Antiparallel Arrangement Research Articles

Emerging Roles for the Mitochondrial ATP Synthase Supercomplexes

As pointed out by Gu et al. (Science 2019) in mammalian mitochondria, the H-shaped tetrameric structure of the ATP synthase, the cell powerhouse, consists of two V-shaped dimers linked by two IF1 in antiparallel arrangement. This supramolecular structure reveals new functional/structural roles of the enzyme complex in mitochondria.

Mesophase Structure‐Enabled Electrostrictive Property in Nylon‐12‐Based Poly(ether‐block‐amide) Copolymers

AbstractTo search for alternative electrostrictive polymers and to understand the underlying mechanism, the structure‐ferroelectric/electrostrictive property relationship for nylon‐12‐based poly(ether‐b‐amide) multiblock copolymers (PEBAX) is investigated. Two PEBAX samples are studied, namely, P6333 and P7033 with 37 and 25 mol.% of soft poly(tetramethylene oxide) (PTMO) blocks, respectively. In both samples, poorly hydrogen‐bonded mesophase facilitates electric field‐induced ferroelectric switching. Meanwhile, the longitudinal electrostrictive strain (S1)–electric field (E) loops are obtained at 2 Hz. Different from conventional poly(vinylidene fluoride‐co‐trifluoroethylene) [P(VDF‐TrFE)]‐based terpolymers, uniaxially stretched nylon‐12‐based PEBAX samples exhibit negative S1, that is, shrinking rather than elongation in the longitudinal direction. This is attributed to the unique conformation transformation of nylon‐12 crystals during ferroelectric switching. Namely, at a zero electric field, crystalline nylon‐12 chains adopt a more or less antiparallel arrangement of amide groups. Upon high‐field poling, ferroelectric domains are enforced with more twisted chains adopting a parallel arrangement of amide groups. Meanwhile, extensional S1 is observed for P6333 at electric fields above 150 MV m−1. This is attributed to the elongation of the amorphous phases (i.e., amorphous nylon‐12 and PTMO). Therefore, competition between shrinking S1 from mesomorphic nylon‐12 crystals (i.e., nanoactuation) and elongational S1 from amorphous phases determines the ultimate electrostriction behavior in stretched PEBAX films.

Antiparallel Arrangement of 2,7-Substituted 9,10-Bis(phenylethynyl)anthracene Assisted by Hydrogen Bonding of Terminal Units

Abstract 2,7-Substituted 9,10-bis(phenylethynyl)anthracenes with bulky phenol residues were synthesized and investigated for their antiparallel molecular arrangement. UV-vis absorption and photoluminescence properties and molecular mechanics calculation indicate that they formed an antiparallel π-π stacked dimer, which was strongly associated by hydrogen bonding and π-π interaction. This strongly associated dimer structure was supported by AFM images of specimens prepared on mica by spin casting dilute chloroform/hexane (2/8 v/v) solution. However, the absence of intradimer hydrogen bonding resulted in the offset stacking, which was confirmed from the single crystal X-ray analysis.

Topological domain-engineered antiferroelectric-like behavior with enhanced energy storage properties in ferroelectric hexagonal Cr-doped YMnO3

We present the observation of the peculiar antiferroelectric (AFE)-like behavior, characterized by the polarization-electric field (P−E) double hysteresis loops and zero remnant polarization (Pr), in the ferroelectric (FE) Cr-doped YMnO3 (YMCO) single crystals. The AFE-like behavior in YMCO is in sharp contrast with the FE P−E single loop with high Pr in the undoped YMnO3 (YMO). The topological cloverleaf domains with ferroelectricity are observed in both YMO and YMCO. It is revealed unambiguously that the AFE-like behavior in YMCO arises from the Cr-substitution induced domain pattern transition from type-II with nonzero net macroscopic polarization to type-I with zero net polarization, as well as the recoverable type-I domain pattern after electric field sweeping. In addition, it is found that both the recoverable energy density and energy storage efficiency are significantly enhanced due to the AFE-like behavior in YMCO compared to YMO. Our results suggest for the first time that, in addition to the mechanism of the antiparallel arrangement of adjacent electric dipoles, the AFE-like behavior can be also achieved by domain engineering in a FE, which provides a possible new strategy to obtain high energy storage performance.

