Structure determination of the seven-helix transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy

Structure determination of membrane proteins by nuclear magnetic resonance spectroscopy

Many biological membranes consist of 50% or more (by weight) membrane proteins, which constitute approximately one-third of all proteins expressed in biological organisms. Helical membrane proteins function as receptors, enzymes, and transporters, among other unique cellular roles. Additionally, most drugs have membrane proteins as their receptors, notably the superfamily of G protein-coupled receptors with seven transmembrane helices. Determining the structures of membrane proteins is a daunting task because of the effects of the membrane environment; specifically, it has been difficult to combine biologically compatible environments with the requirements for the established methods of structure determination. There is strong motivation to determine the structures in their native phospholipid bilayer environment so that perturbations from nonnatural lipids and phases do not have to be taken into account. At present, the only method that can work with proteins in liquid crystalline phospholipid bilayers is solid-state NMR spectroscopy.

Solid-state NMR spectroscopy of proteins

Solid-state NMR spectroscopy proved to be a versatile tool for characterization of structure and dynamics of complex biochemical systems. In particular, magic angle spinning (MAS) solid-state NMR came to maturity for application towards structural elucidation of biological macromolecules. Current challenges in applying solid-state NMR as well as progress achieved recently will be discussed in the following chapter focusing on conceptual aspects important for structural elucidation of proteins.

Solution NMR spectroscopy for the determination of structures of membrane proteins in a lipid environment

Several recent advancements have transformed solution NMR spectroscopy into a competitive, elegant, and eminently viable technique for determining the solution structures of membrane proteins at the level of atomic resolution. Once a good level of cell-based or cell-free expression and purification of a suitably sized membrane protein has been achieved, then NMR offers a combination of several versatile strategies, for example, choice of appropriate deuterated or non-deuterated detergents, temperature, and ionic strength; isotope labelling with (2)H, (13)C, (15)N, with or without protonation of Ile (δ1), Leu, and Val methyl protons; combinatorial labelling of specific amino acids; transverse relaxation-optimized NMR spectroscopy-based, Nonuniform sampling-based, and other NMR experiments; measurement of residual dipolar couplings using stretched polyacrylamide gels or DNA nanotubes; and spin-labelling and paramagnetic relaxation enhancements. Strategic combinations of these advancements together with availability of highly sensitive cryogenically cooled probes equipped high-field NMR spectrometers (up to 1 GHz (1)H frequency) have allowed the perseverant investigator to successfully overcome several of the conventional pitfalls associated with the NMR technique and membrane proteins, viz., low sensitivity, poor sample stability, spectral crowding, and a limited number of NOEs and other constraints for structure calculations. This has resulted in an unprecedented growth in the number of successfully determined NMR structures of large and complex membrane proteins, and this technique now holds great promise for the structure determination of an ever larger body of membrane proteins.

Fragment screening of GPCRs using biophysical methods: identification of ligands of the adenosine A(2A) receptor with novel biological activity

Fragment-based drug discovery (FBDD) has proven a powerful method to develop novel drugs with excellent oral bioavailability against challenging pharmaceutical targets such as protein-protein interaction targets. Very recently the underlying biophysical techniques have begun to be successfully applied to membrane proteins. Here we show that novel, ligand efficient small molecules with a variety of biological activities can be found by screening a small fragment library using thermostabilized (StaR) G protein-coupled receptors (GPCRs) and target immobilized NMR screening (TINS). Detergent-solubilized StaR adenosine A(2A) receptor was immobilized with retention of functionality, and a screen of 531 fragments was performed. Hits from the screen were thoroughly characterized for biochemical activity using the wild-type receptor. Both orthosteric and allosteric modulatory activity has been demonstrated in biochemical validation assays. Allosteric activity was confirmed in cell-based functional assays. The validated fragment hits make excellent starting points for a subsequent hit-to-lead elaboration program.

