Helical Properties Research Articles

N terminal N-methylation modulates chiral centre induced helical (CIH) peptides' biophysical properties.

The effects of N-methylation on CIH peptides' biophysical properties were systematically studied. N-Methylation at the N terminal NH could help improve the peptides' cellular uptake with a retained helical conformation. This N-methylation strategy could also be applied to longer peptides to improve their stability and cellular uptake.

Verification study for an empirical rule in diverse helical conformational behaviors of asymmetric 1,2-diacyl-sn-glycerols in the solution state

Cell-membrane glycerophospholipids and glycolipids have a common asymmetric skeleton of 1,2-diacyl-sn-glycerols. The 1,2-diacyl moiety in solutions permits a rapid equilibrium among three helical conformers, namely gt(+), gg(−), and tg, to display diverse conformational properties. The conformational property changes variably not only by head groups at the sn-3 position, but also by the solvent conditions applied. Recently, we came across an empirical rule in the conformational diversity in the solution state when we assumed the term of ‘helical disparity’ for the equilibrium between gt(+) and gg(−) conformers with reversed helical signs for each other. The sign and magnitude of the helical disparity (%) governs the (+)- or (−)-chirality around the lipid tail and corresponds to the magnitude of the exciton couplet CD (circular dichroism) bands. The empirical rule expresses that the disparity (%) changes linearly by the function of gt(+) population (%). Herein, the rule was verified by 1H NMR spectroscopy using different types of 1,2-diacyl-sn-glycerols as model compounds. The present paper describes that the rule is formulated with a general equation (Eq-1): ‘helical disparity (%)’ = [gt(+)−gg(−)] (%) = A[gt(+)−B], in which A and B are constants taking values around 1.3 and 38, respectively. This rule is maintained regardless of the 1,2-diacyl and sn-3 substituent groups as far as examined here, while affording several exceptions. With Eq-1 (A = 1.3, B = 38), a conformational diagram can be obtained. This allows us to overview the diverse helical conformational properties of the asymmetric 1,2-diacyl-sn-glycerols in the solutions state.

Remarkable functions of sn-3 hydroxy and phosphocholine groups in 1,2-diacyl-sn-glycerolipids to induce clockwise (+)-helicity around the 1,2-diacyl moiety: Evidence from conformation analysis by 1H NMR spectroscopy.

Cell-membrane glycerolipids exhibit a common structural backbone of asymmetric 1,2-diacyl-sn-glycerol bearing polar head groups in the sn-3 position. In this study, the possible effects of sn-3 head groups on the helical conformational property around the 1,2-diacyl moiety in the solution state were examined. 1H NMR Karplus relation studies were carried out using a series of 1,2-dipalmitoyl-sn-glycerols bearing different sn-3 substituents (namely palmitoyl, benzyl, hydrogen, and phosphates). The 1H NMR analysis indicated that the helical property around the 1,2-diacyl moiety is considerably affected by these sn-3 substituents. The sn-3 hydroxy group induced a unique helical property, which was considerably dependent on the solvents used. In CDCl3 solution, three staggered conformers, namely gt(+), gg(−) and tg, were randomized, while in more polar solvents, the gt(+) conformer with (+)-helicity was amplified at the expense of gg(−) and tg conformers. The sn-3 phosphocholine in phosphatidylcholine exhibited a greater effect on the gt(+) conformer, which was independent of the solvents used. From the 1H NMR analysis, the helical conformational properties around the 1,2-diacyl moiety conformed to a simple empirical rule, which permitted the proposal of a conformational diagram for 1,2-dipalmitoyl-sn-glycerols in the solution states.

Characterization of Biomolecular Helices and Their Complementarity Using Geometric Analysis.

A general method is presented to characterize the helical properties of potentially irregular helices, such as those found in protein secondary and tertiary structures and nucleic acids. The method was validated using artificial helices with varying numbers of points, points per helical turn, pitch, and radius. The sensitivity of the method was validated by applying increasing amounts of random perturbation to the coordinates of these helices; 399 360 helices in total were evaluated. In addition, the helical parameters of protein secondary structure elements and nucleic acid helices were analyzed. Generally, at least seven points were required to recapitulate the parameters of a helix using our method. The method can also be used to calculate the helical parameters of nucleic acid-binding proteins, like TALE, enabling direct analysis of their helix complementarity to sequence-dependent DNA distortions.

