A general procedure for building the transmembrane domains of G‐protein coupled receptors

The only results available at present about the structural features of G‐protein coupled receptors are the low resolution electron projection maps obtained from microscopy studies carried out on two‐dimensional crystals of rhodopsin. These studies support previous suggestions that these integral proteins are constituted by seven transmembrane domains. The low resolution electron density map of rhodopsin can be used to extract information about helix relative positions and tilt. This information, together with a reliable procedure to assess the residues involved in each of the transmembrane regions, can be used to construct a model of rhodopsin at atomic resolution. We have developed an algorithm that can be used to generate such a model in a completely automated fashion. The steps involved are: (i) locate the centers of the helices according to the low resolution electron density map; (ii) compute the tilt of each helix based on the elliptical shape observed by each helix in the map; (iii) define a local coordinate system for each of the helices; (iv) bring them together in an antiparallel orientation; (v) rotate each helix through the helical axis in such a way that its hydrophobic moment points in the same direction as the bisector formed between three consecutive helices in the bundle; (vi) rotate each helix through an axis perpendicular to the helical one to assign a proper tilt; (vii) translate each of the helix to its center deduced from the projection map. A major advantage of the procedure presented is its generality and consequently can be used to obtain a model of any G‐protein coupled receptor with the only assumption that the shape of the bundle is the same as found in rhodopsin. This avoids uncertainties found in other procedures that construct models of G‐protein coupled receptors based on sequence homology using rhodopsin as template. This revised version was published online in July 2006 with corrections to the Cover Date.     

Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor

Prediction of 3D structures of membrane proteins, and of G-protein coupled receptors (GPCRs) in particular, is motivated by their importance in biological systems and the difficulties associated with experimental structure determination. In the present study, a novel method for the prediction of 3D structures of the membrane-embedded region of helical membrane proteins is presented. A large pool of candidate models are produced by repacking of the helices of a homology model using Monte Carlo sampling in torsion space, followed by ranking based on their geometric and ligand-binding properties. The trajectory is directed by weak initial restraints to orient helices towards the original model to improve computation efficiency, and by a ligand to guide the receptor towards a chosen conformational state. The method was validated by construction of the β₁ adrenergic receptor model in complex with (S)-cyanopindolol using bovine rhodopsin as template. In addition, models of the dopamine D₂ receptor were produced with the selective and rigid agonist (R)-N-propylapomorphine ((R)-NPA) present. A second quality assessment was implemented by evaluating the results from docking of a library of 29 ligands with known activity, which further discriminated between receptor models. Agonist binding and recognition by the dopamine D₂ receptor is interpreted using the 3D structure model resulting from the approach. This method has a potential for modeling of all types of helical transmembrane proteins for which a structural template with sequence homology sufficient for homology modeling is not available or is in an incorrect conformational state, but for which sufficient empirical information is accessible.     

Analysis of the activation mechanism of the guinea-pig Histamine H<Subscript>1</Subscript>-receptor

The Histamine H(1)-receptor (H1R), belonging to the amine receptor-class of family A of the G-protein coupled receptors (GPCRs) gets activated by agonists. The consequence is a conformational change of the receptor, which may involve the binding-pocket. So, for a good prediction of the binding-mode of an agonist, it is necessary to have knowledge about these conformational changes. Meanwhile some experimental data about the structural changes of GPCRs during activation exist. Based on homology modeling of the guinea-pig H1R (gpH1R), using the crystal structure of bovine rhodopsin as template, we performed several MD simulations with distance restraints in order to get an inactive and an active structure of the gpH1R. The calculations led to a Phe6.44/Trp6.48/Phe6.52-switch and linearization of the proline kinked transmembrane helix VI during receptor activation. Our calculations showed that the Trp6.48/Phe6.52-switch induces a conformational change in Phe6.44, which slides between transmembrane helices III and VI. Additionally we observed a hydrogen bond interaction of Ser3.39 with Asn7.45 in the inactive gpH1R, but because of a counterclockwise rotation of transmembrane helix III Ser3.39 establishes a water-mediated hydrogen bond to Asp2.50 in the active gpH1R. Additionally we simulated a possible mechanism for receptor activation with a modified LigPath-algorithm.     

Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers

The G protein-coupled receptor (GPCR) rhodopsin self-assembles into supramolecular structures in native bilayers, but the structural determinants of receptor oligomerization are not known. We carried out multiple self-assembly coarse-grained molecular dynamics (CGMD) simulations of model membranes containing up to 64 molecules of the visual receptor rhodopsin over time scales reaching 100 μs. The simulations show strong preferential interaction modes between receptors. Two primary modes of receptor-receptor interactions are consistent with umbrella sampling/potential of mean force (PMF) calculations as a function of the distance between a pair of receptors. The preferential interfaces, involving helices (H) 1/8, 4/5 and 5, present no energy barrier to forming a very stable receptor dimer. Most notably, the PMFs show that the preferred rhodopsin dimer exists in a tail-to-tail conformation, with the interface comprising transmembrane H1/H2 and amphipathic H8 at the extracellular and cytoplasmic surfaces, respectively. This dimer orientation is in line with earlier electron microscopy, X-ray, and cross-linking experiments of rhodopsin and other GPCRs. Less stable interfaces, involving H4 and H6, have a free energy barrier for desolvation (delipidation) of the interfaces and appear to be designed to stabilize "lubricated" (i.e., lipid-coated) dimers. The overall CGMD strategy used here is general and can be applied to study the homo- and heterodimerization of GPCRs and other transmembrane proteins. Systematic extension of the work will deepen our understanding of the forces involved in the membrane organization of integral membrane proteins.     

Recent bioorganic studies on rhodopsin and visual transduction

Rhodopsin, the pigment responsible for vision in animals, insect and fish is a typical G protein (guanyl-nucleotide binding protein) consisting of seven transmembrane alpha helices and their interconnecting extramembrane loops. In the case of bovine rhodopsin, the best studied of the visual pigments, the chromophore is 11-cis retinal attached to the terminal amino group of Lys296 through a protonated Schiff base linkage. Photoaffinity labeling with a 3-diazo-4-oxo-retinoid shows that C-3 of the ionone ring moiety is close to Trp265 in helix F (VI) in dark inactivated rhodopsin. Irradiation causes a cis to trans isomerization of the 11-cis double bond giving rise to the highly strained intermediate bathorhodopsin. This undergoes a series of thermal relaxation through lumi-, meta-I and meta-II intermediates after which the retinal chromophore is expelled from the opsin binding pocket. Photoaffinity labeling performed with 3-diazo-4-oxoretinal at -196 degrees C for batho-, -80 degrees C for lumi-, -40 degrees C for meta-I, and 0 degrees C for meta-II rhodopsin showed that in bathorhodopsin the ring is still close to Trp265. However, in lumi-, meta-I and meta-II intermediates crosslinking occurs unexpectedly at A169 in helix D (IV). This shows that large movements in the helical arrangements and a flip over of the ring moiety accompanies the transduction (or bleaching) process. These changes in retinal/opsin interactions are necessarily accompanied by movements of the extramembrane loops, which in turn lead to activation of the G protein residing in the cytoplasmic side. Of the numerous G protein coupled receptors, this is the first time that the outline of transduction pathway has been clarified.     

Reversible Ligand‐Gated Ion Channel via Interconversion between Hollow Single Helix and Intertwined Double Helix

Ligand responsiveness is one of the typical mechanisms in biological organization to trigger sophisticated channel switching. Here, we report a new type of helical trimer which can undergo transition between a hollow single helix and an intertwined double helix with no cavity by complexation and decomplexation of Cu ions. In addition, the one dimensional (1D) hollow helical tubes spontaneously generated from single helices via π‐π interactions embedded into the lipid bilayers and displayed satisfactory channel stability and efficiency. With the addition of Cu^I ions and further extraction with ammonia, the disassembly and reassembly of 1D hollow helical tubes gave rise to the reversible switching of channel activity in situ inside the bilayers. The synthetic helical system provides the first model of reversible ligand‐gated ion channel by means of dynamic transition between single and double helices, which will be available for developing intelligent artificial nanochannels for potential biological and medicinal applications.     