Prediction of fully compensated ferrimagnetic spin-gapless semiconducting FeMnGa/Al/In half Heusler alloys.

Materials with full spin polarization that exhibit zero net magnetization attract great scientific interest because of their potential applications in spintronics. Here, the structural, magnetic and electronic properties of a C1 b -ordered FeMnGa alloy are reported using first-principles calculations. The results indicate that the corresponding band structure exhibits a considerable gap in one of the spin channels and a zero gap in the other thus allowing for high mobility of fully spin-polarized carriers. The localized magnetic moments of Fe and Mn atoms have an antiparallel arrangement leading to fully compensated ferrimagnetism, which possesses broken magnetic inversion symmetry. Such magnetic systems do not produce dipole fields and are extremely stable against external magnetic fields. Therefore, this will improve the performance of spintronic devices. Using this principle, similar band dispersion and compensated magnetic moments were predicted in a C1 b -ordered FeMnAl0.5In0.5 Heusler alloy.

Navigating the Structural Landscape of De Novo α-Helical Bundles.

The association of amphipathic α helices in water leads to α-helical-bundle protein structures. However, the driving force for this-the hydrophobic effect-is not specific and does not define the number or the orientation of helices in the associated state. Rather, this is achieved through deeper sequence-to-structure relationships, which are increasingly being discerned. For example, for one structurally extreme but nevertheless ubiquitous class of bundle-the α-helical coiled coils-relationships have been established that discriminate between all-parallel dimers, trimers, and tetramers. Association states above this are known, as are antiparallel and mixed arrangements of the helices. However, these alternative states are less well understood. Here, we describe a synthetic-peptide system that switches between parallel hexamers and various up-down-up-down tetramers in response to single-amino-acid changes and solution conditions. The main accessible states of each peptide variant are characterized fully in solution and, in most cases, to high resolution with X-ray crystal structures. Analysis and inspection of these structures helps rationalize the different states formed. This navigation of the structural landscape of α-helical coiled coils above the dimers and trimers that dominate in nature has allowed us to design rationally a well-defined and hyperstable antiparallel coiled-coil tetramer (apCC-Tet). This robust de novo protein provides another scaffold for further structural and functional designs in protein engineering and synthetic biology.

KLK4 Inhibition by Cyclic and Acyclic Peptides: Structural and Dynamical Insights into Standard-Mechanism Protease Inhibitors.

Sunflower trypsin inhibitor (SFTI-1) is a 14 amino acid serine protease inhibitor. The dual antiparallel β-sheet arrangement of SFTI-1 is stabilized by an N-terminal-C-terminal backbone cyclization and a further disulfide bridge to form a final bicyclic structure. This constrained structure is further rigidified by an extensive network of internal hydrogen bonds. Thus, the structure of SFTI-1 in solution resembles the protease-bound structure, reducing the entropic penalty upon protease binding. When cleaved at the scissile bond, it is thought that the rigidifying features of SFTI-1 maintain its structure, allowing the scissile bond to be reformed. The lack of structural plasticity for SFTI-1 is proposed to favor initial protease binding and continued occupancy in the protease active site, resulting in an equilibrium between the cleaved and uncleaved inhibitor in the presence of a protease. We have determined, at 1.15 Å resolution, the X-ray crystal structures of complexes between human kallikrein-related peptidase 4 (KLK4) and SFTI-FCQR(Asn14) and between KLK4 and an acyclic form of the same inhibitor, SFTI-FCQR(Asn14)[1,14], with the latter displaying a cleaved scissile bond. Structural analysis and MD simulations together reveal the roles of the altered contact sequence, intramolecular hydrogen bonding network, and backbone cyclization in altering the state of SFTI's scissile bond ligation at the protease active site. Taken together, the data presented reveal insights into the role of dynamics in the standard-mechanism inhibition and suggest that modifications on the non-contact strand may be a useful, underexplored approach for generating further potent or selective SFTI-based inhibitors against members of the serine protease family.

Structural Understanding, Photoswitchability, and Supergelation of a New Class of Four Ring-Based Bent-Shaped Liquid Crystal.

