Helical Angle Research Articles

Correlation between 13Cα chemical shifts and helix content of peptide ensembles

Replica exchange molecular dynamics simulations are used to generate three ensembles of an S-peptide analog (AETAAAKFLREHMDS). Percent helicity of the peptide ensembles calculated using STRIDE is compared to percent helicity calculated from (13)C(alpha) chemical shift deviations (CSD) from random coil in order to test the assumption that CSD can be correlated to percent helicity. The two estimates of helicity, one based on structure and the other on CSD, are in close to quantitative agreement, except at the edges of helical stretches where disagreements of as much as 50% can be found. These disagreements can occur by CSDs both as an under- and an overestimate of peptide helicity. We show that underestimation arises due to ensemble averaging of positive CSDs from conformers with torsion angles in the helical region of Ramachandran space with negative CSDs corresponding to conformers of the peptide in the extended region. In contrast, overestimation comes about due to the fact that a large number of conformations with torsion angles in the helical region are not counted as helical by STRIDE due to a lack of correlated helical torsion angles in neighboring residues.

FTIR Spectroscopy of Secondary-Structure Reorientation of Melibiose Permease Modulated by Substrate Binding

Analysis of infrared polarized absorbance spectra and linear dichroism spectra of reconstituted melibiose permease from Escherichia coli shows that the oriented structures correspond mainly to tilted transmembrane α-helices, forming an average angle of ∼26° with the membrane normal in substrate-free medium. Examination of the deconvoluted linear dichroism spectra in H 2O and D 2O makes apparent two populations of α-helices differing by their tilt angle (helix types I and II). Moreover, the average helical tilt angle significantly varies upon substrate binding: it is increased upon Na + binding, whereas it decreases upon subsequent melibiose binding in the presence of Na +. In contrast, melibiose binding in the presence of H + causes virtually no change in the average tilt angle. The data also suggest that the two helix populations change their tilting and H/D exchange level in different ways depending on the bound substrate(s). Notably, cation binding essentially influences type I helices, whereas melibiose binding modifies the tilting of both helix populations.

The effect of anisotropic systematic errors in estimating helical angles

A common question in movement studies is how the results should be interpreted with respect to systematic and random errors. In this study, simulations are made in order to see how a rigid body's orientation in space (i.e. helical angle between two orientations) is affected by (1) a systematic error added to a single marker (2) a combination of this systematic error and Gaussian white noise. The orientation was estimated after adding a systematic error to one marker within the rigid body. This procedure was repeated with Gaussian noise added to each marker. In conclusion, results show that the systematic error's effect on estimated orientation depends on number of markers in the rigid body and also on which direction the systematic error is added. The systematic error has no effect if the error is added along the radial axis (i.e. the line connecting centre of mass and the affected marker).

Simultaneous extraction of multiple orientational constraints of membrane proteins by 13C-detected N–H dipolar couplings under magic angle spinning

A 13C-detected N–H dipolar coupling technique is introduced for uniaxially mobile membrane proteins for orientation determination using unoriented samples. For proteins undergoing rigid-body uniaxial rotation in the lipid bilayer, the intrinsic equality between the dipolar coupling constants measured in unoriented samples and the anisotropic coupling measured in static oriented samples has been shown recently. Here, we demonstrate that the orientation-sensitive backbone N–H dipolar couplings can be measured with 13C detection using 2D and 3D MAS correlation experiments, so that maximal site resolution can be achieved and multiple orientational constraints can be extracted from each experiment. We demonstrate this technique on the M2 transmembrane peptide of the influenza A virus, where the N–H dipolar couplings of various residues fit to a dipolar wave for a helical tilt angle of 37°, in excellent agreement with data obtained from singly 15N-labeled samples.

