Helical Unwinding Research Articles

Thermal Paper and Time Temperature Integrators Made From a Structural Colored Polymer Crosslinked With Hydrogen Bonded Cyclohexanoic Acid Derivatives

AbstractHydrogen‐bonded cyclohexanoic derivatives are applied in a structural colored cholesteric liquid crystal (CLC) helical polymer that demonstrates an extraordinary dual thermal response. Integration of the dynamic hydrogen‐bonded cyclohexanoic acid derivatives in the CLC polymer as supramolecular crosslinks yields an immediate and irreversible loss of the green structural color upon exposure to temperatures above the cholesteric‐to‐isotropic transition temperature (TNI) caused by the helical order loss. Exposure to temperatures below the TNI yields a gradual irreversible red color shift of the reflected wavelength over broad temperature and time ranges. Most likely due to polymerization confinement in combination with the dynamics of the carboxylic acid hydrogen bonds, helical unwinding takes place over time causing the red shift of the reflected wavelength. The temperature response can be programmed by altering the chemical composition of the liquid crystal mixture. Furthermore, the green, structural color of the polymer can also be easily changed making it possible to print different colored indicators combined with different respective temperature responses on a single substrate. The printed optical sensors can be easily delaminated by dissolving the non‐covalent crosslinked polymer. Such optical polymer materials are attractive for easy processable time–temperature integrators and thermal paper.

Hierarchical self-assembling and helical structure in focal conic domains in meniscus of ferroelectric liquid crystal.

We investigate experimentally the formation of focal conic domains of the ferroelectric phase of a liquid crystal, chiral smectic C (SmC^{*}), in the meniscus geometry. The meniscus geometry is formed in the gap between two glass plates which are placed on a common substrate. This gap is called here a physical cavity. Focal conic domains (FCDs) in the physical cavity with dimensions of micrometer scale are investigated under an optical polarizing microscope which enables us to extract the information on the helical structure formation in the constraint and gradient topological meniscus interface. The helical pitch in the FCD is observed to be shorter than in planar confined geometry. A crucial phenomenon of unwrapping and wrapping of helical structure from one FCD to another is also observed. In-plane application of an electric field on a FCD revealed the asymmetric helical unwinding process whereas an increase in temperature has shown symmetrical unwinding. The helical structure based observation is significant for understanding the ferroelectric phase in focal conic domains and their application in microlenses and optical components.

Alignment layer and helix controlled unconventional operational switching in ferroelectric liquid crystal

Substrate interface driven helical unwinding led dynamical switching is observed and analysed for the low voltage operation switching of ferroelectric liquid crystal (FLC). The surface driven FLC molecules force the bulk molecules to switch the sample cell device at very low voltage as compared to conventional cells. It has been shown in the present investigation using three FLC materials that the surface anchoring of the FLC molecules and the thickness of the cell play a primary role for such devices because these conditions contrive the surface interface particle helical unwinding which is very essential for the low power switching. However, P s, helical pitch value, and the dielectric strength parameters of the FLC materials are also taken into account for the analysis of bulk switching assisted by interfacial switching. Dielectric and electro-optics investigation has proven that once the relaxation process associated with the interface is confirmed by dielectric spectra then only, the low power operation is observed in the sample which is interesting for fundamental and potential electro optical devices application.

Electric field dependence of optical dispersion process in short pitch ferroelectric liquid crystal

The short pitch ferroelectric liquid crystal is also called as deformed helix ferroelectric liquid crystal (DHFLC) due to its property of deformation of helical structure by weak field. The DHFLC material has been studied for the analysis of optical diffraction process by varying the incidence and transmission angles. The applied direct current (DC) field has shown the blocking of dispersed light at various oblique angles of incidence due to the unwinding of helical structure. This confirms the fixed helical pitch unwinding model of DHFLC structure. On the other hand, the application of same DC field has also shown the enhancement in the direct transmission confirming the dispersed light at oblique angle which is realigned to the direct light direction. The application of alternating current (AC) field exhibited the tunability of dispersed transmission as a function of frequency of applied field due to the winding and unwinding process of helical structure. The phenomenon of dispersion in transmission mode due to Bragg diffraction phenomenon is significant for non display application of DHFLCs such as phase grating.

