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Hairpin
Kinds of Hairpin Terms modified by Hairpin Selected AbstractsOne ,,Hairpin after the Other: Exploring Mechanical Unfolding Pathways of the Transmembrane ,-Barrel Protein OmpG,ANGEWANDTE CHEMIE, Issue 44 2009Tanuj Sapra Dr. Sauber auseinandergefädelt: Mithilfe der Einzelmolekül-Rasterkraftspektroskopie wurde erstmals ein äußeres Membranprotein mit ,-Fass-Struktur entfaltet. Überraschenderweise entfalten einzelne ,-Stränge von OmpG aus E. coli nicht individuell, sondern in Form von ,-Haarnadeln. Diese ,-Haarnadeln entfalten eine nach der anderen, bis das gesamte Protein entfaltet ist (siehe Bild). [source] Functionalization of a Diene-Modified Hairpin Mimic via the Diels,Alder Reaction.CHEMINFORM, Issue 51 2004Rolf Tona No abstract is available for this article. [source] Electron Hopping among Cofacially Stacked Perylenediimides Assembled by Using DNA Hairpins,ANGEWANDTE CHEMIE, Issue 13 2010Durchmarsch der Elektronen: Perylendiimid-Chromophore in DNA-Haarnadelstrukturen dienen als Basenpaar-Ersatz und bilden eine reißverschlussartige Einschubstruktur (siehe Bild). Bei der Einelektronenreduktion wurde ein Elektronen-Hüpfen innerhalb der Chromophorenstapel beobachtet. [source] Circular Dichroism of Designed Peptide Helices and ,-Hairpins: Analysis of Trp- and Tyr-Rich PeptidesCHEMBIOCHEM, Issue 12 2005Radhakrishnan Mahalakshmi VCD versus ECD spectroscopy. Peptides rich in aromatic residues yield anomalous far-UV electronic circular dichroism (ECD) spectra that preclude secondary structure assignment. The utility of vibrational circular dichroism (VCD) in conformation analysis is demonstrated by using a set of well-defined peptide helices and hairpins containing proximal aromatic residues. [source] Molecular Conformation and Packing of Peptide , Hairpins in the Solid State: Structures of Two Synthetic Octapeptides Containing 1-Aminocycloalkane-1-Carboxylic Acid Residues at the i+2 Position of the , TurnCHEMISTRY - A EUROPEAN JOURNAL, Issue 12 2005Veldore Vidya Harini Abstract Peptide ,-hairpin formation is facilitated by centrally positioned D -Pro-Xxx segments. The synthetic peptides Boc-Leu-Phe-Val- D -Pro-Ac6c-Leu-Phe-Val-OMe (1) and Boc-Leu-Phe-Val- D -Pro-Ac8c-Leu-Phe-Val-OMe (2) were synthesized in order to explore the role of bulky 1-aminocycloalkane-1-carboxylic acid residues (Acnc, where n is the number of carbon atoms in the ring), at the i+2 position of the nucleating , turn in peptide , hairpins. Peptides 1 and 2 crystallize in the monoclinic space group P21 with two molecules in the asymmetric unit. The crystal structures of 1 and 2 provide conformational parameters for four peptide hairpin molecules. In all cases, the central segments adopts a type II, ,-turn conformation, and three of the four possible cross-strand hydrogen bonds are observed. Fraying of the hairpins at the termini is accompanied by the observation of NH,,,, interaction between the Leu(1)NH group and Phe(7) aromatic group. Cross strand stabilizing interactions between the facing residues Phe(2) and Phe(7) are suggested by the observed orientation of aromatic rings. Anomalous far-UV CD spectra observed in solution suggest that close proximity of the Phe rings is maintained even in isolated molecules. In both peptides 1 and 2, the asymmetric unit consists of approximately orthogonal hairpins, precluding the formation of a planar ,-sheet arrangement in the solid state. Solvent molecules, one dioxane and one water in 1, three water molecules in 2, mediate peptide association. A comparison of molecular conformation and packing motifs in available ,-hairpin structures permits delineation of common features. The crystal structures of ,-hairpin peptides provide a means of visualizing different modes of ,-sheet packing, which may be relevant in developing models for aggregates of polypeptides implicated in disease situations. [source] Salt-resistant homodimeric bactenecin, a cathelicidin-derived antimicrobial peptideFEBS JOURNAL, Issue 15 2008Ju Y. Lee The cathelicidin antimicrobial peptide bactenecin is a ,-hairpin molecule with a single disulfide bond and broad antimicrobial activity. The proform of bactenecin exists as a dimer, however, and it has been proposed that bactenecin is released as a dimer in vivo, although there has been little study of the dimeric form of bactenecin. To investigate the effect of bactenecin dimerization on its biological activity, we characterized the dimer's effect on phospholipid membranes, the kinetics of its bactericidal activity, and its salt sensitivity. We initially synthesized two bactenecin dimers (antiparallel and parallel) and two monomers (,-hairpin and linear). Under oxidative folding conditions, reduced linear bactenecin preferentially folded into a dimer forming a ladder-like structure