Chiral, fully extended helical peptides

Identification of the Cirratiomycin Biosynthesis Gene Cluster in Streptomyces Cirratus: Elucidation of the Biosynthetic Pathways for 2,3-Diaminobutyric Acid and Hydroxymethylserine

Cirratiomycin, a heptapeptide with antibacterial activity, was isolated and characterized in 1981; however, its biosynthetic pathway has not been elucidated. It contains several interesting nonproteinogenic amino acids, such as (2S,3S)-2,3-diaminobutyric acid ((2S,3S)-DABA) and α-(hydroxymethyl)serine, as building blocks. Here, we report the identification of a cirratiomycin biosynthetic gene cluster in Streptomyces cirratus. Bioinformatic analysis revealed that several Streptomyces viridifaciens and Kitasatospora aureofaciens strains also have this cluster. One S. viridifaciens strain was confirmed to produce cirratiomycin. The biosynthetic gene cluster was shown to be responsible for cirratiomycin biosynthesis in S. cirratus in a gene inactivation experiment using CRISPR-cBEST. Interestingly, this cluster encodes a nonribosomal peptide synthetase (NRPS) composed of 12 proteins, including those with an unusual domain organization: a stand-alone adenylation domain, two stand-alone condensation domains, two type II thioesterases, and two NRPS modules that have no adenylation domain. Using heterologous expression and in vitro analysis of recombinant enzymes, we revealed the biosynthetic pathway of (2S,3S)-DABA: (2S,3S)-DABA is synthesized from l-threonine by four enzymes, CirR, CirS, CirQ, and CirB. In addition, CirH, a glycine/serine hydroxymethyltransferase homolog, was shown to synthesize α-(hydroxymethyl)serine from d-serine in vitro. These findings broaden our knowledge of nonproteinogenic amino acid biosynthesis.

Synthesis and Conformational Behaviors of Unnatural Peptides Alternating Chiral and Achiral α,α-Disubstituted α-Amino Acid Units

The development of peptidomimetics to modulate the conformational profile of peptides has been extensively studied in the fields of biological and medicinal chemistry. However, large-scale synthesis of peptidomimetics with both an ordered sequence and a controlled secondary structure is highly challenging. In this paper, the framework of peptidomimetics has been designed to be alternating an achiral α,α-disubstituted α-amino acid unit and a chiral α-methylphenylalanine unit. The polymers are synthesized via invented Ugi reaction-based polycondensation technique. The chiral higher-order structures of the alternating peptides are evaluated mainly through circular dichroism (CD) spectroscopy. The UV-Vis and CD spectra of the polymers in three solvents are systematically measured at various temperatures. The anisotropic factors of CD (gCD ) values are calculated to know the chiroptical response. The results indicate the characteristic conformational behaviors. In a polar solvent, the hydrogen bonds between the N-H group of MePhe unit and the C=O of α,α-diphenylglycine unit outweigh the intraresidue hydrogen bonds in α,α-diphenylglycine unit, leading to the formation of a prevailing preferred-handed 310 -helical conformation. On the other hand, in a less polar solvent, the intrachain hydrogen bonds switch to intraresidue hydrogen bonds in α,α-diphenylglycine unit, which make the polymer adopting a prevailing extended planar C5 -conformation.

Synthetic Mitochondria-Targeting Peptides Incorporating α-Aminoisobutyric Acid with a Stable Amphiphilic Helix Conformation in Plant Cells

In the genetic modification of plant cells, the mitochondrion is an important target in addition to the nucleus and plastid. However, gene delivery into the mitochondria of plant cells has yet to be established by conventional methods, such as particle bombardment, because of the small size and high mobility of mitochondria. To develop an efficient mitochondria-targeting signal (MTS) that functions in plant cells, we designed the artificial peptide (LURL)₃ and its analogues, which periodically feature hydrophobic α-aminoisobutyric acid (Aib, U) and cationic arginine (R), considering the consensus motif recognized by the mitochondrial import receptor Tom20. Circular dichroism measurements and molecular dynamics simulation studies revealed that (LURL)₃ had a propensity to form a stable α-helix in 0.1 M phosphate buffer solution containing 1.0 wt % sodium dodecyl sulfate. After internalization into plant cells via particle bombardment, (LURL)₃ revealed highly selective accumulation in the mitochondria, whereas its analogue (LARL)₃ was predominantly located in the vacuoles in addition to mitochondria. The high selectivity of (LURL)₃ can be attributed to the incorporation of Aib, which promotes the hydrophobic interaction between the MTS and Tom20 by increasing the hydrophobicity and helicity of (LURL)₃. The present study provided a prospective mitochondrial targeting system using the simple design of artificial peptides.

