Helical Elements Research Articles

The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH.

We present the nuclear magnetic resonance spectroscopy (NMR) solution structure of the 5'-terminal stem loop 5_SL1 (SL1) of the SARS-CoV-2 genome. SL1 contains two A-form helical elements and two regions with non-canonical structure, namely an apical pyrimidine-rich loop and an asymmetric internal loop with one and two nucleotides at the 5'- and 3'-terminal part of the sequence, respectively. The conformational ensemble representing the averaged solution structure of SL1 was validated using NMR residual dipolar coupling (RDC) and small-angle X-ray scattering (SAXS) data. We show that the internal loop is the major binding site for fragments of low molecular weight. This internal loop of SL1 can be stabilized by an A12-C28 interaction that promotes the transient formation of an A+•C base pair. As a consequence, the pKa of the internal loop adenosine A12 is shifted to 5.8, compared to a pKa of 3.63 of free adenosine. Furthermore, applying a recently developed pH-differential mutational profiling (PD-MaP) approach, we not only recapitulated our NMR findings of SL1 but also unveiled multiple sites potentially sensitive to pH across the 5'-UTR of SARS-CoV-2.

Hydrophobic core evolution of major histocompatibility complex class I chain-related protein A for dramatic enhancing binding affinity

Interface residues at sites of protein–protein interaction (PPI) are the focus for affinity optimisation. However, protein hydrophobic cores (HCs) play critical roles and shape the protein surface. We hypothesise that manipulating protein HCs can enhance PPI interaction affinities. A cell stress molecule, major histocompatibility complex class I chain-related protein A (MICA), binds to the natural killer group 2D (NKG2D) homodimer to form three molecule interactions. MICA was used as a study subject to support our hypothesis. We redesigned MICA HCs by directed mutagenesis and isolated high-affinity variants through a newly designed partial-denature panning (PDP) method. A few mutations in MICA HCs increased the NKG2D–MICA interaction affinity by 325–5613-fold. Crystal structures of the NKG2D–MICA variant complexes indicated that mutagenesis of MICA HCs stabilised helical elements for decreasing intermolecular interactive free energy (ΔG) of the NKG2D–MICA heterotrimer. The repacking of MICA HC mutants maintained overall surface residues and the authentic binding specificity of MICA. In conclusion, this study provides a new method for MICA redesign and affinity optimisation through HC manipulation without mutating PPI interface residues. Our study introduces a novel approach to protein manipulation, potentially expanding the toolkit for protein affinity optimisation.

Directed Instability as a Mechanism for Fabricating Multistable Twisting Microstructure

Herein, The study of multistable structures, particularly those that can twist, has attracted significant attention in recent years. This ability to transition between multiple stable geometries of these structures paves the way for advances in diverse applications, such as morphing structures and robot actuation mechanisms. Conventional methods of designing and fabricating these structures often involve complex and resource‐intensive fabrication processes, which restrict their widespread adoption and limit their miniaturization. Here, we present a novel inflatable multistable twisting structure, based on helical folds of an elastic tube. Our fabrication approach utilizes directed mechanical instability as a method for a rapid fabrication, which is readily implemented at various length scales. We developed a theoretical model for the deformation of the bistable helical elements comprising the twisting structure, and compared the theoretical results to the experimental data. Furthermore, we demonstrate our fabrication methodology using a variety of polymers, including medical grade polymers, as well as various inner radii ranging from 5 mm to 44 μm and thicknesses of the tubes’ walls ranging from 250 μm to 19 μm.

Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes.

