Sandbox 719: Difference between revisions

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==== 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 ====

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 ==== 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 ====