NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA.

ABSTRACT: Nonspecific protein-DNA interactions are inherently dynamic and involve both diffusion of the protein along the DNA and hopping of the protein from one DNA molecule or segment to another. Understanding how gene regulatory proteins interact nonspecifically with DNA in terms of both structure and dynamics is challenging because the experimental observables are an ensemble average of many rapidly exchanging states. By using a variety of NMR spectroscopic techniques, including relaxation analysis, paramagnetic relaxation enhancement, and residual dipolar couplings, we have characterized structural and kinetic aspects of the interaction of the HoxD9 homeodomain with a nonspecific, 24-bp DNA duplex in a system in which the protein is not constrained to any particular site. The data reveal that H

SUBMITTER: Iwahara J 

PROVIDER: S-EPMC1622777 | biostudies-literature | 2006 Oct

REPOSITORIES: biostudies-literature