and fine tune properties of this pore in detection of analytes.

This <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'>monomeric porin</scene> has features that can be customized as a sensor component, using protein engineering we can develop this protein to be a successful biosensor. Utilizing the flexibility of an extracellular loop, we will append a ligand to help detect our target analyte. <scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'>Location of ligand</scene>
<scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

==Structural Features of OmpG==
OmpG is a 14-stranded beta-barrel and in contrast to most porins, appears to function as a monomer.[1] The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the passive transport of larger oligosaccharides.[1] OmpG adopts two conformations: open and closed. At neutral pH the porin displays an open conformation. However at a more acidic pH the closed conformation is adopted. This closed conformation is a result of OmpG's flexible extracellular loop 6, which folds across the channel blocking the pore opening. The rearrangement of loop 6 appears to be triggered by a pair of histidine residues, which repel one another at acidic pH, resulting in the breakage of neighbouring H-bonds and a lengthening of loop 6 from 10 to 17 residues[2,3]. <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

[[Image:OmpG Conformation.png | thumb|]]
[2IWW]
[http://en.wikipedia.org/wiki/Outer_membrane_protein_G].

==Additional Resources==
Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]
For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]


==References==

[1] Chen M, Li Q-H and Bayley, H (2008) "Orientation of the monomeric porin OmpG in planar lipid bilayers." ChemBioChem 9(18):3029-36

[2] Chen M, Khalid S, Sansom M and Bayley H (2008) "Outer membrane protein G: engineering a quiet pore for biosensing." Proc Natl Acad Sci U S A 105: 6272-6277

[3] Damaghi M, Bippes C, et al. (2010) "pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG." J Mol Biol 397(4):878-82.

File:OmpG top down of net negative loop region.png

2014-12-06T15:33:42Z

Monifa Fahie:

Molecular Playground/OmpG

2014-12-06T15:31:58Z

Monifa Fahie:

<Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'>
==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='3rec' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''>
===Outer Membrane Protein G===
Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores to be used as stochastic sensors, for single molecule detection. The applications of biosensors range from fundamental research, clinical diagnosis, and even advances in homeland security. PCR (Polymerase chain reaction) and ELISA (Enzyme- linked immunosorbent assay) are current sensitive detection methods. However, these methods are time consuming and require laborious effort, where results are provided hours or days later. For this reason alternate approaches are mounting in demands that are rapid in detection time, highly sensitive and reliable.

Through stochastic sensing, we utilize the passage of ionic current through a protein pore containing engineered recognition sites, allowing for monitoring of analytes present. We propose the use of monomeric protein Outer membrane protein G (OmpG) will allow us to tailor and fine tune properties of this pore in detection of analytes.

This <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'>monomeric porin</scene> has features that can be customized as a sensor component, using protein engineering we can develop this protein to be a successful biosensor. Utilizing the flexibility of an extracellular loop, we will append a ligand to help detect our target analyte. <scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'>Location of ligand</scene>
<scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

==Structural Features of OmpG==
OmpG is a 14-stranded beta-barrel and in contrast to most porins, appears to function as a monomer.[1] The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the passive transport of larger oligosaccharides.[1] OmpG adopts two conformations: open and closed. At neutral pH the porin displays an open conformation. However at a more acidic pH the closed conformation is adopted. This closed conformation is a result of OmpG's flexible extracellular loop 6, which folds across the channel blocking the pore opening. The rearrangement of loop 6 appears to be triggered by a pair of histidine residues, which repel each another at acidic pH, resulting in the breakage of neighbouring H-bonds and a lengthening of loop 6 from 10 to 17 residues[2,3]. <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

[[Image:OmpG Conformation.png|thumb|]]
[2IWW]
[http://en.wikipedia.org/wiki/Outer_membrane_protein_G].

The loop environment of OmpG carries a net negative charge. This highly negative character may be implicated in the gating behavior of OmpG. If we can gain a deeper understanding of OmpG gating, we could could use this knowledge to tune it for specific detection of target analytes.

