Distribution by Scientific Domains
Distribution within Chemistry

Terms modified by Helical

  • helical arrangement
  • helical bundle
  • helical chain
  • helical coil
  • helical computed tomography
  • helical conformation
  • helical content
  • helical ct
  • helical domain
  • helical filament
  • helical form
  • helical hairpin
  • helical membrane protein
  • helical monomer
  • helical peptide
  • helical polymer
  • helical propensity
  • helical protein
  • helical region
  • helical regions
  • helical ribbon
  • helical secondary structure
  • helical segment
  • helical sense
  • helical structure
  • helical subdomain
  • helical twisting power

  • Selected Abstracts


    ABSTRACT The proportionality constant, ks, between shear rate, ,, and agitation velocity, N, for a helical ribbon-screw (HRS) agitator was 17.8. Using the HRS agitator, values of consistency index K and the flow behavior index n of 14 apple pulp suspensions at seven different solids concentrations and two average particle diameters 0.71 mm and 1.21 mm were determined; in addition, values of the Casson viscosity ,c and yield stress ,OC were also calculated. The magnitudes of K increased and of n decreased with increase in pulp concentration. Experimental values of the vane yield stress, ,O,, measured with a six-blade vane increased with increase in pulp content. The values of ,OC obtained using the Casson model were close to the experimental values ,O,. The effect of particle size on the relative viscosity, ,r, was correlated with Peclet number. [source]


    JOURNAL OF PHYCOLOGY, Issue 3 2005
    Zhi Ping Wang
    The cyanobacterium Spirulina Turpin is characterized by its regularly coiled trichomes. Under some conditions, its helical filaments can convert to abnormal morphologies, such as irregularly curved and even linear shapes, that had been considered as a permanent degeneration that could not be reversed. However, here we found that the linear filaments of Spirulina platensis Geitler could spontaneously revert to the helical form with the same morphology as the original filaments. Further studies showed that the ultrastructural, physiological, and biochemical characteristics of linear filaments were different from those of the original filaments, whereas they were the same for the reverted and the original filaments. The SDS-PAGE analysis revealed at least four proteins or subunits related to Spirulina morphogenesis: The 21.9-kDa and the 20.3-kDa proteins were highly expressed in the helical filaments, whereas the 52.0-kDa and the 31.8-kDa proteins were highly expressed in the linear filaments. The random amplified polymorphic DNA analysis with 96 random primers showed that the genetic background of the reverted filaments was the same as that of the original filaments but distinct from that of the linear filaments. The results indicated that linear filaments of Spirulina could revert to the original morphology under certain conditions, and their other distinctive traits were regained. [source]

    Helical- and ahelical-dependent chiral recognition mechanisms in capillary electrophoresis using amylose as the selector

    ELECTROPHORESIS, Issue 8 2009
    Weili Wei
    Abstract The present study discovered that helical structures of amylose were not always responsible for its chiral recognition abilities in CE. Several enantiomers with different structures were selected as models. Based on ultraviolet,visible spectroscopy and 13C NMR measurements, it was found that helical structures were gradually destroyed by temperature elevation and almost entirely transformed to extended ahelical structures above 60°C. Then, CE and 1H NMR chiral recognitions were investigated at different temperatures; chiral selectivity of the enantiomers varied in two different ways. Summarily, helical structures were necessary only for chiral separations of the enantiomers with small (<0.78,nm) and flexible molecular structures. However, for the gauche enantiomers (>0.78,nm) with high steric hindrances over their chiral centers, ahelical structures alone can realize chiral recognitions. By using iodine as a helix including competitor, it was further proved that helical structures functioned through the inclusive complexations only in the chiral separations of small enantiomers and had no effect for the others. The underlying mechanisms of the functions of helical and ahelical structures in molecular level were discussed as well. [source]

    Assemblies of Metal Nanoparticles and Self-Assembled Peptide Fibrils,Formation of Double Helical and Single-Chain Arrays of Metal Nanoparticles,

    ADVANCED MATERIALS, Issue 11 2003
    X. Fu
    Double helical and single-chain arrays of Au and Pd metal nanoclusters have been achieved by assembling the corresponding metal nanoparticles on peptide nanofibril templates at different pH values. The assembled metal nanoparticles are useful for studying the superstructures of the peptide nanofibrils. Pd nanowires of different shapes have also been prepared by varying the amount of metal deposition. [source]

    Consequences of Isostructural Main-Chain Modifications for the Design of Antimicrobial Foldamers: Helical Mimics of Host-Defense Peptides Based on a Heterogeneous Amide/Urea Backbone,

