https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Bib+Yang 2026-09-27T17:46:34Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2384190 2015-03-13T19:30:07Z

<p>Bib Yang: Undo revision 2301556 by Michal Harel (Talk)</p> <hr /> <div>==Outer Membrane Protein G==<br /> &lt;Structure load='2iww' size='500' frame='true' align='right' caption='Outer Membrane Protein G complex with glucose, octylglucoside and lauryl dimethylamine oxide (PDB code [[2iww]]).' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'/&gt;<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> <br /> 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.<br /> <br /> [[Image:Open and closed OmpG.jpg|left|thumb|]]<br /> <br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> <br /> Engineering loop 6 to detect large protein analytes<br /> <br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> <br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=2107898 2014-12-18T03:05:01Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='1QOY' size='500' frame='true' align='right' caption='Please select a link from the left to display desired ClyA form' scene='Insert optional scene name here' /&gt;<br /> ==Introduction==<br /> <br /> 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. <br /> <br /> ==About Cytolysin A==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[1QOY]] is a 34 kDa monomer from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli''] (''E. coli''). It is an alpha-PFT comprised of four alpha helicies, a smaller fifth alpha helix, and a &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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.<br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> 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 &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/3'&gt;The oligomeric form of ClyA with a protomer highlighted in crimson&lt;/scene&gt;<br /> <br /> 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].<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> 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. <br /> <br /> Current ClyA projects focus on 3 main areas:<br /> <br /> ClyA non-classical assembly and attack<br /> <br /> ClyA engineered for cancer therapy<br /> <br /> Studies of [http://en.wikipedia.org/wiki/Electro-osmosis, electro-osmosis] using ClyA nanopore<br /> <br /> ==References==<br /> <br /> 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).<br /> <br /> 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).<br /> <br /> 3. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. &amp; Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–30 (2009). <br /> <br /> 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).</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=2107897 2014-12-18T02:58:15Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='1QOY' size='500' frame='true' align='right' caption='Please select a link from the left to display desired ClyA form' scene='Insert optional scene name here' /&gt;<br /> ==Introduction==<br /> <br /> 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. <br /> <br /> ==About Cytolysin A==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[1QOY]] is a 34 kDa monomer from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli''] (''E. coli''). It is an alpha-PFT comprised of four alpha helicies, a smaller fifth alpha helix, and a &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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.<br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> 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 &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> 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].<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> 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. <br /> <br /> Current ClyA projects focus on 3 main areas:<br /> <br /> ClyA non-classical assembly and attack<br /> <br /> ClyA engineered for cancer therapy<br /> <br /> Studies of [http://en.wikipedia.org/wiki/Electro-osmosis, electro-osmosis] using ClyA nanopore<br /> <br /> ==References==<br /> <br /> 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).<br /> <br /> 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).<br /> <br /> 3. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. &amp; Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–30 (2009). <br /> <br /> 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).</div>

Bib Yang https://proteopedia.org/index.php?title=CBI_Molecules&diff=2102924 2014-12-12T22:41:26Z