Herein, we report a new type of azobenzene-based unsymmetrical bent-core molecules exhibiting photoswitchability in the liquid crystalline state, solid state, and solution state and in mixture upon UV irradiation and intense visible light. The compounds exhibited solid-state photochromism upon exposure to UV light, whereas in liquid crystalline state, reversible phase transitions were observed via both UV irradiation and intense visible light exposure. Crystal structure analysis reveals the basic structural understanding such as nonplanar bent molecular shape, antiparallel arrangement of the polar bent molecules, intra- and intermolecular hydrogen bonding, and different π-π interactions and interdigitation of long alkyl chains. The compounds are also found to act as supergelator toward various organic solvents. Hence, this is an excellent example of such potential bent-shaped liquid crystals that promise an immense perspective for device applications such as optical storage, molecular switches, etc.

Understanding structure and dynamics of organic liquid mixtures by molecular simulations

The structure and dynamics of acetonitrile and its mixtures with toluene and water in the whole composition range are investigated by molecular dynamics simulations with several combinations of empirical non-polarizable force fields. The acetonitrile and toluene binary system has been theoretically studied for the first time. One existing force field combination leads to unphysical phase separation in the mixture of acetonitrile with water. Densities, excess molar volumes, dielectric constants, viscosities and self-diffusion coefficients obtained by more suitable force fields are systematically compared with experimental data. For static properties, it is possible to get nearly quantitative agreement for both kinds of mixtures. The evaluation of the dielectric constant illustrates the importance of including the purely electronic component of polarization. The right trends for dynamical properties are captured. The arrangement of the closest acetonitrile molecules is antiparallel in the neat liquid, those with slightly larger separation of molecular centers orientate with respect to each other in various ways without strong preference for any of them. The addition of toluene causes structuring of acetonitrile and enhances the preference of antiparallel arrangement. Water has a smaller effect on the acetonitrile radial distribution functions, but it affects the preferences for individual arrangements.

Probing (UN)Folding Transition Paths of Fast-Folding Proteins by Single-Molecule Fluorescence: Exploring the Role of Secondary Structure, Fold Topology and Sequence

Protein folding involves formation of secondary structural elements and their collapse into well-defined 3-dimensional structure. Attempts to study how these processes cooperate to form the native structure and determine folding mechanisms has been focus of research for decades. Addressing these questions require looking at the distributions of behaviors of individual molecules, which has been successfully attained by theory and computer simulations. Experimentally, the problem must be approached by single-molecule spectroscopic methods, which have not had the required time-resolution. We are investigating protein folding at the single-molecule level combining advanced custom-built fluorescence-based SM-FRET techniques optimized for high-count rates and a maximum likelihood analysis (MLA) of photon arrival times that we developed for the detection of (un)folding transition paths of microsecond folding proteins. To investigate the roles of secondary structure, fold topology, and amino acid sequence we are performing these experiments on three fast-folding protein models, all consisting of three secondary structure elements in an antiparallel arrangement: En-HD (three α-helices), and Nedd4-WW3 and FBP11WW2, which fold onto homologous 3-stranded β-sheets but with different amino acid sequence. We are investigating their folding transition paths by 2-color SM-FRET using variants labeled with FRET pairs at the two ends in free diffusion experiments. Because these proteins fold-unfold in microseconds, free diffusion offers the opportunity to catch folding transitions during the diffusive trajectories without immobilization and thus without significantly perturbing folding landscape. Our analysis of these data using MLA of photon trajectories (rather than binning) provides the free energy landscape as a function of the experimental order parameter (FRET-pair distance) and the intramolecular diffusion coefficient. Subsequent reconstruction of the molecular trajectories from the photon trajectories using stochastic methods provide a direct glimpse of barrier crossing events.

A Single-Channel, 600-MS/s, 12-b, Ringamp-Based Pipelined ADC in 28-nm CMOS

Achieving high linearity and bandwidth with good power efficiency makes the design of ADCs in deep nanoscale CMOS processes very challenging, as the constraints of low-voltage operation and limited intrinsic gain often dictate the use of power-consuming analog circuits and intensive digital calibration. This paper addresses these problems by introducing a pipelined ADC that exploits the low but very constant open-loop gain versus output voltage characteristic of the ring amplifier (ringamp) to achieve both high speed and linearity in low-voltage nanoscale CMOS designs. A tunable ringamp biasing scheme using an anti-parallel arrangement of CMOS transistors and an active ringamp-based common-mode feedback are also introduced. A single-channel prototype ADC is implemented in a standard 28-nm CMOS process, achieving 58.7-dB SNDR and 72.4-dB SFDR at 600 MS/s while consuming 14.5 mW from a single 0.9-V supply, resulting in Walden and Schreier figure-of-merit (FoM) values of 34.4 fJ/conv.-step and 161.9 dB, respectively.

