Influenza M2 Proton Research Articles

A Scalable Synthesis of the Blue Fluorescent Amino Acid 4-Cyanotryptophan and the Fmoc Derivative: Utility Demonstrated with the Influenza M2 Peptide Tetramer.

A scalable synthesis of the Fmoc-protected blue fluorescent amino acid, l-4-cyanotryptophan (W4CN), that exploits an enantioselective phase transfer-catalyzed alkylation is reported. The red-shifted emission of water-exposed W4CN residues was leveraged to investigate the solvation state of tryptophan (Trp) residues within the influenza M2 proton channel. The correlation of the channel's conformation (i.e., open or closed) with the fluorescence spectrum of a mutated W4CN residue suggests that the channel's conformational state does not impact the hydration status of the Trp residues.

Protein structural defects enable pharmaceutical targeting while functionalizing the M2 proton channel

The influenza M2 (22–46) proton channel is therapeutically targetable and a prototype for proton transport across membranes. Conduction initiation, requiring a hydronium formed with exceptionally high pKa, remains nebulous. We tackle the problem by focusing on the dynamic interplay between protein structure and solvent interface. We identify two packing defects in the protein subunits that predict exactly the low and high-affinity drug-binding sites. The latter defect frustrates water coordination, enhancing water basicity and stabilizing the nearby hydronium that forms upon proton penetration in the channel. Thus, the trigger of proton conduction is directly related to the high-affinity binding site. The findings, in quantitative agreement with affinity measurements, are consistent with the targetable functional nature of protein packing defects. These findings enable the design of proton-conducting biomimetic materials, where the epistructure may be engineered to tune the basicity of interfacial water.

Random Mutagenesis Analysis of the Influenza A M2 Proton Channel Reveals Novel Resistance Mutants

The influenza M2 proton channel is a major drug target, but unfortunately, the acquisition of resistance mutations greatly reduces the functional life span of a drug in influenza treatment. New M2 inhibitors that inhibit mutant M2 channels otherwise resistant to the early adamantine-based drugs have been reported, but it remains unclear whether and how easy resistance could arise to such inhibitors. We have combined a newly developed proton conduction assay with an established method for selection and screening, both Escherichia coli-based, to enable the study of M2 function and inhibition. Combining this platform with two groups of structurally different M2 inhibitors allowed us to isolate drug resistant M2 channels from a mutant library. Two groups of M2 variants emerged from this analysis. A first group appeared almost unaffected by the inhibitor, M_089 (N13I, I35L, and F47L) and M_272 (G16C and D44H), and the single-substitution variants derived from these (I35L, L43P, D44H, and L46P). Functionally, these resemble the known drug resistant M2 channels V27A, S31N, and swine flu. In addition, a second group of tested M2 variants were all still inhibited by drugs but to a lesser extent than wild type M2. Molecular dynamics simulations aided in distinguishing the two groups where drug binding to the wild type and the less resistant M2 group showed a stable positioning of the ligand in the canonical binding pose, as opposed to the drug resistant group in which the ligand rapidly dissociated from the complex during the simulations.

Structural characterization of adamantane-resistant mutants of the influenza M2 proton channel

Structural characterization of adamantane-resistant mutants of the influenza M2 proton channel

Interplay between membrane curvature and protein conformational equilibrium investigated by solid-state NMR

Many membrane proteins sense and induce membrane curvature for function, but structural information about how proteins modulate their structures to cause membrane curvature is sparse. We review our recent solid-state NMR studies of two virus membrane proteins whose conformational equilibrium is tightly coupled to membrane curvature. The influenza M2 proton channel has a drug-binding site in the transmembrane (TM) pore. Previous chemical shift data indicated that this pore-binding site is lost in an M2 construct that contains the TM domain and a curvature-inducing amphipathic helix. We have now obtained chemical shift perturbation, protein-drug proximity, and drug orientation data that indicate that the pore-binding site is restored when the full cytoplasmic domain is present. This finding indicates that the curvature-inducing amphipathic helix distorts the TM structure to interfere with drug binding, while the cytoplasmic tail attenuates this effect. In the second example, we review our studies of a parainfluenza virus fusion protein that merges the cell membrane and the virus envelope during virus entry. Chemical shifts of two hydrophobic domains of the protein indicate that both domains have membrane-dependent backbone conformations, with the β-strand structure dominating in negative-curvature phosphatidylethanolamine (PE) membranes. 31P NMR spectra and 1H-31P correlation spectra indicate that the β-strand-rich conformation induces saddle-splay curvature to PE membranes and dehydrates them, thus stabilizing the hemifusion state. These results highlight the indispensable role of solid-state NMR to simultaneously determine membrane protein structures and characterize the membrane curvature in which these protein structures exist.

XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction

The M2 proton channel of influenza A is a drug target that is essential for the reproduction of the flu virus. It is also a model system for the study of selective, unidirectional proton transport across a membrane. Ordered water molecules arranged in "wires" inside the channel pore have been proposed to play a role in both the conduction of protons to the four gating His37 residues and the stabilization of multiple positive charges within the channel. To visualize the solvent in the pore of the channel at room temperature while minimizing the effects of radiation damage, data were collected to a resolution of 1.4 Å using an X-ray free-electron laser (XFEL) at three different pH conditions: pH 5.5, pH 6.5, and pH 8.0. Data were collected on the Inwardopen state, which is an intermediate that accumulates at high protonation of the His37 tetrad. At pH 5.5, a continuous hydrogen-bonded network of water molecules spans the vertical length of the channel, consistent with a Grotthuss mechanism model for proton transport to the His37 tetrad. This ordered solvent at pH 5.5 could act to stabilize the positive charges that build up on the gating His37 tetrad during the proton conduction cycle. The number of ordered pore waters decreases at pH 6.5 and 8.0, where the Inwardopen state is less stable. These studies provide a graphical view of the response of water to a change in charge within a restricted channel environment.

XFEL structures of the influenza M2 proton channel at 1.4 Å: room-temperature water networks and insights into proton conduction

XFEL structures of the influenza M2 proton channel at 1.4 Å: room-temperature water networks and insights into proton conduction

Structural Basis for Asymmetric Conductance of the Influenza M2 Proton Channel Investigated by Solid-State NMR Spectroscopy

The influenza M2 protein forms an acid-activated proton channel that is essential for virus replication. The transmembrane H37 selects for protons under low external pH while W41 ensures proton conduction only from the N terminus to the C terminus and prevents reverse current under low internal pH. Here, we address the molecular basis for this asymmetric conduction by investigating the structure and dynamics of a mutant channel, W41F, which permits reverse current under low internal pH. Solid-state NMR experiments show that W41F M2 retains the pH-dependent α-helical conformations and tetrameric structure of the wild-type (WT) channel but has significantly altered protonation and tautomeric equilibria at H37. At high pH, the H37 structure is shifted toward the π tautomer and less cationic tetrads, consistent with faster forward deprotonation to the C terminus. At low pH, the mutant channel contains more cationic tetrads than the WT channel, consistent with faster reverse protonation from the C terminus. 15N NMR spectra allow the extraction of four H37 pKas and show that the pKas are more clustered in the mutant channel compared to WT M2. Moreover, binding of the antiviral drug, amantadine, at the N-terminal pore at low pH did not convert all histidines to the neutral state, as seen in WT M2, but left half of all histidines cationic, unambiguously demonstrating C-terminal protonation of H37 in the mutant. These results indicate that asymmetric conduction in WT M2 is due to W41 inhibition of C-terminal acid activation by H37. When Trp is replaced by Phe, protons can be transferred to H37 bidirectionally with distinct rate constants.

Drug-Induced Conformational and Dynamical Changes of the S31N Mutant of the Influenza M2 Proton Channel Investigated by Solid-State NMR

The M2 protein of influenza A viruses forms a tetrameric proton channel that is targeted by the amantadine class of antiviral drugs. A S31N mutation in the transmembrane (TM) domain of the protein has caused widespread amantadine resistance in most of the currently circulating flu viruses. Recently, a new family of compounds based on amantadine- and aryl-substituted isoxazole were discovered to inhibit the S31N channel activity and reduce replication of S31N-harboring viruses. We now use solid-state NMR spectroscopy to investigate the effects of one of these isoxazole compounds, WJ352, on the conformation of the S31N TM segment and the dynamics of the proton-selective residue, His37. Chemical shift perturbations show that WJ352 changes the conformational equilibrium of multiple TM residues, with the maximal perturbation occurring at the crucial Asn31. (13)C-(2)H distance measurements and (1)H-(1)H NOE cross peaks indicate that the adamantane moiety of the drug is bound in the spacious pore between Asn31 and Gly34 while the phenyl tail is located near Val27. Thus, the polar amine points to the channel exterior rather than to His37, in contrast to amantadine and rimantadine in the wild-type channel, suggesting that the drug is significantly stabilized by hydrophobic interactions between the adamantane and the TM peptide. (15)N and (13)C chemical shifts indicate that at low pH, His37 undergoes fast exchange among the τ tautomer, the π tautomer, and the cationic state due to proton transfer with water. The exchange rate is higher than the wild-type channel, consistent with the larger single-channel conductance of the mutant. Drug binding at acidic pH largely suppresses this exchange, reverting the histidines to a similar charge distribution as that of the high-pH closed state.

