Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement.
Recent advances in the use of paramagnetic relaxation enhancement (PRE) in structure refinement and in the analysis of transient dynamic processes involved in macromolecular complex formation are presented. In the slow exchange regime, we show, using the SRY/DNA complex as an example, that the PRE provides a powerful tool that can lead to significant increases in the reliability and accuracy of NMR structure determinations. Refinement necessitates the use of an ensemble representation of the paramagnetic center and a model-free extension of the Solomon-Bloembergen equations. In the fast exchange regime, the PRE provides insight into dynamic processes and the existence of transient, low population intermediate species. The PRE allows one to characterize dynamic nonspecific binding of a protein to DNA; to directly demonstrate that the search process whereby a transcription factor locates its specific DNA target site involves both intramolecular (sliding) and intermolecular (hopping and intersegment transfer) translocation; and to detect and visualize the distribution of an ensemble of transient encounter complexes in protein-protein association.
Clore
G Marius
GM
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA. mariusc@intra.niddk.nih.gov
Tang
Chun
C
Iwahara
Junji
J
D004247:DNA / Q000737:chemistry; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D018398:Homeodomain Proteins / Q000737:chemistry; D007091:Image Processing, Computer-Assisted; D046911:Macromolecular Substances / Q000737:chemistry*; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D051876:Sex-Determining Region Y Protein / Q000737:chemistry; D013113:Spin Labels; D013816:Thermodynamics
D018398:Homeodomain Proteins; D046911:Macromolecular Substances; D051876:Sex-Determining Region Y Protein; D013113:Spin Labels; D004247:DNA