Secondary Structure, Dynamics, and Topology of a Seven-Helix Receptor in Native Membranes, Studied by Solid-State NMR Spectroscopy

Complex formation and light activation in membrane-embedded sensory rhodopsin II as seen by solid-state NMR spectroscopy

Microbial rhodopsins execute diverse biological functions in the cellular membrane. A mechanistic understanding of their functional profile is, however, still limited. We used solid-state NMR (ssNMR) spectroscopy to study structure and dynamics of a 2 x 400 amino acid sensory rhodopsin/transducer (SRII/HtrII) complex from Natronomonas pharaonis in a natural membrane environment. We found a receptor-transducer binding interface in the ground state that significantly extends beyond the available X-ray structure. This binding domain involves the EF loop of the receptor and stabilizes the functionally relevant, directly adjacent HAMP domain of the transducer. Using 2D ssNMR difference spectroscopy, we identified protein residues that may act as a functional module around the retinal binding site during the early events of protein activation. These latter protein segments, the inherent plasticity of the HAMP domain, and the observation of an extended SRII/HtrII membrane-embedded interface may be crucial components for optimal signal relay efficiency across the cell membrane.

Assignment strategies for large proteins by magic-angle spinning NMR: the 21-kDa disulfide-bond-forming enzyme DsbA

We present strategies for chemical shift assignments of large proteins by magic-angle spinning solid-state NMR, using the 21-kDa disulfide-bond-forming enzyme DsbA as prototype. Previous studies have demonstrated that complete de novo assignments are possible for proteins up to approximately 17 kDa, and partial assignments have been performed for several larger proteins. Here we show that combinations of isotopic labeling strategies, high field correlation spectroscopy, and three-dimensional (3D) and four-dimensional (4D) backbone correlation experiments yield highly confident assignments for more than 90% of backbone resonances in DsbA. Samples were prepared as nanocrystalline precipitates by a dialysis procedure, resulting in heterogeneous linewidths below 0.2 ppm. Thus, high magnetic fields, selective decoupling pulse sequences, and sparse isotopic labeling all improved spectral resolution. Assignments by amino acid type were facilitated by particular combinations of pulse sequences and isotopic labeling; for example, transferred echo double resonance experiments enhanced sensitivity for Pro and Gly residues; [2-(13)C]glycerol labeling clarified Val, Ile, and Leu assignments; in-phase anti-phase correlation spectra enabled interpretation of otherwise crowded Glx/Asx side-chain regions; and 3D NCACX experiments on [2-(13)C]glycerol samples provided unique sets of aromatic (Phe, Tyr, and Trp) correlations. Together with high-sensitivity CANCOCA 4D experiments and CANCOCX 3D experiments, unambiguous backbone walks could be performed throughout the majority of the sequence. At 189 residues, DsbA represents the largest monomeric unit for which essentially complete solid-state NMR assignments have so far been achieved. These results will facilitate studies of nanocrystalline DsbA structure and dynamics and will enable analysis of its 41-kDa covalent complex with the membrane protein DsbB, for which we demonstrate a high-resolution two-dimensional (13)C-(13)C spectrum.

Broadband Heteronuclear Solid-State NMR Experiments by Exponentially Modulated Dipolar Recoupling without Decoupling

We present a novel solid-state NMR method for heteronuclear dipolar recoupling without decoupling. The method, which introduces the concept of exponentially modulated rf fields, provides efficient broadband recoupling with large flexibility with respect to hetero- or homonuclear applications, sample spinning frequency, and operation without the need for high-power (1)H decoupling. For previous methods, the latter has been a severe source of sample heating which may cause detoriation of costly samples. The so-called EXPonentially mOdulated Recoupling Technique (EXPORT) is described analytically and numerically, and demonstrated experimentally by 1D (13)C spectra and 2D (13)C-(15)N correlation spectra of (13)C,(15)N-labeled samples of GB1, ubiquitin, and fibrils of the SNNFGAILSS fragment of amylin. Through its flexible operation, robustness, and strong performance, it is anticipated that EXPORT will find immediate application for both hetero- and homonuclear dipolar recoupling in solid-state NMR of (13)C,(15)N-labeled proteins and compounds of relevance in chemistry.

