Deuterium-MAS NMR Spectroscopy on Oriented Membrane Proteins: Applications to Photointermediates of Bacteriorhodopsin

Flow Alignment of Extracellular Vesicles: Structure and Orientation of Membrane-Associated Bio-macromolecules Studied with Polarized Light

Extracellular vesicles (EVs) are currently in scientific focus, as they have great potential to revolutionize the diagnosis and therapy of various diseases. However, numerous aspects of these species are still poorly understood, and thus, additional insight into their molecular-level properties, membrane-protein interactions, and membrane rigidity is still needed. We here demonstrate the use of red-blood-cell-derived EVs (REVs) that polarized light spectroscopy techniques, linear and circular dichroism, can provide molecular-level structural information on these systems. Flow-linear dichroism (flow-LD) measurements show that EVs can be oriented by shear force and indicate that hemoglobin molecules are associated to the lipid bilayer in freshly released REVs. During storage, this interaction ceases; this is coupled to major protein conformational changes relative to the initial state. Further on, the degree of orientation gives insight into vesicle rigidity, which decreases in time parallel to changes in protein conformation. Overall, we propose that both linear dichroism and circular dichroism spectroscopy can provide simple, rapid, yet efficient ways to track changes in the membrane-protein interactions of EV components at the molecular level, which may also give insight into processes occurring during vesiculation.

Solid-state nuclear magnetic resonance spectroscopy for membrane protein structure determination

Solid-state NMR (ssNMR) is a versatile technique that can provide high-resolution (sub-angstrom) structural data for integral membrane proteins embedded in native and model membrane environments. The methodologies for a priori structure determination have for the most part been developed using samples with crystalline and fibrous morphologies. However, the techniques are now being applied to large, polytopic membrane proteins including receptors, ion channels, and porins. ssNMR data may be used to annotate and refine existing structures in regions of the protein not fully resolved by crystallography (including ligand-binding sites and mobile solvent accessible loop regions). This review describes the spectroscopic experiments and data analysis methods (including assignment) used to generate high-resolution structural data for membrane proteins. We also consider the range of sample morphologies that are appropriate for study by this method.

Deuterium magic angle spinning NMR used to study the dynamics of peptides adsorbed onto polystyrene and functionalized polystyrene surfaces

LKα14 is a 14 amino acid peptide with a periodic sequence of leucine and lysine residues consistent with an amphipathic α-helix. This "hydrophobic periodicity" has been found to result in an α-helical secondary structure at air-water interfaces and on both polar and nonpolar solid polymer surfaces. In this paper, the dynamics of LKα14 peptides, selectively deuterated at a single leucine and adsorbed onto polystyrene and carboxylated polystyrene beads, are studied using (2)H magic angle spinning (MAS) solid state NMR over a 100 °C temperature range. We first demonstrate the sensitivity enhancement possible with (2)H MAS techniques, which in turn enables us to obtain high-quality (2)H NMR spectra for selectively deuterated peptides adsorbed onto solid polymer surfaces. The extensive literature shows that the dynamics of leucine side chains are sensitive to the local structural environment of the protein. Therefore, the degree to which the dynamics of leucine side chains and the backbone of the peptide LKα14 are influenced by surface proximity and surface chemistry is studied as a function of temperature with (2)H MAS NMR. It is found that the dynamics of the leucine side chains in LKα14 depend strongly upon the orientation of the polymer on the surface, which in turn depends on whether the LKα14 peptide adsorbs onto a polar or nonpolar surface. (2)H MAS line shapes therefore permit probes of surface orientation over a wide temperature range.

Structure elucidation of membrane-associated peptides and proteins in oriented bilayers by solid-state NMR spectroscopy

Solid-state NMR using magnetically oriented bilayer systems provides useful information on the structure and orientation of peptides and proteins bound to lipid bilayers. The ordering of the lipid bilayer along the magnetic field can be achieved in two ways. First, lipid can be macroscopically oriented by pressing lipid-water dispersion between flat glass plates, which is called a mechanically aligned system. Second, lipid molecules themselves can be aligned spontaneously in the magnetic field because of their diamagnetic anisotropy by forming bicelles or magnetically oriented vesicle systems. Structure and orientation of the membrane-associated peptides and proteins can be achieved by analyzing structural constraints obtained from anisotropic chemical shift interactions such as chemical shift oscillation or nuclear dipolar interactions such as dipolar wave and a combination of them such as PISA wheel. Detailed structure elucidation of various kinds of membrane peptides and proteins in such oriented bilayers is presented.