via intermolecular disulfide bonding. As compared to the monomer, the dimer had a greater ability to induce lysis of lipid bilayers and was more rapidly bactericidal. Interestingly, the dimer retained antimicrobial activity at physiological salt concentrations (150 mm NaCl), although the monomer was inactivated. This salt resistance was also seen with bactenecin dimer containing one intermolecular disulfide bond, and the bactenecin dimer appears to undergo multimeric oligomerization at high salt concentrations. Overall, dimeric bactenecin shows potent and rapid antimicrobial activity, and resists salt-induced inactivation under physiological conditions through condensation and oligomerization. These characteristics shed light on the features that a peptide would need to serve as an effective therapeutic agent. [source] Peptides corresponding to helices 5 and 6 of Bax can independently form large lipid poresFEBS JOURNAL, Issue 5 2006Ana J. García-Sáez Proteins of the B-cell lymphoma protein 2 (Bcl2) family are key regulators of the apoptotic cascade, controlling the release of apoptotic factors from the mitochondrial intermembrane space. A helical hairpin found in the core of water-soluble folds of these proteins has been reported to be the pore-forming domain. Here we show that peptides including any of the two ,-helix fragments of the hairpin of Bcl2 associated protein X (Bax) can independently induce release of large labelled dextrans from synthetic lipid vesicles. The permeability promoted by these peptides is influenced by intrinsic monolayer curvature and accompanied by fast transbilayer redistribution of lipids, supporting a toroidal pore mechanism as in the case of the full-length protein. However, compared with the pores made by complete Bax, the pores made by the Bax peptides are smaller and do not need the concerted action of tBid. These data indicate that the sequences of both fragments of the hairpin contain the principal physicochemical requirements for pore formation, showing a parallel between the permeabilization mechanism of a complex regulated protein system, such as Bax, and the much simpler pore-forming antibiotic peptides. [source] Drug recognition of a DNA single strand breakFEBS JOURNAL, Issue 6 2002Nogalamycin intercalation between coaxially stacked hairpins Two DNA hairpin motifs (5,-GCGAAGC-3, and 5,-ACGA AGT-3,), both stabilized by a 5,-GAA loop, have been used to design novel intramolecular double hairpin structures (5,-GCGAAGCACGAAGT-3, and 5,-ACGAAGTGCG AAGC-3,) in which coaxial stacking of the two hairpin components generates a double-stranded stem region effectively with a single-strand break in the middle of the sequence at either the TG or CA step between unconnected 3, and 5, terminal bases. We have investigated by NMR the conformation and dynamics of the DNA at the strand break site. We show that mutual stacking significantly enhances the stability of each hairpin. Further, the anthracycline antibiotic nogalamycin binds cleanly to the 5,-TG (5,-CA) site formed by the mutually stacked hairpins despite the break in the sugar-phosphate backbone on one strand. The complex resembles the structure of nogalamycin,DNA complexes with the drug bound at 5,-TG sites in intact duplex sequences, with ,-stacking interactions probably the single dominant stabilizing interaction. [source] SsrA-mediated protein tagging in the presence of miscoding drugs and its physiological role in Escherichia coliGENES TO CELLS, Issue 7 2002Tatsuhiko Abo Background: We have shown recently that read-through of a normal stop codon by a suppressor tRNA in specific genes possessing a Rho-independent terminator leads to SsrA-mediated tagging of extended proteins in Escherichia coli cells. Miscoding antibiotics such as kanamycin and streptomycin reduce translational fidelity by binding to the 30S ribosomal subunit. The aim of the present study was to address how miscoding antibiotics affect the read-through of stop codons and SsrA-mediated protein tagging. Results: Miscoding antibiotics caused translational read-through of stop codons when added to the culture medium at sublethal concentrations. Under the same conditions, the drugs enhanced SsrA-mediated tagging of bulk cellular proteins, as observed in cells carrying an ochre suppressor tRNA. Translational read-through products generated from the crp gene in the presence of the antibiotics was efficiently tagged by the SsrA system, presumably because the ribosome reached the 3, end of the mRNA defined by the terminator hairpin. The SsrA-defective cells were more sensitive to the miscoding antibiotics compared to the wild-type cells. Conclusion: We conclude that the SsrA system contributes to the survival of cells by dealing with translational errors in the presence of low concentrations of miscoding