Length Of Helix Research Articles

High-amylose wheat and maize starches have distinctly different granule organization and annealing behaviour: A key role for chain mobility

For regular starches, gelatinization occurs over a relatively narrow temperature range in excess water; however, high-amylose starches typically gelatinise over an extended temperature range by a process that is less understood. The present study compared granule organisation of high-amylose starches from wheat (HAWS) and maize (HAMS), and investigated the role of granule organization in determining the gelatinization heterogeneity and different responses to annealing. During gelatinization (starch/water = 1:2), the melting peaks of double helices and amylose-lipid complexes are merged in HAMS, whereas the peaks are separated for HAWS. It is hypothesized that the glucan chains in HAWS are relatively more mobile (i.e., fewer inter-chain interactions), compared to HAMS. Due to this mobility, hot water leaches amylose more readily from HAWS than from HAMS at similar levels of apparent amylose content. After two-step annealing, To (gelatinization onset temperature) of HAWS increased from 58 to 84 °C, while To of HAMS only increased from 70 to 82 °C. For HAWS, annealing apparently extended double helical lengths and made semi-crystalline lamellae more heterogeneous, but reduced double helix content. For HAMS with more organised granular structure, annealing has a relatively limited effect on lamellar layers and chain conformation. The study demonstrates that HAMS and HAWS have distinctly different granule organisation and behaviours during hydrothermal processing and that HAWS, with more mobile chains, has the potential to form thermostable molecular order. The molecular basis for these differences is proposed to be the greater proportion of very long chains/branches in HAWS than HAMS.

Amylosucrase-modified waxy potato starches recrystallized with amylose: The role of amylopectin chain length in formation of low-digestible fractions

This study examined the contribution of amylose to the organization of each starch fraction in recrystallized starch. Amylosucrase (AS)-modified waxy potato starches with different branch chain lengths were completely solubilized with amylose (3:1 ratio) and recrystallized at 4 °C for 48 h. The content of rapidly digestible starch and resistant starch (RS) showed linear change with degree of AS modification, while slowly digestible starch (SDS) did not. The changes in structural characteristics were tracked according to serial removal of each fraction. Results from iodine binding property, branch chain length, X-ray diffraction, and thermal property analysis indicated that branch chain length of amylopectin determined the length of the amylose-amylopectin double helix and the mobility of amylose and that formation of SDS or RS could be induced by controlling the length of amylopectin chains. These findings could be used for production of customized starches with specific digestive properties for health benefits.

Membrane Biology: Transmembrane Helices Need to Fit the Surrounding Fat.

A new study compares two sister species of fission yeast that use very different fatty acids to make membrane lipids and reveals an adaptation in transmembrane helix lengths that maintains membrane protein functions.

Computer-Simulation of the Billet Shape Change during Helical Piercing

In this paper the task of the study of the deformation during helical piercing of the metal was set and solved with the use of the DEFORM-3D software. Methodology, that allows to calculate the length of helix lead along the deformation zone, as well as determine for each lead absolute and relative reduction, the width of the contact area and the metal strain refinement indicator was developed. Based on the developed methodology application the following variation regularities were established: helix lead length (li), quotient reduction (Δr/r0), ratio of the billet radius to the width of the contact area (r0/b), as well as the length of the billet contact surface (l0) with the roll in dependence of the feed angle (β), the roll number of revolutions (N) and the plug nose advancement over the gorge (Cg).

A convenient protein library for spectroscopic calibrations

While several Raman, CD or FTIR spectral libraries are available for well-characterized proteins of known structure, proteins themselves are usually very difficult to acquire, preventing a convenient calibration of new instruments and new recording methods. The problem is particularly critical in the field of FTIR spectroscopy where numerous new methods are becoming available on the market.The present papers reports the construction of a protein library (cSP92) including commercially available products, that are well characterized experimentally for their purity and solubility in conditions compatible with the recording of FTIR spectra and whose high-resolution structure is available.Overall, 92 proteins were selected. These proteins cover well the CATH space at the level of classes and architectures. In terms of secondary structure content, an analysis of their high-resolution structure by DSSP shows that the mean content in the different secondary structures present in cSP92 is very similar to the mean content found in the PDB.The 92-protein set is analyzed in details for the distribution of helix length, number of strands in β- sheets, length of β-strands and amino acid content, all features that may be important for the interpretation of FTIR spectra.

