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

Aromatic spectral editing techniques for magic-angle-spinning solid-state NMR spectroscopy of uniformly (13)C-labeled proteins

The four aromatic amino acids in proteins, namely histidine, phenylalanine, tyrosine, and tryptophan, have strongly overlapping (13)C chemical shift ranges between 100 and 160ppm, and have so far been largely neglected in solid-state NMR determination of protein structures. Yet aromatic residues play important roles in biology through π-π and cation-π interactions. To better resolve and assign aromatic residues' (13)C signals in magic-angle-spinning (MAS) solid-state NMR spectra, we introduce two spectral editing techniques. The first method uses gated (1)H decoupling in a proton-driven spin-diffusion (PDSD) experiment to remove all protonated (13)C signals and retain only non-protonated carbon signals in the aromatic region of the (13)C spectra. The second technique uses chemical shift filters and (1)H-(13)C dipolar dephasing to selectively detect the Cα, Cβ and CO cross peaks of aromatic residues while suppressing the signals of all aliphatic residues. We demonstrate these two techniques on amino acids, a model peptide, and the microcrystalline protein GB1, and show that they significantly simplify the 2D NMR spectra and both reveal and permit the ready assignment of the aromatic residues' signals.

On the problem of resonance assignments in solid state NMR of uniformly ¹⁵N,¹³C-labeled proteins

Determination of accurate resonance assignments from multidimensional chemical shift correlation spectra is one of the major problems in biomolecular solid state NMR, particularly for relative large proteins with less-than-ideal NMR linewidths. This article investigates the difficulty of resonance assignment, using a computational Monte Carlo/simulated annealing (MCSA) algorithm to search for assignments from artificial three-dimensional spectra that are constructed from the reported isotropic (15)N and (13)C chemical shifts of two proteins whose structures have been determined by solution NMR methods. The results demonstrate how assignment simulations can provide new insights into factors that affect the assignment process, which can then help guide the design of experimental strategies. Specifically, simulations are performed for the catalytic domain of SrtC (147 residues, primarily β-sheet secondary structure) and the N-terminal domain of MLKL (166 residues, primarily α-helical secondary structure). Assuming unambiguous residue-type assignments and four ideal three-dimensional data sets (NCACX, NCOCX, CONCA, and CANCA), uncertainties in chemical shifts must be less than 0.4 ppm for assignments for SrtC to be unique, and less than 0.2 ppm for MLKL. Eliminating CANCA data has no significant effect, but additionally eliminating CONCA data leads to more stringent requirements for chemical shift precision. Introducing moderate ambiguities in residue-type assignments does not have a significant effect.

GFT projection NMR spectroscopy for proteins in the solid state

Recording of four-dimensional (4D) spectra for proteins in the solid state has opened new avenues to obtain virtually complete resonance assignments and three-dimensional (3D) structures of proteins. As in solution state NMR, the sampling of three indirect dimensions leads per se to long minimal measurement time. Furthermore, artifact suppression in solid state NMR relies primarily on radio-frequency pulse phase cycling. For an n-step phase cycle, the minimal measurement times of both 3D and 4D spectra are increased n times. To tackle the associated 'sampling problem' and to avoid sampling limited data acquisition, solid state G-Matrix Fourier Transform (SS GFT) projection NMR is introduced to rapidly acquire 3D and 4D spectral information. Specifically, (4,3)D (HA)CANCOCX and (3,2)D (HACA)NCOCX were implemented and recorded for the 6 kDa protein GB1 within about 10% of the time required for acquiring the conventional congeners with the same maximal evolution times and spectral widths in the indirect dimensions. Spectral analysis was complemented by comparative analysis of expected spectral congestion in conventional and GFT NMR experiments, demonstrating that high spectral resolution of the GFT NMR experiments enables one to efficiently obtain nearly complete resonance assignments even for large proteins.

Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of β1 immunoglobulin binding domain of protein G (GB1)

Magic-angle spinning solid-state NMR (MAS SSNMR) represents a fast developing experimental technique with great potential to provide structural and dynamics information for proteins not amenable to other methods. However, few automated analysis tools are currently available for MAS SSNMR. We present a methodology for automating protein resonance assignments of MAS SSNMR spectral data and its application to experimental peak lists of the β1 immunoglobulin binding domain of protein G (GB1) derived from a uniformly ¹³C- and ¹⁵N-labeled sample. This application to the 56 amino acid GB1 produced an overall 84.1% assignment of the N, CO, CA, and CB resonances with no errors using peak lists from NCACX 3D, CANcoCA 3D, and CANCOCX 4D experiments. This proof of concept demonstrates the tractability of this problem.

Structural variations in the cross-beta core of amyloid beta fibrils revealed by deep UV resonance Raman spectroscopy

Understanding fibrillogenesis at a molecular level requires detailed structural characterization of amyloid fibrils. The combination of deep UV resonance Raman (DUVRR) spectroscopy and post mortem hydrogen-deuterium exchange (HX) was utilized for probing parallel vs antiparallel beta-sheets in fibrils prepared from full-length Abeta(1-40) and Abeta(34-42) peptides, respectively. Using previously published structural data based on solid-state NMR analysis, we verified the applicability of Asher's approach for the quantitative characterization of peptide conformation in the Abeta(1-40) fibril core. We found that the conformation of the parallel beta-sheet in the Abeta(1-40) fibril core is atypical for globular proteins, while in contrast, the antiparallel beta-sheet in Abeta(32-42) fibrils is a common structure in globular proteins. In contrast to the case for globular proteins, the conformations of parallel and antiparallel beta-sheets in Abeta fibril cores are substantially different, and their differences can be distinguished by DUVRR spectroscopy.

A Monte Carlo/simulated annealing algorithm for sequential resonance assignment in solid state NMR of uniformly labeled proteins with magic-angle spinning

We describe a computational approach to sequential resonance assignment in solid state NMR studies of uniformly (15)N,(13)C-labeled proteins with magic-angle spinning. As input, the algorithm uses only the protein sequence and lists of (15)N/(13)C(alpha) crosspeaks from 2D NCACX and NCOCX spectra that include possible residue-type assignments of each crosspeak. Assignment of crosspeaks to specific residues is carried out by a Monte Carlo/simulated annealing algorithm, implemented in the program MC_ASSIGN1. The algorithm tolerates substantial ambiguity in residue-type assignments and coexistence of visible and invisible segments in the protein sequence. We use MC_ASSIGN1 and our own 2D spectra to replicate and extend the sequential assignments for uniformly-labeled HET-s(218-289) fibrils previously determined manually by Siemer et al. (J. Biomol. NMR, 34 (2006) 75-87) from a more extensive set of 2D and 3D spectra. Accurate assignments by MC_ASSIGN1 do not require data that are of exceptionally high quality. Use of MC_ASSIGN1 (and its extensions to other types of 2D and 3D data) is likely to alleviate many of the difficulties and uncertainties associated with manual resonance assignments in solid state NMR studies of uniformly labeled proteins, where spectral resolution and signal-to-noise are often sub-optimal.

De novo protein structure generation from incomplete chemical shift assignments

NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments.

Four-dimensional heteronuclear correlation experiments for chemical shift assignment of solid proteins

Chemical shift assignment is the first step in all established protocols for structure determination of uniformly labeled proteins by NMR. The explosive growth in recent years of magic-angle spinning (MAS) solid-state NMR (SSNMR) applications is largely attributable to improved methods for backbone and side-chain chemical shift correlation spectroscopy. However, the techniques developed so far have been applied primarily to proteins in the size range of 5-10 kDa, despite the fact that SSNMR has no inherent molecular weight limits. Rather, the degeneracy inherent to many 2D and 3D SSNMR spectra of larger proteins has prevented complete unambiguous chemical shift assignment. Here we demonstrate the implementation of 4D backbone chemical shift correlation experiments for assignment of solid proteins. The experiments greatly reduce spectral degeneracy at a modest cost in sensitivity, which is accurately described by theory. We consider several possible implementations and investigate the CANCOCX pulse sequence in detail. This experiment involves three cross polarization steps, from H to CA[i], CA[i] to N[i], and N[i] to C'[i-1], followed by a final homonuclear mixing period. With short homonuclear mixing times (<20 ms), backbone correlations are observed with high sensitivity; with longer mixing times (>200 ms), long-range correlations are revealed. For example, a single 4D experiment with 225 ms homonuclear mixing time reveals approximately 200 uniquely resolved medium and long-range correlations in the 56-residue protein GB1. In addition to experimental demonstrations in the 56-residue protein GB1, we present a theoretical analysis of anticipated improvements in resolution for much larger proteins and compare these results in detail with the experiments, finding good agreement between experiment and theory under conditions of stable instrumental performance.

