Right-handed Helical Conformation Research Articles

Cytotoxic Peptaibols from Trichoderma strigosum.

Five new lipopeptaibols (1-5) and eight new 19-residue peptaibols (8-15) along with two known lipopeptaibols, lipovelutibols C (6) and D (7) were isolated from Trichoderma strigosum. The planar structures of the newly discovered peptaibols (1-5, 8-15) were elucidated using 1D and 2D NMR, and UPLC-MS/MS data. The absolute configurations for new peptaibols (1-5, 8-15) were elucidated using the advanced Marfey's method and GITC (2,3,4,6-tetra-O-acetyl-β-d-glucopyranosyl isothiocyanate) derivatization. Through analysis of CD spectra, these peptabols were found to have right-handed helical conformations. While most of the new compounds were significantly more active than the positive control, 9, 10, 12, and 15 containing Ser and Leu at positions 10 and 11, respectively, were the most cytotoxic against MDA-MB-231, SNU449, SKOV3, DU145, and HCT116 cancer cell lines, and the 19-residue peptaibols were generally more potent than lipopeptaibols.

Pseudodiproline (Pro-Cyp) Oligomers Fold into Helical Polyproline Type secondary structures.

The synthesis and conformational properties of oligo-proline mimetics composed of dimeric and tetrameric Pro-Cyp constructs linked by a hydroxymethylene unit are reported. Oligomers were studied both in the solid state and in solution, unveiling right-handed helical conformation depending on the configuration of the vicinally substituted trans-cyclopentane carboxylic acid unit (Cyp). Unlike polyproline oligomers, the alternating synthetic Pro-Cyp counterparts are not stabilized by n-π* interactions but rely instead on the steric demands of the extended backbone conformation within the hydroxymethylene-linked Pro-Cyp repeating units.

Ambidexterity and Left-Handedness Induced by Geminally Disubstituted γ Amino Acid Residues in Chiral 310 Helices.

Chirality is an omnipresent feature in nature's architecture starting from simple molecules like amino acids to complex higher-order structures viz. proteins, DNA, and RNA. The L configuration of proteinogenic amino acids gives rise to right-handed helices. Ambidexterity is as rare in organisms as in molecules. There are only a few reports of ambidexterity in single-peptide molecules composed of either mixed L and D or achiral residues. Here, we report, for the first time, the ambidextrous and left-handed helical conformations in the chiral nonapeptides P1-P3 (Boc-LUVUγx,xULUV-OMe where U = Aib, x,x = 2,2/3,3/4,4), containing chiral L α amino acid residues, in addition to the usually observed right-handed helical conformation. The centrally located achiral γ residue, capable of adopting both left and right-handed helical conformations, induces its handedness on the neighboring chiral and achiral residues, leading to the observation of both left and right-handed helices in P2 and P3. The presence of a single water molecule proximal to the γ residue induces the reversal of helix handedness by forming distinct and stable water-mediated hydrogen bonds. This gives rise to ambidextrous helices as major conformers in P1 and P2. The absence of the observation of ambidexterity in P3 might be due to the inability of γ4,4 in the recruitment of a water molecule. Experiments (NMR, X-ray, and CD) and density functional theory (DFT) calculations suggest that the position of geminal disubstitution is crucial for determining the population of the amenable helical conformations (ambidextrous, left and right-handed) in these chiral peptides.

Peptoids as a Chiral Stationary Phase for Liquid Chromatography: Insights from Molecular Dynamics Simulations.

Peptoids are peptide regioisomers with attractive structural tunability in terms of sequence and three-dimensional arrangement. Peptoids are foreseen to have a great potential for many diverse applications, including their utilization as a chiral stationary phase in chromatography. To achieve chiral recognition, a chiral side chain is required to allow specific interactions with a given enantiomer from a racemic mixture. One of the most studied chiral stationary phases, built with (S)-N-1-phenylethyl (Nspe) units, was shown to be successful in resolving racemic mixtures of binaphthyl derivatives. However, there is currently no description at the atomic scale of the factors favoring its enantioselectivity. Here, we take advantage of steered molecular dynamics simulations to mimic the elution process at the atomic scale and present evidence that the predominantly right-handed helical conformation of Nspe peptoids and their ability to form stronger hydrogen bonds with the (S) enantiomer are responsible for the chiral recognition of the popular chiral probe 2,2'-bihydroxy-1,1'-binaphthyl.