Characterization of the ground state dynamics of proteorhodopsin by NMR and optical spectroscopies

We characterized the dynamics of proteorhodopsin (PR), solubilized in diC7PC, a detergent micelle, by liquid-state NMR spectroscopy at T = 323 K. Insights into the dynamics of PR at different time scales could be obtained and dynamic hot spots could be identified at distinct, functionally relevant regions of the protein, including the BC loop, the EF loop, the N-terminal part of helix F and the C-terminal part of helix G. We further characterize the dependence of the photocycle on different detergents (n-Dodecyl β-D-maltoside DDM; 1,2-diheptanoyl-sn-glycero-3-phosphocholine diC7PC) by ultrafast time-resolved UV/VIS spectroscopy. While the photocycle intermediates of PR in diC7PC and DDM exhibit highly similar spectral characteristics, significant changes in the population of these intermediates are observed. In-situ NMR experiments have been applied to characterize structural changes during the photocycle. Light-induced chemical shift changes detected during the photocycle in diC7PC are very small, in line with the changes in the population of intermediates in the photocycle of proteorhodopsin in diC7PC, where the late O-intermediate populated in DDM is missing and the population is shifted towards an equilibrium of intermediates states (M, N, O) without accumulation of a single populated intermediate.

Role of detergents in conformational exchange of a G protein-coupled receptor

The G protein-coupled β(2)-adrenoreceptor (β(2)AR) signals through the heterotrimeric G proteins G(s) and G(i) and β-arrestin. As such, the energy landscape of β(2)AR-excited state conformers is expected to be complex. Upon tagging Cys-265 of β(2)AR with a trifluoromethyl probe, (19)F NMR was used to assess conformations and possible equilibria between states. Here, we report key differences in β(2)AR conformational dynamics associated with the detergents used to stabilize the receptor. In dodecyl maltoside (DDM) micelles, the spectra are well represented by a single Lorentzian line that shifts progressively downfield with activation by appropriate ligand. The results are consistent with interconversion between two or more states on a time scale faster than the greatest difference in ligand-dependent chemical shift (i.e. >100 Hz). Given that high detergent off-rates of DDM monomers may facilitate conformational exchange between functional states of β(2)AR, we utilized the recently developed maltose-neopentyl glycol (MNG-3) diacyl detergent. In MNG-3 micelles, spectra indicated at least three distinct states, the relative populations of which depended on ligand, whereas no ligand-dependent shifts were observed, consistent with the slow exchange limit. Thus, detergent has a profound effect on the equilibrium kinetics between functional states. MNG-3, which has a critical micelle concentration in the nanomolar regime, exhibits an off-rate that is 4 orders of magnitude lower than that of DDM. High detergent off-rates are more likely to facilitate conformational exchange between distinct functional states associated with the G protein-coupled receptor.

Structure, sulfatide binding properties, and inhibition of platelet aggregation by a disabled-2 protein-derived peptide

Disabled-2 (Dab2) targets membranes and triggers a wide range of biological events, including endocytosis and platelet aggregation. Dab2, through its phosphotyrosine-binding (PTB) domain, inhibits platelet aggregation by competing with fibrinogen for α(IIb)β(3) integrin receptor binding. We have recently shown that the N-terminal region, including the PTB domain (N-PTB), drives Dab2 to the platelet membrane surface by binding to sulfatides through two sulfatide-binding motifs, modulating the extent of platelet aggregation. The three-dimensional structure of a Dab2-derived peptide encompassing the sulfatide-binding motifs has been determined in dodecylphosphocholine micelles using NMR spectroscopy. Dab2 sulfatide-binding motif contains two helices when embedded in micelles, reversibly binds to sulfatides with moderate affinity, lies parallel to the micelle surface, and when added to a platelet mixture, reduces the number and size of sulfatide-induced aggregates. Overall, our findings identify and structurally characterize a minimal region in Dab2 that modulates platelet homotypic interactions, all of which provide the foundation for rational design of a new generation of anti-aggregatory low-molecular mass molecules for therapeutic purposes.

Compressed sensing reconstruction of undersampled 3D NOESY spectra: application to large membrane proteins

Central to structural studies of biomolecules are multidimensional experiments. These are lengthy to record due to the requirement to sample the full Nyquist grid. Time savings can be achieved through undersampling the indirectly-detected dimensions combined with non-Fourier Transform (FT) processing, provided the experimental signal-to-noise ratio is sufficient. Alternatively, resolution and signal-to-noise can be improved within a given experiment time. However, non-FT based reconstruction of undersampled spectra that encompass a wide signal dynamic range is strongly impeded by the non-linear behaviour of many methods, which further compromises the detection of weak peaks. Here we show, through an application to a larger α-helical membrane protein under crowded spectral conditions, the potential use of compressed sensing (CS) l (1)-norm minimization to reconstruct undersampled 3D NOESY spectra. Substantial signal overlap and low sensitivity make this a demanding application, which strongly benefits from the improvements in signal-to-noise and resolution per unit time achieved through the undersampling approach. The quality of the reconstructions is assessed under varying conditions. We show that the CS approach is robust to noise and, despite significant spectral overlap, is able to reconstruct high quality spectra from data sets recorded in far less than half the amount of time required for regular sampling.