Solid-state 2H NMR spectroscopy of retinal proteins in aligned membranes

Solid-state 2H NMR spectroscopy gives a powerful avenue to investigating the structures of ligands and cofactors bound to integral membrane proteins. For bacteriorhodopsin (bR) and rhodopsin, retinal was site-specifically labeled by deuteration of the methyl groups followed by regeneration of the apoprotein. 2H NMR studies of aligned membrane samples were conducted under conditions where rotational and translational diffusion of the protein were absent on the NMR time scale. The theoretical lineshape treatment involved a static axial distribution of rotating C-C2H3 groups about the local membrane frame, together with the static axial distribution of the local normal relative to the average normal. Simulation of solid-state 2H NMR lineshapes gave both the methyl group orientations and the alignment disorder (mosaic spread) of the membrane stack. The methyl bond orientations provided the angular restraints for structural analysis. In the case of bR the retinal chromophore is nearly planar in the dark- and all-trans light-adapted states, as well upon isomerization to 13-cis in the M state. The C13-methyl group at the "business end" of the chromophore changes its orientation to the membrane upon photon absorption, moving towards W182 and thus driving the proton pump in energy conservation. Moreover, rhodopsin was studied as a prototype for G protein-coupled receptors (GPCRs) implicated in many biological responses in humans. In contrast to bR, the retinal chromophore of rhodopsin has an 11-cis conformation and is highly twisted in the dark state. Three sites of interaction affect the torsional deformation of retinal, viz. the protonated Schiff base with its carboxylate counterion; the C9-methyl group of the polyene; and the beta-ionone ring within its hydrophobic pocket. For rhodopsin, the strain energy and dynamics of retinal as established by 2H NMR are implicated in substituent control of activation. Retinal is locked in a conformation that is twisted in the direction of the photoisomerization, which explains the dark stability of rhodopsin and allows for ultra-fast isomerization upon absorption of a photon. Torsional strain is relaxed in the meta I state that precedes subsequent receptor activation. Comparison of the two retinal proteins using solid-state 2H NMR is thus illuminating in terms of their different biological functions.

Separated local field NMR experiments on oriented samples rotating at the magic angle

Biophysical studies on membrane proteins by solid state NMR (SSNMR) can be carried out directly in a membrane environment. Samples are usually prepared in form of multi-lamellar dispersions for magic angle sample spinning or as aligned multi-layers for orientation dependent NMR experiments without sample rotation. A new development is the application of MAS NMR to aligned samples (MAOSS; Magic Angle Oriented Sample Spinning). In combination with separated local field (SLF) experiments, size and orientation of heteronuclear dipolar couplings may be extracted from two-dimensional experiments which correlate dipolar couplings with isotropic chemical shifts. The orientation of these (1)H-X dipolar couplings can be directly related to the orientation of molecular groups in the sample. Here, we demonstrate the feasibility of these experiments on highly ordered polyethylene fibers which serve as model compound. Based on these data, the experiment is also applied to ordered multi-layers of bacteriorhodopsin (purple membrane) which is used as a model for aligned membrane proteins. We present a detailed analysis of different experimental designs with respect to angular sensitivity and the influence of residual sample disorder ("mosaic spread"). The results of the MAOSS-SLF experiment are discussed within the context of established solid state NMR experiments which are usually performed without sample rotation and we compare the data to orientation information obtained from X-ray diffraction.

Characterization of dynamic processes using deuterium in uniformly 2H,13C,15N enriched peptides by MAS solid-state NMR

We present in this paper 2H,13C MAS correlation experiments that are performed on a uniformly 2H,13C,15N labeled sample of Nac-Val, and on the uniformly 2H,15N labeled dipeptide Nac-Val-Leu-OH. The experiments involve the measurement of 2H T1 relaxation times at two different magnetic fields, as well as the measurement of the 2H tensor parameters by evolution of the 2H chemical shift. The data are interpreted quantitatively to differentiate between different side chain motional models.

