Helical Sequences Research Articles

De Novo Design and Characterization of Amphiphilic Peptides with Basic Side Chains for Tailored Interfacial Chemistries.

Lysine-leucine (LK) peptides have been used as model systems and platforms for 2D material design for decades. LK peptides are amphiphilic sequences designed to bind and fold at hydrophobic surfaces through hydrophobic leucine side chains and hydrophilic lysine side chains extending into the aqueous subphase. The hydrophobic periodicity of the sequence dictates the secondary structure at the interface. This robust design makes them ideal candidates for controlling interfacial chemistry. This study presents the de novo design and characterization of two novel peptides: LRα14 and LHα14, which substitute lysine with arginine and histidine, respectively, in the helical LKα14 sequence. This modification is intended to expand the LK peptide platform to a new basic interfacial chemistry. We explore the stability of the new LRα14 and LHα14 designs with respect to changes in pH and salt concentration in bulk solution and at the interface using circular dichroism (UV-CD) and vibrational sum-frequency generation spectroscopy, respectively. Notably, the structural stability of the peptides remains unaffected across a wide range of pH and ionic strength values. At the same time, the variation of side-chain chemistry leads to a wide spectrum of interfacial water structures. By extension of the LK platform to include arginine and histidine, this study broadens the toolbox for designing tailored interfacial chemistries with applications in material and biomedical sciences.

Molecular Origin of Distinct Hydration Dynamics in Double Helical DNA and RNA Sequences.

Water molecules are essential to determine the structure of nucleic acids and mediate their interactions with other biomolecules. Here, we characterize the hydration dynamics of analogous DNA and RNA double helices with unprecedented resolution and elucidate the molecular origin of their differences: first, the localization of the slowest hydration water molecules─in the minor groove in DNA, next to phosphates in RNA─and second, the markedly distinct hydration dynamics of the two phosphate oxygen atoms OR and OS in RNA. Using our Extended Jump Model for water reorientation, we assess the relative importance of previously proposed factors, including the local topography, water bridges, and the presence of ions. We show that the slow hydration dynamics at RNA OR sites is not due to bridging water molecules but is caused by both the larger excluded volume and the stronger initial H-bond next to OR, due to the different phosphate orientations in A-form double helical RNA.

Quantum plasmonics pushes chiral sensing limit to single molecules: a paradigm for chiral biodetections

Chiral sensing of single molecules is vital for the understanding of chirality and their applications in biomedicine. However, current technologies face severe limitations in achieving single-molecule sensitivity. Here we overcome these limitations by designing a tunable chiral supramolecular plasmonic system made of helical oligoamide sequences (OS) and nanoparticle-on-mirror (NPoM) resonator, which works across the classical and quantum regimes. Our design enhances the chiral sensitivity in the quantum tunnelling regime despite of the reduced local E-field, which is due to the strong Coulomb interactions between the chiral OSs and the achiral NPoMs and the additional enhancement from tunnelling electrons. A minimum of four molecules per single-Au particle can be detected, which allows for the detection of an enantiomeric excess within a monolayer, manifesting great potential for the chiral sensing of single molecules.

Numerical and experimental investigations of low-velocity impact on composite overwrapped pressure vessel with different stacking sequences

Composite overwrapped pressure vessels are designed to contain fluids that operate under high pressures. In addition to internal pressure, the design needs to account for out-of-plane loading in the form of low-velocity impact. In this study, a numerical analysis of four models of composite overwrapped pressure vessels with different stacking sequences is performed. A three-dimensional explicit finite element model using multi-layer stacked shell elements was used in the impact zone region to obtain reasonable computation time. Utilizing the bilinear traction-separation law, cohesive zone elements were used to simulate the delamination failure and as bonding between eight layers of CFRP covering the aluminum liner. The simulation results were then validated using drop-weight impact tests, which revealed that the response of contact force to impact time was comparable for both types of analysis. Prediction of failure was carried out by assessing the quantity of energy absorbed by the CFRP layers and was confirmed by shell element data that failed during simulations. In addition, the Hashin damage model confirmed that the matrix tensile failure mode was the predominant failure mode for all discussed impact scenarios. Model-A with Al + [90]8 stacking sequence was found to have the highest impact resistance based on the prediction of the composite’s failure area and the energy absorbed by the CFRP layers. Furthermore, it was found that COPVs with combinations of helical and hoop sequences tend to have larger areas of delamination due to high interlaminar shear stress between the CFRP layers.

A Highly Ordered Nitroxide Side Chain for Distance Mapping and Monitoring Slow Structural Fluctuations in Proteins.

