Kwaku T. Dayie

Structure and mobility of the PUT3 dimer.

The solution structure and backbone dynamics of the transcriptional activator PUTS (31–100) has been characterized using NMR spectroscopy. PUT3 (31–100) contains three distinct domains: a cysteine zinc cluster, linker, and dimerization domain. The cysteine zinc cluster of PUT3 closely resembles the solution structure of GAL4, while the dimerization domain forms a long coiled-coil similar to that observed in the crystal structures of GAL4 and PPR1. However, the residues at the N-terminal end of the coiled-coil behave very differently in each of these proteins. A comparison of the structural elements within this region provides a model for the DMA binding specificity of these proteins. Furthermore, we have characterized the dynamics of PUT3 to find that the zinc cluster and dimerization domains have very diverse dynamics in solution. The dimerization domain behaves as a large protein, while the peripheral cysteine zinc clusters have dynamic properties similar to small proteins.

Heteronuclear Relaxation and the Experimental Determination of the Spectral Density Function

Proteins have always been known as dynamic molecules. With the success of X-ray crystallography in solving protein structures over the past thirty years, the static aspects of proteins have been emphasized, primarily because this technique can only characterize relatively rigid and completely folded proteins. On the other hand, NMR can study partially folded proteins and can characterize well internal motions. Among the most fruitful techniques to characterize internal mobility in proteins are relaxation time measurements, and a large number of studies have focused on that aspect recently (see e.g. Wagner, 1993). Globular proteins must undergo a range of motions in space and time to modulate the stunning array of critical biological processes such as enhance the rate of transcription of DNA, transport electrons, maintain structural integrity, or modulate cellular immune responses (McCammon & Harvey, 1985; Brooks et al., 1988). Understanding such motion inside a protein might thus provide some insight into their behavior. For example, it may allow the elucidation of the potential energy surface on which these proteins move, it may provide some clues on how they fold from a linear chain to three dimensional structure. Finally, dynamics is important in the context of structure refinement. Mobility studies can allow one to detect erroneously too tightly constrained structures, and identify regions that are rigid but appear artifactually disordered in structure calculations due to incomplete data analysis.