Length Of Helix Research Articles

Structural and Functional Implications of Polyarginine Addition to Green Fluorescent Protein Expression in Saccharomyces cerevisiae INVSc1

Green Fluorescent Protein (EGFP) is widely used as a reporter gene, aiding in protein recovery and transduction studies. In this study, EGFP was tagged with eleven arginine residues (PolyR) and six histidine residues (His-tag) for purification. The aim was to enhance the synthesis of EGFP-PolyR in Saccharomyces cerevisiae and evaluate the effects of polyarginine modification on protein stability and expression levels. The expression of EGFP and EGFP-PolyR in S. cerevisiae was assessed through fluorescence measurements and protein levels. Structural analyses were conducted using in silico tools to investigate changes in beta strands and helices, which were validated through Western blots. Results showed that EGFP-PolyR maintained similar fluorescence levels to EGFP, but with notable structural changes. EGFP-PolyR's final beta strand terminates at Ala228, compared to Gly229 in EGFP, affecting the beta sheet's stability. Structural modifications also included altered helix lengths, with a longer helix 10 and shorter helix 9 in EGFP-PolyR. These alterations, along with shifts in helix-helix interactions, contribute to destabilization. Additionally, EGFP-PolyR exhibited unique gamma coils absent in EGFP, further differentiating its structure. The structural changes led to decreased protein expression and solubility, as indicated by Western blot analysis, with EGFP-PolyR showing significantly lower expression levels. The findings suggest that EGFP-PolyR is prone to aggregation and misfolding, characteristics often associated with aggregation-prone proteins.In conclusion, the polyarginine modification significantly impacts the structural integrity, stability, and solubility of EGFP. While fluorescence is retained, these changes hinder protein detectability and purification, highlighting the importance of considering structural alterations when modifying reporter proteins for experimental use.

Experimental Study on Liquid Jet Trajectory in Cross Flow of Swirling Air at Elevated Pressure Condition

Abstract Motivated by fuel atomization applications in gas turbine combustors, this paper presents an experimental examination of liquid jet trajectory and spray dynamics in crossflow of swirling air, at elevated pressure conditions. The study was conducted within an annular passage and was focused on momentum flux ratio and swirl number as the main parameters. The momentum flux ratio was varied from 2 to 25 through incremental adjustments to the liquid injection velocity and the swirl number values of 0.42 and 0.74 were used, representing typical gas turbine fuel atomization conditions. Jet trajectories were captured by imaging the three-dimensional helical path traced by the liquid jet using two mutually perpendicular optical windows. Radial penetration was quantified by solving the equations of a helix. The key findings revealed that radial penetration of the liquid jet is larger for higher momentum flux ratios and is influenced by the helical arc length. Notably, the radial penetration observed at low momentum flux ratios was larger for crossflow with lower swirl number and the radial penetration observed at high momentum flux ratios was more for crossflows with higher swirl number. In comparison to the spray characteristics in swirling crossflows at atmospheric pressure, condition of elevated gaseous pressure resulted in lower radial penetration, jet spread and jet area. Jet trajectory correlations for elevated pressure conditions are additionally presented, developed using curve fitting to the experimental data, which will be useful to the industry for estimation of spray trajectory in swirling crossflows at high pressure conditions.

We are doing it wrong: Putting homology before phylogeny in cyanobacterial taxonomy.