antibiotics. [source] Photocleavage of Peptides and Oligodeoxynucleotides Carrying 2-Nitrobenzyl GroupsHELVETICA CHIMICA ACTA, Issue 4 2009Roger Ramos Abstract Peptides and oligodeoxynucleotides containing photolabile 2-nitrobenzyl groups as mid-sequences were prepared. Photocleavage of aqueous solutions of these compounds neared completion within 30,min to a few hours depending on the photolabile group used. A photolabile group was introduced in the loop of an intramolecular oligodeoxynucleotide hairpin. Melting curves of the hairpin with and without the complementary oligodeoxynucleotide showed a preference for the intramolecular hairpin form, but an intermolecular duplex was observed after photolysis. These results open the possibility of using photolabile DNA hairpins for the fabrication of patterned surfaces. [source] Chemical Approach for the Study of the ,Kissing Complex' of Moloney murine leukaemia VirusHELVETICA CHIMICA ACTA, Issue 7 2008Sébastien Porcher Abstract The replication of Moloney murine leukaemia virus relies on the formation of a stable homodimeric ,kissing complex' of a GACG tetraloop interacting through only two C,G base pairs flanked of 5,-adjacent unpaired adenosines A9. Previous NMR investigations of a model stem loop 1 has not permitted to reveal the origin of this interaction. Therefore, with the aim of deeper comprehension of the phenomena, the model sequence 10 was prepared where position 9 has been substituted for a nucleoside offering a wider , -stacking. In this context, the wyosine phosphoramidite building block 2 was prepared and incorporated by adapting the conditions of the automated synthesis and developing original templated enzymatic ligation. However, no ,kissing interaction' has been observed for this model sequence 10 due to steric hindrance as confirmed by computational simulation. Consequently, several other model sequences, 18, 23,26, containing modified nucleosides were prepared. Finally, the importance of the cross-loop H-bond between G8 and G11 nucleobases was revealed by preparing a 18mer RNA hairpin 27, where the guanosine G8 has been substituted for inosine. The latter, which does not possess a C3 amino function compared to guanosine, is unable to form any ,kissing complex' demonstrating the importance of this secondary interaction in the formation of the complex. [source] Influence of , -Alanine on Hairpin Polyamide Orientation in the DNA Minor GrooveHELVETICA CHIMICA ACTA, Issue 6 2003Victor Antiparallel polyamides containing 1H -pyrrole, 1H -imidazole, and 3-hydroxy-1H -pyrrole amino acids display a preference for minor-groove binding oriented NC with respect to the 5,-3, direction of the DNA helix. We find that replacement of a central Py/Py pair with a ,/, pair within a ten-ring hairpin relaxes the orientation preference and, for some DNA sequences, causes the polyamide to prefer the opposite CN orientation. Substitution of the achiral , -aminobutanoic acid (,) with either (R)(or S)-2-(acetylamino)-4-aminobutanoic acid moderates the orientation preference of the 2- , -2-hairpin. [source] Halloween genes and nuclear receptors in ecdysteroid biosynthesis and signalling in the pea aphidINSECT MOLECULAR BIOLOGY, Issue 2010O. Christiaens Abstract The pea aphid (Acyrthosiphon pisum) is the first whole genome sequenced insect with a hemimetabolic development and an emerging model organism for studies in ecology, evolution and development. The insect steroid moulting hormone 20-hydroxyecdysone (20E) controls and coordinates development in insects, especially the moulting/metamorphosis process. We, therefore present here a comprehensive characterization of the Halloween genes phantom, disembodied, shadow, shade, spook and spookiest, coding for the P450 enzymes that control the biosynthesis of 20E. Regarding the presence of nuclear receptors in the pea aphid genome, we found 19 genes, representing all of the seven known subfamilies. The annotation and phylogenetic analysis revealed a strong conservation in the class of Insecta. But compared with other sequenced insect genomes, three orthologues are missing in the Acyrthosiphon genome, namely HR96, PNR-like and Knirps. We also cloned the EcR, Usp, E75 and HR3. Finally, 3D-modelling of the ligand-binding domain of Ap-EcR exhibited the typical canonical structural scaffold with 12 ,-helices associated with a short hairpin of two antiparallel ,-strands. Upon docking, 20E was located in the hormone-binding groove, supporting the hypothesis that EcR has a role in 20E signalling. [source] A bandpass filter with adjustable bandwidth and predictable transmission zerosINTERNATIONAL JOURNAL OF RF AND MICROWAVE COMPUTER-AIDED ENGINEERING, Issue 2 2010Li Zhu Abstract In this article, a microstrip bandpass filter with an adjustable bandwidth and predictable transmission zeros