Methodological development of solid-state NMR for characterization of membrane proteins

Challenges in numerical simulations of solid-state NMR experiments: spin exchange pulse sequences

While simulations are essential for interpretation of solid-state NMR experiments, large spin systems involved in e.g. spin-diffusion experiments and/or dynamic effects like chemical exchange pose great challenges for the numerical simulations, where we typically want to include effects of finite pulses and other external manipulations in the simulation. In this paper, these topics are reviewed and addressed by simple numerical simulations. The numerical simulations comprise a 2-spin simulation of (2)H two-site jumps and a 332-spin simulation of a CHHC experiment for a small protein.

Optimal control based NCO and NCA experiments for spectral assignment in biological solid-state NMR spectroscopy

We present novel pulse sequences for magic-angle-spinning solid-state NMR structural studies of (13)C,(15)N-isotope labeled proteins. The pulse sequences have been designed numerically using optimal control procedures and demonstrate superior performance relative to previous methods with respect to sensitivity, robustness to instrumental errors, and band-selective excitation profiles for typical biological solid-state NMR applications. Our study addresses specifically (15)N to (13)C coherence transfers being important elements in spectral assignment protocols for solid-state NMR structural characterization of uniformly (13)C,(15)N-labeled proteins. The pulse sequences are analyzed in detail and their robustness towards spin system and external experimental parameters are illustrated numerically for typical (15)N-(13)C spin systems under high-field solid-state NMR conditions. Experimentally the methods are demonstrated by 1D (15)N-->(13)C coherence transfer experiments, as well as 2D and 3D (15)N,(13)C and (15)N,(13)C,(13)C chemical shift correlation experiments on uniformly (13)C,(15)N-labeled ubiquitin.

Determination of the 19F NMR chemical shielding tensor and crystal structure of 5-fluoro-dl-tryptophan

5-Fluoro-dl-tryptophan (5F-Trp) is a very sensitive probe used to investigate orientation and dynamics of biomacromolecules at the in situ level. In order to establish a (19)F NMR strategy, the crystal structure and (19)F chemical shielding tensor of 5F-Trp are reported. A novel approach was developed to use F-F homonuclear dipole-dipole coupling information to analyze single-crystal NMR data without determining crystal orientations. The measured values for the principal components of the shielding tensor are sigma(11)=0.9, sigma(22)=-63.3, and sigma(33)=-82.9 ppm relative to TFA in D(2)O. The principal axes of the shielding tensors coincide with the indole ring symmetry, which makes it a straightforward and powerful tool to monitor protein alignment in oriented environments. Hartree-Fock (HF) and density functional theory (DFT) calculations of the chemical shielding tensors are also reported.

Structural and orientational constraints of bacteriorhodopsin in purple membranes determined by oriented-sample solid-state NMR spectroscopy

We report for the first time, oriented-sample solid-state NMR experiments, specifically polarization inversion spin exchange at the magic angle (PISEMA) and 1H-15N heteronuclear chemical shift correlation (HETCOR), applied to an integral seven-transmembrane protein, bacteriorhodopsin (bR), in natural membranes. The spectra of [15N]Met-bR revealed clearly distinguishable signals from the helical and loop regions. By deconvolution of the helix resonances, it was possible to establish constraints for some helix tilt angles. It was estimated that the extracellular section of helix B has a tilt of less than 5 degrees from the membrane normal, while the tilt of helix A was estimated to be 18-22 degrees , both of which are in agreement with most crystal structures. Comparison of the experimental PISEMA spectrum with simulated spectra based on crystal structures showed that PISEMA and HETCOR experiments are extremely sensitive to the polytopic protein structure, and the solid-state NMR spectra for membrane-embedded bR matched most favorably with the recent 1FBB electron crystallography structure. These results suggest that this approach has the potential to yield structural and orientational constraints for large integral polytopic proteins whilst intercalated and functionally competent in a natural membrane.

Improved pulse sequences for pure exchange solid-state NMR spectroscopy

Spin-exchange experiments are useful for improving the resolution and establishment of sequential assignments in solid-state NMR spectra of uniformly (15)N-labeled proteins oriented macroscopically in phospholipid bilayers. To exploit this advantage fully, it is crucial that the diagonal peaks in the two-dimensional exchange spectra are suppressed. This may be accomplished using the recent pure-exchange (PUREX) experiments, which, however, suffer from up to a threefold reduction of the cross-peak intensity relative to experiments without diagonal-peak suppression. This loss in sensitivity may severely hamper the applicability for the study of membrane proteins. In this paper, we present a two-dimensional exchange experiment (iPUREX) which improves the PUREX sensitivity by 50%. The performance of iPUREX is demonstrated experimentally by proton-mediated (15)N-(15)N spin-exchange experiments for a (15)N-labeled N-acetyl-L-valyl-L-leucine dipeptide. The relevance of exchange experiments with diagonal-peak suppression for large, uniformly (15)N-labeled membrane proteins in oriented phospholipid bilayers is demonstrated numerically for the G-protein coupled receptor rhodopsin.