Dipolar waves

Mesleh MF, Opella SJ. Dipolar waves as NMR maps of helices 62. in proteins. J. Magn. Reson. 2003 163 288-299. 

Figure 18.6 Dipolar wave curves calculated for different orientational states of a-helical peptides (a, c, e), showing the theoretical dipolar splittings for different positions around the helical axis, (b, d, f) The orientation of the peptide is determined from a plot of the tilt angle x versus the azimuthal angle p, where each point in the x/p-plot corresponds to a specific orientation, (a) Helical curve corresponding to an S-state orientation with t = 90°, p = 90° (b) the position of this S-state orientation in the x/p-plot is marked by the center of the concentric circles, (c) Helical curve for a tilted T-state orientation with x 125°, p = 90° (d) the position of this T-state orientation in the x/p-plot. (e) Helical curve for an l-state orientation with x= 10°, p = 90° (f) the position of this l-state orientation in the x/p-plot.

PISA wheels and dipolar waves for oriented proteins... 

To illustrate the power of PISA wheels and dipolar waves to determine the structure of helical peptides and proteins in uniaxiaUy oriented lipid bilayers. Fig. 6a-c show SIMPSON/SIMMOL-simulated PISEMA spectra of an ideal 18-residue a-helix with a tilt angle of 10°-30° relative to Bq. In these simulations, we have tried to mimic experimental conditions by including a random distribution of the principal components of the chemical shift tensor and the dipolar coupling. The chemical shift distribution is 6 ppm for each principal element and has been established as follows we obtained — 85000 N isotropic chemical shifts reported to the BioMagResBank and selected only the — 31000 located in helical secondary stractures to have a data set independent on secondary chemical shifts. The standard deviation on the N chemical shifts for these resonances was — 6 ppm. With the lack of other statistically reliable experimental methods to establish such results for the individual principal elements of the N CSA tensor, we assumed the above variation of 6 ppm for all three principal elements. The variation of the H- N dipolar coupling was estimated by investigating the structures for a small number of a-helical membrane proteins for which the structures were established by liquid-state NMR spectroscopy. These showed standard deviations... 

Fig. 6. (a-c) Simulated PISEMA spectra and (d-f) dipolar waves for an ideal 18-residue a-... 

Despite the fact that the simulated PISEMA spectra in Fig. 6a-c display signihcant fluctuations in the resonance positions relative to the ideal patterns, it is evident that both the PISA wheels and dipolar waves (represented by solid lines in Fig. 6) allow accurate determination of the helix tilt angle. The dipolar wave representation only shows minor differences between the resonance points and the ideal waves, and when trying to fit a dipolar wave to the resonance points, it does not display any visible difference to the ideal curve. 

Fig. 12f-i shows the dipolar waves for a number of different structures, supporting the solid-state NMR stmcture which corresponds to an a-helical stmcture with a kink near the C-terminal end. 

A related application for RDCs has also been described based on the sequence-dependent pattern of RDCs along a helical structure, called a dipolar wave by the Opella group [317, 352, 353]. The magnitude and periodicity of the dipolar wave depends on the orientation of the helix, and can allow irregularities in helix structure to be identified. Most commonly, dipolar waves have been used to help determine the location of helices in a protein sequence, allowing these structural elements to be more rigidly restrained over the course of a structure calculation [57,159, 323, 354]. This is particularly useful for larger helical membrane proteins, since a-helices are not well defined by the NOEs available in sparsely protonated samples [262]. 

Mesleh MF, Veglia G, DeSilva TM, Marassi FM, Opella SJ (2002) Dipolar waves as NMR maps of protein structure. J Am Chem Soc 124 4206 207... 

Park SH, Son WS, Mukhopadhyay R, Valafar H, Opella SJ (2009) Phage-induced alignment of membrane proteins enables the measurement and structural analysis of residual dipolar couplings with dipolar waves and lambda-maps. J Am Chem Soc 131 14140-14141... 

Dipolar waves describe the structure and topology of helices in membrane proteins. The fit of sinusoids with the 3.6 residues per turn period of ideal... 

Residual dipolar couplings have been calculated for four disordered proteins of difierent sizes with secondary structure propensities by Forman-Kay and co-workers using local alignment tensors and compared with the measured RDCs. Using simulations of RDCs in partially unfolded polyalanine chains Jensen and Blackledge have shown that the appearance of the NMR dipolar waves may provide information on the behaviour of the neighbouring capping strands. Bryson et have presented... 

Using model proteins Walsh and Wang have discussed in detail the utilization of dipolar waves to extract structural information such as the periodicity of peptide plane, its planarity, kink or curvature of a-helix and irregularities of P-strand. Veglia and co-workers have exploited the amplitude and average values of dipolar waves in determination of helical membrane protein topology. In the latter studies N-labelled phospholamban protein was used as a test molecule. 

Walsh and Wang showed the periodie behaviour of residual dipolar eouplings (RDCs) arising from nucleic acid and protein secondary structures to be more eomplex and information-rich than previously beheved. They have developed a theoretical framework which allows the bond veetor orientation of nucleie aeids and the peptide plane orientations of protein seeondary structures to be extracted from their dipolar waves. Fushman et al. determined domain orientations in macromolecules by using spin-relaxation and residual dipolar coupling measurements. 

---