Reversible Ligand-Gated Ion Channel via Interconversion between Hollow Single Helix and Intertwined Double Helix

Ligand responsiveness is one of the typical mechanisms in biological organization to trigger sophisticated channel switching. Here, we report a new type of helical trimer which can undergo transition between a hollow single helix and an intertwined double helix with no cavity by complexation and decomplexation of Cu ions. In addition, the one dimensional (1D) hollow helical tubes spontaneously generated from single helices via π-π interactions embedded into the lipid bilayers and displayed satisfactory channel stability and efficiency. With the addition of Cu^I ions and further extraction with ammonia, the disassembly and reassembly of 1D hollow helical tubes gave rise to the reversible switching of channel activity in situ inside the bilayers. The synthetic helical system provides the first model of reversible ligand-gated ion channel by means of dynamic transition between single and double helices, which will be available for developing intelligent artificial nanochannels for potential biological and medicinal applications.     

GXXXG‐Mediated Parallel and Antiparallel Dimerization of Transmembrane Helices and Its Inhibition by Cholesterol: Single‐Pair FRET and 2D IR Studies

Small‐residue‐mediated interhelical packings are ubiquitously found in helical membrane proteins, although their interaction dynamics and lipid dependence remain mostly uncharacterized. We used a single‐pair FRET technique to examine the effect of a GXXXG motif on the association of de novo designed (AALALAA)₃ helices in liposomes. Dimerization occurred with sub‐second lifetimes, which was abolished by cholesterol. Utilizing the nearly instantaneous time‐resolution of 2D IR spectroscopy, parallel and antiparallel helix associations were identified by vibrational couplings across helices at their interface. Taken together, the data illustrate that the GXXXG motif controls helix packing but still allows for a dynamic and lipid‐regulated oligomeric state.     

Compactization of rigid-chain amphiphilic macromolecules with local helical structure

Conformational characteristics of amphiphilic macromolecules with secondary local helical structuring are studied by the method of molecular dynamics for different properties of a helix (bending angles between neighboring vectors of the bond and internal rotation angle) and different rigidities of its fixation. Extended helices with high distances between helical turns and dense helices in which neighboring turns directly adjoin each other are studied. As the quality of a solvent deteriorates, extended helices experience a well-pronounced coil-globule transition, whose amplitude increases with an increase in chain rigidity, while the dimensions of dense helices gradually change. In a poor solvent, extended helices formed “collagen-like” structures, flexible chains of dense helices produce hairpin structures, and rigid macromolecules of dense helices form rodlike globules with an almost ideal local helical order. Independently of helix parameters, a deterioration in solvent quality leads to stabilization of the local secondary structure.     

Evolution of Helical Mesostructures

An intriguing evolution from a simple internal helix to a hierarchical helical (HH) mesostructure with both internal and external helices or a complicated screwlike and concentric circular (CC) mesostructure is successfully observed. The complicated helical structures are determined by TEM studies and 3D electron tomography. We demonstrate a topological helix–coil transition between the internal and external helices to reveal the origin of the HH mesostructure and the relationship between the straight helical and HH rods. Moreover, the boundary condition of the helix–coil transition is clarified to explain in detail the formation of complex helical structures, such as the screwlike mesostructure. It is proposed that the final structural characteristics are determined exactly by the balance between the decrease in the surface free energy and the maintenance of the hexagonal packing in one individual rod, which explains the formation of unusual CC, HH, and screwlike morphologies in one pot. Our success has opened new opportunities in the characterization of complex porous architectures, thus paving a way to remarkable advances in the fields of synthesis, understanding, and application of novel porous materials.     

