Three dimensional NMR spectroscopy

Figure 15.5. Two-dimensional spectrum produced from an F1-F2 slice through the 3-D HMQC-TOCSY spectrum of a pine forest soil fulvic acid at 1.3 ppm on the F3 (proton) axis (Figure 15.2). Labels on cross-peaks correspond to the C-H structures in the aliphatic structures shown. The full 3D cube is superimposed onto the example slice. Reprinted from Simpson, A. I, Kingery, W. L., and Hatcher, R G. (2003a). The identification of plant derived structures in humic materials using three-dimensional NMR spectroscopy. Environ. Sci. Technol. 37,337-342, with permission from the American Chemical Society.

Simpson, A. J., Kingery, W. L., and Hatcher, P. G. (2003a). The identification of plant derived structures in humic materials using three-dimensional NMR spectroscopy. Environ. Sci. Technol. 37,337-342. 

Griesinger, C. Sorensen, O.W. Ernst, R.R. A practical approach to three-dimensional NMR spectroscopy. J. Magn. Reson. 1987, 73, 574-579. 

Eesik, S.W. Zuiderweg, E.R.P. Heteronuclear three-dimensional NMR spectroscopy. A strategy for the simplification of homonuclear two-dimensional NMR spectra. J. Magn. Reson. 1988, 78, 588-593. 

Ikura, M., Kay, L. E., and Bax, A. (1990). A novel approach for sequential assignment of H, C, and N spectra of proteins heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. Biochemistry, 29, 4659 667. 

Three dimensional NMR spectroscopy and improved pulse sequences... 

Clore GM, Bax A, Driscoll PC, Wingfield PT, Gronenbom AM (1990) Assignment of the side-chain H and C resonances of interleukin-1 beta using double- and triple-resonance heteronuclear three-dimensional NMR spectroscopy. Biochemistry 29 8172-8184... 

Bodenhausen G, Ernst RR (1969) The accordion experiment, a simple approach to three-dimensional NMR spectroscopy. J Magn Reson 45(1981) 367-373... 

Stockman, B., Euvrard, A., ScahUl, T. (1993) Heteronuclear three-dimensional NMR spectroscopy of a partially denatured protein The A-state of human ubiquitin. J Biomolec NMR, 3 (3), 285-296. 

NOESY NMR spectroscopy is a homonuclear two-dimensional experiment that identifies proton nuclei that are close to each other in space. If one has already identified proton resonances in one-dimensional NMR spectroscopy or by other methods, it is then possible to determine three dimensional structure through NOESY. For instance, it is possible to determine how large molecules such as proteins fold themselves in three-dimensional space using the NOESY technique. The solution structures thus determined can be compared with solid-state information on the same protein obtained from X-ray crystallographic studies. The pulse sequence for a simple NOESY experiment is shown in Figure 3.23 as adapted from Figure 8.12 of reference 19. 

TTie C-terminal polypeptide block A (residues 462-497) has also been synthesized and its three dimensional structure in solution (90% H2O/10%D2O) was determined by two-dimensional NMR-spectroscopy with a 600 MHz instrument 28. According to this analysis the peptide has a wedge-like shape with dimensions 3 x 1.8 x 1.0 nm. This wedge probably represents the last part in the SAXS model which has a length of about 4 nm and a maximum diameter of 1.4 nm. The principle element of the secondary structure in this part is the conformation. Three antiparallel short jS-sheets composed of residues 466 to 470 ()5j), 485 to 489 and 493 to 496... 

Nuclear magnetic resonance (NMR) spectroscopy is a most effective and significant method for observing the structure and dynamics of polymer chains both in solution and in the solid state [1]. Undoubtedly the widest application of NMR spectroscopy is in the field of structure determination. The identification of certain atoms or groups in a molecule as well as their position relative to each other can be obtained by one-, two-, and three-dimensional NMR. Of importance to polymerization of vinyl monomers is the orientation of each vinyl monomer unit to the growing chain tacticity. The time scale involved in NMR measurements makes it possible to study certain rate processes, including chemical reaction rates. Other applications are isomerism, internal relaxation, conformational analysis, and tautomerism. 

