Gramicidin A aggregation in supported gel state phosphatidylcholine bilayers

Using an atomic force microscope, supported bilayers of saturated phosphatidylcholine (in the gel state) containing various amounts of gramicidin A (gA) were imaged in aqueous solutions and at room temperature. gA clusters were directly observed for the first time under these conditions. It was found that, at a lower gA concentration, gA aggregated into domains, composed of small clusters along with a considerable amount of lipids. This basic aggregation unit, most likely a hexamer, remained the same for acyl chain lengths from 14 to 18 carbons. These small clusters were observed to form elongated aggregates (line type) but never into extended pure gA domains. When gA concentrations were increased, for bilayers with 16 carbons or less, gA aggregated into larger domains but the basic unit remained separated by lipid molecules. At about 5 mol % gA, a percolation-like transition occurred at which the line type aggregates were connected to each other. However, for bilayers with more than 16 carbons, multiple lamellar structures were formed at higher gA fractions and the top layer had a ripple-like surface morphology. The molecular mechanism for the formation of these peculiar structures remains to be elucidated.     

Environmental aspects of near-neutral pH stress corrosion cracking of pipeline steel

The severity of four different soil environments toward the development of near-neutral pH stress corrosion cracking (SCC) of pipeline steel was evaluated using slow strain-rate testing (SSRT). These soils were collected from pipeline sites where near-neutral pH SCC has been observed. It was demonstrated in this investigation that SSRT can differentiate the severity of various soil electrolytes to near-neutral pH SCC. For different soils, the relative susceptibility was found to be determined by the pH values of the soil electrolytes in equilibrium with a given CO₂/N₂ gas mixture. The higher the pH value up to ∼7, the more conducive the soil electrolyte was to near-neutral pH SCC. The pH value in a soil electrolyte was found to depend on the level of CO₂ in the soil solution and the initial HCO ₃ ⁻ concentration before the introduction of CO₂. For a given soil, the susceptibility depends on the actual level of CO₂ in the soil electrolyte. Higher levels of CO₂ lower the pH in the soil electrolyte and tend to increase the susceptibility to SCC. In laboratory tests, cathodic polarization was found to increase the susceptibility to failure, possibly by inhibiting general corrosion, which otherwise removed discrete stress-raising pits and defects from the specimen surface that acted as crack initiation sites or by increasing the extent of hydrogen-induced crack initiation or propagation. In the field, cathodic polarization is likely to prevent near-neutral pH SCC by increasing the pH at the pipe surface to values greater than 7.5. The pH was maintained near-neutral in the lab tests by continuous purging of the test solution with CO₂/N₂. A method is proposed for assessing the relative aggressiveness of various soil extracts to near-neutral pH SCC. Aggressive soil extracts appear to exhibit a narrower variation in pH between solutions purged with N₂ and with CO₂ than that for less-aggressive soil extracts purged with the same gases.     

Sodium dodecyl sulfate-polyacrylamide gel electrophoretic method for assessing the quaternary state and comparative thermostability of avidin and streptavidin

Avidin, a positively charged egg-white protein, aggregates extensively when mixed at ambient temperatures with anionic detergents, such as sodium dodecyl sulfate (SDS). The resultant aggregates fail to penetrate the stacking gel during polyacrylamide gel electrophoresis (PAGE). To prevent the formation of such aggregates, avidin was acetylated and the pI was thus reduced. Acetylated avidin was found to behave in a manner similar to that of streptavidin; under nondenaturing conditions (i.e., incubation of samples at room temperature), both proteins normally migrated mainly as tetramers with a tendency to form oligomers of the tetramer. When samples were boiled, both proteins migrated mainly as the monomer. The comparative stability properties of avidin and streptavidin were also examined using SDS-PAGE by heating samples and determining the extent of dissociation of tetramers to monomers as a function of temperature. A distinctive transition temperature could be defined for individual samples. Using this assay, it was determined that, in the absence of biotin, the quaternary structure of streptavidin is more stable than that of avidin. Biotin appears to stabilize structures of both avidin and streptavidin to a similar degree. Acetylation of avidin thus provides a simple means to analyze the quaternary structure of the molecule using SDS-PAGE.     

