Length Of Helix Research Articles

Peptide Membrane Displaying Membrane Fusion and Fission with Lipid–Raft–Like Organization

Organelles in cells take a wide range of morphologies and convert one morphology to the other for specific biological events. We are trying to construct such complex morphologies allowing transformation from one to the other by using molecular assemblies comprising amphiphilic helical peptides. One key player is poly(sarcosine)–b–(L–Leu- Aib)n having a hydrophilic block of poly(sarcosine) and a helical hydrophobic block of (L–Leu–Aib)n. The driving forces for making these molecular assemblies can be modulated widely by helical block length, knobs-into-holes packing of side chains between helix surfaces, and stereocomplex formation between right- and left–handed helices. Under properly designed amphiphilic polypeptides and their combinations, we can construct morphologies of sheet, tube, and vesicles and even the combination of tube and vesicle, a round–bottomed flask shape. There were several combinations of amphiphilic polypeptides to take the round–bottomed flask morphology. The chimeric morphology is a direct consequence of phase separation of the component polypeptides in one consecutive membrane. The distribution of the components into the round–bottomed or neck moiety was dependent on the combination meaning that lateral diffusion of the components in the membrane led to the phase separation. The vesicle composed of poly(sarcosine)– b–(L–Leu–Aib)6 and poly(sarcosine)–b–(D–Leu–Aib)6 allowed membrane fusion and fission above the phase transition temperature with itself and other vesicle. The monolayer elasticity of vesicles was variable in accordance with the component amphiphilic polypeptides, and the elasticity similar to liposome can be prepared.

Metal-Promoted Assembly of Two Collagen Mimetic Peptides into a Biofunctional "Spiraled Horn" Scaffold.

Biofunctional scaffolds for the delivery of living cells are of the utmost importance for regenerative medicine. Herein, a novel, robust “spiraled horn” scaffold was elucidated through the Co2+-promoted hierarchical assembly of two collagen mimetic peptides, NCoH and HisCol. Each “horn” displayed a periodic banding pattern with band lengths corresponding to the length of the collagen peptide triple helix. Strand exchange between the two peptide trimers resulted in failure to form this intricate morphology, lending support to a precise metal-ligand-based mechanism of assembly. Little change occurred to the observed morphology when the Co2+ concentration was varied from 0.5 to 4.0 mM, and the scaffold was found to be fully formed within two minutes of exposure to the metal ion. The horned network also displayed biological functionality by binding to a His-tagged fluorophore and associating with cells.

Magnetogenesis from axion inflation

In this work we compute the production of magnetic fields in models of axion inflation coupled to the hypercharge sector of the Standard Model through a Chern-Simons interaction term. We make the simplest choice of a quadratic inflationary potential and use lattice simulations to calculate the magnetic field strength, helicity and correlation length at the end of inflation. For small values of the axion-gauge field coupling strength the results agree with no-backreaction calculations and estimates found in the literature. For larger couplings the helicity of the magnetic field differs from the no-backreaction estimate and depends strongly on the comoving wavenumber. We estimate the post-inflationary evolution of the magnetic field based on known results for the evolution of helical and non-helical magnetic fields. The magnetic fields produced by axion inflation with large couplings to U(1)Y can reach Beff ≳ 10−16 G, exhibiting a field strength Bphys ≈ 10−13 G and a correlation length λphys ≈10 pc. This result is insensitive to the exact value of the coupling, as long as the coupling is large enough to allow for instantaneous preheating. Depending on the assumptions for the physical processes that determine blazar properties, these fields can be found consistent with blazar observations based on the value of Beff. Finally, the intensity of the magnetic field for large coupling can be enough to satisfy the requirements for a recently proposed baryogenesis mechanism, which utilizes the chiral anomaly of the Standard Model.

