Empty Structures Research Articles

Proteins as Sponges: A Statistical Journey along Protein Structure Organization Principles

The analysis of a large database of protein structures by means of topological and shape indexes inspired by complex network and fractal analysis shed light on some organizational principles of proteins. Proteins appear much more similar to "fractal" sponges than to closely packed spheres, casting doubts on the tenability of the hydrophobic core concept. Principal component analysis highlighted three main order parameters shaping the protein universe: (1) "size", with the consequent generation of progressively less dense and more empty structures at an increasing number of residues, (2) "microscopic structuring", linked to the existence of a spectrum going from the prevalence of heterologous (different hydrophobicity) to the prevalence of homologous (similar hydrophobicity) contacts, and (3) "fractal shape", an organizing protein data set along a continuum going from approximately linear to very intermingled structures. Perhaps the time has come for seriously taking into consideration the real relevance of time-honored principles like the hydrophobic core and hydrophobic effect.

Role of the Transmembrane Domain 4/Extracellular Loop 2 Junction of the Human Gonadotropin-releasing Hormone Receptor in Ligand Binding and Receptor Conformational Selection

Recent crystal structures of G protein-coupled receptors (GPCRs) show the remarkable structural diversity of extracellular loop 2 (ECL2), implying its potential role in ligand binding and ligand-induced receptor conformational selectivity. Here we have applied molecular modeling and mutagenesis studies to the TM4/ECL2 junction (residues Pro(174(4.59))-Met(180(4.66))) of the human gonadotropin-releasing hormone (GnRH) receptor, which uniquely has one functional type of receptor but two endogenous ligands in humans. We suggest that the above residues assume an α-helical extension of TM4 in which the side chains of Gln(174(4.60)) and Phe(178(4.64)) face toward the central ligand binding pocket to make H-bond and aromatic contacts with pGlu(1) and Trp(3) of both GnRH I and GnRH II, respectively. The interaction between the side chains of Phe(178(4.64)) of the receptor and Trp(3) of the GnRHs was supported by reciprocal mutations of the interacting residues. Interestingly, alanine mutations of Leu(175(4.61)), Ile(177(4.63)), and Met(180(4.66)) decreased mutant receptor affinity for GnRH I but, in contrast, increased affinity for GnRH II. This suggests that these residues make intramolecular or intermolecular contacts with residues of transmembrane (TM) domain 3, TM5, or the phospholipid bilayer, which couple the ligand structure to specific receptor conformational switches. The marked decrease in signaling efficacy of I177A and F178A also indicates that IIe(177(4.63)) and Phe(178(4.64)) are important in stabilizing receptor-active conformations. These findings suggest that the TM4/ECL2 junction is crucial for peptide ligand binding and, consequently, for ligand-induced receptor conformational selection.

Class 1 integrons in environmental and clinical isolates of Pseudomonas aeruginosa

The aims of this study were to ascertain the presence and spread of class 1 integrons amongst environmental and clinical isolates of Pseudomonas aeruginosa and to characterise their variable regions. A total of 76 isolates (56 clinical and 20 environmental) were studied. The presence of plasmids was explored, and polymerase chain reaction (PCR) was used for integron detection. All amplicons were sequenced. PCR detected class 1 integrons in 26 of the 56 clinical isolates; environmental isolates were integron-free. No plasmids were found, thus all the integrons found are possibly on the chromosome. Most isolates presented one amplicon, except PA110514 and PA116136, which showed two PCR products each. Variable regions revealed that 18 strains carried only one gene involved in aminoglycoside resistance, whereas in 3 strains gene cassettes were not found. The most prevalent cassettes amongst isolates were those encoding aminoglycoside adenyltransferase B (aadB). Several of the strains had acquired the same or a highly similar cassette array as those detected in geographically distant P. aeruginosa. This finding suggests that contact with bacterial reservoirs contributes to the evolution of this pathogen towards multiresistance. Empty structures found may represent a reservoir increasing the capacity to adapt to the environment. However, these integrons are not retained when the selective pressure disappears. It is hypothesised that integrons containing gene cassettes are crucial vehicles for the rapid horizontal transfer of resistance. If this is so, reduced use of antibiotics may lead to a significant decrease in the carriage of integrons amongst P. aeruginosa strains.