Control of protein-ligand recognition using a stimuli-responsive polymer

Stimuli-responsive polymers exhibit reversible phase changes in response to changes in environmental factors such as pH or temperature. Conjugating such polymers to antibodies and proteins provides molecular systems for applications such as affinity separations, immunoassays and enzyme recovery and recycling. Here we show that conjugating a temperature-sensitive polymer to a genetically engineered site on a protein allows the protein's ligand binding affinity to be controlled. We synthesized a mutant of the protein streptavidin to enable site-specific conjugation of the responsive polymer near the protein's binding site. Normal binding of biotin to the modified protein occurs below 32 degrees C, whereas above this temperature the polymer collapses and blocks binding. The collapse of the polymer and thus the enabling and disabling of binding, is reversible. Such environmentally triggered control of binding may find many applications in biotechnology and biomedicine, such as the control of enzyme reaction rates and of biosensor activity, and the controlled release of drugs.     

Silicatein filaments and subunits from a marine sponge direct the polymerization of silica and silicones in vitro

Nanoscale control of the polymerization of silicon and oxygen determines the structures and properties of a wide range of siloxane-based materials, including glasses, ceramics, mesoporous molecular sieves and catalysts, elastomers, resins, insulators, optical coatings, and photoluminescent polymers. In contrast to anthropogenic and geological syntheses of these materials that require extremes of temperature, pressure, or pH, living systems produce a remarkable diversity of nanostructured silicates at ambient temperatures and pressures and at near-neutral pH. We show here that the protein filaments and their constituent subunits comprising the axial cores of silica spicules in a marine sponge chemically and spatially direct the polymerization of silica and silicone polymer networks from the corresponding alkoxide substrates in vitro, under conditions in which such syntheses otherwise require either an acid or base catalyst. Homology of the principal protein to the well known enzyme cathepsin L points to a possible reaction mechanism that is supported by recent site-directed mutagenesis experiments. The catalytic activity of the "silicatein" (silica protein) molecule suggests new routes to the synthesis of silicon-based materials.     

Stability of Silicate Coatings on Pyrite Surfaces in a Low pH Environment

The suppression of pyrite oxidation due to the formation of stable coatings of Fe3+–silica and/or Fe3+–hydroxy–silica complexes over pyrite surfaces in near-neutral and neutral solution pHs is well documented. On the contrary, there is currently no convincing experimental evidence that proves the existence of such a coating under low pH environments. Aqueous continuous flow kinetic experiments were conducted using coating solutions containing Na2SiO3?5H2O and H2O2 at pH 6, 4, 3, and 2. Results showed that at pH 2, pyrite oxidation in the presence of silica is pseudofirst order and oxidation is not inhibited by silica. At pH 6, silica significantly reduced pyrite oxidation via a pseudofirst-order reaction that takes on several stages related to changes in the relative contributions of H2O2 and Fe3+. Iron speciation data suggests a surface adsorption mechanism at pH 6 and an electrochemical mechanism at pH 2 for pyrite oxidation. Scanning electron microscopy and energy dispersive x-ray spectroscopy also support the kinetic model and showed the absence of any significant silica coating at pH 2.     

Cloning, expression and reconstitution of the trypanothione-dependent peroxidase system of Crithidia fasciculata

Tyrosine phosphoproteins of size 115-120 kDa were purified from membranes of chicken embryo fibroblasts (CEF) infected with Rous sarcoma virus (RSV). A mouse was immunized with these proteins, and the immune serum was used to screen a CEF cDNA expression library. A highly immunoreactive clone (KS5) was identified and characterized. The cDNA of this clone is 2.3 kb in length with a short 5' UTR and a single major open reading frame (ORF) encoding a polypeptide of 719 amino acids, with a calculated molecular weight of 81.1 kDa. The encoded protein contains an amino terminal PDZ domain, followed by a predicted coiled-coil region, a PEST domain, and a carboxy-terminal SAM domain. Consensus sequence motifs for tyrosine phosphorylation are also present, as are consensus sequences for the binding of SH2 and PDZ domains. Antisera from mice immunized with bacterially expressed fragments of the KS5 protein recognized proteins of size 230, 116, and 65 kDa in CEF. In other chicken embryo tissues, a 116-kDa species was the predominant protein recognized. The 116-kDa species is tyrosine-phosphorylated in RSV-CEF. The presence of PDZ and SAM domains in the KS5 protein suggests that it may act as a molecular adaptor, promoting and relaying information in a signal transduction pathway. It is a member of a family of related proteins, all of which have a highly conserved PDZ domain adjacent to a coiled-coil region. Two other members of this family are the neuronal proteins spinophilin (Allen, P.B., Ouimet, C.C., Greengard, P., 1997. Spinophilin, a novel protein phosphatase 1 binding protein localized to dendritic spines. Proc. Natl. Acad. Sci. USA 94, 9956-9961) and neurabin (Nakanishi, H., Obaishi, H., Satoh, A., Wada, M., Mandai, K., Satoh, K., Nishioka, H., Matsuura, Y., Mizoguchi, A. , Takai, Y., 1997. Neurabin: A novel neural tissue-specific actin filament-binding protein involved in neurite formation. J. Cell Biol. 139, 951-961).     

