Rapid Determination of the Topology of Oligomeric α-Helical Membrane Proteins by Water- and Lipid-Edited Methyl NMR

Solid-State NMR of Virus Membrane Proteins

Enveloped viruses encode ion-conducting pores that permeabilize the host cell membranes and mediate the budding of new viruses. These viroporins are some of the essential membrane proteins of viruses, and have high sequence conservation, making them important targets of antiviral drugs. High-resolution structures of viroporins are challenging to determine by X-ray crystallography and cryoelectron microscopy, because these proteins are small, hydrophobic, and prone to induce membrane curvature. Solid-state NMR (ssNMR) spectroscopy is an ideal method for elucidating the structure, dynamics, and mechanism of action of viroporins in phospholipid membranes. This Account describes our investigations of influenza M2 proteins and the SARS-CoV-2 E protein using solid-state NMR.M2 proteins form acid-activated tetrameric proton channels that initiate influenza uncoating in the cell. 15N and 13C exchange NMR revealed that M2 shuttles protons into the virion using a crucial histidine, whose imidazole nitrogens pick up and release protons on the microsecond time scale at acidic pH. This proton exchange is synchronized with and facilitated by imidazole reorientation, which is observed in NMR spectra. Quantitative 15N NMR spectra yielded the populations of neutral and cationic histidines as a function of pH, giving four proton dissociation constants (pKa's). The pKa's of influenza AM2 indicate that the +3 charged channel has the highest time-averaged single-channel conductance; thus the third protonation event defines channel activation. In comparison, influenza BM2 exhibits lower pKa's due to a second, peripheral histidine, which accelerates proton dissociation from the central proton-selective histidine. Amantadine binding to AM2 suppressed proton exchange and imidazole reorientation, indicating that this antiviral drug acts by inhibiting proton shuttling. Solid-state NMR 13C-2H distance measurements revealed that amantadine binds the N-terminal pore of the channel near a crucial Ser31, whose mutation to asparagine causes amantadine resistance in circulating influenza A viruses. A second binding site, on the lipid-facing surface of the protein, only occurs when amantadine is in large excess in lipid bilayers. M2 not only functions as a proton channel but also conducts membrane scission during influenza budding in a cholesterol-dependent manner. Solid-state NMR distance experiments revealed that two cholesterol molecules bind asymmetrically to the surface of the tetrameric channel, thus recruiting the protein to the cholesterol-rich budding region of the cell membrane to cause membrane scission.To accelerate full structure determination of viroporins, we developed a suite of 19F solid-state NMR techniques that measure interatomic distances to 1-2 nm. Using this approach, we determined the atomic structures of influenza BM2, SARS-CoV-2 E, and EmrE, a multidrug-resistance bacterial transporter. pH-induced structural changes of these proteins gave detailed insights into the activation mechanisms of BM2 and E and the proton-coupled substrate transport mechanism of EmrE. The SARS-CoV-2 E protein forms pentameric helical bundles whose structures are distinct between the closed state at neutral pH and the open state at acidic pH. These 19F-enabled distance NMR experiments are also instrumental for identifying the binding mode and binding site of hexamethylene amiloride in E, paving the way for developing new antiviral drugs that target these pathogenic virus ion channels.

Polar Networks Mediate Ion Conduction of the SARS-CoV-2 Envelope Protein

The SARS-CoV-2 E protein conducts cations across the cell membrane to cause pathogenicity to infected cells. The high-resolution structures of the E transmembrane domain (ETM) in the closed state at neutral pH and in the open state at acidic pH have been determined. However, the ion conduction mechanism remains elusive. Here, we use solid-state NMR spectroscopy to investigate the side chain structure, dynamics, and interactions of five polar residues at the N-terminal entrance of the channel and three polar residues at the C-terminal end. The chemical shifts of the N-terminal Glu8 reveal that the Glu side chain interacts with protons, Ca2+ and two neighboring Thr residues, and adopts distinct motionally averaged conformational ensembles. These polar interactions are sensitive to the presence of negatively charged lipids in the membrane. A T9I mutation, prevalent in the Omicron variants of SARS-CoV-2 E, perturbs these interactions and partially immobilizes the N-terminal segment. Deeper into the channel, two polar residues, Asn15 and Ser16, form interhelical hydrogen bonds in the closed state but become separated by water molecules in the open state. This is manifested by Asn15-Ser16 correlation signals at neutral pH and the loss of these correlations and the appearance of water cross peaks with Ser16 at acidic pH in the presence of Ca2+. Finally, the guanidinium side chain of the C-terminal Arg38 undergoes fast reorientations in the closed state but becomes more restricted in the open state. These results provide evidence for a dynamic and hydrogen-bonded N-terminal polar network that recruits and relays protons and Ca2+ in a lipid-dependent manner. Once inside, the ions permeate past the hydrophobic middle of the transmembrane domain with the help of enhanced hydrophilicity of the C-terminal channel lumen due to the insertion of the Arg38 side chain into the pore.