Empty level structure of boryl-substituted pentacyclic heteroaromatics

Extended π-conjugation in molecular systems is being extensively exploited in a rapidly expanding range of electronic and photonic applications. The modification of such extended systems through the use of heteroatoms allows their tailoring to specific requirements. In particular, the use of the vacant boron p(π) orbital can increase the electron affinity of the extended π system in an analogous fashion to the p-doping of crystalline silicon used in more classical microelectronic devices. Experimental data on such modifications of the empty level structures of boron-containing π-electron materials leading to an increase in their electron affinity are not available in the literature. Using Electron Transmission Spectroscopy, the energies of the vertical anion formation of 5-methyl-2-furanboronic acid pinacol ester (1) and 4-methyl-3-thiopheneboronic acid pinacol ester (2) are measured and compared with those of the reference unsubstituted heteroaromatics furan and thiophene. The results are interpreted with the support of density functional theory (DFT) calculations with the B3LYP functional. DFT calculations are also used to predict the effects of boryl substituents on the electronic and geometrical structures of trans and cis thienyl thiazole.

A novel synthesis method to produce silver-doped CeO2 nanotubes based on Ag nanowire templates

Silver nanowires were used as templates to synthesize silver-doped CeO(2) (Ag-CeO(2)) nanotubes by the precipitation method. The precipitated solid was dried at 100 °C for 24 h and calcined at 500 °C for 5 h. A TEM, HRTEM, LV-SEM and XRD study was carried out to determine the micro and nanostructural characteristics of the samples. LV-SEM analysis allowed us to observe microtubular empty structures constituted by Ce, O and Ag as indicated by EDS. These tubular structures, with an external diameter from 120 to 280 nm and an internal diameter from 40 to 80 nm, were mainly composed of 11 nm ceria nanoparticles. This kind of structures was obtained when CeO(2) nanoparticles covered the Ag nanowires during the synthesis. Due to the presence of ammonium hydroxide used during the synthesis, a fraction of the silver nanowire reacts and Ag atoms begin to migrate outside the ceria microtube. When the sintering process is applied, the Kirkendall effect can occur. So, out-diffusion of the remnant Ag through the interface is faster than the in-diffusion of the shell material (CeO(2)), which eventually results in a coaxial nanotube on completion of the non-equilibrium interdiffusion, leaving the central core completely empty, driving the formation of hollow tubular Ag-CeO(2) structures as a result.

The E6 protein from vaccinia virus is required for the formation of immature virions

An IPTG-inducible mutant in the E6R gene of vaccinia virus was used to study the role of the E6 virion core protein in viral replication. In the absence of the inducer, the mutant exhibited a normal pattern DNA replication, concatemer resolution and late gene expression, but it showed an inhibition of virion structural protein processing it failed to produce infectious particles. Electron microscopic analysis showed that in the absence of IPTG viral morphogenesis was arrested before IV formation: crescents, aberrant or empty IV-like structures, and large aggregated virosomes were observed throughout the cytoplasm. The addition of IPTG to release a 12-h block showed that virus infectious particles could be formed in the absence of de novo DNA synthesis. Our observations show that in the absence of E6 the association of viroplasm with viral membrane crescents is impaired.

The phase diagram of water at negative pressures: Virtual ices

The phase diagram of water at negative pressures as obtained from computer simulations for two models of water, TIP4P/2005 and TIP5P is presented. Several solid structures with lower densities than ice Ih, so-called virtual ices, were considered as possible candidates to occupy the negative pressure region of the phase diagram of water. In particular the empty hydrate structures sI, sII, and sH and another, recently proposed, low-density ice structure. The relative stabilities of these structures at 0 K was determined using empirical water potentials and density functional theory calculations. By performing free energy calculations and Gibbs-Duhem integration the phase diagram of TIP4P/2005 was determined at negative pressures. The empty hydrates sII and sH appear to be the stable solid phases of water at negative pressures. The phase boundary between ice Ih and sII clathrate occurs at moderate negative pressures, while at large negative pressures sH becomes the most stable phase. This behavior is in reasonable agreement with what is observed in density functional theory calculations.

