Interproton distances determination

A combined approach is to use interproton distances determined by simulation and experimental NOE intensities to calculate the dynamic behavior of specific linkages in an oligosaccharide. The MM force field was employed for the computer simulation of calonyctin Ai (40) where interglycosidic NOEs served as experimental distance restraints for the molecular dynamics 104). 

Clearly though, even a purely qualitative evaluation of the geometric influences of the anomeric and exo-anomeric effects based on a new independent measurement tool, has some considerable relevance and further studies on this topic are being actively pursued at this time. And to leave the more sceptical readers of this article with some positive food-for-thought, we summarise below in Table V the interproton distances, determined (22.) by proton relaxation measurement, for an organic molecule, the bicycloheptene portion of XII which is, according to all presently available criteria, tumbling isotropically. 

As anticipated for the 6-4 adduct our interproton distances reflect the R stereochemistry of the linkage between the adjacent thymines found experimentally (50). More interesting from both an experimental and computational perspective is the unusual A4(H1 )-T6(CH3) NOE observed for the 6-4 adduct (50). This NOE was also reflected in the interproton distance determined for these same protons in the simulated structure. In fact, analysis of the simulated structure finds the T6 methyl significantly closer to the A4 deoxyribose than it is in the refined NMR structure. Thus we believe the simulated structure better accounts for the experimental observation of this unusual NOE. On further inspection it is also apparent that the... 

To put the errors in comparative models into perspective, we list the differences among strucmres of the same protein that have been detennined experimentally (Fig. 9). The 1 A accuracy of main chain atom positions corresponds to X-ray structures defined at a low resolution of about 2.5 A and with an / -factor of about 25% [192], as well as to medium resolution NMR structures determined from 10 interproton distance restraints per residue [193]. Similarly, differences between the highly refined X-ray and NMR structures of the same protein also tend to be about 1 A [193]. Changes in the environment... 

This simple relaxation theory becomes invalid, however, if motional anisotropy, or internal motions, or both, are involved. Then, the rotational correlation-time in Eq. 30 is an effective correlation-time, containing contributions from reorientation about the principal axes of the rotational-diffusion tensor. In order to separate these contributions, a physical model to describe the manner by which a molecule tumbles is required. Complete expressions for intramolecular, dipolar relaxation-rates for the three classes of spherical, axially symmetric, and asymmetric top molecules have been evaluated by Werbelow and Grant, in order to incorporate into the relaxation theory the appropriate rotational-diffusion model developed by Woess-ner. Methyl internal motion has been treated in a few instances, by using the equations of Woessner and coworkers to describe internal rotation superimposed on the overall, molecular tumbling. Nevertheless, if motional anisotropy is present, it is wiser not to attempt a quantitative determination of interproton distances from measured, proton relaxation-rates, although semiquantitative conclusions are probably justified by neglecting motional anisotropy, as will be seen in the following Section. 

From the previous discussion, it is clear that relaxation experiments constitute a very powerful tool for investigation of the structure and conformation of carbohydrate molecules in solution. However, the nature of the individual problem may determine which relaxation experiment should be chosen in order to extract interproton distances to the desired accuracy of < 0.2 A. Although the limitations and relative merits of all of the various relaxation methods have not yet been systematically studied, accumulated experience provides some direct knowledge about the range of errors associated with relaxation experiments. 

Combinations of non-selective and/or single-selective relaxation-rates, or both, with n.0.e. values may conveniently be performed with reliable results, especially when other methods seem impractical. However, these experiments are time-consuming, as they entail the determination of a rather large number of experimental values. Moreover, the n.O.e. parameters carry their own systematic and random errors, which are magnified in the calculation of interproton distances. The deuterium-substitution method requires specific deuteration at a strategic position, which, in many cases, may be inconvenient or impractical. Also, this technique is valid only when the relaxation rates obtained after deuterium substitution are at least 5% enhanced, relative to the relaxation rates of the unsubstituted compound, and it requires that, for a meaningful experiment, the following condition " be satisfied. 