Synthesis of Helical Phenolic Resin Bundles through a Sol-Gel Transcription Method.

Chiral and helical polymers possess special helical structures and optical property, and may find applications in chiral catalysis and optical devices. This work presents the preparation and formation process of helical phenolic resins through a sol-gel transcription method. A pair of bola-type chiral low-molecular-weight gelators (LMWGs) derived from valine are used as templates, while 2,4-dihydroxybenzoic acid and formaldehyde are used as precursors. The electron microscopy images show that the phenolic resins are single-handed helical bundles comprised of helical ultrafine nanofibers. The diffused reflection circular dichroism spectra indicate that the helical phenolic resins exhibit optical activity. A possible formation mechanism is proposed, which shows the co-assembly of the LMWGs and the precursors.

Helicity statistics in homogeneous and isotropic turbulence and turbulence models

We study the statistical properties of helicity in direct numerical simulations of fully developed homogeneous and isotropic turbulence and in a class of turbulence shell models. We consider correlation functions based on combinations of vorticity and velocity increments that are not invariant under mirror symmetry. We also study the scaling properties of high-order structure functions based on the moments of the velocity increments projected on a subset of modes with either positive or negative helicity (chirality). We show that mirror symmetry is recovered at small-scales, i.e., chiral terms are subleading and they are well captured by a dimensional argument plus anomalous corrections. These findings are also supported by a high Reynolds numbers study of helical shell models with the same chiral symmetry of Navier-Stokes equations.

Effect of load and speed on warship power rear drive system helical gear anti-scuffing properties in thermal elasto-hydrodynamic lubrication

The key parameters which caused the scoring failure of helical gears are operating load and speed. In this study, the simulations using geometric meshing theory were carried out to investigate the effect of load and speed of warship transmission helical gear system on thermal elasto-hydrodynamic lubrication. The numerical algorithm for the analysis of three-dimensional thermal elasto-hydrodynamic lubrication used in this work has advantage that the film pressure and distributions can be calculated from Reynolds equation for all mixed lubrication regions without any specific boundary condition for the edge of solid contact region. Oil film pressure, film thickness as well as film temperature under different load and speed conditions were obtained and compared. In addition, experimental tests were conducted to determine gear surface temperature under different load and speed conditions. This work provided a guidance to understand the load- and speed-dependent thermal elasto-hydrodynamic lubrication.

Higher helicity invariants and solar dynamo

Modern models of nonlinear dynamo saturation in celestial bodies (specifically, on the Sun) are largely based on the consideration of the balance of magnetic helicity. This physical variable has also a topological meaning: it is associated with the linking coefficient of magnetic tubes. In addition to magnetic helicity, magnetohydrodynamics has a number of topological integrals of motion (the so-called higher helicity moments). We have compared these invariants with magnetic helicity properties and concluded that they can hardly serve as nonlinear constraints on dynamo action.

Helicity within the vortex filament model.

Kinetic helicity is one of the invariants of the Euler equations that is associated with the topology of vortex lines within the fluid. In superfluids, the vorticity is concentrated along vortex filaments. In this setting, helicity would be expected to acquire its simplest form. However, the lack of a core structure for vortex filaments appears to result in a helicity that does not retain its key attribute as a quadratic invariant. By defining a spanwise vector to the vortex through the use of a Seifert framing, we are able to introduce twist and henceforth recover the key properties of helicity. We present several examples for calculating internal twist to illustrate why the centreline helicity alone will lead to ambiguous results if a twist contribution is not introduced. Our choice of the spanwise vector can be expressed in terms of the tangential component of velocity along the filament. Since the tangential velocity does not alter the configuration of the vortex at later times, we are able to recover a similar equation for the internal twist angle to that of classical vortex tubes. Our results allow us to explain how a quasi-classical limit of helicity emerges from helicity considerations for individual superfluid vortex filaments.

Optimal secretion of alkali-tolerant xylanase in Bacillus subtilis by signal peptide screening.