The rapid expansion of whole genome sequencing in bacterial taxonomy has revealed deep evolutionary relationships and speciation signals, but assembly methods often miss true nucleotide diversity in the ribosomal operons. Though it lacks sufficient phylogenetic signal at the species level, the 16S ribosomal RNA gene is still much used in bacterial taxonomy. In cyanobacterial taxonomy, comparisons of 16S-23S Internal Transcribed Spacer (ITS) regions are used to bridge this information gap. Although ITS rRNA region analyses are routinely being used to identify species, researchers often do not identify orthologous operons, which leads to improper comparisons. No method for delineating orthologous operon copies from paralogous ones has been established. A new method for recognizing orthologous ribosomal operons by quantifying the conserved paired nucleotides in a helical domain of the ITS, has been developed. The D1' Index quantifies differences in the ratio of pyrimidines to purines in paired nucleotide sequences of this helix. Comparing 111 operon sequences from 89 strains of Brasilonema, four orthologous operon types were identified. Plotting D1' Index values against the length of helices produced clear separation of orthologs. Most orthologous operons in this study were observed both with and without tRNA genes present. We hypothesize that genomic rearrangement, not gene duplication, is responsible for the variation among orthologs. This new method will allow cyanobacterial taxonomists to utilize ITS rRNA region data more correctly, preventing erroneous taxonomic hypotheses. Moreover, this work could assist genomicists in identifying and preserving evident sequence variability in ribosomal operons, which is an important proxy for evolution in prokaryotes.

Importance of isoleucine residue in ion channel formation ability of 11-residue peptaibols

Peptaibols are a class of short peptides, typically 7 to 20 amino acids long, characterized by noncanonical amino acid residues such as aminoisobutyric acid (Aib). Although the helix length is shorter than the membrane thickness, the 11-residue peptaibol trichorovin-XII (TV-XII) can form ion channels in membranes. Assuming that a higher proportion of isoleucine (Ile) relative to leucine (Leu) residues is crucial for maintaining the ion channel activity of TV-XII, peptide analogs of TV-XII with varying Ile content were designed, synthesized, and evaluated. The secondary structure of all derivatives under hydrophobic conditions was confirmed by CD measurement as an α-helix-like β-bend ribbon spiral structure. The most stable ion channel activity was found in compound 4a with maximum Ile. Furthermore, the C-terminal Ile analog showed greater ion channel activity compared to the Leu analog. This suggests that the choice between Leu and Ile can influence the expression of ion channel activity, which will be crucial for the de novo designed functional peptides.

Synthesis of Aza[n]helicenes up to n = 19: Hydrogen-Bond-Assisted Solubility and Benzannulation Strategy.

Synthetic challenges toward anomalous structures and electronic states often involve handling problems such as insolubility in common organic solvents and oxidative degradation under aerobic conditions. We designed benzo-annulated aza[n]helicenes, which benefit from both the suppressed elevation of highest occupied molecular orbital (HOMO) energies and high solubility due to hydrogen bonding with solvent molecules to overcome these challenges. This strategy enabled the synthesis of six new aza[n]helicenes ([n]AHs) of different lengths (n = 9-19) from acyclic precursors via one-pot intramolecular oxidative fusion reactions. The structures of all of the synthesized aza[n]helicenes were determined by X-ray diffraction (XRD) analysis, and their electrochemical potentials were measured by cyclic voltammetry. Among the synthesized aza[n]helicenes, [17]AH and [19]AH are the first heterohelicenes with a triple-layered helix. The noncovalent interaction (NCI) plots confirm the existence of an effective π-π interaction between the layers. The absorption and fluorescence spectra red-shifted as the helical lengths increased, without any distinct saturation points. The optical resolutions of N-butylated [9]AH, [11]AH, [13]AH, and [15]AH were accomplished, and their circular dichroism (CD) and circularly polarized luminescence (CPL) were measured. Thus, the structural, (chir)optical, and electrochemical properties of the aza[n]helicenes were comprehensively analyzed.

Gramicidin A as a mechanical sensor for mixed nonideal lipid membranes.

Gramicidin A (gA) is a short hydrophobic β-helical peptide that forms cation-selective channels in lipid membranes in the course of transbilayer dimerization. The length of the gA helix is smaller than the thickness of a typical lipid monolayer. Consequently, elastic deformations of the membrane arise in the configurations of gA monomers, conducting dimer, and the intermediate state of coaxial pair, where gA monomers from opposing membrane monolayers are located one on top of the other. The gA channel is characterized by the average lifetime of the conducting state. The elastic properties of the membrane influence the average lifetime, thus making gA a convenient sensor of membrane elasticity. However, the utilization of gA to investigate the elastic properties of mixed membranes comprising two or more components frequently relies on the assumption of ideality, namely that the elastic parameters of mixed-lipid bilayers depend linearly on the concentrations of the components. Here, we developed a general approach that does not rely on the aforementioned assumption. Instead, we explicitly accounted for the possibility of inhomogeneous lateral distribution of all lipid components, as well as for membrane-mediated lateral interactions of gA monomers, dimer, coaxial pair, and minor lipid components. This approach enabled us to derive unknown elastic parameters of lipid monolayer from experimentally determined lifetimes of gA channel in mixed-lipid bilayers. A general algorithm was formulated that allows the unknown elastic parameters of a lipid monolayer to be obtained using gA as a mechanical sensor.