Low-frequency dielectric processes in deformed helix ferroelectric liquid crystals

A low-frequency dielectric relaxation mode in deformed helix ferroelectric liquid crystal (DHFLC) has been observed at the interface of strongly rubbed substrates and DHFLC material which may find applications in low power consumption FLC devices. The surface-induced dielectric relaxation process at the interface of DHFLC and substrate is called the partially unwound helical mode (p-UHM) due to the unwinding of the helical structure at this interface. After investigation of the material under various parameters such as temperature, variation of the amplitude of probing ac voltage and dc bias voltage, the relaxation frequency of p-UHM is found to be shifted towards Goldstone mode and merged with it. The relaxation frequency of Goldstone mode is found to decrease, whereas the relaxation frequency of p-UHM process increases with the increase in temperature of DHFLC. Finally, both the modes merge and the resultant relaxation frequency is found to be lower than Goldstone mode in SmC* phase. It seems that phason mode and partial helical unwinding mode are coupled together due to dipole moment that is resulting in a new relaxation frequency. p-UHM process is significant for low-power displays and non-displays applications like a part of sensor where weak electric signal is required to be realized without pre-amplification.

Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples.

Three-dimensional structures have been solved for several naturally occurring RNA triple helices, although all are limited to six or fewer consecutive base triples, hindering accurate estimation of global and local structural parameters. We present an X-ray crystal structure of a right-handed, U•A-U-rich RNA triple helix with 11 continuous base triples. Due to helical unwinding, the RNA triple helix spans an average of 12 base triples per turn. The double helix portion of the RNA triple helix is more similar to both the helical and base step structural parameters of A′-RNA rather than A-RNA. Its most striking features are its wide and deep major groove, a smaller inclination angle and all three strands favoring a C3′-endo sugar pucker. Despite the presence of a third strand, the diameter of an RNA triple helix remains nearly identical to those of DNA and RNA double helices. Contrary to our previous modeling predictions, this structure demonstrates that an RNA triple helix is not limited in length to six consecutive base triples and that longer RNA triple helices may exist in nature. Our structure provides a starting point to establish structural parameters of the so-called ‘ideal’ RNA triple helix, analogous to A-RNA and B-DNA double helices.

Coupled Transmembrane Substrate Docking and Helical Unwinding in Intramembrane Proteolysis of Amyloid Precursor Protein

Intramembrane-cleaving proteases (I-CLiPs) play crucial roles in physiological and pathological processes, such as Alzheimer’s disease and cancer. However, the mechanisms of substrate recognition by I-CLiPs remain poorly understood. The aspartic I-CLiP presenilin is the catalytic subunit of the γ-secretase complex, which releases the amyloid-β peptides (Aβs) through intramembrane proteolysis of the transmembrane domain of the amyloid precursor protein (APPTM). Here we used solution NMR to probe substrate docking of APPTM to the presenilin homologs (PSHs) MCMJR1 and MAMRE50, which cleaved APPTM in the NMR tube. Chemical shift perturbation (CSP) showed juxtamembrane regions of APPTM mediate its docking to MCMJR1. Binding of the substrate to I-CLiP decreased the magnitude of amide proton chemical shifts δH at the C-terminal half of the substrate APPTM, indicating that the docking to the enzyme weakens helical hydrogen bonds and unwinds the substrate transmembrane helix around the initial ε-cleavage site. The APPTM V44M substitution linked to familial AD caused more CSP and helical unwinding around the ε-cleavage site. MAMRE50, which cleaved APPTM at a higher rate, also caused more CSP and helical unwinding in APPTM than MCMJR1. Our data suggest that docking of the substrate transmembrane helix and helical unwinding is coupled in intramembrane proteolysis and FAD mutation modifies enzyme/substrate interaction, providing novel insights into the mechanisms of I-CLiPs and AD drug discovery.

