Transient NOE-exchange-relay experiment: application to ligand-protein binding under slow exchange conditions.
A new version of one-dimensional (1)H experiment has been developed to probe ligand binding to macromolecular targets. The experiment, called transient NOE-exchange relay, is similar to the 'reverse NOE pumping' technique [A. Chen, M.J. Shapiro, J. Am. Chem. Soc. 122 (2000) 414-415]. The T(2) filter is used to erase protein magnetization, and the saturation then spreads from protein to bound ligand (via NOE) and further to a free ligand (via on-off exchange). The ligand signals, monitored as a function of mixing time, present a familiar 'dip' pattern characteristic of transient NOE or transient exchange experiments. In addition to the T(2) filter, we have also implemented a T(1) filter which makes use of the fact that the selective T(1)(-1) rates in macromolecules are much higher than those in small ligands. To model the experiment, complete relaxation and exchange matrix analysis has been invoked. This formalism was further used as a starting point to develop a simplified treatment where the relaxation and exchange components are represented by 2x2 matrix and, in addition, there is a special term responsible for coupling of ligand magnetization to the protein spin bath. The proposed experimental scheme has been tested on a system of peanut agglutinin complexed with Me-beta-D-galactopyranoside, which is known to be in a slow exchange regime. The results suggest that the NOE-exchange-relay experiment can be used at the advanced stages of the drug development process to confirm high-affinity ligand binding.
Podkorytov
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IS
Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA.
Skrynnikov
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D000465:Algorithms; D003198:Computer Simulation; D005690:Galactose / Q000737:chemistry; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D019887:Peanut Agglutinin / Q000737:chemistry; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*
D008024:Ligands; D019887:Peanut Agglutinin; D011506:Proteins; D005690:Galactose