For a rigidly held, three-spin system, or when existing internal motion is very slow compared to the overall molecular tumbling, all relaxation methods appear to be adequate for structure determination, provided that the following assumptions are valid (a) relaxation occurs mainly through intramolecular, dipolar interactions between protons (b) the motion is isotropic and (c) differences in the relaxation rates between lines of a multiplet are negligibly small, that is, spins are weakly coupled. This simple case is demonstrated in Table V, which gives the calculated interproton distances for the bicycloheptanol derivative (52) of which H-1, -2, and -3 represent a typical example of a weakly coupled, isolated three-spin... 

The significance of n.m.r. spectroscopy for structural elucidation of carbohydrates can scarcely be underestimated, and the field has become vast with ramifications of specialized techniques. Although chemical shifts and spin couplings of individual nuclei constitute the primary data for most n.m.r.-spectral analyses, other n.m.r. parameters may provide important additional data. P. Dais and A. S. Perlin (Montreal) here discuss the measurement of proton spin-lattice relaxation rates. The authors present the basic theory concerning spin-lattice relaxation, explain how reliable data may be determined, and demonstrate how these rates can be correlated with stereospecific dependencies, especially regarding the estimation of interproton distances and the implications of these values in the interpretation of sugar conformations. 

The basis for the determination of solution conformation from NMR data lies in the determination of cross relaxation rates between pairs of protons from cross peak intensities in two-dimensional nuclear Overhauser effect (NOE) experiments. In the event that pairs of protons may be assumed to be rigidly fixed in an isotopically tumbling sphere, a simple inverse sixth power relationship between interproton distances and cross relaxation rates permits the accurate determination of distances. Determination of a sufficient number of interproton distance constraints can lead to the unambiguous determination of solution conformation, as illustrated in the early work of Kuntz, et al. (25). While distance geometry algorithms remain the basis of much structural work done today (1-4), other approaches exist. For instance, those we intend to apply here represent NMR constraints as pseudoenergies for use in molecular dynamics or molecular mechanics programs (5-9). 

Functions such as 1 and 2 permit the inclusion of a pseudoenergy term for all pairs of protons in a molecule, whether or not cross relaxation rates are sufficiently large to be observed. This is made possible by the fact that for sufficiently long distances, the energy contributions from these functions are negligible. For cases where no connectivity is observed between a pair of protons roa6 is set equal to some distance, in our case 4.0A, beyond which a connectivity between protons would be lost in the noise. Inclusion of a pseudoenergy term in the absence of an observed connectivity is important since it serves to exclude conformers with interproton distances short enou to produce a connectivity when none is observed. We shall make limited use of this fact in our structural determinations. 

Quantitative analysis of exchange spectra directly provides data about the chemical exchange and the cross-relaxation rates. Whereas the chemical exchange rate constants are used directly, the cross-relaxation rates are usually processed further for determination of interproton distances and correlation times. 

Equations (33a) and (33b) are of limited value because, most often, /(tc) is not known. Therefore, to determine interproton distance one has to eliminate the correlation time dependence. One possibility is to calibrate crossrelaxation rate by comparing the cross-relaxation rate of a spin pair with known distance [Pg.281]

Besides the advantage of the high-temperature measurements for quantitative interpretation of NOESY spectra, fig. 6 also indicates a special role of the high temperature maximum (note that positive cross-relaxation rates increase downward) of u". If the NOESY spectrum can be recorded at several temperatures around the cr" maximum, than calculated cross-relaxation rates can be used to obtain simultaneously the correlation time and the interproton distances without the necessity of any other knowledge. A typical problem in the cross-relaxation experiments is that cross-relaxation rate depends on two parameters, Tc and r (eq. (la)), and to calculate one of them the other must be independently known. However, the position of the maximum uniquely determines correlation time, and its height uniquely determines interproton distances. 

Nilges, M., Gronenborn, A. M., Brunger, A. T. and Clore, G M. (1988). Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng. 2, 27-38. 

In a typical free NOESY experiment of a molecule in the absence of any interacting protein, cross-peak volumes are interpreted in terms of a set of interproton distances r that can be used as distance restraints in structure determination procedures, like restrained simulated annealing protocols [44], In a tr-NOESY, i.e. a NOESY measured under exchange-transferred conditions in the presence of a protein - i.e., an excess of soluble ligand is in fast exchange equilibrium with a smaller amount of protein-bound ligand -, these r reflect the interproton distances of the ligand in the bound... 

