Single Helix Research Articles

Multiscale structure and precipitation mechanism of debranched starch precipitated by different alcohols

Alcohol solution is a cheap, simple, and effective precipitating solvent frequently used for separating debranched starch (DBS), yet little is known about the precipitation mechanism of DBS by different alcohols. This study precipitated DBS from pullulanase-hydrolyzed starch using ethanol, n-butanol, and isopentanol. The multiscale structures of DBS were characterized, including chain length, single/double helix, and crystalline. The chain conformation and precipitation mechanism of DBS in different alcohols was investigated using molecular dynamics (MD) simulation. DBS precipitated by n-butanol contained the largest proportion of short chain (DP6–24, 83.2 %), the highest V-type crystallinity (21.1 %), and the largest single-helix content (24.7 %). A single helix conformation of DBS chain was determined in alcohols, where alcohol molecules entered the helix cavity. Intra/inter-molecular hydrogen bonds stabilized the helix, with a large number of hydrogen bonds leading to strong molecular interaction and stable helical structure. The solvent accessible surface area of DBS chain decreased by 7.88–19.32 % in alcohols, and the radial distribution function revealed that the first solvent layer of DBS chain at 0.29 nm was closely related to hydrogen bonding. This study provides a basis for the choice of precipitation solvent for preparing DBS with different chain lengths and physicochemical properties.

Rationalizing the Extent of the "Sergeants-and-Soldiers" Effect in Supramolecular Helical Catalysts: Effect of Copper Coordination.

Aggregation of supramolecular helices, for example through interdigitation of their alkyl side chains or through more directional supramolecular interactions, leads to hierarchical architectures with original structural and chiroptical properties. However, when a chiral monomer (the "sergeant") is introduced as a minor component in these assemblies composed of a majority of achiral monomers (the "soldiers"), it is not clear how the aggregation changes the ability of the sergeant to induce a preferential helicity to the polymer main chain (the so-called "sergeants-and-soldiers" effect). This study reports a detailed investigation of the influence of [Cu(OAc)2 ⋅H2 O] coordination on the structure and chiroptical properties of helical hydrogen-bonded co-assemblies composed of a catalytically-active benzene-1,3,5-tricarboxamide (BTA) monomer, acting as the "soldier", and an enantiopure BTA monomer derived from cyclohexylalanine, playing the role of the "sergeant". The copper actually significantly influences the extent of the "sergeants-and-soldiers" effect since it acts as a crosslink that induces some chiral defects in the supramolecular helices. These crosslinks appear to be preserved during the catalytic hydrosilylation of 4-nitroacetophenone. The aggregation of helices through the formation of copper crosslinks is reversible since homochiral single helices are exclusively formed in the case of sergeant-rich assemblies. The fact that both main chain and side chain aggregation affects the chiroptical properties of supramolecular helices must be considered in the design of elaborated chiral materials.

Computer-Aided Design of A-Trail Routed Wireframe DNA Nanostructures with Square Lattice Edges.

In recent years, interest in wireframe DNA origami has increased, with different designs, software, and applications emerging at a fast pace. It is now possible to design a wide variety of shapes by starting with a 2D or 3D mesh and using different scaffold routing strategies. The design choices of the edges in wireframe structures can be important in some applications and have already been shown to influence the interactions between nanostructures and cells. In this work, we increase the alternatives for the design of A-trail routed wireframe DNA structures by using four-helix bundles (4HB). Our approach is based on the incorporation of additional helices to the edges of the wireframe structure to create a 4HB on a square lattice. We first developed the software for the design of these structures, followed by a demonstration of the successful design and folding of a library of structures, and then, finally, we investigated the higher mechanical rigidity of the reinforced structures. In addition, the routing of the scaffold allows us to easily incorporate these reinforced edges together with more flexible, single helix edges, thereby allowing the user to customize the desired stiffness of the structure. We demonstrated the successful folding of this type of hybrid structure and the different stiffnesses of the different parts of the nanostructures using a combination of computational and experimental techniques.

Single Amino Acid Modifications for Controlling the Helicity of Peptide-Based Chiral Gold Nanoparticle Superstructures.

