Measurement of Ligand-Target Residence Times by H Relaxation Dispersion NMR Spectroscopy.

A ligand-observed H NMR relaxation experiment is introduced for measuring the binding kinetics of low-molecular-weight compounds to their biomolecular targets. We show that this approach, which does not require any isotope labeling, is applicable to ligand-target systems involving proteins and nucleic acids of variable molecular size. The experiment is particularly useful for the systematic investigation of low affinity molecules with residence times in the micro- to millisecond time regime.

Ligand-detected relaxation dispersion NMR spectroscopy: dynamics of preQ1-RNA binding.

An NMR-based approach to characterizing the binding kinetics of ligand molecules to biomolecules, like RNA or proteins, by ligand-detected Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments is described. A (15)N-modified preQ1 ligand is used to acquire relaxation dispersion experiments in the presence of low amounts of the Fsu class I preQ1 aptamer RNA, and increasing ligand concentrations to probe the RNA small molecule interaction. Our experimental data strongly support the conformational selection mechanism postulated.

NMR resonance assignments of the archaeal ribosomal protein L7Ae in the apo form and bound to a 25 nt RNA.

The archaeal protein L7Ae forms part of a protein complex in the ribosome that specifically recognizes and binds to kink-turn RNA. In this complex, L7Ae directly interacts with the oligonucleotide and creates a functional arrangement for site-specific 2'-O-methylation. We report the solution NMR backbone assignment of Methanocaldococcus jannaschii L7Ae (117 residues, 12.

A kinetic study of domain swapping of Protein L.

Domain swapping of the B1 domain of Protein L isolated from Peptostreptococcus magnus can be induced by rational mutation. We show that the monomeric and the domain swapped dimeric forms of the G55A mutant of Protein L are directly observable by solution NMR spectroscopy under equilibrium conditions. The kinetics of the domain swapping process can be characterized by real-time NMR spectroscopic techniques, and the free energy landscape for domain swapping of Protein L can be probed by variation of denaturant concentration.