Flat, Cα,β -Didehydroalanine Foldamers with Ferrocene Pendants: Assessing the Role of α-Peptide Dipolar Moments

The foldamer field is continuously expanding as it allows to produce molecules endowed with 3D-structures and functions never observed in nature. We synthesized flat foldamers based on the natural, but non-coded, Cα,β -didehydroalanine α-amino acid, and covalently linked to them two ferrocene (Fc) moieties, as redox probes. These conjugates retain the flat and extended conformation of the 2.05 -helix, both in solution and in the crystal state (X-ray diffraction). Cyclic voltammetry measurements agree with the adoption of the 2.05 -helix, characterized by a negligible dipole moment. Thus, elongated α-peptide stretches of this type are insulators rather than charge conductors, the latter being constituted by peptide α-helices. Also, our homo-tetrapeptide has a N-to-C length of about 18.2 Å, almost double than that (9.7 Å) of an α-helical α-tetrapeptide.

Extent of Helical Induction Caused by Introducing α-Aminoisobutyric Acid into an Oligovaline Sequence

The preferred conformations of a dodecapeptide composed of l-valine (l-Val) and α-aminoisobutyric acid (Aib) residues, Boc-(l-Val-l-Val-Aib)₄-OMe (3), were analyzed in solution and in the crystalline state. Peptide 3 predominantly folded into a mixture of α- and 3₁₀-(P) helical structures in solution and a (P) α helix in the crystalline state.

Development of helix-stabilized antimicrobial peptides composed of lysine and hydrophobic α,α-disubstituted α-amino acid residues

Lysine-based amphipathic nonapeptides, including homochiral peptides [Ac-(l-Lys-l-Lys-Xaa)₃-NH₂ (Xaa=Gly, Ala, Aib, Ac₅c, or Ac₆c) and Ac-(d-Lys-d-Lys-Aib)₃-NH₂], a heterochiral peptide [Ac-(l-Lys-d-Lys-Aib)₃-NH₂], and a racemic mixture of diastereomeric peptides [Ac-(rac-Lys-rac-Lys-Aib)₃-NH₂] were designed and synthesized to investigate the relationship between their preferred secondary structures and their antimicrobial activity. Peptide 5, [Ac-(l-Lys-l-Lys-Ac₆c)₃-NH₂] formed a stable α-helical structure and exhibited strong activity against Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa).

Low pH-triggering changes in peptide secondary structures

An acidic treatment of cyclic α,α-disubstituted α-amino acid-containing peptides changes their conformation from a helical to a random structure.

The 2.0₅-helix in hetero-oligopeptides entirely composed of C(α,α)-disubstituted glycines with both side chains longer than methyls

The existence of the very uncommon, but potentially quite interesting, multiple, consecutive fully-extended conformation (2.0₅-helix) has been already clearly demonstrated in homo-oligopeptides based on quaternary α-amino acids with both side chains longer than methyls, but not cyclized on the α-carbon atom. To extend the scope of this research, in this work we investigated the occurrence of this flat 3D-structure in hetero-oligopeptides, each composed of two or three different residues of that class. The synthesis of a terminally protected peptide series to the tetrapeptide level was carried out by solution methods. The resulting oligomers were chemically and conformationally characterized. The data obtained point to an overwhelming population of the fully-extended conformation in CDCl3. However, a solvent-driven switch to a predominant 3₁₀-helical structure was seen in CD3CN. A delicate, local balance between these two conformations is confirmed to occur in the crystalline state. Molecular dynamics simulations in CHCl3 on a hetero-tetrapeptide converged to the fully-extended conformation even starting from the 3₁₀-helical structure.