Assembling nanoparticles (NPs) into well-defined superstructures can lead to emergent collective properties that depend on their 3-D structural arrangement. Peptide conjugate molecules designed to both bind to NP surfaces and direct NP assembly have proven useful for constructing NP superstructures, and atomic- and molecular-level alterations to these conjugates have been shown to manifest in observable changes to nanoscale structure and properties. The divalent peptide conjugate, C16-(PEPAu)2 (PEPAu = AYSSGAPPMPPF), directs the formation of one-dimensional helical Au NP superstructures. This study examines how variation of the ninth amino acid residue (M), which is known to be a key Au anchoring residue, affects the structure of the helical assemblies. A series of conjugates of differential Au binding affinities based on variation of the ninth residue were designed, and Replica Exchange with Solute Tempering (REST) Molecular Dynamics simulations of the peptides on an Au(111) surface were performed to determine the approximate surface contact and to assign a binding score for each new peptide. A helical structure transition from double helices to single helices is observed as the peptide binding affinity to the Au(111) surface decreases. Accompanying this distinct structural transition is the emergence of a plasmonic chiroptical signal. REST-MD simulations were also used to predict new peptide conjugate molecules that would preferentially direct the formation of single-helical AuNP superstructures. Significantly, these findings demonstrate how small modifications to peptide precursors can be leveraged to precisely direct inorganic NP structure and assembly at the nano- and microscale, further expanding and enriching the peptide-based molecular toolkit for controlling NP superstructure assembly and properties.

Bacterial cellulose: A highly versatile nanomaterial.

Bacterial cellulose: A highly versatile nanomaterial.

Computer modeling of the hexameric channel of VacA from H. pylori.

Helicobacter pylori (H. pylori) infects over half of the human population in the world and is a main cause of stomach ulcers. As one of the major virulence factors secreted by H. pylori, Vacuolating toxin (VacA) molecules can insert into lipid bilayers and oligomerize to form a hexameric membrane channel. It has been proposed that cell vacuolation results primarily from the formation of such channels. However, structural and functional studies of VacA transmembrane (TM) channel have been hindered by the challenge of resolving the structure of this TM domain experimentally. Here, we report a computational protocol for modeling symmetric TM helical bundles and propose a structural model of the hexameric VacA channel. In our model, van der Waals packing and Cα-H···O hydrogen bonding of small residues Gly14 and Gly18 stabilize the association of adjacent helical pairs, consistent with the frequent occurrence of GxxxG motif observed in TM helix-helix interface. Through performing molecular dynamics (MD) simulations iteratively, we refine and validate our model, demonstrating that the resulting channel is stable and supports continuous pore water flow. Additionally, we simulate the single VacA TM helix, capturing the spontaneous partial insertion of the VacA N-terminal hydrophobic region into a lipid bilayer. Our results provide molecular details of how VacA participates in vacuolating the cell and inducing cell apoptosis. The computational protocol thus established may be employed to model other pore-forming toxins without a known structure.

Characterizing the interactions between the LPS transport protein LptC and the ABC transporter LptB2FG.

Synthesis of the essential glycolipid lipopolysaccharide (LPS) in Gram-negative bacteria is completed at the outer leaflet of the inner membrane (IM). Following this process, seven LPS transport (Lpt) proteins facilitate the movement of LPS to the outer membrane (OM). LPS transport to the OM is an essential process and disruption at any stage has detrimental effects on bacterial viability. LptB2FG, the first component of the Lpt system, is a type IV ABC transporter that provides the driving force for LPS extraction from the IM and subsequent transport across a stable protein bridge to the outer leaflet of the OM. LptC is a periplasmic protein anchored to the IM by a single transmembrane helix, which intercalates between the LptF and LptG transmembrane domains, and has been shown to regulate the ATPase activity of LptB2FG. Despite a high level of structural homology between the periplasmic domains of LptF and LptG, the crystal and cryo-EM structures of LptB2FG in complex with LptC show preferential binding of the periplasmic domain of LptC to the periplasmic domain of LptF. Therefore, the role of LptG in this transport process remains unknown. Additionally, we identified six partial loss of function LptC mutations during an in vivo exploratory mutagenesis study. To further investigate the LptB2FGC complex, site-directed spin labeling electron paramagnetic resonance (EPR) spectroscopy, microscale thermophoresis (MST), and an in vitro ATPase assay were employed to characterize differences between the binding partners of periplasmic LptF and LptG along with the mechanistic effects of the LptC loss of function mutants on partner binding and ATPase function or regulation. This work provides evidence suggesting a previously undefined interaction between LptC and LptG while also exploring the role of partial loss of function LptC mutants.

