Transferred NOEs

Post, C. B. Exchange-transferred NOE spectroscopy and bound ligand structure determination. Curr. Opin. Struct. Biol. 2003, 13, 581-588. 

Intermolecular relaxation has little effect on intra-peptide exchange-transferred NOE intensities. J. Biomol. NMR 2002,... 

W. Transferred cross-correlated relaxation complements transferred NOE structure of an IL-4R-derived peptide bound to STAT-6. J. Am. Chem. Soc. 1999, 121, 1949-1953. 

In principle, there are different ways to characterize the complexes On one hand, in favourable cases, it is possible to measure the NMR parameters of the receptor in the free and bound states, i.e., differences in chemical shift and NOE-contacts, before and after the formation of the complex. On the other hand, it is usually more feasible to observe and detect changes in the ligand NMR signals before and after the binding process. In this latter case, the use of STD (saturation transfer difference) and TR-NOE (transferred NOE) experiments is of paramount importance. 

Due to the fact that cross-correlated relaxation depends linearly on the correlation time, it can be used to determine the conformation of ligands when bound to target molecules, provided that the off rate is fast enough to enable detection of the cross-correlated relaxation rate via the free ligand [33, 34]. The conditions under which such an experiment can be performed are similar to those found for transferred NOEs [35], and, for Kd values... 

In the transferred NOE (trNOE) experiment, a ID or 2D NOESY experiment is recorded [31]. The intermolecular NOE build-up to be used as a parameter in Eq. (5) arises from the bound state but is observed via the free ligand, requiring rapid exchange between bound and free states. The technique is described in more detail in Chapt. 16. 

In the transferred NOE experiment, RCIOSS is the cross-relaxation rate of the ligand weighted average over the free and bound state (Eq. 16.7). The experiment works best... 

In the isotope edited/ filtered spectra of a protein-ligand complex, the species actually observed is generally the complex itself. This is an important difference from transferred NOE or saturation difference techniques, where the existence of an equilibrium between free and bound species - and a certain rate of exchange between them - is essential (Chapts. 13 and 16). The general conditions for isotope filtering/editing are therefore identical to those required for standard protein NMR sample concentrations are usually limited by availability and solubility of the components to the order of 1 mM. Considerably lower concentrations will reduce the sensitivity of the experiments to unacceptable levels,... 

In the situation where the interaction is weak, one of the traditional methods that can be applied to obtain structm-al information (internuclear distances) of the bound ligand is the so-called transferred NOE (trNOE) method. Recently, it became possible to use transferred cross-correlated relaxation (trCCR) to directly measure dihedral angles. The combined use of these two techniques significantly improves the precision of the structure determination of ligands weakly bound to macromolecules. 

IKK I/cB kinase NBD NEMO binding domain NEMO NF/cB essential modulator NOE Nuclear Overhauser elfect RDC Residual dipolar coupling SAR Structure-activity relationship trCCR Transferred OCR trNOE Transferred NOE... 

The branched trisaccharide 1 was defined as the minimal carbohydrate epitope for effective binding to anti-GAS Abs [79]. The bound conformation of 1 in complex with the IgG mAb Strep 9 was investigated by transferred NOE experiments and found to correspond to a local minimum conformation, which differed from the predominant conformation in the free state by a rotation around the xj/ angle of the o -(l-2) linkage [123]. STD-NMR ex-... 

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