Evidence of 'genuine empty follicles' in follicular aspirate: a case report

Failure to retrieve oocytes after normal ovarian stimulation has been labeled 'empty follicle syndrome' (EFS). The existence of genuine EFS has been questioned and is still controversial. Here, we report an unusual case in which an extraordinary number of empty follicle-like structures were identified in the ovarian aspirate at the time of retrieval. A 31-year-old woman presented with a 4-year history of primary infertility and underwent ovulation induction. The patient was given hCG and oocyte retrieval was performed 36 h later. During the oocyte retrieval, more than 200 tiny structures resembling pre-antral follicles were noted in the ovarian aspirate. They exhibited two to three layers of granulosa cells and appeared to enclose an immature oocyte. They showed a great variation in size ranging between 40 and 80 microm. These structures were further characterized by electron microscopy and cultivated in vitro to assess hormone secretion. The follicles were found to be devoid of oocytes, but each had a readily identifiable zona. Hormone assays revealed that these follicles were secreting increasing levels of estradiol. A second in vitro fertilization attempt gave similar results. These data are suggestive of some failure in the oocyte maturation process. We speculate that this may be the first actual evidence to support the existence of true empty follicles, which if left to grow in vivo might lead to empty graffian follicles and genuine EFS.

Generalized structural polymorphism in self-assembled viral particles.

The protein shells, called capsids, of nearly all spherical viruses adopt icosahedral symmetry; however, self-assembly of such empty structures often occurs with multiple misassembly steps resulting in the formation of aberrant structures. Using simple models that represent the coat proteins preassembled in the two different predetermined species that are common motifs of viral capsids (i.e., pentameric and hexameric capsomers), we perform molecular dynamics simulations of the spontaneous self-assembly of viral capsids of different sizes containing T = 1,3,4,7,9,12,13,16, and 19 proteins in their icosahedral repeating unit. We observe, in addition to icosahedral capsids, a variety of nonicosahedral yet highly ordered and enclosed capsules. Such structural polymorphism is demonstrated to be an inherent property of the coat proteins, independent of the capsid complexity and the elementary kinetic mechanisms. Moreover, there exist two distinctive classes of polymorphic structures: aberrant capsules that are larger than their respective icosahedral capsids, in T = 1-7 systems; and capsules that are smaller than their respective icosahedral capsids when T = 7-19. Different kinetic mechanisms responsible for self-assembly of those classes of aberrant structures are deciphered, providing insights into the control of the self-assembly of icosahedral capsids.