<p>Bib Yang: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> 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.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> 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 &quot;in progress&quot; until you are finished, and then as &quot;New 2014&quot; or &quot;Revised 2014&quot;. 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).<br /> Follow the instructions at the bottom of this page.<br /> <br /> <br /> ==Molecules==<br /> '''** Designates CBI Molecules Featured on [http://www.umass.edu/cbi/ CBI website]'''<br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> <br /> [http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab]<br /> <br /> : '''[[Molecular Playground/ClyA]]''', Monifa Fahie, Bib Yang '''Revised 2014'''<br /> : '''[[Molecular Playground/OmpG]]''', Christina Chisholm, Monifa Fahie, Bib Yang '''Revised 2014'''<br /> <br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> : '''[[Molecular Playground/ClpP]]''', Lisa Hernandez, Rob Vass '''New 2014'''<br /> : '''[[Molecular Playground/Homo-dimeric RcdA]]''', Kamal K. Joshi <br /> : **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau '''Best CBI Molecule 2011'''<br /> : '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu<br /> <br /> <br /> Farkas Lab<br /> : '''[[Molecular Playground/CLOCK:BMAL1 heterodimer complex]]''', Hui-Hsien Lin, Joseph Hardie, Michael Mingroni '''New 2014''' <br /> <br /> Forbes Lab<br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[Molecular_Playground/DnaK]]''', Joseph Tilitsky, New 2014<br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy '''Best Overall CBI Molecule 2010'''<br /> : '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez<br /> : **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani '''Best CBI Molecule 2012'''<br /> <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : '''[[Molecular Playground/Executioner Caspase-7]]''', Derek MacPherson, Maureen E. Hill<br /> : '''[[Molecular Playground/Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao<br /> : '''[[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay<br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> <br /> Hebert Lab<br /> <br /> : '''[[Molecular_Playground/Hsp70-Hsp90]]''', Jill Graham &quot;Revised 2014&quot;<br /> : '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben<br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : '''[[Molecular_Playground/Pcr H]]''', Fabian Romano, Carolina Morell-Pérez, Yuzhou Tang<br /> <br /> <br /> [http://people.chem.umass.edu/mholden/ Holden Lab]<br /> <br /> : '''[[Molecular Playground/Protective Antigen]]''', Jing Huang<br /> <br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : '''[http://proteopedia.org/wiki/index.php/Chengfeng_Ren Molecular Playground/Inteferon]'''[Revised], Chengfeng Ren<br /> : ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski<br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita<br /> : '''[[Molecular Playground/Antithrombin-Heparin]]''', Yunlong Zhao<br /> <br /> <br /> [http://people.chem.umass.edu/knapplab/?q=knappchem/index.html/ Knapp Lab]<br /> : '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas '''Best CBI Molecule Proteopedia Page 2010''' '''***New Fall 2014***'''<br /> : '''[[Molecular Playground/FIH]]''', Vanessa Chaplin, Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> <br /> <br /> <br /> [http://people.chem.umass.edu/mmaroney/ Maroney Lab]<br /> <br /> : '''[[Molecular Playground/UreE]]''', Priyanka Basak, '''New 2014'''<br /> : '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr<br /> : '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu, Carolyn Carr, Hsin-Ting (Tiffany )Huang, '''Revised 2014'''<br /> : '''[[Molecular Playground/HypA]]''', Heidi Hu<br /> <br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia '''Best CBI Molecule 2011'''<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> : '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> <br /> [http://www.peytonlab.org/ Peyton Lab]<br /> : '''[[Molecular Playground/IntegrinBeta1]]''', Lauren Jansen, Lauren Barney, Elizabeth Brooks, Alyssa Schwartz ***'''NEW FALL 2014''''***<br /> : '''[[Molecular Playground/MMP14]]''', Lauren Jansen<br /> : '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> : '''[[Molecular Playground/FAK]]''', Dannielle Ryman<br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Elizabeth Cummings, Rohan Patil, Sarah Wilson ***'''Revised Fall 2014'''***<br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> <br /> [http://http://www.umass.edu/schiffman/ Schiffman Lab]<br /> : '''[[Molecular Playground/Streptavidin]]''', Katrina Rieger<br /> <br /> <br /> [http://www.biochem.umass.edu/faculty/danny-j-schnell Schnell Lab]<br /> : '''[[Molecular Playground/Tic40]]''', Mine Canakci<br /> <br /> <br /> Tew Lab<br /> <br /> : '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde, Coralie Backlund<br /> <br /> <br /> Thayumanavan Lab<br /> : '''[[Interleukin-1 beta]]''', Huan He<br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> <br /> Thayumanavan &amp; Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson Lab]<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Complex]]''', Elizabeth R. Haglin, Maryam Kashefi<br /> : '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin<br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> : '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : '''[[Molecular Playground/Human Serum Albumin]]''', Mahalia Serrano ''*Revised 2014*''<br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto, Tyler Marcinko ***'''Revised Fall 2014'''*** '''Best CBI Molecule Jmol scenes 2010'''<br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> : '''[[Molecular Playground/Ubiquitin salt bridge discussion]]''', Zhe Zhang<br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> :'''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey, Schnarr lab<br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey, Schnarr lab<br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad, Schnarr lab<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang, Weis lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffi, Bhatia Lab<br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer, Bhatia Lab<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''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.'''<br /> <br /> 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.<br /> <br /> 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.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. <br /> <br /> 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.<br /> <br /> 3. Get started working in Proteopedia. Make yourself a sandbox page: Enter &quot;User:Your Name/Sandbox 1&quot; (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). <br /> <br /> '''Complete the above steps before the CBI Molecule Workshop.'''<br /> <br /> 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.<br /> <br /> 5. Your final pages should be called &quot;Molecular Playground/your molecule&quot; and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them &quot;in progress&quot; until you are finished, and then &quot;new 2014&quot; or &quot;revised 2014&quot;. Minimize text; tell your story with green scenes!<br /> <br /> 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).<br /> <br /> ==Links to HELP pages==<br /> Overview at [[Help:Contents ]]<br /> <br /> See also [[Help:Getting_Started_in_Proteopedia]] <br /> <br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> 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.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=2102923 2014-12-12T22:34:16Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='1QOY' size='500' frame='true' align='right' caption='Please select a link from the left to display desired ClyA form' scene='Insert optional scene name here' /&gt;<br /> ==Introduction==<br /> <br /> 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. <br /> <br /> ==About this Structure==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[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 &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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.<br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> 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 &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> 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].<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> 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. <br /> <br /> Current ClyA projects focus on 3 main areas:<br /> <br /> ClyA non-classical assembly and attack<br /> <br /> ClyA engineered for cancer therapy<br /> <br /> Studies of [http://en.wikipedia.org/wiki/Electro-osmosis, electro-osmosis] using ClyA nanopore<br /> <br /> ==References==<br /> <br /> 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).<br /> <br /> 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).<br /> <br /> 3. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. &amp; Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–30 (2009). <br /> <br /> 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).</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102922 2014-12-12T22:33:50Z

<p>Bib Yang: </p> <hr /> <div>==Outer Membrane Protein G==<br /> &lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'/&gt;<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> <br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> <br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102921 2014-12-12T22:31:50Z

<p>Bib Yang: </p> <hr /> <div>==Outer Membrane Protein G==<br /> &lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'/&gt;<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> <br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> <br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102920 2014-12-12T22:30:06Z

<p>Bib Yang: </p> <hr /> <div><br /> ==Outer Membrane Protein G==<br /> &lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> <br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> <br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102919 2014-12-12T22:29:32Z