Helical unwinding and side-chain unlocking unravel the outward open conformation of the melibiose transporter.

Molecular dynamics simulations have been used to study the alternate access mechanism of the melibiose transporter from Escherichia coli. Starting from the outward-facing partially occluded form, 2 out of 12 simulations produced an outward full open form and one partially open, whereas the rest yielded fully or partially occluded forms. The shape of the outward-open form resembles other outward-open conformations of secondary transporters. During the transporter opening, conformational changes in some loops are followed by changes in the periplasm region of transmembrane helix 7. Helical curvature relaxation and unlocking of hydrophobic and ionic locks promote the outward opening of the transporter making accessible the substrate binding site. In particular, FRET studies on mutants of conserved aromatic residues of extracellular loop 4 showed lack of substrate binding, emphasizing the importance of this loop for making crucial interactions that control the opening of the periplasmic side. This study indicates that the alternate access mechanism for the melibiose transporter fits better into a flexible gating mechanism rather than the archetypical helical rigid-body rocker-switch mechanism.

Unravelling the structural plasticity of stretched DNA under torsional constraint.

Regions of the genome are often held under torsional constraint. Nevertheless, the influence of such constraint on DNA–protein interactions during genome metabolism is still poorly understood. Here using a combined optical tweezers and fluorescence microscope, we quantify and explain how torsional constraint influences the structural stability of DNA under applied tension. We provide direct evidence that concomitant basepair melting and helical unwinding can occur in torsionally constrained DNA at forces >∼50 pN. This striking result indicates that local changes in linking number can be absorbed by the rest of the DNA duplex. We also present compelling new evidence that an overwound DNA structure (likely P-DNA) is created (alongside underwound structures) at forces >∼110 pN. These findings substantiate previous theoretical predictions and highlight a remarkable structural plasticity of torsionally constrained DNA. Such plasticity may be required in vivo to absorb local changes in linking number in DNA held under torsional constraint.

Role of Bilayer Characteristics on the Structural Fate of Aβ(1–40) and Aβ(25–40)

The β-amyloid (Aβ) peptide is derived from the transmembrane (TM) helix of the amyloid precursor protein (APP) and has been shown to interact with membrane surfaces. To understand better the role of peptide-membrane interactions in cell death and ultimately in Alzheimer's disease, a better understanding of how membrane characteristics affect the binding, solvation, and secondary structure of Aβ is needed. Employing a combination of circular dichroism and deep-UV resonance Raman spectroscopies, Aβ(25-40) was found to fold spontaneously upon association with anionic lipid bilayers. The hydrophobic portion of the disease-related Aβ(1-40) peptide, Aβ(25-40), has often been used as a model for how its legacy TM region may behave structurally in aqueous solvents and during membrane encounters. The structure of the membrane-associated Aβ(25-40) peptide was found to depend on both the hydrophobic thickness of the bilayer and the duration of incubation. Similarly, the disease-related Aβ(1-40) peptide also spontaneously associates with anionic liposomes, where it initially adopts mixtures of disordered and helical structures. The partially disordered helical structures then convert to β-sheet structures over longer time frames. β-Sheet structure is formed prior to helical unwinding, implying a model in which β-sheet structure, formed initially from disordered regions, prompts the unwinding and destabilization of membrane-stabilized helical structure. A model is proposed to describe the mechanism of escape of Aβ(1-40) from the membrane surfaces following its formation by cleavage of APP within the membrane.