Betacoronaviruses are a genus within the Coronaviridae family of RNA viruses. They are capable of infecting vertebrates and causing epidemics as well as global pandemics in humans. Mitigating the threat posed by Betacoronaviruses requires an understanding of their molecular diversity. The development of novel antivirals hinges on understanding the key regulatory elements within the viral RNA genomes, in particular the 5'-proximal region, which is pivotal for viral protein synthesis. Using a combination of cryo-electron microscopy, atomic force microscopy, chemical probing, and computational modeling, we determined the structures of 5'-proximal regions in RNA genomes of Betacoronaviruses from four subgenera: OC43-CoV, SARS-CoV-2, MERS-CoV, and Rousettus bat-CoV. We obtained cryo-electron microscopy maps and determined atomic-resolution models for the stem-loop-5 (SL5) region at the translation start site and found that despite low sequence similarity and variable length of the helical elements it exhibits a remarkable structural conservation. Atomic force microscopy imaging revealed a common domain organization and a dynamic arrangement of structural elements connected with flexible linkers across all four Betacoronavirus subgenera. Together, these results reveal common features of a critical regulatory region shared between different Betacoronavirus RNA genomes, which may allow targeting of these RNAs by broad-spectrum antiviral therapeutics.

On the origin of optical rotation changes during the κ-carrageenan disorder-to-order transition

It is well established that solutions of both polymeric and oligomeric κ-carrageenan exhibit a clear change in optical rotation (OR), in concert with gel-formation for polymeric samples, as the solution is cooled in the presence of certain ions. The canonical interpretation – that this OR change reflects a ‘coil-to-helix transition’ in single chains – has seemed unambiguous; the solution- or ‘disordered’-state structure has ubiquitously been assumed to be a ‘random coil’, and the helical nature of carrageenan in the solid-state was settled in the 1970s. However, recent work has found that κ-carrageenan contains substantial helical secondary structure elements in the disordered-state, raising doubts over the validity of this interpretation. To investigate the origins of the OR, density-functional theory calculations were conducted using atomic models of κ-carrageenan oligomers. Changes were found to occur in the predicted OR owing purely to dimerization of chains, and - together with the additional effects of slight changes in conformation that occur when separated helical chains form double-helices - the predicted OR changes are qualitatively consistent with experimental results. These findings contribute to a growing body of evidence that the carrageenan ‘disorder-to-order’ transition is a cooperative process, and have further implications for the interpretation of OR changes demonstrated by macromolecules in general.

Leucine Motifs Stabilize Residual Helical Structure in Disordered Proteins

Many examples are known of regions of intrinsically disordered proteins that fold into α-helices upon binding to their targets. These helical binding motifs (HBMs) can be partially helical also in the unbound state, and this so-called residual structure can affect binding affinity and kinetics. To investigate the underlying mechanisms governing the formation of residual helical structure, we assembled a dataset of experimental helix contents of 65 peptides containing HBM that fold-upon-binding. The average residual helicity is 17% and increases to 60% upon target binding. The helix contents of residual and target-bound structures do not correlate, however the relative location of helix elements in both states shows a strong overlap. Compared to the general disordered regions, HBMs are enriched in amino acids with high helix preference and these residues are typically involved in target binding, explaining the overlap in helix positions. In particular, we find that leucine residues and leucine motifs in HBMs are the major contributors to helix stabilization and target-binding. For the two model peptides, we show that substitution of leucine motifs to other hydrophobic residues (valine or isoleucine) leads to reduction of residual helicity, supporting the role of leucine as helix stabilizer. From the three hydrophobic residues only leucine can efficiently stabilize residual helical structure. We suggest that the high occurrence of leucine motifs and a general preference for leucine at binding interfaces in HBMs can be explained by its unique ability to stabilize helical elements.

The critical role of aromatic residues in the binding of the SARS-CoV-2 fusion peptide to phospholipid bilayer membranes.