The relationship between starch structure and digestibility by time-course digestion of amylopectin-only and amylose-only barley starches

The multi-scale structural dynamics of amylopectin-only barley starch (APBS), normal barley starch (NBS), and amylose-only barley starch (AMBS) digested with amylolytic enzymes for 120 min were investigated in this study. For all starches, 0–20 min was identified as a rapid digestion stage, followed by a 20–120 min slow digestion. For APBS and NBS, the content of short chains (DP ≤ 12) and the thickness of crystalline and amorphous nano-lamellae increased, whereas the crystallinity decreased, and pores were generated on the granular surface during the rapid digestion stage. At the following slow digestion stage, the branching degree and relative amount of double helices increased, the crystalline and lamellar structures were lost, and the hydrolyzed starch segments aggregated. For AMBS, the rapid digestion stage was characterized by an increased content of short chains (DP ≤ 8) and B-type crystals and decreased amounts of V-type crystals. Furthermore, the lamellar and granular structures were lost, and digestion residues aggregated during the first stage of AMBS, which were formed in the second digestion stage of APBS and NBS. The second slow digestion stage of AMBS was characterized by an increased branching degree and a decreased relative content of single helices. It is suggested that the aggregated digestion residues at the initial digestion stage are the main reason for the overall low digestibility of AMBS.

Uncovering the Contributions of Charge Regulation to the Stability of Single Alpha Helices.

The single alpha helix (SAH) is a recurring motif in biology. The consensus sequence has a di-block architecture that includes repeats of four consecutive glutamate residues followed by four consecutive lysine residues. Measurements show that the overall helicity of sequences with consensus E4 K4 repeats is insensitive to a wide range of pH values. Here, we use the recently introduced q-canonical ensemble, which allows us to decouple measurements of charge state and conformation, to explain the observed insensitivity of SAH helicity to pH. We couple the outputs from separate measurements of charge and conformation with atomistic simulations to derive residue-specific quantifications of preferences for being in an alpha helix and for the ionizable residues to be charged vs. uncharged. We find a clear preference for accommodating uncharged Glu residues within internal positions of SAH-forming sequences. The stabilities of alpha helical conformations increase with the number of E4 K4 repeats and so do the numbers of accessible charge states that are compatible with forming conformations of high helical content. There is conformational buffering whereby charge state heterogeneity buffers against large-scale conformational changes thus making the overall helicity insensitive to large changes in pH. Further, the results clearly argue against a single, rod-like alpha helical conformation being the only or even dominant conformation in the ensembles of so-called SAH sequences.

Two-ring chirality generated by the alignment of two achiral phenylacetylene macrocycles.

When two achiral rings are bound mechanically, a chiral source is generated in the assembly. The chiroptical properties could be modulated according to the relative occupation of each ring in the assembly. In fact, we have found that two isomeric assemblies (1 and 2) show unique properties in each assembly with two achiral rings of phenylacetylene macrocycle (PAM). When considering the difference in the chiroptical properties of these two isomeric assemblies (6PAM × 2), no comparison was available based on no activity of the achiral component element itself (6PAM). In this work, we synthesized a two-ring chiral analog (4) by the ring-fusion of two 6PAMs to an 11PAM, and examined the chiroptical properties of 4, since the single helix was imparted as a chiral source. By comparison of the chiroptical properties (molar circular dichroism and molar optical rotation) of 1 and 2 to those of 4, we demonstrated that the disparity was related to the alignment of the two achiral rings.

Experimental Investigation of Helical Pile Performance for Loess Deposits Improvement

Collapsible loess is classified as problematic soil found on most continents. The loess immediately collapses under stresses induced by axial compressive loading or the soil weight when exposed to moisture. In Iran, vast areas of the Golestan province are covered with Aeolian loess deposits. This paper investigates whether the simultaneous effect of inundation and pre-loading in helical pile installation is operative and effective in improving Golestan loess. The effect of installation conditions on loess collapsibility is studied via two main approaches, i.e., field investigations and physical modeling. The experimental studies include the installation of ten single and triple helix piles in the Amirkabir University of Technology Frustum Confining Vessel, i.e., FCV-AUT. Also, ten single and double helix piles with embedment depth of 3 to 6 m and a helix diameter of 250 mm were installed in Golestan province, and full-scale pile static loading tests were performed. The results indicated that the simultaneous application of crowd loading and water pressure during the installation of helical piles results in collapsibility potential reduction due to the soil treatment. Moreover, high or low crowd loads accompanied by water pressure during pile installation bring about similar load-displacement behavior of model piles installed in FCV-AUT and full-scale helical piles. Eventually, it was illustrated that the applied improvement technique is effective on loess soils since it uses the least amount of material, machinery, and equipment while attaining the highest possible bearing capacity ratio regarding sustainability.

Characterization of the role of Ume6 C-terminal tail in C. albicans morphological plasticity.