is proposed. The proposed filter is implemented by combining two hairpin edge-coupled resonators with interdigital capacitors. Compared to typical edge-coupled filters, the proposed filter provides a wider bandwidth resulting from a higher coupling strength between its resonators. To further increase the coupling and consequently the bandwidth, a pair of etched slots in the ground plane is used. By adjusting the geometrical parameters of the interdigital capacitors and etched slots, the bandwidth can be easily adjusted. The filter features two transmission zeros, which are determined by means of the semi-analytical model developed as part of this work. Furthermore, the proposed filters can be cascaded to obtain a sharper cutoff frequency response. Frequency responses of the filters from measurements are in good agreement with those simulated using IE3D in the 5,9 GHz range. © 2009 Wiley Periodicals, Inc. Int J RF and Microwave CAE, 2010. [source] Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and functionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2009Wonpil Im Abstract Understanding the delicate balance of forces governing helix or ,-hairpin interactions in transmembrane (TM) proteins is central to understanding membrane structure and function. These membrane constituent interactions play an essential role in determining the structure and function of membrane proteins, and protein interactions in membranes, and thus form the basis for many vital processes, including TM signaling, transport of ions and small molecules, energy transduction, and cell,cell recognition. "Why does a single-pass TM helix or ,-hairpin have specific orientations in membranes?" "What are the roles of hydrogen bonds, close packing, and helix-lipid or ,-hairpin-lipid interactions in helix or ,-hairpin associations in membranes?" "How do these interactions change the membrane structures?" "How do TM domains transmit signals across membranes?" These are important membrane biophysical questions that can be addressed by understanding the delicate balance of forces governing helix or ,-hairpin interactions with/in membranes. In this work, we summarize a series of helix/,-hairpin restraint potentials that we have developed, and illustrate their applications that begin to address the complicated energetics and molecular mechanisms of these interactions at the atomic level by calculating the potentials of mean force (PMFs) along reaction coordinates relevant to helix/,-hairpin motions in membranes and dissecting the total PMF into the contributions arising from physically important microscopic forces. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009 [source] ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2009Andreas Vitalis Abstract A new implicit solvation model for use in Monte Carlo simulations of polypeptides is introduced. The model is termed ABSINTH for self- Assembly of Biomolecules Studied by an Implicit, Novel, and Tunable Hamiltonian. It is designed primarily for simulating conformational equilibria and oligomerization reactions of intrinsically disordered proteins in aqueous solutions. The paradigm for ABSINTH is conceptually similar to the EEF1 model of Lazaridis and Karplus (Proteins 1999, 35, 133). In ABSINTH, the transfer of a polypeptide solute from the gas phase into a continuum solvent is the sum of a direct mean field interaction (DMFI), and a term to model the screening of polar interactions. Polypeptide solutes are decomposed into a set of distinct solvation groups. The DMFI is a sum of contributions from each of the solvation groups, which are analogs of model compounds. Continuum-mediated screening of electrostatic interactions is achieved using a framework similar to the one used for the DMFI. Promising results are shown for a set of test cases. These include the calculation of NMR coupling constants for short peptides, the assessment of the thermal stability of two small proteins, reversible folding of both an ,-helix and a ,-hairpin forming peptide, and the polymeric properties of intrinsically disordered polyglutamine peptides of varying lengths. The tests reveal that the computational expense for simulations with the ABSINTH implicit solvation model increase by a factor that is in the range of 2.5,5.0 with respect to gas-phase calculations. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] A minor ,-structured conformation is the active state of a fusion peptide of vesicular stomatitis virus glycoprotein,JOURNAL OF PEPTIDE SCIENCE, Issue 4 2008Carolina G. Sarzedas Abstract Entry of enveloped animal viruses into their host cells always depends on a step of membrane fusion triggered by conformational changes in viral envelope glycoproteins. Vesicular stomatitis virus (VSV) infection is mediated by virus spike glycoprotein G, which induces membrane fusion at the acidic environment of the endosomal compartment. In a previous work, we identified a specific sequence in the VSV G protein, comprising the residues 145,164, directly involved in membrane interaction and fusion. In the present work we studied the interaction of pep[145,164] with membranes using NMR to solve the structure of the peptide in two membrane-mimetic systems: SDS micelles and liposomes composed of phosphatidylcholine and phosphatidylserine (PC:PS vesicles). The presence of medium-range NOEs showed that the peptide has a tendency to form N - and C -terminal helical segments in the presence of SDS micelles. Analysis of the chemical shift index indicated helix,coil equilibrium for the C -terminal helix under all conditions studied. At pH 7.0, the N -terminal helix also displayed a helix,coil equilibrium when pep[145-164] was free in solution or in the presence of PC:PS. Remarkably, at the fusogenic pH, the region of the N -terminal helix in the presence of SDS or PC:PS presented a third conformational species that was in equilibrium with the helix and random coil. The N -terminal helix content decreases pH and the minor ,-structured conformation becomes more prevalent at the fusogenic pH. These data point to a ,-conformation as the fusogenic active structure-which is in agreement with the X-ray structure, which shows a ,-hairpin for the region corresponding to pep[145-164]. Copyright © 2007 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 statesJOURNAL OF PEPTIDE SCIENCE, Issue 5 2007Sunita 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] ,-Hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solutionJOURNAL OF PEPTIDE SCIENCE, Issue 9 2004Clara M. Santiveri Abstract The structural properties of a 10-residue and a 15-residue peptide in aqueous solution were investigated by molecular dynamics simulation. The two designed peptides, SYINSDGTWT and SESYINSDGTWTVTE, had been studied previously by NMR at 278 K and the resulting model structures were classified as 3:5 ,-hairpins with a type I + G1 ,-bulge turn. In simulations at 278 K, starting from the NMR model structure, the 3:5 ,-hairpin conformers proved to be stable over the time period evaluated (30 ns). Starting from an extended conformation, simulations of the decapeptide at 278 K, 323 K and 353 K were also performed to study folding. Over the relatively short time scales explored (30 ns at 278 K and 323 K, 56 ns at 353 K), folding to the 3:5 ,-hairpin could only be observed at 353 K. At this temperature, the collapse to ,-hairpin-like conformations is very fast. The conformational space accessible to the peptide is entirely dominated by loop structures with different degrees of ,-hairpin character. The transitions between different types of ordered loops and ,-hairpins occur through two unstructured loop conformations stabilized by a single side-chain interaction between Tyr2 and Trp9, which facilitates the changes of the hydrogen-bond register. In agreement with previous experimental results, ,-hairpin formation is initially driven by the bending propensity of the turn segment. Nevertheless, the fine organization of the turn region appears to be a late event in the folding process. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd. [source] Raman spectra and structure of a 25mer HCV RNAJOURNAL OF RAMAN SPECTROSCOPY, Issue 8 2009Pedro Carmona Abstract We have employed Raman spectroscopy to investigate the conformation of an (Hepatitis C virus) HCV RNA 25mer (1,25 nucleotides) in solution. The principal findings of this study are (1) the A -form secondary structure involving C3,- endo/anti ribofuranose pucker is predominant; (2) some uridine and guanosine nucleoside residues adopt the C2,- endo/anti and C3,- endo/syn conformations, respectively, which appear in looped nucleotide sequences; and (3) six out of nine guanine residues are base-paired probably forming a stem. These results are interpreted as formation of a hairpin whose secondary structure is consistent with that proposed on the basis of phylogenetic comparisons with other viral RNAs. Copyright © 2009 John Wiley & Sons, Ltd. [source] Bayesian analysis of single-molecule experimental dataJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES C (APPLIED STATISTICS), Issue 3 2005S. C. Kou Summary., Recent advances in experimental technologies allow scientists to follow biochemical processes on a single-molecule basis, which provides much richer information about chemical dynamics than traditional ensemble-averaged experiments but also raises many new statistical challenges. The paper provides the first likelihood-based statistical analysis of the single-molecule fluorescence lifetime experiment designed to probe the conformational dynamics of a single deoxyribonucleic acid (DNA) hairpin molecule. The