Structure and Orientation of Peptide Inhibitors Bound to Beta-amyloid Fibrils

Polymerization of the soluble beta-amyloid peptide into highly ordered fibrils is hypothesized to be a causative event in the development of Alzheimer's disease. Understanding the interactions of Abeta with inhibitors on an atomic level is fundamental for the development of diagnostics and therapeutic approaches, and can provide, in addition, important indirect information of the amyloid fibril structure. We have shown recently that trRDCs can be measured in solution state NMR for peptide ligands binding weakly to amyloid fibrils. We present here the structures for two inhibitor peptides, LPFFD and DPFFL, and their structural models bound to fibrillar Abeta(14-23) and Abeta(1-40) based on transferred nuclear Overhauser effect (trNOE) and transferred residual dipolar coupling (trRDC) data. In a first step, the inhibitor peptide structure is calculated on the basis of trNOE data; the trRDC data are then validated on the basis of the trNOE-derived structure using the program PALES. The orientation of the peptide inhibitors with respect to Abeta fibrils is obtained from trRDC data, assuming that Abeta fibrils orient such that the fibril axis is aligned in parallel with the magnetic field. The trRDC-derived alignment tensor of the peptide ligand is then used as a restraint for molecular dynamics docking studies. We find that the structure with the lowest rmsd value is in agreement with a model in which the inhibitor peptide binds to the long side of an amyloid fibril. Especially, we detect interactions involving the hydrophobic core, residues K16 and E22/D23 of the Abeta sequence. Structural differences are observed for binding of the inhibitor peptide to Abeta14-23 and Abeta1-40 fibrils, respectively, indicating different fibril structure. We expect this approach to be useful in the rational design of amyloid ligands with improved binding characteristics.

Investigation of Ligand-Receptor Systems by High-Resolution Solid-State NMR: Recent Progress and Perspectives

Solid-state Nuclear Magnetic Resonance (NMR) provides a general method to study molecular structure and dynamics in a non-crystalline and insoluble environment. We discuss the latest methodological progress to construct 3D molecular structures from solid-state NMR data obtained under magic-angle-spinning conditions. As shown for the neurotensin/NTS-1 system, these methods can be readily applied to the investigation of ligand-binding to G-protein coupled receptors.

The alignment, structure and dynamics of membrane-associated polypeptides by solid-state NMR spectroscopy

Solid-state NMR spectroscopy is being developed at a fast pace for the structural investigation of immobilized and non-crystalline biomolecules. These include proteins and peptides associated with phospholipid bilayers. In contrast to solution NMR spectroscopy, where complete or almost complete averaging leads to isotropic values, the anisotropic character of nuclear interactions is apparent in solid-state NMR spectra. In static samples the orientation dependence of chemical shift, dipolar or quadrupolar interactions, therefore, provides angular constraints when the polypeptides have been reconstituted into oriented membranes. Furthermore, solid-state NMR spectroscopy of aligned samples offers distinct advantages in allowing access to dynamic processes such as topological equilibria or rotational diffusion in membrane environments. Alternatively, magic angle sample spinning (MAS) results in highly resolved NMR spectra, provided that the sample is sufficiently homogenous. MAS spinning solid-state NMR spectra allow to measure distances and dihedral angles with high accuracy. The technique has recently been developed to selectively establish through-space and through-bond correlations between nuclei, similar to the approaches well-established in solution-NMR spectroscopy.

Probing membrane protein orientation and structure using fast magic-angle-spinning solid-state NMR

One and two-dimensional solid-state NMR experiments are discussed that permit probing local structure and overall molecular conformation of membrane-embedded polypeptides under Magic Angle Spinning. The functional dependence of a series of anisotropic recoupling schemes is analyzed using theoretical and numerical methods. These studies lead to the construction of a set of polarization dephasing or transfer units that probe local backbone conformation and overall molecular orientation within the same NMR experiment. Experimental results are shown for a randomly oriented peptide and for two model membrane-peptides reconstituted into lipid bilayers and oriented on polymer films according to a method proposed by Bechinger et al.