==Current OmpG Projects in the Chen Lab==
Engineering loop 6 to detect large protein analytes
Investigating the effect of loop charge on the gating behavior of OmpG

==Additional Resources==
Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]
For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]


==References==

[1] Chen M, Li Q-H and Bayley, H (2008) "Orientation of the monomeric porin OmpG in planar lipid bilayers." ChemBioChem 9(18):3029-36

[2] Chen M, Khalid S, Sansom M and Bayley H (2008) "Outer membrane protein G: engineering a quiet pore for biosensing." Proc Natl Acad Sci U S A 105: 6272-6277

[3] Damaghi M, Bippes C, et al. (2010) "pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG." J Mol Biol 397(4):878-82.
</StructureSection>
===Outer Membrane Protein G===
Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores to be used as stochastic sensors, for single molecule detection. The applications of biosensors range from fundamental research, clinical diagnosis, and even advances in homeland security. PCR (Polymerase chain reaction) and ELISA (Enzyme- linked immunosorbent assay) are current sensitive detection methods. However, these methods are time consuming and require laborious effort, where results are provided hours or days later. For this reason alternate approaches are mounting in demands that are rapid in detection time, highly sensitive and reliable.

Through stochastic sensing, we utilize the passage of ionic current through a protein pore containing engineered recognition sites, allowing for monitoring of analytes present. We propose the use of monomeric protein Outer membrane protein G (OmpG) will allow us to tailor and fine tune properties of this pore in detection of analytes.

This <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'>monomeric porin</scene> has features that can be customized as a sensor component, using protein engineering we can develop this protein to be a successful biosensor. Utilizing the flexibility of an extracellular loop, we will append a ligand to help detect our target analyte. <scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'>Location of ligand</scene>
<scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

==Structural Features of OmpG==
OmpG is a 14-stranded beta-barrel and in contrast to most porins, appears to function as a monomer.[1] The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the passive transport of larger oligosaccharides.[1] OmpG adopts two conformations: open and closed. At neutral pH the porin displays an open conformation. However at a more acidic pH the closed conformation is adopted. This closed conformation is a result of OmpG's flexible extracellular loop 6, which folds across the channel blocking the pore opening. The rearrangement of loop 6 appears to be triggered by a pair of histidine residues, which repel one another at acidic pH, resulting in the breakage of neighbouring H-bonds and a lengthening of loop 6 from 10 to 17 residues[2,3]. <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

[[Image:OmpG Conformation.png|thumb|]]
[2IWW]
[http://en.wikipedia.org/wiki/Outer_membrane_protein_G].

==Additional Resources==
Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]
For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]


==References==

[1] Chen M, Li Q-H and Bayley, H (2008) "Orientation of the monomeric porin OmpG in planar lipid bilayers." ChemBioChem 9(18):3029-36

[2] Chen M, Khalid S, Sansom M and Bayley H (2008) "Outer membrane protein G: engineering a quiet pore for biosensing." Proc Natl Acad Sci U S A 105: 6272-6277

[3] Damaghi M, Bippes C, et al. (2010) "pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG." J Mol Biol 397(4):878-82.

</StructureSection>OmpG is a member of [[CBI Molecules]] being studied in the [http://www.chem.umass.edu/~chenlab/ Chen Lab] 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].

===Outer Membrane Protein G===
Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores to be used as stochastic sensors, for single molecule detection. The applications of biosensors range from fundamental research, clinical diagnosis, and even advances in homeland security. PCR (Polymerase chain reaction) and ELISA (Enzyme- linked immunosorbent assay) are current sensitive detection methods. However, these methods are time consuming and require laborious effort, where results are provided hours or days later. For this reason alternate approaches are mounting in demands that are rapid in detection time, highly sensitive and reliable.

Through stochastic sensing, we utilize the passage of ionic current through a protein pore containing engineered recognition sites, allowing for monitoring of analytes present. We propose the use of monomeric protein Outer membrane protein G (OmpG) will allow us to tailor and fine tune properties of this pore in detection of analytes.

This <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'>monomeric porin</scene> has features that can be customized as a sensor component, using protein engineering we can develop this protein to be a successful biosensor. Utilizing the flexibility of an extracellular loop, we will append a ligand to help detect our target analyte. <scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'>Location of ligand</scene>
<scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

==Structural Features of OmpG==
OmpG is a 14-stranded beta-barrel and in contrast to most porins, appears to function as a monomer.[1] The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the passive transport of larger oligosaccharides.[1] OmpG adopts two conformations: open and closed. At neutral pH the porin displays an open conformation. However at a more acidic pH the closed conformation is adopted. This closed conformation is a result of OmpG's flexible extracellular loop 6, which folds across the channel blocking the pore opening. The rearrangement of loop 6 appears to be triggered by a pair of histidine residues, which repel one another at acidic pH, resulting in the breakage of neighbouring H-bonds and a lengthening of loop 6 from 10 to 17 residues[2,3]. <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

[[Image:OmpG Conformation.png | thumb|]]
[2IWW]
[http://en.wikipedia.org/wiki/Outer_membrane_protein_G].