Implementation and application of helix-helix distance and crossing angle restraint potentials

Based on the definition of helix-helix distance and crossing angle introduced by Chothia et al. (J Mol Biol 1981, 145, 215), we have developed the restraint potentials by which the distance and crossing angle of two selected helices can be maintained around target values during molecular dynamics simulations. A series of assessments show that calculated restraint forces are numerically accurate. Since the restraint forces are only exerted on atoms which define the helical principal axes, each helix can rotate along its helical axis, depending on the helix-helix intermolecular interactions. Such a restraint potential enables us to characterize the helix-helix interactions at atomic details by sampling their conformational space around specific distance and crossing angle with (restraint) force-dependent fluctuations. Its efficacy is illustrated by calculating the potential of mean force as a function of helix-helix distance between two transmembrane helical peptides in an implicit membrane model.     

Determining the orientation of uniaxially rotating membrane proteins using unoriented samples: a 2H, 13C, AND 15N solid-state NMR investigation of the dynamics and orientation of a transmembrane helical bundle

Membrane protein orientation has traditionally been determined by NMR using mechanically or magnetically aligned samples. Here we show a new NMR approach that abolishes the need for preparing macroscopically aligned membranes. When the protein undergoes fast uniaxial rotation around the bilayer normal, the 0 degrees -frequency of the motionally averaged powder spectrum is identical to the frequency of the aligned protein whose alignment axis is along the magnetic field. Thus, one can use unoriented membranes to determine the orientation of the protein relative to the bilayer normal. We demonstrate this approach on the M2 transmembrane peptide (M2TMP) of influenza A virus, which is known to assemble into a proton-conducting tetrameric helical bundle. The fast uniaxial rotational diffusion of the M2TMP helical bundle around the membrane normal is characterized via 2H quadrupolar couplings, C-H and N-H dipolar couplings, 13C chemical shift anisotropies, and 1H T1rho relaxation times. We then show that 15N chemical shift anisotropy and N-H dipolar coupling measured on these powder samples can be analyzed to yield precise tilt angles and rotation angles of the helices. The data show that the tilt angle of the M2TMP helices depends on the membrane thickness to reduce the hydrophobic mismatch. Moreover, the orientation of a longer M2 peptide containing both the transmembrane domain and cytoplasmic residues is similar to the orientation of the transmembrane domain alone, suggesting that the transmembrane domain regulates the orientation of this protein and that structural information obtained from M2TMP may be extrapolated to the longer peptide. This powder-NMR approach for orientation determination is generally applicable and can be extended to larger membrane proteins.     

Systematic Estimates for Possible Regular Helix Models of Heteropolymeric Glucans,Elsinan and Lichenan,Using N-H Mapping Method

Regular helical structures of polysaccharides are most conveniently described by a set of the helix parameters; n for the number of chemical repeating units per turn and h in Å for the rise per unit along the helix axis. A two dimensional mapping of n-h values for possible helix models along with the potential energy surfaces allows one to estimate conformational accessibility of a given posaccharide.^1-3 Recently, we have adopted the method to study an acidic heteropolysaccharide⁴ and a branching glucan.⁵ These polysaccharides involve two or three sets of backbone glycosidic linkages (Φ-Ψ), each of which varies independently, and, therefore, enormous multidimensional spaces must be explored. Their n-h maps were calculated based on the low energy Φ-Ψ values derived from MM3^6-8-generated, relaxed-residue potential energy maps^{9, 10} of the component disaccharides. The present assessment of helix models for the two heteropolymeric glucans is achieved by calculating n-h maps in a similar fashion. These glucans are the two poly(disaccharide)s, poly[(1→3)-α-D-maltotriose] (elsinan) and poly[(1→3)-β-D-cellotriose] (lichenan). In addition to single-stranded helices, three types of mutiple helices; double-parallel, and double-antiparallel, and triple helices have also been examined.     

Electron density redistribution accounts for half the cooperativity of alpha helix formation

The energy of alpha helix formation is well known to be highly cooperative, but the origin and relative importance of the contributions to helical cooperativity have been unclear. Here we separate the energy of helix formation into short range and long range components by using two series of helical dimers of variable length. In one dimer series two monomeric helices interact by forming hydrogen bonds, while in the other they are coupled only through long range, primarily electrostatic interactions. Using Density Functional Theory, we find that approximately half of the cooperativity of helix formation is due to electrostatic interactions between residues, while the other half is due to nonadditive many-body effects brought about by redistribution of electron density with helix length.     

