User:Laura Carbone/Sandbox 1: Difference between revisions
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===Primary & Secondary Structure=== {{STRUCTURE_1ema | PDB=1ema | scene name='User:Laura_Carbone/Sandbox_1/Initial/1' }} | ===Primary & Secondary Structure=== {{STRUCTURE_1ema | PDB=1ema | scene name='User:Laura_Carbone/Sandbox_1/Initial/1' }} | ||
Green fluorescent protein (<scene name='User:Laura_Carbone/Sandbox_1/Initial/1'>default scene</scene>) | Green fluorescent protein (<scene name='User:Laura_Carbone/Sandbox_1/Initial/1'>default scene</scene>) is a 21 kDa protein consisting of 238 residues strung together to form a | ||
<scene name='User:Laura_Carbone/Sandbox_1/Secondary_structure/4'>secondary structure</scene> of five α-helices and one eleven-stranded β-pleated sheet,<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/3'>"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" /> | <scene name='User:Laura_Carbone/Sandbox_1/Secondary_structure/4'>secondary structure</scene> of five α-helices and one eleven-stranded β-pleated sheet,<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/3'>"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" /> | ||