Solid-state C NMR spectroscopy of a C carbonyl-labeled polypeptide

How Does an Amide-N Chemical Shift Tensor Vary in Peptides?

This study addresses a void in the existing literature on the amide-(15)N chemical shift anisotropy (CSA) tensor of peptides: a systematic investigation of how the tensor varies in different peptides. Amide-(15)N CSA tensors for several dipeptides are obtained using quantum chemical calculations, as well as for a series of model Ala-X and X-Ala sequences in both α-helical and β-sheet conformations (where X is one of the naturally occurring amino acids). The calculated values show a significant variation in both isolated and extended peptide structures. Hydrogen bonding at both the carbonyl group and the N-H bond of the peptide plane is shown to affect the principal values of the tensor. Calculations on model peptides indicate that the amide-(15)N CSA tensor is dependent on atoms located within a distance of five bonds. Consequently, the tensor of a given peptide residue is unaffected by residues other than those adjacent to it, which implies that the amide-(15)N CSA tensor should be considered in the context of tripeptide sequences. This further suggests that the amide-(15)N CSA tensor of the second residue of a given tripeptide sequence may be extrapolated to the same sequence in any other polypeptide or protein, given the same backbone conformation and intermolecular environment. These conclusions will facilitate future NMR structural studies of proteins.

Glycyl C(alpha) chemical shielding in tripeptides: measurement by solid-state NMR and correlation with X-ray structure and theory

We report here (13)C(alpha) chemical shielding parameters for central Gly residues in tripeptides adopting alpha-helix, beta-strand, polyglycine II, and fully extended 2 degrees structures. To assess experimental uncertainties in the shielding parameters and the effects of (14)N-(13)C(alpha) or (15)N-(13)C(alpha) dipolar coupling, stationary and magic angle spinning (MAS) spectra with and without (15)N decoupling were obtained from natural abundance and double-labeled samples containing [2-(13)C, (15)N]Gly. We find that accurate (<1 ppm uncertainty) shielding parameters are measured with good sensitivity and resolution in (15)N decoupled 1D or 2D MAS spectra of double-labeled samples. Compared to variations of isotropic shifts with peptide angles, those of (13)C(alpha) shielding anisotropy and asymmetry are greater. Trends relating shielding parameters to the 2 degrees structure are apparent, and the correlation of the experimental values with unscaled ab initio shielding calculations has an rms error of 3 ppm. Using the experimental data and the ab initio shielding values, the empirical trends relating the 2 degrees structure to shielding are extended to the larger range of torsion angles found in proteins.

13C selective polarization and spin diffusion in a lipid bilayer-bound polypeptide by solid-state NMR

While (15)N solid-state NMR has proven to be very advantageous for the development of structural biological methods, (13)C spectroscopy has increased sensitivity and spectral dispersion. However, large natural abundance signals and homonuclear dipolar interactions pose significant problems. Here we have used a pair of (13)C-labeled sites in a lipid-solubilized polypeptide to show the selective polarization can be used in combination with spin diffusion to achieve simplified spectra. Both unoriented and oriented samples have been used, with the latter providing a well-resolved homonuclear dipolar splitting.

Solid-state NMR triple-resonance backbone assignments in a protein

Triple-resonance solid-state NMR spectroscopy is demonstrated to sequentially assign the 13C' and 15N amide backbone resonances of adjacent residues in an oriented protein sample. The observed 13C' chemical shift frequency provides an orientational constraint complementary to those measured from the 1H and 15N amide resonances in double-resonance experiments.

High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints

BACKGROUND

Solid-state nuclear magnetic resonance (NMR) spectroscopy provides novel structural constraints from uniformly aligned samples. These orientational constraints orient specific atomic sites with respect to the magnetic field direction and the unique molecular axis of alignment. Solid-state NMR is uniquely and ideally suited for providing such structural constraints on polypeptides and proteins in a lamellar phase lipid environment. Membrane protein structure represents a great challenge for structural biologists; a new approach for characterizing high resolution three-dimensional structure in such an environment is needed.

RESULTS

The optimal use of orientational constraints for defining three-dimensional structures is demonstrated with the elucidation of the gramicidin A channel structure at high resolution. Initial structures are refined against both the experimental constraints and the CHARMM energy using a novel simulated-annealing protocol to define torsion angle solutions with an error bar of approximately +/- 5 degrees.

CONCLUSIONS

This analysis results in the determination of a high-resolution, time averaged structure of gramicidin A obtained in a lipid bilayer environment above the gel-to-liquid crystalline phase transition temperature. It is demonstrated that solid-state NMR can be used to establish polypeptide, and potentially protein, structures in such an environment. Furthermore, this high-resolution structure is demonstrated to provide new insights into polypeptide function. For the gramicidin A channel the roles of the indole groups that facilitate ion transport and details of the cation solvation environment provided by the amide oxygens are characterized.