NMR Determination of Protein pK(a) Values in the Solid State

Charged residues play an important role in defining key mechanistic features in many biomolecules. Determining the pK(a) values of large, membrane or fibrillar proteins can be challenging with traditional methods. In this study we show how solid-state NMR is used to monitor chemical shift changes during a pH titration for the small soluble β1 immunoglobulin binding domain of protein G. The chemical shifts of all the amino acids with charged side-chains throughout the uniformly-(13)C,(15)N-labeled protein were monitored over several samples varying in pH; pK(a) values were determined from these shifts for E27, D36, and E42, and the bounds for the pK(a) of other acidic side-chain resonances were determined. Additionally, this study shows how the calculated pK(a) values give insights into the crystal packing of the protein.

Structural study of the membrane protein MscL using cell-free expression and solid-state NMR

High-resolution structures of membrane proteins have so far been obtained mostly by X-ray crystallography, on samples where the protein is surrounded by detergent. Recent developments of solid-state NMR have opened the way to a new approach for the study of integral membrane proteins inside a membrane. At the same time, the extension of cell-free expression to the production of membrane proteins allows for the production of proteins tailor made for NMR. We present here an in situ solid-state NMR study of a membrane protein selectively labeled through the use of cell-free expression. The sample consists of MscL (mechano-sensitive channel of large conductance), a 75kDa pentameric alpha-helical ion channel from Escherichia coli, reconstituted in a hydrated lipid bilayer. Compared to a uniformly labeled protein sample, the spectral crowding is greatly reduced in the cell-free expressed protein sample. This approach may be a decisive step required for spectral assignment and structure determination of membrane proteins by solid-state NMR.

Prokaryotic expression, in vitro folding, and molecular pharmacological characterization of the neuropeptide Y receptor type 2

G protein-coupled receptors (GPCRs) are a class of membrane proteins that represent a major target for pharmacological developments. However, there is still little knowledge about GPCR structure and dynamics since high-level expression and characterization of active GPCRs in vitro is extremely complicated. Here, we describe the recombinant expression and functional folding of the human Y(2) receptor from inclusion bodies of E. coli cultures. Milligram protein quantities were produced using high density fermentation and isolated in a single step purification with a yield of over 20 mg/L culture. Extensive studies were carried out on in vitro refolding and stabilization of the isolated receptor in detergent solution. The specific binding of the ligand, the 36 residue neuropeptide Y (NPY), to the recombinant Y(2) receptors in micellar form was shown by several radioligand affinity assays. In competition experiments, an IC(50) value in low nanomolar range could be determined. Further, a K(D) value of 1.9 nM was determined from a saturation assay, where NPY was titrated to the recombinant Y(2) receptors.

Interresidue carbonyl-carbonyl polarization transfer experiments in uniformly 13C,15N-labeled peptides and proteins

In this work, we demonstrate that Homonuclear Rotary Resonance Recoupling (HORROR) can be used to reintroduce carbonyl-carbonyl interresidue dipolar interactions and to achieve efficient polarization transfer between carbonyl atoms in uniformly (13)C,(15)N-labeled peptides and proteins. We show that the HORROR condition is anisotropically broadened and overall shifted to higher radio frequency intensities because of the CSA effects. These effects are analyzed theoretically using Average Hamiltonian Theory. At spinning frequencies used in this study, 22kHz, this broadening is experimentally found to be on the order of a kilohertz at a proton field of 600MHz. To match HORROR condition over all powder orientations, variable amplitude radio frequency (RF) fields are required, and efficient direct transfers on the order of 20-30% can be straightforwardly established. Two- and three-dimensional chemical shift correlation experiments establishing long-range interresidue connectivities (e.g., (N[i]-CO[i-2])) are demonstrated on the model peptide N-acetyl-valine-leucine, and on the third immunoglobulin binding domain of protein G. Possible future developments are discussed.

Atomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy

We show that quantitative internuclear (15)N-(13)C distances can be obtained in sufficient quantity to determine a complete, high-resolution structure of a moderately sized protein by magic-angle spinning solid-state NMR spectroscopy. The three-dimensional ZF-TEDOR pulse sequence is employed in combination with sparse labeling of (13)C sites in the beta1 domain of the immunoglobulin binding protein G (GB1), as obtained by bacterial expression with 1,3-(13)C or 2-(13)C-glycerol as the (13)C source. Quantitative dipolar trajectories are extracted from two-dimensional (15)N-(13)C planes, in which approximately 750 cross peaks are resolved. The experimental data are fit to exact theoretical trajectories for spin clusters (consisting of one (13)C and several (15)N each), yielding quantitative precision as good as 0.1 A for approximately 350 sites, better than 0.3 A for another 150, and approximately 1.0 A for 150 distances in the range of 5-8 A. Along with isotropic chemical shift-based (TALOS) dihedral angle restraints, the distance restraints are incorporated into simulated annealing calculations to yield a highly precise structure (backbone RMSD of 0.25+/-0.09 A), which also demonstrates excellent agreement with the most closely related crystal structure of GB1 (2QMT, bbRMSD 0.79+/-0.03 A). Moreover, side chain heavy atoms are well restrained (0.76+/-0.06 A total heavy atom RMSD). These results demonstrate for the first time that quantitative internuclear distances can be measured throughout an entire solid protein to yield an atomic-resolution structure.

Determination of membrane protein structures using solution and solid-state NMR

NMR is an essential tool to characterize the structure, dynamics, and interactions of biomolecules at an atomic level. Its application to membrane protein (MP) structure determination is challenging and currently an active and rapidly developing field. Main difficulties are the low sensitivity of the technique, the size limitation, and the intrinsic motional properties of the system under investigation. Solution and solid-state NMR (ssNMR) have common and own specific requirements. Solution NMR requires a careful choice of the detergent, elaborated stable isotope labelling schemes to overcome signal overlaps and to collect distance restraints. Excessive spectra crowding hampered large MP structure determination by ssNMR, and so far only high resolution structure of small or fragments of MP have been determined. However, ssNMR provides the unique opportunity to obtain atomic level information of MP in phospholipid bilayers such as orientation of the protein in the membrane. Specific and careful sample preparations are required in combination with uniformly and partially labelled protein for ssNMR spectra assignment. Distance restraints measurements benefit from methodologies currently developed for small soluble proteins in micro-crystalline state.Recent advances in the field increased the releasing rate of high resolution MP structures, providing unprecedented structural and dynamics information making NMR a powerful tool for structural and functional membrane protein studies.

NMR reveals pathway for ferric mineral precursors to the central cavity of ferritin

Ferritin is a multimeric nanocage protein that directs the reversible biomineralization of iron. At the catalytic ferroxidase site two iron(II) ions react with dioxygen to form diferric species. In order to study the pathway of iron(III) from the ferroxidase site to the central cavity a new NMR strategy was developed to manage the investigation of a system composed of 24 monomers of 20 kDa each. The strategy is based on (13)C-(13)C solution NOESY experiments combined with solid-state proton-driven (13)C-(13)C spin diffusion and 3D coherence transfer experiments. In this way, 75% of amino acids were recognized and 35% sequence-specific assigned. Paramagnetic broadening, induced by iron(III) species in solution (13)C-(13)C NOESY spectra, localized the iron within each subunit and traced the progression to the central cavity. Eight iron ions fill the 20-A-long iron channel from the ferrous/dioxygen oxidoreductase site to the exit into the cavity, inside the four-helix bundle of each subunit, contrasting with short paths in models. Magnetic susceptibility data support the formation of ferric multimers in the iron channels. Multiple iron channel exits are near enough to facilitate high concentration of iron that can mineralize in the ferritin cavity, illustrating advantages of the multisubunit cage structure.

Characterization of different water pools in solid-state NMR protein samples

We observed and characterized two distinct signals originating from different pools of water protons in solid-state NMR protein samples, namely from crystal water which exchanges polarization with the protein (on the NMR timescale) and is located in the protein-rich fraction at the periphery of the magic-angle spinning (MAS) sample container, and supernatant water located close to the axis of the sample container. The polarization transfer between the water and the protein can be probed by two-dimensional exchange spectroscopy, and we show that the supernatant water does not interact with protein on the timescale of the experiments. The two water pools have different spectroscopic properties, including resonance frequency, longitudinal, transverse and rotating frame relaxation times. The supernatant water can be removed almost completely physically or can be frozen selectively. Both measures lead to an enhancement of the quality factor of the probe circuit, accompanied by an improvement of the experimental signal/noise, and greatly simplify solvent-suppression by substantially reducing the water signal. We also present a tool, which allows filling solid-state NMR sample containers in a more efficient manner, greatly reducing the amount of supernatant water and maximizing signal/noise.