    ANGEWANDTE CHEMIE, Issue 2 2010
    Paul Claudon
    Wie Zwillinge: Oligoharnstoffe und ,-Peptide sind isostere und quasi-isostrukturelle helicale Foldamere mit besonderen Eigenschaften bei der biomolekularen Erkennung. Die Kombination dieser beiden Rückgrate in Harnstoff-Amid-Hybriden (siehe Bild) ergab wirksamere antimikrobielle helicale Foldamere mit verminderter Cytotoxizität. [source]

    Helical Bis(N-Confused Porphyrins) with Subunits Fused by Double Orthometalation with Platinum: Adaptability of an Apparently Rigid System,

    ANGEWANDTE CHEMIE, Issue 46 2009
    Starr und doch flexibel: Wegen der Flexibilität der Porphyrinringe gelingen Racemisierung oder chirale Induktion auch noch bei helicalen metallierten N-invertierten Biporphyrinen, obwohl das Bipyrrolfragment starr ist. Die Porphyrine sind peripher doppelt mit Platin(II) orthometalliert, und einige Produkte ihrer oxidativen Addition wurden ebenfalls erhalten (siehe die Strukturen des Iodmethyladdukts: grau und braun C; blau N; orange Pt; violett I). [source]

    ChemInform Abstract: Titanium and Zirconium Complexes with Helical Bis(phenolato) Ligands as Hydroamination Catalysts.

    CHEMINFORM, Issue 8 2008
    Klaudia Marcsekova
    Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source]

    Thermal Stability of Dehydrophenylalanine-Containing Model Peptides as Probed by Infrared Spectroscopy: a Case Study of an , -Helical and a 310 -Helical Peptide

    Alka Gupta
    Abstract The temperature-dependent secondary-structural changes in the two known helical model peptides Boc-Val-,Phe-Ala-Leu-Gly-OMe (1; , -helical) and Boc-Leu-Phe-Ala-,Phe-Leu-OMe (2; 310 -helical), which both comprise a single dehydrophenylalanine (,Phe) residue, were investigated by means of FT-IR spectroscopy (peptide film on KBr). Both the first-order and the better-resolved second-order derivative IR spectra of 1 and 2 were analyzed. The ,(NH) (3240,3340,cm,1), the Amide-I (1600,1700,cm,1), and the Amide-II (1510,1580,cm,1) regions of 1 and 2 showed significant differences in thermal-denaturation experiments (22°,144°), with the 310 -helical peptide (2) being considerably more stable. This observation was rationalized by different patterns and strengths of intramolecular H-bonds, and was qualitatively related to the different geometries of the peptides. Also, a fair degree of residual secondary-structural elements were found even in the ,denatured' states above 104° (1) or 134° (2). [source]

    Helical- and ahelical-dependent chiral recognition mechanisms in capillary electrophoresis using amylose as the selector

    ELECTROPHORESIS, Issue 8 2009
    Weili Wei
    Abstract The present study discovered that helical structures of amylose were not always responsible for its chiral recognition abilities in CE. Several enantiomers with different structures were selected as models. Based on ultraviolet,visible spectroscopy and 13C NMR measurements, it was found that helical structures were gradually destroyed by temperature elevation and almost entirely transformed to extended ahelical structures above 60°C. Then, CE and 1H NMR chiral recognitions were investigated at different temperatures; chiral selectivity of the enantiomers varied in two different ways. Summarily, helical structures were necessary only for chiral separations of the enantiomers with small (<0.78,nm) and flexible molecular structures. However, for the gauche enantiomers (>0.78,nm) with high steric hindrances over their chiral centers, ahelical structures alone can realize chiral recognitions. By using iodine as a helix including competitor, it was further proved that helical structures functioned through the inclusive complexations only in the chiral separations of small enantiomers and had no effect for the others. The underlying mechanisms of the functions of helical and ahelical structures in molecular level were discussed as well. [source]

    Insights into the structure of plant ,-type phospholipase D

    FEBS JOURNAL, Issue 10 2007
    Susanne Stumpe
    Phospholipases D play an important role in the regulation of cellular processes in plants and mammals. Moreover, they are an essential tool in the synthesis of phospholipids and phospholipid analogs. Knowledge of phospholipase D structures, however, is widely restricted to sequence data. The only known tertiary structure of a microbial phospholipase D cannot be generalized to eukaryotic phospholipases D. In this study, the isoenzyme form of phospholipase D from white cabbage (PLD,2), which is the most widely used plant phospholipase D in biocatalytic applications, has been characterized by small-angle X-ray scattering, UV-absorption, CD and fluorescence spectroscopy to yield the first insights into its secondary and tertiary structure. The structural model derived from small-angle X-ray scattering measurements reveals a barrel-shaped monomer with loosely structured tops. The far-UV CD-spectroscopic data indicate the presence of ,-helical as well as ,-structural elements, with the latter being dominant. The fluorescence and near-UV CD spectra point to tight packing of the aromatic residues in the core of the protein. From the near-UV CD signals and activity data as a function of the calcium ion concentration, two binding events characterized by dissociation constants in the ranges of 0.1 mm and 10,20 mm can be confirmed. The stability of PLD,2 proved to be substantially reduced in the presence of calcium ions, with salt-induced aggregation being the main reason for irreversible inactivation. [source]

