SNARE proteins: one to fuse and three to keep the nascent fusion pore open

Neurotransmitters are released through nascent fusion pores, which ordinarily dilate after bilayer fusion, preventing consistent biochemical studies. We used lipid bilayer nanodiscs as fusion partners; their rigid protein framework prevents dilation and reveals properties of the fusion pore induced by SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor). We found that although only one SNARE per nanodisc is required for maximum rates of bilayer fusion, efficient release of content on the physiologically relevant time scale of synaptic transmission apparently requires three or more SNARE complexes (SNAREpins) and the native transmembrane domain of vesicle-associated membrane protein 2 (VAMP2). We suggest that several SNAREpins simultaneously zippering their SNARE transmembrane helices within the freshly fused bilayers provide a radial force that prevents the nascent pore from resealing during synchronous neurotransmitter release.     

Structure of the rotor of the V-Type Na+-ATPase from Enterococcus hirae

The membrane rotor ring from the vacuolar-type (V-type) sodium ion-pumping adenosine triphosphatase (Na+-ATPase) from Enterococcus hirae consists of 10 NtpK subunits, which are homologs of the 16-kilodalton and 8-kilodalton proteolipids found in other V-ATPases and in F1Fo- or F-ATPases, respectively. Each NtpK subunit has four transmembrane alpha helices, with a sodium ion bound between helices 2 and 4 at a site buried deeply in the membrane that includes the essential residue glutamate-139. This site is probably connected to the membrane surface by two half-channels in subunit NtpI, against which the ring rotates. Symmetry mismatch between the rotor and catalytic domains appears to be an intrinsic feature of both V- and F-ATPases.     

Structure and molecular mechanism of a nucleobase-cation-symport-1 family transporter

The nucleobase-cation-symport-1 (NCS1) transporters are essential components of salvage pathways for nucleobases and related metabolites. Here, we report the 2.85-angstrom resolution structure of the NCS1 benzyl-hydantoin transporter, Mhp1, from Microbacterium liquefaciens. Mhp1 contains 12 transmembrane helices, 10 of which are arranged in two inverted repeats of five helices. The structures of the outward-facing open and substrate-bound occluded conformations were solved, showing how the outward-facing cavity closes upon binding of substrate. Comparisons with the leucine transporter LeuT(Aa) and the galactose transporter vSGLT reveal that the outward- and inward-facing cavities are symmetrically arranged on opposite sides of the membrane. The reciprocal opening and closing of these cavities is synchronized by the inverted repeat helices 3 and 8, providing the structural basis of the alternating access model for membrane transport.     

Force-clamp spectroscopy monitors the folding trajectory of a single protein

We used force-clamp atomic force microscopy to measure the end-to-end length of the small protein ubiquitin during its folding reaction at the single-molecule level. Ubiquitin was first unfolded and extended at a high force, then the stretching force was quenched and protein folding was observed. The folding trajectories were continuous and marked by several distinct stages. The time taken to fold was dependent on the contour length of the unfolded protein and the stretching force applied during folding. The folding collapse was marked by large fluctuations in the end-to-end length of the protein, but these fluctuations vanished upon the final folding contraction. These direct observations of the complete folding trajectory of a protein provide a benchmark to determine the physical basis of the folding reaction.     

Reversible unfolding of single RNA molecules by mechanical force

Here we use mechanical force to induce the unfolding and refolding of single RNA molecules: a simple RNA hairpin, a molecule containing a three-helix junction, and the P5abc domain of the Tetrahymena thermophila ribozyme. All three molecules (P5abc only in the absence of Mg2+) can be mechanically unfolded at equilibrium, and when kept at constant force within a critical force range, are bi-stable and hop between folded and unfolded states. We determine the force-dependent equilibrium constants for folding/unfolding these single RNA molecules and the positions of their transition states along the reaction coordinate.     