Open-Channel Structures of the Human Glycine Receptor α1 Full-Length Transmembrane Domain

Glycine receptors play a major role in mediating fastinhibitory neurotransmission in the spinal cord and brain stem, yet their high-resolution structures remain unsolved. We determined open-channel structures of the full-length transmembrane domain (TMD) of the human glycine receptor α1-subunit (hGlyR-α1) using nuclear magnetic resonance (NMR) spectroscopy and electron micrographs. hGlyR-α1 TMD spontaneously forms pentameric Cl(-)-conducting channels, with structures sharing overall topology observed in crystal structures of homologous bacterial and nematode pentameric ligand-gated ion channels (pLGICs). However, the mammalian hGlyR-α1 structures present several distinctive features, including a shorter, pore-lining TM2 helix with helical unwinding near the C-terminal end, a TM3 helical kink at A288 that partially overlaps with the homologous ivermectin-binding site in GluCl, and a highly dynamic segment between S267(15') of TM2 and A288 that likely affects allosteric modulations of channel function. Our structures provide additional templates for identifying potential drug targets in GlyRs and other mammalian pLGICs.

Thermodynamic and bias field characterization of a quickly operating antiferroelectric liquid crystal

Dielectric relaxation spectroscopy of a quickly operating antiferroelectric liquid crystal (W-204D) has been carried out under the influence of bias electric field in the frequency range of 20Hz–20MHz in planar aligned cells. W-204D represents both antiferroelectric (SmCA*) and ferroelectric (SmC*) phases. The temperature dependent dielectric investigation has been studied to explore its effect on the dielectric parameters, where a couple of relaxation modes were observed in SmC* phase. Dielectric characterization reveals a Goldstone mode around 32.595kHz and a Soft mode at ~100kHz in the SmC* phase. To study the collective relaxation processes between these two modes W-204D was examined under the influence of DC bias electric field. Due to helical unwinding at 30V bias Goldstone mode get totally suppressed. Experimental data was modeled by Debye and Cole–Cole method indicated that the relaxations are of non-Debye type. Dielectric variations, distribution parameters and relaxation frequencies of these modes have been calculated at various temperatures.

Reversible helical unwinding transition of a self-assembling peptide amphiphile

A designed peptide amphiphile C16-KKFFVLK self-assembles into nanotubes and helical ribbons in aqueous solution at room temperature. A remarkable unwinding transition, leading to twisted tapes, is observed on heating. Nanotubes and ribbons re-form on cooling.

Liquid Crystals Under Two Extremes: (1) High-Power Laser Irradiation, and (2) Single-Photon Level

This paper describes some of my results on liquid crystal investigations under unconventional, incident light powers: (1) under high-power laser irradiation both in free space and inside laser resonators, and (2) in single-photon source applications for quantum information technology. Several effects under high-power, nanosecond laser irradiation are outlined: athermal helical pitch dilation and unwinding of cholesteric mirrors, showing the limits for using them in laser physics; some pitfalls in measurements of thermal-density refractive nonlinearity and the first observation of thermal lens effects in liquid crystals under several nanosecond, low-pulse-repetition rate (2–10 Hz) laser irradiation in the presence of two-photon absorption; feedback-free kaleidoscope of patterns (hexagons, stripes, etc.) in dye-doped liquid crystals. At the single-photon level, definite linear and circular polarizations of single (antibunched) photons for quantum communications were obtained using single-emitter fluorescence in planar-aligned nematic and cholesteric hosts. Circular polarized cholesteric microcavity resonances were also observed under cw-excitation. In addition, using near-field optical microscopy and AFM, 2D-hexagonal arrays made of cholesteric oligomers were investigated. With progress of this technology, similar arrays can be used for fluorescence control of single emitters.