The online version contains supplementary material available at 10.1007/s00723-023-01618-8.

Lipid saturation and head group composition have a pronounced influence on the membrane insertion equilibrium of amphipathic helical polypeptides.

The histidine-rich peptides of the LAH4 family were designed using cationic antimicrobial peptides such as magainin and PGLa as templates. The LAH4 amphipathic helical sequences exhibit a multitude of interesting biological properties such as antimicrobial activity, cell penetration of a large variety of cargo and lentiviral transduction enhancement. The parent peptide associates with lipid bilayers where it changes from an orientation along the membrane interface into a transmembrane configuration in a pH-dependent manner. Here we show that LAH4 adopts a transmembrane configuration in fully saturated DMPC membranes already at pH3.5, i.e. much below the pKa of the histidines whereas the transition pH in POPC correlates closely with histidine neutralization. In contrast in POPG membranes the in-planar configuration is stabilized by about one pH unit. The differences in pH can be converted into energetic contributions for the in-plane to transmembrane transition equilibrium, where the shift in the transition pH due to lipid saturation corresponds to energies which are otherwise obtained by the exchange of several cationic with hydrophobic residues. A similar dependence on lipid saturation has also been observed when the PGLa and magainin antimicrobial peptides interact within lipid bilayers suggesting that the quantitative evaluation presented in this paper also applies to other membrane polypeptides.

Measuring the orbital angular momentum mode of vortex beam based on phase matching sequence

Measuring the orbital angular momentum(OAM) mode of vortex beams is of great significance in applications based on vortex beams.we propose a method of phase matching characteristics of vortex beams to measure the OAM mode. The method first use a high-speed spatial light modulator(SLM) to sequentially load a set of helical phase sequence images, so that the vortex beam is modulated by this SLM. Then obtain the modulated optical field through pinhole filtering, and then the synchronized tilt phase modulation is performed by the 4f system and high-speed SLM. When the OAM mode of vortex beam is opposite to the topological charge of helical phase image, that is, the incident vortex beam degenerates to the fundamental Gaussian mode beam,and through our optical system, the output plane obtained a indicating spot with the position related to the OAM mode. The Simulation and experimental results show that the method obtains a clear OAM mode indicating spot on the final output plane, which verifies the theoretical derivation.

Atomic insight into short helical peptide comprised of consecutive multiple aromatic residues.

The occurrence of sequential multiple aromatic residues in a helical sequence is rare compared to the β-sheet rich structure. Here, using helix promoting α-aminoisobutyric acid (Aib) residues, we unravel atomistic details of the helical secondary structure formation and the super helical assembly of two heptapeptides composed of sequential five and six phenylalanine (Phe) residues.

Deciphering the Backbone Noncovalent Interactions that Stabilize Polyproline II Conformation and Reduce cis Proline Abundance in Polyproline Tracts.

Proline (Pro) has a higher propensity to adopt cis amide geometry than the other natural amino acids, and a poly-Pro (poly-P) tract can adopt either a polyproline I (PPI, all cis amide) or a polyproline II (PPII, all trans amide) helical conformation. Recent studies have revealed a reduced abundance of cis amide geometry among the inner Pro residues of a poly-P tract. However, the forces that stabilize the polyproline helices and the reason for the higher trans amide propensity of the inner Pro residues of a poly-P tract are poorly understood. Herein, we have studied both Pro and non-Pro PPII helical sequences and identified the backbone noncovalent interactions that are crucial to the higher stability of the trans Pro-amide geometry and the preference for a PPII helical conformation. We show the presence of reciprocal CO···CO interactions that extend over the whole PPII helical region. Interestingly, the CO···CO interactions strengthen with the increase in the PPII helical chain length and the inner CO groups possess stronger CO···CO interactions, which could explain the reduced cis abundance of the inner Pro residues of a poly-P tract. We also identified a much stronger (∼0.9 kcal·mol-1) nO → σ*Cα-Cβ interaction between the N-terminal CO oxygen lone pair and the antibonding orbital (σ*) of their Cα-Cβ bonds. As the nO → σ*Cα-Cβ interaction is possible only in the trans isomers of Pro, this interaction should be crucial for the stabilization of a PPII helix. Finally, an unusual nN(amide) → σ*C-N interaction (∼0.3 kcal·mol-1) was observed between the peptidic nitrogen lone pair (nN) and the antibonding orbital (σ*C-N) of the subsequent C-terminal peptide C-N bond. We propose a cumulative effect of these interactions in the stabilization of a PPII helix.