Evidence of “genuine empty follicles”?: A case report

OBJECTIVE: Failure to retrieve oocytes after normal ovarian stimulation has been labeled “empty follicle syndrome” (EFS).This syndrome is not well characterized and its cause remains controversial. The existence of genuine EFS has been questioned and it has been suggested that “unsuccessful oocyte retrieval” would be a more appropriate label. In this report, we describe a an unusual case in which an extraordinary number of empty follicle-like structures were identified in the follicular fluid aspirate of a patient undergoing a routine IVF cycle.DESIGN: Case report.MATERIALS AND METHODS: A 31 year old woman presented with a 4 year history of primary infertility. Ovarian stimulation was carried out using a long luteal phase Lupron protocol with 200 units of recombinant FSH for 10 days. The patient was given hCG and the oocyte retrieval was performed 36 hours later using a standard double lumen needle.RESULTS: During the course of the oocyte retrieval, over 200 tiny structures resembling pre-antral follicles were noted in the follicular aspirate. These pre-antral follicle-like structures were further examined at 300 x magnification using an inverted microsope. They exhibited 2-3 layers of granulose cells and appeared to be surrounding what we presumed was an immature oocyte. They showed a great variation in size ranging from 40-80 microns in diameter. The isolated follicles were placed in culture for 48 hours for maturation. To establish nuclear status and better visualize the oocyte, we treated some of the follicles with hyaluronidase and stripped away the granulose cells. Interestingly, none of the “follicles” contained an oocyte but there was a very thin zona present in each of these entities. We subsequently examined over 40 of these “follicle-like” structures in this manner. All were found to be devoid of an oocyte but each had a readily identifiable zona. Hormone assays on the culture supernatant indicated that these follicle-like structures were secreting increasing levels of estradiol.Electron microscopy was also performed. A second IVF cycle gave similar results.CONCLUSIONS: The identification of over 200 pre-antral follicle-like structures that secreted estradiol and contained a zona devoid of an acutal oocyte is suggestive of some failure in the oocyte maturation process. We speculate that this may be the first actual evidence to support the existence of true empty follicles, which if left to grow in vivo might lead to empty Graffian follicles and genuine EFS. OBJECTIVE: Failure to retrieve oocytes after normal ovarian stimulation has been labeled “empty follicle syndrome” (EFS).This syndrome is not well characterized and its cause remains controversial. The existence of genuine EFS has been questioned and it has been suggested that “unsuccessful oocyte retrieval” would be a more appropriate label. In this report, we describe a an unusual case in which an extraordinary number of empty follicle-like structures were identified in the follicular fluid aspirate of a patient undergoing a routine IVF cycle. DESIGN: Case report. MATERIALS AND METHODS: A 31 year old woman presented with a 4 year history of primary infertility. Ovarian stimulation was carried out using a long luteal phase Lupron protocol with 200 units of recombinant FSH for 10 days. The patient was given hCG and the oocyte retrieval was performed 36 hours later using a standard double lumen needle. RESULTS: During the course of the oocyte retrieval, over 200 tiny structures resembling pre-antral follicles were noted in the follicular aspirate. These pre-antral follicle-like structures were further examined at 300 x magnification using an inverted microsope. They exhibited 2-3 layers of granulose cells and appeared to be surrounding what we presumed was an immature oocyte. They showed a great variation in size ranging from 40-80 microns in diameter. The isolated follicles were placed in culture for 48 hours for maturation. To establish nuclear status and better visualize the oocyte, we treated some of the follicles with hyaluronidase and stripped away the granulose cells. Interestingly, none of the “follicles” contained an oocyte but there was a very thin zona present in each of these entities. We subsequently examined over 40 of these “follicle-like” structures in this manner. All were found to be devoid of an oocyte but each had a readily identifiable zona. Hormone assays on the culture supernatant indicated that these follicle-like structures were secreting increasing levels of estradiol.Electron microscopy was also performed. A second IVF cycle gave similar results. CONCLUSIONS: The identification of over 200 pre-antral follicle-like structures that secreted estradiol and contained a zona devoid of an acutal oocyte is suggestive of some failure in the oocyte maturation process. We speculate that this may be the first actual evidence to support the existence of true empty follicles, which if left to grow in vivo might lead to empty Graffian follicles and genuine EFS.

Probing the Molecular and Electronic Structure of Capsaicin: A Spectroscopic and Quantum Mechanical Study

The conformational preferences of capsaicin were investigated by using the hybrid meta density functional theory (DFT) method MPWB1K. Its flexible, pendant side chain allows for a multitude of conformations only slightly different in energy. The distinctive vibrational features of the most stable conformers were characterized. To elucidate the most favorable reaction sites of capsaicin for radical scavenging, various homolytic bond-dissociation energies were also calculated. Of the possible radical intermediates, the allyl and benzyl radicals are energetically preferred. The filled and empty electronic structures of capsaicin were investigated by exploiting the photoelectron and electron-transmission spectra also of reference molecules and suitable quantum-mechanical calculations. On this basis, a reliable pattern of the vertical ionization energies and electron-attachment energies of capsaicin was proposed. The frontier pi molecular orbitals are concentrated over the vanillyl moiety, with a modest influence of the amidic-aliphatic chain. The (negative) first vertical electron affinity is predicted to be similar to that of benzene. The absorption spectrum of capsaicin and its change by conversion into a phenolic deprotonated anion (modest bathochromic displacement) or a phenoxyl neutral radical (from colorless to red) were interpreted with time-dependent DFT calculations. ESR measurements following chemical or electrochemical reduction of capsaicin did not lead to detection of the corresponding radical anion. The spectra show fragmentation of the original molecule and formation of a variety of radical species which are believed to have a semiquinonic structure.

Morphing Lennard–Jones clusters to TIP4P water clusters: Why do water clusters look like they do?