Multitrack Digital Data Storage: A Reduced Complexity Architecture

We describe a low-complexity noniterative detector for magnetic and optical multitrack high-density data storage. The detector is based on the M-algorithm architecture. It performs limited breadth-first detection on the equivalent one-dimensional (1-D) channel obtained by column-by-column helical unwinding of the two-dimensional (2-D) channel. The detection performance is optimized by the use of a specific 2-D minimum-phase factorization of the channel impulse response by the equalizer. An optimized path selection scheme maintains the complexity close to practical 1-D Viterbi. This scheme is based on an approximate path metric parallel sort network, taking advantage of the metrics' residual ordering from previous M-algorithm iterations. Such an architecture approaches maximum-likelihood performance on a high areal density uncoded channel for a practical number of retained paths M and bit error rate (BER) below 10-4. The performance of the system is evaluated when the channel is encoded with multi-parity check (MPC) block inner code and an outer interleaved Reed-Solomon code. The inner code enhances the minimum error distance of the equalized channel and reduces the correct path losses of the M-algorithm path buffer. The decoding is performed noniteratively. Here, we compare the performance of the system to the soft iterative joint decoding of the read channels for data pages encoded with low-density parity check (LDPC) codes with comparable rates and block length. We provide an approximation of the 2-D channel capacity to further assess the performance of the system

Unexpected twist: harnessing the energy in positive supercoils to control telomere resolution

Negative DNA supercoiling is an important conformational property of bacterial DNA that plays a significant role in a wide variety of DNA transactions. In contrast, positive DNA supercoiling is a by-product of cellular processes that involve helical unwinding or movement of DNA by a fixed translocase, and has generally been considered a necessary evil requiring removal. We now report the first evidence suggesting a physiological role for positive supercoiling; this occurs in telomere resolution in the related Lyme disease and relapsing fever Borrelia spirochetes. Telomere resolution is the process whereby covalently closed hairpin telomeres are generated from replicative intermediates by the telomere resolvase, ResT. We observe a 20-fold and greater stimulation of the reaction by positive supercoiling, which facilitates formation of a previously unobserved reaction intermediate. Our data suggest the possibility that the free energy of positive supercoiling, a resource with no previously described cellular function, may be harnessed and utilized as a regulator of post-replication events.

Pivotal Molecular Determinants of Peptidic and Collagen Triple Helicase Activities Reside in the S3′ Subsite of Matrix Metalloproteinase 8 (MMP-8): THE ROLE OF HYDROGEN BONDING POTENTIAL OF ASN188 AND TYR189 AND THE CONNECTING CIS BOND

The mechanism of triple helical collagen unwinding and cleavage by collagenases in the matrix metalloproteinase (MMP) family is complex and remains enigmatic. Recent reports show that triple helicase activity is initiated by the hemopexin C domain of membrane type 1-MMP, whereas catalytically inactive full-length interstitial collagenase (MMP-1) exhibits full triple helicase functionality pointing to active site determinants that are needed to complete the triple helicase mechanism. In MMP-8, the neutrophil collagenase, a conserved Gly at the S(3)' substrate specificity subsite is replaced by Asn(188) that forms a highly unusual cis bond with Tyr(189), a conserved active site residue in the collagenases. Only in MMP-1 is the S(3)' Gly also replaced, and there too a cis configured Glu-Tyr occurs. Thus, this high energy peptide bond coupled to the canonical Tyr may be important in the collagenolytic process. In a systematic mutagenesis investigation of the MMP-8 S(3)' subsite we found that introducing an S(3)' Gly(188) into MMP-8 reduced collagenolytic efficiency by approximately 30% with a corresponding reduction in cleavage of a synthetic peptide fluorescence resonance energy transfer substrate analogue of the alpha2(I) collagen chain cleavage site. The substitution of Asn(188) to Leu, a hydrophobic residue of similar size to the highly polar Asn and designed to retain the cis bond, revealed the importance of hydrogen bonding to bound substrate with both collagenolytic and peptidic activities reduced approximately 3-fold. In contrast, the specificity for type I collagen of the mutant Y189F dropped 3-fold without any significant alteration in general peptidase activity. Therefore, S(3)' and in particular the hydrogen bonding potential of Tyr(189) is a specific molecular determinant for MMP-8 triple helicase activity. The cis bond connection to Asn(188) juxtaposes these two side chains for closely spaced hydrogen bonding with substrate that improves collagenolytic and general catalytic efficiency that could be exploited for new collagenase-specific inhibitor drugs.