Thermoswitching of Helical Inversion of Dynamic Polyphenylacetylenes through cis-trans Isomerization of Amide Pendants

The cis-trans isomerization of amides plays a vital role in all kinds of structural changes and biological activities, involving protein folding, protein misfolding, and even protein molecular recognition. However, the helical inversion of synthetic macromolecules arising from the cis-trans isomerization of tertiary amides, as a good mimic of natural protein, has been rarely researched. Herein, we synthesized meta-disubstituted polyphenylacetylenes (PPAs) with different N-substituted tertiary amides as one of the pendants, poly{(−)-3-methoxycarbonyl-5-[N-methyl-N-(S)-(1-phenylethyl)carbamoyl]phenylacetylene}(sP-NMe) and poly{(−)-3-methoxycarbonyl-5-[N-propyl -N-(S)-(1-phenylethyl)carbamoyl]phenylacetylene} (sP-NPr). The cis-trans isomerization of amides was investigated by a combinational analysis of 1H/13C nuclear magnetic resonance (NMR), heteronuclear multiple quantum coherence (HMQC), variable-temperature NMR, Raman spectroscopy, ultraviolet–visible (UV–vis) spectroscopy, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and computer calculations. The substituted amide of sP-NMe favors the trans isomer at low temperatures, and the polyene main chain takes the right-handed helical conformation. When increasing the temperature, the ratio of the cis isomer in sP-NMe increases, which causes helical inversion. The screw sense of the polymer backbone of sP-NMe can be thermoreversibly switched upon tuning the cis-trans isomerization equilibrium of the tertiary amide pendant. In comparison, sP-NPr has the left-handed conformation with the majority of the cis isomer owing to the bulky propyl group, and cis-trans isomerization cannot induce helical inversion upon thermal treatment. The results reveal that helical inversion caused by the cis-trans isomerization of amide groups is highly dependent on the size of N-alkyl substituents.

New facets of larger Nest motifs in proteins.

The Nest is a concave-shaped structural motif in proteins formed by consecutive enantiomeric left-handed (L) and right-handed (R) helical conformation of the backbone. This important motif subsumes many turn and helix capping structures and binds electron-rich ligands. Simple Nests are either RL or LR. Larger Nests (>2 residues long) may be RLR, LRL, RLRL, and so forth, being considered as composed of overlapping simple Nests. The larger Nests remain under-explored despite their widely known contributions to protein function. In our study, we address whether the recurrence of enantiomeric geometry in the larger Nests constrains the peptide backbone such that distinct compositional and conformational preferences are seen compared to simple Nests. Our analysis reveals the critical role of the L helical torsion angle in the formation of larger Nests. This can be observed through the higher propensity of residue or secondary structure combinations in LR and LRL backbone conformation in comparison to RL or RLR, although LR/LRL is considerably lower by occurrence. We also find that the most abundant doublets and triplets in Nests have a propensity for particular secondary structures, suggesting a strong sequence-structure relationship in the larger Nest. Overall, our analysis corroborates distinct features of simple and the larger Nests. Such insights would be helpful towards in-vitro design of peptides and peptidomimetic studies.

Development of Helical Aromatic Amide Foldamers with a Diphenylacetylene Backbone.

We designed and synthesized aromatic polyamides with a diphenylacetylene backbone, α-DPA and β-DPA, bearing (S)-α- and (S)-β-methyl-substituted triethyleneglycol (TEG) side chains, respectively, and examined their conformations in solution. Both polymers exhibit strong, solvent polarity-dependent circular dichroism spectra, which indicated that they take helical conformations in low-polarity solvents. The spectra were mirror images, depending on the chiral position of the side chains. Thus, the polyamide α-DPA bearing (S)-α-methyl-substituted TEG groups takes a left-handed helical conformation, while the polyamide β-DPA with (S)-β-methyl-substituted TEG groups takes a right-handed helical conformation. The difference in the screw sense of α-DPA and β-DPA would be caused by the steric interaction between the main chain and the side chain, as observed in poly(p-benzamide) possessing (S)-β-methyl-substituted TEG side chains (β-PA) because the large cavity of the helical structure of DPA would disturb the solvophobically induced helical folding. Detailed conformational analyses of the oligoamides 6-12 with β-methyl-substituted TEG groups were conducted. Theoretical calculations indicated that the oligoamides with β-methyl-substituted TEG groups exist in a helical conformation with a cavity of 7 Å in diameter. The 1H NMR spectra of the oligomers revealed interactions with small anions such as chloride and acetate anions and with pyridinium cations.