A Conserved Hydrophobic Core in Gαi1 Regulates G Protein Activation and Release from Activated Receptor

G protein-coupled receptor-mediated heterotrimeric G protein activation is a major mode of signal transduction in the cell. Previously, we and other groups reported that the α5 helix of Gαi1, especially the hydrophobic interactions in this region, plays a key role during nucleotide release and G protein activation. To further investigate the effect of this hydrophobic core, we disrupted it in Gαi1 by inserting 4 alanine amino acids into the α5 helix between residues Gln(333) and Phe(334) (Ins4A). This extends the length of the α5 helix without disturbing the β6-α5 loop interactions. This mutant has high basal nucleotide exchange activity yet no receptor-mediated activation of nucleotide exchange. By using structural approaches, we show that this mutant loses critical hydrophobic interactions, leading to significant rearrangements of side chain residues His(57), Phe(189), Phe(191), and Phe(336); it also disturbs the rotation of the α5 helix and the π-π interaction between His(57) and Phe(189) In addition, the insertion mutant abolishes G protein release from the activated receptor after nucleotide binding. Our biochemical and computational data indicate that the interactions between α5, α1, and β2-β3 are not only vital for GDP release during G protein activation, but they are also necessary for proper GTP binding (or GDP rebinding). Thus, our studies suggest that this hydrophobic interface is critical for accurate rearrangement of the α5 helix for G protein release from the receptor after GTP binding.

Helix-Grafted Pleckstrin Homology Domains Suppress HIV-1 Infection of CD4-Positive Cells.

The size, functional group diversity and three-dimensional structure of proteins often allow these biomolecules to bind disease-relevant structures that challenge or evade small-molecule discovery. Additionally, folded proteins are often much more stable in biologically relevant environments compared to their peptide counterparts. We recently showed that helix-grafted display-extensive resurfacing and elongation of an existing solvent-exposed helix in a pleckstrin homology (PH) domain-led to a new protein that binds a surrogate of HIV-1 gp41, a validated target for inhibition of HIV-1 entry. Expanding on this work, we prepared a number of human-derived helix-grafted-display PH domains of varied helix length and measured properties relevant to therapeutic and basic research applications. In particular, we showed that some of these new reagents expressed well as recombinant proteins in Escherichia coli, were relatively stable in human serum, bound a mimic of pre-fusogenic HIV-1 gp41 in vitro and in complex biological environments, and significantly lowered the incidence of HIV-1 infection of CD4-positive cells.

Helix Nucleation by the Smallest Known α‐Helix in Water

Cyclic pentapeptides (e.g. Ac-(cyclo-1,5)-[KAXAD]-NH2 ; X=Ala, 1; Arg, 2) in water adopt one α-helical turn defined by three hydrogen bonds. NMR structure analysis reveals a slight distortion from α-helicity at the C-terminal aspartate caused by torsional restraints imposed by the K(i)-D(i+4) lactam bridge. To investigate this effect on helix nucleation, the more water-soluble 2 was appended to N-, C-, or both termini of a palindromic peptide ARAARAARA (≤5 % helicity), resulting in 67, 92, or 100 % relative α-helicity, as calculated from CD spectra. From the C-terminus of peptides, 2 can nucleate at least six α-helical turns. From the N-terminus, imperfect alignment of the Asp5 backbone amide in 2 reduces helix nucleation, but is corrected by a second unit of 2 separated by 0-9 residues from the first. These cyclic peptides are extremely versatile helix nucleators that can be placed anywhere in 5-25 residue peptides, which correspond to most helix lengths in protein-protein interactions.

Helix Nucleation by the Smallest Known α‐Helix in Water

AbstractCyclic pentapeptides (e.g. Ac‐(cyclo‐1,5)‐[KAXAD]‐NH2; X=Ala, 1; Arg, 2) in water adopt one α‐helical turn defined by three hydrogen bonds. NMR structure analysis reveals a slight distortion from α‐helicity at the C‐terminal aspartate caused by torsional restraints imposed by the K(i)–D(i+4) lactam bridge. To investigate this effect on helix nucleation, the more water‐soluble 2 was appended to N‐, C‐, or both termini of a palindromic peptide ARAARAARA (≤5 % helicity), resulting in 67, 92, or 100 % relative α‐helicity, as calculated from CD spectra. From the C‐terminus of peptides, 2 can nucleate at least six α‐helical turns. From the N‐terminus, imperfect alignment of the Asp5 backbone amide in 2 reduces helix nucleation, but is corrected by a second unit of 2 separated by 0–9 residues from the first. These cyclic peptides are extremely versatile helix nucleators that can be placed anywhere in 5–25 residue peptides, which correspond to most helix lengths in protein–protein interactions.