Variation of Absorbance and Helical Unwinding with Electric Field in an Antiferroelectric Liquid Crystal Using Polarized FT-IR Measurements

For a homogeneously aligned cell of an antiferroelectric liquid crystal, infrared spectra have been recorded for SmC*, SmCγ* and SmCA* phases. To investigate the characteristics of absorbance peak and helical structure for each smectic phase, the rotation of the absorbance profiles for phenyl, core carbonyl and chiral carbonyl groups are studied as a function of polarizer angle at various stages of electrically induced transformation of the sample structure. It is found that, the absorbance profile for both the phenyl and the carbonyl groups for the three smectic phases have the same rotational motion for the same polarity of the applied field to the cell. The maximum rotational angle for the absorbance profile of phenyl group for each phase is obtained when the helix structure is completely transformed to an unwound SmC* phase. It is observed that, the helix is already disturbed before the application of electric field to the cell for each molecular group. The results of the measurements are studied in detail and the variation of maximal absorbance in relation to helix unwinding behavior for a surface stabilized cell for each smectic phase is discussed.

Molecular orientation and the infrared dichroism of a chiral smectic liquid crystal in a homogeneously aligned cell at different temperature and bias fields.

The molecular orientation and the dichroic behavior of the vibrational bands of a homogeneously aligned helical cell containing chiral smectic liquid crystal (R)-(-)-1-methylheptyl 4-(4(')-dodecyloxybiphenyl-4-ylcarbonyloxy)-3-fluorobenzoate are studied at various temperatures as a function of the bias field. These temperatures correspond to the various phase states of the sample at zero field. For those bands that exhibit significant dichroism, the field dependencies of the dichroic parameters (the dichroic ratio and the polarization angle of maximum absorbance) are found to be dependent on temperature, phase state, and helical unwinding. For the SmA* and SmC(*)(alpha) phases, the phenyl band dichroic ratio and the corresponding orientational order parameter are found to be almost independent of the bias field. The temperature dependence of the orientational order for zero field is discussed by taking into account the structures of the phases and the molecular tilt angles. The field dependencies of the phenyl band dichroic parameters for the SmC(*)(A) and SmC(*)(gamma) phases yield results about the distribution of directors in the layers of their unit cells and the state of helical unwinding. The azimuthal orientational distribution function of the carbonyl transition moments with respect to the long molecular axis has been determined. It is found that the degrees of the polar and quadrupolar biasing increase with decrease in temperature and the azimuthal biasing angle for the chiral carbonyl group increases significantly with a reduction in temperature.

Resonant x-ray scattering study of the antiferroelectric and ferrielectric phases in liquid crystal devices.

Resonant x-ray scattering has been used to investigate the interlayer ordering of the antiferroelectric and ferrielectric smectic C* subphases in a device geometry. The liquid crystalline materials studied contain a selenium atom and the experiments were carried out at the selenium K edge allowing x-ray transmission through glass. The resonant scattering peaks associated with the antiferroelectric phase were observed in two devices containing different materials. It was observed that the electric-field-induced antiferroelectric to ferroelectric transition coincides with the chevron to bookshelf transition in one of the devices. Observation of the splitting of the antiferroelectric resonant peaks as a function of applied field also confirmed that no helical unwinding occurs at fields lower than the chevron to bookshelf threshold. Resonant features associated with the four-layer ferrielectric liquid crystal phase were observed in a device geometry. Monitoring the electric field dependence of these ferrielectric resonant peaks showed that the chevron to bookshelf transition occurs at a lower applied field than the ferrielectric to ferroelectric switching transition.