Two-dimensional rotational-echo double resonance of Val1-[1-13C]Gly2-[15N]Ala3-gramicidin A in multilamellar dimyristoylphosphatidylcholine dispersions

Hybridization of TEDOR and NCX MAS solid-state NMR experiments for simultaneous acquisition of heteronuclear correlation spectra and distance measurements

Magic angle spinning (MAS) solid-state NMR (ssNMR) spectroscopy is a major technique for the characterization of the structural dynamics of biopolymers at atomic resolution. However, the intrinsic low sensitivity of this technique poses significant limitations to its routine application in structural biology. Here we achieve substantial savings in experimental time using a new subclass of Polarization Optimized Experiments (POEs) that concatenate TEDOR and SPECIFIC-CP transfers into a single pulse sequence. Specifically, we designed new 2D and 3D experiments (2D TEDOR-NCX, 3D TEDOR-NCOCX, and 3D TEDOR-NCACX) to obtain distance measurements and heteronuclear chemical shift correlations for resonance assignments using only one experiment. We successfully tested these experiments on N-Acetyl-Val-Leu dipeptide, microcrystalline U-13C,15N ubiquitin, and single- and multi-span membrane proteins reconstituted in lipid membranes. These pulse sequences can be implemented on any ssNMR spectrometer equipped with standard solid-state hardware using only one receiver. Since these new POEs speed up data acquisition considerably, we anticipate their broad application to fibrillar, microcrystalline, and membrane-bound proteins.

Peptide structural analysis by solid-state NMR spectroscopy

Solid-state nmr spectroscopy provides a robust method for investigating polypeptides that have been prepared by chemical synthesis and that are immobilized by strong interactions with solid surfaces or large macroscopic complexes. Solid-state nmr spectroscopy has been widely used to investigate membrane polypeptides or peptide aggregates such as amyloid fibrils. Whereas magic angle spinning solid-state nmr spectroscopy allows one to measure distances and dihedral angles with high accuracy, static membrane samples that are aligned with respect to the magnetic field direction allow one to determine the secondary structure of bound polypeptides and their orientation with respect to the bilayer normal. Peptide dynamics and the effect of polypeptides on the macroscopic phase preference of phospholipid membranes have been investigated in nonoriented samples. Investigations of the structure and topology of membrane channels, peptide antibiotics, signal sequences as well as model systems that allow one to dissect the interaction contributions in phospholipid membranes will be presented in greater detail.

Solid-state nuclear magnetic resonance investigation of protein and polypeptide structure

Solid-state nuclear magnetic resonance (NMR) is rapidly emerging as a successful and important technique for protein and peptide structural elucidation from samples in anisotropic environments. Because of the diversity of nuclei and nuclear spin interactions that can be observed, and because of the broad range of sample conditions that can be studied by solid-state NMR, the potential for gaining structural constraints is great. Structural constraints in the form of orientational, distance, and torsional constraints can be obtained on proteins in crystalline, liquid-crystalline, or amorphous preparations. Great progress in the past few years has been made in developing techniques for obtaining these constraints, and now it has also been clearly demonstrated that these constraints can be assembled into uniquely defined three-dimensional structures at high resolution. Although much progress toward the development of solid-state NMR as a routine structural tool has been documented, the future is even brighter with the continued development of the experiments, of NMR hardware, and of the molecular biological methods for the preparation of labeled samples.

13C-13C rotational resonance in a transmembrane peptide: a comparison of the fluid and gel phases

