The structure of rabbit muscle phosphoglucomutase at intermediate resolution

The three-dimensional structure of rabbit phosphoglucomutase has been determined to 2.7 A resolution by a combination of isomorphous and molecular replacement techniques. Heavy atom positions were found by using vector search and difference Fourier methods. The two molecules in the asymmetric unit form a dimer with its 2-fold axis perpendicular to and intersecting with a crystallographic 4(1) axis. Thus, the dimers are arranged so that they form fibers that are coincident with the 4(1) axes. A polypeptide model, corresponding with the known residue sequence, has been fitted to the electron density map to produce a structure that consists of four domains. All four have an alpha/beta structure; the first three have a somewhat similar topology that is based on a mixed parallel/antiparallel beta sheet, whereas the fourth is based on an antiparallel sheet. The active site lies between the four domains, with the phosphoserine residue in the first domain and some of the probable substrate-binding residues in the fourth and final domain. The carboxyl edges of all four sheets are directed towards the active site region, which lies in a deep crevice.     

Structure and significance of cruciate flagellar root systems in green algae: Female gametes ofBryopsis lyngbyei (Bryopsidales)

The ultrastructure of the flagellar apparatus in the biflagellate female gametes of the green algaBryopsis lyngbyei has been studied in detail. In the flagellum and basal body, microtubule septations occur in some of the B-tubules. The transition region of the flagellum is extremely long (260–290 nm), exhibits a stellate pattern in cross section but lacks the transverse diaphragm. The two basal bodies form an angle of 180° and overlap at their proximal ends. They are connected by a compound non-striated capping plate. Terminal caps associated with the capping plate partially close the proximal end of each basal body. A cruciate flagellar root system with three different types of microtubular roots is present, i. e. the flagellar apparatus does not show 180° rotational symmetry. One root type contains 2 microtubules which are connected to an elaborate cylindrical structure, presumably a mating structure. The opposite root exhibits 3 microtubules over its entire length and is not associated with a cylindrical structure. In their proximal parts both roots are linked to an underlying crescent body. The other two microtubular roots are probably identical and consist of 4 (or 5) microtubules which show configurational changes. These two identical roots insert into the capping plate and link to the inner side (i. e. the side adjacent to the other basal body) of each basal body, whereas the other two roots attach to the outer sides of each basal body. System I striated fibres are probably associated with each of the four roots, while system II fibres have not been observed. The flagellar apparatus of female gametes ofB. lyngbyei shows many unique features but in some aspects resembles that of ulvalean algae. Functional and phylogenetic aspects of cruciate flagellar root systems in green algae are discussed.     

Production in Escherichia coli and site-directed mutagenesis of a 9-kDa nonspecific lipid transfer protein from wheat.

The sequence encoding a wheat (Triticum durum) nonspecific lipid transfer protein of 9 kDa (nsLTP1) was inserted into an Escherichia coli expression vector, pET3b. The recombinant protein that was expressed accumulated in insoluble cytoplasmic inclusion bodies and was purified and refolded from them. In comparison with the corresponding protein isolated from wheat kernel, the refolded recombinant protein exhibits a methionine extension at its N-terminus but has the same structure and activity as demonstrated by CD, lipid binding and lipid transfer assays. Using the same expression system, four mutants with H5Q, Y16A, Q45R and Y79A replacements were produced and characterized. No significant changes in structure or activity were found for three of the mutants. By contrast, lipid binding experiments with the Y79A mutant did not show any increase of tyrosine fluorescence as observed with the wild-type nsLTP1. Comparison of the two tyrosine mutants suggested that Tyr79 is the residue involved in this phenomenon and thus is located close to the lipid binding site as expected from three-dimensional structure data.     

Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops

We herein report on the formation and high-resolution NMR solution-state structure determination of a G-quadruplex adopted by d[G(3)ATG(3)ACACAG(4)ACG(3)] comprised of four G-tracts with the third one consisting of four guanines that are intervened with non-G streches of different lengths. A single intramolecular antiparallel (3+1) G-quadruplex exhibits three stacked G-quartets connected with propeller, diagonal and edgewise loops of different lengths. The propeller and edgewise loops are well structured, whereas the longer diagonal loop is more flexible. To the best of our knowledge, this is the first high-resolution G-quadruplex structure where all of the three main loop types are present.     