<p>Bib Yang: </p> <hr /> <div><br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> <br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> <br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102918 2014-12-12T22:29:09Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='2GTG' size='350' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> <br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> <br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102917 2014-12-12T22:28:46Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> <br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> <br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102916 2014-12-12T22:28:09Z

<p>Bib Yang: </p> <hr /> <div><br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> <br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> <br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102915 2014-12-12T22:26:01Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> <br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> <br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102914 2014-12-12T22:24:39Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> <br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> <br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102913 2014-12-12T22:23:22Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> ==Outer Membrane Protein G==<br /> <br /> <br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102912 2014-12-12T22:22:20Z

<p>Bib Yang: </p> <hr /> <div>==Outer Membrane Protein G==<br /> <br /> &lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> <br /> <br /> &lt;/StructureSection&gt;</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102911 2014-12-12T22:17:36Z

<p>Bib Yang: /* Outer Membrane Protein G */</p> <hr /> <div>==Outer Membrane Protein G==<br /> &lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> <br /> <br /> &lt;/StructureSection&gt;</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102910 2014-12-12T22:15:29Z

<p>Bib Yang: </p> <hr /> <div>==Outer Membrane Protein G==<br /> &lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> <br /> <br /> &lt;/StructureSection&gt;</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102909 2014-12-12T22:14:45Z

<p>Bib Yang: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> <br /> <br /> &lt;/StructureSection&gt;</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102908 2014-12-12T22:14:14Z

<p>Bib Yang: </p> <hr /> <div><br /> ==Your Heading Here (maybe something like 'Structure')==<br /> &lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> testing<br /> <br /> &lt;/StructureSection&gt;<br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102907 2014-12-12T22:13:45Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> ==Your Heading Here (maybe something like 'Structure')==<br /> &lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> testing<br /> <br /> &lt;/StructureSection&gt;<br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102906 2014-12-12T22:12:07Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> ==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='3rec' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''&gt;<br /> <br /> testing<br /> <br /> &lt;/StructureSection&gt;<br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102905 2014-12-12T22:10:52Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102904 2014-12-12T22:09:26Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102903 2014-12-12T22:08:07Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> ==Outer Membrane Protein G==<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> <br /> <br /> &lt;/StructureSection&gt;</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2102902 2014-12-12T19:28:31Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> ==Outer Membrane Protein G==<br /> &lt;StructureSection load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> 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. <br /> <br /> [[Image:OmpG_top_down_of_net_negative_loop_region.png|left|thumb|]] <br /> <br /> ==Current OmpG Projects in the Chen Lab== <br /> Engineering loop 6 to detect large protein analytes<br /> Investigating the effect of loop charge on the gating behavior of OmpG<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> <br /> <br /> &lt;/StructureSection&gt;</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=2075791 2014-12-03T21:18:57Z

<p>Bib Yang: </p> <hr /> <div>&lt;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' /&gt;<br /> ==Introduction==<br /> <br /> In progress<br /> <br /> ==About this Structure==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[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 &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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.<br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> 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 &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> 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].<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> The Chen Lab, in collaboration with the Heuck lab, recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] assembly. We use a technique commonly used for nanopore sensing called electrophysiology, which allows us to measure the ionic current through the ClyA nanopore.<br /> <br /> ==References==<br /> <br /> 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).<br /> <br /> 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).<br /> <br /> 3. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. &amp; Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–30 (2009). <br /> <br /> 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).</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=2075790 2014-12-03T21:18:28Z

<p>Bib Yang: </p> <hr /> <div>&lt;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' /&gt;<br /> ==Introduction==<br /> <br /> <br /> <br /> ==About this Structure==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[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 &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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.<br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> 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 &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> 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].<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> The Chen Lab, in collaboration with the Heuck lab, recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] assembly. We use a technique commonly used for nanopore sensing called electrophysiology, which allows us to measure the ionic current through the ClyA nanopore.<br /> <br /> ==References==<br /> <br /> 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).<br /> <br /> 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).<br /> <br /> 3. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. &amp; Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–30 (2009). <br /> <br /> 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).</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=2075789 2014-12-03T21:18:05Z

<p>Bib Yang: </p> <hr /> <div>&lt;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' /&gt;<br /> ==Introduction==<br /> <br /> <br /> <br /> ==About this Structure==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[1QOY]] is a 34 kDa monomer from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli''] &quot;E. coli&quot;. It is a pore-forming toxin (PFT) comprised of four alpha helicies, a smaller fifth alpha helix, and a &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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.<br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> 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 &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> 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].<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> The Chen Lab, in collaboration with the Heuck lab, recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] assembly. We use a technique commonly used for nanopore sensing called electrophysiology, which allows us to measure the ionic current through the ClyA nanopore.<br /> <br /> ==References==<br /> <br /> 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).<br /> <br /> 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).<br /> <br /> 3. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. &amp; Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–30 (2009). <br /> <br /> 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).</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=2075788 2014-12-03T21:17:32Z

<p>Bib Yang: </p> <hr /> <div>&lt;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' /&gt;<br /> ==Introduction==<br /> <br /> <br /> <br /> ==About this Structure==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[1QOY]] is a 34 kDa monomer from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli''] ( &quot;E. coli&quot; ). It is a pore-forming toxin (PFT) comprised of four alpha helicies, a smaller fifth alpha helix, and a &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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.<br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> 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 &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> 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].<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> The Chen Lab, in collaboration with the Heuck lab, recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] assembly. We use a technique commonly used for nanopore sensing called electrophysiology, which allows us to measure the ionic current through the ClyA nanopore.<br /> <br /> ==References==<br /> <br /> 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).<br /> <br /> 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).<br /> <br /> 3. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. &amp; Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–30 (2009). <br /> <br /> 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).</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=2075787 2014-12-03T21:16:52Z

