Antiparallel Orientation Research Articles

Highly asymmetrical glycerol diether bolalipids: synthesis and temperature-dependent aggregation behavior.

In the present work, we describe the synthesis and temperature-dependent aggregation behavior of two examples of a new class of highly asymmetrical glycerol diether bolaphospholipids. The bolalipids contain a long alkyl chain (C32) bound to glycerol in the sn-3 position, carrying a hydroxyl group at the ω position. The C16 alkyl chain in the sn-2 position either possesses a racemic methyl branch at the 10 position of the short alkyl chain (lipid II) or does not (lipid I). The sn-1 position of the glycerol is linked to a zwitterionic phosphocholine moiety. The temperature-dependent aggregation behavior of both bolalipids was studied using differential scanning calorimetry (DSC), Fourier-transform infrared (FTIR) spectroscopy, and X-ray scattering. Aggregate structures were visualized by transmission electron microscopy (TEM). We show that both bolalipids self-assemble into large lamellar sheetlike aggregates. Closed lipid vesicles or other aggregate structures such as tubes or nanofibers, as usually found for diglycerol tetraether lipids, were not observed. Within the lamellae the bolalipid molecules are arranged in an antiparallel (interdigitated) orientation. Lipid I, without an additional methyl moiety in the short alkyl chain, shows a lamellar phase with high crystallinity up to a temperature of 34 °C, which was not observed before for other phospholipids.

Noise spectroscopy of CoFeB/MgO/CoFeB magnetic tunnel junctions in the presence of thermal gradients

We present experimental data of the precessional dynamics of the free layer of CoFeB/MgO/CoFeB based magnetic tunnel junctions (MTJ) in the presence of thermal gradients across the MTJ. The free layer precession is investigated by noise spectroscopy. Thermal gradients of the order of tens of mK/nm across the MTJ are generated by electrical heating. Without applied thermal gradients we find spin transfer torque modified magnetization precession. With increasing thermal gradients we generally observe a decrease of the precession frequency which could be related to an increasing overall free layer temperature. However an asymmetry of the line width behavior for parallel and antiparallel orientation points towards additional effects beyond thermal activation. This could be a hint for the modification of the precessional dynamics in magnetic tunnel junctions by thermal spin torques.

Crystal structure analyses of azasulfuryltripeptides reveal potential for γ-turn mimicry.

Azasulfurylpeptides feature an amino acid residue in which the CαH and the carbonyl are replaced respectively by a nitrogen atom and a sulfonyl group. Insight into the conformational preferences of azasulfurylpeptides containing an azasulfurylglycine (AsG) residue has been pursued using X-ray analysis in the solid state. Crystals of N-(Boc)-Pro-AsG-Val-OMe (10) and N-(Cbz)-Ala-AsG-D-Phe-Ot-Bu (11) showed tetrahedral geometries about the sulfur atom with the ω torsion angle preferring a staggered conformation. Furthermore, the ϕ and ψ torsion angles of the central azasulfuryl residue were respectively within close proximity to those of ideal inverse and classical γ-turns. In the crystal lattice, azasulfurylpeptide 11 engaged in intermolecular hydrogen bonds between the sulfonyl oxygen and hydrazide hydrogen in an antiparallel orientation.

First-principles comparative study on the interlayer adhesion and shear strength of transition-metal dichalcogenides and graphene

Due to their layered structure, graphene and transition-metal dichalcogenides (TMDs) are easily sheared along the basal planes. Despite a growing attention towards their use as solid lubricants, so far no head-to-head comparison has been carried out. By means of ab initio modeling of a bilayer sliding motion, we show that graphene is characterized by a shallower potential energy landscape while more similarities are attained when considering the sliding forces; we propose that the calculated interfacial ideal shear strengths afford the most accurate information on the intrinsic sliding capability of layered materials. We also investigate the effect of an applied uniaxial load: in graphene, this introduces a limited increase in the sliding barrier while in TMDs it has a substantially different impact on the possible polytypes. The polytype presenting a parallel orientation of the layers ($R0$) bears more similarities to graphene while that with antiparallel orientation ($R180$) shows deep changes in the potential energy landscape and consequently a sharper increase of its sliding barrier.