Two conformations of EpoA in complex with tubulin have been proposed on the basis of EC [26] and NMR [76, 96] data, respectively (Fig. 11). The tubulin-bound conformation of EpoA was determined by solution NMR spectroscopy [96] before the EC structure of EpoA bound to tubulin was available. The observation that, in a 100 1 mixture with tubulin, NOE cross-peaks of EpoA have negative sign, indicated that there is a fast exchange equilibrium in solution. This offered the opportunity to measure transferred NMR experiments, that report on the bound conformation of the ligand. A total of 46 interproton distances were derived from cross-peak volumes in tr-NOE spectra. However, these distance restraints did not suffice to define a unique conformation, as several distinct structures were consistent with them. Transferred cross-correlated relaxation (Sect. 2.2.1.3) provided the additional dihedral restraints that were crucial to define the bound conformation [96, 97], One requirement to measure CH-CH dipolar and CH-CO dipolar-CSA CCR rates is that the carbon atoms involved in the interaction are labeled with 13C. The availability of a 13C-labeled sample of EpoA offered the opportunity to derive seven of these dihedral angle restraints from tr-CCR measurements (Fig. 12). 

Recently, it was shown that ss-NMR spectroscopy can be used to determine the conformation of EpoB in the solid state [116]. The method relies on the measurement of intramolecular short H-H distances (in the range 1.8-3.0 A) from 2D CHHC correlations under MAS [117]. Regarding the sample preparation, a small amount of 13C labeled compound was diluted with EpoB with natural abundance of carbon isotopes. This reduces the signal to noise but, on the other hand, it excludes contributions from intermolecular H-H polarization transfer. Under these conditions, all CHHC cross-peaks result from intramolecular polarization transfer and reflect intramolecular interproton distances. 

M. Nilges, A. M. Gronenborn, A. T. Brunger, and G. M. Clore, Protein Engin., 2,27 (1988). Determination of Three-Dimensional Structures of Proteins by Simulated Annealing with Interproton Distance Restraints. Application to Crambin, Potato Carboxypeptidase Inhibitor, and Barley Serine Proteinase Inhibitor 2. 

A. T. Briinger, G. M. Clore, A. M. Gronenborn, and M. Karplus, Proc. Natl. Acad. Set. USA, 83, 3801 (1986). Three-Dimensional Structure of Proteins Determined by Molecular Dynamics with Interproton Distance Restraints Applications to Crambin. 

There are three aspects to consider. First, we summarize briefly the underlying computational framework needed and the general strategy used in the structure determination. Second, we cover the use of 2D, 3D, and 4D methods to permit the sequential assignment of peaks to specific amino acids. Finally, we describe the use of nuclear Overhauser enhancements and spin coupling constants to provide restraints on interproton distances and bond angles, and we indicate how dipolar coupling and chemical shifts can sometimes add further information on molecular conformation. 

Chini, M. G. Jones, C. R. ZampeUa, A. D Auria, M. V. Renga, B. Fiorucci, S. Butts, C. P Bifulco, G. Quantitative NMR-derived interproton distances combined with quantum mechanical calculations of chemical shifts in the stmeochemical determination of conicasterol F, a nuclear receptor ligand from theonella swinhoei, ... 

In addition to investigations this important class of compound may also be studied by means of MAS NMR spectroscopy. In fact we have shown that sharp resonances may be obtained from solid state MAS NMR of molecular hydrido carbonyl complexes without recourse either to the multiple pulse methods [22] or to isotopic dilution [23]. This is due to the fact that in these compounds the protons are intramolecularly diluted. We considered again H20s3(CO)io which crystallizes with one molecule as the asymmetric unit, as determined by a neutron diffraction study [24], and displays an interproton distance of 2.38 A. This interproton distance affords a dipolar coupling constant of 8.91 kHz. Now, rotation of the sample at 8.1 kHz allows... 

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