Calculating protein structures directly from anisotropic spin interaction constraints

Protein structure determination by solid-state NMR of aligned samples relies on the fundamental characteristics of the anisotropic nuclear spin interactions present in isotopically labeled proteins. Progress in the implementation of algorithms that calculate protein structures from the orientational constraints in the chemical shift and heteronuclear dipolar coupling interactions is described using both simulated and experimental data.

Double-quantum dipolar recoupling at high magic-angle spinning rates

A full investigation of the possible homonuclear double-quantum recoupling sequences, based on the RN family of sequences with N < or = 20, is given. Several new RN sequences, R16(6)(5), R18(8)(5), and R18(10)(5), were applied at high magic-angle spinning rates and compared with theory. The R18(10)(5) technique can be used to recouple dipolar couplings at spinning rates up to 39 kHz, and the application of the sequence in an INADEQUATE experiment is shown for a spinning rate of 30 kHz.

Specification and visualization of anisotropic interaction tensors in polypeptides and numerical simulations in biological solid-state NMR

Software facilitating numerical simulation of solid-state NMR experiments on polypeptides is presented. The Tcl-controlled SIMMOL program reads in atomic coordinates in the PDB format from which it generates typical or user-defined parameters for the chemical shift, J coupling, quadrupolar coupling, and dipolar coupling tensors. The output is a spin system file for numerical simulations, e.g., using SIMPSON (Bak, Rasmussen, and Nielsen, J. Magn. Reson. 147, 296 (2000)), as well as a 3D visualization of the molecular structure, or selected parts of this, with user-controlled representation of relevant tensors, bonds, atoms, peptide planes, and coordinate systems. The combination of SIMPSON and SIMMOL allows straightforward simulation of the response of advanced solid-state NMR experiments on typical nuclear spin interactions present in polypeptides. Thus, SIMMOL may be considered a "sample changer" to the SIMPSON "computer spectrometer" and proves to be very useful for the design and optimization of pulse sequences for application on uniformly or extensively isotope-labeled peptides where multiple-spin interactions need to be considered. These aspects are demonstrated by optimization and simulation of novel DCP and C7 based 2D N(CO)CA, N(CA)CB, and N(CA)CX MAS correlation experiments for multiple-spin clusters in ubiquitin and by simulation of PISA wheels from PISEMA spectra of uniaxially oriented bacteriorhodopsin and rhodopsin under conditions of finite RF pulses and multiple spin interactions.

Solid-state NMR data support a helix-loop-helix structural model for the N-terminal half of HIV-1 Rev in fibrillar form

Rev is a 116 residue basic protein encoded by the genome of human immunodeficiency virus type 1 (HIV-1) that binds to multiple sites in the Rev response element (RRE) of viral mRNA transcripts in nuclei of host cells, leading to transport of incompletely spliced and unspliced viral mRNA to the cytoplasm of host cells in the latter phases of the HIV-1 life cycle. Rev is absolutely required for viral replication. Because Rev aggregates and fibrillizes in solution at concentrations required for crystal growth or liquid state NMR measurements, high-resolution structural characterization of full-length Rev has not been possible. Previously, circular dichroism studies have shown that approximately 50 % of the Rev sequence adopts helical secondary structure, predicted to correspond to a helix-loop-helix structural motif in the N-terminal half of the protein. We describe the application of solid-state NMR techniques to Rev fibrils as a means of obtaining site-specific, atomic-level structural constraints without requiring a high degree of solubility or crystallinity. Solid-state NMR measurements, using the double-quantum chemical shift anisotropy and constant-time double-quantum-filtered dipolar recoupling techniques, provide constraints on the phi and psi backbone dihedral angles at sites in which consecutive backbone carbonyl groups are labeled with (13)C. Quantitative analysis of the solid-state NMR data, by comparison with numerical simulations, indicates helical phi and psi angles at residues Leu13 and Val16 in the predicted helix 1 segment, and at residues Arg39, Arg 42, Arg43, and Arg44 in the predicted helix 2 segment. These data represent the first site-specific structural constraints from NMR spectroscopy on full-length Rev, and support the helix-loop-helix structural model for its N-terminal half.