Solution structure of a DNA quadruplex containing ALS and FTD related GGGGCC repeat stabilized by 8-bromodeoxyguanosine substitution.

A prolonged expansion of GGGGCC repeat within non-coding region of C9orf72 gene has been identified as the most common cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), which are devastating neurodegenerative disorders. Formation of unusual secondary structures within expanded GGGGCC repeat, including DNA and RNA G-quadruplexes and R-loops was proposed to drive ALS and FTD pathogenesis. Initial NMR investigation on DNA oligonucleotides with four repeat units as the shortest model with the ability to form an unimolecular G-quadruplex indicated their folding into multiple G-quadruplex structures in the presence of K+ ions. Single dG to 8Br-dG substitution at position 21 in oligonucleotide d[(G4C2)3G4] and careful optimization of folding conditions enabled formation of mostly a single G-quadruplex species, which enabled determination of a high-resolution structure with NMR. G-quadruplex structure adopted by d[(G4C2)3GGBrGG] is composed of four G-quartets, which are connected by three edgewise C-C loops. All four strands adopt antiparallel orientation to one another and have alternating syn-anti progression of glycosidic conformation of guanine residues. One of the cytosines in every loop is stacked upon the G-quartet contributing to a very compact and stable structure.

Structures of the Alzheimer's Wild-Type Aβ1-40 Dimer from Atomistic Simulations.

We have studied the dimer of amyloid beta peptide Aβ of 40 residues by means of all-atom replica exchange molecular dynamics. The Aβ-dimers have been found to be the smallest toxic species in Alzheimer's disease, but their inherent flexibilities have precluded structural characterization by experimental methods. Though the 24-μs-scale simulation reveals a mean secondary structure of 18% β-strand and 10% α helix, we find transient configurations with an unstructured N-terminus and multiple β-hairpins spanning residues 17-21 and 30-36, but the antiparallel and perpendicular peptide orientations are preferred over the parallel organization. Short-lived conformational states also consist of all α topologies, and one compact peptide with β-sheet structure stabilized by a rather extended peptide with α-helical content. Overall, this first all-atom study provides insights into the equilibrium structure of the Aβ1-40 dimer in aqueous solution, opening a new avenue for a comprehensive understanding of the impact of pathogenic and protective mutations in early-stage Alzheimer's disease on a molecular level.

Poly(ADP-ribose)polymerase 1 stimulates the AP-site cleavage activity of tyrosyl-DNA phosphodiesterase 1.

The influence of poly(ADP-ribose)polymerase 1 (PARP1) on the apurinic/apyrimidinic (AP)-site cleavage activity of tyrosyl-DNA phosphodiesterase 1 (TDP1) and interaction of PARP1 and TDP1 were studied. The efficiency of single or clustered AP-site hydrolysis catalysed by TDP1 was estimated. It was shown that the efficiency of AP-site cleavage increases in the presence of an additional AP-site in the opposite DNA strand depending on its position. PARP1 stimulates TDP1; the stimulation effect was abolished in the presence of NAD(+). The interaction of these two proteins was characterized quantitatively by measuring the dissociation constant for the TDP1-PARP1 complex using fluorescently-labelled proteins. The distance between the N-termini of the proteins within the complex was estimated using FRET. The data obtained suggest that PARP1 and TDP1 bind in an antiparallel orientation; the N-terminus of the former protein interacts with the C-terminal domain of the latter. The functional significance of PARP1 and TDP1 interaction in the process of DNA repair was demonstrated for the first time.

Synthesis and DNA/RNA Binding Properties of Conformationally Constrained Pyrrolidinyl PNA with a Tetrahydrofuran Backbone Deriving from Deoxyribose.

Sugar-derived cyclic β-amino acids are important building blocks for designing of foldamers and other biomimetic structures. We report herein the first synthesis of a C-activated N-Fmoc-protected trans-(2S,3S)-3-aminotetrahydrofuran-2-carboxylic acid as a building block for Fmoc solid phase peptide synthesis. Starting from 2-deoxy-d-ribose, the product is obtained in a 6.7% overall yield following an 11-step reaction sequence. The tetrahydrofuran amino acid is used as a building block for a new peptide nucleic acid (PNA), which exhibits excellent DNA binding affinity with high specificity. It also shows preference for binding to DNA over RNA and specifically in the antiparallel orientation. In addition, the presence of the hydrophilic tetrahydrofuran ring in the PNA structure reduces nonspecific interactions and self-aggregation, which is a common problem in PNA due to its hydrophobic nature.