conformational change is initially treated as a continuous time two-state Markov chain, which is not observable and must be inferred from changes in photon emissions. This model is further complicated by unobserved molecular Brownian diffusions. Beyond the simple two-state model, a competing model that models the energy barrier between the two states of the DNA hairpin as an Ornstein,Uhlenbeck process has been suggested in the literature. We first derive the likelihood function of the simple two-state model and then generalize the method to handle complications such as unobserved molecular diffusions and the fluctuating energy barrier. The data augmentation technique and Markov chain Monte Carlo methods are developed to sample from the posterior distribution desired. The Bayes factor calculation and posterior estimates of relevant parameters indicate that the fluctuating barrier model fits the data better than the simple two-state model. [source] Design of microstrip bandpass and lowpass filters using coupling matrix method and a new hairpin defected ground structureMICROWAVE AND OPTICAL TECHNOLOGY LETTERS, Issue 11 2008Ahmed Boutejdar Abstract In this work, we present a novel compact hairpin defected ground structure (DGS) bandpass and lowpass microstrip filter using two hairpin-slots etched in the ground plane. A compact microstrip BPF using coupled DGS resonators is designed using coupling matrix method. The designed BPF showed very wide stopband with two transmission zeros. Furthermore, a simple technique to transform the designed BPF to a LPF was presented. The BPF was fabricated and measured. The measurement results showed good agreement with the theoretical and simulation results. © 2008 Wiley Periodicals, Inc. Microwave Opt Technol Lett 50: 2898,2901, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.23794 [source] Characterization of CetA and CetB, a bipartite energy taxis system in Campylobacter jejuniMOLECULAR MICROBIOLOGY, Issue 5 2008Kathryn T. Elliott Summary The energy taxis receptor Aer, in Escherichia coli, senses changes in the redox state of the electron transport system via an flavin adenine dinucleotide cofactor bound to a PAS domain. The PAS domain (a sensory domain named after three proteins Per, ARNT and Sim, where it was first identified) is thought to interact directly with the Aer HAMP domain to transmit this signal to the highly conserved domain (HCD) found in chemotaxis receptors. An apparent energy taxis system in Campylobacter jejuni is composed of two proteins, CetA and CetB, that have the domains of Aer divided between them. CetB has a PAS domain, while CetA has a predicted transmembrane region, HAMP domain and the HCD. In this study, we examined the expression of cetA and cetB and the biochemical properties of the proteins they encode. cetA and cetB are co-transcribed independently of the flagellar regulon. CetA has two transmembrane helices in a helical hairpin while CetB is a peripheral membrane protein tightly associated with the membrane. CetB levels are CetA dependent. Additionally, we demonstrated that both CetA and CetB participate in complexes, including a likely CetB dimer and a complex that may include both CetA and CetB. This study provides a foundation for further characterization of signal transduction mechanisms within CetA/CetB. [source] Systematic mutagenesis of the thymidine tract of the pyrBI attenuator and its effects on intrinsic transcription termination in Escherichia coliMOLECULAR MICROBIOLOGY, Issue 1 2007Katalin Sipos Summary The pyrBI attenuator of Escherichia coli is an intrinsic transcription terminator composed of DNA with a hyphenated dyad symmetry and an adjacent 8 bp T:A tract (T-tract). These elements specify a G+C-rich terminator hairpin followed by a run of eight uridine residues (U-tract) in the RNA transcript. In this study, we examined the effects on in vivo transcription termination of systematic base substitutions in the T/U-tract of the pyrBI attenuator. We found that these substitutions diminished transcription termination efficiency to varying extents, depending on the nature and position of the substitution. In general, substitutions closer to the dyad symmetry/terminator hairpin exhibited the most significant effects. Additionally, we examined the effects on in vivo transcription termination of mutations that insert from 1 to 4 bases between the terminator hairpin and U-tract specified by the pyrBI attenuator. Our results show an inverse relationship between termination efficiency and the number of bases inserted. The effects of the substitution and insertion mutations on termination efficiency at the pyrBI attenuator were also measured in vitro, which corroborated the in vivo results. Our results are discussed in terms of the current models for intrinsic transcription