A comparative study of two doubly 13C labeled amphiphilic transmembrane peptides was undertaken to determine the potential of rotational resonance for measuring internuclear distances through the direct dipolar coupling in the presence of motion. The two peptides, having the sequence acetyl-K2-G-L16-K2-A-amide, differed only in the position of 13C labels. The first peptide, [1-13C]leu(11):[alpha-13C]leu(12), had labels on adjacent residues, at the carbonyl of leu(11) and the alpha carbon of leu(12). The second, [1-13C]leu(8):[alpha-(13)/C]leu(11), was labeled on consecutive turns of the alpha-helical peptide. The internuclear distance between labeled positions of the first peptide, which for an ideal alpha helix has a value of 2.48 A, is relatively independent of internal flexibility or peptide conformational change. The dipolar coupling between these two nuclei is sensitive to motional averaging by molecular reorientation, however, making this peptide ideal for investigating these motions. The internuclear distance between labels on the second peptide has an expected static ideal alpha-helix value of 4.6 A, but this is sensitive to internal flexibility. In addition, the dipolar coupling between these two nuclei is much weaker because of their larger separation, making this peptide a much more difficult test of the rotational resonance technique. The dipolar couplings between the labeled nuclei of these two peptides were measured by rotational resonance in the dry peptide powders and in multilamellar dispersions with dimyristoylphosphatidylcholine in the gel phase, at -10 degrees C, and in the fluid phase, at 40 degrees C. The results for the peptide having adjacent labels can be readily interpreted in terms of a simple model for the peptide motion. The results for the second peptide show that, in the fluid phase, the motionally averaged dipolar coupling is too small to be measured by rotational resonance. Rotational resonance, rotational echo double resonance, and related techniques can be used to obtain reliable and valuable dipolar couplings in static solid and membrane systems. The interpretation of these couplings in terms of internuclear distances is straightforward in the absence of molecular motion. These techniques hold considerable promise for membrane protein structural studies under conditions, such as at low temperatures, where molecular motion does not modulate the dipolar couplings. However, a typical membrane at physiological temperatures exhibits complex molecular motions. In the absence of an accurate and detailed description of both internal and whole body molecular motions, it is unlikely that techniques of this type, which are based on extracting distances from direct internuclear dipolar couplings, can be used to study molecular structure under these conditions. Furthermore, the reduction in the strengths of the dipolar couplings by these motions dramatically reduces the useful range of distances which can be measured.

REDOR-determined distances from heterospins to clusters of 13C labels

The use of rotational-echo double resonance NMR to measure distances from an observed tightly coupled cluster of 13C spins to a distant 15N, 31P, or 19F is practical if all homonuclear 13C-13C dipolar interactions are suppressed by multiple-pulse decoupling during heteronuclear dipolar evolution. This scheme is first calibrated by experiments performed on multiply labeled alanines and then applied in the measurement of 19F-13C distances in p-trifluoromethylphenyl [1,2-13C2]acetate.

A new monofluorinated phosphatidylcholine forms interdigitated bilayers

16-Fluoropalmitic acid was synthesized from 16-hydroxypalmitic acid using diethylaminosulfur trifluoride. This monofluorinated fatty acid then was used to make 1-palmitoyl-2-[16-fluoropalmitoyl]-phosphatidylcholine (F-DPPC) as a fluorinated analog of dipalmitoylphosphatidylcholine (DPPC). Surprisingly, we found that the phase transition temperature (Tm) of F-DPPC occurs near 50 degrees C, approximately 10 degrees C higher than its nonfluorinated counterpart, DPPC, as judged by both differential scanning calorimetry and infrared spectroscopy. The pretransition observed for DPPC is absent in F-DPPC. A combination of REDOR, rotational-echo double-resonance, and conventional solid-state NMR experiments demonstrates that F-DPPC forms a fully interdigitated bilayer in the gel phase. Electron paramagnetic resonance experiments show that below Tm, the hydrocarbon chains of F-DPPC are more motionally restricted than those of DPPC. X-ray scattering experiments confirm that the thickness and packing of gel phase F-DPPC is similar to that of heptanetriol-induced interdigitated DPPC. F-DPPC is the first phosphoglyceride containing sn-1 and sn-2 ester-linked fatty acyl chains of equal length that spontaneously forms interdigitated bilayers in the gel state in the absence of inducing agents such as alcohols.