Analysis of the flanking sequences of the heterochromatic JNK region in Secale vavilovii chromosomes

The JNK motif is repeated 4 000 times in an additional heterochromatin band. Flanking sequences of a JNK region, which form extra heterochromatin in 2R rye (Secale vavilovii Grossh.) chromosomes, were studied using a genome walking technique. The results clearly indicate that there were blocks of JNK sequences adjacent to the R173 family of repeated sequences. Moreover, it appears that the R173 are sequences flanking in both directions, i.e., upstream and downstream. Downstream, the R173 is adjacent to the JNKs in an anti-parallel orientation, whereas upstream it is adjacent in a parallel orientation. In order to confirm the presence of the R173 sequence, fluorescence in situ hybridization was carried out. Using both JNK and R173 molecular probes, overlapping hybridization signals in the 2RL pair of chromosomes were observed, indicating an identical location of the two sequence elements.

Topological chirality of a type of DNA and protein polyhedral links

Polyhedral links, interlinked and interlocked architectures, have been proposed for the description and characterization of DNA and protein polyhedra. In this paper, we study the topological chirality of a type of DNA polyhedral links constructed by the strategy of “n-point stars” and a type of protein polyhedral links constructed by “three-cross curves and untwisted double-line” covering. Furthermore, we prove that links corresponding to bipartite plane graphs have antiparallel orientations, and under these orientations, their writhes are not zero. As a result, the type of double crossover DNA polyhedral links are topologically chiral. We also prove that the unoriented link corresponding to a connected, even, bipartite plane graph always has self-writhe 0. Using the Jones polynomial for unoriented links we derive two simple criteria for chirality of unoriented alternating links with self-writhe 0. By applying this criterion we show that 3-regular protein polyhedral links are also topologically chiral. Topological chirality always implies chemical chirality, hence the corresponding DNA and protein polyhedra are all chemically chiral. Our chiral criteria may be used to detect the topological chirality of more complicated DNA and protein polyhedral links that may be synthesized by chemists and biologists in the future.

Conformational Changes in the Orai1 C-Terminus Evoked by STIM1 Binding.

Store-operated CRAC channels regulate a wide range of cellular functions including gene expression, chemotaxis, and proliferation. CRAC channels consist of two components: the Orai proteins (Orai1-3), which form the ion-selective pore, and STIM proteins (STIM1-2), which form the endoplasmic reticulum (ER) Ca2+ sensors. Activation of CRAC channels is initiated by the migration of STIM1 to the ER-plasma membrane (PM) junctions, where it directly interacts with Orai1 to open the Ca2+-selective pores of the CRAC channels. The recent elucidation of the Drosophila Orai structure revealed a hexameric channel wherein the C-terminal helices of adjacent Orai subunits associate in an anti-parallel orientation. This association is maintained by hydrophobic interactions between the Drosophila equivalents of human Orai1 residues L273 and L276. Here, we used mutagenesis and chemical cross-linking to assess the nature and extent of conformational changes in the self-associated Orai1 C-termini during STIM1 binding. We find that linking the anti-parallel coiled-coils of the adjacent Orai1 C-termini through disulfide cross-links diminishes STIM1-Orai1 interaction, as assessed by FRET. Conversely, prior binding of STIM1 to the Orai1 C-terminus impairs cross-linking of the Orai1 C-termini. Mutational analysis indicated that a bend of the Orai1 helix located upstream of the self-associated coils (formed by the amino acid sequence SHK) establishes an appropriate orientation of the Orai1 C-termini that is required for STIM1 binding. Together, our results support a model wherein the self-associated Orai1 C-termini rearrange modestly to accommodate STIM1 binding.