<p>Bib Yang: </p> <hr /> <div>&lt;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' /&gt;<br /> ==Introduction==<br /> <br /> <br /> <br /> ==About this Structure==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[1QOY]] is a 34 kDa monomer from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli''] (&quot;E. coli&quot;). It is a pore-forming toxin (PFT) comprised of four alpha helicies, a smaller fifth alpha helix, and a &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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.<br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> 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 &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> 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].<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> The Chen Lab, in collaboration with the Heuck lab, recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] assembly. We use a technique commonly used for nanopore sensing called electrophysiology, which allows us to measure the ionic current through the ClyA nanopore.<br /> <br /> ==References==<br /> <br /> 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).<br /> <br /> 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).<br /> <br /> 3. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. &amp; Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–30 (2009). <br /> <br /> 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).</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=2075785 2014-12-03T21:09:55Z

<p>Bib Yang: </p> <hr /> <div>&lt;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' /&gt;<br /> ==About this Structure==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[1QOY]] is a monomer from the dodecameric pore-forming toxin (PFT) from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli''] (&quot;E. coli&quot;). It is a 34kDa protein comprised of four alpha helicies, a smaller fifth alpha helix, and a &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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.<br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> 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 &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> 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].<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> The Chen Lab, in collaboration with the Heuck lab, recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] assembly. We use a technique commonly used for nanopore sensing called electrophysiology, which allows us to measure the ionic current through the ClyA nanopore.<br /> <br /> ==References==<br /> <br /> 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).<br /> <br /> 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).<br /> <br /> 3. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. &amp; Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–30 (2009). <br /> <br /> 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).</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2065638 2014-11-19T18:13:58Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> ==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='3rec' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''&gt;<br /> ===Outer Membrane Protein G===<br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> &lt;/StructureSection&gt;<br /> ===Outer Membrane Protein G===<br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> <br /> <br /> &lt;/StructureSection&gt;OmpG is a member of [[CBI Molecules]] being studied in the [http://www.chem.umass.edu/~chenlab/ Chen Lab] in the &lt;span class=&quot;plainlinks&quot;&gt;[http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program]&lt;/span&gt; at UMass Amherst and on display at the &lt;span class=&quot;plainlinks&quot;&gt;[http://www.molecularplayground.org/ Molecular Playground]&lt;/span&gt;.<br /> <br /> <br /> <br /> <br /> <br /> ===Outer Membrane Protein G===<br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png | thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2065634 2014-11-19T18:13:12Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> ===Outer Membrane Protein G===<br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2065626 2014-11-19T18:11:01Z

<p>Bib Yang: </p> <hr /> <div>&lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> ===Outer Membrane Protein G===<br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> <br /> <br /> &lt;/StructureSection&gt;OmpG is a member of [[CBI Molecules]] being studied in the [http://www.chem.umass.edu/~chenlab/ Chen Lab] in the &lt;span class=&quot;plainlinks&quot;&gt;[http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program]&lt;/span&gt; at UMass Amherst and on display at the &lt;span class=&quot;plainlinks&quot;&gt;[http://www.molecularplayground.org/ Molecular Playground]&lt;/span&gt;.<br /> <br /> <br /> <br /> <br /> <br /> ===Outer Membrane Protein G===<br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png | thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2065589 2014-11-19T18:03:12Z

<p>Bib Yang: </p> <hr /> <div>===Outer Membrane Protein G===<br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png|thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> <br /> <br /> &lt;/StructureSection&gt;OmpG is a member of [[CBI Molecules]] being studied in the [http://www.chem.umass.edu/~chenlab/ Chen Lab] in the &lt;span class=&quot;plainlinks&quot;&gt;[http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program]&lt;/span&gt; at UMass Amherst and on display at the &lt;span class=&quot;plainlinks&quot;&gt;[http://www.molecularplayground.org/ Molecular Playground]&lt;/span&gt;.<br /> <br /> <br /> &lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> <br /> ===Outer Membrane Protein G===<br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png | thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2065588 2014-11-19T18:02:14Z

<p>Bib Yang: </p> <hr /> <div>===Outer Membrane Protein G===<br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png | thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> <br /> <br /> &lt;/StructureSection&gt;OmpG is a member of [[CBI Molecules]] being studied in the [http://www.chem.umass.edu/~chenlab/ Chen Lab] in the &lt;span class=&quot;plainlinks&quot;&gt;[http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program]&lt;/span&gt; at UMass Amherst and on display at the &lt;span class=&quot;plainlinks&quot;&gt;[http://www.molecularplayground.org/ Molecular Playground]&lt;/span&gt;.<br /> <br /> <br /> &lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> <br /> ===Outer Membrane Protein G===<br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png | thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2065586 2014-11-19T18:01:16Z