Numerical investigation of mixing performance for a helical tangential porous tube-in-tube microchannel reactor

The tube-in-tube microchannel reactor (TMCR) is widely applied in chemical engineering and material industries. Two or more fluids are mixed in the annular channel of TMCR. This work aims to introduce a helical tangential porous tube-in-tube microchannel reactor (HTP-TMCR). The performance of HTP-TMCR is analyzed using computational fluid dynamics (CFD) method, focusing on three aspects: mixing index, pressure drop, and velocity distribution. Additionally, this study investigates the impacts of four geometric parameters, including left and right helical directions, pitch, pore size, and length of the non-porous zone, on the mixing performance of HTP-TMCR. The simulation results reveal that the mixing index initially decreases as the flow rate increases, reaching its lowest point (approximately 75%) at Q=2 L/h. Subsequently, there is a sharp rise to a second inflection point at Q=10 L/h, followed by a gradual progression stabilizing around 95%. Specifically, the left helical configuration demonstrates superior performance compared to the right one. Optimal mixing is achieved at low flow rates when the pitch is 4 mm and the pore size is 0.4 mm. Designing the length of the non-porous zone to be 5 mm is recommended. Furthermore, the characteristic of pressure drop for HTP-TMCR indicates its potential for commercial applications.

Helical Nanographenes Bearing Pentagon-Heptagon Pairs by Stepwise Dehydrocyclization.

The incorporation of pentagon-heptagon pairs into helical nanographenes lacks a facile synthetic route, and the impact of these pairs on chiroptical properties remains unclear. In this study, a method for the stepwise construction of pentagon-heptagon pairs in helical nanographenes by the dehydrogenation of [6]helicene units was developed. Three helical nanographenes containing pentagon-heptagon pairs were synthesized and characterized using this approach. A wide variation in the molecular geometries and photophysical properties of these helical nanographenes was observed, with changes in the helical length of these structures and the introduction of the pentagon-heptagon pairs. The embedded pentagon-heptagon pairs reduced the oxidation potential of the synthesized helical nanographenes. The high isomerization energy barriers enabled the chiral resolution of the helicene enantiomers. Chiroptical investigations revealed remarkably enhanced circularly polarized luminescence and luminescence dissymmetry factors with an increasing number of the pentagon-heptagon pairs.

Helical Nanographenes Bearing Pentagon‐Heptagon Pairs by Stepwise Dehydrocyclization

AbstractThe incorporation of pentagon‐heptagon pairs into helical nanographenes lacks a facile synthetic route, and the impact of these pairs on chiroptical properties remains unclear. In this study, a method for the stepwise construction of pentagon‐heptagon pairs in helical nanographenes by the dehydrogenation of [6]helicene units was developed. Three helical nanographenes containing pentagon‐heptagon pairs were synthesized and characterized using this approach. A wide variation in the molecular geometries and photophysical properties of these helical nanographenes was observed, with changes in the helical length of these structures and the introduction of the pentagon‐heptagon pairs. The embedded pentagon‐heptagon pairs reduced the oxidation potential of the synthesized helical nanographenes. The high isomerization energy barriers enabled the chiral resolution of the helicene enantiomers. Chiroptical investigations revealed remarkably enhanced circularly polarized luminescence and luminescence dissymmetry factors with an increasing number of the pentagon‐heptagon pairs.