Precise binding of single-stranded DNA termini by human RAD52 protein

The human RAD52 protein, which exhibits a heptameric ring structure, has been shown to bind resected double strand breaks (DSBs), consistent with an early role in meiotic recombination and DSB repair. In this work, we show that RAD52 binds single-stranded and tailed duplex DNA molecules via precise interactions with the terminal base. When probed with hydroxyl radicals, ssDNA-RAD52 complexes exhibit a four-nucleotide repeat hypersensitivity pattern. This unique pattern is due to the interaction of RAD52 with either a 5' or a 3' terminus of the ssDNA, is sequence independent and is phased precisely from the terminal nucleotide. Hypersensitivity is observed over approximately 36 nucleotides, consistent with the length of DNA that is protected by RAD52 in nuclease protection assays. We propose that RAD52 binds DNA breaks via specific interactions with the terminal base, leading to the formation of a precisely organized ssDNA-RAD52 complex in which the DNA lies on an exposed surface of the protein. This protein-DNA arrangement may facilitate the DNA-DNA interactions necessary for RAD52-mediated annealing of complementary DNA strands.     

OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences.

A novel folding motif has been observed in four different proteins which bind oligonucleotides or oligosaccharides: staphylococcal nuclease, anticodon binding domain of asp-tRNA synthetase and B-subunits of heat-labile enterotoxin and verotoxin-1. The common fold of the four proteins, which we call the OB-fold, has a five-stranded beta-sheet coiled to form a closed beta-barrel. This barrel is capped by an alpha-helix located between the third and fourth strands. The barrel-helix frameworks can be superimposed with r.m.s. deviations of 1.4-2.2 A, but no similarities can be observed in the corresponding alignment of the four sequences. The nucleotide or sugar binding sites, known for three of the four proteins, are located in nearly the same position in each protein: on the side surface of the beta-barrel, where three loops come together. Here we describe the determinants of the OB-fold, based on an analysis of all four structures. These proposed determinants explain how very different sequences adopt the OB-fold. They also suggest a reinterpretation of the controversial structure of gene 5 ssDNA binding protein, which exhibits some topological and functional similarities with the OB-fold proteins.     

A NEW BASAL PTEROSAUR GENUS FROM THE UPPER TRIASSIC OF THE NORTHERN CALCAREOUS ALPS OF SWITZERLAND

Abstract:  A lower jaw with multicusped teeth and a number of unique characteristics was discovered in an extensive exposure of the Upper Triassic Kössen Formation in the Northern Calcareous Alps. The ramus of the jaw is high and dominated by a row of large, oval foramina that lies parallel to the tooth row. In addition, the anterior portion of the dentary exhibits a large number of nutritive foramina and small pits, which might indicate an association with a soft tissue structure and/or the presence of a keratinous cover of that area during life. All elements of the jaw are thin-walled and hollow, possibly pneumatic. Two teeth are preserved within the dentary. One is tricuspid and the other bears four cuSPS. The teeth are noticeably small in comparison with the overall size of the ramus, being only one-third of the height of the ramus. The teeth show a strong similarity to those of the well-known basal pterosaur genus Eudimorphodon , whose jaw morphology, however, clearly differs from the specimen described in this study. The dentition and the pneumatic bone structure make an assignment to the Pterosauria plausible. Based on the great number of distinct morphological characters the specimen is described as Caviramus schesaplanensis gen. et sp. nov.     

Structural variation in the inner ears of four deep-sea elopomorph fishes

Deep-sea fishes have evolved in dark or dimly lit environments devoid of the visual cues available to shallow-water species. Because of the limited opportunity for visual scene analysis by deep-sea fishes, it is reasonable to hypothesize that the inner ears of at least some such species may have evolved structural adaptations to enhance hearing capabilities in lieu of vision. As an initial test of this hypothesis, scanning electron microscopy was used to examine the structure of the inner ears of four deep-sea elopomorph species inhabiting different depths: Synaphobranchus kaupii, Synaphobranchus bathybius, Polyacanthonotus challengeri, and Halosauropsis macrochir. The shape of the sensory epithelia and hair cell ciliary bundle orientation of the saccule, lagena, and utricle, the three otolithic organs associated with audition and vestibular function, are described. The saccules of all four species have a common, alternating ciliary bundle orientation pattern. In contrast, the lagena exhibits more interspecific diversity in shape and ciliary bundle orientation, suggesting that it has special adaptations in these species. The macula neglecta, a sensory epithelium of unknown function, is present in all four species.     