Figures 13.7 and 13.8 are two examples of two-dimensional NMR spectroscopy applied to polymers. Figure 13.7 is the proton homonuclear correlated spectroscopy (COSY) contour plot of Allied 8207A poly(amide) 6 [29]. In this experiment, the normal NMR spectrum is along the diagonal. Whenever a cross peak occurs, it is indicative of protons that are three bonds apart. Consequently, the backbone methylenes of this particular polymer can be traced through their J-coupling. Figure 13.8 is the proton-carbon correlated (HETCOR) contour plot of Nylon 6 [29]. This experiment permits the mapping of the proton resonances into the carbon-13 resonances.

In future, the methods of two-dimensional NMR spectroscopy (Section 2.10) will be the ones used for the unequivocal signal identifications of longer chain peptides. Complete 13C shift assignments are achieved from carbon-proton shift correlations via two- and three-bond couplings, as is demonstrated for the orange-red chromopeptide antibiotic actinomycin D (Fig. 5.13, Table 5.28, [603, 812]). 

CHAPTER 36, FIGURE 5 Motif structures within coagulation proteins. Common motifs are found in the amino terminal regions of the proteinase precursor molecules. Shown are the kringle motifs and EGF-like motifs found in the vitamin K-dependent proteins and in plasminogen. Fibronectin (types I and II) motifs and apple motifs (named from their two-dimensional representations) are also present but not shown. Some epidermal growth factor-like domains contain P-hydroxylated Asp residues. The cartoon structures for the motifs are derived from three-dimensional structures determined by x-ray crystallography or by two-dimensional NMR spectroscopy. 

Equation (4.2.11) describes the response to three delta pulses separated by ti =oi — 02 >0, t2 = 02 — 03 > 0, and t3 = 03 > 0. Writing the multi-pulse response as a function of the pulse separations is the custom in multi-dimensional Fourier NMR [Eml ]. Figure 4.2.3 illustrates the two time conventions used for the nonlinear impulse response and in multi-dimensional NMR spectroscopy for n = 3. Fourier transformation of 3 over the pulse separations r, produces the multi-dimensional correlation spectra of pulsed Fourier NMR. Foinier transformation over the time delays <7, produces the nonlinear transfer junctions known from system theory or the nonlinear susceptibilities of optical spectroscopy. The nonlinear susceptibilities and the multi-dimensional impulse-response functions can also be measured with multi-resonance CW excitation, and with stochastic excitation piul]. 

We have also begun to structurally characterize fibrillar states of a-synuclein (140 residues) and of the K19 domain of protein tau. Both systems are involved in possibly related neuro-degenerative diseases.Preliminary results of two- and three-dimensional correlation spectroscopy, as outlined above, reveal that many of the NMR detectable resonances exhibit narrow or line widths, consistent with the occurrence of well-ordered domains in both proteins. On the other hand, other segments of the considered proteins cannot readily be detected suggesting that they may display static or dynamic disorder under the experimental conditions considered. While the effect of molecular dynamics of NMR relaxation parameters has been studied in the context of solution- or solid-state NMR for a long time, recent progress in the study of uniformly labelled proteins by MAS NMR has created novel means by which to study dynamics of entire polypeptide sequences using 2D methods. For example, Bockmann and Emsley have... 

Meunier, S., Bernassau, J. M., Guillemot, J. C., Eerrara, P., and Darbon, H. (1997). Determination of the three-dimensional structure of CC chemokine monocyte chemoattractant protein 3 by IH two dimensional NMR spectroscopy. Biochemistry 36, 4412 422. 

Two- and three-dimensional or even higher-dimensional NMR spectroscopy is changing from specialised techniques to more commonly used ones. As the complexity of the acquired NMR data increases, the task of analysing these data constantly becomes more and more demanding and new methods are required to facilitate the analysis. With one-dimensional NMR data multivariate data analysis has proven to be a strong tool, but how should one analyse higher-dimensional NMR data in order to extract as much relevant information as possible without having to break data down into smaller dimensions and thus lose the inherent structure A class of... 

Peptides consisting exclusively of fS- or y-amino acids (amino acids) have emerged as a promising new class of nonnatural oligomers (foldamers) that are able to fold into well-defined secondary structures [41--47]. So far, three different helical secondary structures and two turn motifs [177-181] as well as a parallel [177,179] and an antiparallel [179,182] sheet structure have been identified by two-dimensional NMR spectroscopy, circular dichroism (CD), and/or X-ray diffraction studies. In addition, cyclo- -tetrapeptides have been found to form nanotubes in the solid state [183] and have been used as transmembrane ion channels [184]. All these studies have demon-... 

---