Crystal structure of Escherichia coli MscS,a voltage-modulated and mechanosensitive channel

The mechanosensitive channel of small conductance (MscS) responds both to stretching of the cell membrane and to membrane depolarization. The crystal structure at 3.9 angstroms resolution demonstrates that Escherichia coli MscS folds as a membrane-spanning heptamer with a large cytoplasmic region. Each subunit contains three transmembrane helices (TM1, -2, and -3), with the TM3 helices lining the pore, while TM1 and TM2, with membrane-embedded arginines, are likely candidates for the tension and voltage sensors. The transmembrane pore, apparently captured in an open state, connects to a large chamber, formed within the cytoplasmic region, that connects to the cytoplasm through openings that may function as molecular filters. Although MscS is likely to be structurally distinct from other ion channels, similarities in gating mechanisms suggest common structural elements.     

丙型肝炎病毒NS4B蛋白调控Hep3B细胞非折叠蛋白质反应研究

研究表达的丙型肝炎病毒(HCV)NS4B对Hep3B细胞非折叠蛋白质反应的影响。NS4B重组真核表达质粒pcDNA3.1(-)NS4B通过脂质体转染Hep3B细胞,G418筛选和Western blot鉴定稳定转染细胞;RT-PCR检测稳定转染细胞内XBP1 mRNA剪接,Western blot鉴定ATF6蛋白切割,荧光素酶试验检测稳定转染细胞内GRP78和XBP1启动子活性。G418筛选和Western Blot鉴定证实获得稳定表达NS4B的Hep3B细胞;在该细胞内,XBP1 mRNA剪接、ATF6切割、XBP1和Grp78启动子激活均被检测到。NS4B在Hep3B的稳定表达诱导了非折叠蛋白质反应。     

Long unfolded linkers facilitate membrane protein import through the nuclear pore complex

Active nuclear import of soluble cargo involves transport factors that shuttle cargo through the nuclear pore complex (NPC) by binding to phenylalanine-glycine (FG) domains. How nuclear membrane proteins cross through the NPC to reach the inner membrane is presently unclear. We found that at least a 120-residue-long intrinsically disordered linker was required for the import of membrane proteins carrying a nuclear localization signal for the transport factor karyopherin-α. We propose an import mechanism for membrane proteins in which an unfolded linker slices through the NPC scaffold to enable binding between the transport factor and the FG domains in the center of the NPC.     

南丰蜜橘化渣性评价及不同结果习性果实的品质比较

【目的】建立南丰蜜橘化渣性品质的量化指标,比较不同结果习性果实的品质差异,为制定改善南丰蜜橘化渣性品质的栽培措施提供依据。【方法】以南丰蜜橘为材料,用感官品尝的方法区分果实的化渣性,并测定化渣性不同果实的囊衣厚度和囊瓣剪切力、硬度、咀嚼度等化渣性品质指标,分析果实化渣性和这些指标的相关性。进一步测定不同结果习性果实的化渣性品质与常规品质（维生素C、可溶性固形物和可滴定酸）的差异。【结果】囊瓣剪切力和囊衣厚度能够客观反映果实的化渣程度,利用这两个指标可对果实化渣性进行量化;根据品尝试验、囊衣厚度和囊瓣剪切力的结果范围,可将南丰蜜橘果实的化渣性分为3个等级：“化渣”果实的囊瓣剪切力为1.15-1.64 kg,囊衣中间处厚度为0.09-0.12 cm;“较化渣”果实的囊瓣剪切力为1.64-2.63 kg,囊衣中间处厚度为0.12-0.14 cm;“不化渣”果实的囊瓣剪切力为2.63-5.70 kg,囊衣中间处厚度为0.14-0.17 cm;比较不同结果习性果实的品质表明：大果的化渣性优于中果和小果,而中果的常规品质优于小果和大果;短枝果实的化渣性优于长枝果实的,但两者的常规品质没有差异;高负载枝果实化渣性显著优于低负载枝果实,但不同负载量枝条上果实的常规品质没有差异;外膛果的常规品质和化渣性均优于内膛果实;树冠中层果实的化渣性较好,且上层和中层果实的常规品质优于下层果实。【结论】化渣性是南丰蜜橘重要的品质指标,可用囊瓣剪切力及囊衣厚度进行量化评价;不同结果习性的果实品质有差异,化渣性品质与常规品质没有相关性,但化渣性品质好的果实,其常规品质也较好。     