Cluster structures with globally minimal energy have been determined for a potential that was varied smoothly between an isotropic Lennard–Jones pair potential and the full TIP4P water potential, for cluster sizes between 4 and 22 molecules. Intermediate rhombohedral structures have been discovered that directly link the close-packed Lennard–Jones structures with the typical water cluster building blocks, explaining the occurence of the latter. Among these rhombohedral intermediates are the highly symmetric rhombic dodecahedron, which seeds the typical water-centered cage structures, and a 6-ring nanotube around a water dimer, which is directly related to the Lennard–Jones double icosahedron. The known qualitative defect of the TIP4P potential (preference of empty prismatic structures over molecule-centered cages at larger cluster sizes) would almost disappear at a 30% damping of the Coulomb term, without deterioration of the results at other cluster sizes.

Doping Golden Buckyballs: Cu@Au16‐ and Cu@Au17‐ Cluster Anions.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

Doping Golden Buckyballs: Cu@Au16− and Cu@Au17− Cluster Anions

The discovery of the unique catalytic effects of gold nanoparticles on oxide substrates has stimulated a flurry of research into the structures and properties of free gold nanoclusters, which may hold the key to elucidating the catalytic mechanisms of supported gold clusters. One of the most remarkable results has been the discovery of planar gold cluster anions (Aun_) of up to twelve gold atoms and the 2D to 3D transition for clusters with n larger than 12. Among larger gold clusters, Au20 has been found to be a perfect tetrahedron. A more recent study of the structures of Aun_ cluster anions in the medium size range (n=15–19) has shown that clusters with n=16–18 possess unprecedented empty cage structures. In particular, the Au16_ cluster anion has an interesting tetrahedral structure with an inner diameter of about 5.5 0 and can be compared to the fullerenes (buckyballs). Although Au32 was first suggested to be a “24- carat golden fullerene”, subsequent studies showed that the Au32_ ion is in fact a low-symmetry compact 3D structure. Other larger gold cage clusters have also been proposed computationally, but none has been observed or is expected to be the global minimum. The cage structures of themore » cluster anions Au16_ and Au17_ have recently been confirmed by electron diffraction and thus they are the first experimentally confirmed and the smallest possible gold cages. The large empty space inside these cage clusters immediately suggested that they can be doped with a foreign atom to produce a new class of endohedral gold cages analogous to endohedral fullerenes.« less

Temporary anion states and dissociative electron attachment to nitrobenzene derivatives

The nitrobenzene derivatives 1,2-nitrotoluene, 1,3-nitrotoluene, 1,2-fluoronitrobenzene, 1,3-fluoronitrobenzene, 1,4-fluoronitrobenzene, 1,2-chloronitrobenzene, 1,3-chloronitrobenzene and 1,4-chloronitrobenzene are investigated by means of electron transmission spectroscopy (ETS), dissociative electron attachment spectroscopy (DEAS) and negative ion mass spectrometry (NIMS). The observed energies of electron attachment to π* MOs were interpreted with the support of the empty level structures of the neutral molecules supplied by HF/6-31G and B3LYP/6-31G* calculations. In the chlorine-substituted derivatives three main long-lived negative ions (NIs) (M −, Cl −, and NO 2 −) are observed, only M − and NO 2 − in the other investigated compounds. The detection of the metastable NIs corresponding to the process M* − → R − + (M–R) suggests that the molecular NIs formed near thermal electron energy dissociate on a microsecond timescale. Mean autodetachment lifetimes of the molecular NIs as a function of electron energy are evaluated.

A Guest‐Free Germanium Clathrate.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

A guest-free germanium clathrate

The challenges associated with synthesizing expanded semiconductor frameworks with cage-like crystal structures continue to be of interest. Filled low-density germanium and silicon framework structures have distinct properties that address important issues in thermoelectric phonon glass-electron crystals, superconductivity and the possibility of Kondo insulators. Interest in empty framework structures of silicon and germanium is motivated by their predicted wide optical bandgaps of the same magnitude as quantum dots and porous silicon, making them and their alloys promising materials for silicon-based optoelectronic devices. Although almost-empty Na(1-x)Si136 has already been reported, the synthesis of guest-free germanium clathrate has so far been unsuccessful. Here we report the high-yield synthesis and characteristics of germanium with the empty clathrate-II structure through the oxidation of Zintl anions in ionic liquids under ambient conditions. The approach demonstrates the potential of ionic liquids as media for the reactions of polar intermetallic phases.

