Orientation Of Helices Research Articles

Left Ventricular Twist and the "Rigid Body Rotation" Pattern in Patients Treated with Anthracyclines or Anti-HER2.

Background: During the physiological cardiac cycle, the helix orientation of the muscle fibres induces the rotation of the apex relative to the base of the left ventricular (LV). In heart failure, LV torsion is impaired, and rotation at basal and apical levels occurs in the same direction, a phenomenon called rigid body rotation (RBR). We aimed to evaluate whether the RBR pattern and GLS together could improve the diagnosis of cardiotoxicity in patients treated with anthracyclines and/or anti-HER2. Methods: With an observational, retrospective study involving 175 patients (mean age 55 ± 12 years, 94% females), we evaluated the development of cancer therapeutic-related cardiac dysfunction (CTRCD) defined according to ESC guidelines. We characterised LV dysfunction by echocardiographic standard and speckle-tracking (GLS and RBR pattern) measurements. Patients with a previous diagnosis of structural heart disease or atrial fibrillation were excluded. Results: At the time of enrolment, the chemotherapy regimen included trastuzumab (96%), pertuzumab (21%), and anthracyclines (13%). Twenty-two patients (12.5%) developed cardiotoxicity, and thirteen patients developed an RBR within 6 months of follow-up. In all cases, the RBR pattern was associated with cardiotoxicity (p < 0.001), reporting an optimal specificity but poor sensitivity at three and six months. However, the addition of the RBR pattern to the global longitudinal strain (GLS) ≥ -16% increased the odds ratio (OR) from 25.6 to 32.6 at three months and from 32.5 to 49.6 at six months rather than GLS alone. Conclusions: The RBR pattern improves the diagnostic accuracy of GLS for the detection of cardiotoxicity secondary to anthracyclines and anti-HER2-based treatments.

Domain Swapping in Abiotic Foldamers.

Foldamer sequences that adopt tertiary helix-turn-helix folds mediated by helix-helix hydrogen bonding in organic solvents have been previously reported. In an attempt to create genuine abiotic quaternary structures, i.e. assemblies of tertiary structures, new sequences were prepared that possess additional hydrogen bond donors at positions that may promote an association between the tertiary folds. However, a solid state structure and extensive solution state investigations by Nuclear Magnetic Resonance (NMR) and Circular Dichroism (CD) show that, instead of forming a quaternary structure, the tertiary folds assemble into stable domain-swapped dimer motifs. Domain swapping entails a complete reorganization of the arrays of hydrogen bonds and changes in relative helix orientation and handedness that can all be rationalized.

Domain Swapping in Abiotic Foldamers

AbstractFoldamer sequences that adopt tertiary helix‐turn‐helix folds mediated by helix‐helix hydrogen bonding in organic solvents have been previously reported. In an attempt to create genuine abiotic quaternary structures, i.e. assemblies of tertiary structures, new sequences were prepared that possess additional hydrogen bond donors at positions that may promote an association between the tertiary folds. However, a solid state structure and extensive solution state investigations by Nuclear Magnetic Resonance (NMR) and Circular Dichroism (CD) show that, instead of forming a quaternary structure, the tertiary folds assemble into stable domain‐swapped dimer motifs. Domain swapping entails a complete reorganization of the arrays of hydrogen bonds and changes in relative helix orientation and handedness that can all be rationalized.

Insights on the G protein-coupled receptor helix 8 solution structure and orientation using a neurotensin receptor 1 peptide.

G-protein coupled receptors (GPCRs) are the largest class of membrane proteins encoded in the human genome with high pharmaceutical relevance and implications to human health. These receptors share a prevalent architecture of seven transmembrane helices followed by an intracellular, amphipathic helix 8 (H8) and a disordered C-terminal tail (Ctail). Technological advancements have led to over 1000 receptor structures in the last two decades, yet frequently H8 and the Ctail are conformationally heterogeneous or altogether absent. Here we synthesize a peptide comprising the neurotensin receptor 1 (NTS1) H8 and Ctail (H8-Ctail) to investigate its structural stability, conformational dynamics, and orientation in the presence of detergent and phospholipid micelles, which mimic the membrane. Circular dichroism (CD) and nuclear magnetic resonance (NMR) measurements confirm that zwitterionic 1,2-diheptanoyl-sn-glycero-3-phosphocholine is a potent stabilizer of H8 structure, whereas the commonly-used branched detergent lauryl maltose neopentyl glycol (LMNG) is unable to completely stabilize the helix - even at amounts four orders of magnitude greater than its critical micellar concentration. We then used NMR spectroscopy to assign the backbone chemical shifts. A series of temperature and lipid titrations were used to define the H8 boundaries as F376-R392 from chemical shift perturbations, changes in resonance intensity, and chemical-shift-derived phi/psi angles. Finally, the H8 azimuthal and tilt angles, defining the helix orientation relative of the membrane normal were measured using paramagnetic relaxation enhancement NMR. Taken together, our studies reveal the H8-Ctail region is sensitive to membrane physicochemical properties and is capable of more adaptive behavior than previously suggested by static structural techniques.