積層造形内耳モデルを用いた半規管の計測

Three dimensional analysis of the plane that includes each semicircular canal is essential for understanding the vestibule-ocular reflex evoked in each plane. The fact that the semicircular canals do not lie in single planes has been reported. We measured the helical angle of the plane where each semicircular canal existed using a simulated 3D model of the inner ear and a software-based three-dimensional computed tomographic (3D-CT) imaging program. The diameter of each semicircular canal was also measured. The helical angle was the greatest in the anterior semicircular canal both in measurement of the models and the software-based images. The diameter was the greatest in the anterior semicircular canal when measured in the models. It is suggested that the helical angle of the semicircular canal potentially influences the sensitivity of the vestibulo-ocular reflex (VOR) that the semicircular canal evokes in each plane. A sufficient VOR may be evoked in the plane less strictly determined.

TOWARDS THE DISPERSION RELATIONS FOR DIELECTRIC OPTICAL FIBERS WITH HELICAL WINDINGS UNDER SLOW- AND FAST-WAVE CONSIDERATIONS - A COMPARATIVE ANALYSIS

The paper presents the electromagnetic (EM) wave propagation in cylindrical optical fibers with helical windings under slow- and fast-wave considerations. Field components are deduced for both the cases, and also, the dispersion relations are obtained by applying the boundary conditions, as modified by the presence of conducting helical windings. Two special cases are considered corresponding to the values of the helical pitch angle as 0 degrees and 90 degrees. A comparison of the dispersion relations is presented.

Head Shape and Winding Angle Optimization of Composite Pressure Vessels Based on a Multi-level Strategy

This paper presents a multi-level strategy for the optimization of composite pressure vessels with nonmetallic liners. The design variables for composite vessels include the head shape, the winding angle, the layer thickness, the number of layers, and the stacking sequence. A parameter called “modified shape factor” is introduced as an objective function. This parameter takes into account the effects of the internal pressure and volume, the vessel weight, and the composite material properties. The proposed algorithm uses genetic algorithm and finite element analysis to optimize the design parameters. As a few examples, this procedure is implemented on geodesic and ellipsoidal heads. The results show that for the given vessel conditions, the geodesic head shape with helical winding angle of nine degrees has the better performance.

Synthesis, Crystal Structure and Electrochemistry of Ferrocene‐Containing Diketoimines

Acetoacetylferrocene reacted with benzidine and 4,4′‐diaminodiphenylmethane in absolute ethanol to give the diketoimines 2a–b in high yields. Determined by X‐ray structure analysis, 2a crystallized in monoclinic crystal system—space group P21/c with cell parameters: a=10.8595(2), b=12.4095(2), c=12.2021(2) Å, β=97.6390(10), Z=2, V=1631.10(5) Å3. The unit cell contains two independent molecules to form helical crystal structure stabilized by hydrogen bond interactions with helical angle is 39.3°.

Model for Self-Propulsive Helical Filaments: Kink-Pair Propagation

Spiroplasma bacteria propel through viscous fluids by sending kinks or domain walls between regions of opposite handedness down their helical body. A simple elastic model for the domain-wall propagation is formulated and studied using hydrodynamic simulations and scaling arguments, giving good agreement with recent video-microscopy observations. It is shown that the observed helical bacterial pitch angle psi approximately 35 degrees is optimized for maximal speed and efficiency.

Discussion on the problems related to NC machining of toroid-shaped taper cutter with constant angle between cutting edge and the cutter axis

Defining the helical angle as the angle between the cutting edge and revolving axis of the cutter presents the designing models of the cutting edge and helical groove of a toroid shaped taper cutter. Under the condition of a certain revolving speed, the relative radial and axial feeding speeds of the grinding wheel in two-axis NC machining of the cutter are deduced. The models for calculating the actual obtained groove and the simulation-method of computer are also provided.The surface near to the top of the end cutter has no helical cutting edges and infinite feeding speeds of NC machine. It is necessary to adopt a supplementary cutting edge. A supplementary cutting edge is designed as a cutting edge with a constant pitch. This paper provides valuable reference for the design and NC machining of this kind of toroid shaped taper cutter.