Kinetic behavior of the network structure changes in funoran gelation studied by rheological and NMR measurements

Funoran is a promising food polysaccharide with unique gelling properties but understanding its gelation behaviors remains inadequate. This study aimed to investigate the influence of cooling and heating rates on funoran gelation properties and study its gelation mechanism by dynamic rheology and NMR studies. With constant heating rates, the melting point was unaffected by changing cooling rates, whereas higher cooling and heating rates enhance the gel strength and thermal hysteresis. The gelation kinetics mechanism of the funoran solution was elucidated at different quenching temperatures. The rheological measurement results indicated that the funoran solution quenched to lower temperatures resulted in higher G` in the gel state, and faster gelation rate compared with the solution quenched at higher temperatures. 1H NMR results revealed a slow decay in funoran signal intensity at higher temperatures (20 °C) and a fast signal decay at 2 °C. A theoretical model involving second and first-order reactions was proposed to describe the gelation kinetic process of funoran at different quenching temperatures. It was shown longer helix lengths were required for stable intermolecular association and gel formation at higher temperatures than at lower temperatures. These results offer valuable insights for optimizing the funoran gelation properties for various food applications.

Influence of idler misalignment fault on contact and dynamic characteristics of helical gear

Due to the advantages of stable helical gear transmission, it is widely used in industry, agriculture, and national defense. Shaft misalignment has a great influence on the vibration, bearing capacity, and life of gear transmission. Based on the idler wheel drive system as the research object, according to the principle of gear meshing, the helical gear time-varying contact wire length model was deduced. The dynamic model of the gear transmission system with faults is established considering the faults of the idler's center distance error and angle error, and the influence law of idler misalignment fault on the vibration of the idler transmission system is revealed. On this basis, the finite element model under angle error is established to analyze the contact stress of the tooth surface under different faults and reveal the contact stress distribution law of the tooth surface. The results show that the misalignment fault will change the length of the helical gear contact line. When the gear shaft misaligns, it will increase the axial force of the gear and increase the axial vibration of the gear. Moreover, the angle error will cause uneven load distribution on the tooth surface of the helical gear, which will reduce the contact area of the gear and increase the contact stress. The phenomenon of off-load of gear accelerates the wear of the gear tooth surface and shortens the life of the gear. The study of idler misalignment fault is of great significance for prolonging the life of gear and providing the basis for gear fault diagnosis.

Structural basis for evolutionarily conserved interactions between TFIIS and Paf1C

The elongation factor TFIIS interacts with Paf1C complex to facilitate processive transcription by Pol II. We here determined the crystal structure of the trypanosoma TFIIS LW domain in a complex with the LFG motif of Leo1, as well as the structures of apo-form TFIIS LW domains from trypanosoma, yeast and human. We revealed that all three TFIIS LW domains possess a conserved hydrophobic core that mediates their interactions with Leo1. Intriguingly, the structural study revealed that trypanosoma Leo1 binding induces the TFIIS LW domain to undergo a conformational change reflected in the length and orientation of α6 helix that is absent in the yeast and human counterparts. These differences explain the higher binding affinity of the TFIIS LW domain interacting with Leo1 in trypanosoma than in yeast and human, and indicate species-specific variations in the interactions. Importantly, the interactions between the TFIIS LW domain and an LFG motif of Leo1 were found to be critical for TFIIS to anchor the entire Paf1C complex. Thus, in addition to revealing a detailed structural basis for the TFIIS-Paf1C interaction, our studies also shed light on the origin and evolution of the roles of TFIIS and Paf1C complex in regulation of transcription elongation.

Determination of the optimal connector length to enhance stability of backbone-circularized granulocyte colony-stimulating factor.

Improving protein stability is important for industrial applications, and one promising method for achieving this is backbone circularization. As connector length affects stability, predicting and elucidating a more stable connector length is necessary for development of the backbone circularization method. However, the relationship between connector length and protein stability has not been completely elucidated. Here, we determined the most stable connector length for granulocyte colony-stimulating factor by changing one residue at a time to produce connector length variants and then measuring their thermal stability. Analysis of the local structures obtained from the predicted structures of the circularized variants revealed that an approach using helix length, dihedral backbone angle, and number of unbonded hydrogen bond donors and acceptors is suitable for identifying connector lengths with higher stability.

