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Hairpin Structure (hairpin + structure)
Selected AbstractsDesign of Neutral Metallomesogens from 5,5-Dimethyldipyrromethane: Metal Ion Mediated Control of Folding and Hairpin StructuresEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 32 2008Kelly A. Ames Abstract New ligands derived from 5,5-dimethyldipyrromethane and their corresponding neutral complexes with ZnII and PdII are described. The ligands incorporate either a hexacatenar [H2(1n), n = 1, 10, 12, 14 and 16], tetracatenar [H2(2n), n = 1 and 16] or an extended dicatenar structure [H2(3n), n = 1and 16]. Single-crystal X-ray structure determinations of [Zn2(11)2] and [Zn2(31)2] confirm a distorted tetrahedral geometry at ZnII to afford double-stranded helical structures, while the PdII species [Pd(31)] shows a distorted square-planar geometry with the ligand adopting an alternative hairpin conformation. The metal-free hexacatenar ligands H2(1n) (n = 10, 12, 14, 16) and the corresponding complexes [Zn2(116)2] and [Pd(1n)] (n = 12, 14, 16) are not mesomorphic. However, the tetracatenar complex [Zn2(216)2] generates a smectic mesophase, as confirmed by X-ray diffraction, while [Pd(216)] and the metal-free ligand H2(216) show no mesomorphic behaviour. Two of the extended dicatenar compounds, H2(316) and [Zn2(316)2] are non-mesomorphic, while [Pd(316)] displays a smectic A phase.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] NMR investigations of subunit c of the ATP synthase from Propionigenium modestum in chloroform/methanol/water (4 : 4 : 1)FEBS JOURNAL, Issue 7 2002Ulrich Matthey The subunit c from the ATP synthase of Propionigenium modestum was studied by NMR in chloroform/methanol/water (4 : 4 : 1). In this solvent, subunit c consists of two helical segments, comprised of residues L5 to I26 and G29 to N82, respectively. On comparing the secondary structure of subunit c from P. modestum in the organic solvent mixture with that in dodecylsulfate micelles several deviations became apparent: in the organic solvent, the interruption of the ,,helical structure within the conserved GXGXGXGX motif was shortened from five to two residues, the prominent interruption of the ,,helical structure in the cystoplasmic loop region was not apparent, and neither was there a break in the ,,helix after the sodium ion-binding Glu65 residue. The folding of subunit c of P. modestum in the organic solvent also deviated from that of Escherichia coli in the same environment, the most important difference being that subunit c of P. modestum did not adopt a stable hairpin structure like subunit c of E. coli. [source] Efficient downregulation of alb1 gene using an AMA1-based episomal expression of RNAi construct in Aspergillus fumigatusFEMS MICROBIOLOGY LETTERS, Issue 2 2007Vahid Khalaj Abstract An episomal RNAi silencing construct containing the inducible cbhB promoter and a hairpin structure has been made to downregulate the alb1 gene in the human pathogen Aspergillus fumigatus. Transformation of fungal protoplasts resulted in a high number of transformants with an inducible silenced phenotype (white spores). Efficient downregulation of the alb1 gene using this system suggests that this approach may overcome the variable downregulation observed with integrative constructs. [source] The mitochondrial genome of the Korean hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae)INSECT MOLECULAR BIOLOGY, Issue 2 2006I. Kim Abstract We determined the complete nucleotide sequences of the mitochondrial genome (mitogenome) of the Korean hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae). The entire mitochondrial DNA (mtDNA) molecule was 15 314 bp long. The C. raphaelis genes were in the same order and orientation as the completely sequenced mitogenomes of other lepidopteran species, except for the presence of an extra copy of tRNASer(AGN). High similarity in primary sequence and secondary structure between the two tandemly located copies of the tRNASer(AGN) suggest a recent duplication of an original single tRNASer(AGN). The DHU arm of the two copies of tRNASer(AGN) formed a simple loop as seen in many other metazoan mt tRNASer(AGN). The putative initiation codon for the C. raphaelis COI gene appears to be a tetranucleotide, TTAG, found commonly in the sequenced lepidopterans. ATPase8, ATPase6, ND4L and ND6 genes, which are next to another protein-coding gene at their 3, end all had the sequences potential to form a hairpin structure, suggesting the importance of such a structure for precise cleavage of the mature protein-coding genes. [source] The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2009Michio Iwaoka Abstract Molecular simulation by using force field