==Additional Resources==
Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]
For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]


==References==

[1] Chen M, Li Q-H and Bayley, H (2008) "Orientation of the monomeric porin OmpG in planar lipid bilayers." ChemBioChem 9(18):3029-36

[2] Chen M, Khalid S, Sansom M and Bayley H (2008) "Outer membrane protein G: engineering a quiet pore for biosensing." Proc Natl Acad Sci U S A 105: 6272-6277

[3] Damaghi M, Bippes C, et al. (2010) "pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG." J Mol Biol 397(4):878-82.

MonifaFahie/sandbox

2014-11-19T18:15:33Z

Monifa Fahie: /* Momo's CBI Molecule */

==Momo's CBI Molecule==
<StructureSection load='2wiv' size='340' side='right' caption='Caption for this structure' scene=''>

OmpG is a member of [[CBI Molecules]] being studied in the [http://www.chem.umass.edu/~chenlab/index.HTML/ Chen Lab] 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='2IWW' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'>

<scene name='60/609792/2_ompg/1'>TextToBeDisplayed<2 OmpG /scene>

==Outer Membrane Protein G==
Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores to be used as stochastic sensors, for single molecule detection. The applications of biosensors range from fundamental research, clinical diagnosis, and even advances in homeland security. PCR (Polymerase chain reaction) and ELISA (Enzyme- linked immunosorbent assay) are current sensitive detection methods. However, these methods are time consuming and require laborious effort, where results are provided hours or days later. For this reason alternate approaches are mounting in demands that are rapid in detection time, highly sensitive and reliable.

Through stochastic sensing, we utilize the passage of ionic current through a protein pore containing engineered recognition sites, allowing for monitoring of analytes present. We propose the use of monomeric protein Outer membrane protein G (OmpG) will allow us to tailor and fine tune properties of this pore in detection of analytes.

This <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'>monomeric porin</scene> has features that can be customized as a sensor component, using protein engineering we can develop this protein to be a successful biosensor. Utilizing the flexibility of an extracellular loop, we will append a ligand to help detect our target analyte. <scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'>Location of ligand</scene>
<scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

==Structural Features of OmpG==
OmpG is a 14-stranded beta-barrel and in contrast to most porins, appears to function as a monomer.[1] The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the passive transport of larger oligosaccharides.[1] OmpG adopts two conformations: open and closed. At neutral pH the porin displays an open conformation. However at a more acidic pH the closed conformation is adopted. This closed conformation is a result of OmpG's flexible extracellular loop 6, which folds across the channel blocking the pore opening. The rearrangement of loop 6 appears to be triggered by a pair of histidine residues, which repel one another at acidic pH, resulting in the breakage of neighbouring H-bonds and a lengthening of loop 6 from 10 to 17 residues[2,3]. <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

[[Image:OmpG Conformation.png | thumb| ]]
[2IWW]
[http://en.wikipedia.org/wiki/Outer_membrane_protein_G].

==Additional Resources==
Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]
For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]
 

==References==

[1] Chen M, Li Q-H and Bayley, H (2008) "Orientation of the monomeric porin OmpG in planar lipid bilayers." ChemBioChem 9(18):3029-36

[2] Chen M, Khalid S, Sansom M and Bayley H (2008) "Outer membrane protein G: engineering a quiet pore for biosensing." Proc Natl Acad Sci U S A 105: 6272-6277

[3] Damaghi M, Bippes C, et al. (2010) "pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG." J Mol Biol 397(4):878-82.

MonifaFahie/sandbox

2014-11-19T18:11:00Z

Monifa Fahie:

==Momo's CBI Molecule==
<StructureSection load='2wiv' size='340' side='right' caption='Caption for this structure' scene=''>

OmpG is a member of [[CBI Molecules]] being studied in the [http://www.chem.umass.edu/~chenlab/index.HTML/ Chen Lab] 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='2IWW' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'>

==Outer Membrane Protein G==
Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores to be used as stochastic sensors, for single molecule detection. The applications of biosensors range from fundamental research, clinical diagnosis, and even advances in homeland security. PCR (Polymerase chain reaction) and ELISA (Enzyme- linked immunosorbent assay) are current sensitive detection methods. However, these methods are time consuming and require laborious effort, where results are provided hours or days later. For this reason alternate approaches are mounting in demands that are rapid in detection time, highly sensitive and reliable.