    Evaluation of detergents for the soluble expression of ,-helical and ,-barrel-type integral membrane proteins by a preparative scale individual cell-free expression system

    FEBS JOURNAL, Issue 23 2005
    Christian Klammt
    Cell-free expression has become a highly promising tool for the fast and efficient production of integral membrane proteins. The proteins can be produced as precipitates that solubilize in mild detergents usually without any prior denaturation sttif. Alternatively, membrane proteins can be synthesized in a soluble form by adding detergents to the cell-free system. However, the effects of a representative variety of detergents on the production, solubility and activity of a wider range of membrane proteins upon cell-free expression are currently unknown. We therefore analyzed the cell-free expression of three structurally very different membrane proteins, namely the bacterial ,-helical multidrug transporter, EmrE, the ,-barrel nucleoside transporter, Tsx, and the porcine vasopressin receptor of the eukaryotic superfamily of G-protein coupled receptors. All three membrane proteins could be produced in amounts of several mg per one ml of reaction mixture. In general, the detergent 1-myristoyl-2-hydroxy- sn -glycero-3-[phospho- rac -(1-glycerol)] was found to be most effective for the resolubilization of membrane protein precipitates, while long chain polyoxyethylene-alkyl-ethers proved to be most suitable for the soluble expression of all three types of membrane proteins. The yield of soluble expressed membrane protein remained relatively stable above a certain threshold concentration of the detergents. We report, for the first time, the high-level cell-free expression of a ,-barrel type membrane protein in a functional form. Structural and functional variations of the analyzed membrane proteins are evident that correspond with the mode of expression and that depend on the supplied detergent. [source]

    Structural model for an AxxxG-mediated dimer of surfactant-associated protein C

    FEBS JOURNAL, Issue 11 2004
    Visvaldas Kairys
    The pulmonary surfactant prevents alveolar collapse and is required for normal pulmonary function. One of the important components of the surfactant besides phospholipids is surfactant-associated protein C (SP-C). SP-C shows complex oligomerization behavior and a transition to ,-amyloid-like fibril structures, which are not yet fully understood. Besides this nonspecific oligomerization, MS and chemical cross-linking data combined with CD spectra provide evidence of a specific, mainly ,-helical, dimer at low to neutral pH. Furthermore, resistance to CNBr cleavage and dual NMR resonances of porcine and human recombinant SP-C with Met32 replaced by isoleucine point to a dimerization site located at the C-terminus of the hydrophobic ,-helix of SP-C, where a strictly conserved heptapeptide sequence is found. Computational docking of two SP-C helices, described here, reveals a dimer with a helix,helix interface that strikingly resembles that of glycophorin A and is mediated by an AxxxG motif similar to the experimentally determined GxxxG pattern of glycophorin A. It is highly likely that mature SP-C adopts such a dimeric structure in the lamellar bilayer systems found in the surfactant. Dimerization has been shown in previous studies to have a role in sorting and trafficking of SP-C and may also be important to the surfactant function of this protein. [source]

    SMAP-29 has two LPS-binding sites and a central hinge

    FEBS JOURNAL, Issue 4 2002
    Brian F. Tack
    The CD spectra of SMAP-29, an antimicrobial peptide from sheep, showed disordered structure in aqueous buffers, and significant helicity in membrane-like environments, including SDS micelles, lipopolysaccharide (LPS) dispersions, and trifluoroethanol buffer systems. A structure determined by NMR in 40% perdeuterated trifluoroethanol indicated that residues 8,17 were helical, residues 18,19 formed a hinge, and residues 20,28 formed an ordered, hydrophobic segment. SMAP-29 was flexible in 40% trifluoroethanol, forming two sets of conformers that differed in the relative orientation of the N-terminal domain. We used a chromogenic Limulus assay to determine the EC50 of the peptide (the concentration that bound 50% of the added LPS). Studies with full-length and truncated SMAP-29 molecules revealed that each end of the holopeptide contained an LPS-binding domain. The higher affinity LPS-binding domain was situated in the flexible N-terminal portion. LPS binding to full-length SMAP-29 showed positive cooperativity, so the EC50 of the peptide (2.6 µm) was considerably lower than that of the individual LPS-binding domains. LPS-binding studies with a mixture of truncated peptides revealed that this cooperativity was primarily intramolecular (i.e. involving the N- and C-terminal LPS-binding sites of the same peptide molecule). CAP-18[106,142], an antimicrobial cathelicidin peptide of rabbits, resembled SMAP-29 in that it contained N- and C-terminal LPS-binding domains, had an EC50 of 2.5 µm, and bound LPS with positive cooperativity. We conclude that the presence of multiple binding sites that function cooperatively allow peptides such as SMAP-29 and CAP-18 to bind LPS with high affinity. [source]