parameters has been widely applied in the fields of peptide and protein research for various purposes. We recently proposed a new all-atom protein force field, called the SAAP force field, which utilizes single amino acid potentials (SAAPs) as the fundamental elements. In this article, whole sets of the SAAP force field parameters in vacuo, in ether, and in water have been developed by ab initio calculation for all 20 proteinogenic amino acids and applied to Monte Carlo molecular simulation for two short peptides. The side-chain separation approximation method was employed to obtain the SAAP parameters for the amino acids with a long side chain. Monte Carlo simulation for Met-enkephalin (CHO-Tyr-Gly-Gly-Phe-Met-NH2) by using the SAAP force field revealed that the conformation in vacuo is mainly controlled by strong electrostatic interactions between the amino acid residues, while the SAAPs and the interamino acid Lennard-Jones potentials are predominant in water. In ether, the conformation would be determined by the combination of the three components. On the other hand, the SAAP simulation for chignolin (H-Gly-Tyr-Asp-Pro-Glu-Thr-Gly-Thr-Trp-Gly-OH) reasonably reproduced a native-like ,-hairpin structure in water although the C-terminal and side-chain conformations were different from the native ones. It was suggested that the SAAP force field is a useful tool for analyzing conformations of polypeptides in terms of intrinsic conformational propensities of the single amino acid units. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Applications of model ,-hairpin peptidesJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 12 2004Carol E. Stotz Abstract In recent years, ,-hairpin peptides have been studied in great detail. Much of the focus has been on the thermodynamic stability of ,-hairpin structure. Structural measurements have been conducted with nuclear magnetic resonance, with additional information obtained from circular dichroism, Fourier transform infrared, and molecular dynamic simulation studies. Point mutations, both in the ,-strands and in the turn region, have systematically explored the role of turn sequence, side-chain,side-chain interactions, intramolecular hydrogen bonding, and ,-strand length on ,-hairpin peptide conformational stability. In addition to studying the elements of structural stability independently, the cooperative nature of the individual components to combine to form the overall structure has also been investigated. Because the ,-hairpin peptides often spontaneously form their conformation, they have begun to serve as models for studying peptide binding and therapeutic agents. © 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93:2881,2894, 2004 [source] Characterization of the binding surface of the translocated intimin receptor, an essential protein for EPEC and EHEC cell adhesionPROTEIN SCIENCE, Issue 12 2007Nathan T. Ross Abstract The translocated intimin receptor (TIR) of enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC) is required for EPEC and EHEC infections, which cause widespread illness across the globe. TIR is translocated via a type-III secretion system into the intestinal epithelial cell membrane, where it serves as an anchor for E. coli attachment via its binding partner intimin. While many aspects of EPEC and EHEC infection are now well understood, the importance of the intermolecular contacts made between intimin and TIR have not been thoroughly investigated. Herein we report site-directed mutagenesis studies on the intimin-binding domain of EPEC TIR, and how these mutations affect TIR-intimin association, as analyzed by isothermal titration calorimetry and circular dichroism. These results show how two factors govern TIR's binding to intimin: A three-residue TIR hot spot is identified that largely mediates the interaction, and mutants that alter the ,-hairpin structure of TIR severely diminish binding affinity. In addition, peptides incorporating key TIR residues identified by mutagenesis are incapable of binding intimin. These results indicate that hot spot residues and structural orientation/preorganization are required for EPEC, and likely EHEC, TIR-intimin binding. [source] Sequence dependence of ,-hairpin structure: Comparison of a salt bridge and an aromatic interactionPROTEIN SCIENCE, Issue 12 2003Sarah E. Kiehna Abstract A comparison of the contributions and position dependence of cross-strand electrostatic and aromatic side-chain interactions to ,-sheet stability has been performed by using nuclear magnetic resonance in a well-folded ,-hairpin peptide of the general sequence XRTVXVdPGOXITQX. Phe,Phe and Glu,Lys pairs were varied at the internal and terminal non,hydrogen-bonded