Competing forces in the self-assembly of amide-functionalized discotic mesogens.

The effect of incorporating a single amide group on the self-assembly of discotic mesogens was examined. Two series of tetraalkoxydibenzophenazines amides were prepared: tertiary diethyl amides, dEt(n) incapable of hydrogen bonding, and secondary amides HBu(n) that can act as both H-bond donors and acceptors. These compounds exhibit markedly different behavior in solution; NMR studies of dEt(n) show no evidence of self-association, whereas HBu(n) strongly associate via H-bonding and π-stacking. Compounds HBu(n) also act as small molecule gelators in a range of solvents, a property not observed for the corresponding tertiary amides. All compounds were found to form Colh liquid crystal phases; variable temperature XRD experiments indicate that each column has a diameter approximately equal to that of a single molecule. A comparison of the phase behavior of HBu(n) and dEt(n) suggests that the columnar phases of the former are stabilized by hydrogen bonding, likely at the expense of local parallel alignment of these molecules. Single crystal X-ray diffraction studies revealed that dEt(6) adopts an antiparallel arrangement in the solid state, in keeping with previous theories of packing within columnar LC phases. These studies highlight the interplay between competing factors, such as hydrogen bonding, π-stacking and dipole-dipole interactions that affect the stability of the LC phases.

Alkyl chain-dependent cyano-stilbene derivative's molecular stacking, emission enhancement and fluorescent response to the mechanical force and thermal stimulus

Two cyano-stilbene derivatives with butyl (C4MPA) and octyl groups (C8MPA) were synthesized to investigate the effects of alkyl chains on molecular stacking, emission enhancement, and mechanofluorochromism. The two compounds displayed weak emissions in monomolecular state and emitted an enhanced fluorescence in crystal state. However, the fluorescence quantum yield of C4MPA (19%) was lower than that of C8MPA (76%). Face-to-face dimer stacking was found only in the C4MPA crystal, in which molecules adopted a nonplanar configuration. The C8MPA crystal presented two kinds of antiparallel 1D arrangement. One involved the antiparallel stacking of nonplanar aromatic moieties. The other consisted of coplanar molecules without π-π stacking, which were responsible for the higher luminescence yield. Moreover, the emission of the C4MPA solid was quenched under mechanical force, whereas the C8MPA solid still emitted a strong fluorescence after grinding. C8MPA lost fluorescence when heated at above 60 °C because of its low melting point, and the supercooling viscous liquid without fluorescence was observed even the sample was cooled to room temperature for 10 h, meaning a very slowly crystallization process. Such non-emissive supercooling viscous liquid might rapidly transform into strongly emissive solid under the mechanical force shearing stimulus. Thus, C8MPA films could be used as sensors for mechanical force and thermal stimuli.

Ca2+-Sensor Neurocalcin δ and Hormone ANF Modulate ANF-RGC Activity by Diverse Pathways: Role of the Signaling Helix Domain.

Prototype member of the membrane guanylate cyclase family, ANF-RGC (Atrial Natriuretic Factor Receptor Guanylate Cyclase), is the physiological signal transducer of two most hypotensive hormones ANF and BNP, and of the intracellular free Ca2+. Both the hormonal and the Ca2+-modulated signals operate through a common second messenger, cyclic GMP; yet, their operational modes are divergent. The hormonal pathways originate at the extracellular domain of the guanylate cyclase; and through a cascade of structural changes in its successive domains activate the C-terminal catalytic domain (CCD). In contrast, the Ca2+ signal operating via its sensor, myristoylated neurocalcin δ both originates and is translated directly at the CCD. Through a detailed sequential deletion and expression analyses, the present study examines the role of the signaling helix domain (SHD) in these two transduction pathways. SHD is a conserved 35-amino acid helical region of the guanylate cyclase, composed of five heptads, each meant to tune and transmit the hormonal signals to the CCD for their translation and generation of cyclic GMP. Its structure is homo-dimeric and the molecular docking analyses point out to the possibility of antiparallel arrangement of the helices. Contrary to the hormonal signaling, SHD has no role in regulation of the Ca2+- modulated pathway. The findings establish and define in molecular terms the presence of two distinct non-overlapping transduction modes of ANF-RGC, and for the first time demonstrate how differently they operate, and, yet generate cyclic GMP utilizing common CCD machinery.