    Assemblies of Metal Nanoparticles and Self-Assembled Peptide Fibrils,Formation of Double Helical and Single-Chain Arrays of Metal Nanoparticles,

    ADVANCED MATERIALS, Issue 11 2003
    X. Fu
    Double helical and single-chain arrays of Au and Pd metal nanoclusters have been achieved by assembling the corresponding metal nanoparticles on peptide nanofibril templates at different pH values. The assembled metal nanoparticles are useful for studying the superstructures of the peptide nanofibrils. Pd nanowires of different shapes have also been prepared by varying the amount of metal deposition. [source]

    Prediction of protein folding rates from primary sequences using hybrid sequence representation

    Yingfu Jiang
    Abstract The ability to predict protein folding rates constitutes an important step in understanding the overall folding mechanisms. Although many of the prediction methods are structure based, successful predictions can also be obtained from the sequence. We developed a novel method called prediction of protein folding rates (PPFR), for the prediction of protein folding rates from protein sequences. PPFR implements a linear regression model for each of the mainstream folding dynamics including two-, multi-, and mixed-state proteins. The proposed method provides predictions characterized by strong correlations with the experimental folding rates, which equal 0.87 for the two- and multistate proteins and 0.82 for the mixed-state proteins, when evaluated with out-of-sample jackknife test. Based on in-sample and out-of-sample tests, the PPFR's predictions are shown to be better than most of other sequence only and structure-based predictors and complementary to the predictions of the most recent sequence-based QRSM method. We show that simultaneous incorporation of several characteristics, including the sequence, physiochemical properties of residues, and predicted secondary structure provides improved quality. This hybridized prediction model was analyzed to reveal the complementary factors that can be used in tandem to predict folding rates. We show that bigger proteins require more time for folding, higher helical and coil content and the presence of Phe, Asn, and Gln may accelerate the folding process, the inclusion of Ile, Val, Thr, and Ser may slow down the folding process, and for the two-state proteins increased ,-strand content may decelerate the folding process. Finally, PPFR provides strong correlation when predicting sequences with low similarity. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source]

    Time-averaged predictions of folded and misfolded peptides using a reduced physicochemical model

    Oliver J. Clarke
    Abstract Energy-based methods for calculating time-averaged peptide structures are important for rational peptide design, for defining local structure propensities in large protein chains, and for exploring the sequence determinants of amyloid formation. High-end methods are currently too slow to be practicable, and will remain so for the foreseeable future. The challenge is to create a method that runs quickly on limited computer resources and emulates reality sufficiently well. We have developed a simplified off-lattice protein model, incorporating semi-empirical physicochemical potentials, and combined it with an efficient Monte Carlo method for calculating time-averaged peptide structures. Reasonably accurate predictions are found for a set of small ,-helical and ,-hairpin peptides, and we demonstrate a potential application in measuring local structure propensities in protein chains. Time-averaged structures have also been calculated for a set of small peptides known to form ,-amyloid fibrils. The simulations were of three interacting peptides, and in each case the time-averaged structure describes a three-stranded ,-sheet. The performance of our method in measuring the propensities of small peptides to self-associate into possible prefibrillar species compares favorably with more detailed and CPU-intensive approaches. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source]

    Semiautomatic sequence-specific assignment of proteins based on the tertiary structure,The program st2nmr

    Primo, Pristov
    Abstract The sequence-specific assignment of resonances is still the most time-consuming procedure that is necessary as the first step in high-resolution NMR studies of proteins. In many cases a reliable three-dimensional (3D) structure of the protein is available, for example, from X-ray spectroscopy or homology modeling. Here we introduce the st2nmr program that uses the 3D structure and Nuclear Overhauser Effect spectroscopy (NOESY) peak list(s) to evaluate and optimize trial sequence-specific assignments of spin systems derived from correlation spectra to residues of the protein. A distance-dependent target function that scores trial assignments based on the presence of expected NOESY crosspeaks is optimized in a Monte Carlo fashion. The performance of the program st2nmr is tested on real NMR data of an ,-helical (cytochrome c) and ,-sheet (lipocalin) protein using homology models and/or X-ray structures; it succeeded in completely reproducing the correct sequence-specific assignments in most cases using 2D and/or 15N/13C Nuclear Overhauser Effect (NOE) data. Additionally to amino acid residues the program can also handle ligands that are bound to the protein, such as heme, and can be used as a complementary tool to fully automated assignment procedures. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 335,340, 2002 [source]