The Striated Bands of Paramecium Are Immunologically Distinct from the Centrin-Specific Infraciliary Lattice and Cytostomal Cord

The pellicle of Paramecium has three two-dimensionally arrayed systems that occupy separate but closely paralleling planes. All three systems are now distinguishable by their differing immunological properties. This study focused on the two deeper systems. The infraciliary lattice lies innermost and labels with centrin-specific antibodies. The middle system, the striated bands, is specifically labeled with a monoclonal antibody that we have raised to a 110 kDa conical antigen in P. multimicronucleatum. This antibody labels a similar geometric cortical pattern in at least two species, P. multimicronucleatum and P. tetraurelia. Centrin-specific structures appear to be net-like in the above two species but show a more interrupted pattern in P. caudatum. The cytostomal cord is an essentially unbranched extension of the net-like infraciliary lattice and, like it, is centrin-specific. The cord has a unique association with the alveolar sacs which suggest these calcium-storing compartments contribute to the calcium fluxes required for contraction of the cord. A structural rather than a contractile function is favored for the striated bands, based solely on their morphology.     

Crystal structure of auracyanin, a "blue" copper protein from the green thermophilic photosynthetic bacterium Chloroflexus aurantiacus

Auracyanin B, one of two similar blue copper proteins produced by the thermophilic green non-sulfur photosynthetic bacterium Chloroflexus aurantiacus, crystallizes in space group P6(4)22 (a=b=115.7 A, c=54.6 A). The structure was solved using multiple wavelength anomalous dispersion data recorded about the CuK absorption edge, and was refined at 1.55 A resolution. The molecular model comprises 139 amino acid residues, one Cu, 247 H(2)O molecules, one Cl(-) and two SO(4)(2-). The final residual and estimated standard uncertainties are R=0.198, ESU=0.076 A for atomic coordinates and ESU=0.05 A for Cu---ligand bond lengths, respectively. The auracyanin B molecule has a standard cupredoxin fold. With the exception of an additional N-terminal strand, the molecule is very similar to that of the bacterial cupredoxin, azurin. As in other cupredoxins, one of the Cu ligands lies on strand 4 of the polypeptide, and the other three lie along a large loop between strands 7 and 8. The Cu site geometry is discussed with reference to the amino acid spacing between the latter three ligands. The crystallographically characterized Cu-binding domain of auracyanin B is probably tethered to the periplasmic side of the cytoplasmic membrane by an N-terminal tail that exhibits significant sequence identity with known tethers in several other membrane-associated electron-transfer proteins.     

Later Middle Pleistocene human remains from the Almonda Karstic system, Torres Novas, Portugal

Later Middle Pleistocene archeological deposits of the Galeria Pesada (Gruta da Aroeira), Almonda Karstic System, Torres Novas, Portugal, yielded two archaic human teeth, a mandibular canine and a maxillary third molar. The C(1)presents moderate and asymmetrical shoveling with a stout root. The slightly worn M(3)exhibits at least four cusps with a large hypocone, three roots with large radicular plates, and an absence of taurodontism. They are moderately large for later Middle Pleistocene humans in their buccolingual crown diameters, although the M(3)mesiodistal diameter is modest. The C(1)exhibits labial calculus and multiple linear hypoplastic defects, but the M(3)is lesion free. Both teeth are morphologically similar to those of other Middle Pleistocene European humans and reinforce a pattern of dental hypertrophy among these archaic Homo.     

Structure and significance of cruciate flagellar root systems in green algae: Zoospores ofUlva lactuca (Ulvales,Chlorophyceae)

The ultrastructure of the flagellar apparatus in the quadriflagellate zoospores ofUlva lactuca was examined. The two L-shaped pairs of basal bodies are arranged in mirror image relation. Two apical capping plates connect adjacent basal bodies of different pairs with each other. The flagellar root system is cruciate and exhibits a microtubular part (4-2-4-2 system) and a complex and elaborate fibrillar part. The latter consists of two striated fibres (striation pattern 32 nm) closely associated with the two-stranded roots and four differently patterned fibres (striation pattern 150–160 nm) which are more internally located and run parallel to all four microtubular roots. The presence of four microtubular roots and six striated fibres is at present not known for any other green alga and taxonomic implications are discussed.     