Two-dimensional transferred-echo double resonance study of molecular motion in a fluorinated polycarbonate

A two-dimensional version of the transferred-echo double resonance (TEDOR) experiment is introduced to measure strong heteronuclear magnetic dipolar interactions between rare spins. A quantitative description of this 2D-TEDOR experiment is given for an I-S pair of spins undergoing relative motion. 2D-TEDOR calculations are consistent with data for a calibration model: the directly bound 13C-31P pair in [3-13C]glyphosate, HO31(3)P13CH2NHCH2COOH. Analysis shows that the indirect spin-spin interaction and the dipole-dipole interaction have opposite signs in this system. The 2D-TEDOR experiment is then used to measure heteronuclear 13C-19F interactions in a fluorinated polycarbonate in which an aromatic proton is replaced by a fluorine on every fourth ring. Results from the 2D-TEDOR experiment show that the aromatic ring flips that occur in ordinary polycarbonate are blocked for a fluorinated ring.

Solid-state NMR for the study of membrane systems: the use of anisotropic interactions

The use of solid-state nuclear magnetic resonance (NMR) as a tool to determine the structure of membrane molecules is reviewed with a particular emphasis on techniques that provide information on orientation or order. Experiments reported here have been performed in membranes, rather than in micelles or organic solvents. Several ways to prepare and handle the samples are discussed, like sample orientation and magic-angle spinning (MAS). Results concerning lipids, membrane peptides and proteins are included, as well as a discussion regarding the potential of such methods and their pitfalls.

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.

REDOR dephasing by multiple spins in the presence of molecular motion

Closed-form, numerical algorithms are presented for calculating REDOR dephasing for three general cases: (i) collections of isolated I-S spin pairs; (ii) many S spins coupled to an I spin; and (iii) an I-S spin pair in relative motion. For the case when more than one S spin is dipolar coupled to an I spin, the calculation assumes that the S-S homonuclear interaction does not affect REDOR dephasing. Full numerical simulations show that this assumption is true if the S-spin lineshapes are inhomogeneously broadened, the S-spin chemical shifts are far from rotational resonance, and a version of REDOR is used which minimizes the number of S-spin pi pulses. For the rapidly rotating -CF3 group of poly(trifluoroethyl methacrylate), the formalisms of (ii) and (iii) are combined to calculate the dephasing. The experimentally measured dephasing matches theory when the wiggling motion of the -OCH2CF3 moiety of the polymer is taken into account.

Prospects for resonance assignments in multidimensional solid-state NMR spectra of uniformly labeled proteins

The feasibility of assigning the backbone 15N and 13C NMR chemical shifts in multidimensional magic angle spinning NMR spectra of uniformly isotopically labeled proteins and peptides in unoriented solid samples is assessed by means of numerical simulations. The goal of these simulations is to examine how the upper limit on the size of a peptide for which unique assignments can be made depends on the spectral resolution, i.e., the NMR line widths. Sets of simulated three-dimensional chemical shift correlation spectra for artificial peptides of varying length are constructed from published liquid-state NMR chemical shift data for ubiquitin, a well-characterized soluble protein. Resonance assignments consistent with these spectra to within the assumed spectral resolution are found by a numerical search algorithm. The dependence of the number of consistent assignments on the assumed spectral resolution and on the length of the peptide is reported. If only three-dimensional chemical shift correlation data for backbone 15N and 13C nuclei are used, no residue-specific chemical shift information, information from amino acid side-chain signals, and proton chemical shift information are available, a spectral resolution of 1 ppm or less is generally required for a unique assignment of backbone chemical shifts for a peptide of 30 amino acid residues.

Characterization of two forms of cadmium phosphide by magic-angle spinning 31P NMR

Annealing of commercial grade cadmium phosphide (CD3P2) at 600 K produces a material which, in magic-angle spinning spin-lattice 31P NMR relaxation experiments, has broad lines and multiple T1 values. By contrast, sublimation at 900 K results in a crystalline material with narrow lines and a single T1. However, both materials have the same Cd-P lattice spacings as determined by rotational-echo, double-resonance 31P NMR with 113Cd dephasing. Both materials also have closely similar X-ray diffraction powder patterns. These results are interpreted in terms of a distribution of lattice vacancies in the annealed material, creating structural heterogeneity but with no substantial change in lattice parameters from those of the sublimed cadmium phosphide.