<p>Bib Yang: </p> <hr /> <div>==Your Heading Here (maybe something like 'Structure')==<br /> &lt;StructureSection load='3rec' size='350' side='right' caption='Escherichia coli reca protein-bound DNA (PDB entry [[3rec]])' scene=''&gt;<br /> <br /> <br /> ===Outer Membrane Protein G===<br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png | thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.<br /> <br /> <br /> &lt;/StructureSection&gt;OmpG is a member of [[CBI Molecules]] being studied in the [http://www.chem.umass.edu/~chenlab/ Chen Lab] in the &lt;span class=&quot;plainlinks&quot;&gt;[http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program]&lt;/span&gt; at UMass Amherst and on display at the &lt;span class=&quot;plainlinks&quot;&gt;[http://www.molecularplayground.org/ Molecular Playground]&lt;/span&gt;.<br /> <br /> <br /> &lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> <br /> ===Outer Membrane Protein G===<br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png | thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/OmpG&diff=2065584 2014-11-19T18:00:18Z

<p>Bib Yang: </p> <hr /> <div>OmpG is a member of [[CBI Molecules]] being studied in the [http://www.chem.umass.edu/~chenlab/ Chen Lab] in the &lt;span class=&quot;plainlinks&quot;&gt;[http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program]&lt;/span&gt; at UMass Amherst and on display at the &lt;span class=&quot;plainlinks&quot;&gt;[http://www.molecularplayground.org/ Molecular Playground]&lt;/span&gt;.<br /> <br /> <br /> &lt;Structure load='2GTG' size='500' frame='true' align='right' caption='Outer Membrane Protein G' scene='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/5'&gt;<br /> <br /> <br /> ===Outer Membrane Protein G===<br /> 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. <br /> <br /> 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. <br /> <br /> This &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/4'&gt;monomeric porin&lt;/scene&gt; 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. &lt;scene name='User:Christina_Chisholm/Sandbox_1/224highlighted_ompg/5'&gt;Location of ligand&lt;/scene&gt;<br /> &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> <br /> ==Structural Features of OmpG==<br /> 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]. &lt;scene name='User:Christina_Chisholm/Sandbox_1/Greenwoselection_ompg/3'&gt;&lt;/scene&gt;<br /> <br /> [[Image:OmpG Conformation.png | thumb|]]<br /> [2IWW]<br /> [http://en.wikipedia.org/wiki/Outer_membrane_protein_G].<br /> <br /> ==Additional Resources==<br /> Current applications using nanopores for protein detection [https://www.nanoporetech.com/technology/analytes-and-applications-dna-rna-proteins/protein-analysis-]<br /> For additional information, see: Nanobiotechnology Review [http://www.nature.com/nnano/journal/v6/n4/full/nnano.2011.52.html]<br /> &lt;/br&gt;<br /> <br /> ==References==<br /> <br /> [1] Chen M, Li Q-H and Bayley, H (2008) &quot;Orientation of the monomeric porin OmpG in planar lipid bilayers.&quot; ChemBioChem 9(18):3029-36<br /> <br /> [2] Chen M, Khalid S, Sansom M and Bayley H (2008) &quot;Outer membrane protein G: engineering a quiet pore for biosensing.&quot; Proc Natl Acad Sci U S A 105: 6272-6277 <br /> <br /> [3] Damaghi M, Bippes C, et al. (2010) &quot;pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG.&quot; J Mol Biol 397(4):878-82.</div>

Bib Yang https://proteopedia.org/index.php?title=File:Protopedia_protomer.pdb&diff=2065574 2014-11-19T17:52:13Z

<p>Bib Yang: </p> <hr /> <div></div>

Bib Yang https://proteopedia.org/index.php?title=File:Protopedia_oligomer.pdb&diff=2065569 2014-11-19T17:46:33Z

<p>Bib Yang: </p> <hr /> <div></div>

Bib Yang https://proteopedia.org/index.php?title=CBI_Molecules&diff=1926671 2014-05-13T16:00:48Z