Crystal structure of cholesterol oxidase from Brevibacterium sterolicum refined at 1.8 A resolution

Cholesterol oxidase (3 beta-hydroxysteroid oxidase, EC 1.1.3.6) is an FAD-dependent enzyme that carries out the oxidation and isomerization of steroids with a trans A : B ring junction. The crystal structure of the enzyme from Brevibacterium sterolicum has been determined using the method of isomorphous replacement and refined to 1.8 A resolution. The refined model includes 492 amino acid residues, the FAD prosthetic group and 453 solvent molecules. The crystallographic R-factor is 15.3% for all reflections between 10.0 A and 1.8 A resolution. The structure is made up of two domains: an FAD-binding domain and a steroid-binding domain. The FAD-binding domain consists of three non-continuous segments of sequence, including both the N terminus and the C terminus, and is made up of a six-stranded beta-sheet sandwiched between a four-stranded beta-sheet and three alpha-helices. The overall topology of this domain is very similar to other FAD-binding proteins. The steroid-binding domain consists of two non-continuous segments of sequence and contains a six-stranded antiparallel beta-sheet forming the "roof" of the active-site cavity. This large beta-sheet structure and the connections between the strands are topologically similar to the substrate-binding domain of the FAD-binding protein para-hydroxybenzoate hydroxylase. The active site lies at the interface of the two domains, in a large cavity filled with a well-ordered lattice of 13 solvent molecules. The flavin ring system of FAD lies on the "floor" of the cavity with N-5 of the ring system exposed. The ring system is twisted from a planar conformation by an angle of approximately 17 degrees, allowing hydrogen-bond interactions between the protein and the pyrimidine ring of FAD. The amino acid residues that line the active site are predominantly hydrophobic along the side of the cavity nearest the benzene ring of the flavin ring system, and are more hydrophilic on the opposite side near the pyrimidine ring. The cavity is buried inside the protein molecule, but three hydrophobic loops at the surface of the molecule show relatively high temperature factors, suggesting a flexible region that may form a possible path by which the substrate could enter the cavity. The active-site cavity contains one charged residue, Glu361, for which the side-chain electron density suggests a high degree of mobility for the side-chain. This residue is appropriately positioned to act as the proton acceptor in the proposed mechanism for the isomerization step.     

Atomic resolution structure of cucurmosin, a novel type 1 ribosome-inactivating protein from the sarcocarp of Cucurbita moschata

A novel type 1 ribosome-inactivating protein (RIP) designated cucurmosin was isolated from the sarcocarp of Cucurbita moschata (pumpkin). Besides rRNA N-glycosidase activity, cucurmosin exhibits strong cytotoxicities to three cancer cell lines of both human and murine origins, but low toxicity to normal cells. Plant genomic DNA extracted from the tender leaves was amplified by PCR between primers based on the N-terminal sequence and X-ray sequence of the C-terminal. The complete mature protein sequence was obtained from N-terminal protein sequencing and partial DNA sequencing, confirmed by high resolution crystal structure analysis. The crystal structure of cucurmosin has been determined at 1.04A, a resolution that has never been achieved before for any RIP. The structure contains two domains: a large N-terminal domain composed of seven alpha-helices and eight beta-strands, and a smaller C-terminal domain consisting of three alpha-helices and two beta-strands. The high resolution structure established a glycosylation pattern of GlcNAc(2)Man(3)Xyl. Asn225 was identified as a glycosylation site. Residues Tyr70, Tyr109, Glu158 and Arg161 define the active site of cucurmosin as an RNA N-glycosidase. The structural basis of cytotoxicity difference between cucurmosin and trichosanthin is discussed.     

Evolution of Structural Shape in Bacterial Globin-Related Proteins

The globin family of proteins has a characteristic structural pattern of helix interactions that nonetheless exhibits some variation. A simplified model for globin structural evolution was developed in which protein shape evolved by random change of contacts between helices. A conserved globin domain of 15 bacterial proteins representing four structural families was studied. Using a parsimony approach ancestral structural states could be reconstructed. The distribution of number of contact changes per site for a fixed topology tree fit a gamma distribution. Homoplasy was high, with multiple changes per site and no support for an invariant class of residue-residue contacts. Contacts changed more slowly than sequence. A phylogenetic reconstruction using a distance measure based on the proportion of shared contacts was generally consistent with a sequence-based phylogeny but not highly resolved. Contact pattern convergence between members of different globin family proteins could not be detected. Simulation studies indicated the convergence test was sensitive enough to have detected convergence involving only 10% of the contacts, suggesting a limit on the extent of selection for a specific contact pattern. Contact site methods may provide additional approaches to study the relationship between protein structure and sequence evolution. [Reviewing Editior: Dr. Lauren Ancel Meyers]     

A new flagellate <Emphasis Type="Italic">Percolomonas lacustris</Emphasis> sp. n. (Excavata,Percolozoa) from an inland saline lake (Southeastern European Russia)