Biomolecular solid state NMR: advances in structural methodology and applications to peptide and protein fibrils

Solid state nuclear magnetic resonance (NMR) methods can provide atomic-level structural constraints on peptides and proteins in forms that are not amenable to characterization by other high-resolution structural techniques, owing to insolubility, high molecular weight, noncrystallinity, or other characteristics. Important examples include peptide and protein fibrils and membrane-bound peptides and proteins. Recent advances in solid state NMR methodology aimed at structural problems in biological systems are reviewed. The power of these methods is illustrated by experimental results on amyloid fibrils and other protein fibrils.

Solid-state NMR as a probe of amyloid fibril structure

Amyloid fibrils are intrinsically noncrystalline, insoluble, high-molecular-weight aggregates of peptides and proteins, with considerable biomedical and biophysical significance. Solid-state NMR techniques are uniquely capable of providing high-resolution, site-specific structural constraints for amyloid fibrils, at the level of specific interatomic distances and torsion angles. So far, a relatively small number of solid-state NMR studies of amyloid fibrils have been reported. These have addressed issues about the supramolecular organization of beta-sheets in the fibrils and the peptide conformation in the fibrils, and have concentrated on the beta-amyloid peptide of Alzheimer's disease. Many additional applications of solid-state NMR to amyloid fibrils from a variety of sources are anticipated in the near future, as these systems are ideally suited for the technique and are of widespread current interest.

Analysis of dipolar-coupling-mediated coherence transfer in a homonuclear two spin-12 solid-state system

Homonuclear dipolar-mediated coherence transfer (DCT), a through-space transfer of magnetization between like spins, can yield otherwise difficult-to-obtain structural information for macromolecules by measuring the internuclear distances between two sites of interest. The behavior of a spin-12 system under DCT is analyzed in detail by computing the time development of the density matrix using the product operator formalism. The effect of coherence transfer (CT) via the homonuclear isotropic scalar coupling on DCT is examined. Analytical and computational results that yield useful information on the frequencies, first-maxima, and first-zero of CT for a uniaxially oriented or a single-crystal solid-state system are presented. The results predict that the evolution of the spin angular momentum operators under the homonuclear dipolar coupling Hamiltonian leads to "cylindrical mixing" unlike "isotropic mixing" due to the strong scalar coupling Hamiltonian. These results will find relevance in both the design of RF pulse sequences for the structural studies of uniaxially oriented biological solids and the interpretation of solution NMR results from proteins embedded in partially oriented bicelles. Copyright 1999 Academic Press.

Determination of multiple ***&phi;***-torsion angles in proteins by selective and extensive (13)C labeling and two-dimensional solid-state NMR

We describe an approach to efficiently determine the backbone conformation of solid proteins that utilizes selective and extensive (13)C labeling in conjunction with two-dimensional magic-angle-spinning NMR. The selective (13)C labeling approach aims to reduce line broadening and other multispin complications encountered in solid-state NMR of uniformly labeled proteins while still enhancing the sensitivity of NMR spectra. It is achieved by using specifically labeled glucose or glycerol as the sole carbon source in the protein expression medium. For amino acids synthesized in the linear part of the biosynthetic pathways, [1-(13)C]glucose preferentially labels the ends of the side chains, while [2-(13)C]glycerol labels the C(alpha) of these residues. Amino acids produced from the citric-acid cycle are labeled in a more complex manner. Information on the secondary structure of such a labeled protein was obtained by measuring multiple backbone torsion angles phi; simultaneously, using an isotropic-anisotropic 2D correlation technique, the HNCH experiment. Initial experiments for resonance assignment of a selectively (13)C labeled protein were performed using (15)N-(13)C 2D correlation spectroscopy. From the time dependence of the (15)N-(13)C dipolar coherence transfer, both intraresidue and interresidue connectivities can be observed, thus yielding partial sequential assignment. We demonstrate the selective (13)C labeling and these 2D NMR experiments on a 8.5-kDa model protein, ubiquitin. This isotope-edited NMR approach is expected to facilitate the structure determination of proteins in the solid state.