position, and the resulting stability was measured by the effects on ,-hydrogen and aromatic hydrogen chemical shifts. It was determined that the introduction of a Phe,Phe pair resulted in a more folded peptide, regardless of position, and a more tightly folded core. Substitution of the Glu,Lys pair at the internal position results in a less folded peptide and increased fraying at the terminal residues. Upfield shifting of the aromatic hydrogens provided evidence for an edge-face aromatic interaction, regardless of position of the Phe,Phe pair. In peptides with two Phe,Phe pairs, substitution with Glu,Lys at either position resulted in a weakening of the aromatic interaction and a subsequent decrease in peptide stability. Thermal denaturation of the peptides containing Phe,Phe indicates that the aromatic interaction is enthalpically favored, whereas the folding of hairpins with cross-strand Glu,Lys pairs was less enthalpically favorable but entropically more favorable. [source] Elongation of the BH8 ,-hairpin peptide: Electrostatic interactions in ,-hairpin formation and stabilityPROTEIN SCIENCE, Issue 7 2001Marina Ramírez-Alvarado Abstract An elongated version of the de novo designed ,-hairpin peptide, BH8, has allowed us to gain insight into the role of electrostatic interactions in ,-hairpin stability. A Lys,Glu electrostatic pair has been introduced by adding a residue at the beginning and at the end of the N-terminal and C-terminal strands, respectively, of the ,-hairpin structure, in both orientations. The two resulting peptides and controls having Ala residues at these positions and different combinations of Ala with Lys, or Glu residues, have been analyzed by nuclear magnetic resonance (NMR), under different pH and ionic strength conditions. All of the NMR parameters, in particular the conformational shift analysis of C, protons and the coupling constants, 3JHN,, correlate well and the population estimates are in reasonable agreement among the different methods used. In the most structured peptides, we find an extension of the ,-hairpin structure comprising the two extra residues. Analysis of the pH and salt dependence shows that ionic pairs contribute to ,-hairpin stability. The interaction is electrostatic in nature and can be screened by salt. There is also an important salt-independent contribution of negatively charged groups to the stability of this family of ,-hairpin peptides. [source] Lentiviral vectors that carry anti-HIV shRNAs: problems and solutionsTHE JOURNAL OF GENE MEDICINE, Issue 9 2007Olivier ter Brake Abstract Background HIV-1 replication can be inhibited with RNA interference (RNAi) by expression of short hairpin RNA (shRNA) from a lentiviral vector. Because lentiviral vectors are based on HIV-1, viral sequences in the vector system are potential targets for the antiviral shRNAs. Here, we investigated all possible routes by which shRNAs can target the lentiviral vector system. Methods Expression cassettes for validated shRNAs with targets within HIV-1 Leader, Gag-Pol, Tat/Rev and Nef sequences were inserted in the lentiviral vector genome. Third-generation self-inactivating HIV-1-based lentiviral vectors were produced and lentiviral vector capsid production and transduction titer determined. Results RNAi against HIV-1 sequences within the vector backbone results in a reduced transduction titer while capsid production was unaffected. The notable exception is self-targeting of the shRNA encoding sequence, which does not affect transduction titer. This is due to folding of the stable shRNA hairpin structure, which masks the target for the RNAi machinery. Targeting of Gag-Pol mRNA reduces both capsid production and transduction titer, which was improved with a human codon-optimized Gag-Pol construct. When Rev mRNA was targeted, no reduction in capsid production and transduction titer was observed. Conclusions Lentiviral vector titers can be negatively affected when shRNAs against the vector backbone and the Gag-Pol mRNA are expressed during lentiviral vector production. Titer reductions due to targeting of the Gag-Pol mRNA can be avoided with a human codon-optimized Gag-Pol packaging plasmid. The remaining targets in the vector backbone may be modified by point mutations to resist RNAi-mediated degradation during vector production. Copyright © 2007 John Wiley & Sons, Ltd. [source] Novel CNBP- and La-based translation control systems for mammalian cellsBIOTECHNOLOGY & BIOENGINEERING, Issue 1 2003Stefan Schlatter Abstract Throughout the development of Xenopus, production of ribosomal proteins (rp) is regulated at the translational level. Translation control is mediated by a terminal oligopyrimidine element (TOP) present in the 5, untranslated