Ambidextrous α,γ-Hybrid Peptide Foldamers.

Molecular chirality is ubiquitous in nature. The natural biopolymers, proteins and DNA, preferred a right-handed helical bias due to the inherent stereochemistry of the monomer building blocks. Here, we are reporting a rare co-existence of left- and right-handed helical conformations and helix-terminating property at the C-terminus within a single molecule of α,γ-hybrid peptide foldamers composed of achiral Aib (α-aminoisobutyric acid) and 3,3-dimethyl-substituted γ-amino acid (Adb; 4-amino-3,3-dimethylbutanoic acid). At the molecular level, the left- and right-handed helical screw sense of α,γ-hybrid peptides are representing a macroscopic tendril perversion. The pronounced helix-terminating behaviour of C-terminal Adb residues was further explored to design helix-Schellman loop mimetics and to study their conformations in solution and single crystals. The stereochemical constraints of dialkyl substitutions on γ-amino acids showed a marked impact on the folding behaviour of α,γ-hybrid peptides.

Synthesis and Light‐Mediated Structural Disruption of an Azobenzene‐Containing Helical Poly(isocyanide)

Helical poly(isocyanide)s are an important class of synthetic polymers possessing a static helical structure. Since their initial discovery, numerous examples of these helices have been fabricated. In this contribution, the synthesis of a chiral, azobenzene (azo)-containing isocyanide monomer is reported. Upon polymerization with nickel(II) catalysts, a well-defined circular dichroism (CD) trace is obtained, corresponding to the formation of a right-handed polymeric helix. The helical polymer, dissolved in chloroform and irradiated with UV light (365 nm), undergoes a cis to trans isomerization of the azobenzene side-chains. After the isomerization, a change in conformation of the helix occurs, as evidenced by CD spectroscopy. When the solution is irradiated with LED light, the polymer returns to a right-handed helical conformation. To open up the possibility for chain-end post-polymerization modification of this light-responsive system, an alkyne-functionalized nickel(II) catalyst is also used in the polymerization of the azobenzene monomer, resulting in a stimuli-responsive, terminal-alkyne-containing helical poly(isocyanide).

Three-State Switchable Chiral Stationary Phase Based on Helicity Control of an Optically Active Poly(phenylacetylene) Derivative by Using Metal Cations in the Solid State.

An unprecedented three-state switchable chiral stationary phase (CSP) for high-performance liquid chromatography (HPLC) was developed using a helical poly(phenylacetylene) bearing a chiral ( R)-α-methoxyphenylacetic acid residue as the pendant (poly-1). The left- and right-handed helical conformations were induced in poly-1-based CSP upon coordination with a catalytic amount of soluble sodium and cesium tetrakis[3,5-bis(trifluoromethyl)phenyl]borate salts (MBArF), respectively, which are soluble in the HPLC conditions [hexane-2-propanol (95:5, v/v)]. The switch between the two different helical states of poly-1 can be easily achieved by rinsing the poly-1-based CSP with MeOH and the subsequent addition of the proper MBArF salt. Using this dynamic helical CSP, we demonstrate how changes on the orientation of the secondary structure of a chiral polymer (right-handed, left-handed, and racemic helices) can alter and even invert the elution order of the enantiomers. This study was done without adding chiral additives or changing the mobile phase, which could produce changes on the retention times and make it more difficult to determine the role of the secondary structure during the chiral recognition process.

Effect of the α-substituted chiral side chain on the helical conformation of N-substituted poly(p-benzamide)

The effect of the side chain chiral center position on the secondary structure of oligomers and polymers of N-substituted 4-aminobenzoic acid was studied. Monomer 1 was prepared from l-alanine methyl ester hydrochloride in seven steps. The poly(p-benzamide) having an α-substituted side chain at the nitrogen atom (α-Me-PA) was obtained from the polymerization of 1 with triethylsilane, CsF, and 18-crown-6 in THF. The circular dichroism (CD) studies in solution demonstrated that α-Me-PA adopted a right-handed helical conformation in protic polar solvents, such as water and methanol, and a random structure in chloroform, indicating that solvophobic interactions played an important role in the helical folding of α-Me-PA. The tetramer of (S)-4-(sec-butylamino)benzoic acid was synthesized as a model compound of α-Me-PA. The single crystal X-ray analysis of the tetramer revealed that the right- and left-handed helical molecules existed in a one-to-one ratio in the crystal, and that the screw pitch of the right-handed helix was shorter than the left-handed helix.

