Conformation exchange

Moseley, H. N. B., Curto, E. V., Krishna, N. R. Complete Relaxation and Conformational Exchange Matrix (CORCEMA) analysis of NOESY spectra of interacting systems two-dimensional transferred NOESY. J. Magn. Reson. Sen B 1995, 108, 243-261. 

The first experiment to be recorded on isotope-labeled proteins is the [ N/HJ-HSQC experiment. Inspection of the [ N. HJ-correlalion map and simple counting of cross peaks reveals whether multiple conformers exist, whether some parts of the backbone signals are broadened, possibly because of slow conformational exchange, or whether parts of the sequence are not visible at all. As mentioned above, the spectrum will also show whether the protein is well folded or not. 

In principle, TROSY is not limited to interference between dipole-dipole coupling and CSA. Pervushin [50] proposed the use of the differential conformational exchange-in-... 

Fig. 12.6 Identification of the residues undergoing conformational exchange based on the field dependence of relaxation parameters a the comparison of 2R 2-R ] values measured at three fields, 9.4, 11.7, and 14.1 T (shown as grey, white, and black bars, respectively) b the values of Rex + 2czJ(0) at 500 MHz directly derived from the difference between the 2R 2-R values (Eq. (17)) at 600 and 500 MHz (as described in Ref. [16]). This analysis does not require structural information. A strong increase in 2R 2—R] with the field in panel a could be indicative of the conformational exchange, as further quantified in b. Although the contributions from CSA and R cannot be sepa-...

It should be mentioned that rotational anisotropy of the molecule will result in an increase in the R2 values for NH vectors having particular orientation with respect to the diffusion tensor frame [46]. This increase could be misinterpreted as conformational exchange contributions, and, vice versa, small values of Rex, usually of the order or 1 s 1 or less, could be mistaken for the manifestation of the rotational anisotropy. Therefore, identification of residues subjected to conformational exchange is critical for accurate analysis of relaxation data. Additional approaches are necessary to distinguish between the two effects. As suggested earlier [27] (see also Ref. [26]), a comparison between R2 and the cross-correlation rate r]xy could serve this purpose, as tjxy contains practically the same combination of spec-... 

Experimental approaches to direct characterization of the conformational exchange motions in proteins have been suggested earlier [67-69]. The most recent methods [66, 70-73] are based on a relaxation-compensated version of CPMG that alleviates the previous restriction on the duration of the refocusing delay due to evolution of magnetization from scalar couplings and dipole-dipole cross-correlations. 

Alternatively, the much more common situation in trNOE studies involves fast exchange on the chemical shift time scale where the observed resonance shifts are weighted averages of the corresponding shift in the free and bound state [13]. A full account of the complete relaxation matrix and conformational exchange effects for n spins has been performed by London et al. [13], and a similar treatment was later incorporated into the programme CORCEMA [14]. 

The basic theoretical formulation for the quantitative analysis of the STD-NMR data is similar to the one we developed for the analysis of transferred NOESY data, and is based on a complete relaxation and conformational exchange matrix (CORCEMA) theory [33]. 

The chemical shift dispersion (Table 1) and the temperature dependence of the resonance hne shape provides a qualitative measure of whether the structure is well ordered [2]. However, NMR spectroscopy also provides information relevant to the problem of protein folding in the study of the molten globule states. NMR spectroscopic investigations of molten globules may be more demanding than those of ordered proteins due to spectral overlap arising from poor shift dispersion and to short relaxation times that are due to conformational exchange at intermediate rates on the NMR time scale. 

Fig. 7. One-dimensional NMR spectra of the designed four-helix bundles SA-42 (lower trace) and GTD-43 (top two traces). The chemical shift dispersion of SA-42 in 90% H2O and 10% D2O at 323 K and pH 4.5 is poor and the resonances are severely broadened due to conformational exchange. The chemical shift dispersion of GTD-43 in the same solvent at 288 K and pH 3.0 is comparable to that of the naturally occurring four-helix bundle IL-4 and the resonances are not significantly affected by conformational exchange. Upon raising the temperature to 298 K line broadening is observed (top trace) which shows that GTD-43 is in slow exchange on the NMR time scale, unlike SA-42 where an increased temperature reduces the line width. These spectra are therefore diagnostic of structures with disordered (SA-42) and ordered (GTD-43) hydrophobic cores...

In an alternative approach the site-selective functionalization reaction has been used to incorporate a galactose derivative into a folded foux-hehx bundle protein and the effect of glycosylation on the structure of the folded protein has been identified [65]. The unfunctionalized designed four-helix bundle did not have a well-defined tertiary structure but the introduction of the sugar improved the helical content and reduced the rate of conformational exchange. Glycosylation may therefore play a role in the maturation of poorly folded proteins. 

Myrtaceae), from which the related 2, 4, 6 -trihydroxy-3 -formyl-5 -methyldihydrochal-cone was also obtained. The NMR spectra of the synthetic formyl derivative show evidence for exchange broadening, which was attributed to conformational exchange between two stable hydrogen-bonded rotamers from molecular mechanics and ab initio calculations ... 

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