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====Secondary Structure====

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 tetramer Interface ====

[[Image:Tetramer-interface.jpg |200px|left|thumb|Figure 1: Ribbon diagram of the DsRed tetramer, produced by MOLSCRIPT (28). Monomers are labeled with uppercase A–D, and the carboxy termini are labeled with lowercase a– d. The amino termini are obscured in this view. Note the antenna-like array of the chromophores, antiparallel in pairs.]]

The most striking feature of DsRed is that, as shown in Figure 1, it exists as an extremely close-packed tetramer, quite unlike the primarily monomeric avGFP. The tetramer is a square prism with remarkably flat sides and a small elliptical hole directly through the center. The hole is lined with polar residues and salt bridges and localizes a number of solvent molecules.

The most striking feature of DsRed is that, as shown in Figure 1, it exists as an extremely close-packed tetramer, quite unlike the primarily monomeric avGFP. It is a dimer of dimer. The whole tetramer is a square prism with remarkably flat sides and a small elliptical hole directly through the center. The hole is lined with polar residues and salt bridges and localizes a number of solvent molecules.

The accessible surface area of the isolated monomer <ref>The interpretation of protein structures: estimation of static accessibility. Lee B, Richards FM. PubMed : [http://www.ncbi.nlm.nih.gov/pubmed?term=The%20interpretation%20of%20protein%20structures%3A%20estimation%20of%20static%20accessibility here]</ref> ~~is around 10,230 Å², and that of the tetramer is 31,420 Å2, so roughly 25% of the monomer surface is not solvent accessible in the tetramer~~.

The accessible surface area of the isolated monomer is around 10,230 Å², and that of the tetramer is 31,420 Å², so roughly 25% of the monomer surface is not solvent accessible in the tetramer<ref>The interpretation of protein structures: estimation of static accessibility. Lee B, Richards FM. PubMed : [http://www.ncbi.nlm.nih.gov/pubmed?term=The%20interpretation%20of%20protein%20structures%3A%20estimation%20of%20static%20accessibility here]</ref>.

The AB interface does not seem to have particularly notable features and consists of hydrophobic interactions between small side chains, although a few hydrogen bonds and salt bridges are also present.

On the other hand, interactions in the AC (and BD) interface consist largely of salt bridges and hydrogen bonds, many of which are mediated by buried water molecules, as well a surprisingly large number of interactions involving aromatic residues.

A unique feature of the DsRed tetramer is the carboxy termini, which in avGFP are flexible [only residues 2–229 are visible of the 238 in the mature protein]<ref>Crystal structure of the Aequorea victoria green fluorescent protein. Ormö M, Cubitt AB, Kallio K, Gross LA, Tsien RY, Remington SJ. . PubMed : [http://www.ncbi.nlm.nih.gov/pubmed/8703075 8703075]</ref>. In DsRed, the carboxy terminus of the A monomer embraces the C monomer and vice versa, forming a ‘‘clasp’’ about a local 2-fold.

Although the carboxyl-terminal carboxylates are partially exposed to solvent, the intimate association of Leu-225 with another protomer in the tetramer will likely result in nonfunctional carboxyl-terminal fusion constructions with DsRed. Much of the AC interface involves the bulge region of the fold (which contacts the chromophore), suggesting that tetramer formation may be important for correct folding and/or proper establishment of the chromophore environment

==== The Chromophore environment ====

[[Image:Chromophore1G7K.gif |250px|right|thumb|Figure 2: Chromophore of the DsRed protein]]

Structure of the chromophore was predicted by sequence comparisons. ~~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 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.

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.

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.

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@@ Line 18: / Line 18: @@
 ====Secondary Structure====
-<Structure load='1G7K' size='370' frame='true' align='right' scene='Insert optional scene name here' />
+<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 tetramer Interface ====
 [[Image:Tetramer-interface.jpg |200px|left|thumb|Figure 1: Ribbon diagram of the DsRed tetramer, produced by MOLSCRIPT (28). Monomers are labeled with uppercase A–D, and the carboxy termini are labeled with lowercase a– d. The amino termini are obscured in this view. Note the antenna-like array of the chromophores, antiparallel in pairs.]]
-The most striking feature of DsRed is that, as shown in Figure 1, it exists as an extremely close-packed tetramer, quite unlike the primarily monomeric avGFP. The tetramer is a square prism with remarkably flat sides and a small elliptical hole directly through the center. The hole is lined with polar residues and salt bridges and localizes a number of solvent molecules.
+The most striking feature of DsRed is that, as shown in Figure 1, it exists as an extremely close-packed tetramer, quite unlike the primarily monomeric avGFP. It is a dimer of dimer. The whole tetramer is a square prism with remarkably flat sides and a small elliptical hole directly through the center. The hole is lined with polar residues and salt bridges and localizes a number of solvent molecules.
-The accessible surface area of the isolated monomer <ref>The interpretation of protein structures: estimation of static accessibility. Lee B, Richards FM. PubMed : [http://www.ncbi.nlm.nih.gov/pubmed?term=The%20interpretation%20of%20protein%20structures%3A%20estimation%20of%20static%20accessibility here]</ref> is around 10,230 Å², and that of the tetramer is 31,420 Å2, so roughly 25% of the monomer surface is not solvent accessible in the tetramer.
+The accessible surface area of the isolated monomer is around 10,230 Å², and that of the tetramer is 31,420 Å², so roughly 25% of the monomer surface is not solvent accessible in the tetramer<ref>The interpretation of protein structures: estimation of static accessibility. Lee B, Richards FM. PubMed : [http://www.ncbi.nlm.nih.gov/pubmed?term=The%20interpretation%20of%20protein%20structures%3A%20estimation%20of%20static%20accessibility here]</ref>.
 The AB interface does not seem to have particularly notable features and consists of hydrophobic interactions between small side chains, although a few hydrogen bonds and salt bridges are also present.
 On the other hand, interactions in the AC (and BD) interface consist largely of salt bridges and hydrogen bonds, many of which are mediated by buried water molecules, as well a surprisingly large number of interactions involving aromatic residues.
-A unique feature of the DsRed tetramer is the carboxy termini, which in avGFP are flexible [only residues 2–229 are visible of the 238 in the mature protein]<ref>Crystal structure of the Aequorea victoria green fluorescent protein. Ormö M, Cubitt AB, Kallio K, Gross LA, Tsien RY, Remington SJ. . PubMed : [http://www.ncbi.nlm.nih.gov/pubmed/8703075 8703075]</ref>. In DsRed, the carboxy terminus of the A monomer embraces the C monomer and vice versa, forming a ‘‘clasp’’ about a local 2-fold.
-Although the carboxyl-terminal carboxylates are partially exposed to solvent, the intimate association of Leu-225 with another protomer in the tetramer will likely result in nonfunctional carboxyl-terminal fusion constructions with DsRed. Much of the AC interface involves the bulge region of the fold (which contacts the chromophore), suggesting that tetramer formation may be important for correct folding and/or proper establishment of the chromophore environment
 ==== The Chromophore environment ====
-<Structure load='1G7K' size='470' frame='true' align='left' scene='Insert optional scene name here' />
+<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]]
-Structure of the chromophore was predicted by sequence comparisons. 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 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.
+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.
 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.