<p>Bib Yang: </p> <hr /> <div>These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].<br /> 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.<br /> <br /> UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.<br /> <br /> Fall 2013: CBI Molecules are due 12/4/13 and should be added at the TOP of the list from your lab. Label it as &quot;in progress&quot; until you are finished, and then as &quot;New 2013&quot; or &quot;Revised 2013&quot;. For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not).<br /> <br /> <br /> ==Molecules==<br /> '''** Designates CBI Molecules Featured on [http://http://www.umass.edu/cbi/ CBI website]'''<br /> <br /> Bhatia Lab<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin<br /> <br /> : '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer<br /> <br /> <br /> [http://chamberslab.com/wp/ Chambers Lab]<br /> <br /> : '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab]<br /> <br /> : New Fall 2013!! '''[[Molecular Playground/ClyA]]''', Bib Yang<br /> : Updated Fall 2013!! '''[[Molecular Playground/OmpG]]''', Christina Chisholm<br /> <br /> [http://openwetware.org/wiki/Chien Chien Lab]<br /> <br /> New Fall 2013! : **'''[[Molecular Playground/Homo-dimeric RcdA]]''', Kamal K. Joshi <br /> <br /> : **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau <br /> :: Best CBI Molecule 2011<br /> <br /> : '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu<br /> <br /> <br /> Forbes Lab<br /> <br /> : '''[[Molecular Playground/CheR]]''', Miaomin Zhang<br /> <br /> : '''[[Molecular Playground/RBP]]''', Jan Panteli<br /> <br /> : '''[[Molecular Playground/TRAIL]]''', Charley Swofford<br /> <br /> <br /> [http://www.biochem.umass.edu/garman/index.html Garman Lab]<br /> <br /> : '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon<br /> <br /> : '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli<br /> <br /> <br /> [http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]<br /> <br /> : '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy<br /> :: Best Overall CBI Molecule 2010<br /> <br /> : '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez<br /> (compare this to the previous version above to see what's new)<br /> <br /> : **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani <br /> :: Best CBI Molecule 2012<br /> <br /> <br /> [http://people.chem.umass.edu/jhardy/ Hardy Lab]<br /> <br /> : New Fall 2013!! '''[[Molecular Playground/Executioner Caspase-7]]''', Derek MacPherson, Maureen E. Hill<br /> <br /> : '''[[Molecular Playground/[[Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao<br /> <br /> : ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay<br /> <br /> : '''[[Molecular Playground/Caspase-7 Dynamics]]'''<br /> <br /> : '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber<br /> <br /> : '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez<br /> <br /> : '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls<br /> <br /> : '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz<br /> <br /> <br /> Hebert Lab<br /> <br /> : New Fall 2013!! '''[[Molecular_Playground/Hsp70-Hsp90]]''', Jill Graham<br /> : New Fall 2012!! '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben<br /> : '''[[Molecular Playground/Saposin C]]''', Abla Tannous<br /> : '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd<br /> <br /> <br /> [http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]<br /> <br /> : Updated Fall 2012!! '''[[Molecular_Playground/Pcr H]]''', Fabian Romano, Carolina Morell-Pérez<br /> <br /> <br /> [http://people.chem.umass.edu/mholden/ Holden Lab]<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/Protective Antigen]]''', Jing Huang<br /> <br /> <br /> <br /> [http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]<br /> <br /> : New 2013! '''[http://proteopedia.org/wiki/index.php/Chengfeng_Ren Molecular Playground/Inteferon]''', Chengfeng Ren<br /> <br /> : Updated Fall 2012!! ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski<br /> <br /> : '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita<br /> <br /> : New Summer 2014!! '''[[Molecular Playground/Antithrombin-Heparin]]''', Yunlong Zhao<br /> <br /> <br /> <br /> <br /> Knapp lab<br /> <br /> : Updated Fall 2013!! '''[[Molecular Playground/FIH]]''', Vanessa Chaplin, Cornelius Taabazuing, Breanne Holmes, John Hangasky<br /> <br /> : Updated Fall 2012!! '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas<br /> :: Best CBI Molecule Proteopedia Page 2010<br /> <br /> <br /> <br /> <br /> [http://people.chem.umass.edu/mmaroney/ Maroney Lab]<br /> <br /> : '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr<br /> : Updated Fall 2013!! '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu, Carolyn Carr<br /> : '''[[Molecular Playground/HypA]]''', Heidi Hu<br /> <br /> <br /> [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> : **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia <br /> :: Best CBI Molecule 2011<br /> : '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia<br /> <br /> : '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan <br /> <br /> <br /> [http://www.peytonlab.org/ Peyton Lab]<br /> : New Fall 2013! '''[[Molecular Playground/MMP14]]''', Lauren Jansen<br /> <br /> : '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen<br /> <br /> : '''[[Molecular Playground/FAK]]''', Dannielle Ryman<br /> <br /> [http://roberts.openwetware.org/ Roberts Lab]<br /> <br /> : '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson<br /> <br /> : '''[[Molecular Playground/Insulin]]''', Whitney Stoppel<br /> <br /> <br /> [http://www.umass.edu/rotellogroup/ Rotello Lab]<br /> <br /> : '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino<br /> <br /> : '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang<br /> <br /> : '''[[Molecular playground/Chymotrypsin]]''', Brad<br /> <br /> : '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell<br /> <br /> [http://http://www.umass.edu/schiffman/ Schiffman Lab]<br /> :New Fall 2013! '''[[Molecular Playground/Streptavidin]]''', Katrina Rieger<br /> <br /> [https://elements.chem.umass.edu/schnarrlab/ Schnarr Lab] <br /> <br /> : New Fall 2012!! '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey <br /> <br /> : '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey<br /> <br /> : '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad<br /> <br /> <br /> [http://www.biochem.umass.edu/faculty/danny-j-schnell Schnell Lab]<br /> : New Fall 2012!! '''[[Molecular Playground/Tic40]]''', Mine Canakci<br /> <br /> <br /> <br /> <br /> Tew Lab<br /> <br /> : Updated Fall 2013!! '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde<br /> <br /> <br /> Thayumanavan Lab<br /> : New Fall 2013!! '''[[Interleukin-1 beta]]''', Huan He<br /> <br /> : '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez<br /> <br /> : '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura<br /> <br /> : '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi<br /> <br /> : '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy<br /> <br /> : '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado <br /> <br /> : '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang<br /> <br /> : ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo<br /> <br /> : '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko<br /> <br /> Thayumanavan &amp; Vachet Labs<br /> <br /> : '''[[Molecular Playground/Trypsin]]''', Gladys Murage<br /> <br /> <br /> [http://people.chem.umass.edu/thompson/index.html Thompson] &amp; [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs<br /> <br /> : New Fall 2013!! '''[[Molecular Playground/Bacterial Chemotaxis Complex]]''', Elizabeth R. Haglin, Maryam Kashefi<br /> <br /> : New Fall 2012!! '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin<br /> <br /> : '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones<br /> <br /> : '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang<br /> <br /> : Updated 2013!! '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li<br /> <br /> <br /> [http://www.chem.umass.edu/~vachet/index.html Vachet Lab]<br /> <br /> : New Fall 2013!! '''[[Molecular Playground/Human Serum Albumin]]''', Mahalia Serrano<br /> <br /> : '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto<br /> :: Best CBI Molecule Jmol scenes 2010<br /> <br /> : '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou <br /> <br /> :'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne<br /> <br /> : '''[[Molecular Playground/Ubiquitin salt bridge discussion]]''', Zhe Zhang<br /> <br /> <br /> Other Molecules of interest<br /> <br /> : '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]<br /> <br /> <br /> Other Laboratories<br /> <br /> : '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]<br /> <br /> : '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab<br /> <br /> : '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab<br /> <br /> ==Instructions==<br /> <br /> '''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.'''<br /> <br /> Fall 2013: Complete steps 1-2 by 10/18, and bring your computer to the CBI Molecule Workshop on Wed 10/23 in ISB 321. <br /> <br /> A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). It's great if you can end with a brief statement about how it relates to your group's research goals.<br /> <br /> 1. If you don't already have one, request a Proteopedia account and log in. <br /> <br /> 2. Read through the rest of the instructions and look at any existing CBI Molecules from your research group. Talk with other Chalk Talk students in your research group and think about how you can make a new or improved CBI Molecule related to your group's research. Develop ideas for the scenes you wish to show. You will work learn how to make scenes during the workshop. <br /> <br /> 3. Get started working in Proteopedia by using the links at [[Help:Contents]]. Make yourself a sandbox page: Enter &quot;User:Your Name/Sandbox 1&quot; (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made). <br /> <br /> 4. For those editing an existing CBI Molecule, start from that entry 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 do some editing of the molecule so that they each appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.<br /> <br /> 5. Your final pages should be called &quot;Molecular Playground/your molecule&quot; and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them &quot;in progress&quot; until you are finished, and then &quot;new 2013&quot; or &quot;revised 2013&quot;.<br /> <br /> ==Links to HELP pages==<br /> Overview at [[Help:Contents ]]<br /> <br /> See also [[Help:Getting_Started_in_Proteopedia]] <br /> <br /> Videos showing how to use Proteopedia:<br /> [[Proteopedia:Video_Guide]]<br /> (Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)<br /> <br /> [[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]<br /> gives succinct step by step instructions on how to create a molecular scene.<br /> <br /> 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.<br /> [http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]<br /> <br /> [[Proteopedia:Guidelines for Ethical Writing]].<br /> Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.<br /> <br /> For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=1926670 2014-05-13T15:58:12Z