Selective Methods Promote Protein Solid-State NMR

Solid-state nuclear magnetic resonance (ssNMR) is indispensable for studying the structures, dynamics, and interactions of insoluble proteins in native or native-like environments. While ssNMR includes numerous nonselective techniques for general analysis, it also provides various selective methods that allow for the extraction of precise details about proteins. This perspective highlights three key aspects of selective methods: selective signals of protein segments, selective recoupling, and site-specific insights into proteins. These methods leverage protein topology, labeling strategies, and the tailored manipulation of spin interactions through radio frequency (RF) pulses, significantly promoting the field of protein ssNMR. With ongoing advancements in higher magnetic fields and faster magic angle spinning (MAS), there remains an ongoing need to enhance the selectivity and efficiency of selective ssNMR methods, facilitating deeper atomic-level insights into complex biological systems.

Oligomeric State and Drug Binding of the SARS-CoV-2 Envelope Protein Are Sensitive to the Ectodomain

The envelope (E) protein of SARS-CoV-2 is the smallest of the three structural membrane proteins of the virus. E mediates budding of the progeny virus in the endoplasmic reticulum Golgi intermediate compartment of the cell. It also conducts ions, and this channel activity is associated with the pathogenicity of SARS-CoV-2. The structural basis for these functions is still poorly understood. Biochemical studies of E in detergent micelles found a variety of oligomeric states, but recent 19F solid-state NMR data indicated that the transmembrane domain (ETM, residues 8-38) forms pentamers in lipid bilayers. Hexamethylene amiloride (HMA), an E inhibitor, binds the pentameric ETM at the lipid-exposed helix-helix interface. Here, we investigate the oligomeric structure and drug interaction of an ectodomain-containing E construct, ENTM (residues 1-41). Unexpectedly, 19F spin diffusion NMR data reveal that ENTM adopts an average oligomeric state of dimers instead of pentamers in lipid bilayers. A new amiloride inhibitor, AV-352, shows stronger inhibitory activity than HMA in virus-like particle assays. Distance measurements between 13C-labeled protein and a trifluoromethyl group of AV-352 indicate that the drug binds ENTM with a higher stoichiometry than ETM. We measured protein-drug contacts using a sensitivity-enhanced two-dimensional 13C-19F distance NMR technique. The results indicate that AV-352 binds the C-terminal half of the TM domain, similar to the binding region of HMA. These data provide evidence for the existence of multiple oligomeric states of E in lipid bilayers, which may carry out distinct functions and may be differentially targeted by antiviral drugs.

The plant rhabdovirus viroporin P9 facilitates insect-mediated virus transmission in barley

Potassium (K+) plays crucial roles in both plant development and immunity. However, the function of K+ in plant-virus interactions remains largely unknown. Here, we utilized Barley yellow striate mosaic virus (BYSMV), an insect-transmitted plant cytorhabdovirus, to investigate the interplay between viral infection and plant K+ homeostasis. The BYSMV accessory P9 protein exhibits viroporin activity by enhancing membrane permeability in Escherichia coli. Additionally, P9 increases K+ uptake in yeast (Saccharomyces cerevisiae) cells, which is disrupted by a point mutation of glycine 14 to threonine (P9G14T). Furthermore, BYSMV P9 forms oligomers and targets to both the viral envelope and the plant membrane. Based on the recombinant BYSMV-GFP (BYGFP) virus, a P9-deleted mutant (BYGFPΔP9) was rescued and demonstrated infectivity within individual plant cells of Nicotiana benthamiana and insect vectors. However, BYGFPΔP9 failed to infect barley plants after transmission by insect vectors. Furthermore, infection of barley plants was severely impaired for BYGFP-P9G14T lacking P9 K+ channel activity. In vitro assays demonstrate that K+ facilitates virion disassembly and the release of genome RNA for viral mRNA transcription. Altogether, our results show that the K+ channel activity of viroporins is conserved in plant cytorhabdoviruses and plays crucial roles in insect-mediated virus transmission.

Transmembrane conformation of the envelope protein of an alpha coronavirus, NL63

The envelope (E) proteins of coronaviruses (CoVs) form cation-conducting channels that are associated with the pathogenicity of these viruses. To date, high-resolution structural information about these viroporins is limited to the SARS-CoV E protein. To broaden our structural knowledge of other members of this family of viroporins, we now investigate the conformation of the E protein of the human coronavirus (hCoV), NL63. Using two- and three-dimensional magic-angle-spinning NMR, we have measured 13 C and 15 N chemical shifts of the transmembrane domain of E (ETM), which yielded backbone (ϕ, ψ) torsion angles. We further measured the water accessibility of NL63 ETM at neutral pH versus acidic pH in the presence of Ca2+ ions. These data show that NL63 ETM adopts a regular α-helical conformation that is unaffected by pH and the N-terminal ectodomain. Interestingly, the water accessibility of NL63 ETM increases only modestly at acidic pH in the presence of Ca2+ compared to neutral pH, in contrast to SARS ETM, which becomes much more hydrated at acidic pH. This difference suggests a structural basis for the weaker channel conductance of α-CoV compared to β-CoV E proteins. The weaker E channel activity may in turn contribute to the reduced virulence of hCoV-NL63 compared to SARS-CoV viruses.