Membrane protein structure: the contribution and potential of novel solid state NMR approaches

Alternative methods for describing molecular detail for large integral membrane proteins are required in the absence of routine crystallographic approaches. Novel solid state NMR methods, devised for the study of large molecular assemblies, are now finding applications in biological systems, including integral membrane proteins. Wild-type and genetically engineered proteins can be investigated and detailed information about side chains, prosthetic groups, ligands (e.g. drugs) and binding sites can be deduced. The molecular structure and dynamics of selected parts of the proteins are accessible by a range of different solid state NMR approaches. Inter- and intra-atomic distances can be determined rather accurately (within ångströms) and the orientation of molecular bonds (within 2 degrees) can be measured in ideal cases. Here, a brief description of the methods is given and then some specific examples described with an indication of the future potential for the approaches in studying membrane proteins. It is anticipated that this emerging NMR methodology will be more widely used in the future, not only for resolving local structure, but also for more expansive descriptions of membrane protein structure at atomic resolution.

Lipid-mediated a-factor interactions with artificial membranes

Our understanding of the cellular export of a-factor and its interaction with the receptor do not yet allow for a description of the phenomena on a molecular level. Synthesis of a-factor analogs and biophysical studies of the lipopeptides in the presence of artificial membranes provide insights which can be analyzed with respect to the biological potency of the molecules. It is through the study of the interaction of the lipopeptides with membranes at varying levels of complexity that we will be able to develop a molecular description of the biological processes.

Sodium ion binding in the gramicidin A channel. Solid-state NMR studies of the tryptophan residues

Gramicidin A analogs, labeled with 13C in the backbone carbonyl groups and the C-2 indole carbons of the tryptophan-11 and tryptophan-13 residues, were synthesized using t-Boc-protected amino acids. The purified analogs were incorporated into phosphatidylcholine bilayers at a 1:15 molar ratio and macroscopically aligned between glass coverslips. The orientations of the labeled groups within the channel were investigated using solid-state NMR and the effect of a monovalent ion (Na+) on the orientation of these groups determined. The presence of sodium ions did not perturb the 13C spectra of the tryptophan carbonyl groups. These results contrast with earlier results in which the Leu-10, Leu-12, and Leu-14 carbonyl groups were found to be significantly affected by the presence of sodium ions and imply that the tryptophan carbonyl groups are not directly involved in ion binding. The channel form of gramicidin A has been demonstrated to be the right-handed form of the beta 6.3 helix: consequently, the tryptophan carbonyls would be directed away from the entrance to the channel and take part in internal hydrogen bonding, so that the presence of cations in the channel would have less effect than on the outer leucine residues. Sodium ions also had no effect on the C-2 indole resonance of the tryptophan side chains. However, a small change was observed in Trp-11 when the ether lipid, ditetradecylphosphatidylcholine, was substituted for the ester lipid, dimyristoylphosphatidylcholine, indicating some sensitivity of the gramicidin side chains to the surrounding lipid.

Conformational analysis of the Saccharomyces cerevisiae tridecapeptide mating pheromone by 13C,15N rotational-echo double resonance nuclear magnetic resonance spectroscopy

The solid-state conformation of [Nle12]alpha-factor, the Saccharomyces cerevisiae tridecapeptide mating pheromone (WHWLQLKPGQPNleY), was investigated by 13C,15N rotational-echo double resonance (REDOR) nuclear magnetic resonance spectroscopy (NMR). Previous high-resolution NMR studies of [Nle12]alpha-factor in solution revealed a transient Type II beta-turn spanning residues 7-10 of the peptide. To investigate this region of [Nle12]alpha-factor in the solid state, a series of four selectively 13C,15N-enriched tridecapeptides were synthesized by solid-phase methods. Carbon-nitrogen distances between the labeled sites in lyophilized samples of [Nle12]alpha-factor were accurately measured by REDOR NMR. Experimentally determined distances were compared with those from calculated models for Type I and Type II beta-turns and for an extended chain. The measured distances indicate that, in a lyophilized powder, the central region of the [Nle12]alpha-factor is not in an extended conformation. The experimental data was most consistent with distances obtained from a distorted Type I beta-turn model.