region (UTR) of rp -encoding mRNAs. TOP elements adopt a specific secondary structure that prevents ribosome-binding and translation-initiation of rp -encoding mRNAs. However, binding of CNBP (cellular nucleic acid binding protein) or La proteins to the TOP hairpin structure abolishes the TOP-mediated transcription block and induces rp production. Based on the specific CNBP-TOP/La-TOP interactions we have designed a translation control system (TCS) for conditional as well as adjustable translation of desired transgene mRNAs in mammalian cells. The generic TCS configuration consists of a plasmid encoding CNBP or La under control of the tetracycline-responsive expression system (TETOFF) and a target expression vector containing a TOP module between a constitutive PSV40 promoter and the human model product gene SEAP (human secreted alkaline phosphatase) (PSV40 -TOP- SEAP -pA). The TCS technology showed excellent SEAP regulation profiles in transgenic Chinese hamster ovary (CHO) cells. Alternatively to CNBP and La, TOP-mediated translation control can also be adjusted by artificial phosphorothioate anti-TOP oligodeoxynucleotides. Confocal laser-scanning microscopy demonstrated cellular uptake of FITC-labeled oligodeoxynucleotides and their localization in perinuclear organelles within 24 hours. Besides their TOP-based translation-controlling capacity, CNBP and La were also shown to increase cap-independent translation from polioviral internal ribosomal entry sites (IRES) and La alone to boost cap-dependent translation initiation. CNBP and La exemplify for the first time the potential of RNA-binding proteins to exert translation control of desired transgenes and to increase heterologous protein production in mammalian cells. We expect both of these assets to advance current gene therapy and biopharmaceutical manufacturing strategies. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 81: 1,12, 2003. [source] Aminoglycoside,Quinacridine Conjugates: Towards Recognition of the P6.1 Element of Telomerase RNACHEMBIOCHEM, Issue 2 2006Markus Kaiser Dr. Abstract A modular synthesis has been developed which allows easy and rapid attachment of one or two aminoglycoside units to a quinacridine intercalator, thereby leading to monomeric and dimeric conjugates. Melting temperature (Tm) experiments show that the tobramycin dimeric conjugate TD1 exhibits strong binding to the P6.1 element of human telomerase RNA. By contrast, tobramycin alone is much less efficient and the monomeric compound TM1 elicits a poor binding ability. Monitoring of the interaction by an electrophoretic mobility shift assay shows a 1:1 stoichiometry for the binding of the dimeric compound to the hairpin structure and confirms the lower affinity for a control duplex. Protection experiments with RNase T1 indicate interaction of the drug both in the stem and in the loop of the hairpin. Taken together, the data suggest a binding of TD1 inside the hairpin at the stem-loop junction. The same trends are observed with paromomycin and kanamycin analogues but with a lower affinity. [source] Folding Dynamics of 10-Residue ,-Hairpin Peptide ChignolinCHEMISTRY - AN ASIAN JOURNAL, Issue 5 2007Atsushi Suenaga Dr. Abstract Short peptides that fold into ,-hairpins are ideal model systems for investigating the mechanism of protein folding because their folding process shows dynamics typical of proteins. We performed folding, unfolding, and refolding molecular dynamics simulations (total of 2.7,,s) of the 10-residue ,-hairpin peptide chignolin, which is the smallest ,-hairpin structure known to be stable in solution. Our results revealed the folding mechanism of chignolin, which comprises three steps. First, the folding begins with hydrophobic assembly. It brings the main chain together; subsequently, a nascent turn structure is formed. The second step is the conversion of the nascent turn into a tight turn structure along with interconversion of the hydrophobic packing and interstrand hydrogen bonds. Finally, the formation of the hydrogen-bond network and the complete hydrophobic core as well as the arrangement of side-chain,side-chain interactions occur at approximately the same time. This three-step mechanism appropriately interprets the folding process as involving a combination of previous inconsistent explanations of the folding mechanism of the ,-hairpin, that the first event of the folding is formation of hydrogen bonds and the second is that of the hydrophobic core, or vice versa. [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] A HYPOTHESIS FOR IMPORT OF THE NUCLEAR-ENCODED PsaE PROTEIN OF PAULINELLA CHROMATOPHORA (CERCOZOA, RHIZARIA) INTO ITS CYANOBACTERIAL ENDOSYMBIONTS/PLASTIDS VIA THE ENDOMEMBRANE SYSTEM,JOURNAL