Conformations of signal peptides induced by lipids suggest initial steps in protein export

Despite the requirement for a functional signal sequence in protein export, little is known of the conformational properties and membrane interactions of these highly hydrophobic amino terminal extensions on nearly all exported proteins. The Escherichia coli lambda phage receptor signal sequence was studied in phospholipid monolayers by circular dichroism and Fourier transform infrared spectroscopy; the signal peptide was shown to prefer an alpha-helical conformation when inserted into the lipid phase. However, interaction with the lipid surface without insertion induced the signal sequence, which is unstructured in bulk aqueous solution, to adopt a beta structure. These observations are combined in a model for the initial steps in signal sequence-membrane interaction in vivo.     

Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase

The structure of a 20-amino acid peptide inhibitor bound to the catalytic subunit of cyclic AMP-dependent protein kinase, and its interactions with the enzyme, are described. The x-ray crystal structure of the complex is the basis of the analysis. The peptide inhibitor, derived from a naturally occurring heat-stable protein kinase inhibitor, contains an amphipathic helix that is followed by a turn and an extended conformation. The extended region occupies the cleft between the two lobes of the enzyme and contains a five-residue consensus recognition sequence common to all substrates and peptide inhibitors of the catalytic subunit. The helical portion of the peptide binds to a hydrophobic groove and conveys high affinity binding. Loops from both domains converge at the active site and contribute to a network of conserved residues at the sites of magnesium adenosine triphosphate binding and catalysis. Amino acids associated with peptide recognition, nonconserved, extend over a large surface area.     

The structure of a complex of recombinant hirudin and human alpha-thrombin

The crystallographic structure of a recombinant hirudin-thrombin complex has been solved at 2.3 angstrom (A) resolution. Hirudin consists of an NH2-terminal globular domain and a long (39 A) COOH-terminal extended domain. Residues Ile1 to Tyr3 of hirudin form a parallel beta-strand with Ser214 to Glu217 of thrombin with the nitrogen atom of Ile1 making a hydrogen bond with Ser195 O gamma atom of the catalytic site, but the specificity pocket of thrombin is not involved in the interaction. The COOH-terminal segment makes numerous electrostatic interactions with an anion-binding exosite of thrombin, whereas the last five residues are in a helical loop that forms many hydrophobic contacts. In all, 27 of the 65 residues of hirudin have contacts less than 4.0 A with thrombin (10 ion pairs and 23 hydrogen bonds). Such abundant interactions may account for the high affinity and specificity of hirudin.     

Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects

The magnitude of the hydrophobic effect, as measured from the surface area dependence of the solubilities of hydrocarbons in water, is generally thought to be about 25 calories per mole per square angstrom (cal mol-1 A-2). However, the surface tension at a hydrocarbon-water interface, which is a "macroscopic" measure of the hydrophobic effect, is approximately 72 cal mol-1 A-2. In an attempt to reconcile these values, alkane solubility data have been reevaluated to account for solute-solvent size differences, leading to a revised "microscopic" hydrophobic effect of 47 cal mol-1 A-2. This value, when used in a simple geometric model for the curvature dependence of the hydrophobic effect, predicts a macroscopic alkane-water surface tension that is close to the macroscopic value.     

Solid-state defect mechanism in vanadyl pyrophosphate catalysts: implications for selective oxidation

High-resolution and in situ electron microscopy of vanadyl pyrophosphate catalysts reacted in alkane (n-butane) and other reducing environments have shown evidence for surface structure modifications accompanied by two sets of symmetry-related extended defects. Defect analysis reveals that the defects are formed by pure (glide) shear mechanism. The defect mechanism suggests the presence of basal (coplanar) anion vacancies, associated with Lewis acid centers, at oxygen sites linking corner-sharing phosphorus tetrahedra and vanadyl octahedra in the active plane. These in-plane defect sites may be key to the activation of the alkane, especially in the dehydrogenation.     

Triple-stranded polynucleotide helix containing only purine bases

The structure of the complex involving one polyadenylic acid and two polyinosinic acid chains has been determined by x-ray diffraction. The three coaxial, helical chains have conformations like conventional RNA double helices despite the absence of purine-pyrimidine pairing. Formation of hypoxanthine pairs in codon-anticodon interactions therefore requires only trivial changes in the conformation of a standard nucleotide. Evolution of the contemporary genetic code involving purine-pyrimidine complementarity from a primeval code with only adenine-hypoxanthine pairing would have been possible without major discontinuities in molecular geometry.     