J-Based 3D sidechain correlation in solid-state proteins

Scalar-based three-dimensional homonuclear correlation experiments are reported for (13)C sidechain correlation in solid-state proteins. These experiments are based on a sensitive constant-time format, in which homonuclear scalar couplings are utilized for polarization transfer, but decoupled during chemical shift evolution, to yield highly resolved indirect dimensions and band selectivity as desired. The methods therefore yield spectra of high quality that give unique sets of sidechain correlations for small proteins even at 9.4 Tesla (400 MHz (1)H frequency). We demonstrate versions of the pulse sequence that enable correlation from the sidechain to the backbone carbonyl as well as purely sidechain correlation sets; together these two data sets provide the majority of (13)C-(13)C correlations for assignment. The polarization transfer efficiency is approximately 30% over two bonds. In the protein GB1 (56 residues), we find essentially all cross peaks uniquely resolved. We find similar efficiency of transfer (approximately 30%) in the 140 kDa tryptophan synthase (TS), since the relaxation rates of immobilized solid proteins are not sensitive to global molecular tumbling, as long as the correlation time is much longer than the magic-angle spinning rotor period. In 3D data sets of TS at 400 MHz, some peaks are resolved and, in combination with higher field data sets, we anticipate that assignments will be possible; in this vein, we demonstrate 2D (13)C-(13)C spectra of TS at 900 MHz that are well resolved. These results together provide optimism about the prospects for assigning the spectra of such large enzymes in the solid state.

Retinal dynamics during light activation of rhodopsin revealed by solid-state NMR spectroscopy

Rhodopsin is a canonical member of class A of the G protein-coupled receptors (GPCRs) that are implicated in many of the drug interventions in humans and are of great pharmaceutical interest. The molecular mechanism of rhodopsin activation remains unknown as atomistic structural information for the active metarhodopsin II state is currently lacking. Solid-state (2)H NMR constitutes a powerful approach to study atomic-level dynamics of membrane proteins. In the present application, we describe how information is obtained about interactions of the retinal cofactor with rhodopsin that change with light activation of the photoreceptor. The retinal methyl groups play an important role in rhodopsin function by directing conformational changes upon transition into the active state. Site-specific (2)H labels have been introduced into the methyl groups of retinal and solid-state (2)H NMR methods applied to obtain order parameters and correlation times that quantify the mobility of the cofactor in the inactive dark state, as well as the cryotrapped metarhodopsin I and metarhodopsin II states. Analysis of the angular-dependent (2)H NMR line shapes for selectively deuterated methyl groups of rhodopsin in aligned membranes enables determination of the average ligand conformation within the binding pocket. The relaxation data suggest that the beta-ionone ring is not expelled from its hydrophobic pocket in the transition from the pre-activated metarhodopsin I to the active metarhodopsin II state. Rather, the major structural changes of the retinal cofactor occur already at the metarhodopsin I state in the activation process. The metarhodopsin I to metarhodopsin II transition involves mainly conformational changes of the protein within the membrane lipid bilayer rather than the ligand. The dynamics of the retinylidene methyl groups upon isomerization are explained by an activation mechanism involving cooperative rearrangements of extracellular loop E2 together with transmembrane helices H5 and H6. These activating movements are triggered by steric clashes of the isomerized all-trans retinal with the beta4 strand of the E2 loop and the side chains of Glu(122) and Trp(265) within the binding pocket. The solid-state (2)H NMR data are discussed with regard to the pathway of the energy flow in the receptor activation mechanism.

Assigning large proteins in the solid state: a MAS NMR resonance assignment strategy using selectively and extensively 13C-labelled proteins