Molecular Modulator Approach for Controlling the Length of Chiral 1D Single-Helical Gold Nanoparticle Superstructures.

Peptide-based methods have proven useful for constructing helical gold nanoparticle superstructures that exhibit strong plasmonic chiroptical activity. Superstructure syntheses using the amphiphilic peptide conjugate C16-(AYSSGAPPMoxPPF)2 typically yield 1D helices with a broad length distribution. In this study, we introduce a molecular modulator approach for controlling helix length. It represents a first step toward achieving narrowly disperse populations of single helices fabricated using peptide-based methods. Varying amounts of modulator, C16-(AYSSGA)2, were added to C16-(AYSSGAPPMoxPPF)2-based single-helix syntheses, resulting in decreased helix length and narrowing of the helix length distribution. Kinetic studies of fiber assembly were performed to investigate the mechanism by which the modulator affects helix length. It was found that the modulator leads to rapid peptide conjugate nucleation and fiber growth, which in turn results in large amounts of short fibers that serve as the underlying scaffold for the single-helix superstructures. These results constitute important advances toward generating monodisperse samples of plasmonic helical colloids.

Visualization and comparison of CT dose distribution between axial and helical acquisitions.

It is challenging to assess the accuracy of volume CT Dose Index (CTDIvol ) when the axial scan modes corresponding to a helical scan protocol are not available. An alternative approach was proposed to directly measure using helical acquisitions and relatively small differences (<20%) from CTDIvol were observed. To visually demonstrate the 3D dose distribution for both axial and helical CT acquisitions and quantitively compare and CTDIvol . 3D dose distribution within the standard CTDI phantoms (16 and 32cm diameter) from a single CT projection, Dp (x,y,z) was first generated using Monte Carlo simulation (GEANT4) with 9×108 photons per combination of tube voltage (80-140kV), collimation width (1-8cm), and z-axis location of the central ray of the x-ray beam, with a spatial resolution of 1 mm3 . These dose distributions from one single projection were analytically ensembled to simulate 3D dose volumes DA (x,y,z) and DH (x,y,z) for axial and helical scans, respectively, with different helical pitches (0.3-2) and scan lengths (100-150mm). 2D planar dose distributions were obtained by integrating the inside 100mm of the dose volumes. CTDIvol and were calculated using the planar dose data at corresponding pencil chamber locations and the percentage differences (PD) were reported. High spatial resolution 3D CT dose volumes were generated and visualized. PDs between and CTDIvol had strong dependency on scan length and peripheral chamber locations, with subtle dependency on collimation width and pitch. PDs were mostly within the range of±3% for a scan length of 150mm with four peripheral chamber locations. With a scan length covering the entire phantom length, directly measured from helical scans can serve as an alternative to CTDIvol only if all four peripheral locations were measured.

Inner surface peening for long and narrow helical pipe using acoustic cavitation

The inner surface peening of helical pipes is highly challenging due to the inaccessibility of the inner surface. To the end, we propose to peen the inner surface by introducing acoustic cavitation inside the pipe. We also provide a theory to account for how the inner surface peening can be achieved by the acoustic cavitation for a long helical pipe. We evaluate the validity of theory with experiments conducted on helical pipe specimens. The experimental results well agree with the theorical predictions. Also, it was found that a significant amount of compressive residual stress was achieved by the acoustic cavitation on the inner surface. The experimental results imply that the acoustic-cavitation-generation of compressive residual stress is effective regardless of pipe length, which promises that the present peening method will be applicable for a wide range of helical pipe length.

Negative fragmentation approach for investigating the depolarization effect of neighboring residues on hydrogen bonds in π-helix

We systematically analyzed hydrogen bond (HB) interaction energies in π-helix with alanine peptide models using the negative fragmentation approach (NFA) combined with the precise density functional theory (DFT) and the molecular mechanics calculation. We conclude that the weaker HB energies in the helical structure as compared with those of the isolated ones originate from the depolarization of both acceptor and donor groups of HB. It was also observed that the longer the helical length, the more stable the HB, suggesting the HB cooperativity.