In-tube passive heat transfer enhancement in the process industry

Enhanced heat transfer surfaces are used in heat exchangers to improve performance and to decrease system volume and cost. In-tube heat transfer enhancement usually takes the form of either micro-fin tubes (of the helical micro-fin or herringbone varieties), or of helical wire inserts. Despite a substantial increase in heat transfer, these devices also cause non-negligible pressure drops. By making use of well-proven flow pattern maps for smooth tubes and the new ones for smooth and enhanced tubes, it is shown from the refrigerant condensation data that flow patterns have a strong influence on heat transfer and pressure drop. This is done for data obtained from in-tube condensation experiments for mass fluxes ranging from 300 to 800 kg/m 2 s at a saturation temperature of 40 °C, for refrigerants R-22, R-134a, and R-407C. The flow regimes, pressure drops, heat transfer coefficients, and the overall performance of three different tubes, namely a smooth-, 18° helical micro-fin-, and a herringbone micro-fin tube (each having a nominal diameter of 9.51 mm), are presented and compared to the performance of smooth tubes with helical wire inserts (with pitches of 5 mm, 7.77 mm and 11 mm corresponding to helical angles of 78.2°, 72°, and 65.3°, respectively).

Determining the Helical Tilt Angle of a Transmembrane Helix in Mechanically Aligned Lipid Bilayers Using EPR Spectroscopy

This study demonstrates the feasibility of obtaining structural topology and helical tilt information of an integral transmembrane helix inserted into aligned planner-supported phospholipid bilayers (mechanically aligned bilayers) using a spin-label EPR approach. Significant changes are observed in the hyperfine splitting values at various orientations of the spin-labeled transmembrane helix with respect to the static magnetic field (B0). The hyperfine splitting values gleaned from the orientational dependent EPR spectra allow the helical tilt of the transmembrane helix to be determined.

Developmental evolution of sexual ornamentation: model and a test of feather growth and pigmentation

A tremendous diversity of avian color displays has stimulated numerous studies of natural and sexual selection. Yet, the developmental mechanisms that produce such diversification, and thus the proximate targets of selection pressures, are rarely addressed and poorly understood. In particular, because feathers are colored during growth, the dynamics of feather growth play a deterministic role in the variation in ornamentation. No study to date, however, has addressed the contribution of feather growth to the expression of carotenoid-based ornamentation. Here, we examine the developmental basis of variation in ornamental feather shapes in male house finches (Carpodacus mexicanus)-a species in which carotenoid displays are under strong natural and sexual selection. First, we use geometric morphometrics to partition the observed shape variation in fully grown feathers among populations, ages, degrees of elaboration, ornamental body parts, and individuals. Second, we use a biologically informed mathematical model of feather growth to predict variation in shape of ornamental feathers due to simulated growth rate, angle of helical growth of feather barbs, initial number of barb ridges, rate of addition of new barbs, barb diameter, and ramus-expansion angle. We find close concordance between among-individual variation in feather shape and hue of entire ornament, and show that this concordance can be attributed to a shared mechanism-growth rate of feather barbs. Predicted differences in feather shape due to rate of addition of barbs and helical angle of feather growth explained observed variation in ornamental area both among individuals and between populations, whereas differences in helical angle of growth and the number of barbs in the feather follicle explained differences in feather shape between ornamental parts and among males of different ages. The findings of a close association of feather growth dynamics and overall ornamentation identify the proximate targets of selection for elaboration of sexual displays. Moreover, the close association of feather growth and pigmentation not only can reinforce condition-dependence in color displays, but can also enable phenotypic and genetic accommodation of novel pigments into plumage displays providing a mechanism for the observed concordance of within-population developmental processes and between-population diversification of color displays.