The Floral Scales in Hellmuthia (Cyperaceae, Cyperoideae) and Paramapania (Cyperaceae, Mapanioideae): An Ontogenetic Study

In 1976 the monotypic genus Hellmuthia was placed in the Hypolytreae s.l., but was subsequently ascribed to the Mapanioideae, tribe Chrysitricheae, mainly because of the presence in Hellmuthia of two lateral, mapanioid-like floral scales with ciliated keels, the anatomy of the nutlet, the embryo and the inflorescence. Recently, based on cladistic analyses and supported by pollen ontogenetic evidence, Hellmuthia was transferred to a Cyperaceae, tribe Cypereae, clade mainly consisting of Ficinia and Isolepis. In this study, the floral ontogeny in Hellmuthia was investigated and compared with the floral ontogeny in Paramapania, with special attention for the floral scales. Freshly collected inflorescences of Hellmuthia membranacea and Paramapania parvibractea were investigated using scanning electron and light microscopy. In the conical 'spikelet' in Hellmuthia, proximal bracts occur, each axillating an axis with empty glume-like structures, or a reduced spikelet. Hence, it is a reduced partial inflorescence. In Hellmuthia, the stamen primordia originate before the primordia of the perianth-gynoecium appear. Moreover, a third adaxially positioned 'floral scale' was observed for the first time. The position and relative time of appearance of the floral scales in Hellmuthia are typical for perianth parts in Cyperoideae. The basal position of Hellmuthia within a clade of species with usually perianthless flowers, allows the presence of rudiments of a perianth in Hellmuthia to be interpreted as a primitive state. Development of the lateral 'scales' in Paramapania follows a different pattern. Therefore, it was decided that the lateral 'scales' in Paramapania are different from the lateral perianth parts in Hellmuthia. The pollen grains in Hellmuthia are cyperoid, with one polar and five lateral apertures, of which the membrane is covered with sexinous bodies. The pollen surface is granulate and perforate with microspines. The floral ontogeny in Hellmuthia occurs according to the general cyperoid pattern. The lateral scales in Hellmuthia are perianth parts, and they are not homologous to the lateral 'scales' in Paramapania.

Ultrastructure of maize necrotic streak virus infections.

Maize necrotic streak virus (MNeSV) has 32 nm isometric particles that encapsidate a single stranded RNA genome ca. 4.3 kb in size, and is a tentative member of the genus Tombusvirus. Since tombusviruses elicit the formation of cytopathological structures known as “multivesicular bodies” that assist in their classification at the genus level, the cytology of thin-sectioned maize leaf tissues 7, 15, and 45 days after inoculation was investigated. The prominent cytopathological features were: (i) an extensive accumulation of virus particles scattered throughout the cytoplasm or in crystalline arrays in the cytoplasm or, occasionally, in intercellular spaces; (ii) extensive plasmolysis and the appearance of small patches of amorphous, dark-staining material in the cytoplasm; (iii) the proliferation of membranes and the presence of empty double membrane-bound vesicular structures of various sizes. No apparent connection between these membranous elements and the nuclear envelope was detected, even when large clusters of vesicles were adpressed to the nuclei. Some of the largest double-membrane bound structures had rows of small vesicles located inside peripheral dilations of the bounding membrane. Although most of these structures appeared to originate from disintegrating mitochondria, they bore little resemblance to genuine multivesicular bodies like those arising from the modified mitochondria that follow infection by certain members of the family Tombusviridae, i.e. Carnation Italian ringspot virus, Pelargonium necrotic spot virus (PNSV), Galinsoga mosaic virus (GaMV), and Turnip crinkle virus (TCV). Immunogold labelling using antibodies to virus particles was detected over cytoplasm associated with virus particles and patches of electrondense amorphous material, suggesting that this material consists of virus coat protein.

Account of three-body interactions in the lattice dynamics method

The lattice dynamics method is extended with the account of three-body interaction potential in the harmonic approximation. Analytic expressions for the force constants and dynamical matrix elements are presented. Dynamical matrix element responsible for indirect interaction of atoms is single out. Modeling calculations of phonon spectra at the center of Brillouin zone for empty silicon clathrate structures Si 34 and Si 46 have been performed.