Thermal response of energy foundations installed in unsaturated residual soils

This study focuses on the thermal response of energy foundations with different piping geometries installed in unsaturated soil. Energy foundations are an efficient alternative to traditional space heating and cooling approaches and can reduce energy demand for air conditioning in Brazil, where unsaturated residual soil deposits are abundant. A three-dimensional numerical model for heat transfer and subsurface flow is first validated against field data from a thermal response test at the University of São Paulo. The model is then used to compare the performance of triple and quadruple U-tube piping geometries and helical piping geometries of equivalent length. The helical geometries resulted in initial less uniformly heated foundations and lower heat flux at the foundation boundary compared with the U-tubes, but the differences between the U-tube geometries and their equivalent length helices were less than 1°C. All piping geometries exhibited increased heat output as the length of heat exchanger piping increased. The infinite line source solution was compared with the model results. The infinite line source solution underestimated the thermal response of the system during the first 25-30 days and overestimated it afterwards.

Influence of interfacial tryptophan residues on an arginine-flanked transmembrane helix

The transmembrane helices of membrane proteins often are flanked by interfacial charged or aromatic residues that potentially help to anchor the membrane-spanning protein. For isolated single-span helices, the interfacial residues may be especially important for stabilizing particular tilted transmembrane orientations. The peptide RWALP23 (acetyl-GR2ALW(LA)6LWLAR22A-amide) has been employed to investigate the interplay between interfacial arginines and tryptophans. Here we replace the tryptophans of RWALP23 with A5 and A19, to investigate arginines alone with respect to helix fraying and orientation in varying lipid bilayers. Deuterated alanines incorporated into the central sequence allow the orientation and stability of the core helix to be assessed by means of solid -state 2H NMR in bilayers of DOPC, DMPC and DLPC. The helix tilt from the bilayer normal is found to increase slightly when R2 and R22 are present, and increases still further when the tryptophans W5 and W19 are replaced by alanines. The extent of helix dynamic averaging remains low in all cases. The preferred helix azimuthal rotation is essentially constant for all of the helices in each of the lipid membranes considered here. The alanines located outside of the core region of the peptide are sensitive to helical integrity. The new alanines, A5 and A19, therefore, provide new information about the length of the core helix and the onset of unraveling of the terminals. Residue A19 remains essentially on the central helix in each lipid membrane, while residues A3, A5 and A21 deviate from the core helix to an extent that depends on the membrane thickness. Differential unraveling of the two ends to expose peptide backbone groups for hydrogen bonding therefore acts together with specific interfacial side chains to stabilize a transmembrane helix.

Complex viscosity of helical and doubly helical polymeric liquids from general rigid bead-rod theory

With general rigid bead-rod modeling, we recreate shapes of complex macromolecular structures with beads, by rigidly fixing bead positions relative to one another. General rigid-bead rod theory then attributes the elasticity of polymeric liquids to the orientation that their macromolecules develop during flow. For linear viscoelastic behaviors, this theory has been evaluated for just a few very simple structures: rigid rings, the rigid tridumbbell, and three quadrafunctional branched structures. For oscillatory shear flow, the frequency dependencies of both parts of the complex viscosity are, at least qualitatively, predicted correctly. In this paper, we use general rigid-bead rod theory for the most complex macromolecular architectures to date. We thus explore the role of helix geometry on the complex viscosity of a helical polymeric liquid. Specifically, for both singly and doubly helical structures, we investigate the effects of helix radius, flight length, helix length, and the number of beads per flight on the complex viscosity function, the fluid relaxation time, and the zero-shear values of the steady shear viscosity and of the first normal stress coefficient. As a worked example, we examine specifically deoxyribonucleic acid (DNA). Using general rigid bead-rod theory, we dissect the DNA to see how the first helix, second helix, and then the base pairs each contribute to the complex viscosity. We next explore the rheological implications of gene replication to find that the unzipping of DNA into a pair of single strands is viscostatic.