Synthesis of Altrose Poly-amido-saccharides with β-N-(1→2)-d-amide Linkages: A Right-Handed Helical Conformation Engineered in at the Monomer Level.

The design and synthesis of amide-linked saccharide oligomers and polymers, which are predisposed to fold into specific ordered secondary structures, is of significant interest. Herein, right-handed helical poly amido-saccharides (PASs) with β-N-(1→2)-d-amide linkages are synthesized by the anionic ring-opening polymerization of an altrose β-lactam monomer (alt-lactam). The right-handed helical conformation is engineered into the polymers by preinstalling the β configuration of the lactam ring in the monomer via the stereospecific [2+2] cycloaddition of trichloroacetyl isocyanate with a d-glycal possessing a 3-benzyloxy group oriented to the α-face of the pyranose. The tert-butylacetyl chloride initiated polymerization of the alt-lactam proceeds smoothly to afford stereoregular polymers with narrow dispersities. Birch reduction of the benzylated polymers gives water-soluble altrose PASs (alt-PASs) in high yields without degradation of the polymer backbone. Circular dichroism analysis shows the alt-PASs adopt a right-handed helical conformation in aqueous solutions. This secondary conformation is stable over a wide range of different conditions, such as pH (2.0 to 12.0), temperature (5 to 75 °C), ionic salts (2.0 M LiCl, NaCl, and KCl), as well as in the presence of protein denaturants (4.0 M urea and guanidinium chloride). Cytotoxicity studies reveal that the alt-PASs are nontoxic to HEK, HeLa, and NIH3T3 cells. The results showcase the ability to direct solution conformation of polymers through monomer design. This approach is especially well-suited and straightforward for PASs as the helical conformations formed result from constraints imposed by the relatively rigid and sterically bulky repeating units.

Novel NMR Techniques to Study Structural and Dynamical Properties of DNA Quadruplexes

Since the right-handed double helical conformation was first described by Watson and Crick (1), we have realized that DNA is highly polymorphic as evidenced by left-handed DNA (2), parallel-stranded DNA (3), DNA quadruplexes (4), and DNA i-motifs (5), to name a few. The conformation a particular segment of DNA assumes, as well as its thermodynamic stability and ligand binding properties, depend highly upon its sequence context and also on environmental conditions (e.g., temperature, cations present, pH, and so on).

Synthesis of Bradyrhizose Oligosaccharides Relevant to the Bradyrhizobium O-Antigen.

The unique α-(1→7)-bradyrhizoside linkages are constructed for the first time via judicious choice of the glycosylation partners and conditions, thus tetra- and penta-bradyrhizosides relevant to the peculiar O-antigen of Bradyrhizobium are synthesized, which are shown to adopt the defined right-handed helical conformations and to be unable to induce innate immune responses in plants.

12/10-Helical β-Peptide with Dynamic Folding Propensity: Coexistence of Right- and Left-Handed Helices in an Enantiomeric Foldamer.

We present the first examples of atomic-resolution crystal data for the β-peptide 12/10-helix from oligomers of cis-2-aminocyclohexane carboxylic acid (cis-ACHC) with alternating chirality. The local conformations of two enantiomeric cis-ACHC dimer units suggested that a chiral β-peptide may adopt both right-handed and left-handed helical conformations in solution. To probe the conformational behavior of 12/10-helical β-peptides, the two reference helices with a single handedness were synthesized with a more rigidified cis-ACHC derivative. Comparison with these reference helices at low temperature revealed that a chiral cis-ACHC oligomer with alternating chirality indeed displays 12/10-helical conformations with both handedness that equilibrate rapidly in solution. This is a very rare example of chiral oligomers with helix inversion ability. The 12/10-helical backbone should be a valuable addition to potential scaffolds for applications involving helices with dynamic folding propensity.

Ribbon structure stabilized by C10 and C12 turns in αγ hybrid peptide

The present study describes the synthesis and crystallographic analysis of αγ hybrid peptides, Boc-Gpn-L-Pro-NHMe (1), Boc-Aib-Gpn-L-Pro-NHMe (2), and Boc-L-Pro-Aib-Gpn-L-Pro-NHMe (3). Peptides 1 and 2 adopt expanded 12-membered (C12 ) helical turn over γα segment. Peptide 3 promotes the ribbon structure stabilized by type II β-turn (C10 ) followed by the expanded C12 helical γα turn. Both right-handed and left-handed helical conformations for Aib residue are observed in peptides 2 and 3, respectively.