Based on the SARS-CoV-2 fusion peptide (FP) structure determined from the NMR experiment, we created six FP models under different environmental conditions to explore the effects of salt and cholesterol on FP-membrane binding. The all-atom molecular dynamics (MD) simulation results indicated that ionic environments notably impact the FP structure as well as the stability of the helical elements within the peptide. Our findings highlighted the unpredictable influence of ions on the secondary structures and dynamics of the FP, emphasizing the complexity and sensitivity of the peptide's conformations to ionic conditions. When exploring the peptide's interaction with a cholesterol-free phospholipid bilayer membrane, we found that the helical elements of the FP remain stable irrespective of the salt type (Na+ or Ca2+). This result emphasizes the crucial role of phospholipid bilayer membranes in supporting the secondary structures of the FP. The MD simulation results showed that Ca2+ ions facilitated deeper membrane penetration than Na+ ions, highlighting the critical role of calcium ions in the FP-membrane binding. Our study indicates the essential role of the aromatic residues (such as Phe833 and Tyr837) in the FP-membrane binding process. Finally, we investigated the FP-membrane binding patterns in the presence of cholesterol. The MD simulation results demonstrated that the coupling of Ca2+ ions and cholesterol would also benefit the FP-membrane binding. Furthermore, our findings reveal that while the type of ion and cholesterol content exert varied and unpredictable influences on FP-membrane binding patterns, aromatic residues like tyrosine (Tyr) and phenylalanine (Phe) play an essential role in FP-membrane binding. In particular, deep mutational scanning (DMS) experiments have confirmed that mutating phenylalanine in the FP significantly decreases viral mutational fitness, emphasizing the pivotal role of phenylalanine residues in membrane fusion. This knowledge can aid in developing more effective therapeutic strategies targeting the viral fusion peptide and its key amino acids, ultimately contributing to developing treatments and vaccines against the virus.

Recruitment of trimeric eIF2 by phosphatase non-catalytic subunit PPP1R15B

Regulated protein phosphorylation controls most cellular processes. The protein phosphatase PP1 is the catalytic subunit of many holoenzymes that dephosphorylate serine/threonine residues. How these enzymes recruit their substrates is largely unknown. Here, we integrated diverse approaches to elucidate how the PP1 non-catalytic subunit PPP1R15B (R15B) captures its full trimeric eIF2 substrate. We found that the substrate-recruitment module of R15B is largely disordered with three short helical elements, H1, H2, and H3. H1 and H2 form a clamp that grasps the substrate in a region remote from the phosphorylated residue. A homozygous N423D variant, adjacent to H1, reducing substrate binding and dephosphorylation was discovered in a rare syndrome with microcephaly, developmental delay, and intellectual disability. These findings explain how R15B captures its 125kDa substrate by binding the far end of the complex relative to the phosphosite to present it for dephosphorylation by PP1, a paradigm of broad relevance.

Fluoride-Salt-cooled high-Temperature Advanced Reactor (FuSTAR): An integrated nuclear-based energy production and conversion system

Based on the analysis of energy structure and the development trends of advanced nuclear energy technology, combining the complementary advantages of nuclear energy and other energy sources in China, the Fluoride-Salt-cooled high-Temperature Advanced Reactor (FuSTAR) system has been proposed. FuSTAR system is designed to address production capacity issues in areas with energy shortages or resource concentration and can be combined with high-temperature process heat to achieve high-value-added processes such as hydrogen production. In this paper, the Tri-structural isotropic fuel combined with helical cruciform elements has been studied in detail on the neutron physics and thermal-hydraulic properties, and the flow and heat transfer experiment is carried out for the first time. The multilayer nonlinear programming method has been applied to the design of thermal transport systems. Then the optimal parameters and configuration of the thermoelectric conversion system are obtained by the superstructure optimization method. The inherent safety of FuSTAR is demonstrated through deterministic safety analysis. In addition, the iodine-sulfur cycle technology and the characteristics of tritium production are also analyzed. This study highlights the significant potential of integrating nuclear energy with other energy sources in an optimized energy-production system.