Restraint potential and free energy decomposition formalism for helical tilting

A restraint potential for the helical tilt angle has been developed and its efficacy is illustrated by calculating the potentials of mean force (PMFs) as a function of WALP19’s tilt angle in vacuum. Based on our formalism to calculate the projection forces acting along the tilt, the thermodynamic integration yields a free energy profile that is in good agreement with the PMF obtained by the weighted-histogram analysis method. The present work provides a rigorous framework to decompose the total PMF into any microscopic contributions, which will be useful to explore the helix tilting in membranes due to a hydrophobic mismatch.

Heat transfer enhancement in circular tubes using helical swirl generator insert at the entrance

This paper presents an experimental study of heat transfer and friction characteristics in decaying turbulent swirl flow generated by a short helical tape placed at the entrance of the test section. In the experiments, total mass flux was varied from 160 kg m −2 s −1 to 1628 kg m −2 s −1 and the momentum ratio ( M h / M T ) was varied from 0 to 8.6. The experiments were conducted for water flow rates in the range of 5000 ⩽ Re ⩽ 30 000 . Three different helical tapes with helical angels of 30°, 45° and 60° were used. Experimental results confirm that, the use of a helical tape inserted to the tube leads to a higher heat transfer rate than the non-swirling flow. The local heat transfer coefficients were found to be increasing to very high values along the downstream of the helical tape, and then decreasing with the distance ( x / L ). The augmentation of heat transfer was found to be the function of the momentum ratio, M h / M T and Reynolds number. No pronounced effect of the number of the helical channels ( N h ), and helical angle ( α) on heat transfer was observed. It is found that using the helical tape can help to increase the heat transfer rate up to 20% depending on M h / M T and Re at constant pumping power. Enhancement efficiency increases with increasing momentum ratio and decreases with increasing Reynolds number.

Influence of the proximity of a N*–SmA–SmC* multicritical point on the electroclinic effect in the cholesteric phase

Chiral liquid crystal material (C12 homologue of biphenyl benzoate series) exhibiting the cholesteric (N*), smectic A (SmA) and ferroelectric smectic C (SmC*) phases have been studied by structural, thermodynamic, electrooptical and dielectric investigations. The helical pitch, tilt angle and spontaneous polarization have been determined. In the dielectric measurements, we have studied the soft mode in the SmC* and SmA phases. From experimental data, we have evaluated the soft‐mode rotational viscosity and the electroclinic coefficient in the SmA phase. All results are discussed and compared with previous studies performed on other homologues of the same series. The main result is that the relaxation process detected in the N* phase for the C8, C10 and C11 homologues and explained as a soft‐mode‐like mechanism, is not observed for C12. This corroborates the idea that this mechanism is related to the appearance of smectic order fluctuations within N* phase, the amplitude of which is increased when approaching the SmC*–SmA–N* multicritical point.

3D kinematics of the equine metacarpophalangeal joint at walk and trot

The metacarpophalangeal (MCP) joint and its supporting soft tissues are common sites of injury in athletic horses. Equine gait analysis has focused on 2D analysis in the sagittal plane and little information is available which describes 3D motions of the MCP joint and their possible role in the development of injuries. The aim was to characterize the 3D rotations of the equine MCP joint during walking and trotting. Three-dimensional trajectories of marker triads fixed rigidly to the third metacarpus and proximal phalanx of the right forelimb of healthy horses were recorded at walk (n = 4) and trot (n = 6) at 120 Hz using eight infra-red cameras. Kinematics of the MCP joint were calculated in terms of helical angles between the two segments using singular-value decomposition and spatial attitude methods. The ranges of motion were: flexion/extension: 62 +/- 7 degrees at walk, 77 +/- 5 degrees at trot; adduction/abduction: 13 +/- 7 degrees at walk, 18 +/- 7 degrees at trot; and axial rotation: 6 +/- 3 degrees at walk, 9 +/- 5 degrees at trot. Flexion/extension had a consistent pattern and amplitude in all horses and appeared to be coupled with adduction/abduction, such that stance phase extension was accompanied by abduction and swing phase flexion was accompanied by adduction. Axial rotation was small in amount and the direction varied between horses but was consistent within an individual for the two gaits.