termination and estimating termination efficiencies at intrinsic terminators of other bacteria. [source] Inactivation of the decay pathway initiated at an internal site by RNase E promotes poly(A)-dependent degradation of the rpsO mRNA in Escherichia coliMOLECULAR MICROBIOLOGY, Issue 4 2003Paulo E. Marujo Summary In Escherichia coli, RNA degradation is mediated by endonucleolytic processes, frequently mediated by RNase E, and also by a poly(A)-dependent mechanism. The dominant pathway of decay of the rpsO transcripts is initiated by an RNase E cleavage occurring at a preferential site named M2. We demonstrate that mutations which prevent this cleavage slow down degradation by RNase E. All these mutations reduce the single-stranded character of nucleotides surrounding the cleavage site. Moreover, we identify two other cleavage sites which probably account for the slow RNase E-mediated degradation of the mutated mRNAs. Failure to stabilize the rpsO transcript by appending a 5, hairpin indicates that RNase E is not recruited by the 5, end of mRNA. The fact that nucleotide substitutions which prevent cleavage at M2 facilitate the poly(A)-dependent degradation of the rpsO transcripts suggest an interplay between the two mechanisms of decay. In the discussion, we speculate ,that ,a ,structural ,feature ,located ,in ,the ,vicinity of M2 could be an internal degradosome entry site promoting both RNase E cleavages and poly(A)-dependent degradation of the rpsO mRNA. We also discuss the role of poly(A)-dependent decay in mRNA metabolism. [source] Beta-helix model for the filamentous haemagglutinin adhesin of Bordetella pertussis and related bacterial secretory proteinsMOLECULAR MICROBIOLOGY, Issue 2 2001Andrey V. Kajava Bordetella pertussis establishes infection by attaching to epithelial cells of the respiratory tract. One of its adhesins is filamentous haemagglutinin (FHA), a 500-Å-long secreted protein that is rich in ,-structure and contains two regions, R1 and R2, of tandem 19-residue repeats. Two models have been proposed in which the central shaft is (i) a hairpin made up of a pairing of two long antiparallel ,-sheets; or (ii) a ,-helix in which the polypeptide chain is coiled to form three long parallel ,-sheets. We have analysed a truncated variant of FHA by electron microscopy (negative staining, shadowing and scanning transmission electron microscopy of unstained specimens): these observations support the latter model. Further support comes from detailed sequence analysis and molecular modelling studies. We applied a profile search method to the sequences adjacent to and between R1 and R2 and found additional ,covert' copies of the same motifs that may be recognized in overt form in the R1 and R2 sequence repeats. Their total number is sufficient to support the tenet of the ,-helix model that the shaft domain , a 350 Å rod , should consist of a continuous run of these motifs, apart from loop inserts. The N-terminus, which does not contain such repeats, was found to be weakly homologous to cyclodextrin transferase, a protein of known immunoglobulin-like structure. Drawing on crystal structures of known ,-helical proteins, we developed structural models of the coil motifs putatively formed by the R1 and R2 repeats. Finally, we applied the same profile search method to the sequence database and found several other proteins , all large secreted proteins of bacterial provenance , that have similar repeats and probably also similar structures. [source] The solution structure of ZNF593 from Homo sapiens reveals a zinc finger in a predominately unstructured proteinPROTEIN SCIENCE, Issue 3 2008Paulette L. Hayes Abstract Here, we report the solution structure of ZNF593, a protein identified in a functional study as a negative modulator of the DNA-binding activity of the Oct-2 transcription factor. ZNF593 contains a classic C2H2 zinc finger domain flanked by about 40 disordered residues on each terminus. Although the protein contains a high degree of intrinsic disorder, the structure of the zinc finger domain was resolved by NMR spectroscopy without a need for N- or C-terminal truncations. The tertiary structure of the zinc finger domain is composed of a ,-hairpin that positions the cysteine side chains for zinc coordination, followed by an atypical kinked ,-helix containing the two histidine side chain ligands. The structural topology of ZNF593 is similar to a fragment of the double-stranded RNA-binding protein Zfa and the C-terminal zinc finger of MBP-1, a human enhancer binding protein. The structure presented here will provide a guide for future functional studies of how ZNF593 negatively modulates the DNA-binding activity of Oct-2, a POU domain-containing transcription factor. Our work illustrates the unique capacity of NMR spectroscopy for structural analysis