<p>Bib Yang: /* References */</p> <hr /> <div>&lt;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' /&gt;<br /> ==About this Structure==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[1QOY]] is a monomer from the dodecameric pore-forming toxin (PFT) from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli''] (&quot;E. coli&quot;). It is a 34kDa protein comprised of four alpha helicies, a smaller fifth alpha helix, and a &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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.<br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> 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 &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> 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].<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> The Chen Lab, in collaboration with the Heuck lab, recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] assembly. Currently, we are investigating electroosmotic flow and electrophoretic force, the forces that influence polymer translocation through ClyA. We use a technique commonly used for nanopore sensing called electrophysiology which allows us to measure the current passing through the ClyA nanopore.<br /> <br /> ==References==<br /> <br /> 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).<br /> <br /> 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).<br /> <br /> 3. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. &amp; Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–30 (2009). <br /> <br /> 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).</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=1926669 2014-05-13T15:57:56Z

<p>Bib Yang: </p> <hr /> <div>&lt;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' /&gt;<br /> ==About this Structure==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[1QOY]] is a monomer from the dodecameric pore-forming toxin (PFT) from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli''] (&quot;E. coli&quot;). It is a 34kDa protein comprised of four alpha helicies, a smaller fifth alpha helix, and a &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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.<br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> 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 &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> 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].<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> The Chen Lab, in collaboration with the Heuck lab, recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] assembly. Currently, we are investigating electroosmotic flow and electrophoretic force, the forces that influence polymer translocation through ClyA. We use a technique commonly used for nanopore sensing called electrophysiology which allows us to measure the current passing through the ClyA nanopore.<br /> <br /> ==References==<br /> <br /> 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).<br /> <br /> <br /> 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).<br /> <br /> <br /> 3. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. &amp; Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–30 (2009). <br /> <br /> <br /> 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).</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=1926668 2014-05-13T15:57:27Z

<p>Bib Yang: </p> <hr /> <div>&lt;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' /&gt;<br /> ==About this Structure==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[1QOY]] is a monomer from the dodecameric pore-forming toxin (PFT) from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli''] (&quot;E. coli&quot;). It is a 34kDa protein comprised of four alpha helicies, a smaller fifth alpha helix, and a &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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.<br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> 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 &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> 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].<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> The Chen Lab, in collaboration with the Heuck lab, recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] assembly. Currently, we are investigating electroosmotic flow and electrophoretic force, the forces that influence polymer translocation through ClyA. We use a technique commonly used for nanopore sensing called electrophysiology which allows us to measure the current passing through the ClyA nanopore.<br /> <br /> ==References==<br /> <br /> 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).<br /> 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).<br /> 3. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. &amp; Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–30 (2009). <br /> 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).</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=1926667 2014-05-13T15:50:19Z