Estimation of helical angles of myosin and collagen by second harmonic generation imaging microscopy

We performed Second Harmonic Generation (SHG) imaging microscopy of endogeneous myosin-rich and collagen-rich tissues in amphibian and mammals. We determined the relative components of the macroscopic susceptibility tensor chi((2)) from polarization dependence of SHG intensity. The effective orientation angle theta(e) of the harmonophores has been determined for each protein. For myosin we found theta(e) approximately 62 degrees and this value was unchanged during myofibrillogenesis. It was also independent of the animal species (xenopus, dog and human). For collagen we found theta(e) approximately 49 degrees for both type I- and type III- rich tissues. From these results we localized the source of SHG along the single helix of both myosin and collagen.

An analysis of the spatial arrangement of the myocardial aggregates making up the wall of the left ventricle

We used the technique of peeling of myocardial aggregates, usually described as 'fibres', to determine the spatial arrangement of the myocytes in the left ventricular wall of a healthy autopsied human heart. We digitised the left ventricular outer and inner boundaries, as well as the pathways in space, of almost 3000 aggregates harvested from the left ventricular myocardium. During the process of gradual peeling, we sought to identify the myocardial aggregates as uniformly as possible. Despite this, interpolation was necessary to complete the pattern so as to construct a unit vector field that represented the preferred direction of the myocardial aggregates throughout the entirety of the walls of the left ventricle of this individual human heart. Apart from the overall systematic arrangement of the aggregates necessary to achieve physiologic ventricular contraction, we documented substantial local heterogeneities in the orientation of the myocardial aggregates. In particular, a significant proportion of aggregates was found to intrude obliquely with respect to the ventricular boundaries, with markedly heterogeneous distribution. Moreover, the distribution of the helical angle of the aggregates relative to the ventricular base varied notably throughout the left ventricular free walls and the septum. Within the generally quite uniform and continuous structure of the ventricular mass, we were, however, unable to identify any organised tracts or functional subunits such as a 'helical ventricular band', nor did we find radial fibrous lamellas coursing across the ventricular wall. We suggest that the impact of local anatomical inhomogeneities, associated with gradients in regional contractile function on global ventricular dynamics, has been systematically underestimated in the past. Our analysis confirms furthermore the continuous nature of the myocardium associated with an overall gross organisation of the fibre direction field; however, there is no evidence of substructures compartmentalising the ventricles.

Structure and Dynamics of Membrane-associated ICP47, a Viral Inhibitor of the MHC I Antigen-processing Machinery

To evade the host's immune response, herpes simplex virus employs the immediate early gene product ICP47 (IE12) to suppress antigen presentation to cytotoxic T-lymphocytes by inhibition of the ATP-binding cassette transporter associated with antigen processing (TAP). ICP47 is a membrane-associated protein adopting an alpha-helical conformation. Its active domain was mapped to residues 3-34 and shown to encode all functional properties of the full-length protein. The active domain of ICP47 was reconstituted into oriented phospholipid bilayers and studied by proton-decoupled 15N and 2H solid-state NMR spectroscopy. In phospholipid bilayers, the protein adopts a helix-loop-helix structure, where the average tilt angle of the helices relative to the membrane surface is approximately 15 degrees (+/- 7 degrees ). The alignment of both structured domains exhibits a mosaic spread of approximately 10 degrees . A flexible dynamic loop encompassing residues 17 and 18 separates the two helices. Refinement of the experimental data indicates that helix 1 inserts more deeply into the membrane. These novel insights into the structure of ICP47 represent an important step toward a molecular understanding of the immune evasion mechanism of herpes simplex virus and are instrumental for the design of new therapeutics.