NMR Structure of Retinal Guanylate Cyclase Activating Protein 5 (GCAP5) with R22A Mutation That Abolishes Dimerization and Enhances Cyclase Activation.

Guanylate cyclase activating protein-5 (GCAP5) in zebrafish photoreceptors promotes the activation of membrane receptor retinal guanylate cyclase (GC-E). Previously, we showed the R22A mutation in GCAP5 (GCAP5R22A) abolishes dimerization of GCAP5 and activates GC-E by more than 3-fold compared to that of wild-type GCAP5 (GCAP5WT). Here, we present ITC, NMR, and functional analysis of GCAP5R22A to understand how R22A causes a decreased dimerization affinity and increased cyclase activation. ITC experiments reveal GCAP5R22A binds a total of 3 Ca2+, including two sites in the nanomolar range followed by a single micromolar site. The two nanomolar sites in GCAP5WT were not detected by ITC, suggesting that R22A may affect the binding of Ca2+ to these sites. The NMR-derived structure of GCAP5R22A is overall similar to that of GCAP5WT (RMSD = 2.3 Å), except for local differences near R22A (Q19, W20, Y21, and K23) and an altered orientation of the C-terminal helix near the N-terminal myristate. GCAP5R22A lacks an intermolecular salt bridge between R22 and D71 that may explain the weakened dimerization. We present a structural model of GCAP5 bound to GC-E in which the R22 side-chain contacts exposed hydrophobic residues in GC-E. Cyclase assays suggest that GC-E binds to GCAP5R22A with ∼25% higher affinity compared to GCAP5WT, consistent with more favorable hydrophobic contact by R22A that may help explain the increased cyclase activation.

Computational Insights into the Conformational Dynamics of HIV-1 Vpr in a Lipid Bilayer for Ion Channel Modeling.

HIV-1 Vpr is a multifunctional accessory protein consisting of 96 amino acids that play a critical role in viral pathogenesis. Among its diverse range of activities, Vpr can create a cation-selective ion channel within the plasma membrane. However, the oligomeric state of this channel has not yet been elucidated. In this study, we investigated the conformational dynamics of Vpr helices to model the ion channel topology. First, we employed a series of multiscale simulations to investigate the specific structure of monomeric Vpr in a membrane model. During the lipid bilayer self-assembly coarse grain simulation, the C-terminal helix (residues 56-77) effectively formed the transmembrane region, while the N-terminal helix exhibited an amphipathic nature by associating horizontally with a single leaflet. All-atom molecular dynamics (MD) simulations of full-length Vpr inside a phospholipid bilayer show that the C-terminal helix remains very stable inside the bilayer core in a vertical orientation. Subsequently, using the predicted C-terminal helix orientation and conformation, various oligomeric states (ranging from tetramer to heptamer) possibly forming the Vpr ion channel were built and further evaluated. Among these models, the pentameric form exhibited consistent stability in MD simulations and displayed a compatible conformation for a water-assisted ion transport mechanism. This study provides structural insights into the ion channel activity of the Vpr protein and the foundation for developing therapeutics against HIV-1 Vpr-related conditions.

Attractant and repellent induce opposing changes in the four-helix bundle ligand-binding domain of a bacterial chemoreceptor.

Motile bacteria navigate toward favorable conditions and away from unfavorable environments using chemotaxis. Mechanisms of sensing attractants are well understood; however, molecular aspects of how bacteria sense repellents have not been established. Here, we identified malate as a repellent recognized by the MCP2201 chemoreceptor in a bacterium Comamonas testosteroni and showed that it binds to the same site as an attractant citrate. Binding determinants for a repellent and an attractant had only minor differences, and a single amino acid substitution in the binding site inverted the response to malate from a repellent to an attractant. We found that malate and citrate affect the oligomerization state of the ligand-binding domain in opposing way. We also observed opposing effects of repellent and attractant binding on the orientation of an alpha helix connecting the sensory domain to the transmembrane helix. We propose a model to illustrate how positive and negative signals might be generated.