Helical screw-sense preferences of peptides based on chiral, Cα-tetrasubstituted α-amino acids

The preferred helical screw senses of chiral α-amino acids with a C(α)-tetrasubstituted α-carbon atom, as determined in the crystal state by X-ray diffraction analyses on derivatives and peptides, are reviewed. This survey covers C(α)-methylated and C(α)-ethylated α-amino acids, as well as α-amino acids cyclized on the α-carbon, including those characterized by the combination of lack of chirality at the α-carbon with either side-chain or axial chirality. Although, in general, chiral C(α)-tetrasubstituted α-amino acids show a less pronounced bias toward a single helical screw sense than their proteinogenic (C(α)-trisubstituted) counterparts, our analysis highlights significant differences in terms of magnitude and direction of such a bias among the various sub-families of residues, and between individual amino acids within each sub-family as well. The experimental findings can be rationalized, at least in part, on the basis of steric considerations.

Multiple, consecutive, fully-extended 2.0₅-helix peptide conformation

The peptide 2.0(5)-helix does exist. It has been experimentally authenticated both in the crystalline state (by X-ray diffraction) and in solution (by several spectroscopic techniques). It is the most common conformation for C(α)-tetrasubstituted α-amino acids with at least two atoms in each side chain, provided that cyclization on the C(α)-atom is absent. X-Ray diffraction has allowed a detailed description of its geometrical and three-dimensional (3D)-structural features. The infrared absorption and the nuclear magnetic resonance parameters characteristics of this multiple, consecutive, fully-extended structure have been described. Conformational energy calculations are in agreement with the experimental findings. As the contribution per amino acid residue to the length of this helix is the longest possible, its exploitation as a molecular spacer is quite promising. However, it is a rather fragile 3D-structure and particularly sensitive to solvent polarity. Interestingly, in such a case, it may reversibly convert to the much shorter 3(10)-helix, thus generating an attractive molecular spring.

Topological Study of the Structures of Heterochiral Peptides Containing Equal Amounts of l-Leu and d-Leu

We designed and synthesized two dodecapeptides, Boc-(l-Leu-l-Leu-Aib-d-Leu-d-Leu-Aib)2-OMe (5) and Boc-l-Leu-l-Leu-Aib-(d-Leu-d-Leu-Aib)2-l-Leu-l-Leu-Aib-OMe (6), that contain equal amounts of l-Leu, d-Leu, and achiral Aib residues. The conformations of peptides 5 and 6 in the crystalline state were studied using X-ray crystallographic analysis. Peptide 5 formed a left-handed (M) α-helical structure, whereas peptide 6 was composed of a combination of fused (M) α-helical and right-handed (P) 310-helical structures. In solution, roughly equivalent amounts of (P) and (M) helices were present in 5, whereas the (M) α-helix was present in 6 as its dominant conformation.

Conformational preferences of Ac-Gly-NHMe in solution

The conformational behaviour of Ac-Gly-NHMe and its fluorinated [CF₃-C(O)-Gly-NHMe] and N-methyl[Ac-Gly-N(Me)₂] derivatives is investigated in nonpolar, polar and polar protic solutions by NMR and IR spectroscopies and theoretical calculations.

Exploring the consequences of a representative "disallowed" conformation of Aib on a 3₁₀-helical fold

The structural effects of a representative "disallowed" conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D ((1)H, (13)C) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)-helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib*-Oxa) of 2, in a conformation (ϕ, ψ = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)-helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations.

Conformation of a terminally protected βγ hybrid dipeptide Boc-Ant-Gpn-OMe stabilized by C6/C7 hydrogen bonds

The hybrid βγ dipeptide, methyl 2-[1-({2-[(tert-butoxycarbonyl)amino]benzamido}methyl)cyclohexyl]acetate (Boc-Ant-Gpn-OMe), C22H32N2O5, adopts a folded conformation stabilized by intramolecular six- (C6) and seven-membered (C7) hydrogen-bonded rings, together with weak C-H...O and C-H...π interactions, resulting in a ribbon-like structure.