The external and internal morphology of a new species of excavate flagellate which inhabits the saline Novoe Lake (Orenburg oblast, Russia) is considered. A cell of the flagellate has four naked flagella (one long and three short) extending parallel to each other. The long and one short flagella terminate with an acroneme. Three microtubular bands reinforce the longitudinal ventral groove. The vesicular nucleus lies in the anterior part of the cell. The mithochondria have discoid cristae. The system of submembrane microtubules originates from the fibrils close to the kinetosome and extends to the end of the posterior cell. A small bulbous projection is seen at the tip of the end of the posterior cell. Dictyosomes of the Golgi apparatus are not found. The lifecycle includes spherical thick-walled cysts that have a single hole with a plug. The external structure of the cell and cysts of a similar species, Percolomonas cosmopolitus, is compared to that in P. lacustris. The new species differs from the known ones by the presence of a posterior bulbous projection, a hole and plug inside the cyst, an acroneme of one short flagellum, and other features.     

A comparative study of electronic and neural networks involved in pattern recognition

The comparative study of electronic and neural networks involved in pattern recognition starts with the analogies of structure and function which exist between the electronic “basic integrative unit” and the neuron. Both elements represent the basic components in each system of networks and may be considered as functionally equivalent.According to the kind of response given to a standard input signal, four types of integrative units, either electronic or neural, may be distinguished: the fixed, the accommodative, the signal prolongating and the adaptive type.The integrative units perform many different functions. Those involved in pattern recognition, however, can all be grouped into three categories according to one of the following functions they perform: contrast detection, pattern detection and pattern discrimination. A “contrast detecting unit” gives responses in two senses, positive or negative, according to the position of the stimulus over its receptive field. A “pattern detecting unit” gives responses in one sense only, with a maximum for a pattern having the spatial distribution corresponding to the positive acting receptors of its receptive field. For performing the function of discrimination, which leads to reliable identification of any pattern, a network arrangement called a “maximum amplitude filter” is necessary. Examples of such units and arrangements existing in the nervous system are provided.It is concluded that a “logical analysis of neural networks” based on engineering principles is possible and that this could provide a new tool to the neurophysiologist in the study of the nervous system.     

嘉庚蛸雌性生殖系统组织学观察

对象山港自然海区中的嘉庚蛸(Octopus tankahkeei)雌性生殖系统的组织学结构进行了研究.结果表明,雌性生殖系统由卵巢、输卵管、输卵管腺组成.卵巢单个、球形,内包裹滤泡细胞围成的卵子,输卵管1对,开口于外套腔中部,每条输卵管中部膨大形成圆球状的输卵管腺.近端输卵管内具两瓣蘑菇状突起,上有不规则短指状分枝,突...     

Structure of poly (dT).poly (dA).poly (dT)

The molecular structure of poly (dT).poly (dA).poly (dT) has been determined and refined using the continuous x-ray intensity data on layer lines in the diffraction pattern obtained from an oriented fiber of the DNA. The final R-value for the preferred structure is 0.29 significantly lower than that for plausible alternatives. The molecule forms a 12-fold right-handed triple-helix of pitch 38.4 A and each base triplet is stabilized by a set of four Crick-Watson-Hoogsteen hydrogen bonds. The deoxyribose rings in all the three strands have C2'-endo conformations. The grooveless cylindrical shape of the triple-helix is consistent with the lack of lateral organization in the fiber.     

Enhancing the activity of insulin at the receptor interface: crystal structure and photo-cross-linking of A8 analogues

The receptor-binding surface of insulin is broadly conserved, reflecting its evolutionary optimization. Neighboring positions nevertheless offer an opportunity to enhance activity, through either transmitted structural changes or introduction of novel contacts. Nonconserved residue A8 is of particular interest as Thr(A8) --> His substitution (a species variant in birds and fish) augments the potency of human insulin. Diverse A8 substitutions are well tolerated, suggesting that the hormone-receptor interface is not tightly packed at this site. To resolve whether enhanced activity is directly or indirectly mediated by the variant A8 side chain, we have determined the crystal structure of His(A8)-insulin and investigated the photo-cross-linking properties of an A8 analogue containing p-azidophenylalanine. The structure, characterized as a T(3)R(3)(f) zinc hexamer at 1.8 A resolution, is essentially identical to that of native insulin. The photoactivatable analogue exhibits efficient cross-linking to the insulin receptor. The site of cross-linking lies within a 14 kDa C-terminal domain of the alpha-subunit. This contact, to our knowledge the first to be demonstrated from the A chain, is inconsistent with a recent model of the hormone-receptor complex derived from electron microscopy. Optimizing the binding interaction of a nonconserved side chain on the surface of insulin may thus enhance its activity.