Comparison of fragments comprising the first two helices of the human Y4 and the yeast Ste2p G-protein-coupled receptors

Solution NMR techniques are used to determine the structure and the topology of micelle integration of a large fragment of the Y4 receptor, a human G-protein-coupled receptor, that contains the entire N-terminal domain plus the first two transmembrane (TM) segments. The structure calculations reveal that the putative TM helices are indeed helical to a large extent, but that interruptions of secondary structure occur close to internal polar or charged residues. This view is supported by (15)N relaxation data, amide-water exchange rates, and attenuations from micelle-integrating spin labels. No contacts between different helices are observed. This is in contrast to a similar TM1-TM2 fragment from the yeast Ste2p receptor for which locations of the secondary and the tertiary structure agreed well with the predictions from a homology model. The difference in structure is discussed in terms of principal biophysical properties of residues within central regions of the putative TM helices. Overall, using the biophysical scale of Wimley and White the TM regions of Ste2p display much more favorable free energies for membrane integration. Accordingly, the full secondary structure and the tertiary structure in TM1-TM2 of the Y4 receptor is likely to be formed only when tertiary contacts with other TM segments are created during folding of the receptor.

Eukaryotic N-glycosylation occurs via the membrane-anchored C-terminal domain of the Stt3p subunit of oligosaccharyltransferase

N-glycosylation is an essential and highly conserved protein modification. In eukaryotes, it is catalyzed by a multisubunit membrane-associated enzyme, oligosaccharyltransferase (OT). We report the high resolution structure of the C-terminal domain of eukaryotic Stt3p. Unlike its soluble β-sheet-rich prokaryotic counterparts, our model reveals that the C-terminal domain of yeast Stt3p is highly helical and has an overall oblate spheroid-shaped structure containing a membrane-embedded region. Anchoring of this protein segment to the endoplasmic reticulum membrane is likely to bring the membrane-embedded donor substrate closer, thus facilitating glycosylation efficiency. Structural comparison of the region near the WWDYG signature motif revealed that the acceptor substrate-binding site of yeast OT strikingly resembles its prokaryotic counterparts, suggesting a conserved mechanism of N-glycosylation from prokaryotes to eukaryotes. Furthermore, comparison of the NMR and cryo-EM structures of yeast OT revealed that the molecular architecture of this acceptor substrate-recognizing domain has interesting spatial specificity for interactions with other essential OT subunits.

Topogenesis of heterologously expressed fragments of the human Y4 GPCR

Fragments of large membrane proteins have the potential to facilitate structural analysis by NMR, but their folding state remains a concern. Here we determined the quality of folding upon heterologous expression for a series of N- or C-terminally truncated fragments of the human Y4 G-protein coupled receptor, amounting to six different complementation pairs. As the individual fragments lack a specific function that could be used to ascertain proper folding, we instead assessed folding on a basic level by studying their membrane topology and by comparing it to well-established structural models of GPCRs. The topology of the fragments was determined using a reporter assay based on C-terminal green fluorescent protein- or alkaline phosphatase-fusions. N-terminal fusions to Lep or Mistic were used if a periplasmic orientation of the N-terminus of the fragments was expected based on predictions. Fragments fused to Mistic expressed at comparably high levels, whereas Lep fusions were produced to a much lower extent. Though none of the fragments exclusively adopted one orientation, often the correct topology predominated. In addition, systematic analysis of the fragment series suggested that the C-terminal half of the Y4 receptor is more important for adopting the correct topology than the N-terminal part. Using the detergent dodecylphosphocholine, selected fragments were solubilized from the membrane and proved sufficiently stable to allow purification. Finally, as a first step toward reconstituting a functional receptor from two fragments, we observed a physical interaction between complementing fragments pairs upon co-expression.

Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples

We have developed an approach for determining NMR structures of proteins over 20 kDa that utilizes sparse distance restraints obtained using transverse relaxation optimized spectroscopy experiments on perdeuterated samples to guide RASREC Rosetta NMR structure calculations. The method was tested on 11 proteins ranging from 15 to 40 kDa, seven of which were previously unsolved. The RASREC Rosetta models were in good agreement with models obtained using traditional NMR methods with larger restraint sets. In five cases X-ray structures were determined or were available, allowing comparison of the accuracy of the Rosetta models and conventional NMR models. In all five cases, the Rosetta models were more similar to the X-ray structures over both the backbone and side-chain conformations than the "best effort" structures determined by conventional methods. The incorporation of sparse distance restraints into RASREC Rosetta allows routine determination of high-quality solution NMR structures for proteins up to 40 kDa, and should be broadly useful in structural biology.

Facile backbone structure determination of human membrane proteins by NMR spectroscopy

Although nearly half of today's major pharmaceutical drugs target human integral membrane proteins (hIMPs), only 30 hIMP structures are currently available in the Protein Data Bank, largely owing to inefficiencies in protein production. Here we describe a strategy for the rapid structure determination of hIMPs, using solution NMR spectroscopy with systematically labeled proteins produced via cell-free expression. We report new backbone structures of six hIMPs, solved in only 18 months from 15 initial targets. Application of our protocols to an additional 135 hIMPs with molecular weight <30 kDa yielded 38 hIMPs suitable for structural characterization by solution NMR spectroscopy without additional optimization.

Biosynthesis and spectroscopic characterization of 2-TM fragments encompassing the sequence of a human GPCR, the Y4 receptor

This paper presents a divide-and-conquer approach towards obtaining solution structures of G protein-coupled receptors. The human Y4 receptor was dissected into two to three transmembrane helix fragments, which were individually studied by solution NMR. We systematically compared various biosynthetic routes for the expression of the fragments in Escherichia coli and discuss purification strategies. In particular, we have compared the production of transmembrane (TM) fragments as inclusion bodies by using the ΔTrp leader sequence, with membrane-directed expression by using Mistic as the fusion partner, and developed methods for enzymatic cleavage. In addition, direct expression of two-TM fragments into inclusion bodies is a successful route in some cases. With the exception of TM13, we could produce all fragments in isotope-labeled form in quantities sufficient for NMR studies. Almost complete backbone resonance assignment was obtained for the first two helices, as well as for helices 5 and 7, and a high degree was obtained for TM6, while conformational exchange processes resulted in the disappearance of many signals from TM4. In addition, complete assignments were obtained for all residues of the N-terminal domain, as well as the extracellular and cytosolic loops (with the exception of an undecapeptide segment in the second extracellular loop, EC2) and for the complete cytosolic C-terminal tail. In total, backbone resonances of 78 % of all residues were assigned for the Y4 receptor. Predictions of secondary structure based on backbone chemical shifts indicate that most residues from the TM regions adopt helical conformations, with exception of those around polar residues or prolines. However, the domain boundaries differ slightly from those predicted for homology models. We suggest that the obtained chemical shifts might be useful in assigning the full-length receptor.

Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling

The fast Fourier transformation has been the gold standard for transforming data from time to frequency domain in many spectroscopic methods, including NMR. While reliable, it has as a drawback that it requires a grid of uniformly sampled data points. This needs very long measuring times for sampling in multidimensional experiments in all indirect dimensions uniformly and even does not allow reaching optimal evolution times that would match the resolution power of modern high-field instruments. Thus, many alternative sampling and transformation schemes have been proposed. Their common challenges are the suppression of the artifacts due to the non-uniformity of the sampling schedules, the preservation of the relative signal amplitudes, and the computing time needed for spectra reconstruction. Here we present a fast implementation of the Iterative Soft Thresholding approach (istHMS) that can reconstruct high-resolution non-uniformly sampled NMR data up to four dimensions within a few hours and make routine reconstruction of high-resolution NUS 3D and 4D spectra convenient. We include a graphical user interface for generating sampling schedules with the Poisson-Gap method and an estimation of optimal evolution times based on molecular properties. The performance of the approach is demonstrated with the reconstruction of non-uniformly sampled medium and high-resolution 3D and 4D protein spectra acquired with sampling densities as low as 0.8%. The method presented here facilitates acquisition, reconstruction and use of multidimensional NMR spectra at otherwise unreachable spectral resolution in indirect dimensions.

Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment

Obtaining NMR assignments for slowly tumbling molecules such as detergent-solubilized membrane proteins is often compromised by low sensitivity as well as spectral overlap. Both problems can be addressed by amino-acid specific isotope labeling in conjunction with (15)N-(1)H correlation experiments. In this work an extended combinatorial selective in vitro labeling scheme is proposed that seeks to reduce the number of samples required for assignment. Including three different species of amino acids in each sample, (15)N, 1-(13)C, and fully (13)C/(15)N labeled, permits identification of more amino acid types and sequential pairs than would be possible with previously published combinatorial methods. The new protocol involves recording of up to five 2D triple-resonance experiments to distinguish the various isotopomeric dipeptide species. The pattern of backbone NH cross peaks in this series of spectra adds a new dimension to the combinatorial grid, which otherwise mostly relies on comparison of [(15)N, (1)H]-HSQC and possibly 2D HN(CO) spectra of samples with different labeled amino acid compositions. Application to two α-helical membrane proteins shows that using no more than three samples information can be accumulated such that backbone assignments can be completed solely based on 3D HNCA/HN(CO)CA experiments. Alternatively, in the case of severe signal overlap in certain regions of the standard suite of triple-resonance spectra acquired on uniformly labeled protein, or missing signals due to a lack of efficiency of 3D experiments, the remaining gaps can be filled.

Cell-free synthesis of membrane subunits of ATP synthase in phospholipid bicelles: NMR shows subunit a fold similar to the protein in the cell membrane

NMR structure determination of large membrane proteins is hampered by broad spectral lines, overlap, and ambiguity of signal assignment. Chemical shift and NOE assignment can be facilitated by amino acid selective isotope labeling in cell-free protein synthesis system. However, many biological detergents are incompatible with the cell-free synthesis, and membrane proteins often have to be synthesized in an insoluble form. We report cell-free synthesis of subunits a and c of the proton channel of Escherichia coli ATP synthase in a soluble form in a mixture of phosphatidylcholine derivatives. In comparison, subunit a was purified from the cell-free system and from the bacterial cell membranes. NMR spectra of both preparations were similar, indicating that our procedure for cell-free synthesis produces protein structurally similar to that prepared from the cell membranes.

Large multiple transmembrane domain fragments of a G protein-coupled receptor: biosynthesis, purification, and biophysical studies

To conduct biophysical analyses on large domains of GPCRs, multimilligram quantities of highly homogeneous proteins are necessary. This communication discusses the biosynthesis of four transmembrane and five transmembrane-containing fragments of Ste2p, a GPCR recognizing the Saccharomyces cerevisiae tridecapeptide pheromone α-factor. The target fragments contained the predicted four N-terminal Ste2p[G(31) -A(198) ] (4TMN), four C-terminal Ste2p[T(155) -L(340) ] (4TMC), or five C-terminal Ste2p[I(120) -L(340) ] (5TMC) transmembrane segments of Ste2p. 4TMN was expressed as a fusion protein using a modified pMMHa vector in L-arabinose-induced Escherichia coli BL21-AI, and cleaved with cyanogen bromide. 4TMC and 5TMC were obtained by direct expression using a pET21a vector in IPTG-induced E. coli BL21(DE3) cells. 4TMC and 5TMC were biosynthesized on a preparative scale, isolated in multimilligram amounts, characterized by MS and investigated by biophysical methods. CD spectroscopy indicated the expected highly α-helical content for 4TMC and 5TMC in membrane mimetic environments. Tryptophan fluorescence showed that 5TMC integrated into the nonpolar region of 1-stearoyl-2-hydroxy-sn-glycero-3-phospho-(1'-rac-glycerol) micelles. HSQC-TROSY investigations revealed that [(15) N]-labeled 5TMC in 50% trifluoroethanol-d(2) /H(2) O/0.05%-trifluoroacetic acid was stable enough to conduct long multidimensional NMR measurements. The entire Ste2p GPCR was not readily reconstituted from the first two and last five or first three and last four transmembrane domains.

'q-Titration' of long-chain and short-chain lipids differentiates between structured and mobile residues of membrane proteins studied in bicelles by solution NMR spectroscopy