Identifying anisotropic constraints in multiply labeled bacteriorhodopsin by 15N MAOSS NMR: a general approach to structural studies of membrane proteins

Structural models of membrane proteins can be refined with sets of multiple orientation constraints derived from structural NMR studies of specifically labeled amino acids. The magic angle oriented sample spinning (MAOSS) NMR approach was used to determine a set of orientational constraints in bacteriorhodopsin (bR) in the purple membrane (PM). This method combines the benefits of magic angle spinning (MAS), i.e., improved sensitivity and resolution, with the ability to measure the orientation of anisotropic interactions, which provide important structural information. The nine methionine residues in bacteriorhodopsin were isotopically (15)N labeled and spectra simplified by deuterium exchange before cross-polarization magic angle spinning (CPMAS) experiments. The orientation of the principal axes of the (15)N chemical shift anisotropy (CSA) tensors was determined with respect to the membrane normal for five of six residual resonances by analysis of relative spinning sideband intensities. The applicability of this approach to large proteins embedded in a membrane environment is discussed in light of these results.

Deuterium solid-state NMR investigations of exchange labeled oriented purple membranes at different hydration levels

Oriented purple membranes were equilibrated under controlled (2)H(2)O relative humidity ranging from 15% to 93% and introduced into the magnetic field of an NMR spectrometer with the membrane normal parallel to the magnetic field direction. Deuterium solid-state NMR spectra of these samples resolved four deuteron populations. Deuterons that have exchanged with amide protons of the protein exhibited a broad spectral line shape (<150 kHz). Furthermore, a broadened signal of deuterons tightly associated with protein and lipid is detected at low hydration, as well as two additional water populations that were present when the samples were equilibrated at >/=75% relative humidity. These latter ones are characterized by narrow quadrupolar splittings (<2.5 kHz) and orientation-dependent chemical shifts. Their deuterium relaxation times, measured as a function of temperature, indicate correlation times in the fast regime (10(-10) s) and activation energies of 13 kJ/mol (at 86% relative humidity). Differences in T(1) and T(2) relaxation together with small residual quadrupole splittings show that the mobility of the deuterons is anisotropic. The occurrence of these mobile water populations at high levels of purple membrane hydration (>/=75% relative humidity) correlate with proton pumping activity of bacteriorhodopsin, the fast kinetics of M-decay in the bacteriorhodopsin photocycle, and structural alterations of the protein during the M-state, which have been described previously.

Membrane proteins: the 'Wild West' of structural biology

Historically, the task of determining the structure of membrane proteins has been hindered by experimental difficulties associated with their lipid-embedded domains. Here, we provide an overview of recently developed experimental and predictive tools that are changing our view of this largely unexplored territory - the 'Wild West' of structural biology. Crystallography, single-particle methods and atomic force microscopy are being used to study huge membrane proteins with increasing detail. Solid-state nuclear magnetic resonance strategies provide orientational constraints for structure determination of transmembrane (TM) alpha-helices and accurate measurements of intramolecular distances, even in very complex systems. Longer distance constraints are determined by site-directed spin-labelling electron paramagnetic resonance, but current labelling strategies still constitute some limitation. Other methods, such as site-specific infrared dichroism, enable orientational analysis of TM alpha-helices in aligned bilayers and, combined with novel computational and predictive tools that use evolutionary conservation data, are being used to analyze TM alpha-helical bundles.

Solid-state 19F-NMR analysis of 19F-labeled tryptophan in gramicidin A in oriented membranes

The response of membrane-associated peptides toward the lipid environment or other binding partners can be monitored by solid-state NMR of suitably labeled side chains. Tryptophan is a prominent amino acid in transmembrane helices, and its (19)F-labeled analogues are generally biocompatible and cause little structural perturbation. Hence, we use 5F-Trp as a highly sensitive NMR probe to monitor the conformation and dynamics of the indole ring. To establish this (19)F-NMR strategy, gramicidin A was labeled with 5F-Trp in position 13 or 15, whose chi(1)/chi(2) torsion angles are known from previous (2)H-NMR studies. First, the alignment of the (19)F chemical shift anisotropy tensor within the membrane was deduced by lineshape analysis of oriented samples. Next, the three principal axes of the (19)F chemical shift anisotropy tensor were assigned within the molecular frame of the indole ring. Finally, determination of chi(1)/chi(2) for 5F-Trp in the lipid gel phase showed that the side chain alignment differs by up to 20 degrees from its known conformation in the liquid crystalline state. The sensitivity gain of (19)F-NMR and the reduction in the amount of material was at least 10-fold compared with previous (2)H-NMR studies on the same system and 100-fold compared with (15)N-NMR.