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.

Chiral Supramolecular Assemblies: Controllable Construction and Biological Activity.

Chiral supramolecular assemblies with helical structures (e. g., proteins with α-helix, DNA with double helix, collagen with triple-helix) as the central structure motifs in biological systems play a crucial role in various physiological activities of living organisms. Variations in chiral structure can cause many abnormal physiological activities. To gain insight into the construction, structural transition, and related physiological functions of these complex helix in natural systems, it is necessary to fabricate artificial supramolecular assemblies with controllable helix orientation as research platform. This review discusses recent advances in chiral supramolecular assembly, including the precise construction and regulation of assembled chiral nanostructures with tunable chirality. Chiral structure-dependent biological activities, including cell proliferation, cell differentiation, antibacterial activity and tissue regeneration, are also discussed. This review not only contributes to further understanding of the importance of chirality in the physiological environment, but also plays an important role in the development of chiral biomedical materials for the treatment of diseases (e. g., tissue engineering regeneration, stem cell transplantation therapy).

Synthesis and Crystallographic Characterization of Helical Hairpin Oligourea Foldamers.

Oligomers designed to form a helix-turn-helix super-secondary structure have been prepared by covalently bridging aliphatic oligourea foldamer helices with either rigid aromatic or more flexible aliphatic spacers. The relative helix orientation in these dimers has been investigated at high resolution using X-ray diffraction analysis. In several cases, racemic crystallography was used to facilitate crystallization and structure determination. All structures were solved by direct methods. Well-defined parallel helical hairpin motifs were observed in all cases when 4,4'-methylene diphenyl diisocyanate was employed as a dimerizing agent, irrespective of primary sequence and chain length.

Multiresponsive Cylindrically Symmetric Cholesteric Liquid Crystal Elastomer Fibers Templated by Tubular Confinement.

Cylindrically symmetric cholesteric liquid crystal elastomer (CLCE) fibers templated by tubular confinement are reported, displaying mechanochromic, thermochromic, and thermomechanical responses. The synthesis inside a sacrificial tube secures radial orientation of the cholesteric helix, and the ground state retroreflection wavelength is easily tuned throughout the visible spectrum or into the near-infrared by varying the concentration of a chiral dopant. The fibers display continuous, repeatable, and quantitatively predictable mechanochromic response, reaching a blue shift of more than -220 nm for 180% elongation. The cylindrical symmetry renders the response identical in all directions perpendicular to the fiber axis, making them exceptionally useful for monitoring complex strains, as demonstrated in revealing local strain during tying of different knots. The CLCE reflection color can be revealed with high contrast against any background by taking advantage of the circularly polarized reflection. Upon heating, the fibers respond-fully reversibly-with red shift and radial expansion/axial contraction. However, there is no transition to an isotropic state, confirming a largely forgotten theoretical prediction by de Gennes. These fibers and the easy way of making them may open new windows for large-scale application in advanced wearable technology andbeyond.

Tilted State Population of Antimicrobial Peptide PGLa Is Coupled to the Transmembrane Potential.

Cationic antimicrobial peptide PGLa gets into close contact with the anionic bacterial cell membrane, facilitating cross-membrane transport phenomena and membrane disruption depending on the concentration. The mechanisms of action are closely associated with the tilted insertion geometry of PGLa. Therefore, we aimed to understand the interaction between the transmembrane potential (TMP) and the orientation of the membrane-bound PGLa helix. Molecular dynamics simulations were performed with TMP, and we found that the PGLa tilt angle relative to the membrane is coupled with the TMP. Elevated TMP increases the population of the tilted state. We observed positive feedback between the tilt angle and the TMP, which occurs due to the electrostatic interaction between the peptidic helix and the Na+ cations at the membrane–water interface. These TMP coupled phenomena can contribute to understanding the direct antimicrobial and adjuvant effects of PGLa in combination with regular antibiotics.

New Method for a SEM-Based Characterization of Helical-Fiber Nonwovens.