Experience in Gas Dynamic Tests of Model Bundles of Self-Separating Helical Fuel Elements Made Using Additive Technologies

Experience in Gas Dynamic Tests of Model Bundles of Self-Separating Helical Fuel Elements Made Using Additive Technologies

DNAJB6 mutants display toxic gain of function through unregulated interaction with Hsp70 chaperones

Molecular chaperones are essential cellular components that aid in protein folding and preventing the abnormal aggregation of disease-associated proteins. Mutations in one such chaperone, DNAJB6, were identified in patients with LGMDD1, a dominant autosomal disorder characterized by myofibrillar degeneration and accumulations of aggregated protein within myocytes. The molecular mechanisms through which such mutations cause this dysfunction, however, are not well understood. Here we employ a combination of solution NMR and biochemical assays to investigate the structural and functional changes in LGMDD1 mutants of DNAJB6. Surprisingly, we find that DNAJB6 disease mutants show no reduction in their aggregation-prevention activity in vitro, and instead differ structurally from the WT protein, affecting their interaction with Hsp70 chaperones. While WT DNAJB6 contains a helical element regulating its ability to bind and activate Hsp70, in LGMDD1 disease mutants this regulation is disrupted. These variants can thus recruit and hyperactivate Hsp70 chaperones in an unregulated manner, depleting Hsp70 levels in myocytes, and resulting in the disruption of proteostasis. Interfering with DNAJB6-Hsp70 binding, however, reverses the disease phenotype, suggesting future therapeutic avenues for LGMDD1.

Exploring the Bioenergy Potential of Microfluidics: The Case of a T-Micromixer with Helical Elements for Sustainable Energy Solutions

This study explores the potential application of microfluidics in the field of bioenergy, with a particular focus on the energy potential of biogas derived from vine shoots, a locally abundant waste material. The enhanced mixing capability of a micromixer has been analyzed to make it suitable for microfluidic energy applications. Mixing index, pressure drop, and kinematic measurements within the T-micromixer with helical elements and their related mixing performances have been studied and validated using CFD for different values of Reynolds number (0.1–60) for laminar Newtonian miscible fluid. Geometrical characteristics were further examined to improve the mixing performance. Various values of twisted angles were evaluated and compared to choose the optimal angle. A new parameter, Q, was introduced to represent the ratio of vorticity square over the sum of vorticity square and deformation square intensities. Furthermore, the results of the numerical simulation were compared with the given data in the literature, showing a significant agreement, in addition to the fact that a high-quality mixture can be created with a geometry angle of 90°, and a mixing index above 0.99 can be obtained at low Reynolds numbers. The numerical investigation of the flow regimes of miscible fluid in the T-microkenics with the proposed angle can be utilized to develop the mixing performance of the micromixers in a wide variety of processes.

Influence Of Helical Confinement On Crack Development In RCC Beams

Structures made of reinforced concrete are susceptible to developing cracks when they are in the path of earthquakes, strong winds, or increased structural loading. It is therefore possible that it will be necessary to manage structural cracking in the Service Limit State to maximise the lifetime and strength of the structural components under any stress. Helical containment is superior to rectangular containment in terms of its ability to strengthen and ductile the Reinforced Concrete (RC) structural member. In the current work, six distinct beams were each subjected to a series of tests to see how they behaved in terms of cracking when subjected to bending loads. Each of these tests used a unique helical pitch space distance. The beams all measured 150 mm by 150 mm and 750 mm in length. They were designed in accordance with the criteria of Euro code 2, with the identical dimensions. Both 50 and 100 mm were used to take the measurement for the helical pitch. The findings indicate that the utilisation of helical elements does influence the cracking behaviour of the beams. The most important finding was that the measurement of the crack’s thickness was slightly reduced when the beams were restricted to a helical zone with a closer spacing between them. The fact that the theoretical crack is longer than the actual crack that was measured experimentally demonstrates that the Euro code 2 standard provides a more accurate forecast as well as a higher factor of safety. This is demonstrated by the fact that the theoretical crack is larger than the actual crack that was measured.

Pathogen-specific structural features of Candida albicans Ras1 activation complex: uncovering new antifungal drug targets.