In recent years, solid-state magic-angle spinning nuclear magnetic resonance spectroscopy (MAS NMR) has been growing into an important technique to study the structure of membrane proteins, amyloid fibrils and other protein preparations which do not form crystals or are insoluble. Currently, a key bottleneck is the assignment process due to the absence of the resolving power of proton chemical shifts. Particularly for large proteins (approximately >150 residues) it is difficult to obtain a full set of resonance assignments. In order to address this problem, we present an assignment method based upon samples prepared using [1,3-13C]- and [2-13C]-glycerol as the sole carbon source in the bacterial growth medium (so-called selectively and extensively labelled protein). Such samples give rise to higher quality spectra than uniformly [13C]-labelled protein samples, and have previously been used to obtain long-range restraints for use in structure calculations. Our method exploits the characteristic cross-peak patterns observed for the different amino acid types in 13C-13C correlation and 3D NCACX and NCOCX spectra. An in-depth analysis of the patterns and how they can be used to aid assignment is presented, using spectra of the chicken alpha-spectrin SH3 domain (62 residues), alphaB-crystallin (175 residues) and outer membrane protein G (OmpG, 281 residues) as examples. Using this procedure, over 90% of the Calpha, Cbeta, C' and N resonances in the core domain of alphaB-crystallin and around 73% in the flanking domains could be assigned (excluding 24 residues at the extreme termini of the protein).

Structure and dynamics of membrane proteins by magic angle spinning solid-state NMR

Membrane proteins remain difficult to study by traditional methods. Magic angle spinning solid-state NMR (MAS SSNMR) methods present an important approach for studying membrane proteins of moderate size. Emerging MAS SSNMR methods are based on extensive assignments of the nuclei as a basis for structure determination and characterization of function. These methods have already been used to characterize fibrils and globular proteins and are being increasingly used to study membrane proteins embedded in lipids. This review highlights recent applications to intrinsic membrane proteins and summarizes recent technical advances that will enable these methods to be utilized for more complex membrane protein systems in the near future.

Retinal conformation and dynamics in activation of rhodopsin illuminated by solid-state H NMR spectroscopy

Solid-state NMR spectroscopy gives a powerful avenue for investigating G protein-coupled receptors and other integral membrane proteins in a native-like environment. This article reviews the use of solid-state (2)H NMR to study the retinal cofactor of rhodopsin in the dark state as well as the meta I and meta II photointermediates. Site-specific (2)H NMR labels have been introduced into three regions (methyl groups) of retinal that are crucially important for the photochemical function of rhodopsin. Despite its phenomenal stability (2)H NMR spectroscopy indicates retinal undergoes rapid fluctuations within the protein binding cavity. The spectral lineshapes reveal the methyl groups spin rapidly about their three-fold (C(3)) axes with an order parameter for the off-axial motion of SC(3) approximately 0.9. For the dark state, the (2)H NMR structure of 11-cis-retinal manifests torsional twisting of both the polyene chain and the beta-ionone ring due to steric interactions of the ligand and the protein. Retinal is accommodated within the rhodopsin binding pocket with a negative pretwist about the C11=C12 double bond. Conformational distortion explains its rapid photochemistry and reveals the trajectory of the 11-cis to trans isomerization. In addition, (2)H NMR has been applied to study the retinylidene dynamics in the dark and light-activated states. Upon isomerization there are drastic changes in the mobility of all three methyl groups. The relaxation data support an activation mechanism whereby the beta-ionone ring of retinal stays in nearly the same environment, without a large displacement of the ligand. Interactions of the beta-ionone ring and the retinylidene Schiff base with the protein transmit the force of the retinal isomerization. Solid-state (2)H NMR thus provides information about the flow of energy that triggers changes in hydrogen-bonding networks and helix movements in the activation mechanism of the photoreceptor.

Comparative analysis of NMR chemical shift predictions for proteins in the solid phase

A comparative analysis of nuclear chemical shift predictions of proteins in the solid state by rapid algorithms trained on and verified with solution-state NMR assignments is presented. The precision of predictions by four dedicated computer programs (SHIFTS, PROSHIFTS, SHIFTX and SPARTA) was found to be close to values obtained for proteins in solution. Correlation coefficients depend on the NMR nucleus (N, C', C(alpha) and C(beta)) and on secondary structure (beta-strand, random coil and alpha-helix), but also on the molecular environment (membrane-integral or not). The findings establish a quantitative basis for using chemical shift prediction programs for solid-state NMR applications. On the other hand, prediction inaccuracies identified for certain resonance kind, residue type, and molecular environment point to possible areas of methodological improvement.

Ion channels: from conductance to structure

In this perspective I tell the story (albeit a clearly abridged version) of how our knowledge of ion conduction through ion channels has evolved from a purely electrical concept to a structural dynamics view of ions interacting with a membrane protein. Our progress in this field has shown steady growth over the years but has also been interspersed with sudden jumps of discovery. These leaps have normally been associated with the introduction of a new technical advance or the development of a new biological preparation; therefore, it is quite certain that we have not seen them all.

