The integral membrane protein M2 of influenza virus forms pH-gated proton channels in the viral lipid envelope. The low pH of an endosome activates the M2 channel before haemagglutinin-mediated fusion. Conductance of protons acidifies the viral interior and thereby facilitates dissociation of the matrix protein from the viral nucleoproteins--a required process for unpacking of the viral genome. In addition to its role in release of viral nucleoproteins, M2 in the trans-Golgi network (TGN) membrane prevents premature conformational rearrangement of newly synthesized haemagglutinin during transport to the cell surface by equilibrating the pH of the TGN with that of the host cell cytoplasm. Inhibiting the proton conductance of M2 using the anti-viral drug amantadine or rimantadine inhibits viral replication. Here we present the structure of the tetrameric M2 channel in complex with rimantadine, determined by NMR. In the closed state, four tightly packed transmembrane helices define a narrow channel, in which a 'tryptophan gate' is locked by intermolecular interactions with aspartic acid. A carboxy-terminal, amphipathic helix oriented nearly perpendicular to the transmembrane helix forms an inward-facing base. Lowering the pH destabilizes the transmembrane helical packing and unlocks the gate, admitting water to conduct protons, whereas the C-terminal base remains intact, preventing dissociation of the tetramer. Rimantadine binds at four equivalent sites near the gate on the lipid-facing side of the channel and stabilizes the closed conformation of the pore. Drug-resistance mutations are predicted to counter the effect of drug binding by either increasing the hydrophilicity of the pore or weakening helix-helix packing, thus facilitating channel opening.

Summary Many immune system receptors signal through cytoplasmic tyrosine-based motifs (ITAMs), but how receptor ligation results in ITAM phosphorylation remains unknown. Live cell imaging studies showed a close interaction of the CD3ε cytoplasmic domain of the T cell receptor (TCR) with the plasma membrane through fluorescence resonance energy transfer (FRET) between a C-terminal fluorescent protein and a membrane fluorophore. Electrostatic interactions between basic CD3ε residues and acidic phospholipids enriched in the inner leaflet of the plasma membrane were required for binding. The nuclear magnetic resonance (NMR) structure of the lipid-bound state of this cytoplasmic domain revealed deep insertion of the two key tyrosines into the hydrophobic core of the lipid bilayer. Receptor ligation thus needs to result in unbinding of the CD3ε ITAM from the membrane to render these tyrosines accessible to Src kinases. Sequestration of key tyrosines into the lipid bilayer represents a previously unrecognized mechanism for control of receptor activation.

SUMMARY MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression. Among these, members of the let-7 miRNA family control many cell fate determination genes to influence pluripotency, differentiation, and transformation. Lin28 is a specific, post-transcriptional inhibitor of let-7 biogenesis. We report crystal structures of mouse Lin28 in complex with sequences from let-7d, let-7-f1, and let-7g precursors. The two folded domains of Lin28 recognize two distinct regions of the RNA and are sufficient for inhibition of let-7 in vivo. We also show by NMR spectroscopy that the linker connecting the two folded domains is flexible, accommodating Lin28 binding to diverse let-7 family members. Protein-RNA complex formation imposes specific conformations on both components that could affect downstream recognition by other processing factors. Our data provide a molecular explanation for Lin28 specificity and a model for how it regulates let-7.

We report the solution structure of BID, an intracellular cross-talk agent that can amplify FAS/TNF apoptotic signal through the mitochondria death pathway after Caspase 8 cleavage. BID contains eight alpha helices where two central hydrophobic helices are surrounded by six amphipathic ones. The fold resembles poreforming bacterial toxins and shows similarity to BCL-XL although sequence homology to BCL-XL is limited to the 16-residue BH3 domain. Furthermore, we modeled a complex of BCL-XL and BID by aligning the BID and BAK BH3 motifs in the known BCL-XL-BAK BH3 complex. Additionally, we show that the overall structure of BID is preserved after cleavage by Caspase 8. We propose that BID has both BH3 domain-dependent and -independent modes of action in inducing mitochondrial damage.