Salt Dependence of A-Form RNA Duplexes: Structures and Implications.

The biological functions of RNA range from gene regulation through catalysis and depend critically on its structure and flexibility. Conformational variations of flexible, non-base-paired components, including RNA hinges, bulges, or single-stranded tails, are well documented. Recent work has also identified variations in the structure of ubiquitous, base-paired duplexes found in almost all functional RNAs. Duplexes anchor the structures of folded RNAs, and their surface features are recognized by partner molecules. To date, no consistent picture has been obtained that describes the range of conformations assumed by RNA duplexes. Here, we apply wide angle, solution X-ray scattering (WAXS) to quantify these variations, by sampling length scales characteristic of helical geometries under different solution conditions. To identify the radius, helical rise, twist, and length of dsRNA helices, we exploit molecular dynamics generated structures, explicit solvent models, and ensemble optimization methods. Our results quantify the substantial and salt-dependent deviations of double-stranded (ds) RNA duplexes from the assumed canonical A-form conformation. Recent experiments underscore the need to properly describe the structures of RNA duplexes when interpreting the salt dependence of RNA conformations.

Starch: Granule, Amylose-Amylopectin, Feed Preparation, and Recovery by the Fowl's Gastrointestinal Tract

SUMMARY Starch exists as glucose polymers of amylose and amylopectin. Amylose involves 10–30 glucose units having α-1,4-linkages enabling self-association into a helix. Amylopectin is assembled from a large number of helices interconnected by α-1,6-branching to dominate each granule. Granules have amorphous branching alternate with layers of crystallized helices. Crystallization involves helices laterally held together with either intermediary water (A) or is direct H-bonded (B) to resist digestion. Granule digestion by α-amylase depends on attachment along the helix length with release of maltose and maltotriose which includes α-limit dextrins from amylopectin. Amyloplasts progressively assemble each granule with sequential cell filling from aleurone to core during endosperm maturation. Incomplete development reduces endosperm starch content and energy value while losses from germination are less influential. High temperature drying of moist grain creates resistant granules due to annealing and partial loss of bound water from A- to form H-bonding and B-crystals. Further annealing and additional resistance occurs with high temperature pelleting. Extrusion extends annealing together with granule gelatinization which frees polymers enabling retrogradion into resistant crystallites of amylose while amylopectin remains amorphous and digestible. Pellet stability reduces feed loss and work of prehension. Gastric digestion improves granule exposure. Pancreatic α-amylase erodes granules within the small intestine with products transferring to the unstirred water layer where microvilli enzymes generate glucose for absorption. Resistance delays granule erosion with potential continuance and fermentation in the large intestine that reduces NE then AME if excreted. Starch resistance influences location of digestion by the gastrointestinal tract and product use.

Cryo-EM structure of TRPC5 at 2.8-Å resolution reveals unique and conserved structural elements essential for channel function.

The transient receptor potential canonical subfamily member 5 (TRPC5), one of seven mammalian TRPC members, is a nonselective calcium-permeant cation channel. TRPC5 is of considerable interest as a drug target in the treatment of progressive kidney disease, depression, and anxiety. Here, we present the 2.8-Å resolution cryo-electron microscopy (cryo-EM) structure of the mouse TRPC5 (mTRPC5) homotetramer. Comparison of the TRPC5 structure to previously determined structures of other TRPC and TRP channels reveals differences in the extracellular pore domain and in the length of the S3 helix. The disulfide bond at the extracellular side of the pore and a preceding small loop are essential elements for its proper function. This high-resolution structure of mTRPC5, combined with electrophysiology and mutagenesis, provides insight into the lipid modulation and gating mechanisms of the TRPC family of ion channels.