Arginine dynamics in a membrane-bound cationic beta-hairpin peptide from solid-state NMR

The site-specific motion of Arg residues in a membrane-bound disulfide-linked antimicrobial peptide, protegrin-1 (PG-1), was investigated by using magic-angle-spinning solid-state NMR spectroscopy to better understand the membrane insertion and lipid interaction of this cationic membrane-disruptive peptide. The C-H and N-H dipolar couplings and 13C chemical shift anisotropies were measured in the anionic POPE/POPG membrane, and were found to be reduced from the rigid-limit values by varying extents; this indicates the presence of segmental motion. An Arg residue at the beta-turn region of the peptide showed much weaker spin interactions, which indicates larger amplitudes of motion than an Arg residue in the beta-strand region of the peptide. This is consistent with the exposure of the beta turn to the membrane surface and the immersion of the beta strand in the hydrophobic middle of the membrane, and supports the previously proposed oligomerization of the peptide into beta barrels in the anionic membrane. The 13C T2 and 1H T(1rho) relaxation times indicate that the beta-turn backbone undergoes large-amplitude intermediate-timescale motion in the fluid phase of the membrane; this causes significant line broadening and loss of spectral intensity. This study illustrates the strong correlation between the dynamics and structure of membrane proteins, and the capability of solid-state NMR spectroscopy to provide detailed information on site-specific dynamics in complex membrane-protein assemblies.

Solid-state NMR adiabatic TOBSY sequences provide enhanced sensitivity for multidimensional high-resolution magic-angle-spinning 1H MR spectroscopy

We propose a solid-state NMR method that maximizes the advantages of high-resolution magic-angle-spinning (HRMAS) applied to intact biopsies when compared to more conventional liquid-state NMR approaches. Theoretical treatment, numerical simulations and experimental results on intact human brain biopsies are presented. Experimentally, it is proven that an optimized adiabatic TOBSY (TOtal through Bond correlation SpectroscopY) solid-state NMR pulse sequence for two-dimensional 1H-1H homonuclear scalar-coupling longitudinal isotropic mixing provides a 20%-50% improvement in signal-to-noise ratio relative to its liquid-state analogue TOCSY (TOtal Correlation SpectroscopY). For this purpose we have refined the C9(15)1 symmetry-based 13C TOBSY pulse sequence for 1H MRS use and compared it to MLEV-16 TOCSY sequence. Both sequences were rotor-synchronized and implemented using WURST-8 adiabatic inversion pulses. As discussed theoretically and shown in simulations, the improved magnetization-transfer comes from actively removing residual dipolar couplings from the average Hamiltonian. Importantly, the solid-state NMR techniques are tailored to perform measurements at low temperatures where sample degradation is reduced. This is the first demonstration of such a concept for HRMAS metabolic profiling of disease processes, including cancer, from biopsies requiring reduced sample degradation for further genomic analysis.

Asymmetric insertion of membrane proteins in lipid bilayers by solid-state NMR paramagnetic relaxation enhancement: a cell-penetrating Peptide example

A novel solid-state NMR technique for identifying the asymmetric insertion depths of membrane proteins in lipid bilayers is introduced. By applying Mn (2+) ions on the outer but not the inner leaflet of lipid bilayers, the sidedness of protein residues in the lipid bilayer can be determined through paramagnetic relaxation enhancement (PRE) effects. Protein-free lipid membranes with one-side Mn (2+)-bound surfaces exhibit significant residual (31)P and lipid headgroup (13)C intensities, in contrast to two-side Mn (2+)-bound membranes, where lipid headgroup signals are mostly suppressed. Applying this method to a cell-penetrating peptide, penetratin, we found that at low peptide concentrations, penetratin is distributed in both leaflets of the bilayer, in contrast to the prediction of the electroporation model, which predicts that penetratin binds to only the outer lipid leaflet at low peptide concentrations to cause an electric field that drives subsequent peptide translocation. The invalidation of the electroporation model suggests an alternative mechanism for intracellular import of penetratin, which may involve guanidinium-phosphate complexation between the peptide and the lipids.