From the Micelle to the Membrane: Molecular Dynamics Simulations of Solution NMR Structures of Membrane Proteins

The physiological environment of membrane proteins is a complex membrane yet structural studies by necessity are largely based on solubilisation in detergent micelles or model lipid bilayers and bicelles. The choice of solubilising environment has been shown to have some impact on the conformation of membrane proteins; understanding the basis of these changes is critical in linking experimental structures to the conformations expected in native environments.Here we use a combination of coarse-grained (CG) and atomistic (AT) molecular dynamics (MD) simulations to probe the effects of experimental conditions on structure, with particular emphasis on the solution NMR structures of alpha helical membrane proteins including the influenza M2 proton channel and a mitochondrial carrier protein.We show that this multiscale simulation approach may be used to improve the packing of solution NMR structures in a lipid bilayer environment. This technique is also used to probe the roles of specific native lipids (e.g. cardiolipin) on membrane protein structure and dynamics.

Hydrogen-bonding partner of the proton-conducting histidine in the influenza M2 proton channel revealed from 1H chemical shifts.

The influenza M2 protein conducts protons through a critical histidine (His) residue, His37. Whether His37 only interacts with water to relay protons into the virion or whether a low-barrier hydrogen bond (LBHB) also exists between the histidines to stabilize charges before proton conduction is actively debated. To address this question, we have measured the imidazole (1)H(N) chemical shifts of His37 at different temperatures and pH using 2D (15)N-(1)H correlation solid-state NMR. At low temperature, the H(N) chemical shifts are 8-15 ppm at all pH values, indicating that the His37 side chain forms conventional hydrogen bonds (H-bonds) instead of LBHBs. At ambient temperature, the dynamically averaged H(N) chemical shifts are 4.8 ppm, indicating that the H-bonding partner of the imidazole is water instead of another histidine in the tetrameric channel. These data show that His37 forms H-bonds only to water, with regular strength, thus supporting the His-water proton exchange model and ruling out the low-barrier H-bonded dimer model.

Paramagnetic Cu(II) for Probing Membrane Protein Structure and Function: Inhibition Mechanism of the Influenza M2 Proton Channel

Paramagnetic Cu(II) ions enhance nuclear spin relaxation in a distance-dependent fashion and can be used as a structural probe of proteins. Cu(II) can also serve as a functionally important ligand in proteins. Here we investigate the structural basis of Cu(II) inhibition of the influenza M2 proton channel through Cu(II)-induced paramagnetic relaxation enhancement (PRE). (13)C T(1) relaxation rates of the central residues of the transmembrane (TM) domain of M2 are significantly enhanced by Cu(II), and pronounced spectral broadening is observed for the proton-selective residue, His37. These data yielded quantitative distances of (13)C spins to the Cu(II) center and identified the Cu(II) binding site to be Nε2 of His37. This binding site is surrounded by four imidazole rings from the top and four indole rings of Trp41 from the bottom, thus explaining the high affinity of Cu(II) binding. Bound at this location, Cu(II) can inhibit proton currents by perturbing histidine-water proton exchange, preventing histidine conformational dynamics, and interfering with His-Trp cation-π interaction. The Cu(II) binding site is distinct from the binding site of the hydrophobic drug amantadine, which is about 10 Å N-terminal to His37. Consistently, Cu(II) and amantadine induce distinct conformational changes at several key residues, suggesting the possibility of designing new drugs that target the His37 site to inhibit amantadine-resistant mutant M2 proteins. In addition to the high-affinity His37 binding site, we also examined the weaker and nonspecific binding of Cu(II) to membrane-surface lipid phosphates and the extent of the resulting PRE to surface-proximal protein residues. This study demonstrates the feasibility of NMR studies of paramagnetic-ion-complexed membrane proteins, where the ion serves as both a functional ligand and a distance probe.