Determination of membrane Peptide orientation by 1H-detected 2H NMR spectroscopy

We demonstrate the application of the proton inverse detected deuteron (PRIDE) NMR technique to the measurement of the orientation of membrane-bound peptides with enhanced sensitivity. Gramicidin D, a transmembrane peptide, and ovispirin, a surface-bound peptide, were used as model systems. The peptides were 2H-labeled by 1H/2H exchange and oriented uniaxially on glass plates. The directly detected 2H spectra of both peptides showed only a strong D(2)O signal and no large quadrupolar splittings. In contrast, the PRIDE spectrum of gramicidin exhibited quadrupolar splittings as large as 281 kHz, consistent with its transmembrane orientation. Moreover, the large D(2)O signal in the directly detected 2H spectra was cleanly suppressed in the PRIDE spectrum. For ovispirin, the 1H indirectly detected 2H spectrum revealed a 104 kHz splitting and a zero-frequency peak. The former reflects the in-plane orientation of most of the helix axis, while the latter results from residues with a magic-angle orientation of the N-D bonds. These are consistent with previous 15N NMR results on ovispirin. The combination of PRIDE and exchange labeling provides an economical and sensitive method of studying membrane peptide orientations in lipid bilayers without the influence of D(2)O and with the ability to detect N-D bonds at the magic angle from the bilayer normal.

Bilayer sample for fast or slow magic angle oriented sample spinning solid-state NMR spectroscopy

An alternative setup for Magic Angle Oriented Spinning Spectroscopy is proposed. Samples were prepared by orienting lipid bilayers onto polymer films, which were wrapped into a spiral so as to fit into 4 or 7 mm MAS rotors. This geometry resulted in narrow line widths and a higher upper spinning limit when compared to the conventional MAOSS setup with stacked glass plates. Whereas orientational information was extracted from low spinning spectra, fast spinning will be applicable to high-resolution multidimensional NMR pulse sequences.

Evidence of a tendency to self-association of the transmembrane domain of ErbB-2 in fluid phospholipid bilayers

The transmembrane domains of receptor tyrosine kinases are single-span helical structures suggested to participate directly in the formation of side-to-side receptor homodimers/homooligomers that modulate signal transduction. Transmembrane peptides from the class I receptor tyrosine kinase, ErbB-2, were examined directly by 2H NMR spectroscopy as a means of following such phenomena under the dynamic conditions that characterize fluid, fully hydrated bilayers of natural phospholipids. Appropriate peptides were expressed as 50-mers, containing the transmembrane domain of ErbB-2 plus contiguous stretches of amino acids from the cytoplasmic and extracellular domains. Deuterium probes were incorporated in place of 1H at a site within the helical intramembranous portion (the -CH3 side chain of Ala657), and the peptides were assembled into bilayers of 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) for study. An analogous peptide corresponding to the oncogenic variant characterized by a Val659-->Glu point mutation was also examined. At high peptide concentration, prominent spectral features could be assigned to rapidly rotating transmembrane monomers and to large oligomers rotating very slowly relative to a time scale of 10(-5) s. As peptide concentration was lowered, the latter feature was greatly reduced, and an additional population of mobile species became identifiable, consistent with the presence of homodimers and/or small oligomers. The defined nature of these latter spectral features suggests that preferred interaction sites exist on the peptides. The appearance of similar phenomena in the case of transmembrane peptides from both wild-type ErbB-2 and the transforming mutant argues for the involvement of additional factors in signal modulation, such as limitations normally imposed by the missing extramembranous portions.

Membrane protein topology probed by (1)H spin diffusion from lipids using solid-state NMR spectroscopy

We describe a two-dimensional solid-state NMR technique to investigate membrane protein topology under magic-angle spinning conditions. The experiment detects the rate of (1)H spin diffusion from the mobile lipids to the rigid protein. While spin diffusion within the rigid protein is fast, magnetization transfer in the mobile lipids is an inefficient and slow process. Qualitative analysis of (1)H spin-diffusion build-up curves from the lipid chain-end methyl groups to the protein allows the identification of membrane-embedded domains in the protein. Numerical simulations of spin-diffusion build-up curves yield the approximate insertion depth of protein segments in the membrane. The experiment is demonstrated on the selectively (13)C labeled colicin Ia channel domain, known to have a membrane-embedded domain, and on DNA/cationic lipid complexes where the DNA rods are bound to the membrane surface. The experiment is designed for X-nucleus detection, which could be (13)C or (15)N in the protein and (31)P for the DNA. Finally, we show that a qualitative distinction between membrane proteins with and without a membrane-embedded domain can be made even by using an unlabeled protein, by detection of lipid signals. This spin-diffusion experiment is simple to perform and requires no oriented bilayer preparations and only standard NMR hardware.