Proton-detected scalar coupling based assignment strategies in MAS solid-state NMR spectroscopy applied to perdeuterated proteins

Assignment of proteins in MAS (magic angle spinning) solid-state NMR relies so far on correlations among heteronuclei. This strategy is based on well dispersed resonances in the (15)N dimension. In many complex cases like membrane proteins or amyloid fibrils, an additional frequency dimension is desirable in order to spread the amide resonances. We show here that proton detected HNCO, HNCA, and HNCACB type experiments can successfully be implemented in the solid-state. Coherences are sufficiently long lived to allow pulse schemes of a duration greater than 70 ms before incrementation of the first indirect dimension. The achieved resolution is comparable to the resolution obtained in solution-state NMR experiments. We demonstrate the experiments using a triply labeled sample of the SH3 domain of chicken alpha-spectrin, which was re-crystallized in H(2)O/D(2)O using a ratio of 1/9. We employ paramagnetic relaxation enhancement (PRE) using EDTA chelated Cu(II) to enable rapid data acquisition.

Advances towards resonance assignments for uniformly--13C, 15N enriched bacteriorhodopsin at 18.8 T in purple membranes

Solid state NMR spectra from uniformly (13)C, (15)N enriched bacteriorhodospin (bR) purified from H. salinarium were acquired at 18.8 T using magic angle spinning methods. Isolated resonances of 2D (13)C-(13)C spectra exhibited 0.50-0.55 ppm line-widths. Several amino acid types could be assigned, and at least 12 out of 15 Ile peaks could be resolved clearly and identified based on their characteristic chemical shifts and connectivities. This study confirms that high resolution solid state NMR spectra can be obtained for a 248 amino acid uniformly labeled membrane protein in its native membrane environment and indicates that site-specific assignments are likely to be feasible with heteronuclear multidimensional spectra.

Two-dimensional homonuclear chemical shift correlation established by the cross-relaxation driven spin diffusion in solids

A new type of spin diffusion, cross-relaxation driven spin diffusion (CRDSD), is investigated using (15)N NMR on a N-acetyl-L-valyl-L-leucine (NAVL) single crystal under stationary condition. A two-dimensional (2D) pulse sequence that correlates the chemical shifts of (15)N nuclei, with a radio-frequency spin lock on the (15)N channel during the mixing time, is used to observe CRDSD. Experimental results obtained using CRDSD, rf-driven spin diffusion, and proton driven spin diffusion approaches on the NAVL single crystal are compared. Our experimental results suggest that the (15)N spin diffusion rate can be enhanced by about 1000 times using CRDSD than by the normal proton driven spin diffusion. Interestingly, the required spin-locking rf field strength for CRDSD is much lower than that used for the rf-driven spin diffusion experiments. The cross-peak patterns observed in 2D (15)N-(15)N correlation spectra using CRDSD and RFDSD are very different as they arise from different spin-spin interactions. A detailed theory describing CRDSD and RFDSD processes is also presented using a thermodynamic model. The speedy spin diffusion process rendered by the CRDSD approach will be useful to assign resonances from a uniformly (15)N or (13)C labeled proteins and peptides, particularly in aligned samples.

Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR

Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhauser effect (NOE) routinely used in solution NMR. Here, we present a complementary approach for using relative orientations of molecular fragments, determined from dipolar line shapes. Whereas SSNMR distance restraints typically have an uncertainty of approximately 1 A, the tensor-based experiments report on relative vector (pseudobond) angles with precision of a few degrees. By using 3D techniques of this type, vector angle (VEAN) restraints were determined for the majority of the 56-residue B1 immunoglobulin binding domain of protein G [protein GB1 (a total of 47 HN-HN, 49 HN-HC, and 12 HA-HB restraints)]. By using distance restraints alone in the structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 +/- 0.13 A (1.52 +/- 0.12 A for all heavy atoms), which improved to 0.49 +/- 0.05 A (1.19 +/- 0.07 A) on the addition of empirical chemical shift [torsion angle likelihood obtained from shift and sequence similarity (TALOS)] restraints. VEAN restraints further improved the ensemble to 0.31 +/- 0.06 A bbRMSD (1.06 +/- 0.07 A); relative to the structure with distances alone, most of the improvement remained (bbRMSD 0.64 +/- 0.09 A; 1.29 +/- 0.07 A) when TALOS restraints were removed before refinement. These results represent significant progress toward atomic-resolution protein structure determination by SSNMR, capabilities that can be applied to a large range of membrane proteins and fibrils, which are often not amenable to solution NMR or x-ray crystallography.