Contraction and relaxation of heart muscle cells is regulated by cycling of calcium between cytoplasm and sarcoplasmic reticulum. Human phospholamban (PLN), expressed in the sarcoplasmic reticulum membrane as a 30-kDa homopentamer, controls cellular calcium levels by a mechanism that depends on its phosphorylation. Since PLN was discovered Ϸ30 years ago, extensive studies have aimed to explain how it influences calcium pumps and to determine whether it acts as an ion channel. We have determined by solution NMR methods the atomic resolution structure of an unphosphorylated PLN pentamer in dodecylphosphocholine micelles. The unusual bellflower-like assembly is held together by leucine͞isoleucine zipper motifs along the membrane-spanning helices. The structure reveals a channel-forming architecture that could allow passage of small ions. The central pore gradually widens toward the cytoplasmic end as the transmembrane helices twist around each other and bend outward. The dynamic Nterminal amphipathic helices point away from the membrane, perhaps facilitating recognition and inhibition of the calcium pump.leucine͞isoleucine zipper ͉ membrane channel ͉ NMR ͉ dipolar couplings P hospholamban (PLN) in the sarcoplasmic reticulum (SR) membrane of cardiomyocytes regulates the level of intracellular calcium, the main determinant of muscle contraction and relaxation. In the unphosphorylated form, PLN has an inhibitory effect on the sarco(endo)plasmic reticulum calcium ATPase (SERCA), a membrane protein responsible for pumping most of the calcium from the cytoplasm into the SR, thereby causing relaxation of myofibrils. Heart stimulants, such as adrenaline, set off a chain of signal transduction events that among other effects lead to PLN phosphorylation. Phosphorylated PLN no longer inhibits SERCA, allowing for more efficient pumping of calcium. Imbalance in the PLN-SERCA interaction leads to deterioration of heart function and cardiomyopathy (1). In vitro experiments have suggested that SERCA binds PLN by stripping a subunit away from the unphosphorylated 30-kDa pentamer, thereby depolymerizing PLN assembly (2, 3), but the nature of this interaction is still not understood. In addition to its role as a calcium pump regulator, there have been early ion conductance studies suggesting that PLN is also an ion channel (4). This hypothesis has not been tested further due in part to the lack of structural information on the PLN pentamer.To elucidate a potential dual function of PLN, we have determined the structure of the unphosphorylated human PLN pentamer by solution NMR methods at 30°C and compared it with that of a monomeric mutant (5). The pentamer structure reveals a number of previously undescribed features. The unusual axial orientation and flexibility of the extramembrane helices in the pentamer may facilitate recognition by SERCA, whereas the supercoiling and bending of the membrane-spanning helices leads to formation of a funnel-like channel with a hydrophobic neck, as in many known ion channels. MethodsProtein Preparat...

Using a set of six 1H-detected triple-resonance NMR experiments, we establish a method for sequence-specific backbone resonance assignment of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of 5–30 kDa proteins. The approach relies on perdeuteration, amide 2H/1H exchange, high magnetic fields, and high-spinning frequencies (ωr/2π ≥ 60 kHz) and yields high-quality NMR data, enabling the use of automated analysis. The method is validated with five examples of proteins in different condensed states, including two microcrystalline proteins, a sedimented virus capsid, and two membrane-embedded systems. In comparison to contemporary 13C/15N-based methods, this approach facilitates and accelerates the MAS NMR assignment process, shortening the spectral acquisition times and enabling the use of unsupervised state-of-the-art computational data analysis protocols originally developed for solution NMR.

Mitochondrial solute carriers are a family of membrane proteins that catalyze the transport of small molecules across the mitochondrial inner membrane1. We describe here a solution nuclear magnetic resonance (NMR) method for structural characterization of mitochondrial uncoupling protein 2 (UCP2), a member of the carrier family that translocates protons across the mitochonrial inner membrane2. The method, which overcomes some of the challenges associated with membrane-protein structure determination3, combines orientation restraints derived from NMR residual dipolar couplings (RDCs) and semi-quantitative distance restraints from paramagnetic relaxation enhancement (PRE) measurements. The local and secondary structures of the protein were determined by piecing together molecular fragments from the Protein Data Bank (PDB) that best fit experimental RDCs from samples weakly aligned in a DNA nanotube liquid crystal. The RDCs also determine the relative orientation of the secondary structural segments, and the PRE restraints provide their spatial arrangement in the tertiary fold. We determined the structure of UCP2 in the presence of GDP. We also mapped the interaction between UCP2 and GDP by measuring paramagnetic broadening of the protein NMR resonances from nitroxide-labeled GDP. UCP2 closely resembles the bovine ADP/ATP carrier (the only carrier protein of known structure4), but the relative orientations of the helical segments are different, resulting in a wider opening on the matrix side of the inner membrane. Moreover, the nitroxide-labeled GDP binds inside the channel and appears to be closer to transmembrane helix 1–4. We believe this biophysical approach, based on solution NMR spectroscopy, can be applied broadly to other membrane proteins and in particular to other mitochondrial carriers, not only for structure determination but also for characterizing various conformational states of these proteins linked to substrate transport.

The Hepatitis C virus (HCV) has developed a small membrane protein, p7, which remarkably can self-assemble into a large channel complex that selectively conducts cations1-4. We are curious as to what structural solution has the viroporin adopted to afford selective cation conduction because p7 has no homology with any of the known prokaryotic or eukaryotic channel proteins. The p7 activity can be inhibited by amantadine and rimantadine2,5, which also happen to be potent blockers of the influenza M2 channel6 and licensed drugs against influenza infections7. The adamantane derivatives were subjects of HCV clinical trials8, but large variation in drug efficacy among the various HCV genotypes has been difficult to explain without detailed molecular structures. Here, we determined the structures of this HCV viroporin as well as its drug-binding site using the latest nuclear magnetic resonance (NMR) technologies. The structure exhibits an unusual mode of hexameric assembly, where the individual p7 monomers, i, not only interact with their immediate neighbors, but also reach farther to associate with the i+2 and i+3 monomers, forming a sophisticated, funnel-like architecture. The structure also alludes to a mechanism of cation selection: an asparagine/histidine ring that constricts the narrow end of the funnel serves as a broad cation selectivity filter while an arginine/lysine ring that defines the wide end of the funnel may selectively allow cation diffusion into the channel. Our functional investigation using whole-cell channel recording showed that these residues are indeed critical for channel activity. NMR measurements of the channel-drug complex revealed six equivalent hydrophobic pockets between the peripheral and pore-forming helices to which amantadine or rimantadine binds, and compound binding specifically to this position may allosterically inhibit cation conduction by preventing the channel from opening. Our data provide molecular explanation for p7-mediated cation conductance and its inhibition by adamantane derivatives.