Efficient peptide based gelators for aromatic organic solvents and vegetable oils: application in phase selective gelation and dye entrapment

The examples of organogel in vegetable oil are limited and the illustration of single amphiphile showing organogel in a lot of vegetable oils are rare. Hence, invention of a new type of amphiphile capable to gelate different vegetable oils are demanding and challenging aspect to us. In this article, we have synthesized two peptide based low molecular weight organic gelators, [11-(2-tert-Butoxycarbonylamino-3-methyl-butyrylamino)-undecanoylamino]-acetic acid (TBMBUA) and [11-(2-tert-Butoxycarbonylamino-3-methyl-pentanoylamino)-undecanoylamino]-acetic acid (TBMPUA) and have demonstrated their excellent gelation ability towards a number of aromatic organic solvents and different edible vegetable oils. FT-IR and temperature dependence 1H-NMR spectroscopy studies confirmed that hydrogen bonding interaction among the amide linkages plays significant role for formation of gel in organic solvents. XRD and FT-IR measurements suggested anti-parallel beta sheet arrangement between the peptide chains in the self-assembled state. The study revealed that the synthesized amphiphile TBMBUA is a good phase selective gelator of aromatic organic solvents in water-solvent mixture and both the gelators are able to entrap toxic dyes from aqueous dye solution. Hence the gelators can be successfully utilized to remove the toxic aromatic organic solvents and toxic dyes present in waste water which is one of the serious problems in recent years.

Dimensional change of the quadrupole order in pseudospin- 12 pyrochlore magnets under magnetic field in the [111] direction

We have studied long range orders of electric quadrupole moments described by an effective pseudospin-$\frac{1}{2}$ Hamiltonian representing pyrochlore magnets with non-Kramers ions under [111] magnetic field, in relevance to Tb$_{2}$Ti$_{2}$O$_{7}$. Order parameters and phase transitions of this frustrated system are investigated using classical Monte-Carlo simulations. In zero field, the model undergoes a first-order phase transition from a paramagnetic state to an ordered state with an antiparallel arrangement of pseudospins. This pseudospin order is characterized by the wavevector $\boldsymbol{k}=0$ and is selected by an energetic or an order-by-disorder mechanism from degenerate $\boldsymbol{k}=(h,h,h)$ mean-field orders. Under [111] magnetic field this three-dimensional quadrupole order is transformed to a quasi two-dimensional quadrupole order on each kagom\'{e} lattice separated by field-induced ferromagnetic triangular lattices. We discuss implication of the simulation results with respect to experimental data of Tb$_{2}$Ti$_{2}$O$_{7}$.

Bromine-terminated azobenzene liquid crystals

ABSTRACTA series of liquid crystals (LCs) of bromine-terminated azobenzene were synthesised and characterised. The LCs were composed of an azobenzene core, an alkyl chain and a flexible spacer with a bromine atom at a remote position. Mesomorphic properties were dependent on both the alkyl chain length and the relative position of the bromine atom at the end of the spacer group. The nematic phase was favoured over the smectic A phase for alkyl chains with one and seven carbon atoms. However, the SmA mesophase was dominant for compounds with 10-carbon alkyl chains. The remote bromine atom in the spacer group favoured SmA for homologous with n-decyl chains and the nematic phase for n-heptyl and methyl groups. Molecular modelling showed that the azobenzene LCs tended to adopt the all trans-conformation in the gas phase as the number of carbon atoms increased. For short spacer groups, bent conformations contributed to the level population proportion of conformers. For the non-LC 5a, the gauche conformation became the most stable with a torsional angle of –68.9°. X-ray experiments showed a monolamellar SmA mesophase in an antiparallel arrangement. Absorption maxima at 360 and 440 nm were assigned to π–π* and n–π* transitions, respectively.