The lack of tools particularly designed for the quantification of the fiber morphology in nonwovens, especially the multi-level structured fibers, is the main reason for the limited research studies on the establishment of realistic nonwoven structure. In this study, two polymers, cellulose acetate (CA) and thermoplastic polyurethane (TPU), which have different molecular flexibility, were chosen to produce nonwovens with helical nanofibers. Focusing on the nonwovens with helical fibers, a soft package was developed to characterize fiber morphologies, including fiber orientation, helix diameter, and curvature of helix. The novelty of this study is the proposal of a method for the characterization of nanofibrous nonwovens with special fiber shape (helical fibers) which can be used for curve fibers. The characterization results for the helical-fiber nonwoven sample and the nonwoven sample with straight fibers were compared and analyzed.

Spin-Decoupled Transflective Spatial Light Modulations Enabled by a Piecewise-Twisted Anisotropic Monolayer.

Wavefront control lies at the heart of modern optics. Metasurfaces with specifically tailored resonators can encode different phases to two orthogonal polarization components, but suffer from wavelength‐dependent efficiency, sophisticated fabrication, and limited size. Liquid crystals, another excellent candidate for planar optics, are restricted to spin‐coupled conjugated phase modulations. Planar optics with spin‐decoupled functions is expected to release the multifunctionality of modern optics. Here, a spin‐decoupled transflective spatial light modulator is presented with a piecewise‐twisted anisotropic monolayer. The phases of reflected and transmitted light can be independently customized by preprogramming the initial orientations of the periodic helix and mirror‐symmetric dual‐twist configuration, respectively. A transflective orbital angular momentum encoder and decoder is demonstrated, which is simultaneously compatible with different multiplexing techniques. This work releases the multifunctionality of advanced planar optics and may upgrade existing devices in optical informatics.

αα-hub coregulator structure and flexibility determine transcription factor binding and selection in regulatory interactomes

Formation of transcription factor (TF)–coregulator complexes is a key step in transcriptional regulation, with coregulators having essential functions as hub nodes in molecular networks. How specificity and selectivity are maintained in these nodes remain open questions. In this work, we addressed specificity in transcriptional networks using complexes formed between TFs and αα-hubs, which are defined by a common αα-hairpin secondary structure motif, as a model. Using NMR spectroscopy and binding thermodynamics, we analyzed the structure, dynamics, stability, and ligand-binding properties of the Arabidopsis thaliana RST domains from TAF4 and known binding partner RCD1, and the TAFH domain from human TAF4, allowing comparison across species, functions, and architectural contexts. While these αα-hubs shared the αα-hairpin motif, they differed in length and orientation of accessory helices as well as in their thermodynamic profiles of ligand binding. Whereas biologically relevant RCD1–ligand pairs displayed high affinity driven by enthalpy, TAF4–ligand interactions were entropy driven and exhibited less binding-induced structuring. We in addition identified a thermal unfolding state with a structured core for all three domains, although the temperature sensitivity differed. Thermal stability studies suggested that initial unfolding of the RCD1–RST domain localized around helix 1, lending this region structural malleability, while effects in TAF4–RST were more stochastic, suggesting variability in structural adaptability upon binding. Collectively, our results support a model in which hub structure, flexibility, and binding thermodynamics contribute to αα-hub–TF binding specificity, a finding of general relevance to the understanding of coregulator–ligand interactions and interactome sizes.

Phenomenological theory of the magnetic 90∘ helical state

We explore a phenomenological phase diagram for the magnetic helical state with ${90}^{\ensuremath{\circ}}$ turn angle between neighboring spins in the external magnetic field. Such a state is formed by the Eu spin layers in the superconducting iron arsenide ${\mathrm{RbEuFe}}_{4}{\mathrm{As}}_{4}$. The peculiarity of this spin configuration is that it is not realized in the standard Heisenberg model with bilinear exchange interactions. A minimum model allowing for such a state requires the biquadratic nearest-neighbor interaction term. In addition, in tetragonal materials, the ${90}^{\ensuremath{\circ}}$ helix state may be stabilized by the in-plane fourfold anisotropy term, which also fixes helix orientation with respect to the crystal lattice. Such a system has a very rich behavior in the external magnetic field. The magnetic field induces the metamagnetic transition to the double-periodic state with the moment angles ($\ensuremath{\alpha}$, $\ensuremath{\alpha}$, $\ensuremath{-}\ensuremath{\alpha}$, $\ensuremath{-}\ensuremath{\alpha}$) with respect to the field for the four subsequent spins. The transition field to this state from the deformed helix is determined by the strength of biquadratic interaction. The transition is second-order for small biquadratic coupling and becomes first-order when this coupling exceeds the critical value. On the other hand, the aligned state at high magnetic field becomes unstable with respect to the formation of an incommensurate fan state, which transforms into the double-periodic state with decreasing magnetic field. The range of this incommensurate state near the saturation field is proportional to square of the biquadratic coupling. In addition, when the magnetic field is applied along one of four the equilibrium moment directions, the deformed helix state experience the first-order rotation transition at the field determined by the fourfold anisotropy.