Structural Investigation of Rimantadine Inhibition of the AM2-BM2 Chimera Channel of Influenza Viruses

The M2 channel of influenza A is a target of the adamantane family antiviral drugs. Two different drug-binding sites have been reported: one inside the pore, and the other is a lipid-facing pocket. A previous study showed that a chimera of M2 variants from influenza A and B that contains only the pore-binding site is sensitive to amantadine inhibition, suggesting that the primary site of inhibition is inside the pore. To obtain atomic details of channel-drug interaction, we determined the structures of the chimeric channel with and without rimantadine. Inside the channel and near the N-terminal end, methyl groups of Val27 and Ala30 from four subunits form a hydrophobic pocket around the adamantane, and the drug amino group appears to be in polar contact with the backbone oxygen of Ala30. The structures also reveal differences between the drug-bound and -unbound states of the channel that can explain drug resistance.

Inhibition of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) by Influenza M2 Proton Channel

Lung ion channels are essential for keeping the lung clear of inhaled particles and pathogens by regulation of airway surface liquid. Influenza M2 protein forms a pH activated, homotetramer proton channel that inhibits the expression and the activity of the amiloride sensitive sodium channel (ENaC) (Lazrak et al. 2009 FASEB J. 2009 Nov;23(11):3829–42). In order to determine the effect of Influenza M2 on fluid regulation it is necessary to understand how it affects other important ion channels. CFTR is an ABC ion transporter that regulates fluid balance in the lung as well as performing many other vital functions. Xenopus oocytes were co-injected with human CFTR (0.25–0.5ng) and Udorn strain M2 (25ng) cRNAs and allowed to express for 72 hours. Whole cell currents were recorded using the two electrode voltage clamp technique. Forskolin activated current was inhibited with GlyH-101 while M2 current was inhibited with Amantadine. Protein concentration was measured via Western Blot. Co-expression of Influenza M2 and CFTR decreased CFTR current and protein expression. Inhibition was seen at 24 hours post M2 injection and continued at least to 72 hours. The decrease was not caused by translational competition as co-expression of CFTR with Influenza M1 protein had no effect. Suppression was independent of ion channel activity as an inactive mutant (M2-G34V) also decreased CFTR current. Funding provided by NIHR01-HL031197

Identification of a novel interaction between the M2 proton channel of influenza A virus and cyclin D3: consequences for cell cycle progression

To define cellular factors involved in the life cycle of influenza virus, we have used a genome-wide yeast-two-hybrid screening approach. Interestingly, we have identified a novel interaction between the 54 amino-acid cytosolic tail of influenza A virus M2 proton channel protein and the cyclin D3 cellular protein, a key regulator of the cell cycle G1-S transition. Very little is known about crosstalks between influenza A virus and the cellular machineries that regulate the cell cycle. We confirmed the physical interaction between M2 and Cyclin D3, by co-immunoprecipitation studies in human epithelial cells. We then conducted immunofluorescence assays to analyze the relative distribution of cyclin D3 and M2 in infected A549 lung epithelial cells. Interestingly, we observed that cyclin D3 is relocated to or retained at the Golgi apparatus, where M2 is concentrated, at 5 hours post infection. In contrast, cyclin D3 was mainly present in the nucleus, with occasional localization in the cytoplasm, in non-infected cells. More importantly, at 10 hours post infection cyclin D3 was detected in the cytoplasm and at 24 hours post infection expression levels were much reduced. To further study the consequences of influenza virus infection on cyclin D3 expression levels, we infected A549 cells for increasing time points and MOI and analyzed protein levels by western blotting. We found that level of expressed cyclin D3 is decreased upon infection and that this effect is dependent on both time of infection and MOI used. Those data suggest that cyclin D3 is either degraded or its expression down regulated upon influenza virus infection. Interestingly, protein levels of downstream effectors, namely cyclin dependent kinases CDK4 and 6, retinoblastoma protein RB, and cyclin E and A, were also diminished upon infection. By contrast, levels of the CDK inhibitors P15 and P16, which are upstream regulators of the G1-S transition, were unchanged. Together, our data strongly suggest that influenza virus infection alters normal cell cycle progression by interfering with expression levels of cell cycle regulators. Most likely, the newly identified interaction between influenza M2 proton channel and cyclin D3 is involved in this process. We will further investigate the effects of infection on the cell cycle progression by flow cytometry and decipher the molecular mechanism responsible for the down-regulation of cell cycle regulators in influenza infected cells. We will determine whether alteration of cell cycle progression is a strategy used by influenza virus to better replicate in host cells.

Mechanisms of proton conduction and gating in influenza M2 proton channels from solid-state NMR.