Structural evolution of mesomorphic propylene–1‐butene random copolymer during heating process

AbstractThe study of the transition of mesophase to α‐crystal (meso–α transition) is of great significance for understanding the crystallization, morphology as well as processability of polypropylene materials. The structural evolution of mesomorphic isotactic propylene–1‐butene (iPPBu) random copolymer during the continuous heating process was investigated using in situ Fourier transform infrared spectroscopy, differential scanning calorimetry, wide‐angle X‐ray diffraction and dynamic mechanical analysis. The presence of the butene comonomer influences the meso–α transition behavior. Compared with the mesomorphic iPP homopolymer, the presence of butene comonomer reduces both onset temperature (Tonset) and end temperature (Tend) of the meso–α transition, and narrows the transition temperature range. The content of the 31 helical sequence with 12 monomers remains invariant during the meso–α transition, differing from that of mesomorphic iPP homopolymer. Similar to mesomorphic iPP homopolymer, the 31 helical sequence with monomer number n ≤ 12 is found to exist in the rigid amorphous fraction of iPPBu, but is different from that of a mesomorphic propylene–ethylene random copolymer. In the meso–α transition (from 60 to 100 °C), the redshift of the peak position of the band at ca 841 cm−1 provides new information for the approaching of adjacent stems at the molecular level. Moreover, a new peak at around Tend is found in the tan(δ)–T plot, and is correlated with the meso–α transition. The activation energy of the meso–α transition of mesomorphic iPPBu is 32.5 kJ mol−1, which is slightly lower than that of mesomorphic iPP homopolymer. This work sheds new light on further understanding of the meso–α transition mechanism of iPPBu copolymer at the molecular level and elucidates the effect of butene comonomer on the meso–α transition. © 2021 Society of Industrial Chemistry.

Probing Protein Folding with Sequence-Reversed α-Helical Bundles.

Recurrent protein folding motifs include various types of helical bundles formed by α-helices that supercoil around each other. While specific patterns of amino acid residues (heptad repeats) characterize the highly versatile folding motif of four-α-helical bundles, the significance of the polypeptide chain directionality is not sufficiently understood, although it determines sequence patterns, helical dipoles, and other parameters for the folding and oligomerization processes of bundles. To investigate directionality aspects in sequence-structure relationships, we reversed the amino acid sequences of two well-characterized, highly regular four-α-helical bundle proteins and studied the folding, oligomerization, and structural properties of the retro-proteins, using Circular Dichroism Spectroscopy (CD), Size Exclusion Chromatography combined with Multi-Angle Laser Light Scattering (SEC-MALS), and Small Angle X-ray Scattering (SAXS). The comparison of the parent proteins with their retro-counterparts reveals that while the α-helical character of the parents is affected to varying degrees by sequence reversal, the folding states, oligomerization propensities, structural stabilities, and shapes of the new molecules strongly depend on the characteristics of the heptad repeat patterns. The highest similarities between parent and retro-proteins are associated with the presence of uninterrupted heptad patterns in helical bundles sequences.

Type I and type V procollagen triple helix uses different subsets of the molecular ensemble for lysine posttranslational modifications in the rER

Collagen is the most abundant protein in humans. It has a characteristic triple-helix structure and is heavily posttranslationally modified. The complex biosynthesis of collagen involves processing by many enzymes and chaperones in the rough endoplasmic reticulum. Lysyl hydroxylase 1 (LH1) is required to hydroxylate lysine for cross-linking and carbohydrate attachment within collagen triple helical sequences. Additionally, a recent study of prolyl 3-hydroxylase 3 (P3H3) demonstrated that this enzyme may be critical for LH1 activity; however, the details surrounding its involvement remain unclear. If P3H3 is an LH1 chaperone that is critical for LH1 activity, P3H3 and LH1 null mice should display a similar deficiency in lysyl hydroxylation. To test this hypothesis, we compared the amount and location of hydroxylysine in the triple helical domains of type V and I collagen from P3H3 null, LH1 null, and wild-type mice. The amount of hydroxylysine in type V collagen was reduced in P3H3 null mice, but surprisingly type V collagen from LH1 null mice contained as much hydroxylysine as type V collagen from wild-type mice. In type I collagen, our results indicate that LH1 plays a global enzymatic role in lysyl hydroxylation. P3H3 is also involved in lysyl hydroxylation, particularly at cross-link formation sites, but is not required for all lysyl hydroxylation sites. In summary, our study suggests that LH1 and P3H3 likely have two distinct mechanisms to recognize different collagen types and to distinguish cross-link formation sites from other sites in type I collagen.