Atomistic insights into rhodopsin activation from a dynamic model

Rhodopsin, the light sensitive receptor responsible for blue-green vision, serves as a prototypical G protein-coupled receptor (GPCR). Upon light absorption, it undergoes a series of conformational changes that lead to the active form, metarhodopsin II (META II), initiating a signaling cascade through binding to the G protein transducin (G(t)). Here, we first develop a structural model of META II by applying experimental distance restraints to the structure of lumi-rhodopsin (LUMI), an earlier intermediate. The restraints are imposed by using a combination of biased molecular dynamics simulations and perturbations to an elastic network model. We characterize the motions of the transmembrane helices in the LUMI-to-META II transition and the rearrangement of interhelical hydrogen bonds. We then simulate rhodopsin activation in a dynamic model to study the path leading from LUMI to our META II model for wild-type rhodopsin and a series of mutants. The simulations show a strong correlation between the transition dynamics and the pharmacological phenotypes of the mutants. These results help identify the molecular mechanisms of activation in both wild type and mutant rhodopsin. While static models can provide insights into the mechanisms of ligand recognition and predict ligand affinity, a dynamic model of activation could be applicable to study the pharmacology of other GPCRs and their ligands, offering a key to predictions of basal activity and ligand efficacy.     

Lipid-rhodopsin hydrophobic mismatch alters rhodopsin helical content

The ability of photoactivated rhodopsin to achieve the enzymatically active metarhodopsin II conformation is exquisitely sensitive to bilayer hydrophobic thickness. The sensitivity of rhodopsin to the lipid matrix has been explained by the hydrophobic matching theory, which predicts that lipid bilayers adjust elastically to the hydrophobic length of transmembrane helices. Here, we examined if bilayer thickness adjusts to the length of the protein or if the protein alters its conformation to adapt to the bilayer. Purified bovine rhodopsin was reconstituted into a series of mono-unsaturated phosphatidylcholines with 14-20 carbons per hydrocarbon chain. Changes of hydrocarbon chain length were measured by (2)H NMR, and protein helical content was quantified by synchrotron radiation circular dichroism and conventional circular dichroism. Experiments were conducted on dark-adapted rhodopsin, the photo-intermediates metarhodopsin I/II/III, and opsin. Changes of bilayer thickness upon rhodopsin incorporation and photoactivation were mostly absent. In contrast, the helical content of rhodopsin increased with membrane hydrophobic thickness. Helical content did not change measurably upon photoactivation. The increases of bilayer thickness and helicity of rhodopsin are accompanied by higher metarhodopsin II/metarhodopsin I ratios, faster rates of metarhodopsin II formation, an increase of tryptophan fluorescence, and higher temperatures of rhodopsin denaturation. The data suggest a surprising adaptability of this G protein-coupled membrane receptor to properties of the lipid matrix.     

Chalcogen-Bond-Induced Double Helix Based on Self-Assembly of a Small Planar Building Block

As a rule, helical structures at the molecular level are formed by non-planar units. This makes the design of helices, starting from planar building blocks via self-assembly, even more fascinating. Until now, however, this has only been achieved in rare cases, where hydrogen and halogen bonds were involved. Here, we show that the carbonyl-tellurium interaction motif is suitable to assemble even small planar units into helical structures in solid phase. We found two different types of helices: both single and double helices, depending on the substitution pattern. In the double helix, the strands are connected by additional Te⋅⋅⋅Te chalcogen bonds. In the case of the single helix, a spontaneous enantiomeric resolution occurs in the crystal. This underlines the potential of the carbonyl-tellurium chalcogen bond to generate complex three-dimensional patterns.     