Xylanases are industrially important enzymes for xylan digestion. We experimentally screened over 114 Sec and 24 Tat pathway signal peptides, with two different promoters, for optimal production of an alkaline active xylanase (XynBYG) from Bacillus pumilus BYG in a Bacillus subtilis host. Though both promoters yielded highly consistent secretion levels (0.97 Pearson correlation coefficient), the Sec pathway was found to be more efficient than the Tat pathway for XynBYG secretion. Furthermore, the optimal signal peptide (phoB) for XynBYG secretion was found to be different from the optimal peptides for cutinase and esterase reported in previous studies. A partial least squares regression analysis further identified several statistically important variables: helical properties, amino acid composition bias, and the discrimination score in Signal P. These variables explain the observed 23% variance in the secretion yield of XynBYG by the different signal peptides. The results also suggest that the helical propensity of a signal peptide plays a significant role in the beta-rich xylanase, but not in the helix-rich cutinase, suggesting a coupling of the conformations between the signal peptide and its cargo protein for optimal secretion.

Current-induced three-dimensional domain wall propagation in cylindrical NiFe nanowires

We report on the magnetization configurations in single NiFe cylindrical nanowires grown by template-assisted electrodeposition. Angular anisotropic magnetoresistance measurements reveal that a three-dimensional helical domain wall is formed naturally upon relaxation from a saturated state. Micromagnetic simulations support the helical domain wall properties and its reversal process, which involves a splitting of the clockwise and anticlockwise vortices. When a pulsed current is applied to the nanowire, the helical domain wall propagation is observed with a minimum current density needed to overcome its intrinsic pinning.

Spatial evolution of the helical behavior and the 2/3 power-law in single-square-grid-generated turbulence

Direct numerical simulations are performed to investigate the helical properties of single-square-grid-generated turbulence. The streamwise evolution of the probability density functions of the relative helicity density h reveals the existence of a transition from a quasi-two-dimensional state to a three-dimensional state. The correlations between the helicity and the enstrophy level as well as the dissipation level are examined. When conditioned on a high level of dissipation or enstrophy, in the energy decay region the velocity and vorticity vectors in both instantaneous and fluctuating fields become more aligned. However, this correlation does not hold in the production region. We also study the second-order structure function and reveal that a well-defined power-law can be found at a location quite close to the grid, where the turbulent flow is still in the transition state.

Understanding and tuning the properties of redox-accumulating manganese helicates.

The pentanuclear Mn complex [Mn5(μ3-O)(bpp)6]n+ can access six consecutive total oxidation levels from Mn(ii)5 to Mn(iii)5. The electronic structure and redox behavior of this cluster are studied computationally and the results are compared with experimental data. The tunability of the redox potential span and of the absolute potential position is explored through systematic modifications of the 3,5-bis(pyridin-2-yl)-pyrazole (Hbpp) ligand. By substitutions with electron-donating and electron-withdrawing groups, the position of the redox events can be shifted by ca. 1 eV, however no ligand modification is predicted to alter the total redox span. By changing the pyridyl groups to benzimidazole groups, yielding the 3,5-bis(benzimidazol-2-yl)pyrazole (H3bbp) ligand, it is predicted that higher oxidation states can be stabilized, from Mn(iii)4Mn(iv) up to Mn(iv)5. In this system, the redox span for the same number of redox equivalents accumulated is slightly smaller than that in the original system. The manganese system is compared with its pentanuclear iron analogue that was recently reported to be catalytically active in oxygen evolution (Okamura et al., Nature, 2016, 530, 465). The electronic and structural requirements for utilization of the stored oxidizing equivalents in water oxidation are discussed.

Tunable Helicity, Stability and DNA-Binding Properties of Short Peptides with Hybrid Metal Coordination Motifs.