Through stochastic sensing, we utilize the passage of ionic current through a protein pore containing engineered recognition sites, allowing for monitoring of analytes present. We propose the use of monomeric protein Outer membrane protein G (OmpG) will allow us to tailor and fine tune properties of this pore in detection of analytes.

This <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'>monomeric porin</scene> has features that can be customized as a sensor component, using protein engineering we can develop this protein to be a successful biosensor. Utilizing the flexibility of an extracellular loop, we will append a ligand to help detect our target analyte. <scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'>Location of ligand</scene>
<scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

==Structural Features of OmpG==
OmpG is a 14-stranded beta-barrel and in contrast to most porins, appears to function as a monomer.[1] The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the passive transport of larger oligosaccharides.[1] OmpG adopts two conformations: open and closed. At neutral pH the porin displays an open conformation. However at a more acidic pH the closed conformation is adopted. This closed conformation is a result of OmpG's flexible extracellular loop 6, which folds across the channel blocking the pore opening. The rearrangement of loop 6 appears to be triggered by a pair of histidine residues, which repel one another at acidic pH, resulting in the breakage of neighbouring H-bonds and a lengthening of loop 6 from 10 to 17 residues[2,3]. <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

[[Image:OmpG Conformation.png | thumb| ]]
[2IWW]
[http://en.wikipedia.org/wiki/Outer_membrane_protein_G].

==Additional Resources==
Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]
For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]
 

==References==

[1] Chen M, Li Q-H and Bayley, H (2008) "Orientation of the monomeric porin OmpG in planar lipid bilayers." ChemBioChem 9(18):3029-36

[2] Chen M, Khalid S, Sansom M and Bayley H (2008) "Outer membrane protein G: engineering a quiet pore for biosensing." Proc Natl Acad Sci U S A 105: 6272-6277

[3] Damaghi M, Bippes C, et al. (2010) "pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG." J Mol Biol 397(4):878-82.

MonifaFahie/sandbox

2014-11-19T18:08:08Z

Monifa Fahie: /* Momo's CBI Molecule */

==Momo's CBI Molecule==
<StructureSection load='2wiv' size='340' side='right' caption='Caption for this structure' scene=''>

OmpG is a member of [[CBI Molecules]] being studied in the [http://www.chem.umass.edu/~chenlab/index.HTML/ Chen Lab] 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='2IWW' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'>

==Outer Membrane Protein G==
Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores to be used as stochastic sensors, for single molecule detection. The applications of biosensors range from fundamental research, clinical diagnosis, and even advances in homeland security. PCR (Polymerase chain reaction) and ELISA (Enzyme- linked immunosorbent assay) are current sensitive detection methods. However, these methods are time consuming and require laborious effort, where results are provided hours or days later. For this reason alternate approaches are mounting in demands that are rapid in detection time, highly sensitive and reliable.

Through stochastic sensing, we utilize the passage of ionic current through a protein pore containing engineered recognition sites, allowing for monitoring of analytes present. We propose the use of monomeric protein Outer membrane protein G (OmpG) will allow us to tailor and fine tune properties of this pore in detection of analytes.

This <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'>monomeric porin</scene> has features that can be customized as a sensor component, using protein engineering we can develop this protein to be a successful biosensor. Utilizing the flexibility of an extracellular loop, we will append a ligand to help detect our target analyte. <scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'>Location of ligand</scene>
<scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

==Structural Features of OmpG==
OmpG is a 14-stranded beta-barrel and in contrast to most porins, appears to function as a monomer.[1] The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the passive transport of larger oligosaccharides.[1] OmpG adopts two conformations: open and closed. At neutral pH the porin displays an open conformation. However at a more acidic pH the closed conformation is adopted. This closed conformation is a result of OmpG's flexible extracellular loop 6, which folds across the channel blocking the pore opening. The rearrangement of loop 6 appears to be triggered by a pair of histidine residues, which repel one another at acidic pH, resulting in the breakage of neighbouring H-bonds and a lengthening of loop 6 from 10 to 17 residues[2,3]. <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

[[Image:OmpG Conformation.png | thumb| ]]
[2IWW]
[http://en.wikipedia.org/wiki/Outer_membrane_protein_G].