Effect of degree of crystallinity on charge transport in ferroelectric semicrystalline polymer film

This paper describes 3D particle-in-cell (PIC) simulation of charge injection and transport through ferroelectric semicrystalline polymer (e.g. PVDF) film comprised of nanocrystallites in an amorphous matrix with varying degrees of crystallinity. The classical electrical double layer (EDL) model for a monopolar core is extended (eEDL) to represent the nanocrystallite by replacing it with a dipolar core. Charge injection at the electrodes assumes metal-polymer Schottky emission at low to moderate fields and Fowler-Nordheim tunneling at high fields. Injected particles propagate via field-dependent Poole-Frenkel mobility. In the eEDL model, the initial attachment of charge particles forms the bound Stern-Helmholtz layer leading to Maxwell-Wagner-Sillars polarization. Subsequent waves of charge particles are repelled by the attached charge resulting in the diffuse Gouy- Chapman transport layer. The simulation algorithm uses a boundary integral equation method (BIEM) for solution of the Poisson equation coupled with a second-order predictorcorrector scheme for robust time integration of the equations of motion. The stability criterion of the explicit algorithm conforms to the Courant-Friedrichs-Levy (CFL) limit assuring robust and rapid convergence. The model is capable of simulating a wide dynamic range spanning leakage current to pre-breakdown levels. Simulation results for semicrystalline film with varying degrees of crystallinity indicate that charge transport behavior depends on nanoparticle polarization with anti-parallel orientation showing the highest conduction and therefore lowest level of charge trapping in the interaction zone. Charge attachment to nanocrystallites increase with vol% loading or degree of crystallinity, and saturates at 40 vol% for the set of simulation parameters. The eEDL model predicts the intuitive meandering pathways of charge particle trajectories, which get progressively more inclined from normal incidence with increasing vol% loading.

Insights into the Hendra virus NTAIL–XD complex: Evidence for a parallel organization of the helical MoRE at the XD surface stabilized by a combination of hydrophobic and polar interactions

The Hendra virus is a member of the Henipavirus genus within the Paramyxoviridae family. The nucleoprotein, which consists of a structured core and of a C-terminal intrinsically disordered domain (NTAIL), encapsidates the viral genome within a helical nucleocapsid. NTAIL partly protrudes from the surface of the nucleocapsid being thus capable of interacting with the C-terminal X domain (XD) of the viral phosphoprotein. Interaction with XD implies a molecular recognition element (MoRE) that is located within NTAIL residues 470–490, and that undergoes α-helical folding. The MoRE has been proposed to be embedded in the hydrophobic groove delimited by helices α2 and α3 of XD, although experimental data could not discriminate between a parallel and an antiparallel orientation of the MoRE. Previous studies also showed that if the binding interface is enriched in hydrophobic residues, charged residues located close to the interface might play a role in complex formation. Here, we targeted for site directed mutagenesis two acidic and two basic residues within XD and NTAIL. ITC studies showed that electrostatics plays a crucial role in complex formation and pointed a parallel orientation of the MoRE as more likely. Further support for a parallel orientation was afforded by SAXS studies that made use of two chimeric constructs in which XD and the MoRE were covalently linked to each other. Altogether, these studies unveiled the multiparametric nature of the interactions established within this complex and contribute to shed light onto the molecular features of protein interfaces involving intrinsically disordered regions.

Dimerization of Terminal Domains in Spiders Silk Proteins Is Controlled by Electrostatic Anisotropy and Modulated by Hydrophobic Patches.

The well-tuned spinning technology from spiders has attracted many researchers with the promise of producing high-performance, biocompatible, and yet biodegradable fibers. So far, the intricate chemistry and rheology of spinning have eluded us. A breakthrough was achieved recently, when the 3D structures of the N and C terminal domains of spider dragline silk were resolved and their pH-induced dimerization was revealed. To understand the terminal domains' dimerization mechanisms, we developed a protein model based on the experimental structures that reproduces charge and hydrophobic anisotropy of the complex protein surfaces. Monte Carlo simulations were used to study the thermodynamic dimerization of the N-terminal domain as a function of pH and ionic strength. We show that the hydrophobic and electrostatic anisotropies of the N-terminal domain cooperate constructively in the association process. The dipolar attractions at pH 6 lead to weakly bound dimers by forcing an antiparallel monomer orientation, stabilized by hydrophobic locking at close separations. Elevated salt concentrations reduce the thermodynamic dimerization constant due to screened electrostatic dipolar attraction. Moreover, the mutations on ionizable residues reveal a free energy of binding, proportional to the dipole moment of the mutants. It has previously been shown that dimers, formed at pH 6, completely dissociate at pH 7, which is thought to be due to altered protein charges. In contrast, our study indicates that the pH increase has no influence on the charge distribution of the N-terminal domain. Instead, the pH-induced dissociation is due to an adapted, loose conformation at pH 7, which significantly hampers both electrostatic and hydrophobic attractive interactions.