Given the prevalent role of α-helical motifs on protein surfaces in mediating protein-protein and protein-DNA interactions, there have been significant efforts to develop strategies to induce α-helicity in short, unstructured peptides to interrogate such interactions. Toward this goal, we have recently introduced hybrid metal coordination motifs (HCMs). HCMs combine a natural metal-binding amino acid side chain with a synthetic chelating group that are appropriately positioned in a peptide sequence to stabilize an α-helical conformation upon metal coordination. Here, we present a series of short peptides modified with HCMs consisting of a His and a phenanthroline group at i and i+7 positions that can induce α-helicity in a metal-tunable fashion as well as direct the formation of discrete dimeric architectures for recognition of biological targets. We show that the induction of α-helicity can be further modulated by secondary sphere interactions between amino acids at the i+4 position and the HCM. A frequently cited drawback of the use of peptides as therapeutics is their propensity to be quickly digested by proteases; here, we observe an enhancement of up to ∼100-fold in the half-lifes of the metal-bound HCM-peptides in the presence of trypsin. Finally, we show that an HCM-bearing peptide sequence, which contains the DNA-recognition domain of a bZIP protein but is devoid of the obligate dimerization domain, can dimerize with the proper geometry and in an α-helical conformation to bind a cognate DNA sequence with high affinities (Kd≥ 65 nM), again in a metal-tunable manner.

Comparative analyses of helical properties in asymmetric 1,2-diacyl-sn-glycerols by means of circular dichroism and proton NMR spectroscopies: notable effects of substituting groups at sn-3 position

The titled 1,2-diacyl-sn-glycerol constitutes a common asymmetric backbone of cell-membrane phospholipids and glycolipids. The acyclic sn-glycerol skeleton allows flexible conformational changes by free rotation along each of the glycerol sn-1,2 and sn-2,3 C–C single bonds in solution. It is generally believed, however, that the sn-1,2 tail position adopts two gauche conformers [gt-(+) and gg-(−)] near exclusively to display an ordered conformation. In the present study, our interest was focused on the fact that the two gauche conformers possess helical signs which are the reverse of each other. We examined (+)- and (−)-chirality arising from the disparity between the two helical conformers using a series of 1,2-dibenzoyl-sn-glycerols 2–8 as model compounds, which possess 1,2-dibenzoate chromophore for circular dichroism analysis, while having variable substituent groups at the sn-3 position. First, the analysis was conducted with the circular dichroism ‘dibenzoate exciton coupling methodology’ of Nakanishi and Harada followed by 1H NMR analysis to calculate the time-averaged populations (%) of the three staggered conformers, that is, gt-(+), gg-(−) and tg. The results are discussed in terms of the ‘helicity index’ which covers information on the sign and intensity of circular dichroism bands in circular dichroism analysis as well as on the helical disparity (%) and the total volume (%) of the two helical conformers in 1H NMR analysis. The two independent spectroscopic approaches were well matched in the estimation of the helical index, which in turn allowed us to conclude that the sn-3 substituting groups have diverse effects on the helical properties of 1,2-diacyl-sn-glycerols in solution.

Microwave magnetoelectric fields: helicities and reactive power flows

The dual symmetry between the electric and magnetic fields underlies Maxwell’s electrodynamics. Due to this symmetry, one can describe topological properties of an electromagnetic field in free space and obtain the conservation law of optical (electromagnetic) helicity. What kind of the field helicity one can expect to see when the electromagnetic-field symmetry is broken? The near fields originated from small ferrite particles with magnetic-dipolar-mode oscillations are the fields with the electric and magnetic components, but with broken dual (electric–magnetic) symmetry. These fields—called magnetoelectric (ME) fields—have topological properties different from such properties of electromagnetic fields. The helicity states of ME fields are topologically protected quantum-like states. In this paper, we study the helicity properties of ME fields. We analyze conservation laws of the ME-field helicity and show that the helicity density is related to an imaginary part of the complex power-flow density. We show also that the helicity of ME fields can be a complex value. The shown topological properties of the ME fields can be useful for novel near- and far-field microwave applications. The obtained results can find application for development of novel microwave metamaterials. Strongly localized ME fields, having both the real and imaginary helicity parameters, open unique perspective for sensitive microwave probing of structural characteristics of chemical and biological objects.

Robust helical edge transport in gated InAs/GaSb bilayers.

