Protein L : Amide Proton Exchange

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Overall Architecture of Peptostreptococcal Protein L.

The protein is shown as Cartoons with Structure coloring. The a-helix is a magenta-colored spiral; the b-strands are yellow-colored arrows (pointing from the N- to the C-terminus); regular turns are colored light blue; and unspecified (mostly connecting) segments are colored white.

The exchange of amide protons (N-H) with solvent D2O was studied by Yi and Baker, Protein Sci5, 1060-1066 (1996) using NMR and mass spectrometry. The NMR experiments showed that the exchange rates fell into three classes.
Color each residue by class:
Red: Rapidly exchanging protons on the surface (>105/sec).
Green: Intermediate exchange rates.
Blue: Slowly exchanging protons found mostly in the interior of the protein. Mass spectrometry showed that this class exchanged in "all-or-none" fashion with a rate similar to the unfolding kinetics (0.06/sec).

Color and spacefill only the amide protons in each class. After coloring the amide protons, choose additional displays from the Chime menu to examine the "visual accessibility" of each proton.

Viewing tips:
Use the buttons to the right of the image to show only portions of the structure; then use the Chime menu to display or color the molecule. The rotate buttons act on the entire structure. Remove the distance monitors with a second click.

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The coordinate file used here is derived from 2ptl.pdb.
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