<p>Bib Yang: </p> <hr /> <div>&lt;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' /&gt;<br /> ==About this Structure==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[1QOY]] is a monomer from the dodecameric pore-forming toxin (PFT) from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli''] (&quot;E. coli&quot;). It is a 34kDa protein comprised of four alpha helicies, a smaller fifth alpha helix, and a &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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.<br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> 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 &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> 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].<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> The Chen Lab, in collaboration with the Heuck lab, recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] assembly. Currently, we are investigating electroosmotic flow and electrophoretic force, the forces that influence polymer translocation through ClyA. We use a technique commonly used for nanopore sensing called electrophysiology which allows us to measure the current passing through the ClyA nanopore.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=1926666 2014-05-13T15:48:17Z

<p>Bib Yang: </p> <hr /> <div>&lt;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' /&gt;<br /> ==About this Structure==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[1QOY]] is a monomer from the dodecameric pore-forming toxin (PFT) from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli'']. It is a 34kDa protein comprised of four alpha helicies, a smaller fifth alpha helix, and a &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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.<br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> 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 &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> 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].<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> The Chen Lab, in collaboration with the Heuck lab, recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] assembly. Currently, we are investigating electroosmotic flow and electrophoretic force, the forces that influence polymer translocation through ClyA. We use a technique commonly used for nanopore sensing called electrophysiology which allows us to measure the current passing through the ClyA nanopore.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=1926661 2014-05-13T15:31:46Z

<p>Bib Yang: </p> <hr /> <div>&lt;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' /&gt;<br /> ==About this Structure==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[1QOY]] is a monomer from the dodecameric pore-forming toxin (PFT) from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli'']. It is a 34kDa protein comprised of four alpha helicies, a smaller fifth alpha helix, and a &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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. <br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> 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 &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> Its crystal structure, [[2WCD]], reveals a dodecamer. Larger [http://pubs.acs.org/doi/abs/10.1021/ja4053398 pores] have been isolated, as well. <br /> <br /> ==Research on ClyA at UMass Amherst==<br /> The Chen Lab, in collaboration with the Heuck lab, recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] assembly. Currently, we are investigating electroosmotic flow and electrophoretic force, the forces that influence polymer translocation through ClyA. We use a technique commonly used for nanopore sensing called electrophysiology which allows us to measure the current passing through the ClyA nanopore.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=1926660 2014-05-13T15:26:21Z

<p>Bib Yang: </p> <hr /> <div>&lt;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' /&gt;<br /> ==About this Structure==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[1QOY]] is a monomer from the dodecameric pore-forming toxin (PFT) from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli'']. It is a 34kDa protein comprised of four alpha helicies, a smaller fifth alpha helix, and a &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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. <br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> The protomer of ClyA reveals slight differences between the monomer and protomer (from the dodecamer). The major conformational changes between the monomer and the protomer are the positions of the &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminal helix&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta-tongue&lt;/font&gt;&lt;/B&gt;. 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> Its crystal structure, [[2WCD]], reveals a dodecamer. Larger [http://pubs.acs.org/doi/abs/10.1021/ja4053398 pores] have been isolated, as well.<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> The Chen Lab, in collaboration with the Heuck lab, recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] assembly. Currently, we are investigating electroosmotic flow and electrophoretic force, the forces that influence polymer translocation through ClyA.</div>

Bib Yang https://proteopedia.org/index.php?title=Molecular_Playground/ClyA&diff=1926659 2014-05-13T15:23:36Z

<p>Bib Yang: </p> <hr /> <div>&lt;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' /&gt;<br /> ==About this Structure==<br /> &lt;scene name='57/571278/Clya_monomer/2'&gt;ClyA monomer in its inactive form&lt;/scene&gt;<br /> <br /> [[1QOY]] is a monomer from the dodecameric pore-forming toxin (PFT) from [http://en.wikipedia.org/wiki/Escherichia_coli ''Escherichia coli'']. It is a 34kDa protein comprised of four alpha helicies, a smaller fifth alpha helix, and a &lt;B&gt;&lt;font color=&quot;purple&quot;&gt;beta tongue&lt;/font&gt;&lt;/B&gt;. The &lt;B&gt;&lt;font color=&quot;blue&quot;&gt;N-terminus&lt;/font&gt;&lt;/B&gt; and the &lt;B&gt;&lt;font color=&quot;red&quot;&gt;C-terminus&lt;/font&gt;&lt;/B&gt; 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. <br /> <br /> &lt;scene name='57/571278/Clya_protomer/1'&gt;ClyA protomer&lt;/scene&gt;<br /> <br /> The protomer of ClyA reveals slight differences between the monomer and protomer (from the dodecamer). 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.<br /> <br /> &lt;scene name='57/571278/Clya_oligomer/1'&gt;The oligomeric form of ClyA&lt;/scene&gt;<br /> <br /> Its crystal structure, [[2WCD]], reveals a dodecamer. Larger [http://pubs.acs.org/doi/abs/10.1021/ja4053398 pores] have been isolated, as well.<br /> <br /> ==Research on ClyA at UMass Amherst==<br /> The Chen Lab, in collaboration with the Heuck lab, recently published a paper on [http://www.jbc.org/content/288/43/31042.short, ClyA] assembly. Currently, we are investigating electroosmotic flow and electrophoretic force, the forces that influence polymer translocation through ClyA.</div>

Bib Yang