Water-inserted alpha-helical segments implicate reverse turns as folding intermediates

Information relevant to the folding and unfolding of alpha helices has been extracted from an analysis of protein structures. The alpha helices in protein crystal structures have been found to be hydrated, either externally by a water molecule hydrogen bonding to the backbone carbonyl oxygen atom, or internally by inserting into the helix hydrogen bond and forming a hydrogen-bonded bridge between the backbone carbonyl oxygen and the amide nitrogen atoms. The water-inserted alpha-helical segments display a variety of reverse-turn conformations, such as type III, type II, type I, and opened out, that can be considered as folding intermediates that are trapped in the folding-unfolding process of alpha helices. Since the alpha helix, most turns, and the extended beta strand occupy contiguous regions in the conformational space of phi, psi dihedral angles, a plausible pathway can be proposed for the folding-unfolding process of alpha helices in aqueous solution.     

Structure of a site-2 protease family intramembrane metalloprotease

Regulated intramembrane proteolysis by members of the site-2 protease (S2P) family is an important signaling mechanism conserved from bacteria to humans. Here we report the crystal structure of the transmembrane core domain of an S2P metalloprotease from Methanocaldococcus jannaschii. The protease consists of six transmembrane segments, with the catalytic zinc atom coordinated by two histidine residues and one aspartate residue approximately 14 angstroms into the lipid membrane surface. The protease exhibits two distinct conformations in the crystals. In the closed conformation, the active site is surrounded by transmembrane helices and is impermeable to substrate peptide; water molecules gain access to zinc through a polar, central channel that opens to the cytosolic side. In the open conformation, transmembrane helices alpha1 and alpha6 separate from each other by 10 to 12 angstroms, exposing the active site to substrate entry. The structure reveals how zinc embedded in an integral membrane protein can catalyze peptide cleavage.     

Activation of integrin alphaIIbbeta3 by modulation of transmembrane helix associations

Transmembrane helices of integrin alpha and beta subunits have been implicated in the regulation of integrin activity. Two mutations, glycine-708 to asparagine-708 (G708N)and methionine-701 to asparagine-701, in the transmembrane helix of the beta3 subunit enabled integrin alphaIIbbeta3 to constitutively bind soluble fibrinogen. Further characterization of the G708N mutant revealed that it induced alphaIIbbeta3 clustering and constitutive phosphorylation of focal adhesion kinase. This mutation also enhanced the tendency of the transmembrane helix to form homotrimers. These results suggest that homomeric associations involving transmembrane domains provide a driving force for integrin activation. They also suggest a structural basis for the coincidence of integrin activation and clustering.     

The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism

The ABC transporters are ubiquitous membrane proteins that couple adenosine triphosphate (ATP) hydrolysis to the translocation of diverse substrates across cell membranes. Clinically relevant examples are associated with cystic fibrosis and with multidrug resistance of pathogenic bacteria and cancer cells. Here, we report the crystal structure at 3.2 angstrom resolution of the Escherichia coli BtuCD protein, an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and appears to represent a conserved motif among the ABC transporters.     

Genome-wide identification,expression and functional analysis of sugar transporters in sorghum (Sorghum bicolor L.)

Sugar transporters are essential for osmotic process regulation, various signaling pathways and plant growth and development. Currently, few studies are available on the function of sugar transporters in sorghum(Sorghum bicolor L.). In this study, we performed a genome-wide survey of sugar transporters in sorghum. In total, 98 sorghum sugar transporters(SSTs) were identified via BLASTP. These SSTs were classified into three families based on the phylogenetic and conserved domain analysis, includ...     

Atomic force microscopy and dissection of gap junctions

An atomic force microscope (AFM) was used to study the structure of isolated hepatic gap junctions in phosphate-buffered saline (PBS). The thickness of these gap junctions appears to be 14.4 nanometers, close to the dimensions reported by electron microscopy (EM). When an increasing force is applied to the microscope tip, the top membrane of the gap junction can be "dissected" away, leaving the extracellular domains of the bottom membrane exposed. When such "force dissection" is performed on samples both trypsinized and fixed with glutaraldehyde, the hexagonal array of gap junction hemichannels is revealed, with a center-to-center spacing of 9.1 nanometers.     