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.

An optimal strategy for recovering the deuterium (2H) quadrupolar interaction under magic-angle spinning NMR

By exploiting the homology in the form of the truncated high-field homonuclear dipole-dipole and quadrupole coupling Hamiltonians, we have previously demonstrated that a simple adaptation of a rotor-synchronized pulse sequence (DRAMA) used for the recovery of dipole-dipole couplings can also be used to resurrect quadrupole couplings (QUADRAMA). In the canonical implementation of these recovery pulse sequences, the couplings are not significantly scaled down from their static sample values. While such minimal scaling is of course desirable in the recovery of typical homonuclear dipolar couplings (< or =2 kHz) and small quadrupole couplings, it is clearly not ideal for the recovery of the much larger quadrupole couplings (20-200 kHz) often encountered in solid-state 2H NMR. In such a case, some prior knowledge of the order of magnitude of the coupling is required to optimize the experimental conditions for QUADRAMA. In order to overcome this drawback, in this study, we have developed a general and optimized strategy for implementing the QUADRAMA technique which does not require any knowledge of the size of the coupling vQ. Experimental tests of the optimized protocol demonstrate that by judicious choices of a combination of scaling factors and recoupling times, 2H quadrupole couplings ranging over an order of magnitude from 3 to 42 kHz can be measured. Since this optimized protocol can reliably be used to recover couplings over a broad range, it expands the range of systems accessible to study by 2H NMR into a realm where static sample NMR and simple MAS NMR may fail.

REDOR NMR on a hydrophobic peptide in oriented membranes

A method is presented for the calculation of REDOR dephasing for specifically labeled membrane-spanning peptides in uniformly aligned lipid bilayers under magic angle oriented sample spinning (MAOSS) conditions. Numerical simulations are performed for dephasing of (13)C signal by (15)N when the labels are placed in an alpha-helical peptide at the carbonyl of residue (i) and amide nitrogen of residue (i + 2) to show the dependency of REDOR echo intensity on the peptide tilt angle relative to the membrane normal. The approach was applied to the labeled transmembrane domain of phospholamban ([(15)N-Leu(37), (13)C-Leu(39)]PLBTM) incorporated into dimyristoylphosphatidylcholine bilayers. The dephasing observed for a random membrane dispersion showed that the peptide was alpha-helical in the region including the two labels, and dephasing in oriented membranes showed that the peptide helix was tilted by 25 degrees +/- 7 degrees relative to the bilayer normal. These results agree with those obtained by other spectroscopic methods.

Solid-state NMR spectroscopy applied to membrane proteins

One major remaining problem in structural biology is to elucidate the structure and mechanism of function of membrane proteins. On the basis of preliminary information from genome projects, it is now estimated that up to 50,000 different membrane proteins may exist in the human being and that virtually every life process proceeds, sooner or later, through a membrane protein. Solid-state NMR spectroscopy in high magnetic field is rapidly developing into a widely applicable tool to describe the structure and help understand the mechanism of function of a membrane protein. Recent work in applied solid-state NMR spectroscopy crosses the boundary between the biological and the physical sciences, and aims at increasing the predictive range of this biophysical method.

Chromophore reorientation during the photocycle of bacteriorhodopsin: experimental methods and functional significance

Light-induced isomerization leads to orientational changes of the retinylidene chromophore of bacteriorhodopsin in its binding pocket. The chromophore reorientation has been characterized by the following methods: polarized absorption spectroscopy in the visible, UV and IR; polarized resonance Raman scattering; solid-state deuterium nuclear magnetic resonance; neutron and X-ray diffraction. Most of these experiments were performed at low temperatures with bacteriorhodopsin trapped in one or a mixture of intermediates. Time-resolved measurements at room temperature with bacteriorhodopsin in aqueous suspension can currently only be carried out with transient polarized absorption spectroscopy in the visible. The results obtained to date for the initial state and the K, L and M intermediates are presented and discussed. The most extensive data are available for the M intermediate, which plays an essential role in the function of bacteriorhodopsin. For this intermediate the various methods lead to a consistent picture: the curved all-trans polyene chain in the initial state straightens out in the M intermediate (13-cis) and the chain segment between C(5) and C(13) tilts upwards in the direction of the cytoplasmic surface. The kink at C(13) allows the positions of beta-ionone ring and Schiff base nitrogen to remain approximately fixed.