of folded domains in a predominantly disordered protein. [source] Unfolding of the loggerhead sea turtle (Caretta caretta) myoglobin: A 1H-NMR and electronic absorbance studyPROTEIN SCIENCE, Issue 9 2002Daniela Delli Castelli Abstract The effect of urea concentration on the backbone solution structure of the cyanide derivative of ferric Caretta caretta myoglobin (at pH 5.4) is reported. By addition of urea, sequential and long-range nuclear Overhauser effects (NOEs) are gradually lost. By using the residual NOE constraints to build the molecular model, a picture of the unfolding pathway was obtained. When the urea concentration is raised to 2.2 M, helices A and B appear largely disordered; helices C, D, and F loose structural constraints at 3.0 M urea. At urea concentration >6 M, the protein appears to be fully unfolded, including the GH hairpin and helix E stabilizing the prosthetic group. Reversible and cooperative denaturation isotherms obtained by following NOE peaks are considerably different from those obtained by monitoring electronic absorption changes. The reversible and cooperative urea-dependent folding-unfolding process of C. caretta myoglobin follows the minimum three-state mechanism N,X,D, where X represents a disordered globin structure (occurring at ,4 M urea) that still binds the heme. [source] Alternative type I and I, turn conformations in the ,8/,9 ,-hairpin of human acidic fibroblast growth factorPROTEIN SCIENCE, Issue 3 2002Jaewon Kim Abstract Human acidic fibroblast growth factor (FGF-1) has a ,-trefoil structure, one of the fundamental protein superfolds. The X-ray crystal structures of wild-type and various mutant forms of FGF-1 have been solved in five different space groups: C2, C2221, P21 (four molecules/asu), P21 (three molecules/asu), and P212121. These structures reveal two characteristically different conformations for the ,8/,9 ,-hairpin comprising residue positions 90,94. This region in the wild-type FGF-1 structure (P21, four molecules/asu), a his-tagged His93,Gly mutant (P21, three molecules/asu) and a his-tagged Asn106,Gly mutant (P212121) adopts a 3:5 ,-hairpin known as a type I (1,4) G1 ,-bulge (containing a type I turn). However, a his-tagged form of wild-type FGF-1 (C2221) and a his-tagged Leu44,Phe mutant (C2) adopt a 3:3 ,-hairpin (containing a type I, turn) for this same region. A feature that distinguishes these two types of ,-hairpin structures is the number and location of side chain positions with eclipsed C, and main-chain carbonyl oxygen groups (, , +60°). The effects of glycine mutations upon stability, at positions within the hairpin, have been used to identify the most likely structure in solution. Type I, turns in the structural data bank are quite rare, and a survey of these turns reveals that a large percentage exhibit crystal contacts within 3.0 Å. This suggests that many of the type I, turns in X-ray structures may be adopted due to crystal packing effects. [source] Synthesis and NMR solution structure of an ,-helical hairpin stapled with two disulfide bridgesPROTEIN SCIENCE, Issue 5 2000Philippe Barthe Abstract Helical coiled-coils and bundles are some of the most common structural motifs found in proteins. Design and synthesis of ,-helical motifs may provide interesting scaffolds that can be useful as host structures to display functional sites, thus allowing the engineering of novel functional miniproteins. We have synthesized a 38-amino acid peptide, ,2p8, encompassing the ,-helical hairpin present in the structure of p8MTCP1, as an ,-helical scaffold particularly promising for its stability and permissiveness of sequence mutations. The three-dimensional structure of this peptide has been solved using homonuclear two-dimensional NMR techniques at 600 MHz. After sequence specific assignment, a total of 285 distance and 29 dihedral restraints were collected. The solution structure of ,2p8 is presented as a set of 30 DIANA structures, further refined by restrained molecular dynamics, using simulated annealing protocol with the AMBER force field. The RMSD values for the backbone and all heavy atoms are 0.65 ± 0.25 and 1.51 ± 0.21 Å, respectively. Excised from its protein context, the ,-hairpin keeps its native structure: an ,-helical coiled-coil, similar to that found in superhelical structures, with two helices spanning residues 4-16 and 25,36, and linked by a short loop. This motif is stabilized by two interhelical disulfide bridges and several hydrophobic interactions at the helix interface, leaving most of its solvent-exposed surface available for mutation. This ,-helical hairpin, easily amenable to synthetic chemistry and biological expression system, may represent a stable and versatile scaffold to display new functional sites and peptide libraries. [source] | ||||||||||||||||||||||||||||||||||