Partial symmetrization of the photosynthetic reaction center

The bacterial photosynthetic reaction center (RC) is a pigmented intrinsic membrane protein that performs the primary charge separation event of photosynthesis, thereby converting light to chemical energy. The RC pigments are bound primarily by two homologous peptides, the L and M subunits, each containing five transmembrane helices. These alpha helices and pigments are arranged in an approximate C2 symmetry and form two possible electron transfer pathways. Only one of these pathways is actually used. In an attempt to identify nonhomologous residues that are responsible for functional differences between the two branches, homologous helical regions that interact extensively with the pigments were genetically symmetrized (that is, exchanged). For example, replacement of the fourth transmembrane helix (D helix) in the M subunit with the homologous helix from the L subunit yields photosynthetically inactive RCs lacking a critical photoactive pigment. Photosynthetic revertants have been isolated in which single amino acid substitutions (intragenic suppressors) compensate for this partial symmetrization.     

杂种牛CAPN4基因第六内含子的遗传变异与牛肉嫩度的关联分析

以CAPN4基因作为肉牛肉品质嫩度性状的候选基因,利用PCR-RFLP方法在牛CAPN4基因内发现了1个变异酶切位点,为intron6上的HhaI-RFLP。对此多态性片段进行克隆测序分析,结果表明此酶切位点是由于488位的碱基T→C的突变引起。此多态位点有A、B两个等位基因,其频率分别为0.7和0.3,在所研究的群体中,该位点处于Hardy-Weiberg平衡状态。利用最小二乘法拟合线性模型对不同分子标记基因型效应值间肉品质嫩度性状差异显著性检验,结果表明差异不显著(P>0.05)。     

Entropically driven helix formation

The helix is a ubiquitous motif for biopolymers. We propose a heuristic, entropically based model that predicts helix formation in a system of hard spheres and semiflexible tubes. We find that the entropy of the spheres is maximized when short stretches of the tube form a helix with a geometry close to that found in natural helices. Our model could be directly tested with wormlike micelles as the tubes, and the effect could be used to self-assemble supramolecular helices.     

Voltage sensor of Kv1.2: structural basis of electromechanical coupling

Voltage-dependent ion channels contain voltage sensors that allow them to switch between nonconductive and conductive states over the narrow range of a few hundredths of a volt. We investigated the mechanism by which these channels sense cell membrane voltage by determining the x-ray crystal structure of a mammalian Shaker family potassium ion (K+) channel. The voltage-dependent K+ channel Kv1.2 grew three-dimensional crystals, with an internal arrangement that left the voltage sensors in an apparently native conformation, allowing us to reach three important conclusions. First, the voltage sensors are essentially independent domains inside the membrane. Second, they perform mechanical work on the pore through the S4-S5 linker helices, which are positioned to constrict or dilate the S6 inner helices of the pore. Third, in the open conformation, two of the four conserved Arg residues on S4 are on a lipid-facing surface and two are buried in the voltage sensor. The structure offers a simple picture of how membrane voltage influences the open probability of the channel.     

Unfolded proteins are Ire1-activating ligands that directly induce the unfolded protein response

The unfolded protein response (UPR) detects the accumulation of unfolded proteins in the endoplasmic reticulum (ER) and adjusts the protein-folding capacity to the needs of the cell. Under conditions of ER stress, the transmembrane protein Ire1 oligomerizes to activate its cytoplasmic kinase and ribonuclease domains. It is unclear what feature of ER stress Ire1 detects. We found that the core ER-lumenal domain (cLD) of yeast Ire1 binds to unfolded proteins in yeast cells and to peptides primarily composed of basic and hydrophobic residues in vitro. Mutation of amino acid side chains exposed in a putative peptide-binding groove of Ire1 cLD impaired peptide binding. Peptide binding caused Ire1 cLD oligomerization in vitro, suggesting that direct binding to unfolded proteins activates the UPR.