NMR structural studies of membrane proteins

The three-dimensional structures of membrane proteins are essential for understanding their functions, interactions and architectures. Their requirement for lipids has hampered structure determination by conventional approaches. With optimized samples, it is possible to apply solution NMR methods to small membrane proteins in micelles; however, lipid bilayers are the definitive environment for membrane proteins and this requires solid-state NMR methods. Newly developed solid-state NMR experiments enable completely resolved spectra to be obtained from uniformly isotopically labeled membrane proteins in phospholipid lipid bilayers. The resulting operational constraints can be used for the determination of the structures of membrane proteins.

Intrinsic asymmetry in multidimensional solid-state NMR correlation spectra

Solid-state MAS correlation spectra involving cross polarization will generally provide spectra which are asymmetric about the main diagonal. A quantitative treatment of this effect is provided and is demonstrated experimentally with examples of two-dimensional spin-diffusion spectra. The effect, which is due to the nonuniform nonequilibrium initial coherent state induced by cross polarization, is usually pronounced, and cannot be eliminated simply. It must be taken into account when quantifying solid-state CPMAS correlation spectra.

Magic angle-oriented sample spinning (MAOSS): A new approach toward biomembrane studies

The application of magic angle sample spinning (MAS) NMR to uniformly aligned biomembrane samples is demonstrated as a new general approach toward structural studies of membrane proteins, peptides, and lipids. The spectral linewidth from a multilamellar lipid dispersion is dominated, in the case of protons, by the dipolar coupling. For low-gamma or dilute spins, however, the chemical shift anisotropy dominates the spectral linewidth, which is reduced by the two-dimensional order in a uniformly aligned lipid membrane. The remaining line broadening, which is due to orientational defects ("mosaic spread") can be easily removed at low spinning speeds. This orientational order in the sample also allows the anisotropic intermolecular motions of membrane components (such as rotational diffusion, tauc = 10(-10) s) for averaging dipolar interactions to be utilized, e.g., by placing the membrane normal parallel to the rotor axis. The dramatic resolution improvement for protons which are achieved in a lipid sample at only 220 Hz spinning speed in a 9.4 T field is slightly better than any data published to date using ultra-high fields (up to 17.6 T) and high-speed spinning (14 kHz). Additionally, the analysis of spinning sidebands provides valuable orientational information. We present the first 1H, 31P, and 13C MAS spectra of uniformly aligned dimyristoylphosphatidylcholine (DMPC) bilayers. Also, 1H resolution enhancement for the aromatic region of the M13 coat protein reconstituted into DMPC bilayers is presented. This new method combines the high resolution usually achieved by MAS with the advantages of orientational constraints obtained by working with macroscopically oriented samples. We describe the general potential and possible perspectives of this technique.

Nuclear magnetic resonance characterization of the myristoylated, N-terminal fragment of ADP-ribosylation factor 1 in a magnetically oriented membrane array

The behavior of the N-terminal fragment of human ADP-ribosylation factor 1 (ARF1) in a membranelike environment is described. This is accomplished using heteronuclear liquid crystal NMR techniques in a magnetically oriented membrane array on a selectively 13C- and 15N-labeled peptide. After full assignment of the labeled sites, residual dipolar couplings (13C-13C, 15N-1H and, 13C-15N) and chemical shift anisotropy effects (amide 13C and 15N) were measured. The experimental data were interpreted using order matrix calculations to yield orientational and dynamic information for four separate, rigid amide planes. The experimental data obtained proves that the amphipathic peptide interacts with the bilayer in a mode that is consistent with an alpha-helix having its axis parallel to the membrane surface. Possibilities of extending the employed techniques to larger and uniformly labeled systems are discussed.

Solution NMR spectroscopy beyond 25 kDa

Improvements in NMR instrumentation, higher magnetic field strengths, novel NMR experiments and new deuterium-labeling strategies have significantly increased the scope of structural problems that can now be addressed by solution NMR methods. To date, a number of structures of proteins of 30 kDa have been solved using multidimensional 15N,13C,2H NMR techniques, and this molecular weight limit will probably be surpassed in the near future.