A switch from parallel to antiparallel strand orientation in a coiled-coil X-ray structure via two core hydrophobic mutations.

The coiled-coil is one of the most ubiquitous and well studied protein structural motifs. Significant effort has been devoted to dissecting subtle variations of the typical heptad repeat sequence pattern that can designate larger topological features such as relative α-helical orientation and oligomer size. Here we report the X-ray structure of a model coiled-coil peptide, HA2-Del-L2seM, which forms an unanticipated core antiparallel dimer with potential sites for discrete higher-order multimerization (trimer or tetramer). In the X-ray structure, a third, partially-ordered α-helix is weakly associated with the antiparallel dimer and analytical ultracentrifugation experiments indicate the peptide forms a well-defined tetramer in solution. The HA2-Del-L2seM sequence is closely related to a parent model peptide, HA2-Del, which we previously reported adopts a parallel trimer; HA2-Del-L2seM differs by only hydrophobic leucine to selenomethione mutations and thus this subtle difference is sufficient to switch both relative α-helical topology and number of α-helices participating in the coiled-coil. Comparison of the X-ray structures of HA2-Del-L2seM (reported here) with the HA2-Del parent (reported previously) reveals novel interactions involving the selenomethionine residues that promote antiparallel coiled-coil configuration and preclude parallel trimer formation. These novel atomic insights are instructive for understanding subtle features that can affect coiled-coil topology and provide additional information for design of antiparallel coiled-coils.

Weird Ion…Weird Ion Channels Mediating Resistance to Fluoride Toxicity

F‐ specific ion channels of the newly discovered “Fluc” family act as F‐ exporters protect many microorganisms from the toxic effects of this environmentally pervasive halide. The channel is constructed as an four‐TM helix dual‐topology homodimer, in which the two subunits adopt antiparallel orientation within the membrane. We previously used fibronectin domain‐based “monobodies” selected by phage display methods to establish this unusual membrane architecture, showing that these small proteins block single Fluc channels from either side of the membrane. We now ask whether the two blocking sites on opposite sides of the membrane can both be occupied simultaneously by monobodies. Our analysis examines the dependence of single‐channel block‐times as a function of monobody concentration varied symmetrically on the two sides of the channel. If both sides can be blocked symmetrically, a linear blocking scheme should be followed:
Open ‐‐‐‐ Block(1) ‐‐‐‐Block(2),Where both blocked states are nonconducting. This scheme makes quantitative predictions for the increase in block‐times with monobody concentration that provide information about any cooperativity, negative or positive, that may operate between the two sites.

Orienting tetramolecular G-quadruplex formation: the quest for the elusive RNA antiparallel quadruplex.

DNA and RNA G-quadruplexes (G4) are unusual nucleic acid structures involved in a number of key biological processes. RNA G-quadruplexes are less studied although recent evidence demonstrates that they are biologically relevant. Compared to DNA quadruplexes, RNA G4 are generally more stable and less polymorphic. Duplexes and quadruplexes may be combined to obtain pure tetrameric species. Here, we investigated whether classical antiparallel duplexes can drive the formation of antiparallel tetramolecular quadruplexes. This concept was first successfully applied to DNA G4. In contrast, RNA G4 were found to be much more unwilling to adopt the forced antiparallel orientation, highlighting that the reason RNA adopts a different structure must not be sought in the loops but in the G-stem structure itself. RNA antiparallel G4 formation is likely to be restricted to a very small set of peculiar sequences, in which other structural features overcome the formidable intrinsic barrier preventing its formation.