    Characterization of conantokin Rl -A: molecular phylogeny as structure/function study

    Konkallu H. Gowd
    Abstract A multidisciplinary strategy for discovery of new Conus venom peptides combines molecular genetics and phylogenetics with peptide chemistry and neuropharmacology. Here we describe application of this approach to the conantokin family of conopeptides targeting NMDA receptors. A new conantokin from Conus rolani, ConRl -A, was identified using molecular phylogeny and subsequently synthesized and functionally characterized. ConRl -A is a 24-residue peptide containing three ,-carboxyglutamic acid residues with a number of unique sequence features compared to conantokins previously characterized. The HPLC elution of ConRl -A suggested that this peptide exists as two distinct, slowly exchanging conformers. ConRl -A is predominantly helical (estimated helicity of 50%), both in the presence and absence of Ca++. The order of potency for blocking the four NMDA receptor subtypes by ConRl -A was NR2B > NR2D > NR2A > NR2C. This peptide has a greater discrimination between NR2B and NR2C than any other ligand reported so far. In summary, ConRl -A is a new member of the conantokin family that expands our understanding of structure/function of this group of peptidic ligands targeted to NMDA receptors. Thus, incorporating phylogeny in the discovery of novel ligands for the given family of ion channels or receptors is an efficient means of exploring the megadiverse group of peptides from the genus Conus. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd. [source]

    The sequence TGAAKAVALVL from glyceraldehyde-3-phosphate dehydrogenase displays structural ambivalence and interconverts between ,-helical and ,-hairpin conformations mediated by collapsed conformational states

    Sunita Patel
    Abstract The peptide TGAAKAVALVL from glyceraldehyde-3-phosphate dehydrogenase adopts a helical conformation in the crystal structure and is a site for two hydrated helical segments, which are thought to be helical folding intermediates. Overlapping sequences of four to five residues from the peptide, sample both helical and strand conformations in known protein structures, which are dissimilar to glyceraldehyde-3-phosphate dehydrogenase suggesting that the peptide may have a structural ambivalence. Molecular dynamics simulations of the peptide sequence performed for a total simulation time of 1.2 µs, starting from the various initial conformations using GROMOS96 force field under NVT conditions, show that the peptide samples a large number of conformational forms with transitions from ,-helix to ,-hairpin and vice versa. The peptide, therefore, displays a structural ambivalence. The mechanism from ,-helix to ,-hairpin transition and vice versa reveals that the compact bends and turns conformational forms mediate such conformational transitions. These compact structures including helices and hairpins have similar hydrophobic radius of gyration (Rgh) values suggesting that similar hydrophobic interactions govern these conformational forms. The distribution of conformational energies is Gaussian with helix sampling lowest energy followed by the hairpins and coil. The lowest potential energy of the full helix may enable the peptide to take up helical conformation in the crystal structure of the glyceraldehyde-3-phosphate dehydrogenase, even though the peptide has a preference for hairpin too. The relevance of folding and unfolding events observed in our simulations to hydrophobic collapse model of protein folding are discussed. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source]

    Structural studies and model membrane interactions of two peptides derived from bovine lactoferricin

    Leonard T. Nguyen
    Abstract The powerful antimicrobial properties of bovine lactoferricin (LfcinB) make it attractive for the development of new antimicrobial agents. An 11-residue linear peptide portion of LfcinB has been reported to have similar antimicrobial activity to lactoferricin itself, but with lower hemolytic activity. The membrane-binding and membrane-perturbing properties of this peptide were studied together with an amidated synthetic version with an added disulfide bond, which was designed to confer increased stability and possibly activity. The antimicrobial and cytotoxic properties of the peptides were measured against Staphylococcus aureus and Escherichia coli and by hemolysis assays. The peptides were also tested in an anti-cancer assay against neuroblastoma cell lines. Vesicle disruption caused by these LfcinB derivatives was studied using the fluorescent reporter molecule calcein. The extent of burial of the two Trp residues in membrane mimetic environments were quantitated by fluorescence. Finally, the solution NMR structures of the peptides bound to SDS micelles were determined to provide insight into their membrane bound state. The cyclic peptide was found to have greater antimicrobial potency than its linear counterpart. Consistent with this property, the two Trp residues of the modified peptide were suggested to be embedded deeper into the membrane. Although both peptides adopt an amphipathic structure without any regular ,-helical or ß-sheet conformation, the 3D-structures revealed a clearer partitioning of the cationic and hydrophobic faces for the cyclic peptide. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd. [source]