C. albicans is an important human fungal pathogen and filamentation is essential for its virulence. Ume6 is a transcription factor critical for filamentation. Ume6 is composed of three domains, a long N terminal domain, Zn-finger domain, and a C-terminal domain. Previously, it was shown that the Zn-finger domain is essential for filamentation, as removal of this domain led to a lack of filamentation. However, the role for the C-terminal domain has not been defined. We find deletion of the C-terminal domain leads to a filamentation defect and the defect is not as severe as removal of the Zn-finger or ume6 deletion. We mutated a number of residues in the C-terminal domain to try to identify specific residues important for filamentation, but all of our mutants displayed wild type filamentation. Alpha fold predictions suggest the C-terminal domain forms a single alpha helix that is predicted to interact with the Zn-finger domain via hydrogen bond. Our data suggests the C-terminal domain binds the Zn-finger domain and through this interaction is important for filamentation.

The structural integrity of the membrane-embedded bacterial division complex FtsQBL studied with molecular dynamics simulations

The FtsQBL is an essential molecular complex sitting midway through bacterial divisome assembly. To visualize and understand its structure, and the consequences of its membrane anchorage, we produced a model of the E. coli complex using the deep-learning prediction utility, AlphaFold 2. The heterotrimeric model was inserted into a 3-lipid model membrane and subjected to a 500-ns atomistic molecular dynamics simulation. The model is superb in quality and captures most experimentally derived structural features, at both the secondary structure and the side-chain levels. The model consists of a uniquely interlocking module contributed by the C-terminal regions of all three proteins. The functionally important constriction control domain residues of FtsB and FtsL are located at a fixed vertical position of ∼43–49 Å from the membrane surface. While the periplasmic domains of all three proteins are well-defined and rigid, the single transmembrane helices of each are flexible and their collective twisting and bending contribute to most structural variations, according to principal component analysis. Considering FtsQ only, the protein is more flexible in its free state relative to its complexed state—with the biggest structural changes located at the elbow between the transmembrane helix and the α-domain. The disordered N-terminal domains of FtsQ and FtsL associate with the cytoplasmic surface of the inner membrane instead of freely venturing into the solvent. Contact network analysis highlighted the formation of the interlocking trimeric module in FtsQBL as playing a central role in mediating the overall structure of the complex.

Assessment of order of helical structures of retrograded starch by Raman spectroscopy

In this study, the long- and short-range order of retrograded starch was evaluated using Fourier-transform infrared spectroscopy (FTIR), wide-angle X-ray diffraction (XRD), and Raman spectroscopy. FTIR and XRD could not assess the degree of order of various helical structures. Raman spectroscopy was used to establish a method for evaluating the order of the helical structures of the retrograded starch. The characteristic peaks of the Raman bands around 865, 1343, and 2908 cm −1 were related to the amylose double helix, amylose single helix, and amylopectin double helix, respectively. The full width at half maximum (FWHM) of the characteristic peaks was used to assess the order of the helical structure. During retrogradation, the order of all helical structures increased, which was greater for the amylose double helix than that of other helical structures in the early stage of storage. The crystallization rate of the amylose double helix was also higher than that of other helical structures. • A method for assessing the order of helical structures was established. • The order of all helical structures increased during starch retrogradation. • Crystallization rate of various helical structures were obtained.

Controlling aromatic helix dimerization in water by tuning charge repulsions.

Several helically folded aromatic oligoamides were designed and synthesized. The sequences were all water-soluble thanks to the charged side chains borne by the monomers. Replacing a few, sometimes only two, charged side chains by neutral methoxy groups was shown to trigger the formation of various aggregates which could be tentatively assigned to head-to-head stacked dimers of single helices, double helical duplexes and a quadruplex, none of which would form in organic solvent with organic-soluble analogues. The nature of the aggregates was supported by concentration and solvent dependent NMR studies, 1H DOSY experiments, mass spectrometry, and X-ray crystallography or energy-minimized models, as well as analogies with earlier studies. The hydrophobic effect appears to be the main driving force for aggregation but it can be finely modulated by the presence or absence of a small number of charges to an extent that had no precedent in aromatic foldamer architectures. These results will serve as a benchmark for future foldamer design in water.

SNARE Proteins in Synaptic Vesicle Fusion.