C repeats of the streptococcal M1 protein achieve the human serum albumin binding ability by flanking regions which stabilize the coiled-coil conformation

The M and M-like proteins of Streptococcus pyogenes are fibrous cell surface proteins. They have multiple binding sites for several human proteins and are composed of the C-terminal anchor domain, the alpha-helical coiled-coil domain, and the N-terminal non-coiled-coil domain. The coiled-coil domain of the M1 protein consists of repeat units called B, C, and D and a spacer unit S between B and C. Recombinant fragments A-B-S-C-D, A-B-S, B-S-C, S-C, S-C-D, C-D, and C of the coiled-coil domain were studied by analyzing their secondary structures and binding affinities to human serum albumin (HSA). As shown by circular dichroism, all fragments are in an alpha-helical conformation. C-D and S-C-D form coiled coils at room temperature and bind below 37 degrees C with high affinity to HSA. C-D and S-C-D unfold in two steps with Tm values of approximately 31 and approximately 65 degrees C; complex formation with HSA increases the unfolding temperatures. B-S-C has a lower alpha-helical content, a less pronounced coiled-coil conformation, and a reduced thermal stability, binds HSA weaker, and is only slightly stabilized by HSA binding in comparison to C-D and S-C-D. C and S-C are less stable than the other fragments and are not organized as coiled coils showing some features of alpha-helical single strands only below 20 degrees C, and binding of HSA was not observed. The results indicate that the formation of coiled-coil structures, supported by flanking D regions and, to a lesser extent also B regions, is essential for the binding of C repeat units to HSA.     

A controlled-release microchip

Much previous work in methods of achieving complex drug-release patterns has focused on pulsatile release from polymeric materials in response to specific stimuli, such as electric or magnetic fields, exposure to ultrasound, light or enzymes, and changes in pH or temperature. An alternative method for achieving pulsatile release involves using microfabrication technology to develop active devices that incorporate micrometre-scale pumps, valves and flow channels to deliver liquid solutions. Here we report a solid-state silicon microchip that can provide controlled release of single or multiple chemical substances on demand. The release mechanism is based on the electrochemical dissolution of thin anode membranes covering microreservoirs filled with chemicals in solid, liquid or gel form. We have conducted proof-of-principle release studies with a prototype microchip using gold and saline solution as a model electrode material and release medium, and we have demonstrated controlled, pulsatile release of chemical substances with this device.     

Staf, a promiscuous activator for enhanced transcription by RNA polymerases II and III

A monoclonal antibody, CML-1, raised against carrot (Daucus carota L.) nuclear-matrix proteins selectively labeled the nuclear periphery of carrot protoplasts when visualized by confocal and electron microscopy. To identify the constituent proteins of higher plant cells structurally homologous to the vertebrate nuclear lamina, we cloned overlapping cDNAs partially encoding a CML-1-recognized protein and determined the entire sequence including the open reading frame. When the deduced amino acid sequence was compared with other known protein sequences contained in major databases, no protein was found to show high sequence identity across the whole region of the protein, while the partial sequence showed strong similarities with myosin, tropomyosin, and some intermediate filament proteins. The protein, designated NMCP1, had an estimated molecular mass of 133.6 kDa and showed three characteristic domains. The central domain contains long alpha-helices exhibiting heptad repeats of apolar residues, demonstrating structural similarity to that of filament-forming proteins. The terminal domains are predominantly nonhelical and contain potential sequence motifs for nuclear localization signals. NMCP1 has many recognition motifs for different types of protein kinases, including cdc2 kinase and PKC. These results suggest that NMCP1 protein forms coiled-coil filaments and is a constituent of the peripheral architecture of the higher plant cell nucleus.     

