Stanley J. Opella

Structure of the chemokine receptor CXCR1 in phospholipid bilayers

CXCR1 is one of two high-affinity receptors for the CXC chemokine interleukin-8 (IL-8), a major mediator of immune and inflammatory responses implicated in many disorders, including tumour growth. IL-8, released in response to inflammatory stimuli, binds to the extracellular side of CXCR1. The ligand-activated intracellular signalling pathways result in neutrophil migration to the site of inflammation. CXCR1 is a class A, rhodopsin-like G-protein-coupled receptor (GPCR), the largest class of integral membrane proteins responsible for cellular signal transduction and targeted as drug receptors. Despite its importance, the molecular mechanism of CXCR1 signal transduction is poorly understood owing to the limited structural information available. Recent structural determination of GPCRs has advanced by modifying the receptors with stabilizing mutations, insertion of the protein T4 lysozyme and truncations of their amino acid sequences, as well as addition of stabilizing antibodies and small molecules that facilitate crystallization in cubic phase monoolein mixtures. The intracellular loops of GPCRs are crucial for G-protein interactions, and activation of CXCR1 involves both amino-terminal residues and extracellular loops. Our previous nuclear magnetic resonance studies indicate that IL-8 binding to the N-terminal residues is mediated by the membrane, underscoring the importance of the phospholipid bilayer for physiological activity. Here we report the three-dimensional structure of human CXCR1 determined by NMR spectroscopy. The receptor is in liquid crystalline phospholipid bilayers, without modification of its amino acid sequence and under physiological conditions. Features important for intracellular G-protein activation and signal transduction are revealed. The structure of human CXCR1 in a lipid bilayer should help to facilitate the discovery of new compounds that interact with GPCRs and combat diseases such as breast cancer.

Structures of the M2 channel-lining segments from nicotinic acetylcholine and NMDA receptors by NMR spectroscopy

The structures of functional peptides corresponding to the predicted channel-lining M2 segments of the nicotinic acetylcholine receptor (AChR) and of a glutamate receptor of the NMDA subtype (NMDAR) were determined using solution NMR experiments on micelle samples, and solid-state NMR experiments on bilayer samples. Both M2 segments form straight transmembrane α-helices with no kinks. The AChR M2 peptide inserts in the lipid bilayer at an angle of 12° relative to the bilayer normal, with a rotation about the helix long axis such that the polar residues face the N-terminal side of the membrane, which is assigned to be intracellular. A model built from these solid-state NMR data, and assuming a symmetric pentameric arrangement of M2 helices, results in a funnel-like architecture for the channel, with the wide opening on the N-terminal intracellular side.

Two-dimensional 1H NMR experiments show that the 23-residue magainin antibiotic peptide is an alpha-helix in dodecylphosphocholine micelles, sodium dodecylsulfate micelles, and trifluoroethanol/water solution.

Magainin2 is a 23-residue antibiotic peptide that disrupts the ionic gradient across certain cellmembranes. Two-dimensional 1H NMR spectroscopy was used to investigate the structure ofthe peptide in three of the membrane environments most commonly employed in biophysicalstudies. Sequence-specific resonance assignments were determined for the peptide inperdeuterated dodecylphosphocholine (DPC) and sodium dodecylsulfate micelles andconfirmed for the peptide in 2,2,2-trifluoroethanol solution. The secondary structure is shownto be helical in all of the solvent systems. The NMR data were used as a set of restraints fora simulated annealing protocol that generated a family of three-dimensional structures of thepeptide in DPC micelles, which superimposed best between residues 4 and 20. For theseresidues, the mean pairwise rms difference for the backbone atoms is 0.47 ± 0.10Å from the average structure. The calculated peptide structures appear to be curved,with the bend centered at residues Phe12 and Gly13.

Molecular and structural information from 14N–13C dipolar couplings manifested in high resolution 13C NMR spectra of solids

The dipolar coupling between 14N and 13C is not suppressed by magic angle sample spinning because the relatively large 14N quadrupole interaction shifts the axis of quantization of the 14N spins away from the direction of the applied field. The resulting 13C resonance line shapes are influenced by the sign, magnitude, and asymmetry parameter of the 14N quadrupole coupling tensor; the internuclear distance; the magnitude of the applied magnetic field; and the orientation of the internuclear vector in the principal axis system of the electric field gradient. It is demonstrated that one or more of these parameters can be determined from the 13C NMR data if the others are known by virtue of single crystal studies or molecular symmetry.

Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints

A solid‐state NMR approach for simultaneous resonance assignment and three‐dimensional structure determination of a membrane protein in lipid bilayers is described. The approach is based on the scattering, hence the descriptor “shotgun,” of 15N‐labeled amino acids throughout the protein sequence (and the resulting NMR spectra). The samples are obtained by protein expression in bacteria grown on media in which one type of amino acid is labeled and the others are not. Shotgun NMR short‐circuits the laborious and time‐consuming process of obtaining complete sequential assignments prior to the calculation of a protein structure from the NMR data by taking advantage of the orientational information inherent to the spectra of aligned proteins. As a result, it is possible to simultaneously assign resonances and measure orientational restraints for structure determination. A total of five two‐dimensional 1H/15N PISEMA (polarization inversion spin exchange at the magic angle) spectra, from one uniformly and four selectively 15N‐labeled samples, were sufficient to determine the structure of the membrane‐bound form of the 50‐residue major pVIII coat protein of fd filamentous bacteriophage. Pisa (polarity index slat angle) wheels are an essential element in the process, which starts with the simultaneous assignment of resonances and the assembly of isolated polypeptide segments, and culminates in the complete three‐dimensional structure of the protein with atomic resolution. The principles are also applicable to weakly aligned proteins studied by solution NMR spectroscopy.

Solid-state NMR structural studies of peptides and proteins in membranes

Abstract Solid-state NMR spectroscopy is emerging as a new approach in the structural investigations of peptides and proteins in membrane bilayers. Orientational parameters obtained from samples aligned on glass plates have been used to determine their secondary structures and orientations in the bilayer. They have also been used in the determination of the high resolution structure of gramicidin. Additional structural information, distance measurements between pairs of different nuclei and between pairs of like nuclei has been obtained on peptides in bilayers using magic angle spinning methods.

Protein structure by solid-state NMR spectroscopy.

The three-dimensional structures of proteins are among the most valuable contributions of biophysics to the understanding of biological systems (Dickerson & Geis, 1969; Creighton, 1983). Protein structures are utilized in the description and interpretation of a wide variety of biological phenomena, including genetic regulation, enzyme mechanisms, antibody recognition, cellular energetics, and macroscopic mechanical and structural properties of molecular assemblies. Virtually all of the information currently available about the structures of proteins at atomic resolution has been obtained from diffraction studies of single crystals of proteins (Wyckoff et al , 1985). However, recently developed NMR methods are capable of determining the structures of proteins and are now being applied to a variety of systems, including proteins in solution and other non-crystalline environments that are not amenable for X-ray diffraction studies. Solid-state NMR methods are useful for proteins that undergo limited overall reorientation by virtue of their being in the crystalline solid state or integral parts of supramolecular structures that do not reorient rapidly in solution. For reviews of applications of solid-state NMR spectroscopy to biological systems see Torchia and VanderHart (1979), Griffin (1981), Oldfield et al . (1982), Opella (1982), Torchia (1982), Gauesh (1984), Torchia (1984) and Opella (1986). This review describes how solid-state NMR can be used to obtain structural information about proteins. Methods applicable to samples with macroscopic orientation are emphasized.

Orientations of amphipathic helical peptides in membrane bilayers determined by solid-state NMR spectroscopy

SummarySolid-state NMR spectroscopy was used to determine the orientations of two amphipathic helical peptides associated with lipid bilayers. A single spectral parameter provides sufficient orientational information for these peptides, which are known, from other methods, to be helical. The orientations of the peptides were determined using the15N chemical shift observed for specifically labeled peptide sites. Magainin, an antibiotic peptide from frog skin, was found to lie in the plane of the bilayer. M2δ, a helical segment of the nicotinic acetylcholine receptor, was found to span the membrane, perpendicular to the plane of the bilayer. These findings have important implications for the mechanisms of biological functions of these peptides.

Two‐dimensional 13C NMR of highly oriented polyethylene

The two‐dimensional NMR procedure of separated local field spectroscopy [J. S. Waugh, Proc. Natl. Acad. Sci. USA 73, 1394 (1976)] is applied to fibers of highly oriented polyethylene. The 1H decoupled 13C chemical shift spectrum of the fiber oriented parallel to the external magnetic field is a single line, while a distinctive powder pattern results from the perpendicular orientation that is in excellent agreement with calculations. The 13C–1H dipolar splitting is 45 kHz at σ33 and nonexistent at σ22 consistent with perfectly aligned methylene groups with C–H bond length of 1.10 a.u. The splitting at σ11 is somewhat reduced from the predicted value; this finding, along with the temperature invariance of parameters, is discussed in terms of the molecular disorder and motion of the polymer.

NMR Structural Studies of Membrane Proteins

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