In vivo function and membrane binding properties are correlated for Escherichia coli lamB signal peptides

Wild-type and pseudorevertant signal peptides of the lamB gene product of Escherichia coli interact with lipid systems whereas a nonfunctional deletion mutant signal peptide does not. This conclusion is based on interaction of synthetic signal peptides with a lipid monolayer-water surface, conformational changes induced by presence of lipid vesicles in an aqueous solution of signal peptide, and capacities of the peptides to promote vesicle aggregation. Analysis of the signal sequences and previous conformational studies suggest that these lipid interaction properties may be attributable to the tendency of the functional signal peptides to adopt alpha-helical conformations. Although the possibility of direct interaction between the signal peptide and membrane lipids during protein secretion is controversial, the results suggest that conformationally related amphiphilicity and consequent membrane affinity of signal sequences are important for function in vivo.     

Three-dimensional structure of the LDL receptor-binding domain of human apolipoprotein E

Human apolipoprotein E, a blood plasma protein, mediates the transport and uptake of cholesterol and lipid by way of its high affinity interaction with different cellular receptors, including the low-density lipoprotein (LDL) receptor. The three-dimensional structure of the LDL receptor-binding domain of apoE has been determined at 2.5 angstrom resolution by x-ray crystallography. The protein forms an unusually elongated (65 angstroms) four-helix bundle, with the helices apparently stabilized by a tightly packed hydrophobic core that includes leucine zipper-type interactions and by numerous salt bridges on the mostly charged surface. Basic amino acids important for LDL receptor binding are clustered into a surface patch on one long helix. This structure provides the basis for understanding the behavior of naturally occurring mutants that can lead to atherosclerosis.     

Transmembrane helical interactions and the assembly of the T cell receptor complex

Studies of the subunit interactions of the multicomponent T cell antigen receptor (TCR) revealed that specific pairs of chains have the ability to assemble after transfection into fibroblasts. For one such pair, TCR-alpha and CD3-delta, their ability to assemble was encoded by their transmembrane domains. The specificity of this interaction suggests that well-defined helical interactions in the membrane can explain the assembly of some multichain membrane complexes.     

Hydrophobic organization of membrane proteins

Membrane-exposed residues are more hydrophobic than buried interior residues in the transmembrane regions of the photosynthetic reaction center from Rhodobacter sphaeroides. This hydrophobic organization is opposite to that of water-soluble proteins. The relative polarities of interior and surface residues of membrane and water soluble proteins are not simply reversed, however. The hydrophobicities of interior residues of both membrane and water-soluble proteins are comparable, whereas the bilayer-exposed residues of membrane proteins are more hydrophobic than the interior residues, and the aqueous-exposed residues of water-soluble proteins are more hydrophilic than the interior residues. A method of sequence analysis is described, based on the periodicity of residue replacement in homologous sequences, that extends conclusions derived from the known atomic structure of the reaction center to the more extensive database of putative transmembrane helical sequences.     

Conformation of blood-group and virus receptor glycoproteins from red cells and secretions

Optical rotatory dispersion of human blood-group and virus receptor glycoproteins from erythrocytes and secretions was studied in the far-ultraviolet. Erythrocyte membrane blood-group glycoproteins, with potent virus receptor activities, contained significant alpha-helical and extended beta conformations, whereas the glycoproteins of secretions were largely disordered. These conclusions were supported by determination of the Moffitt constants (b(0)) and by measurements of circular dichroism.     

Hyaluronates: relation between molecular conformations

The discovery that both potassium and sodium salts of hyaluronic acid can exist in a double-strand helical conformation that will convert to the already known single-strand helical structures illustrates the remarkable conformational versatility of this biopolymer. X-ray diffraction was used to monitor variations in molecular conformation as a function of several independent, controllable variables, such as relative humidity, temperature, and applied tension. A scheme is presented for the interrelation of a range of hyaluronate conformations.     

NMR structure of Mistic, a membrane-integrating protein for membrane protein expression

Although structure determination of soluble proteins has become routine, our understanding of membrane proteins has been limited by experimental bottlenecks in obtaining both sufficient yields of protein and ordered crystals. Mistic is an unusual Bacillus subtilis integral membrane protein that folds autonomously into the membrane, bypassing the cellular translocon machinery. Using paramagnetic probes, we determined by nuclear magnetic resonance (NMR) spectroscopy that the protein forms a helical bundle with a surprisingly polar lipid-facing surface. Additional experiments suggest that Mistic can be used for high-level production of other membrane proteins in their native conformations, including many eukaryotic proteins that have previously been intractable to bacterial expression.     

