Structure determination in "shiftless" solid state NMR of oriented protein samples.

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Structure determination in "shiftless" solid state NMR of oriented protein samples.

Structure determination in "shiftless" solid state NMR of oriented protein samples.

J Magn Reson. 2011 Jul 6;

Authors: Yin Y, Nevzorov AA

An efficient formalism for calculating protein structures from oriented-sample NMR data in the torsion-angle space is presented. Angular anisotropies of the NMR observables are treated by utilizing an irreducible spherical basis of rotations. An intermediate rotational transformation is introduced that greatly speeds up structural fitting by rendering the dependence on the torsion angles ? and ? in a purely diagonal form. Back-calculation of the simulated solid-state NMR spectra of protein G involving (15)N chemical shift anisotropy (CSA), and (1)H-(15)N and (1)H(?)-(13)C(?) dipolar couplings was performed by taking into account non-planarity of the peptide linkages and experimental uncertainty. Even a relatively small (to within 1ppm) random variation in the CSA values arising from uncertainties in the tensor parameters yields the RMSD's of the back-calculated structures of more than 10Å. Therefore, the (15)N CSA has been substituted with heteronuclear dipolar couplings which are derived from the highly conserved bond lengths and bond angles associated with the amino-acid covalent geometry. Using the additional (13)C(?)-(15)N and (13)C'-(15)N dipolar couplings makes it possible to calculate protein structures entirely from "shiftless" solid-state NMR data. With the simulated "experimental" uncertainty of 15Hz for protein G and 120Hz for a helical hairpin derived from bacteriorhodopsin, back-calculation of the synthetic dipolar NMR spectra yielded a converged set of solutions. The use of distance restraints dramatically improves structural convergence even if larger experimental uncertainties are assumed.

PMID: 21741286 [PubMed - as supplied by publisher]



Source: PubMed