    Crystal-state 3D-structural characterization of novel 310 -helical peptides

    Dr Marco Crisma
    Abstract The crystal-state conformations of two octapeptides, pBrBz-(D -Iva)8 -OtBu (8I) and Ac-[L -(,Me)Val]8 -OH (8II), the heptapeptide Z-[L -(,Me)Val]7 -OH (7), the hexapeptide Z-[L -(,Me)Leu]6 -OtBu (6) and the tetrapeptide alkylamide Z-(Aib)2 - L -Glu(OMe)- L -Ala- L -Lol (5) were assessed by x-ray diffraction analyses. Two independent molecules are observed in the asymmetric unit of each L -(,Me)Val homo-peptide. All four homo-peptides are folded in a regular 310 -helical structure (only the C -terminal H-bonded conformation of the D -Iva octapeptide is distorted to a type-I ,-turn). The hydroxyl groups of the C -terminal carboxyl moieties of the two L -(,Me)Val homo-peptides participate in an oxy-analogue of the type-III ,-turn conformation. While the two L -(,Me)Val 310 -helices are right-handed, the D -Iva and L -(,Me)Leu helices are left-handed. The tetrapeptide alkylamide is 310 -helical at the N -terminus, but it is mixed 310/,-helical at the C -terminus. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd. [source]

    Effects of detergents on the secondary structures of prion protein peptides as studied by CD spectroscopy

    Dr Yoshihiro Kuroda
    Abstract Pathogenic prion proteins (PrPSc) are thought to be produced by ,-helical to ,-sheet conformational changes in the normal cellular prion proteins (PrPC) located solely in the caveolar compartments. In order to inquire into the possible conformational changes due to the influences of hydrophobic environments within caveolae, the secondary structures of prion protein peptides were studied in various kinds of detergents by CD spectra. The peptides studied were PrP(129,154) and PrP(192,213); the former is supposed to assume ,-sheets and the latter ,-helices, in PrPSc. The secondary structure analyses for the CD spectra revealed that in buffer solutions, both PrP(129,154) and PrP(192,213) mainly adopted random-coils (,60%), followed by ,-sheets (30%,40%). PrP(129,154) showed no changes in the secondary structures even in various kinds of detergents such as octyl-,- D -glucopyranoside (OG), octy-,- D -maltopyranoside (OM), sodium dodecyl sulfate (SDS), Zwittergent 3,14 (ZW) and dodecylphosphocholine (DPC). In contrast, PrP(192,213) changed its secondary structure depending on the concentration of the detergents. SDS, ZW, OG and OM increased the ,-helical content, and decreased the ,-sheet and random-coil contents. DPC also increased the ,-helical content, but to a lesser extent than did SDS, ZW, OG or OM. These results indicate that PrP(129,154) has a propensity to adopt predominantly ,-sheets. On the other hand, PrP(192,213) has a rather fickle propensity and varies its secondary structure depending on the environmental conditions. It is considered that the hydrophobic environments provided by these detergents may mimic those provided by gangliosides in caveolae, the head groups of which consist of oligosaccharide chains containing sialic acids. It is concluded that PrPC could be converted into a nascent PrPSc having a transient PrPSc like structure under the hydrophobic environments produced by gangliosides. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd. [source]

    Investigation of penetratin peptides Part 1.