An important feature associated with Candida albicans pathogenicity is its ability to switch between yeast and hyphal forms, a process in which CaRas1 plays a key role. CaRas1 is activated by the guanine nucleotide exchange factor (GEF) CaCdc25, triggering hyphal growth-related signaling pathways through its conserved GTP-binding (G)-domain. An important function in hyphal growth has also been proposed for the long hypervariable region downstream the G-domain, whose unusual content of polyglutamine stretches and Q/N repeats make CaRas1 unique within Ras proteins. Despite its biological importance, both the structure of CaRas1 and the molecular basis of its activation by CaCdc25 remain unexplored. Here, we show that CaRas1 has an elongated shape and limited conformational flexibility and that its hypervariable region contains helical structural elements, likely forming an intramolecular coiled-coil. Functional assays disclosed that CaRas1-activation by CaCdc25 is highly efficient, with activities up to 2,000-fold higher than reported for human GEFs. The crystal structure of the CaCdc25 catalytic region revealed an active conformation for the α-helical hairpin, critical for CaRas1-activation, unveiling a specific region exclusive to CTG-clade species. Structural studies on CaRas1/CaCdc25 complexes also revealed an interaction surface clearly distinct from that of homologous human complexes. Furthermore, we identified an inhibitory synthetic peptide, prompting the proposal of a key regulatory mechanism for CaCdc25. To our knowledge, this is the first report of specific inhibition of the CaRas1-activation via targeting its GEF. This, together with their unique pathogen-structural features, disclose a set of novel strategies to specifically block this important virulence-related mechanism. IMPORTANCE Candida albicans is the main causative agent of candidiasis, the commonest fungal infection in humans. The eukaryotic nature of C. albicans and the rapid emergence of antifungal resistance raise the challenge of identifying novel drug targets to battle this prevalent and life-threatening disease. CaRas1 and CaCdc25 are key players in the activation of signaling pathways triggering multiple virulence traits, including the yeast-to-hypha interconversion. The structural similarity of the conserved G-domain of CaRas1 to those of human homologs and the lack of structural information on CaCdc25 has impeded progress in targeting these proteins. The unique structural and functional features for CaRas1 and CaCdc25 presented here, together with the identification of a synthetic peptide capable of specifically inhibiting the GEF activity of CaCdc25, open new possibilities to uncover new antifungal drug targets against C. albicans virulence.

Development of a mathematical model of a chiral metamaterial based on a cylindrical helical elements accounting for the dispersion and concentration of elements

Background. Interest in the study of microwave metamaterials is associated with the possibility of using them to achieve the required frequency and polarization selective properties of interaction with electromagnetic radiation, which can’t be obtained for structures based on homogeneous media. Aim. The mathematical model of a chiral metamaterial based on a periodic matrix of arbitrarily oriented conducting thin-wire cylindrical helices located in a homogeneous isotropic container creation is considered. Unlike known models, it takes into account the explicit form of the dependence of the effective permittivity and the relative chirality parameter on the helices concentration. Methods. The heterogeneity of a chiral metamaterial based on the Maxwell Garnett formula, which makes it possible to determine the effective dielectric permittivity from the permeabilities of the container and the region occupied by conducting mirror asymmetric inclusions is taken into account when creating a mathematical model. The dispersion of permittivity using the quadratic Lorentz formula and the dispersion of the chirality parameter based on the Condon model are taken into account. Results. Analytical frequency-dependent expressions for the effective permittivity and the chirality parameter taking into account the concentration of helices and their geometric parameters, were obtained in the work. The expression for the relationship between the dimensionless volume concentration of inclusions and the distance between adjacent elements is obtained. The quasi-static approach is used to calculate the resonant frequency of conducting thin-wire cylindrical helices. Conclusion. The proposed method for constructing a mathematical model can be applied to chiral metamaterials based on periodic matrices of conductive elements of an arbitrary mirror asymmetric spatial configuration.

