Sandbox Reserved 1083

From Proteopedia

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{{UniHelsinki_ProteinCourse_2015}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
{{UniHelsinki_ProteinCourse_2015}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
==Your Heading Here (maybe something like 'Structure')==
==Your Heading Here (maybe something like 'Structure')==
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<StructureSection load='1ema' size='340' side='right' caption='Caption for this structure' scene=''>
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<StructureSection load='2f1m' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
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== Example page for Green fluorescent protein ("GFP") ==
 
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Green fluorescent protein (1ema)
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== AcrA ==
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Green fluorescent protein (1ema)
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AcrA is a Multidrug efflux system protein. It belongs to resistance nodulation cell division (RND) family protein, which utilize electrochemical gradient to energize efflux of antibiotics and other compounds out of the bacterial cells (Putman et al 2000). RND system consists of large complexes of three essential proteins and work together as a multiprotein [http://en.wikipedia.org/wiki/Efflux_%28microbiology%29 efflux system]. Two most studied RND systems are E. coli AcrA-AcrB-TolC and P. aeruginosa MexA-MexB-OprM, which are known to efflux antibiotics, heavy metals, dyes, detergents, solvents, plus many other substrates (Ayush Kumar, Herbert P. Schweizer 2005).
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Green fluorescent <scene name='69/699996/1ema/1'>protein</scene> ('''GFP'''), originally isolated from the jellyfish Aequorea victoria (PDB entry 1ema), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement.
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== Stable core of AcrA ==
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Exploring the Structure
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GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The chromophore, responsible for the fluorescent properties of the protein, is buried inside the beta barrel as part of the central alpha helix passing through the barrel. The chromophore forms via spontaneous cyclization and oxidation of three residues in the central alpha helix: -Thr65 (or Ser65)-Tyr66-Gly67. This cyclization and oxidation creates the chromophore's five-membered ring via a new bond between the threonine and the glycine residues.[1]
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Four molecules of AcrA (45-312 residues) in asymmetric unit of the crystal pack as an apparent dimer of dimers. Each monomers are labeled as A (in blue), B (in orange), C (in green) and D (in pink). A, B / C, D are related to one another by approximate <scene name='69/699996/Acra/1'>dyad symmetry</scene>. Each set of dimers are related to one another by approximate 2 fold axis (Jonathan Mikolosko, Kostyantyn Bobyk, Helen I. Zgurskaya, and Partho Ghosh, 2006).
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Each monomer is a sickle shaped molecule comprising three domains viz. β-barrel domain, lipoyl domain, and coiled coil α-helical hairpin domain. β-barrel domain comprises six anti-parallel β-sheets and a short α-helix. Lipoyl domain is present in the central part of the AcrA monomer made up of two half motifs interrupted by an α-helical hairpin. Each half of the lipoyl motif is homologous to each other and consist of four β-strands in the form of a β-sandwich. A conserved lysine residue on the connecting loop of two half motifs serve as carrier of lipoyl or biotinyl co-factors. The coiled coil domain consists of five heptad repeats per helix. Two α-helices are packed together as a canonical knobs-into-holes by hydrophobic side chains in the a and d positions of the heptad repeats (Johnson and Church 1999, Akama et al 2004). Crystal structure provide evidence for the flexibility of the hinge region between α-helical hairpin and lipoyl domain. The difference in hinge angle in case of B and C chain varies approximately by 15o overall and 21 Å at the loop located at the top of the hairpin.
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== Assembly within biological system ==
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== Function ==
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AcrA is present within E. coli cells as a part of tripartite membrane associated efflux system along with AcrB and TolC. AcrA is present in the periplasmic space of cell with the proton antiporter AcrB in the inner-membrane and channel TolC in the outer membrane. It can it can remain free or form bipartite complexes with AcrB and TolC. The lipoyl and β-barrel domain of AcrA interact with AcrB, whereas the α-helical hairpin domain interact with TolC (Qiang Ge et al, 2009). ArcA remains attached to the inner membrane via lipid acylation of Cys-25. N and C termini of AcrA form two β-stand, β1 (54-61) and β14 (292-297). A 28 flexible residues connects acylated Cys-25 with the β-barrel domain and allow the protein to reach the periplasmic top of AcrB (Yu et al 2003). A short α-helix (222-230) located between β-10 and β-11 closes off the end of the β-barrel near the C-terminus of AcrA fragment. Approximately 100 residues in the C-terminal are predicted to be important for AcrAB-TolC interaction.
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== Disease ==
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== Relevance ==
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== Structural highlights ==
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This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
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</StructureSection>
</StructureSection>
== References ==
== References ==
<references/>
<references/>

Revision as of 07:20, 22 April 2015

This Sandbox is Reserved from 15/04/2015, through 15/06/2015 for use in the course "Protein structure, function and folding" taught by Taru Meri at the University of Helsinki. This reservation includes Sandbox Reserved 1081 through Sandbox Reserved 1090.
To get started:
  • Click the edit this page tab at the top. Save the page after each step, then edit it again.
  • Click the 3D button (when editing, above the wikitext box) to insert Jmol.
  • show the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.
  • Add a description of your scene. Use the buttons above the wikitext box for bold, italics, links, headlines, etc.

More help: Help:Editing

Your Heading Here (maybe something like 'Structure')

Caption for this structure

Drag the structure with the mouse to rotate

References

  1. Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
  2. Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
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