    The environment dependent conformational properties of penetratin, two of its derivatives
    Abstract The homeodomain, the DNA-binding domain of Antennapedia homeoprotein, is composed of three ,-helices and one ,-turn between helices II and III. Its third helix from the N -terminal (helix III) can translocate through the cell membrane into the nucleus and can be used as an intracellular vehicle for the delivery of oligopeptides and oligonucleotides. To the best of our knowledge, this helix III, called penetratin, which consists of 16 amino acids, is internalized by cells in a specific, non-receptor-mediated manner. For a better understanding of the mechanism of the transfer, the structure of penetratin was examined in both extracellular matrix-mimetic and membrane-mimetic environments; 1H-NMR and CD spectroscopic measurements were performed in mixtures of TFE/water with different ratios. The molecular conformations of two analogue peptides [(6,14-Phe)-penetratin and a 12 amino acid penetratin derivative (peptide 3)] were also studied. An atomic level comprehensive analysis of penetratin and its two analogues was performed. In a membrane-mimetic solvent system (TFEd2/water = 9 : 1), on the basis of 553 distance restraints, the 4,12 region of penetratin exhibits a bent, irregular helical structure on NMR examination. Interactions between hydrophobic amino acid residues in conjunction with H-bonds stabilize the secondary structure of the molecule. Thus, both derivatives adopt a helix-like conformation. However, while (6,14-Phe)-penetratin displays both ,-helical and 310 -helical features, the structure of peptide 3 is predominantly a 310 -helix. Of the three peptides, surprisingly (6,14-Phe)-penetratin has the largest helical content. An increase in the polarity of the molecular environment gradually disintegrates these helix-like secondary structures. In a highly aqueous molecular system (TFEd2/water = 1 : 9), the fast exchange of multiple conformers leads to too few distance restraints being extracted, therefore the NMR structures can no longer be determined. The NMR data show that only short-range order can be traced in these peptides. Under these conditions, the molecules adopt nascent helix-like structures. On the other hand, CD spectra could be recorded at any TFE/water ratio and the conformational interconversion could therefore be monitored as a function of the polarity of the molecular environment. The CD data were analysed comprehensively by the quantitative deconvolution method (CCA+). All three penetratin peptides display helical conformational features in a low dielectric medium, with significant differences as a function of their amino acid composition. However, these conformational features are gradually lost during the shift from an apolar to a polar molecular environment. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd. [source]

    Densely grafted polyisocyanides synthesized by two types of polymerization techniques

    Yanqing Tian
    Abstract A series of novel polyisocyanide- graft -polystyrenes and polyisocyanide- graft -[polystyrene- block -poly(butyl acrylate)]s were synthesized through the grafting-through and grafting-from routes with two types of living polymerization techniques: polymerization with the Pd,Pt ,-ethynediyl dinuclear complex as the initiator and catalyst for the polyisocyanide backbone and atom transfer radical polymerization for the grafted side chain. Through the introduction of a chiral center at the side chain of the polyisocyanide backbone, helical grafted and graft block polyisocyanides were prepared through the grafting-from method. All of the obtained polymers exhibited polydispersities in the range of 1.07,1.41. This might have been the first time grafted polyisocyanides were prepared, especially helical grafted polyisocyanides, through the operation of two living polymerization techniques. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 1871,1880, 2003 [source]

    The changing faces of Streptococcus antigen I/II polypeptide family adhesins

    L. Jeannine Brady
    Summary Streptococcus mutans antigen I/II (AgI/II) protein was one of the first cell wall-anchored adhesins identified in Gram-positive bacteria. It mediates attachment of S. mutans to tooth surfaces and has been a focus for immunization studies against dental caries. The AgI/II family polypeptides recognize salivary glycoproteins, and are also involved in biofilm formation, platelet aggregation, tissue invasion and immune modulation. The genes encoding AgI/II family polypeptides are found among Streptococcus species indigenous to the human mouth, as well as in Streptococcus pyogenes, S. agalactiae and S. suis. Evidence of functionalities for different regions of the AgI/II proteins has emerged. A sequence motif within the C-terminal portion of Streptococcus gordonii SspB (AgI/II) is bound by Porphyromonas gingivalis, thus promoting oral colonization by this anaerobic pathogen. The significance of other epitopes is now clearer following resolution of regional crystal structures. A new picture emerges of the central V (variable) region, predicted to contain a carbohydrate-binding trench, being projected from the cell surface by a stalk formed by an unusual association between an N-terminal ,-helix and a C-terminal polyproline helix. This presentation mode might be important in determining functional conformations of other Gram-positive surface proteins that have adhesin domains flanked by ,-helical and proline-rich regions. [source]

    Novel ultrastructures of Treponema primitia and their implications for motility

    Gavin E. Murphy
    Summary Members of the bacterial phylum Spirochaetes are generally helical cells propelled by periplasmic flagella. The spirochete Treponema primitia is interesting because of its mutualistic role in the termite gut, where it is believed to cooperate with protozoa that break down cellulose and produce H2 as a by-product. Here we report the ultrastructure of T. primitia as obtained by electron cryotomography of intact, frozen-hydrated cells. Several previously unrecognized external structures were revealed, including bowl-like objects decorating the outer membrane, arcades of hook-shaped proteins winding along the exterior and tufts of fibrils extending from the cell tips. Inside the periplasm, cone-like structures were found at each pole. Instead of the single peptidoglycan layer typical of other Gram-negative bacteria, two distinct periplasmic layers were observed. These layers formed a central open space that contained two flagella situated adjacent to each other. In some areas, the inner membrane formed flattened invaginations that protruded into the cytoplasm. High-speed light microscopic images of swimming T. primitia cells showed that cell bodies remained rigid and moved in a helical rather than planar motion. Together, these findings support the ,rolling cylinder' model for T. primitia motility that posits rotation of the protoplasmic cylinder within the outer sheath. [source]