The M2 protein of influenza viruses forms an acid-activated tetrameric proton channel. We used solid-state nuclear magnetic resonance spectroscopy to determine the structure and functional dynamics of the pH-sensing and proton-selective histidine-37 in M2 bound to a cholesterol-containing virus-envelope-mimetic membrane so as to better understand the proton conduction mechanism. In the high-pH closed state, the four histidines form an edge-face π-stacked structure, preventing the formation of a hydrogen-bonded water chain to conduct protons. In the low-pH conducting state, the imidazoliums hydrogen-bond extensively with water and undergo microsecond ring reorientations with an energy barrier greater than 59 kilojoules per mole. This barrier is consistent with the temperature dependence of proton conductivity, suggesting that histidine-37 dynamically shuttles protons into the virion. We propose a proton conduction mechanism in which ring-flip-assisted imidazole deprotonation is the rate-limiting step.

Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers.

The M2 protein of influenza A virus is a membrane-spanning tetrameric proton channel targeted by the antiviral drugs amantadine and rimantadine 1. Resistance to these drugs has compromised their effectiveness against many influenza strains, including pandemic H1N1. A recent crystal structure of M2(22-46) showed electron densities attributed to a single amantadine in the N-terminal half of the pore 2, suggesting a physical occlusion mechanism for inhibition. However, a solution NMR structure of M2(18-60) showed four rimantadines bound to the C-terminal lipid-facing surface of the helices 3, suggesting an allosteric mechanism. Here we show by solid-state NMR spectroscopy that two amantadine-binding sites exist in M2 in phospholipid bilayers. The high-affinity site, occupied by a single amantadine, is located in the N-terminal channel lumen, surrounded by residues mutated in amantadine-resistant viruses. Quantification of the protein – amantadine distances resulted in a 0.3 Å-resolution structure of the high-affinity binding site. The second, low-affinity, site was observed on the C-terminal protein surface, but only when the drug reaches high concentrations in the bilayer. The orientation and dynamics of the drug are distinct in the two sites, as shown by 2H NMR. These results indicate that amantadine physically occludes the M2 channel, thus paving the way for developing new antiviral drugs against influenza viruses. The study demonstrates the ability of solid-state NMR to elucidate small-molecule interactions with membrane proteins and determine high-resolution structures of their complexes.

Site‒specific IR spectroscopy and molecular modelling combined towards solving transmembrane protein structure

Membrane protein structures are underrepresented in structural databases despite their abundance and biomedical importance. This review focuses on the novel method of site-specific infrared dichroism (SSID) combined with constraint molecular dynamics simulation, which has recently emerged as a powerful method to obtain structures of transmembrane α-helical bundles. The theory of SSID including its latest developments is reviewed with the aim to encourage widespread application of this method. This is followed by an outline of the conformational search using experimentally constraint molecular dynamics simulations. Finally a critical evaluation of recent applications, namely the Influenza M2 proton channel, the vpu ion channel of HIV-1 and the MHC-class II associated invariant chain, is conducted.

Influenza M2 Proton Channel Activity Selectively Inhibits Trans-Golgi Network Release of Apical Membrane and Secreted Proteins in Polarized Madin-Darby Canine Kidney Cells

The function of acidification in protein sorting along the biosynthetic pathway has been difficult to elucidate, in part because reagents used to alter organelle pH affect all acidified compartments and are poorly reversible. We have used a novel approach to examine the role of acidification in protein sorting in polarized Madin-Darby canine kidney (MDCK) cells. We expressed the influenza virus M2 protein, an acid-activated ion channel that equilibrates lumenal and cytosolic pH, in polarized MDCK cells and examined the consequences on the targeting and delivery of apical and basolateral proteins. M2 activity affects the pH of only a subset of acidified organelles, and its activity can be rapidly reversed using ion channel blockers (Henkel, J.R., G. Apodaca, Y. Altschuler, S. Hardy, and O.A. Weisz. 1998. Mol. Biol. Cell. 8:2477-2490; Henkel, J.R., J.L. Popovich, G.A. Gibson, S.C. Watkins, and O.A. Weisz. 1999. J. Biol. Chem. 274:9854-9860). M2 expression significantly decreased the kinetics of cell surface delivery of the apical membrane protein influenza hemagglutinin, but not of the basolaterally delivered polymeric immunoglobulin receptor. Similarly, the kinetics of apical secretion of a soluble form of gamma-glutamyltranspeptidase were reduced with no effect on the basolaterally secreted fraction. Interestingly, M2 activity had no effect on the rate of secretion of a nonglycosylated protein (human growth hormone [hGH]) that was secreted equally from both surfaces. However, M2 slowed apical secretion of a glycosylated mutant of hGH that was secreted predominantly apically. Our results suggest a role for acidic trans-Golgi network pH in signal-mediated loading of apical cargo into forming vesicles.