Molecular and structural insight into the differences among common and rare Alzheimer's disease-associated apoE variants.

Alzheimer's Disease (AD) is the leading cause of dementia worldwide with multiple risk modifying factors identified through GWAS including common apoE variants (apoE2, apoE3, apoE4). Additionally, rare apoE variants including apoE3-R136S (Christchurch), apoE3-V236E (Jacksonville), and apoE4-R251G may alter AD risk. ApoE interacts with AD-associated proteins TREM2 and amyloid-beta (Aβ), holding interactions at the hinge and LDL receptor binding domain (LDLRBD) for TREM2 and the N-terminal helices and lipid binding domain (LBD) for Aβ. The structure, conformation, and dynamics differences among these apoE variants that may alter apoE interactions with TREM2 and Aβ are unknown. In this study, we investigated how these apoE isoforms differ in secondary structure, conformation, and dynamics using molecular dynamics (MD) simulations. The apoE variants’ structures were obtained by mutating the known NMR structure of lipid-free apoE3 (PDBID: 2L7B). We performed 500 ns MD simulations for the six apoE variants with the last 250 ns of equilibrated trajectories used for analysis. The apoE variants differed primarily in the conformational stability of the N-terminal, hinge, and LBD regions. Further, apoE variants differed in secondary structure, and specifically in the length, occupancy, and type of helices that make up the N-terminal, hinge, and LBD regions. Our dynamic cross-correlated motion analysis revealed variations in the correlated motions between the hinge, LDLRBD, and LBD regions of apoE variants. The conformational stability, secondary structure, and dynamic motion differences among the apoE variants provide important insight into how these common and rare apoE variants may alter interactions with TREM2, Aβ, and other AD-associated proteins to affect the risk of developing AD. Acknowledgements: This work was supported by the NIH 1R01AG068395-01A1, NIH 5T32EB023872-04, and Alzheimer's Drug Discovery Foundation.

HACS: Helical Auxetic Yarn Capacitive Strain Sensors with Sensitivity Beyond the Theoretical Limit.

The development of flexible strain sensors over the past decade has focused on accessing high strain percentages and high sensitivity (i.e., gauge factors). Strain sensors that employ capacitance as the electrical signal to correlate to strain are typically restricted in sensitivity because of the Poisson effect. By employing auxetic structures, the limits of sensitivity for capacitive sensors have been exceeded, which has improved the competitiveness of this modality of sensing. In this work, the first employment of helical auxetic yarns as capacitive sensors is presented. It is found that the response of the helical auxetic yarn capacitive sensors (termed as HACS) is dependent on the two main fabrication variables-the ratio of diameters and the helical wrapping length. Depending on these variables, sensors that respond to strain with increasing or decreasing capacitance values can be obtained. A greater auxetic character results in larger sensitivities accessible at smaller strains-a characteristic that is not commonly found when accessing high gauge factors. In addition, the highest sensitivity for auxetic capacitive sensors reported thus far is obtained. A mechanism of sensor response that explains both the variable capacitance response and the high gauge factors obtained experimentally is proposed.

Effect of heat-moisture treatment (HMT) on thermal stability of starch gel and the surface adhesiveness of vermicelli

The molecular structure has an important influence on the surface adhesion of starch gel. In the present study, the surface adhesiveness of vermicelli after cooking was reduced by heat-moisture treatment (HMT), and the mechanism underlying the increased thermal stability was explored by measuring the changes in short-range order, crystallinity, the thickness of the crystalline layer, and the length of the double helix in the dry starch gel. The surface adhesiveness decreased by 72.12 % when the moisture content was 26 %. HMT increased the crystallinity, and the thickness of the crystalline layer of the starch gel increased from 14.61 nm to 14.83–17.30 nm at 20–26 % moisture content. The molecular rearrangement and destruction of unstable short double helixes increased the proportion of long double helixes, resulting in an increased crystallinity and layer thickness.