Molecular weight recognition in the multiple-stranded helix of a synthetic polymer without specific monomer-monomer interaction

Stereoregular isotactic and syndiotactic poly(methyl methacrylate)s (it- and st-PMMAs) are known to form a multiple-stranded complementary helix, so-called stereocomplex (SC) through van der Waals interactions, which is a rare example of helical supramolecular structures formed by a commodity polymer. In this study, we prepared SCs by using uniform it- and st-PMMAs and those with a narrow molecular weight distribution having different molecular weights and investigated their structures in detail using high-resolution atomic force microscopy as a function of the molecular weight and molecular weight distribution of the component PMMAs. We found that complementary it- and st-PMMAs with the longer molecular length determine the total length of the SC, and molecules of the shorter component associate until they fill up or cover the longer component. These observations support a supramolecular triple-stranded helical structure of the SCs composed of a double-stranded helix of two intertwined it-PMMA chains included in a single helix of st-PMMA, and this triple-stranded helix model of the SCs appears to be applicable to the it- and st-PMMAs having a wide range of molecular weights we employed in this study. In homogeneous double-stranded helices of it-PMMA, it has been found that, in mixtures of two it-PMMAs with different molecular weights, chains of the same molecular weight selectively form a double-stranded it-PMMA helix, or recognize the molecular weights of each other ("molecular sorting"). We thus demonstrate that molecular weight recognition is possible, without any specific interaction between monomer units, through the formation of a topological multiple-stranded helical structure based upon van der Waals interaction.     

Heavy‐Atom Labeled Transmembrane β‐Peptides: Synthesis,CD‐Spectroscopy,and X‐ray Diffraction Studies in Model Lipid Multilayer

Transmembrane β‐peptides are promising candidates for the design of well‐controlled membrane anchors in lipid membranes. Here, we present the synthesis of transmembrane β‐peptides with and without tryptophan anchors, as well as a novel iodine‐labeled d ‐β³‐amino acid. By using one or more of the heavy‐atom labeled amino acids as markers, the orientation of the helical peptide was inferred based on the electron‐density profile determined by X‐ray reflectivity. The β‐peptides were synthesized through manual Fmoc‐based solid‐phase peptide synthesis (SPPS) and reconstituted in unilamellar vesicles forming a right‐handed 3₁₄‐helix secondary structure, as shown by circular dichroism spectroscopy. We then integrated the β‐peptide into solid‐supported membrane stacks and carried out X‐ray reflectivity and grazing incidence small‐angle X‐ray scattering to determine the β‐peptide orientation and its effect on the membrane bilayers. These β‐peptides adopt a well‐ordered transmembrane motif in the solid‐supported model membrane, maintaining the basic structure of the original bilayer with some distinct alterations. Notably, the helical tilt angle, which accommodates the positive hydrophobic mismatch, induces a tilt of the acyl chains. The tilted chains, in turn, lead to a membrane thinning effect.     

Ab initio computational modeling of long loops in G-protein coupled receptors

A newly developed approach for predicting the structure of segments that connect known elements of secondary structure in proteins has been applied to some of the longer loops in the G-protein coupled receptors (GPCRs) rhodopsin and the dopamine receptor D2R. The algorithm uses Monte Carlo (MC) simulation in a temperature annealing protocol combined with a scaled collective variables (SCV) technique to search conformation space for loop structures that could belong to the native ensemble. Except for rhodopsin, structural information is only available for the transmembrane helices (TMHs), and therefore the usual approach of finding a single conformation of lowest energy has to be abandoned. Instead the MC search aims to find the ensemble located at the absolute minimum free energy, i.e., the native ensemble. It is assumed that structures in the native ensemble can be found by an MC search starting from any conformation in the native funnel. The hypothesis is that native structures are trapped in this part of conformational space because of the high-energy barriers that surround the native funnel. In this work it is shown that the crystal structure of the second extracellular loop (e2) of rhodopsin is a member of this loop’s native ensemble. In contrast, the crystal structure of the third intracellular loop is quite different in the different crystal structures that have been reported. Our calculations indicate, that of three crystal structures examined, two show features characteristic of native ensembles while the other one does not. Finally the protocol is used to calculate the structure of the e2 loop in D2R. Here, the crystal structure is not known, but it is shown that several side chains that are involved in interaction with a class of substituted benzamides assume conformations that point into the active site. Thus, they are poised to interact with the incoming ligand.