Secondary Structure of Decorin-Derived Peptides in Solution

ABSTRACTDecorin is a small leucine-rich repeat proteoglycan supporting collagen fibril formation by controlling the rate of collagen fibrillogenesis and fibril dimensions. Peptides derived from the inner surface of decorin have been shown to bind to collagen, while peptides derived from the outer surface do not display such binding affinity. As typical secondary structural elements such as β-sheets and α-helical regions were found in the decorin X-ray crystal structure, here it was investigated by Circular Dichroism (CD) spectroscopy in solution, whether the same structural elements can be found in the derived peptides. Here it is shown that the peptide derived from decorin’s outer surface has the propensity to adopt helical conformation, as it was found in the crystal structure. The results were more pronounced in 80 vol% TFE solution, which led to an increase in the number as well as the length of helices. In contrast, peptides derived from the inner surface had a higher tendency to adopt β-sheet conformation, also in TFE, which corresponds to the conformation of the original sequence in the crystal structure of decorin. This suggests that the peptides derived from decorin adopt the structures present in the native protein.

X-ray diffraction from nonuniformly stretched helical molecules.

The fibrous proteins in living cells are exposed to mechanical forces interacting with other subcellular structures. X-ray fiber diffraction is often used to assess deformation and movement of these proteins, but the analysis has been limited to the theory for fibrous molecular systems that exhibit helical symmetry. However, this approach cannot adequately interpret X-ray data from fibrous protein assemblies where the local strain varies along the fiber length owing to interactions of its molecular constituents with their binding partners. To resolve this problem a theoretical formulism has been developed for predicting the diffraction from individual helical molecular structures nonuniformly strained along their lengths. This represents a critical first step towards modeling complex dynamical systems consisting of multiple helical structures using spatially explicit, multi-scale Monte Carlo simulations where predictions are compared with experimental data in a 'forward' process to iteratively generate ever more realistic models. Here the effects of nonuniform strains and the helix length on the resulting magnitude and phase of diffraction patterns are quantitatively assessed. Examples of the predicted diffraction patterns of nonuniformly deformed double-stranded DNA and actin filaments in contracting muscle are presented to demonstrate the feasibly of this theoretical approach.

Effects of conformational ordering on protein/polyelectrolyte electrostatic complexation: ionic binding and chain stiffening.

Coupling of electrostatic complexation with conformational transition is rather general in protein/polyelectrolyte interaction and has important implications in many biological processes and practical applications. This work studied the electrostatic complexation between κ-carrageenan (κ-car) and type B gelatin, and analyzed the effects of the conformational ordering of κ-car induced upon cooling in the presence of potassium chloride (KCl) or tetramethylammonium iodide (Me4NI). Experimental results showed that the effects of conformational ordering on protein/polyelectrolyte electrostatic complexation can be decomposed into ionic binding and chain stiffening. At the initial stage of conformational ordering, electrostatic complexation can be either suppressed or enhanced due to the ionic bindings of K+ and I− ions, which significantly alter the charge density of κ-car or occupy the binding sites of gelatin. Beyond a certain stage of conformational ordering, i.e., helix content θ > 0.30, the effect of chain stiffening, accompanied with a rapid increase in helix length ζ, becomes dominant and tends to dissociate the electrostatic complexation. The effect of chain stiffening can be theoretically interpreted in terms of double helix association.

New Design of Ranque–Hilsch Vortex Tube: Helical Multi-Intake Vortex Generator

An experimental study is conducted to investigate the thermal energy separation in a counterflow vortex tube. The effects of the cold orifice diameter (), the number of tangential intakes (), and the helical length of intakes () on thermal separation and cold temperature of the vortex tube are investigated. Finally, the results are compared with the conventional tangential nozzle under the same experimental conditions. It is observed that the cold temperature difference of the new Ranque–Hilsch design was greater than the cold temperature difference of the classical Ranque–Hilsch vortex tube. Also, the vortex generator with , and has the highest effect on the vortex tube energy separation.

Biological insertion of computationally designed short transmembrane segments.

The great majority of helical membrane proteins are inserted co-translationally into the ER membrane through a continuous ribosome-translocon channel. The efficiency of membrane insertion depends on transmembrane (TM) helix amino acid composition, the helix length and the position of the amino acids within the helix. In this work, we conducted a computational analysis of the composition and location of amino acids in transmembrane helices found in membrane proteins of known structure to obtain an extensive set of designed polypeptide segments with naturally occurring amino acid distributions. Then, using an in vitro translation system in the presence of biological membranes, we experimentally validated our predictions by analyzing its membrane integration capacity. Coupled with known strategies to control membrane protein topology, these findings may pave the way to de novo membrane protein design.