'q-Titration' refers to the systematic comparison of signal intensities in solution NMR spectra of uniformly (15)N labeled membrane proteins solubilized in micelles and isotropic bicelles as a function of the molar ratios (q) of the long-chain lipids (typically DMPC) to short-chain lipids (typically DHPC). In general, as q increases, the protein resonances broaden and correspondingly have reduced intensities due to the overall slowing of protein reorientation. Since the protein backbone signals do not broaden uniformly, the differences in line widths (and intensities) enable the narrower (more intense) signals associated with mobile residues to be differentiated from the broader (less intense) signals associated with "structured" residues. For membrane proteins with between one and seven trans-membrane helices in isotropic bicelles, we have been able to find a value of q between 0.1 and 1.0 where only signals from mobile residues are observed in the spectra. The signals from the structured residues are broadened so much that they cannot be observed under standard solution NMR conditions. This q value corresponds to the ratio of DMPC:DHPC where the signals from the structured residues are "titrated out" of the spectrum. This q value is unique for each protein. In magnetically aligned bilayers (q>2.5) no signals are observed in solution NMR spectra of membrane proteins because the polypeptides are "immobilized" by their interactions with the phospholipid bilayers on the relevant NMR timescale (∼10(5)Hz). No signals are observed from proteins in liposomes (only long-chain lipids) either. We show that it is feasible to obtain complementary solution NMR and solid-state NMR spectra of the same membrane protein, where signals from the mobile residues are present in the solution NMR spectra, and signals from the structured residues are present in the solid-state NMR spectra. With assigned backbone amide resonances, these data are sufficient to describe major features of the secondary structure and basic topology of the protein. Even in the absence of assignments, this information can be used to help establish optimal experimental conditions.

Solution NMR studies of integral polytopic α-helical membrane proteins: the structure determination of the seven-helix transmembrane receptor sensory rhodopsin II, pSRII

About 30% of the proteins encoded in the genome are expressed as membrane proteins but these represent <1% of all the structures solved today. In view of the physiological and pharmaceutical significance of membrane proteins it is clear that a better and more comprehensive understanding of their three-dimensional (3D) structures at atomic resolution is required. α-Helical integral membrane proteins are generally more difficult to work with than β-barrel-type proteins and this has particularly been true for the polytopic members such as the large family of seven-helical proteins. In this chapter we describe the practical aspects of the solution-state NMR spectroscopy structure determination of the seven-helical transmembrane (7-TM) protein receptor sensory rhodopsin pSRII from the haloalkaliphilic archaeon Natronomonas pharaonis reconstituted in detergent micelles. This is the first time that a three-dimensional structure of a 7-TM protein has been determined by NMR.

Bacterial production and solution NMR studies of a viral membrane ion channel

Advances in solution nuclear magnetic resonance (NMR) methodology that enable studies of very large proteins have also paved the way for studies of membrane proteins that behave like large proteins due to the added weight of surfactants. Solution NMR has been used to determine the high-resolution structures of several small, membrane proteins dissolved in detergent micelles and small bicelles. However, the usual difficulties with membrane proteins in producing, purifying, and stabilizing the proteins away from native membranes remain, requiring intensive screening efforts. Low levels of heterologous expression can be the most detrimental aspect to studying membrane proteins. This is exacerbated for NMR studies because of the costs of isotopically enriched media. Thus, solution NMR studies have tended to focus on relatively small, membrane proteins that can be expressed into inclusion bodies and refolded. Here, we describe the methods used to produce, purify, and refold the proton channel M2 into detergent micelles, and the procedures used to determine chemical shift assignments and the atomic level structure of the closed form of the homotetrameric channel.

Prokaryotic diacylglycerol kinase and undecaprenol kinase

Prokaryotic diacylglycerol kinase (DAGK) and undecaprenol kinase (UDPK) are the lone members of a family of multispan membrane enzymes that are very small, lack relationships to any other family of proteins-including water soluble kinases-and exhibit an unusual structure and active site architecture. Escherichia coli DAGK plays an important role in recycling diacylglycerol produced as a by-product of biosynthesis of molecules located in the periplasmic space. UDPK seems to play an analogous role in gram-positive bacteria, where its importance is evident because UDPK is essential for biofilm formation by the oral pathogen Streptococcus mutans. DAGK has also long served as a model system for studies of membrane protein biocatalysis, folding, stability, and structure. This review explores our current understanding of the microbial physiology, enzymology, structural biology, and folding of the prokaryotic DAGK family, which is based on over 40 years of studies.

High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data

X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 Å crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 Å in the transmembrane region, a 58% enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22% of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals.