We have engineered electron-hole bilayers of inverted InAs/GaSb quantum wells, using dilute silicon impurity doping to suppress residual bulk conductance. We have observed robust helical edge states with wide conductance plateaus precisely quantized to 2e^{2}/h in mesoscopic Hall samples. On the other hand, in larger samples the edge conductance is found to be inversely proportional to the edge length. These characteristics persist in a wide temperature range and show essentially no temperature dependence. The quantized plateaus persist to a 12T applied in-plane field; the conductance increases from 2e^{2}/h in strong perpendicular fields manifesting chiral edge transport. Our study presents a compelling case for exotic properties of a one-dimensional helical liquid on the edge of InAs/GaSb bilayers.

Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions.

Ebola, considered till recently as a rare and endemic disease, has dramatically transformed into a potentially global humanitarian crisis. The genome of Ebola, a member of the Filoviridae family, encodes seven proteins. Based on the recently implemented software (PAGAL) for analyzing the hydrophobicity and amphipathicity properties of alpha helices (AH) in proteins, we characterize the helices in the Ebola proteome. We demonstrate that AHs with characteristically unique features are involved in critical interactions with the host proteins. For example, the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain has an AH with a large hydrophobic moment. The neutralizing antibody (KZ52) derived from a human survivor of the 1995 Kikwit outbreak recognizes a protein epitope on this AH, emphasizing the critical nature of this secondary structure in the virulence of the Ebola virus. Our method ensures a comprehensive list of such `hotspots'. These helices probably are or can be the target of molecules designed to inhibit AH mediated protein-protein interactions. Further, by comparing the AHs in proteins of the related Marburg viruses, we are able to elicit subtle changes in the proteins that might render them ineffective to previously successful drugs. Such differences are difficult to identify by a simple sequence or structural alignment. Thus, analyzing AHs in the small Ebola proteome can aid rational design aimed at countering the `largest Ebola epidemic, affecting multiple countries in West Africa' ( http://www.cdc.gov/vhf/ebola/outbreaks/2014-west-africa/index.html).

A statistical analysis of current helicity and twist in solar active regions over the phases of the solar cycle using the spectro-polarimeter data of Hinode

Abstract Current helicity and twist of solar magnetic fields are important in characterizing the dynamo mechanism working in the convection zone of the Sun. We have carried out a statistical study on the current helicity of solar active regions observed with the spectro-polarimeter (SP) of the Hinode Solar Optical Telescope (SOT). We used SOT-SP data of 558 vector magnetograms of a total of 80 active regions obtained during the period from 2006 to 2012. We have applied spatial smoothing and division of data points into weak and strong field ranges to compare the contributions from different scales and field strengths. We found that the current helicity follows the “hemispheric sign rule” when weak magnetic fields (absolute field strength < 300 gauss) are considered and no smoothing is applied. On the other hand, the pattern of current helicity fluctuates and violates the hemispheric sign rule when stronger magnetic fields are considered and smoothing of 2${^{\prime\prime}_{.}}$0 (modeled on ground-based observations) is applied. Furthermore, we found a tendency that weak and inclined fields conform to the hemispheric sign rule and strong and vertical fields violate it. These different properties of helicity through the strong and weak magnetic field components give important clues in understanding the solar dynamo as well as the mechanism of formation and evolution of solar active regions.

Magnetic antenna excitation of whistler modes. II. Antenna arrays

The excitation of whistler modes from magnetic loop antennas has been investigated experimentally. The field topology of the excited wave driven by a single loop antenna has been measured for different loop orientations with respect to the uniform background field. The fields from two or more antennas at different locations are then created by superposition of the single-loop data. It is shown that an antenna array can produce nearly plane waves which cannot be achieved with single antennas. By applying a phase shift along the array, oblique wave propagation is obtained. This allows a meaningful comparison with plane wave theory. The Gendrin mode and oblique cyclotron resonance are demonstrated. Wave helicity and polarization in space and time are demonstrated and distinguished from the magnetic helicity of the wave field. The superposition of two oblique plane whistler modes produces in a “whistler waveguide” mode whose polarization and helicity properties are explained. The results show that single point measurements cannot properly establish the wave character of wave packets. The laboratory observations are relevant for excitation and detection of whistler modes in space plasmas.