Synthesis of polyisocyanides bearing oligothiophene pendants: higher-order structural control through pendant framework design

L-Alanine-based polyisocyanides bearing oligothiophene (OT) pendants (poly-3a and poly-3b) were synthesized and the influence of the OT pendants on the chiroptical properties and helix-forming abilities of the polymers was investigated. Poly-3a bearing a quinquethiophene unit with two n-hexyl chains successfully formed a preferred-handed helical conformation by simultaneous interactions of the OT-pendant π–π stacking and hydrogen bonding of the amide groups. In contrast, poly-3b, which possesses a branched alkyl chain on behalf of the terminal n-hexyl chain of poly-3a, did not form a higher-ordered helical conformation. The results suggest that the structure of the alkyl chains positioned far from the polymer backbones remotely and sensitively affected the ability of the polymer to form a helical conformation. We also found that the structure of the OT pendants significantly affect the molecular weight as observed by AFM measurements. The polyisocyanide poly-3c bearing a bithiophene unit was additionally synthesized to examine the influence of the number of thiophene rings within the OT pendants on the higher-order structure formation. L-Alanine-based polyisocyanides bearing oligothiophene (OT) pendants were synthesized and the influence of the OT pendants on the helix-forming abilities of the polymers was investigated. The polyisocyanide possessing quinquethiophene units with two n-hexyl chains readily formed a right-handed helical conformation with a helical array of the OT pendants biased by the chirality of the L-alanine residues. This study revealed that the simultaneous interactions of the π–π stacking and the hydrogen bonding between the pendants are required to arrange the OT units into a helically twisted manner along the backbone.

Triangular prism-shaped β-peptoid helices as unique biomimetic scaffolds

β-Peptoids are peptidomimetics based on N-alkylated β-aminopropionic acid residues (or N-alkyl-β-alanines). This type of peptide mimic has previously been incorporated in biologically active ligands and has been hypothesized to be able to exhibit foldamer properties. Here we show, for the first time, that β-peptoids can be tuned to fold into stable helical structures. We provide high-resolution X-ray crystal structures of homomeric β-peptoid hexamers, which reveal right-handed helical conformations with exactly three residues per turn and a helical pitch of 9.6–9.8 Å between turns. The presence of folded conformations in solution is supported by circular dichroism spectroscopy showing length- and solvent dependency, and molecular dynamics simulations provide further support for a stabilized helical secondary structure in organic solvent. We thus outline a framework for future design of novel biomimetics that display functional groups with high accuracy in three dimensions, which has potential for development of new functional materials.

Conformation of dehydropentapeptides containing four achiral amino acid residues - controlling the role of L-valine.

Structural studies of pentapeptides containing an achiral block, built from two dehydroamino acid residues (ΔZPhe and ΔAla) and two glycines, as well as one chiral L-Val residue were performed using NMR spectroscopy. The key role of the L-Val residue in the generation of the secondary structure of peptides is discussed. The obtained results suggest that the strongest influence on the conformation of peptides arises from a valine residue inserted at the C-terminal position. The most ordered conformation was found for peptide Boc-Gly-ΔAla-Gly-ΔZPhe-Val-OMe (3), which adopts a right-handed helical conformation.

Polymorphism Complexity and Handedness Inversion in Serum Albumin Amyloid Fibrils

Protein-based amyloid fibrils can show a great variety of polymorphic structures within the same protein precursor, although the origins of these structural homologues remain poorly understood. In this work we investigate the fibrillation of bovine serum albumin--a model globular protein--and we follow the polymorphic evolution by a statistical analysis of high-resolution atomic force microscopy images, complemented, at larger length scales, by concepts based on polymer physics formalism. We identify six distinct classes of coexisting amyloid fibrils, including flexible left-handed twisted ribbons, rigid right-handed helical ribbons and nanotubes. We show that the rigid fibrils originate from flexible fibrils through two diverse polymorphic transitions, first, via a single-fibril transformation when the flexible left-handed twisted ribbons turn into the helical left-handed ribbons, to finally evolve into nanotube-like structures, and second, via a double-fibril transformation when two flexible left-handed twisted ribbons wind together resulting in a right-handed twisted ribbon, followed by a rigid right-handed helical ribbon polymorphic conformation. Hence, the change in handedness occurs with an increase in the level of the fibril's structural organization.