Refinement of the geometry of the retinal binding pocket in dark-adapted bacteriorhodopsin by heteronuclear solid-state NMR distance measurements

The bacterial proton pump bacteriorhodopsin (BR) is a 26.5 kDa seven-transmembrane helical protein. Several structural models have been published at > or =1.55 A resolution. The initial cis-trans isomerization of the retinal moiety involves structural changes within <1 A. To understand the chromophore-protein interactions that are important for light-driven proton transport, very accurate measurements of the protein geometry are required. To reveal more structural details at the site of the retinal, we have, therefore, selectively labeled the tryptophan side chains of BR with (15)N and metabolically incorporated retinal, (13)C-labeled at position 14 or 15. Using these samples, heteronuclear distances were measured with high accuracy using SFAM REDOR magic angle spinning solid-state NMR spectroscopy in dark-adapted bacteriorhodopsin. This NMR technique is applied for the first time to a high-molecular mass protein. Two retinal conformers are distinguished by their different isotropic 14-(13)C chemical shifts. Whereas the C14 position of 13-cis-15-syn-retinal is 4.2 A from [indole-(15)N]Trp86, this distance is 3.9 A in the all-trans-15-anti conformer. This latter distance allows us to check on the details of the active center of BR in the various published models derived from X-ray and electron diffraction data. The experimental approach and the results reported in this paper enforce the notion that distances between residues of a membrane protein binding pocket and a bound ligand can be determined at subangstrom resolution.

Observations of light-induced structural changes of retinal within rhodopsin

Photo-isomerization of the 11-cis retinal chromophore activates the mammalian light-receptor rhodopsin, a representative member of a major superfamily of transmembrane G-protein-coupled receptor proteins (GPCRs) responsible for many cell signal communication pathways. Although low-resolution (5 A) electron microscopy studies confirm a seven transmembrane helix bundle as a principal structural component of rhodopsin, the structure of the retinal within this helical bundle is not known in detail. Such information is essential for any theoretical or functional understanding of one of the fastest occurring photoactivation processes in nature, as well as the general mechanism behind GPCR activation. Here we determine the three-dimensional structure of 11-cis retinal bound to bovine rhodopsin in the ground state at atomic level using a new high-resolution solid-state NMR method. Significant structural changes are observed in the retinal following activation by light to the photo-activated M(I) state of rhodopsin giving the all-trans isomer of the chromophore. These changes are linked directly to the activation of the receptor, providing an insight into the activation mechanism of this class of receptors at a molecular level.

Structural and orientational information of the membrane embedded M13 coat protein by (13)C-MAS NMR spectroscopy

Oriented and unoriented M13 coat protein, incorporated into dimyristoyl phosphatidylcholine bilayers, has been studied by (13)C-magic angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy. Rotational resonance experiments provided two distance constraints between Calpha and C&z.dbnd6;O positions of the labelled residues Val-29/Val-30 (0.4+/-0.5nm) and Val-29/Val-31 (0.45+/-0. 5nm) in its hydrophobic domain. The derived dihedral angles (Phi, Psi) for Val-30 revealed a local alpha-helical conformation. (13)C-CP-MAS experiments on uniformly aligned samples (MAOSS experiments) using the (13)C&z.dbnd6;O labelled site of Val-30 allowed the determination of the helix tilt (20 degrees +/-10 degrees ) in the membrane. It is shown that one uniform MAS high-resolution solid state NMR approach can be used to obtain structural and orientational data.

Biomolecular NMR: recent advances in liquids, solids and screening

The past year has witnessed significant advances in NMR analysis of bio-macromolecules from a broad array of disciplines. First, great progress in the development of methods for measuring residual dipolar couplings in nematic media promises to increase both the size of systems to be studied and the accuracy with which structures can be determined. Second, the ability of solid-state NMR to provide structural information on biological systems is undergoing rapid expansion as a result of recent developments. The structural details that can be derived for biomolecules in the liquid and solid states can be used for the rational design of high-affinity ligands. Such studies are now complemented by NMR screening of synthetic and natural molecular libraries. Several NMR screening protocols have been designed that employ both rational and random elements.