Assessment of a fully active class A G protein-coupled receptor isolated from in vitro folding

We provide a protocol for the preparation of fully active Y2 G protein-coupled receptors (GPCRs). Although a valuable target for pharmaceutical research, information about the structure and dynamics of these molecules remains limited due to the difficulty in obtaining sufficient amounts of homogeneous and fully active receptors for in vitro studies. Recombinant expression of GPCRs as inclusion bodies provides the highest protein yields at lowest costs. But this strategy can only successfully be applied if the subsequent in vitro folding results in a high yield of active receptors and if this fraction can be isolated from the nonactive receptors in a homogeneous form. Here, we followed that strategy to provide large quantities of the human neuropeptide Y receptor type 2 and determined the folding yield before and after ligand affinity chromatography using a radioligand binding assay. Directly after folding, we achieved a proportion of ~25% active receptor. This value could be increased to ~96% using ligand affinity chromatography. Thus, a very homogeneous sample of the Y2 receptor could be prepared that exhibited a K(D) value of 0.1 ± 0.05 nM for the binding of polypeptide Y, which represents one of the natural ligands of the Y2 receptor.

Fast NMR data acquisition from bicelles containing a membrane-associated peptide at natural-abundance

In spite of recent technological advances in NMR spectroscopy, its low sensitivity continues to be a major limitation particularly for the structural studies of membrane proteins. The need for a large quantity of a membrane protein and acquisition of NMR data for a long duration are not desirable. Therefore, there is considerable interest in the development of methods to speed up the NMR data acquisition from model membrane samples. In this study, we demonstrate the feasibility of acquiring two-dimensional spectra of an antimicrobial peptide (MSI-78; also known as pexiganan) embedded in isotropic bicelles using natural-abundance (15)N nuclei. A copper-chelated lipid embedded in bicelles is used to speed-up the spin-lattice relaxation of protons without affecting the spectral resolution and thus enabling fast data acquisition. Our results suggest that even a 2D SOFAST-HMQC spectrum can be obtained four times faster using a very small amount (∼3 mM) of a copper-chelated lipid. These results demonstrate that this approach will be useful in the structural studies of membrane-associated peptides and proteins without the need for isotopic enrichment for solution NMR studies.

New amphiphiles for membrane protein structural biology

A challenging requirement for X-ray crystallography or NMR structure determination of membrane proteins (MPs), in contrast to soluble proteins, is the necessary use of amphiphiles to mimic the hydrophobic environment of membranes. A number of new detergents, lipids and non-detergent-like amphiphiles have been developed that stabilize MPs, and these have contributed to increased success in MP structural determinations in recent years. Despite some successes, currently available reagents are inadequate and there remains a pressing need for new amphiphiles. Literature examples and some new developments are selected here as a framework for discussing desirable properties of new amphiphiles for MP structural biology.

Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching

Mitochondrial uncoupling protein 2 (UCP2) is an integral membrane protein in the mitochondrial anion carrier protein family, the members of which facilitate the transport of small molecules across the mitochondrial inner membrane. When the mitochondrial respiratory complex pumps protons from the mitochondrial matrix to the intermembrane space, it builds up an electrochemical potential. A fraction of this electrochemical potential is dissipated as heat, in a process involving leakage of protons back to the matrix. This leakage, or 'uncoupling' of the proton electrochemical potential, is mediated primarily by uncoupling proteins. However, the mechanism of UCP-mediated proton translocation across the lipid bilayer is unknown. Here we describe a solution-NMR method for structural characterization of UCP2. The method, which overcomes some of the challenges associated with membrane-protein structure determination, combines orientation restraints derived from NMR residual dipolar couplings (RDCs) and semiquantitative distance restraints from paramagnetic relaxation enhancement (PRE) measurements. The local and secondary structures of the protein were determined by piecing together molecular fragments from the Protein Data Bank that best fit experimental RDCs from samples weakly aligned in a DNA nanotube liquid crystal. The RDCs also determine the relative orientation of the secondary structural segments, and the PRE restraints provide their spatial arrangement in the tertiary fold. UCP2 closely resembles the bovine ADP/ATP carrier (the only carrier protein of known structure), but the relative orientations of the helical segments are different, resulting in a wider opening on the matrix side of the inner membrane. Moreover, the nitroxide-labelled GDP binds inside the channel and seems to be closer to transmembrane helices 1-4. We believe that this biophysical approach can be applied to other membrane proteins and, in particular, to other mitochondrial carriers, not only for structure determination but also to characterize various conformational states of these proteins linked to substrate transport.