==Additional Resources==
Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]
For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]
 

==References==

[1] Chen M, Li Q-H and Bayley, H (2008) "Orientation of the monomeric porin OmpG in planar lipid bilayers." ChemBioChem 9(18):3029-36

[2] Chen M, Khalid S, Sansom M and Bayley H (2008) "Outer membrane protein G: engineering a quiet pore for biosensing." Proc Natl Acad Sci U S A 105: 6272-6277

[3] Damaghi M, Bippes C, et al. (2010) "pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG." J Mol Biol 397(4):878-82.

This is a default text for your page '''MonifaFahie/sandbox'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

MonifaFahie/sandbox

2014-11-19T18:04:33Z

Monifa Fahie: /* Momo's CBI Molecule */

==Momo's CBI Molecule==
<StructureSection load='2wiv' size='340' side='right' caption='Caption for this structure' scene=''>

OmpG is a member of [[CBI Molecules]] being studied in the [http://www.chem.umass.edu/~chenlab/ Chen Lab] 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='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'>

==Outer Membrane Protein G==
Protein biosensors serve as an analytical device combining a biological component with a physiochemical detector. Through protein engineering we are able to utilize pores to be used as stochastic sensors, for single molecule detection. The applications of biosensors range from fundamental research, clinical diagnosis, and even advances in homeland security. PCR (Polymerase chain reaction) and ELISA (Enzyme- linked immunosorbent assay) are current sensitive detection methods. However, these methods are time consuming and require laborious effort, where results are provided hours or days later. For this reason alternate approaches are mounting in demands that are rapid in detection time, highly sensitive and reliable.

Through stochastic sensing, we utilize the passage of ionic current through a protein pore containing engineered recognition sites, allowing for monitoring of analytes present. We propose the use of monomeric protein Outer membrane protein G (OmpG) will allow us to tailor and fine tune properties of this pore in detection of analytes.

This <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'>monomeric porin</scene> has features that can be customized as a sensor component, using protein engineering we can develop this protein to be a successful biosensor. Utilizing the flexibility of an extracellular loop, we will append a ligand to help detect our target analyte. <scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'>Location of ligand</scene>
<scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

==Structural Features of OmpG==
OmpG is a 14-stranded beta-barrel and in contrast to most porins, appears to function as a monomer.[1] The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the passive transport of larger oligosaccharides.[1] OmpG adopts two conformations: open and closed. At neutral pH the porin displays an open conformation. However at a more acidic pH the closed conformation is adopted. This closed conformation is a result of OmpG's flexible extracellular loop 6, which folds across the channel blocking the pore opening. The rearrangement of loop 6 appears to be triggered by a pair of histidine residues, which repel one another at acidic pH, resulting in the breakage of neighbouring H-bonds and a lengthening of loop 6 from 10 to 17 residues[2,3]. <scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'></scene>

[[Image:OmpG Conformation.png | thumb| ]]
[2IWW]
[http://en.wikipedia.org/wiki/Outer_membrane_protein_G].

==Additional Resources==
Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]
For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]
 

==References==

[1] Chen M, Li Q-H and Bayley, H (2008) "Orientation of the monomeric porin OmpG in planar lipid bilayers." ChemBioChem 9(18):3029-36

[2] Chen M, Khalid S, Sansom M and Bayley H (2008) "Outer membrane protein G: engineering a quiet pore for biosensing." Proc Natl Acad Sci U S A 105: 6272-6277

[3] Damaghi M, Bippes C, et al. (2010) "pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG." J Mol Biol 397(4):878-82.

This is a default text for your page '''MonifaFahie/sandbox'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

MonifaFahie/sandbox

2014-11-19T17:35:57Z

Monifa Fahie:

==Momo's CBI Molecule==
<StructureSection load='2wiv' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''MonifaFahie/sandbox'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

MonifaFahie/sandbox

2014-11-19T17:32:15Z

Monifa Fahie: /* Your Heading Here (maybe something like 'Structure') */

==Momo's CBI Molecule==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''MonifaFahie/sandbox'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

MonifaFahie/sandbox

2014-11-19T17:28:19Z

Monifa Fahie: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''MonifaFahie/sandbox'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>