Low-power synchronous helical pulse sequences for large anisotropic interactions in MAS NMR: Double-quantum excitation of 14N.

We develop a theoretical framework for a class of pulse sequences in the nuclear magnetic resonance (NMR) of rotating solids, which are applicable to nuclear spins with anisotropic interactions substantially larger than the spinning frequency, under conditions where the radiofrequency amplitude is smaller than or comparable to the spinning frequency. The treatment is based on average Hamiltonian theory and allows us to derive pulse sequences with well-defined relationships between the pulse parameters and spinning frequency for exciting specific coherences without the need for any detailed calculations. This framework is applied to the excitation of double-quantum spectra of 14N and is used both to evaluate the existing low-power pulse schemes and to predict the new ones, which we present here. It is shown that these sequences can be designed to be γ-encoded and therefore allow the acquisition of sideband-free spectra. It is also shown how these new double-quantum excitation sequences are incorporated into heteronuclear correlation NMR, such as 1H-14N dipolar double-quantum heteronuclear multiple-quantum correlation spectroscopy. The new experiments are evaluated both with numerical simulations and experiments on glycine and N-acetylvaline, which represent cases with "moderate" and "large" quadrupolar interactions, respectively. The analyzed pulse sequences perform well for the case of a "moderate" quadrupolar interaction, however poorly with a "large" quadrupolar interaction, for which future work on pulse sequence development is necessary.

Structure, membrane topology and influence of cholesterol of the membrane proximal region: transmembrane helical anchor sequence of gp41 from HIV

During the first steps of HIV infection the Env subunit gp41 is thought to establish contact between the membranes and to be the main driver of fusion. Here we investigated in liquid crystalline membranes the structure and cholesterol recognition of constructs made of a gp41 external region carrying a cholesterol recognition amino acid consensus (CRAC) motif and a hydrophobic membrane anchoring sequence. CD- und ATR-FTIR spectroscopies indicate that the constructs adopt a high degree of helical secondary structure in membrane environments. Furthermore, 15N and 2H solid-state NMR spectra of gp41 polypeptides reconstituted into uniaxially oriented bilayers agree with the CRAC domain being an extension of the transmembrane helix. Upon addition of cholesterol the CRAC NMR spectra remain largely unaffected when being associated with the native gp41 transmembrane sequence but its topology changes when anchored in the membrane by a hydrophobic model sequence. The 2H solid-state NMR spectra of deuterated cholesterol are indicative of a stronger influence of the model sequence on this lipid when compared to the native gp41 sequence. These observations are suggestive of a strong coupling between the transmembrane and the membrane proximal region of gp41 possibly enforced by oligomerization of the transmembrane helical region.

Design and Synthesis of Helical N-Terminal L-Prolyl Oligopeptides Possessing Hydrocarbon Stapling.

We designed and synthesized helical short oligopeptides with an l-proline on the N-terminus and hydrocarbon stapling on the side chain. Side-chain stapling is a frequently used method for the development of biologically active peptides. Side-chain stapling can stabilize the secondary structures of peptides, and, therefore, stapled peptides may be applicable to peptide-based organocatalysts. Olefin-tethered cis-4-hydroxy-l-proline 1 and l-serine 2 and 8, and (R)-α-allyl-proline 18 were used as cross-linking motifs and incorporated into helical peptide sequences. The Z- and E-selectivities were observed for the ring-closing metathesis reactions of peptides 3 and 11 (i,i+1 series), respectively, while no E/Z-selectivity was observed for that of 19 (i,i+3 series). The stapled peptide B’ catalyzed the Michael addition reaction of 1-methylindole to α,β-unsaturated aldehyde, which was seven times faster than that of unstapled peptide B. Furthermore, the high catalytic activity was retained even at lower catalyst loadings (5 mol %) and lower temperatures (0 °C). The circular dichroism spectra of stapled peptide B’ showed a right-handed helix with a higher intensity than that of unstapled peptide B. These results indicate that the introduction of side-chain stapling is beneficial for enhancing the catalytic activity of short oligopeptide catalysts.

Chiral Phosphathiahelicenes: Improved Synthetic Approach and Uses in Enantioselective Gold(I)-Catalyzed [2 + 2] Cycloadditions of N-Homoallenyl Tryptamines

A chiral phosphathiahelicene scaffold displaying a phosphole and a thiophene unit as the terminal rings of the helical sequence has been synthesized and characterized by spectroscopic methods and X...