Flexoelectricity in antiferroelectrics

Flexoelectricity (coupling between polarization and strain gradients) is a property of all dielectric materials that has been theoretically known for decades, but only relatively recently it has begun to attract experimental attention. As a consequence, there are still entire families of materials whose flexoelectric performance is unknown. Such is the case of antiferroelectrics: materials with an antiparallel but switchable arrangement of dipoles. These materials are expected to be flexoelectrically relevant because it has been hypothesised that flexoelectricity could be linked to the origin of their antiferroelectricity. In this work, we have measured the flexoelectricity of two different antiferroelectrics (PbZrO3 and AgNbO3) as a function of temperature, up to and beyond their Curie temperature. Although their flexocoupling shows a sharp peak at the antiferroelectric phase transition, neither flexoelectricity nor the flexocoupling coefficients are anomalously high, suggesting that it is unlikely that flexoelectricity causes antiferroelectricity.

Revised Crystal Structure of Human Adenovirus Reveals the Limits on Protein IX Quasi-Equivalence and on Analyzing Large Macromolecular Complexes

We report the revised crystal structure of a pseudo-typed human adenovirus at 3.8-Å resolution that is consistent with the atomic models of minor proteins determined by cryo-electron microscopy. The diffraction data from multiple crystals were rescaled and merged to increase the data completeness. The densities for the minor proteins were initially identified in the phase-refined omit maps that were further improved by the phases from docked poly-alanine models to build atomic structures. While the trimeric fiber molecules are disordered due to flexibility and imposition of 5-fold symmetry, the remaining major capsid proteins hexon and penton base are clearly ordered, with the exception of hypervariable region 1 of hexons, the RGD containing loop, and the N-termini of the penton base. The exterior minor protein IX together with the interior minor proteins IIIa and VIII stabilizes the adenovirus virion. A segment of N-terminal pro-peptide of VI is found in the interior cavities of peripentonal hexons, and the rest of VI is disordered. While the triskelion substructures formed by the N-termini of IX conform to excellent quasi 3-fold symmetry, the tetrameric coiled-coils formed by the C-termini and organized in parallel and anti-parallel arrangement do not exhibit any quasi-symmetry. This observation also conveys the pitfalls of using the quasi-equivalence as validation criteria for the structural analysis of extended (non-modular) capsid proteins such as IX. Together, these results remedy certain discrepancies in the previous X-ray model in agreement with the cryo-electron microscopy models.

Molecular Simulation Studies of Cyanine‐Based Chromonic Mesogens: Spontaneous Symmetry Breaking to Form Chiral Aggregates and the Formation of a Novel Lamellar Structure

AbstractAll‐atom molecular dynamics simulations are performed on two chromonic mesogens in aqueous solution: 5,5′‐dimethoxy‐bis‐(3,3′‐di‐sulphopropyl)‐thiacyanine triethylammonium salt (Dye A) and 5,5′‐dichloro‐bis‐(3,3′‐di‐sulphopropyl)‐thiacyanine triethylammonuim salt (Dye B). Simulations demonstrate the formation of self‐assembled chromonic aggregates with an interlayer distance of ≈0.35 nm, with neighboring molecules showing a predominantly head‐to‐tail antiparallel stacking arrangement to minimize electrostatic repulsion between hydrophilic groups. Strong overlap of the aromatic rings occurs within the self‐assembled columns, characteristic of H‐aggregation in aqueous solution. At low concentrations, aggregates of Dye A form chiral columns, despite the presence of strictly achiral species. Chirality arises out of the minimization of steric repulsion between methoxy groups, which would otherwise disrupt the stacking of aromatic molecular cores. At higher concentrations, simulations suggest the interaction of short columns leads to the formation of an achiral‐layered structure in which hydrophobic aromatic regions of the molecule are sandwiched between two layers of hydrophilic groups. This novel lamellar structure is suggested as a likely candidate for the structure of a J‐aggregate. The latter is known to exhibit intense red‐shifted absorption peaks in solution but their structure has not yet been characterized. Self‐organization of such structures provides a route to the formation of “smectic” chromonic mesophases.