Homeotropic Concentric Helix Orientations in Chiral Nematic Cellulose Nanocrystal Films by Local Magnetic Fields

AbstractMany fascinating device applications of chiral nematic materials are determined by their helical axis orientations. Cellulose nanocrystals (CNCs) self‐assemble producing left‐handed chiral nematic films with predominant planar textures. While varied techniques have been exploited to tune the helical axis orientations, it remains challenging to produce concentrically aligned chiral nematic state. Herein, the authors report novel findings that left‐handed chiral nematic CNC films formed with homeotropic concentric helix orientations in the planar textures can be realized by local radial magnetic field‐directed self‐assembly of CNCs. These chiral nematic CNC films display left‐handed circular polarization patterns and transform spontaneous luminescence to right‐handed circularly polarized luminescence on both film plane and lateral surfaces owing to the underlying photonic bandgaps. These plane‐lateral chiroptical properties can be tuned simultaneously from the visible to the near‐infrared spectral regime. Their work presents a step towards the development of self‐organized chiroptical materials encoded with complex polarization features for photonic applications.

Dissymmetric Chiral Poly(diphenylacetylene)s: Secondary Structure Elucidation and Dynamic Luminescence

AbstractThe secondary structure of a dissymmetric and chiral poly(diphenylacetylene) (PDPA) is elucidated by combining the data from NMR experiments (regioregular head to tail structure), Raman and IR studies (E configuration of the polyene double bonds), and high‐resolution AFM images (helical pitch, packing angle and orientation of the external helix). As a result, an E‐transoidal polyene backbone describing three coaxial helices is obtained. Theoretical electronic circular dichroism (ECD) studies of the structure show a good correspondence between experimental and theoretical data and allow one to decipher that the first Cotton band is generated by the poly(diphenylacetylene) core and not only by the polyene backbone. The dynamic behavior of poly‐(S)‐2 is also demonstrated by a helix inversion effect produced by conformational changes at the pendant groups when annealed in solvents with different donor abilities. This phenomenon is accompanied by an inversion of the circular polarized luminescence of the PDPA (CPL switch).

Dissymmetric Chiral Poly(diphenylacetylene)s: Secondary Structure Elucidation and Dynamic Luminescence.

The secondary structure of a dissymmetric and chiral poly(diphenylacetylene) (PDPA) is elucidated by combining the data from NMR experiments (regioregular head to tail structure), Raman and IR studies (E configuration of the polyene double bonds), and high-resolution AFM images (helical pitch, packing angle and orientation of the external helix). As a result, an E-transoidal polyene backbone describing three coaxial helices is obtained. Theoretical electronic circular dichroism (ECD) studies of the structure show a good correspondence between experimental and theoretical data and allow one to decipher that the first Cotton band is generated by the poly(diphenylacetylene) core and not only by the polyene backbone. The dynamic behavior of poly-(S)-2 is also demonstrated by a helix inversion effect produced by conformational changes at the pendant groups when annealed in solvents with different donor abilities. This phenomenon is accompanied by an inversion of the circular polarized luminescence of the PDPA (CPL switch).

Mapping the helix arrangement of the reconstituted ETR1 ethylene receptor transmembrane domain by EPR spectroscopy.

The plant ethylene receptor ETR1 is a key player in the perception of the phytohormone and subsequent downstream ethylene signal transmission, crucial for processes such as ripening, senescence and abscission. However, to date, there is sparse structural knowledge about the transmembrane sensor domain (TMD) of ETR1 that is responsible for the binding of the plant hormone and initiates the downstream signal transmission. Sequence information and ab initio modelling suggest that the TMD consists of three transmembrane helices. Here, we combined site-directed spin labelling with electron paramagnetic resonance spectroscopy and obtained distance restraints for liposome-reconstituted ETR1_TMD on the orientation and arrangement of the transmembrane helices. We used these data to scrutinize different computational structure predictions of the TMD.