Photodynamic modification of proteins in human red blood cell membranes, induced by protoporphyrin

Illumination of erythrocytes or erythrocyte membranes with visible light in the presence of protoporphyrin causes photodynamic damage of the cell membrane. This process is reflected a.o. by a mutilated ultrastructure and changes of the physical properties of the membrane proteins. Illumination in the presence of protoporphyrin causes association of membrane proteins, leading to blurring of the protein bands in electropheretograms, disappearance of bands and the appearance of protein aggregates on top of the gels. The formation of large protein aggregates is also indicated by Sephadex gel filtration of the solubilized membrane proteins. In kinetic studies it appeared that spectrin and the bands 2.1, 2.2, 2.3 and 6 are most susceptible and that band 3 is least susceptible to this cross-linking reaction. Experimental results indicate that this cross-linking is caused by direct photooxidation of membrane proteins. Peroxidation of unsaturated fatty acids is not involved in the process. The significance of this process for studies on membrane structure and on photodynamic membrane damage is discussed.     

The coiled-coil helix in the neck of kinesin

Kinesin is a microtubule-dependent motor protein. We have recently determined the X-ray structure of monomeric and dimeric kinesin from rat brain. The dimer consists of two motor domains, held together by their alpha-helical neck domains forming a coiled coil. Here we analyze the nature of the interactions in the neck domain (residues 339-370). Overall, the neck helix shows a heptad repeat (abcdefg)n typical of coiled coils, with mostly nonpolar residues in positions a and d. However, the first segment (339-355) contains several nonclassical residues in the a and d positions which tend to weaken the hydrophobic interaction along the common interface. Instead, stabilization is achieved by a hydrophobic "coat" formed by the a and d residues and the long aliphatic moieties of lysines and glutamates, extending away from the coiled-coil core. By contrast, the second segment of the kinesin neck (356-370) shows a classical leucine zipper pattern in which most of the hydrophobic residues are buried at the highly symmetrical dimer interface. The end of the neck reveals the structure of a potential coiled-coil "trigger" sequence.     

Precipitation and densification of magnetic iron compounds from aqueous solutions at room temperature

The advantages of generating stable and compact spinel-type precipitates from aqueous solutions at ambient temperature, instead of the amorphous and voluminous hydroxides obtained by conventional treatment of effluents are supported by experimental evidence. As a first step, the study of magnetite formation by controlled aerial oxidation of ferrous solutions at ambient temperature was considered. The parameters studied were: aerial oxidation intensity, precipitation pH, SO₄²⁻ concentration, initial Fe²⁺ concentration and aging of the sludges. The results suggest a close relation between precipitation pH and the kinetics of conversion of intermediate green rust-II into γ-FeOOH and/or Fe₃O₄. A precipitation pH between 10 and 11 and a well-controlled oxidant environment achieved by a moderate aeration of the solutions promoted suitable physical and chemical stability characteristics of quickly generated magnetite at ambient temperature. Furthermore, the minimum concentration of ferrous ions conducive to magnetite formation will be limited by the preexistent amount of dissolved oxygen in the starting solutions. Generated information was related to a laboratory-scale simulation of the `Recycle Process', but applied to the generation and densification of magnetic sludges. The stability conditions of iron precipitates allowed a better understanding of those transformations that occur in the stages of this process: aerated alkaline precipitation, solid/liquid separation, chemical conditioning of settled solids and their recycling to the precipitation stage.     

Identification of homo- and heteromeric interactions between members of the breast carcinoma-associated D52 protein family using the yeast two-hybrid system

The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family. Since D52-like protein sequences are all predicted to contain a coiled-coil domain, we used the yeast two-hybrid system and glutathione S-transferase pull-down assays to investigate whether homo- and/or heteromeric interactions occur between D52-like proteins. Analyses of yeast strains co-transfected with paired D52-like constructs indicated that D52-like fusion proteins interact in homo- and heteromeric fashions through their predicted coiled-coil domains. Similarly, extensive two-hybrid screenings of a human breast carcinoma expression library identified hD53 and hD52 as potential interactors for both hD52 and hD53 baits. Thus, D52-like proteins appear to exert and/or regulate their activities through specific interactions with other D52-like proteins, which in turn may be intrinsic to potential roles of these molecules in controlling cell proliferation.     

