Sandbox 719: Difference between revisions

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==== The Chromophore environment ====
 
=== Fluorescence ===
 
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=== The Chromophore environment ===
<Structure load='1G7K' size='300' frame='true' align='left' caption='Insert caption here' scene='Insert optional scene name here' />
<Structure load='1G7K' size='300' frame='true' align='left' caption='Insert caption here' scene='Insert optional scene name here' />
[[Image:Chromophore1G7K.gif |250px|right|]]
[[Image:Chromophore1G7K.gif |250px|right|]]
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===Analisys and comparison between DsRed and GFP chromophore===
=== Fluorescence ===
[[Image:ABC.png |210px|left|thumb||(A) A portion of the experimental multiwave- length anomalous dispersion-phased electron density map at 2.0-Å resolution,(B) Ball-and-stick diagram of the DsRed chromophore and environment. (C) Schematic diagram of the chromophore environment showing salt bridges and/or hydrogen bonds|]]
These experiments shown the existence of a green fluorescent protein intermediate, very close to GFP, and suggests that there are several steps in the overall reaction (Matz et al.). Studies of Baird et al. shown there are two key conserved amino acids : Gln-66 and Gln-215. When we do the comparison of chromophore of DsRed and GFP, two points seems to be important. First Gln-66 of DsRed had a sp2 hybridization while Thr/Ser-65 (which are at the same place in the molecule) of GFP have a sp3 hybridization. Secondly, the conserved glutamate Glu-215 of DsRed is closer of the chromophore and is bonded to a water molecule close to GlN-66, which becomes oxidized. So this positionning of Gln-66 and Glu-215 should have a big influence in the red fluorescence, and Glu-215 could have two roles : In the formation of green fluorescence intermediate, and, by its environment, is crucial for formation of green or red emitting species.
Matz et al. Suggested that GFP is a “broken” version of an ancestral red fluorescent protein, due to these obsevations.


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*In a high quantity, it could cytotoxic and forms aggregates.
*In a high quantity, it could cytotoxic and forms aggregates.
The aim of the studies on this protein is to understand how it work exactly, and find solutions to avoid these problems.
The aim of the studies on this protein is to understand how it work exactly, and find solutions to avoid these problems.
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===Analisys and comparison between DsRed and GFP chromophore===
[[Image:ABC.png |210px|left|thumb||(A) A portion of the experimental multiwave- length anomalous dispersion-phased electron density map at 2.0-Å resolution,(B) Ball-and-stick diagram of the DsRed chromophore and environment. (C) Schematic diagram of the chromophore environment showing salt bridges and/or hydrogen bonds|]]
These experiments shown the existence of a green fluorescent protein intermediate, very close to GFP, and suggests that there are several steps in the overall reaction (Matz et al.). Studies of Baird et al. shown there are two key conserved amino acids : Gln-66 and Gln-215. When we do the comparison of chromophore of DsRed and GFP, two points seems to be important. First Gln-66 of DsRed had a sp2 hybridization while Thr/Ser-65 (which are at the same place in the molecule) of GFP have a sp3 hybridization. Secondly, the conserved glutamate Glu-215 of DsRed is closer of the chromophore and is bonded to a water molecule close to GlN-66, which becomes oxidized. So this positionning of Gln-66 and Glu-215 should have a big influence in the red fluorescence, and Glu-215 could have two roles : In the formation of green fluorescence intermediate, and, by its environment, is crucial for formation of green or red emitting species.
Matz et al. Suggested that GFP is a “broken” version of an ancestral red fluorescent protein, due to these obsevations.
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