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Dynamics of the GCN4 Basic Leusine Zipper Domain

Clay Bracken, Peter A. Carr, John Cavanaugh, & A.G. Palmer (1999) Temperature Dependence of Intramolecular Dynamics of the Basic Leucine Zipper of GCN4: Implications for the Entropy of Association with DNA, J. Mol. Biol. 285, 2133-2146.

Structure and sequence of GCN4-58. Top, ribbon and diagram of the GCN4bZip DNA-binding domain and dimerization domain complexed with DNA. The Figure was drawn from the coordinates of PBD file 1ysa using Insight (Molecular Simulations). Bottom, the amino acid sequence of GCN4-58 DNA-binding domain and dimerization domain is shown using one letter amino acid codes. The amino acid residues are numbered in numerical order above the sequence. Residues 3 through 48 in GCN4-58 correspond with residues 26 through 281 in the full-length GCN4 protein. The N-terminal Met-Lys dipeptide of GCN4-58 is not part of the GCN4 sequence.

The 1H-15N HSQC correlation spectrum of GCN4-58 in the absence of DNA (pH = 4.7, T = 310 K) at 600 MHz 1H frequency. The resonances for the backbone amide of Gly56 (boxed in the Figure) and for the Arg N spins (circled) are aliased. The resonances for the N and C-terminal residues, the basic region, and the leucine zipper are depicted in green blue, and red, respectively.

Backbone motions of GC4-58 at 290, 300, and 310 K. The width and color of the backbone tube are proportional to the inverse of J(0.87H). Values of J(0.87H) were interpolated for residues for which relaxation data was not obtained. The Figure was drawn using MOLMOL (Koradi et al., 1996). The graph shows the temperature dependence of intramolecular dynamics of GCN4-58. The slopes of linear least-squares fits of J(0.87H) versus temperature are graphed for those residues for which data are available at all three temperatures.

Amplitudes of intramolecular motions in GCN4-58 in the absence of DNA. The order parameter S2 at 310 K derived from spectral density mapping is graphed versus amino acid sequence. The increase in the amplitude of motion (reduction in S2) in the N-terminal basic region implies that DNA-binding is accompanied by a large unfavorable decrease in conformational chain entropy of the backbone of GCN4-58.

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Last modified 7/25/02 Kemal Eren. Send comments to agp6@columbia.edu