Contact nuclear Overhauser effects

Nuclear magnetic resonance (NMR) S Chemical shift, coupling constants, and spectroscopy nuclear Overhauser effect allows calculation of contact points, distances, and conformation... 

The detailed nuclear Overhauser effect (NOE) analysis of contacts between Pl and its flanking thymidine residues involving imino and methyl protons attested to a stacked-in conformation for this base, with a regular right-handed helical conformation [69]. Cross-strand NOE patterns between protons on adjacent triplexes suggested no structural distortions with an altered width for the groove formed by purines and pyrimidines in the third strand. The Pl base was found to be readily accommodated in an otherwise all-pyrimidine third... 

Many other intermolecular and intramolecular contacts are described by distances (hydrogen bond lengths, van der Waals contact, experimentally determined distances from nuclear Overhauser effect (NOE) spectra, fluorescence energy transfer, etc.) so that the distance matrix representation can be used to specify all the known information about a molecular structure. These bounds are entered into a distance geometry program, as are other bounds that specify constraints on modeling problems, such as constraints to superimpose atoms in different molecules. Hypotheses about intra- or intermolecular conformations and interactions are easily specified with distance constraints models can be built quickly to test different hypotheses simply by changing the distance constraints. 

The most important structural probe is the nuclear Overhauser effect (NOE), which provides valuable information on the structure of linear peptides. Briefly, the observation of a direct NOE between a pair of protons indicates the presence of a significant population of conformers in which the distance between these two proteins is relatively short. The overall pattern of connectivity therefore corresponds to a particular conformation. Constraints on both backbone and side chain dihedral angles are obtained from coupling contacts. An example of a two-dimensional NMR spectrum for a synthetic peptide related to residues 6-13 of human growth hormone is shown in Figure 8. 

Fig. 9. Backbone folding of short neurotoxin molecule as derived from Naja naja neurotoxin II study. Additional contacts from the studies of other neurotoxin are indicated as follows Mos - neurotoxin III Naja mossambica mossambica (36), Erb - erabutoxin b Laticauda semifasciata(40) and Ct - cobrotoxin Naja Naja atra(39). Abbreviation pK -deprotonation of ionogenic group influence on chemical shifts, + - charge effect on pK values, NOE - nuclear Overhauser effect, CS - chemical shift changes upon selective modification, SL - spin label broadening effects.

Basic data obtained from NMR studies consist of distance and torsion angle restraints. Once resonances have been assigned, nuclear Overhauser effect (NOE) contacts are selected and their intensities are used to calculate interproton distances. Information on torsion angles are based on the measurement of coupling constants and analysis of proton chemical shifts. Together, this information is used to formulate a nonlinear optimization problem, the solution of which should provide the correct protein structure. Typically, a hybrid energy function of the following form is employed ... 

To determine whether the catalyst remains in this conformation in solution, heteronuclear NOESY experiments were set up. If one of the ligands flips, nOe (nuclear Overhauser effect) contacts between the side chain protons and the phthaloyl carbons should be visible. No cross peaks were detected in the case of 20, meaning that the all-up conformation is also predominant in solution, whereas cross peaks in the spectrum of 19 indicated that the C4 symmetry is not maintained in solution. Variable temperature NMR experiments with 20 confirmed this, as the aromatic carbon atoms give rise to two singlets at room temperature, which merge into one broad singlet at higher temperatures (comparable to the spectmm of 19 at room temperature). 

Energy levels with Overhauser effect (a) Relaxation due to a time-dependent isotropic contact electron-spin-nuclear-spin hyperfine interaction a(t)l S which has a zero time-average, but allows processes X and Y and enhances nuclear spin transitions when the electron populations are made equal by saturation, (b) Relaxation is due to all dipole-dipole interactions, which allow processes X, V, and PNi nuclear spin transitions are forced into emission by the Overhauser effect. In (a) the relative Boltzmann populations before saturation are shown. 

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