Comparative NMR analysis of an 80-residue G protein-coupled receptor fragment in two membrane mimetic environments

Fragments of integral membrane proteins have been used to study the physical chemical properties of regions of transporters and receptors. Ste2p(G31-T110) is an 80-residue polypeptide which contains a portion of the N-terminal domain, transmembrane domain 1 (TM1), intracellular loop 1, TM2 and part of extracellular loop 1 of the α-factor receptor (Ste2p) from Saccharomyces cerevisiae. The structure of this peptide was previously determined to form a helical hairpin in lyso-palmitoylphosphatidyl-glycerol micelles (LPPG) [1]. Herein, we perform a systematic comparison of the structure of this protein fragment in micelles and trifluoroethanol (TFE):water in order to understand whether spectra recorded in organic:aqueous medium can facilitate the structure determination in a micellar environment. Using uniformly labeled peptide and peptide selectively protonated on Ile, Val and Leu methyl groups in a perdeuterated background and a broad set of 3D NMR experiments we assigned 89% of the observable atoms. NOEs and chemical shift analysis were used to define the helical regions of the fragment. Together with constraints from paramagnetic spin labeling, NOEs were used to calculate a transiently folded helical hairpin structure for this peptide in TFE:water. Correlation of chemical shifts was insufficient to transfer assignments from TFE:water to LPPG spectra in the absence of further information.

Biophysical characterization of G-protein coupled receptor-peptide ligand binding

G-protein coupled receptors (GPCRs) are ubiquitous membrane proteins allowing intracellular responses to extracellular factors that range from photons of light to small molecules to proteins. Despite extensive exploitation of GPCRs as therapeutic targets, biophysical characterization of GPCR-ligand interactions remains challenging. In this minireview, we focus on techniques that have been successfully used for structural and biophysical characterization of peptide ligands binding to their cognate GPCRs. The techniques reviewed include solution-state nuclear magnetic resonance (NMR) spectroscopy, solid-state NMR, X-ray diffraction, fluorescence spectroscopy and single-molecule fluorescence methods, flow cytometry, surface plasmon resonance, isothermal titration calorimetry, and atomic force microscopy. The goal herein is to provide a cohesive starting point to allow selection of techniques appropriate to the elucidation of a given GPCR-peptide interaction.

Solution NMR studies of polytopic α-helical membrane proteins

NMR spectroscopy has established itself as one of the main techniques for the structural study of integral membrane proteins. Remarkably, over the last few years, substantial progress has been achieved in the structure determination of increasingly complex polytopical α-helical membrane proteins, with their size approaching ∼100kDa. Such advances are the result of significant improvements in NMR methodology, sample preparation and powerful selective isotope labelling schemes. We review the requirements facilitating such work based on the more recent solution NMR studies of α-helical proteins. While the majority of such studies still use detergent-solubilized proteins, alternative more native-like lipid-based media are emerging. Recent interaction, dynamics and conformational studies are discussed that cast a promising light on the future role of NMR in this important and exciting area.

Polymer-based cell-free expression of ligand-binding family B G-protein coupled receptors without detergents

G-protein coupled receptors (GPCRs) constitute the largest family of intercellular signaling molecules and are estimated to be the target of more than 50% of all modern drugs. As with most integral membrane proteins (IMPs), a major bottleneck in the structural and biochemical analysis of GPCRs is their expression by conventional expression systems. Cell-free (CF) expression provides a relatively new and powerful tool for obtaining preparative amounts of IMPs. However, in the case of GPCRs, insufficient homogeneity of the targeted protein is a problem as the in vitro expression is mainly done with detergents, in which aggregation and solubilization difficulties, as well as problems with proper folding of hydrophilic domains, are common. Here, we report that using CF expression with the help of a fructose-based polymer, NV10 polymer (NVoy), we obtained preparative amounts of homogeneous GPCRs from the three GPCR families. We demonstrate that two GPCR B family members, corticotrophin-releasing factor receptors 1 and 2β are not only solubilized in NVoy but also have functional ligand-binding characteristics with different agonists and antagonists in a detergent-free environment as well. Our findings open new possibilities for functional and structural studies of GPCRs and IMPs in general.

Overcoming barriers to membrane protein structure determination

After decades of slow progress, the pace of research on membrane protein structures is beginning to quicken thanks to various improvements in technology, including protein engineering and microfocus X-ray diffraction. Here we review these developments and, where possible, highlight generic new approaches to solving membrane protein structures based on recent technological advances. Rational approaches to overcoming the bottlenecks in the field are urgently required as membrane proteins, which typically comprise ~30% of the proteomes of organisms, are dramatically under-represented in the structural database of the Protein Data Bank.