Thermal analysis of a triple helix ground heat exchanger using numerical simulation and multiple linear regression

Geothermal heat exchangers, one of the main components of shallow geothermal systems, have been investigated by many researchers in recent years to exploit clean and renewable energies. Most of the previous studies have mostly concentrated on the common types of ground heat exchangers including U-tube and helical ground heat exchangers. In the case of helical type, only two types of heat exchanger, with an inner outlet or with an outer outlet, have been examined. In order to increase the surface interaction between heat exchanger and backfill to improve the heat transfer rate, this study intends to present a new generation of helical ground heat exchangers called triple helix. Three helical branches are considered for both inlet and outlet of triple helix ground heat exchanger. The influences of geometric parameters such as helix pitch, helix diameter, helical coil length, the distance between centers of inner and outer helical coil branches, and the distance between centers of inner/outer helical coil branches on the efficacy of the heat transfer process are investigated by a numerical study. The results indicate that the most effective geometric parameter on the performance of the triple helix ground heat exchanger is the length of the helical coil, while the two parameters of the distance between centers of inner/outer helical coil branches, as well as the distance between centers of inner and outer helical coil branches, have the least effect. Along with the numerical results, multiple regression method accompanies with the artificial neural network are used to propose effective formulations to predict thermal properties of a triple helix ground heat exchanger.

Magnetic Phase Transition in MnSi Based on the First Principle Calculations of Electronic Structure and Spin Fluctuation Theory

Based on the spin-fluctuation theory and LSDA + U + SO-calculations of the electronic structure, the spin states arising in the region of the magnetic phase transition in the helicoidal ferromagnet MnSi are studied. Within the framework of the stated model of the electronic structure, a temperature dependence of the homogeneous magnetic susceptibility is obtained near the temperature of the magnetic phase transition, which is in good agreement with experiment. At the temperature of the transition to the paramagnetic state, the left chirality vanishes, and spin correlations arise with a radius equal to the length of the spin helix, which then decreases with temperature. The results were obtained within the framework of the assignment of the Ministry of Education and Science of the Russian Federation, contract 3.9521.2017 / 8.9

The Transmembrane Conformation of the Influenza B Virus M2 Protein in Lipid Bilayers

Influenza A and B viruses cause seasonal flu epidemics. The M2 protein of influenza B (BM2) is a membrane-embedded tetrameric proton channel that is essential for the viral lifecycle. BM2 is a functional analog of AM2 but shares only 24% sequence identity for the transmembrane (TM) domain. The structure and function of AM2, which is targeted by two antiviral drugs, have been well characterized. In comparison, much less is known about the structure of BM2 and no drug is so far available to inhibit this protein. Here we use solid-state NMR spectroscopy to investigate the conformation of BM2(1–51) in phospholipid bilayers at high pH, which corresponds to the closed state of the channel. Using 2D and 3D correlation NMR experiments, we resolved and assigned the 13C and 15N chemical shifts of 29 residues of the TM domain, which yielded backbone (φ, ψ) torsion angles. Residues 6–28 form a well-ordered α-helix, whereas residues 1–5 and 29–35 display chemical shifts that are indicative of random coil or β-sheet conformations. The length of the BM2-TM helix resembles that of AM2-TM, despite their markedly different amino acid sequences. In comparison, large 15N chemical shift differences are observed between bilayer-bound BM2 and micelle-bound BM2, indicating that the TM helix conformation and the backbone hydrogen bonding in lipid bilayers differ from the micelle-bound conformation. Moreover, HN chemical shifts of micelle-bound BM2 lack the periodic trend expected for coiled coil helices, which disagree with the presence of a coiled coil structure in micelles. These results establish the basis for determining the full three-dimensional structure of the tetrameric BM2 to elucidate its proton-conduction mechanism.

3D-Spatial encoding with permanent magnets for ultra-low field magnetic resonance imaging

We describe with a theoretical and numerical analysis the use of small permanent magnets moving along prescribed helical paths for 3D spatial encoding and imaging without sample adjustment in ultra-low field magnetic resonance imaging (ULF-MRI). With our developed method the optimal magnet path and orientation for a given encoding magnet number and instrument architecture can be determined. As a proof-of-concept, we studied simple helical magnet paths and lengths for one and two encoding magnets to evaluate the imaging efficiency for a mechanically operated ULF-MRI instrument with permanent magnets. We demonstrate that a single encoding magnet moving around the sample in a single revolution suffices for the generation of a 3D image by back projection.