Neurotransmitters are stored in small membrane-bound vesicles at synapses; a subset of synaptic vesicles is docked at release sites. Fusion of docked vesicles with the plasma membrane releases neurotransmitters. Membrane fusion at synapses, as well as all trafficking steps of the secretory pathway, is mediated by SNARE proteins. The SNAREs are the minimal fusion machinery. They zipper from N-termini to membrane-anchored C-termini to form a 4-helix bundle that forces the apposed membranes to fuse. At synapses, the SNAREs comprise a single helix from syntaxin and synaptobrevin; SNAP-25 contributes the other two helices to complete the bundle. Unc13 mediates synaptic vesicle docking and converts syntaxin into the permissive "open" configuration. The SM protein, Unc18, is required to initiate and proofread SNARE assembly. The SNAREs are then held in a half-zippered state by synaptotagmin and complexin. Calcium removes the synaptotagmin and complexin block, and the SNAREs drive vesicle fusion. After fusion, NSF and alpha-SNAP unwind the SNAREs and thereby recharge the system for further rounds of fusion. In this chapter, we will describe the discovery of the SNAREs, their relevant structural features, models for their function, and the central role of Unc18. In addition, we will touch upon the regulation of SNARE complex formation by Unc13, complexin, and synaptotagmin.

Settlement based load capacity curve for single helix helical pile in c - ϕ soil

Helical piles are getting increasingly popular for lightweight engineering applications. Currently, the helical pile is mostly designed with torque capacity; however, it cannot explain the foundation's anticipated settlement. The current study developed a settlement-based design technique to determine the capacity of a single helix in small diameter helical piles. A three-dimensional nonlinear finite element analysis (FEA) was conducted using PLAXIS 3D. At first, the numerical models were calibrated and verified using load testing data from representative soil properties and realistic modeling assumptions. Then a parametric study was extended to determine the load settlement curve in different c- ϕ soil types, along with varying helix and shaft configurations. The load-deformation curves were grouped to develop multiple load capacity curves. Finally, the load capacity curve was validated by load test data. The range of calculated vs measured (from load tests) capacities (Qc/Qm) is 0.68 to 2.67, where the mean Qc/Qm is 1.10.

Protein engineering of antifreeze proteins reveals that their activity scales with the area of the ice-binding site.

Antifreeze proteins (AFPs) protect organisms from freezing by binding to ice crystals to prevent their growth. Here, we have investigated how the area of an AFP's ice-binding site (IBS) changes its antifreeze activity. The polyproline type II helical bundle fold of the 9.6-kDa springtail (Collembola) AFP from Granisotoma rainieri (a primitive arthropod) facilitates changes to both IBS length and width. A one quarter decrease in area reduced activity to less than 10%. A one quarter increase in IBS width, through the addition of a single helix, tripled antifreeze activity. However, increasing IBS length by a similar amount actually reduced activity. Expanding the IBS area can greatly increase antifreeze activity but needs to be evaluated by experimentation on a case-by-case basis.

Whirling instability of an eccentric coated fibre

We study a gravity-driven viscous flow coating a vertical cylindrical fibre. The destabilisation of a draining liquid column into a downward moving train of beads has been linked to the conjunction of the Rayleigh–Plateau and Kapitza instabilities in the limit of small Bond numbers $Bo$ . Here, we focus on quasi-inertialess flows (large Ohnesorge number $Oh$ ) and conduct a linear stability analysis on a unidirectional flow along a rigid eccentric fibre for intermediate to large $Bo$ . We show the existence of two unstable modes, namely pearl and whirl modes. The pearl mode depicts asymmetric beads, similar to that of the Rayleigh–Plateau instability, whereas a single helix forms along the axis in the whirl mode instability. The geometric and hydrodynamic thresholds of the whirl mode instability are investigated, and phase diagrams showing the transition thresholds between different regimes are presented. Additionally, an energy analysis is carried out to elucidate the whirl formation mechanism. This analysis reveals that despite the unfavourable capillary energy cost, the asymmetric interface shear distribution, caused by the fibre eccentricity, has the potential to sustain a whirling interface. In general, small fibre radius and large eccentricity tend to foster the whirl mode instability, while reducing $Bo$ tends to favour the dominance of the pearl mode instability. Finally, we compare the predictions of our model with the results of some illustrative experiments, using highly viscous silicone oils flowing down fibres. Whirling structures are observed for the first time, and the measured wavenumbers match our stability analysis prediction.

Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations.

Molecular dynamics simulations and geometry optimizations carried out at the quantum level as well as by quantum mechanical/molecular mechanics methods predict that short, single-stranded DNA oligonucleotides adopt conformations very similar to those observed in crystallographic double-stranded B-DNA, with rise coordinates close to ≈3.3 Å. In agreement with the experimental evidence, the computational results show that DNA single strands rich in adjacent purine nucleobases assume more regular arrangements than poly-thymine. The preliminary results suggest that single-stranded poly-cytosine DNA should also retain a substantial helical order in solution. A comparison of the structures of single and double helices confirms that the B-DNA motif is a favorable arrangement also for single strands. Indeed, the optimal geometry of the complementary single helices is changed to a very small extent in the formation of the duplex.