OF PHYCOLOGY, Issue 5 2010Mackiewicz The cyanobacterial endosymbionts of Paulinella chromatophora can shed new light on the process of plastid acquisition. Their genome is devoid of many essential genes, suggesting gene transfer to the host nucleus and protein import back into the endosymbionts/plastids. Strong evidence for such gene transfer is provided by the psaE gene, which encodes a PSI component that was efficiently transferred to the Paulinella nucleus. It remains unclear, however, how this protein is imported into the endosymbionts/plastids. We reanalyzed the sequence of Paulinella psaE and identified four potential non-AUG translation initiation codons upstream of the previously proposed start codon. Interestingly, the longest polypeptide, starting from the first UUG, contains a clearly identifiable signal peptide with very high (90%) predictability. We also found several downstream hairpin structures that could enhance translation initiation from the alternative codon. These results strongly suggest that the PsaE protein is targeted to the outer membrane of Paulinella endosymbionts/plastids via the endomembrane system. On the basis of presence of respective bacterial homologs in the Paulinella endosymbiont/plastid genome, we discuss further trafficking of PsaE through the peptidoglycan wall and the inner envelope membrane. It is possible that other nuclear-encoded proteins of P. chromatophora also carry signal peptides, but, alternatively, some may be equipped with transit peptides. If this is true, Paulinella endosymbionts/plastids would possess two distinct targeting systems, one cotranslational and the second posttranslational, as has been found in higher plant plastids. Considering the endomembrane system-mediated import pathway, we also discuss homology of the membranes surrounding Paulinella endosymbionts/plastids. [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 Ĺ. This suggests that many of the type I, turns in X-ray structures may be adopted due to crystal packing effects. [source] Hexamer oligonucleotide topology and assembly under solution phase NMR and theoretical modeling scrutinyBIOPOLYMERS, Issue 12 2010Maxim P. Evstigneev Abstract The entire family of noncomplementary hexamer oligodeoxyribonucleotides d(GCXYGC) (X and Y = A, G, C, or T) were assessed for topological indicators and equilibrium thermodynamics using a priori molecular modeling and solution phase NMR spectroscopy. Feasible modeled hairpin structures formed a basis from which solution structure and equilibria for each oligonucleotide were considered. 1H and 31P variable temperature-dependent (VT) and concentration-dependent NMR data, NMR signal assignments, and diffusion parameters led to d(GCGAGC) and d(GCGGGC) being understood as exceptions within the family in terms of self-association and topological character. A mean diffusion coefficient D298 K = (2.0 ± 0.07) × 10,10 m2 s,1 was evaluated across all hexamers except for d(GCGAGC) (D298 K = 1.7 × 10,10 m2 s,1) and d(GCGGGC) (D298 K = 1.2 × 10,10 m2 s,1). Melting under VT analysis (Tm = 323 K) combined with supporting NMR evidence confirmed d(GCGAGC) as the shortest tandem sheared GA mismatched duplex. Diffusion measurements were used to conclude that d(GCGGGC) preferentially exists as the shortest stable quadruplex structure. Thermodynamic analysis of all data led to the assertion that, with the exception of XY = GA and GG, the remaining noncomplementary oligonucleotides adopt equilibria between monomer and duplex, contributed largely by monomer random-coil forms. Contrastingly, d(GCGAGC) showed preference for tandem sheared GA mismatch duplex formation with an association constant K = 3.9 × 105M,1. No direct evidence was acquired for hairpin formation in any instance although its potential existence is considered possible for d(GCGAGC) on the basis of molecular modeling studies. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 1023,1038, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Identification of Trinucleotide Repeat Ligands with a FRET Melting AssayCHEMBIOCHEM, Issue 8 2008Samir Amrane Dr. Abstract DNA hairpin structures formed within a repeated tract might be a causative factor for triplet expansion observed in several debilitating diseases. We have designed and used a fluorescence resonance energy transfer (FRET) melting assay to screen for ligands that bind specifically to the CNG triplet repeats. Using this assay, we screened a panel of 33 chemicals that were previously designed to bind DNA or RNA secondary structures. Remarkably, we found that macrocyclic compounds, such as acridine dimers and trimers, exhibit interesting affinities and specificities for this motif. [source] | |||||||||||||