Model for Charge Transport in Ferroelectric Nanocomposite Film

This paper describes 3D particle-in-cell simulation of charge injection and transport through nanocomposite film comprised of ferroelectric ceramic nanofillers in an amorphous polymer matrix and/or semicrystalline ferroelectric polymer with varying degrees of crystallinity. The classical electrical double layer model for a monopolar core is extended to represent the nanofiller/nanocrystallite by replacing it with a dipolar core. Charge injection at the electrodes assumes metal-polymer Schottky emission at low to moderate fields and Fowler-Nordheim tunneling at high fields. Injected particles propagate via field-dependent Poole-Frenkel mobility. The simulation algorithm uses a boundary integral equation method for solution of the Poisson equation coupled with a second-order predictor-corrector scheme for robust time integration of the equations of motion. The stability criterion of the explicit algorithm conforms to the Courant-Friedrichs-Levy limit assuring robust and rapid convergence. Simulation results for BaTiO3 nanofiller in amorphous polymer matrix and semicrystalline PVDF with varying degrees of crystallinity indicate that charge transport behavior depends on nanoparticle polarization with antiparallel orientation showing the highest conduction and therefore the lowest level of charge trapping in the interaction zone. Charge attachment to nanofillers and nanocrystallites increases with vol% loading or degree of crystallinity and saturates at 30–40 vol% for the set of simulation parameters.

Simulation of bipolar charge transport in nanocomposite polymer films

This paper describes 3D particle-in-cell simulation of bipolar charge injection and transport through nanocomposite film comprised of ferroelectric ceramic nanofillers in an amorphous polymer matrix. The classical electrical double layer (EDL) model for a monopolar core is extended (eEDL) to represent the nanofiller by replacing it with a dipolar core. Charge injection at the electrodes assumes metal-polymer Schottky emission at low to moderate fields and Fowler-Nordheim tunneling at high fields. Injected particles migrate via field-dependent Poole-Frenkel mobility and recombine with Monte Carlo selection. The simulation algorithm uses a boundary integral equation method for solution of the Poisson equation coupled with a second-order predictor-corrector scheme for robust time integration of the equations of motion. The stability criterion of the explicit algorithm conforms to the Courant-Friedrichs-Levy limit assuring robust and rapid convergence. The model is capable of simulating a wide dynamic range spanning leakage current to pre-breakdown. Simulation results for BaTiO3 nanofiller in amorphous polymer matrix indicate that charge transport behavior depend on nanoparticle polarization with anti-parallel orientation showing the highest leakage conduction and therefore lowest level of charge trapping in the interaction zone. Charge recombination is also highest, at the cost of reduced leakage conduction charge. The eEDL model predicts the meandering pathways of charge particle trajectories.

Duplex DNA and DNA-RNA hybrids with parallel strand orientation: 2'-deoxy-2'-fluoroisocytidine, 2'-deoxy-2'-fluoroisoguanosine, and canonical nucleosides with 2'-fluoro substituents cause unexpected changes on the double helix stability.

Oligonucleotides with parallel or antiparallel strand orientation incorporating 2'-fluorinated 2'-deoxyribonucleosides with canonical nucleobases or 2'-deoxy-2'-fluoroisocytidine ((F)iCd, 1c) and 2'-deoxy-2'-fluoroisoguanosine ((F)iGd, 3c) were synthesized. To this end, the nucleosides 1c and 3c as well as the phosphoramidite building blocks 19 and 23 were prepared and employed in solid-phase oligonucleotide synthesis. Unexpectedly, (F)iCd is not stable during oligonucleotide deprotection (55 °C, aq NH3) and was converted to a cyclonucleoside (14). Side product formation was circumvented when oligonucleotides were deprotected under mild conditions (aq ammonia-EtOH, rt). Oligonucleotides containing 2'-fluoro substituents ((F)iCd, (F)iGd and fluorinated canonical 2'-deoxyribonucleosides) stabilize double-stranded DNA, RNA, and DNA-RNA hybrids with antiparallel strand orientation. Unexpected strong stability changes are observed for oligonucleotide duplexes with parallel chains. While fluorinated oligonucleotides form moderately stable parallel stranded duplexes with complementary DNA, they do not form stable hybrids with RNA. Furthermore, oligoribonucleotide duplexes with parallel strand orientation are extremely unstable. It is anticipated that nucleic acids with parallel chains might be too rigid to accept sugar residues in the N-conformation as observed for ribonucleosides or 2'-deoxy-2'-fluororibonucleosides. These observations might explain why nature has evolved the principle of antiparallel chain orientation and has not used the parallel chain alignment.