Investigating the Nucleation Effect of DMDBS on Syndiotactic Polypropylene from the Perspective of Chain Conformation

The mechanism of nucleating agents (NAs) accelerating the crystallization of semi-crystalline polymers has received continuous attention due to the extreme importance in academic research and industry application. In this work, the nucleation effect and probable mechanism of 1,3:2,4-bis(3,4-dimethylbenzylidene)sorbitol (DMDBS) on promoting the crystallization of syndiotactic polypropylene (sPP) was systematically investigated. Our results showed that DMDBS could significantly accelerate the crystallization process and did not change the crystalline form of sPP. The in situ infrared spectra recorded in the crystallization process showed that in pristine sPP the tttt conformers decreased and the ttgg conformers increased subsequently. In sPP/DMDBS system, DMDBS could promote the increase of ttgg conformers rather than the decrease of tttt conformers. The further analysis by 2D-IR spectra revealed that ttgg conformers increased prior to the decrease of tttt conformers in the sPP/DMDBS system comparing with pristine sPP. Considering that ttgg conformers were basic elements of helical conformation of Form I crystal for sPP, we proposed a probable nucleation mechanism of DMDBS for sPP:DMDBS could stabilize the ttgg conformers which induced these ttgg conformers to pre-orientate and aggregate into helical conformation sequences as initial nuclei quickly and early to promote the sPP crystallization. Our work provides some new insights into the nucleation mechanism of NAs for sPP.

Hybrid Helical Polymer Nanochannels Constructed by Combining Aromatic Amide and Pyridine‐Oxadiazole Structural Sequences

An effective method is reported to synthesize aromatic helical polymer nanochannels by combining both the well-studied aromatic amide helical codons with pyridine-oxadiazole helical codons into helical structure sequences. With this strategy, a type of helical polymer nanochannel that shows structure-directed transmembrane transport functions is synthesized. Although such nanochannels show relatively weak selectivity for the transportation of alkali metal ions, accessible chemical mutation of helical structure sequences will provide a great chance for the design of desired channel property. The straightforward preparation of well-established pyridine-oxadiazole helical structure will significantly promote the synthesis of this kind of aromatic helical polymer nanochannels. With the development of aromatic amide foldamers, moreover, a number of "monomers" will be available for the preparation of helical polymer nanochannels.

Evolution, characterization and phylogenetic utility of ITS2 gene in Orthoptera and some Polyneoptera: Highly variable at the order level and highly conserved at the species level

ITS2 is often suggested as a potential marker for evolutionary studies and species barcoding. However, there are many lineages have not been studied. This study focuses on ITS2 in Polyneoptera at the order and species levels. ITS2 sequences representing six polyneopteran orders and 15 species in the genus Anterastes are studied. We arrived at the following conclusions: (i) ITS2 is highly variable and contains little phylogenetic information in Polyneoptera, (ii) the shortest length and the highest GC content of ITS2 is found in Orthoptera among insects, (iii) the secondary structure exhibits general characteristics of eukaryotes especially in helices II and III, and with no order-specific architecture, (iv) ITS2 is highly conserved at the species level, both in linear sequences and secondary structures, (v) helices I, IA, II, IIA and III almost invariable in nucleotide sequence shared by all species in the genus. At the generic level, the most conspicuous result is the variable pattern in ITS2. It is highly conserved in helical sequences, but highly variable in non/peri-helical regions which we considered to be mutation islands. These frequently mutated regions contain a significant amount of molecular homoplasy, thus, the utility of ITS2 in phylogenetic analyses and species barcoding is low, at least in Polyneoptera.

Stimuli-Responsive Conformational Transformation of Peptides for Tunable Cytotoxicity.

The stimuli-responsive conformational transformation of peptides possessing a constrained form triggered by specific biological microenvironment would provide an effective strategy for the development of highly specific peptide therapeutics. Here, we developed a peptide containing a cytotoxic helical KLA sequence with therapeutic specificity through the use of stimuli-responsive conformational transformation. The KLA peptide is modified to form a cyclic structure to allow for constrained helicity that confers low cytotoxicity. The modified KLA peptide is electrostatically complexed to hyaluronic acid to facilitate enhanced endocytosis into the cancer cells. After endocytosis, the peptide is released from the complex into the cellular cytoplasm by hyaluronidases on the surface of the cellular membrane. Specific intracellular stimuli then trigger the release of the strain that suppresses peptide helicity, and the inherent helical conformation of the KLA peptide is restored. Therefore, the stimuli-responsive conformational transformation of a peptide from low to high helicity selectively induces cell death by disruption of the plasma and mitochondrial membrane.