Solid-state nuclear magnetic resonance characterization of gramicidin channel structure

The method of using orientational constraints derived from solid-state NMR for structural characterization of polypeptides in heterogeneous environments has now been demonstrated. A very high resolution structure has been achieved that has led to greater functional understanding of this channel. Much can be done to improve this structural technique to make it more efficient and more generally applicable. Others as well as ourselves are applying this approach to membrane proteins. Although solid-phase synthesis and specific site isotopic labeling has been essential for the development described here, one of the primary challenges is to be able to use amino acid-specific and uniform labeling of peptides and proteins by biosynthetic means for isotopic incorporation. This will allow for the study of many more proteins and significantly large proteins. Unlike solution NMR structural methods, there are no intrinsic molecular weight limitations. In fact, as the molecular weight increases the molecular motion will become less and the spectroscopic properties will improve. The major limitation will be sensitivity: as the molecular weight increases the number of moles will decrease in the samples, causing sensitivity to decrease. Advances in field strength and NMR technology help to address this problem. With larger molecules and more isotopically labeled sites resolution could also be a problem; however, the two- and three-dimensional methods demonstrated by Opella and co-workers clearly show the potential for enormous resolving power. In the 15N dimension alone it is shown that the resolution is greater than in solution NMR. Although challenges such as spectral assignments have yet to be completely solved, several approaches have been described, and the prospects are excellent for solving this and other problems facing the development of this novel approach for structural elucidation. Although there is an attempt to get away from solid-phase synthesis to solve larger molecular weight structures, peptide synthesis will continue to be important for generating single- and double-site labeled model compounds for characterizations of spin interaction tensors. Such characterizations will continue to be a very important aspect of this structural approach.

Reconstitution of membrane proteins into lipid-rich bilayered mixed micelles for NMR studies

This paper describes a study undertaken to assess the possibility and practical consequences of reconstituting integral and peripheral membrane proteins into bilayered discoidal mixed micelles ("bicelles") composed of dimyristoylphosphatidylcholine and smaller amounts of either CHAPSO or short-chain phosphatidylcholine. The amphiphilic assemblies in these mixtures are uniquely suited for use in NMR structural studies because they can be magnetically oriented with experimentally-tunable system order. The first step of this study was to test about 15 membrane-associating polypeptides and proteins for their ability to interfere with magnetic orientation of the bicellar assemblies. A variety of results were obtained ranging from no perturbation to a complete disruption of orientation. Second, the suitability of bicelles as mimics of natural bilayers was tested by reconstituting diacylglycerol kinase, an integral membrane enzyme. The kinase was observed to be functional and completely stable for at least 24 h when incubated at 38 degrees C in bicelles. Third, the NMR spectra from a number of bicelle-reconstituted proteins were examined. In some cases, 13C NMR resonances from reconstituted proteins were extremely broad and asymmetric. In other cases, resonances from reconstituted proteins were moderately broad, but much less so than resonances from proteins reconstituted into multilayers oriented by mechanical methods. In the cases of two surface-associating proteins (cytochrome c and leucine enkephalin), oriented sample 13C NMR spectra of extremely high resolution were obtained. For these proteins it was also demonstrated that the experimentally variable order of the bicellar assemblies could be exploited to provide a means of screening for detergent-specific structural perturbations, for making spectral assignments, and for measuring chemical shift anisotropies and dipolar couplings. Taken as a whole, these results indicate that bicelles may be uniquely and effectively employed as model membranes to facilitate NMR structural studies of many, but not all, membrane proteins.

A method for studying the structure of uniaxially aligned biopolymers using solid state 15N-nmr: application to Bombyx mori silk fibroin fibers

Recent advances in the application of solid state nmr spectroscopy to uniformly aligned biopolymers have opened a window through which to view the detailed structure of biological macromolecules that are unable to be seen with standard techniques for structure determination such as x-ray diffraction. Atomic resolution structural details are obtained from solid state nmr data in the form of bond orientations, which yield the relative positions of specific atoms within the molecule. For static aligned systems such as fibers, in which rapid reorientation about the axis of alignment does not occur, it has generally been necessary to perform trial and error line-shape simulations to extract structural details from nmr spectra arising from a single type of nuclear spin interaction. In the present work, a new method is developed in which solid state 15N-nmr spectra obtained from uniaxially aligned molecules placed with the axis of alignment both parallel and perpendicular to the magnetic field are analyzed to yield the orientations of specific molecular bonds. Analytical expressions are derived that utilize spectral features read from 15N chemical shift anisotropy line shapes to calculate a discrete number of possible orientations for a specific site. The 15N-1H dipolar interaction is employed to further narrow the number of unique orientations possible for a given site. With this method, a neighborhood of possible orientations is quickly determined, and full line-shape simulations within this region of allowed space can be performed to refine the limits of orientation. This technique demonstrates the use of a single type of isotopic label to determine the orientation of a specific molecular group such as a peptide plane within a protein. Results from the application of this method to the Bombyx mori silk fibroin protein provide structural detail that is consistent with currently accepted structural models based on fiber diffraction studies.

Orientational constraints as three-dimensional structural constraints from chemical shift anisotropy: the polypeptide backbone of gramicidin A in a lipid bilayer

Chemical shifts observed from samples that are uniformly aligned with respect to the magnetic field can be used as very high-resolution structural constraints. This constraint takes the form of an orientational constraint rather than the more familiar distance constraint. The accuracy of these constraints is dependent upon the quality of the tensor characterization. Both tensor element magnitudes and tensor orientations with respect to the molecular frame need to be considered. Here these constraints have been used to evaluate models for the channel conformation of gramicidin A. Of the three models used, the one experimentally derived model of gramicidin in sodium dodecyl sulfate micelles fits the data least well.