Study of the Tubular Billets Geometric Characteristics during Computer Simulation of the Rotary Piercing Process

The results of the computer simulation of the tubular billet rotary piercing process are presented. The research methodology of the deformation zone geometric ratios with due regard for the tubular billet change of shape at each helical curve step was developed .The changes pattern of the helical curve step length (li), quotient reduction (Δr/r0), ratio of the tubular billet radius to the contact surface width (r/b), contact surface length of the tubular billet (l0) with a roll, depending on the feed angle (β), roll rotation frequency (N) and plug nose extension at the gorge (Сg) was established.

Spinning spin density vectors along the propagation direction.

It has been known that light possesses both spin and orbital angular momenta (AM) arising from the twisting behaviors of the electric (and magnetic) field vector and the wavefront of the field, respectively. The spin (AM) density is also a vector in the field of three dimensions (3D), since its orientation can be in any direction. In this Letter, we show that through focusing a Gaussian beam with both on-axis and off-axis vortices in a high-numerical-aperture system, the spin (AM) density vector in the focal region exhibits nontrivial behaviors: rotating around the central axis along the propagation direction. We demonstrate that this helical behavior of the spin (AM) density vector is mainly caused by the different Gouy phases of the three field components. By changing the position of the off-axis vortex and the semiaperture angle, the helical shape and the helical length can be adjusted. This is a new type of optical twist, to the best of our knowledge, and it may supply another rotational degree of freedom in optical tweezers.

Bir gövde borulu ısı değiştiricisinde farklı levha türlerinin ısıl performansa etkisinin sayısal olarak incelenmesi

In this study, the thermal performance of a small scale shell and tube heat exchanger was performed according to the baffle type by using three dimensional Computational Fluid Dynamics (CFD) method. In numerical calculations, segmental and continuous helical baffle types were selected to get the comparative results. For helical baffle type, we used two different models that the numbers of helical rotations and baffle spacing length were different. Thus, we determined five different numerical models and the thermal performance of each models were evaluated under different inlet temperature values selected as 50, 60 and 70°C for the tube side. The inlet temperature value and the mass flow rate of shell side were kept constant during all the numerical calculations. The heat transfer calculations were achieved by using Logarithmic Mean Temperature Difference (LMTD) method. We also employed the Bell-Delaware method which can be used accurately for shell and tube heat exchangers. The highest thermal performance was determined in Case-IV which had equal baffle spacing and the maximum number of rotations for continuous helical baffle. The predicted total pressure drop results obtained from the numerical calculations were in good agreement with the calculated total pressure drop from Bell-Delaware method. The lowest pressure drop and the highest thermal performance were achieved for continuous helical baffle type compared to the segmental equal spacing baffle type. The numerical simulations based on CFD analysis can provide more information about heat exchangers and this tool can be used to improve both design and the thermal performance of heat exchangers.

Strong deformations of DNA: Effect on the persistence length

.Extreme deformations of the DNA double helix attracted a lot of attention during the past decades. Particularly, the determination of the persistence length of DNA with extreme local disruptions, or kinks, has become a crucial problem in the studies of many important biological processes. In this paper we review an approach to calculate the persistence length of the double helix by taking into account the formation of kinks of arbitrary configuration. The reviewed approach improves the Kratky-Porod model to determine the type and nature of kinks that occur in the double helix, by measuring a reduction of the persistence length of the kinkable DNA.Graphical abstract

Stretch-Induced Coil–Helix Transition in Isotactic Polypropylene: A Molecular Dynamics Simulation

The stretch-induced coil–helix transition (CHT) of isotactic polypropylene (iPP) was studied with full-atom molecular dynamics (MD) simulations during the uniaxial stretch process. The results show that imposing stretch induces CHT, which increases both the content and the average length of helices. As strain exceeding a certain value, long helices initially not presented in melt start to emerge, which mainly follow a kinetic pathway of merging adjacent short helices, while overstretch at large strain leads to the helix-extended coil transition. Based on statistics on the distribution of helical length and theoretical calculation, stretch is found to reduce free energy gap for CHT. At small strain, the single-chain model is sufficient to account stretch-induced CHT for the formation of short helices, but the gap reduction is mainly contributed by intrachain energy rather than entropy, which is different from current theories for stretch-induced CHT. While the formation of long helices at large strain requ...