PAI-1 secretion and matrix deposition in human peritoneal mesothelial cell cultures: transcriptional regulation by TGF-beta 1

The thermally sensitive block copolymer, poly(N-isopropylacrylamide-b-dl-lactide) (PIPAAm-PLA), was synthesized by ring-opening polymerization of dl-lactide initiated from hydroxy-terminated poly (N-isopropylacrylamide) (PIPAAm). A PIPAAm bearing a single terminal hydroxyl group was prepared by telomerization using 2-hydroxyethanethiol as a chain-transfer agent. Successful preparation of PIPAAm and the PIPAAm-PLA block copolymer was verified by gel permeation chromatography (GPC) and 1H-NMR spectroscopy. Polymeric micelles were prepared from block copolymers using a dialysis method. Their solutions showed reversible changes in optical properties: transparent below a lower critical solution temperature (LCST) and opaque above the LCST. Dynamic light scattering measurements were used to observe the formation of micellar structures approximately 40 nm in diameter, which do not change between 20 degreesC and 30 degreesC. Above the LCST, polymer micelles aggregated, a phenomenon found to be reversible since the aggregates dissociated again by cooling below the LCST. Further observations using atomic force microscopy (AFM) confirmed this behaviour. The properties of this block copolymer system are interesting from both applied and fundamental perspectives, particularly for active targeting as drug carriers.     

Development of cellulose derivatives as novel enteric coating agents soluble at pH 3.5-4.5 and higher

Hydroxypropyl methylcellulose (HPMC) was selected as a base polymer to develop novel enteric coating agents for acid protection which can dissolve at pH around 4, and was modified with trimellitic acid or maleic acid at various degrees of substitution. These carboxylic acids have higher dissociation constants and higher solubility in water than the carboxylic acids of existing enteric coating polymers. The synthesized polymers were micronized and dispersed in aqueous medium to determine their pKa values by potentiometric titration. The pH of dissolution and the water vapor permeability of the cast films prepared from organic solutions were also evaluated. Hydroxypropyl methylcellulose trimellitate (HPMCT) showed good acid resistance, and the pH at which it dissolves can be controlled in the range of pH 3.5 to 4.5 by varying the content of trimellityl groups and the methoxyl substitution of the base polymer.     

The human LARGE gene from 22q12.3-q13.1 is a new, distinct member of the glycosyltransferase gene family

Meningioma, a tumor of the meninges covering the central nervous system, shows frequent loss of material from human chromosome 22. Homozygous and heterozygous deletions in meningiomas defined a candidate region of >1 Mbp in 22q12.3-q13.1 and directed us to gene cloning in this segment. We characterized a new member of the N-acetylglucosaminyltransferase gene family, the LARGE gene. It occupies >664 kilobases and is one of the largest human genes. The predicted 756-aa N-acetylglucosaminyltransferase encoded by LARGE displays features that are absent in other glycosyltransferases. The human like-acetylglucosaminyltransferase polypeptide is much longer and contains putative coiled-coil domains. We characterized the mouse LARGE ortholog, which encodes a protein 97.75% identical with the human counterpart. Both genes reveal ubiquitous expression as assessed by Northern blot analysis and in situ histochemistry. Chromosomal mapping of the mouse gene reveals that mouse chromosome 8C1 corresponds to human 22q12.3-q13.1. Abnormal glycosylation of proteins and glycosphingolipids has been shown as a mechanism behind an increased potential of tumor formation and/or progression. Human tumors overexpress ganglioside GD3 (NeuAcalpha2,8NeuAcalpha2, 3Galbeta1,4Glc-Cer), which in meningiomas correlates with deletions on chromosome 22. It is the first time that a glycosyltransferase gene is involved in tumor-specific genomic rearrangements. An abnormal function of the human like-acetylglucosaminyltransferase protein may be linked to the development/progression of meningioma by altering the composition of gangliosides and/or by effect(s) on other glycosylated molecules in tumor cells.     

Geometrical criteria for formation of coiled-coil structures of polypeptide chains

Crick's general formulas describing a coiled coil are expressed in a different form to combine the parameters of a coiled coil with the backbone dihedral angles of a polypeptide chain, assuming that the bond lengths and bond angles of the chain are fixed. While the existence of a low-energy coiled-coil conformation depends on energetic considerations, these formulas, which pertain to single-stranded structures and, by application of symmetry operations, to multistranded structures, provide the geometrical criteria for the existence of coiled coils. The concept of "the averaged structure of the minor helix", introduced here, makes it possible to relate the shape of the major helix to that of the minor helix. It is shown, in the analysis of a simple model of a single-stranded coiled-coil beta structure, that strong geometrical restrictions exist for the formation of coiled-coil structures from a given minor helix conformation of a polypeptide chain; these restrictions are expressed in a general form that is applicable to any coiled-coil of any number of residues in a repeat unit. As an application, the possible existence of a two-stranded coiled-coil antiparallel beta structure is considered, both geometrically and energetically, and discussed in relation to the observed twisted beta structures in globular proteins. The proposed coiled-coil models of alpha-helical proteins are also examined briefly.