Isotope effect on the structural evolution process in the isothermal crystallization phenomenon of polyoxymethylene

Isotope effect on the structural evolution process in the melt-isothermal crystallization phenomenon of polyoxymethylene (POM) has been studied on the basis of the time-resolved simultaneous measurements of FTIR spectra, small-angle X-ray scattering (SAXS) and wide-angle X-ray diffraction (WAXD) for a series of copolymers with the different D/H contents. The quantitative analysis of FTIR band intensities for a series of POM D/H random copolymers revealed the critical sequence lengths or the minimal helical segmental lengths necessary for the detection of the IR band intensity. The quantitative analysis of the time-resolved SAXS and WAXD data revealed the formation of the domains of higher density in the melt, the increasing correlation between these domains and the growth of the crystalline lamellae. The time-resolved FTIR data gave the generation and growth of the helical segments in parallel. By combining all the data collected simultaneously, the following observations have been deduced about the structural evolution process from the melt: (1) immediately after the temperature jump, some portions of random coils in the melt regularize into the domains consisting of the aggregation of the short helical segments of 3–5 turns, (2) these domains approach each other to have stronger correlation, (3) and they form the crystalline lamellae. These lamellae grow furthermore by adding the helical segments on the surface. (4) When the degree of supercooling (the difference between the equilibrium melting point and the crystallization temperature) is high, the insertion of new lamellae into the originally-generated lamellae occurs. These structural evolution processes were found to be common to all the isotopic species including a normal POM (POM-H), a fully-deuterated POM (POM-D) and the random copolymer of deuterated (CD2O) and hydrogeneous (CH2O) monomeric units. However, these processes were found to occur at the different rate depending sensitively on the D/H content: the slowest POM-D << D/H-random copolymer << the fastest POM-H. These different structural evolutions were found to be scaled systematically by shifting along the time axis over a wide range of the degree of supercooling.

Two chiroptical modes of silver nanospirals

As an emerging three-dimensional chiral metamaterial, plasmonic nanospirals (NSs) possess inherent chiroptical activity that has attracted increasing attention for developing potential photonic applications. However, the study of chiroptical activity of plasmonic NSs is still in its infancy, especially for NSs made of silver, which is a typical plasmonic material with high plasmonic quality. Herein, we present a systematic study of circular dichroism (CD) of silver NSs (AgNSs) that are fabricated and engineered in helical lengths by glancing-angle deposition (GLAD) and dispersed in ethanol. The CD spectrum is composed of a bisignated mode of two peaks, one in the UV regime and the other in the visible. The UV mode has a resonance wavelength saturating at ∼375 nm and a linewidth decoupled from the helical elongation, while the visible mode tends to have a redshift and its linewidth broadens linearly with the elongation of AgNS. Helical elongation generally amplifies the chiroptical activity of both modes. Finite-element simulation shows good agreement with the experimental CD results, and accounts for the wavelength-related chiroptical distinction in terms of the resonance wavelength. This work contributes to understanding the bisignated chiroptical responses of plasmonic nanospirals, and introduces a simple method to tailor the visible chiroptical activity that is strongly desired to explore a wide range of chirality-related bio-applications.

Enabling Light Work in Helical Self-Assembly for Dynamic Amplification of Chirality with Photoreversibility.

Light-driven transcription and replication are always subordinate to a delicate chirality transfer. Enabling light work in construction of the helical self-assembly with reversible chiral transformation becomes attractive. Herein we demonstrate that a helical hydrogen-bonded self-assembly is reversibly photoswitched between photochromic open and closed forms upon irradiation with alternative UV and visible light, in which molecular chirality is amplified with the formation of helixes at supramolecular level. The characteristics in these superhelixes such as left-handed or right-handed twist and helical length, height, and pitch are revealed by SEM and AFM. The helical photoswitchable nanostructure provides an easily accessible route to an unprecedented photoreversible modulation in morphology, fluorescence, and helicity, with precise assembly/disassembly architectures similar to biological systems such as protein and DNA.

