Sandbox 719: Difference between revisions
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==== The tetramer Interface ==== | ==== The tetramer Interface ==== | ||
[[Image:Tetramer-interface.jpg |200px|left|thumb|] | [[Image:Tetramer-interface.jpg |200px|left|thumb|]] | ||
The most striking feature of DsRed is that, as shown in Fig. 2, 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 Fig. 2, 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 accessible surface area of the isolated monomer (21) is 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 (21) is 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. | ||
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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. | 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 (7)]. In DsRed, the carboxy terminus of the A monomer embraces the C monomer and vice versa, forming a ‘‘clasp’’ about a local 2-fold. | 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 (7)]. 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 | 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 ==== | ==== The Chromophore environment ==== | ||