    A comparison between EAM interatomic potentials for Al and Ni: from bulk systems to nanowires

    S. Pelįez
    Abstract Two different kinds of interatomic potentials within the Embedded Atom Method (EAM) have been used to study several properties of selected crystalline structures and nanowire configurations (ordered and helical) for Al and Ni based systems. Reliability of these potentials has been explored when describing cohesive energy and geometrical properties of the systems under consideration as the atomic coordination number decreases. Results provide a criteria for stablishing the limits of validity of EAM potentials when applied to such systems as metallic ultra-narrow or single atom nanowires. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

    Effect of steady torque twisting on the orientation of cortical microtubules in the epidermis of the sunflower hypocotyl

    PLANT BIOLOGY, Issue 4 2008
    J. Elsner
    Abstract Orientation of cortical microtubules (cMTs) is suggested to be affected by mechanical stress existing in cell walls. However, in mutants exhibiting helical (chiral) growth, there is a correlation between orientation of cMTs in outer tissues and helical growth direction. The aim of this research was to examine the effect of a chiral mechanical stimulation on cMTs. For this purpose, the orientation of cMTs was investigated in hypocotyls subjected to either a right- or a left-handed twist, resulting from a steady torque. cMTs were visualised in fixed material using the immunofluorescence method. The cMTs in untouched control hypocotyls were mostly transverse with respect to the cell long axis. In immobilised, but not twisted control hypocotyls, the transverse orientation was also most frequent, while applied twisting resulted in a change in cMT orientation from transverse to oblique. The data provide additional evidence that changes in tissue stress can be reorganized by cortical microtubules. [source]

    The spatial pattern of air seeding thresholds in mature sugar maple trees

    PLANT CELL & ENVIRONMENT, Issue 9 2005
    ABSTRACT Air seeding threshold (Pa) of xylem vessels from current year growth rings were measured along the vertical axis of mature sugar maple trees (Acer saccharum Marsh.), with sampling points in primary leaf veins, petioles, 1-, 3-, and 7-year-old branches, large branches, the trunk and roots. The air seeding threshold was taken as the pressure required to force nitrogen gas through intervessel pit membranes. Although all measurements were made on wood produced in the same year, Pa varied between different regions of A. saccharum, with distal organs such as leaves and petioles having lower Pa than basal regions. Mean (SE) Pa ranged from 1.0 (± 0.1) MPa in primary leaf veins to 4.8 (± 0.1) MPa in the main trunk. Roots exhibited a Pa of 2.8 (± 0.2) MPa, lower than all other regions of the tree except leaf veins and petioles. Mean xylem vessel diameter increased basipetally, with the widest vessels occurring in the trunk and roots. Within the shoot, wider vessels had greater air seeding thresholds, contrasting with trends previously reported. However, further experimentation revealed that differences in Pa between regions of the stem were driven by the presence of primary xylem conduits, rather than differences in vessel diameter. In 1-year-old branches, Pa was significantly lower in primary xylem vessels than in adjacent secondary xylem vessels. This explained the lower values of Pa measured in petioles and leaf veins, which possessed a greater ratio of primary xylem to secondary xylem than other regions. The difference in Pa between primary and secondary xylem was attributed to the greater area of primary cell wall (pit membrane) exposed in primary xylem conduits with helical or annular thickening. [source]

    Mistic: Cellular localization, solution behavior, polymerization, and fibril formation,

    PROTEIN SCIENCE, Issue 7 2009
    Hay Dvir
    Abstract Mistic represents a family of unique membrane-associating proteins originally found in Bacillus subtilis (M110). As a fusion partner, it has been shown to assist overexpression of foreign integral membrane proteins in E. coli. We have expressed shorter Mistic homologs from other Bacillus species and surprisingly, unlike M110, found them abundant in the cytoplasm. These Mistic homologs including the corresponding shorter sequence (amino acids 27 through 110 of M110) exist as multimeric assemblies in solution in the absence of detergent. Crystals of Mistic from B. leicheniformis (M2) diffracted to 3.2 Å resolution, indicating that it exists as a multimer in the crystalline state as well. Moreover, we show that although M2 is mostly ,-helical, it tends to polymerize and form fibrils. Such oligomerization could potentially mask the charged surface of the monomeric Mistic to assist membrane integration. [source]