User:Laura Carbone/Sandbox 1: Difference between revisions

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{{STRUCTURE_1ema |  PDB=1ema  |  scene name='User:Laura_Carbone/Sandbox_1/Initial/1'  }}
{{STRUCTURE_1ema |  PDB=1ema  |  scene name='User:Laura_Carbone/Sandbox_1/Initial/1'  }}
<scene name='User:Laura_Carbone/Sandbox_1/Initial/1'>Green fluorescent protein</scene> consists of 238 residues strung together to form  
<scene name='User:Laura_Carbone/Sandbox_1/Initial/1'>Green fluorescent protein</scene> consists of 238 residues strung together to form  
<scene name='User:Laura_Carbone/Sandbox_1/Secondary_structure/3'>five α-helices and one β-pleated sheet</scene> consisting of eleven strands,<ref name="PDBsum" /> where each strand contains nine to thirteen residues each.<ref name="Ormo" />  (To view the primary and secondary structure of GFP, go to [[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1ema&template=protein.html&r=wiring&l=1&chain=A www.ebi.aci.uk]].)  These β-strands display an almost “seamless symmetry” in which only two of the strands vary in structural content.<ref name="Phillips">Phillips GN Jr.  1997.  Structure and dynamics of green fluorescent protein.  Curr Opin Struct Biol.  7(6):821-827.  DOI 10.1016/S0959-440X(97)80153-4.</ref>  This β-sheet conforms itself through regular hydrogen bonding into a β-barrel.<ref name="Yang" />  In GFP, the structure is so regular that “stripes” of water molecules can be seen following the structure of the barrel.<ref name="Phillips" />  Together with the α-helices at either end of the molecule, a nearly perfect cylinder is produced, 42Å long and 24Å in diameter,<ref name="Ormo" /> creating what is referred to as a “β-can” formation.<ref name="Phillips" />  The short helical segments at either end of the cylinder form “caps” to further protect the interior of the β-barrel.<ref name="Phillips" />  Overall stability is maintained by this β-can structure, helping to resist unfolding from heat and other denaturants.<ref name="Yang" />
<scene name='User:Laura_Carbone/Sandbox_1/Secondary_structure/3'>five α-helices and one β-pleated sheet</scene> consisting of eleven strands,<ref name="PDBsum" /> where each strand contains nine to thirteen residues each.<ref name="Ormo" />  (To view the primary and secondary structure of GFP, go to [[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1ema&template=protein.html&r=wiring&l=1&chain=A www.ebi.aci.uk]].)  These β-strands display an almost “seamless symmetry” in which only two of the strands vary in structural content.<ref name="Phillips">Phillips GN Jr.  1997.  Structure and dynamics of green fluorescent protein.  Curr Opin Struct Biol.  7(6):821-827.  DOI 10.1016/S0959-440X(97)80153-4.</ref>  This β-sheet conforms itself through regular hydrogen bonding into a β-barrel.<ref name="Yang" />  In GFP, the structure is so regular that <scene name='User:Laura_Carbone/Sandbox_1/Stripes_of_water/1'>"stripes"</scene> of water molecules (red) can be seen following the structure of the barrel.<ref name="Phillips" />  Together with the α-helices at either end of the molecule, a nearly perfect cylinder is produced, 42Å long and 24Å in diameter,<ref name="Ormo" /> creating what is referred to as a “β-can” formation.<ref name="Phillips" />  The short helical segments at either end of the cylinder form “caps” to further protect the interior of the β-barrel.<ref name="Phillips" />  Overall stability is maintained by this β-can structure, helping to resist unfolding from heat and other denaturants.<ref name="Yang" />


One <scene name='User:Laura_Carbone/Sandbox_1/Central_helix/1'>α-helix</scene> can be found running through the central axis of the β-barrel,<ref name="Haldar" /> roughly <scene name='User:Laura_Carbone/Sandbox_1/Perpendicular/2'>perpendicular</scene> to the symmetry axis of the barrel.<ref name="Ormo">Ormo M, Cubitt AB, Kallio K, Gross LA, Tsien RY, Remington SJ.  1996.  Crystal structure of the ''Aequorea victoria'' green fluorescent protein.  Science.  273(5280):1392-1395.  DOI 10.1126/science.273.5280.1392.</ref>  This helix is extremely important as it contains the fluorophore responsible for fluorescence.<ref name="Yang" /><ref name="Haldar" />  This α-helix in particular is highly stabilized by the many contacts that are made with each strand of the barrel.<ref name="Andrews">Andrews BT, Gosavi S, Finke JM, Onuchic JN, Jennings PA.  2008.  The dual-basin landscape in GFP.  Proceedings of the National Academy of Sciences.  105(34):12283-12288.  DOI 10.1073/pnas.0804039105.</ref>
One <scene name='User:Laura_Carbone/Sandbox_1/Central_helix/1'>α-helix</scene> can be found running through the central axis of the β-barrel,<ref name="Haldar" /> roughly <scene name='User:Laura_Carbone/Sandbox_1/Perpendicular/2'>perpendicular</scene> to the symmetry axis of the barrel.<ref name="Ormo">Ormo M, Cubitt AB, Kallio K, Gross LA, Tsien RY, Remington SJ.  1996.  Crystal structure of the ''Aequorea victoria'' green fluorescent protein.  Science.  273(5280):1392-1395.  DOI 10.1126/science.273.5280.1392.</ref>  This helix is extremely important as it contains the fluorophore responsible for fluorescence.<ref name="Yang" /><ref name="Haldar" />  This α-helix in particular is highly stabilized by the many contacts that are made with each strand of the barrel.<ref name="Andrews">Andrews BT, Gosavi S, Finke JM, Onuchic JN, Jennings PA.  2008.  The dual-basin landscape in GFP.  Proceedings of the National Academy of Sciences.  105(34):12283-12288.  DOI 10.1073/pnas.0804039105.</ref>
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