Sandbox 719: Difference between revisions
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====Secondary Structure==== | ====Secondary Structure==== | ||
<Structure load='1G7K' size=' | <Structure load='1G7K' size='510' frame='true' align='right' scene='Insert optional scene name here' /> | ||
The DsRed is a 28kDa polypeptide that emits a red color after an excitation because of the presents of a chromophore composed by 3 amino acids –Gln-Tyr-Gly- (residues 66-68)<ref>Fluorescent proteins from nonbioluminescent Anthozoa species. Matz MV, Fradkov AF, Labas YA, Savitsky AP, Zaraisky AG, Markelov ML, Lukyanov SA.. PubMed : [http://www.ncbi.nlm.nih.gov/pubmed/10504696 10504696]</ref>. The fold of our protein is very closed to the most common fluorescent protein, the ''Aequorea victoria'' Green Fluorescent Protein (avGFP). The primary sequence of those two proteins is 23% similar but in the immediate vicinity of the chromophore the primary structure is strictly conserved and theses several amino acid are probably essential for the chromophore formation. The DsRed protein is obligatory a tetramer in solution. The monomer is composed by 11-strand <scene name='Sandbox_719/Sheet/1'>beta sheet</scene> with a coaxial <scene name='Sandbox_719/Helix/1'>helix</scene>. | The DsRed is a 28kDa polypeptide that emits a red color after an excitation because of the presents of a chromophore composed by 3 amino acids –Gln-Tyr-Gly- (residues 66-68)<ref>Fluorescent proteins from nonbioluminescent Anthozoa species. Matz MV, Fradkov AF, Labas YA, Savitsky AP, Zaraisky AG, Markelov ML, Lukyanov SA.. PubMed : [http://www.ncbi.nlm.nih.gov/pubmed/10504696 10504696]</ref>. The fold of our protein is very closed to the most common fluorescent protein, the ''Aequorea victoria'' Green Fluorescent Protein (avGFP). The primary sequence of those two proteins is 23% similar but in the immediate vicinity of the chromophore the primary structure is strictly conserved and theses several amino acid are probably essential for the chromophore formation. The DsRed protein is obligatory a tetramer in solution. The monomer is composed by 11-strand <scene name='Sandbox_719/Sheet/1'>beta sheet</scene> with a coaxial <scene name='Sandbox_719/Helix/1'>helix</scene>. | ||
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==== The Chromophore environment ==== | ==== The Chromophore environment ==== | ||
<Structure load='1G7K' size=' | <Structure load='1G7K' size='490' frame='true' align='left' scene='Insert optional scene name here' /> | ||
[[Image:Chromophore1G7K.gif |250px|right|thumb|Figure 2: Chromophore of the DsRed protein]] | [[Image:Chromophore1G7K.gif |250px|right|thumb|Figure 2: Chromophore of the DsRed protein]] | ||
Structure of the chromophore was predicted by sequence comparisons. | Structure of the chromophore was predicted by sequence comparisons. The chromophore of the DsRed is localized in a very polar cavity, and results to the autocatalytic cyclization and hydrogenation of the<scene name='Sandbox_719/Chromophore/1'> -Gln66-Tyr67-Gly68- tripeptide</scene>. Environment of DsRed chromophore is much more complicated in DsRd than in GFP, cause to the hydrogen bond and salt bridge network. There are more charges in DsRed than in GFP, due to three lysine (residues 70,83 and 163) and glutamic acid (residue 148) wich interact very closely with the chromophore. These charges are localized in two perpendicular band : the positive one is parallel to the axis of the chromophore, and the negative one perpendicular to this axis. | ||
The Phenolate oxygen of the chromophore forms a hydrogen bond with Ser-146 and a nearly water molecule, and it also forms a charge-charge with the Lys-163 residue. To forms all these interactions, the necessarily always charged. | The Phenolate oxygen of the chromophore forms a hydrogen bond with Ser-146 and a nearly water molecule, and it also forms a charge-charge with the Lys-163 residue. To forms all these interactions, the necessarily always charged. | ||
There is an other important residue in the struture of the chromophore, the residue Glu-215 (equivalent to the residue Glu-222 in GFP). This residue is highly close to the chromophore, and it also interacts with a water molecule localized near GLN-66. But Glu-215 also interacts with the positively charged chain of Lys-70, and it forms a hydrogen with Ser-205 side chain, like in GFP. | There is an other important residue in the struture of the chromophore, the residue Glu-215 (equivalent to the residue Glu-222 in GFP). This residue is highly close to the chromophore, and it also interacts with a water molecule localized near GLN-66. But Glu-215 also interacts with the positively charged chain of Lys-70, and it forms a hydrogen with Ser-205 side chain, like in GFP. | ||