植物叶面铺展剂复配规律 Ⅵ.SDS和DTAB混合水溶液体相和表面层行为

ＳＤＳ／ＤＴＡＢ复配体系在体相及气／液表面层中相互作用行为研究表明,添加适量ＤＴＡＢ,混合溶液的胶束生成、表面张力降低能力和表面张力降低效率均得到明显改善,这３项指标均在较大浓度比例范围内产生增效效应．分子相互作用理论计算结果显示,ＳＤＳ和ＤＴＡＢ不论在混合胶束还是在混合表面层中均产生强烈相互作用．两亲分子碳氢链之间的疏水相互作用和相反电性离子头基之间的库仑引力是混合体系产生高表面活性的主要原因,等链长的正／负离子铺展剂复配为较大浓度范围内的表面张力降低能力增效提供了条件．     

The gramicidin pore: crystal structure of a cesium complex

Gramicidin, a linear polypeptide composed of hydrophobic amino acids with alternating L- and D- configurations, forms transmembrane ion channels. The crystal structure of a gramicidin-cesium complex has been determined at 2.0 angstrom resolution. In this structure, gramicidin forms a 26 angstrom long tube comprised of two polypeptide chains arranged as antiparallel beta strands that are wrapped into a left-handed helical coil with 6.4 residues per turn. The polypeptide backbone forms the interior of the hydrophilic, solvent-filled pore and the side chains form a hydrophobic and relatively regular surface on the outside of the pore. This example of a crystal structure of a solvent-filled ion pore provides a basis for understanding the physical nature of ion translocation.     

The structures of COPI-coated vesicles reveal alternate coatomer conformations and interactions

Transport between compartments of eukaryotic cells is mediated by coated vesicles. The archetypal protein coats COPI, COPII, and clathrin are conserved from yeast to human. Structural studies of COPII and clathrin coats assembled in vitro without membranes suggest that coat components assemble regular cages with the same set of interactions between components. Detailed three-dimensional structures of coated membrane vesicles have not been obtained. Here, we solved the structures of individual COPI-coated membrane vesicles by cryoelectron tomography and subtomogram averaging of in vitro reconstituted budding reactions. The coat protein complex, coatomer, was observed to adopt alternative conformations to change the number of other coatomers with which it interacts and to form vesicles with variable sizes and shapes. This represents a fundamentally different basis for vesicle coat assembly.     

Characterization of a helical protein designed from first principles

The question of how the primary amino acid sequence of a protein determines its three-dimensional structure is still unanswered. One approach to this problem involves the de novo design of model peptides and proteins that should adopt desired three-dimensional structures. A systematic approach was aimed at the design of a four-helix bundle protein. The gene encoding the designed protein was synthesized and the protein was expressed in Escherichia coli and purified to homogeneity. The protein was shown to be monomeric, highly helical, and very stable to denaturation by guanidine hydrochloride (GuHCl). Thus a globular protein has been designed that is capable of adopting a stable, folded structure in aqueous solution.     

Multicompartment micelles from ABC miktoarm stars in water

By combining three mutually immiscible polymeric components in a mixed-arm star block terpolymer architecture, we have observed the formation of a previously unknown class of multicompartment micelles in dilute aqueous solution. Connection of water-soluble poly(ethylene oxide) and two hydrophobic but immiscible components (a polymeric hydrocarbon and a perfluorinated polyether) at a common junction leads to molecular frustration when dispersed in aqueous solution. The incompatible hydrophobic blocks form cores that are protected from the water by the poly(ethylene oxide) blocks, but both are forced to make contact with the poly(ethylene oxide) by virtue of the chain architecture. The structures that emerge depend on the relative lengths of the blocks and can be tuned from discrete multicompartment micelles to extended wormlike structures with segmented cores.     

Nanomechanical basis of selective gating by the nuclear pore complex

The nuclear pore complex regulates cargo transport between the cytoplasm and the nucleus. We set out to correlate the governing biochemical interactions to the nanoscopic responses of the phenylalanineglycine (FG)-rich nucleoporin domains, which are involved in attenuating or promoting cargo translocation. We found that binding interactions with the transport receptor karyopherin-beta1 caused the FG domains of the human nucleoporin Nup153 to collapse into compact molecular conformations. This effect was reversed by the action of Ran guanosine triphosphate, which returned the FG domains into a polymer brush-like, entropic barrier conformation. Similar effects were observed in Xenopus oocyte nuclei in situ. Thus, the reversible collapse of the FG domains may play an important role in regulating nucleocytoplasmic transport.     

不同烘烤方式烘烤过程中烟叶表面烷烃类物质变化的研究

研究了不同烘烤方式对烘烤过程中烟叶表面烷烃类物质含量变化与损失的影响。结果表明,采用挂竿密集烤房烤后烟叶烷烃类物质总量损失最多,比烘烤前减少58.9%,损失主要发生在变黄期和干筋期;筐装密集烤房烤后烟叶烷烃类物质总量损失最少,仅比烘烤前减少13.8%,损失主要发生在干叶期(烤后72~96 h);散叶密集烤房和传统普通烤房烤后烟叶烷烃类物质总量损失居中,分别比烘烤前减少35.8%和32.3%,损失也主要发生在干筋期。因此,筐装密集烤房是解决目前挂竿密集烤房烟叶香气量损失较大的有效措施之一。