3D analysis of the geometrically nonlinear deformation of beams by the method of basic helical elements

3D analysis of the geometrically nonlinear deformation of beams by the method of basic helical elements

Analysis of heat transfer enhancement due to helical static mixing elements inside cooling channels in machine tools

In this contribution, the effectiveness of helical static mixers in different arrangements and flow configurations/regimes is explored. By means of a thorough numerical analysis, the application limits of helical static mixers for the heat transfer enhancement inside cooling channels of machine tools are provided. The numerical simulations were processed with the commercial finite volume Computational Fluid Dynamics (CFD) code, ANSYS Fluent 2020 R2. This study shows that there exists an optimal range of application for static mixers as heat exchange intensifier depending on the flow speed, the transmitted heat flow and the thermal conductivity of the tool. The investigations of this contribution are restricted to single-phase flow in circular cross-sections and straight channel geometries. As a representative application example for a machine tooling, the cooling of a simple injection mold is investigated. The research carried out reveals that the application of static mixing elements for enhancement of heat transfer is very effective, particularly for fluid flow with low to medium Reynolds numbers, close-contour cooling, high values of heat fluxes, and high thermal conductivity of the tooling material.

Numerical Investigation of Flow Patterns and Mixing Characteristics in a 3D Micromixer with Helical Elements over Wide Reynolds Numbers (Adv. Theory Simul. 5/2023)

Micromixers play a crucial role in the microreactions to offer rapid and homogenous mixing. In article number 2200671, Bo Liu, Jing Jin, Yonggang Zhu, and co-workers innovatively develop a high-performance 3D micromixer with helical elements over an ultra-wide range of Reynolds numbers to achieve efficient mixing, and build a validated coupled model to systematically investigate flow patterns and mixing characteristics of the micromixer.

Numerical Investigation of Flow Patterns and Mixing Characteristics in a 3D Micromixer with Helical Elements over Wide Reynolds Numbers

AbstractMicromixers play an important role in the micro total analysis systems (µTAS) that require rapid and effective mixing. However, current micromixers are usually designed to meet the need for mixing at limited Reynolds numbers. Herein, this paper presents a high‐performance 3D micromixer with helical elements over wide Reynolds numbers to achieve efficient mixing and has numerically investigated flow patterns and mixing characteristics accordingly. A coupled numerical model is built to analyze the flow pattern, mixing behavior, residence time distribution (RTD), and mixing performance of the 3D micromixer. Helical elements inside could greatly enhance a secondary flow and induce chaotic advection around. Dean vortices are observed in the micromixer, enormously shortening the RTD and promoting the related mixing effect. Furthermore, the effects of various geometric parameters are systematically investigated to optimize the performance of this 3D micromixer. The optimized micromixer shows excellent mixing ability over wide Reynolds numbers ranging from 0.01 to 2333.3, with an efficiency of over 94%. In addition, the numerical results are proved well consistent with analytical and experimental data correspondingly. Therefore, this work would potentially expand the use scope of 3D micromixers and provide a constructive strategy to develop essential parts involving the mixing or reacting process in µTAS.

Radial Line Planar Phased Array Using Electromechanically Rotated Helical Antennas

In this paper, we propose a novel radial line planar phased array in which helical antenna elements are individually rotated by their respective connected micromotors to realize dynamic beam-scanning. To our knowledge, this is the first radial line planar array (RLPA) that has antenna elements electromechanically rotated by their individual micromotors. To facilitate its fabrication, helix and its probe are directly metallized on a plastic shaft using molded interconnect device technology, and a motor shaft is press-fitted into the plastic shaft. We also present a new design methodology for RLPA, which combines the equivalent circuit theory and electromagnetic simulations of the unit cell element. The proposed procedure is practical to design an RLPA of antenna elements with arbitrary probe shape without large-scale full-wave analysis of the whole structure of the RLPA. We design, fabricate, and evaluate a 7-circle array with 168 helical antenna elements fabricated using molded interconnect device technology. The prototype antenna exhibits dynamic and accurate beam-scanning performance. Furthermore, the prototype antenna exhibits a low reflection coefficient (less than -17dB) and high antenna efficiency (above 77%), which validates the proposed design methodology.