Chemical shift assignment of the transmembrane helices of DsbB, a 20-kDa integral membrane enzyme, by 3D magic-angle spinning NMR spectroscopy

The Escherichia coli inner membrane enzyme DsbB catalyzes disulfide bond formation in periplasmic proteins, by transferring electrons to ubiquinone from DsbA, which in turn directly oxidizes cysteines in substrate proteins. We have previously shown that DsbB can be prepared in a state that gives highly resolved magic-angle spinning (MAS) NMR spectra. Here we report sequential 13C and 15N chemical shift assignments for the majority of the residues in the transmembrane helices, achieved by three-dimensional (3D) correlation experiments on a uniformly 13C, 15N-labeled sample at 750-MHz 1H frequency. We also present a four-dimensional (4D) correlation spectrum, which confirms assignments in some highly congested regions of the 3D spectra. Overall, our results show the potential to assign larger membrane proteins using 3D and 4D correlation experiments and form the basis of further structural and dynamical studies of DsbB by MAS NMR.

J-based 2D homonuclear and heteronuclear correlation in solid-state proteins

Scalar-based two-dimensional heteronuclear experiments are reported for NCO and NCA chemical shift correlation in the solid state. In conjunction with homonuclear CACO correlation, these experiments form a useful set for tracing connectivities and assigning backbone resonances in solid-state proteins. The applicability of this approach is demonstrated on two proteins, the β 1 immunoglobulin binding domain of protein G at 9.4 T and reassembled thioredoxin at 14.1 T, using different decoupling conditions and MAS frequencies. These constant-time J-based correlation experiments exhibit increased resolution in the indirect dimension owing to homonuclear and heteronuclear decoupling, and because the indirect evolution and transfer periods are combined into a single constant time interval, this increased resolution is not obtained at the cost of sensitivity. These experiments are also shown to be compatible with in-phase anti-phase (IPAP) selection, giving increased resolution in the directly detected dimension.

Magic-angle spinning solid-state NMR spectroscopy of nanodisc-embedded human CYP3A4

Cytochrome P450 (CYP) 3A4 contributes to the metabolism of approximately 50% of commercial drugs by oxidizing a large number of structurally diverse substrates. Like other endoplasmic reticulum-localized P450s, CYP3A4 contains a membrane-anchoring N-terminal helix and a significant number of hydrophobic domains, important for the interaction between CYP3A4 and the membrane. Although the membrane affects specificity of CYP3A4 ligand binding, the structural details of the interaction have not been revealed so far because X-ray crystallography studies are available only for the soluble domain of CYP3A4. Here we report sample preparation and initial magic-angle spinning (MAS) solid-state NMR (SSNMR) of CYP3A4 (Delta3-12) embedded in a nanoscale membrane bilayer, or Nanodisc. The growth protocol yields approximately 2.5 mg of the enzymatically active, uniformly 13C,15N-enriched CYP3A4 from 1 L of growth medium. Polyethylene glycol 3350-precipitated CYP3A4 in Nanodiscs yields spectra of high resolution and sensitivity, consistent with a folded, homogeneous protein. CYP3A4 in Nanodiscs remains enzymatically active throughout the precipitation protocol as monitored by bromocriptine binding. The 13C line widths measured from 13C-13C 2D chemical shift correlation spectra are approximately 0.5 ppm. The secondary structure distribution within several amino acid types determined from 13C chemical shifts is consistent with the ligand-free X-ray structures. These results demonstrate that MAS SSNMR can be performed on Nanodisc-embedded membrane proteins in a folded, active state. The combination of SSNMR and Nanodisc methodologies opens up new possibilities for obtaining structural information on CYP3A4 and other integral membrane proteins with full retention of functionality.

Magic-angle-spinning NMR spectroscopy applied to small molecules and peptides in lipid bilayers

ssNMR (solid-state NMR) spectroscopy provides increasing possibilities to study the structural and dynamic aspects of biological membranes. Here, we review recent ssNMR experiments that are based on MAS (magic angle spinning) and that provide insight into the structure and dynamics of membrane systems at the atomic level. Such methods can be used to study membrane architecture, domain formation or molecular complexation in a way that is highly complementary to other biophysical methods such as imaging or calorimetry.

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.

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.