Comparative study of four physical approaches about allergenicity of soybean protein isolate for infant formula

ABSTRACTThe objective of this study was to investigate the influences of microwaving, high-intensity ultrasound (HIU), high-pressure homogenization (HPH) and high hydrostatic pressure (HHP) on the allergenicity and structural properties of soy protein isolate (SPI) for infant formula. Microwaving, HIU, HPH and HHP reduced allergenicity by 24.7%, 18.9%, 29.8% and 46.6%, respectively. Western blotting (WB) results indicated the allergens for Chinese soy-allergic childrens encompass 130 kD, 115 kD, lipoxidase, α and γ subunit of β-conglycinin, Chain A of glycinin, P34, 30 kD, 28 kD, Chain B of glycinin. SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) (with 2-ME) and WB patterns did not show significant differences among the native and modified SPIs. These four approaches influenced molecular interactions such as free sulfhydryl, hydrophobicity and zeta potential, compositions of secondary structures containing helices, strands, turns and unordered, and structural parameters including helices and strands (per 100 residues), average length of helices and strands. The epitopes of SPI allergens could be closely related to α-helix and β-sheet. In case of magnitude of secondary structure composition and parameter changes, HHP ranked top compared with other three methods. Therefore, the allergenicity reducing efficiency of HHP is much higher than those of other three treatments.

Tuning RNA Flexibility with Helix Length and Junction Sequence

The increasing awareness of RNA’s central role in biology calls for a new understanding of how RNAs, like proteins, recognize biological partners. Because RNA is inherently flexible, it assumes a variety of conformations. This conformational flexibility can be a critical aspect of how RNA attracts and binds molecular partners. Structurally, RNA consists of rigid basepaired duplexes, separated by flexible non-basepaired regions. Here, using an RNA system consisting of two short helices, connected by a single-stranded (non-basepaired) junction, we explore the role of helix length and junction sequence in determining the range of conformations available to a model RNA. Single-molecule Förster resonance energy transfer reports on the RNA conformation as a function of either mono- or divalent ion concentration. Electrostatic repulsion between helices dominates at low salt concentration, whereas junction sequence effects determine the conformations at high salt concentration. Near physiological salt concentrations, RNA conformation is sensitive to both helix length and junction sequence, suggesting a means for sensitively tuning RNA conformations.

A Naturally Occurring Repeat Protein with High Internal Sequence Identity Defines a New Class of TPR-like Proteins

Linear repeat proteins often have high structural similarity and low (∼25%) pairwise sequence identities (PSI) among modules. We identified a unique P. anserina (Pa) sequence with tetratricopeptide repeat (TPR) homology, which contains longer (42 residue) repeats (42PRs) with an average PSI >91%. We determined the crystal structure of five tandem Pa 42PRs to 1.6 Å, and examined the stability and solution properties of constructs containing three to six Pa 42PRs. Compared with 34-residue TPRs (34PRs), Pa 42PRs have a one-turn extension of each helix, and bury more surface area. Unfolding transitions shift to higher denaturant concentration and become sharper as repeats are added. Fitted Ising models show Pa 42PRs to be more cooperative than consensus 34PRs, with increased magnitudes of intrinsic and interfacial free energies. These results demonstrate the tolerance of the TPR motif to length variation, and provide a basis to understand the effects of helix length on intrinsic/interfacial stability.

Thermally Controlled Collagen Peptide Cages for Biopolymer Delivery.

The hierarchical assembly of collagen-based triple helical peptides into disks, followed by metal-promoted assembly into microcages is described. The length of the triple helix was found to correlate to the height of the disks that formed, providing mechanistic insights into their formation. The encapsulation of fluorescently labeled dextrans within the peptide microcages, and their subsequent thermal release is detailed. The half-life for thermal release of the encapsulated cargo from the cages was found to increase as the peptide triple helix stability increased, providing a means to engineer cargo delivery rates through peptide design.

Deformation and shape of flexible, microscale helices in viscous flow.

We examine experimentally the deformation of flexible, microscale helical ribbons with nanoscale thickness subject to viscous flow in a microfluidic channel. Two aspects of flexible microhelices are quantified: the overall shape of the helix and the viscous frictional properties. The frictional coefficients determined by our experiments are consistent with calculated values in the context of resistive-force theory. The deformation of helices by viscous flow is well described by nonlinear finite extensibility. Under distributed loading, the pitch distribution is nonuniform, and from this we identify both linear and nonlinear behavior along the contour length of a single helix. Moreover, flexible helices are found to display reversible global to local helical transitions at a high flow rate.