Right-handed Helical Structure Research Articles

A Chirally Stable, Atropoisomeric,Cα-Tetrasubstitutedα-Amino Acid: Incorporation into Model Peptides and Conformational Preference

A variety of model peptides, including four complete homologous series, to the pentamer level, characterized by the recently proposed binaphthyl-based, axially chiral, Cα-tetrasubstituted, cyclic α-amino acid Bin, in combination with Ala, Gly, or Aib residues, was synthesized by solution methods and fully characterized. The solution conformational propensity of these peptides was determined by FT-IR absorption and 1H-NMR techniques. Moreover, the molecular structures of the free amino acid (S)-enantiomer and an Nα-acylated dipeptide alkylamide with the heterochiral sequence -(R)-Bin-Phe- were assessed in the crystal state by X-ray diffraction. Taken together, the results point to the conclusion that β-bends and 310 helices are preferentially adopted by Bin-containing peptides, although the fully extended conformation would also be adopted in solution by the short oligomers to some extent. We also confirmed the tendency of (R)-Bin to fold a peptide chain into right-handed bend and helical structures. The absolute configuration of the Bin residue(s) was correlated with the typically intense exciton-split Cotton effect of the 1Bb binaphthyl transition near 225 nm.

Conformational Free Energy Surfaces of Ala10and Aib10Peptide Helices in Solution

A newly developed molecular simulation algorithm, the multidimensional conformational free energy thermodynamic integration (CFTI) method, has been applied to describe the conformational free energy surfaces of regular peptide helices in solution. The systems studied are (Ala)10 and (Aib)10 peptides, where Aib is α-methylalanine, in water and DMSO solution. The CFTI approach was used to calculate two-dimensional maps of the conformational free energy and its gradient as a function of the peptide backbone dihedrals (φ,ψ). In the region of right-handed helical structures of (Ala)10 and (Aib)10, the α-helix and π-helix were found to be locally stable states, corresponding to free energy minima. The location of the minima was refined by free energy optimization. Unexpectedly, solvation by both water and DMSO tended to strongly stabilize the π-helix relative to the standard α-helical structure. The π and α-helices had essentially identical stability for (Ala)10 in water and DMSO. The (Ala)10 π-helical free ene...

Assemblies of aziridinemethanols

Two novel long chain aziridinemethanols (1b, c) are described and their molecular organisation in the bulk and self-assembling properties in aqueous dispersion are reported. The orientation of the NH hydrogen of the aziridinealcohol moiety in 1b can be changed by introducing a methyl substituent into the rigid three-membered ring (1c), leading to a change in the hydrogen bonding pattern interconnecting these molecules. This change in configuration leads to marked differences in the ordering of these molecules in the solid state. Although compounds 1b and 1c both form highly organised structures in aqueous media and on the air–water interface, noteworthy differences are observed. Compound 1c yields left-handed helical ribbons whereas no chiral aggregates are found for 1b. However, the addition of 2-acetoxybenzoic acid (aspirin) to an aqueous dispersion of 1b leads to the generation of both left- and right-handed helical structures. Under these conditions a reaction had taken place that was specific for the ortho-isomer of acetoxybenzoic acid.

Helical superstructure from an achiral banana-shaped liquid crystal

In the banana-shaped achiral molecular system reported here, 1,3-phenylene bis[4-(3-chloro-4-n-octyloxy-phenyliminomethyl) benzoate] (PBCOB) and 1,3-phenylene bis[4-(3-fluoro-4-n-octyloxy-phenyliminomethyl) benzoate] (PBFOB), their smectic mesophases, including a switchable banana phase B7, were identified by differential scanning calorimetry (DSC), X-ray scattering and polarizing optical microscopy (POM) studies. Both the left- and right-handed helical domains are spontaneously formed upon cooling from isotropic liquid to the switchable banana phase (By). The homeotropic alignment and ferroelectric properties of banana-shaped liquid crystal are investigated. The spontaneous polarization for PBCOB is about 50 nC/cm2. Doping the PBCOB with a cyanohydrin-contain chiral smectic liquid crystal resulted in more right-handed helical structures.

Cryoatomic Force Microscopy of Filamentous Actin

Cryoatomic force microscopy (cryo-AFM) was used to image phalloidin-stabilized actin filaments adsorbed to mica. The single filaments are clearly shown to be right-handed helical structures with a periodicity of ∼38 nm. Even at a moderate concentration (∼10 μg/ml), narrow, branched rafts of actin filaments and larger aggregates have been observed. The resolution achieved is sufficient to resolve actin monomers within the filaments. A closer examination of the images shows that the branched rafts are composed of up to three individual filaments with a highly regular lateral registration with a fixed axial shift of ∼13 nm. The implications of these higher-order structures are discussed in terms of x-ray fiber diffraction and rheology of actin gels. The cryo-AFM images also indicate that the recently proposed model of left-handed F-actin is likely to be an artifact of preparation and/or low-resolution AFM imaging.

Solution structure of an 11-mer duplex containing the 3, N4-ethenocytosine adduct opposite 2′-deoxycytidine: implications for the recognition of exocyclic lesions by DNA glycosylases

Lipid peroxidation products, as well as the metabolic products of vinyl chloride, react with cellular DNA producing the mutagenic adduct 3, N 4-etheno-2′-deoxycytidine (ϵdC), along with several other exocyclic derivatives. High-resolution NMR spectroscopy and restrained molecular dynamics simulations were used to establish the solution structure of an 11-mer duplex containing an ϵdC·dC base-pair at its center. The NMR data suggested a regular right-handed helical structure having all residues in the anti orientation around the glycosydic torsion angle and Watson-Crick alignments for all canonical base-pairs of the duplex. Restrained molecular dynamics generated a three-dimensional model in excellent agreement with the spectroscopic data. The (ϵdC·dC)-duplex structure is a regular right-handed helix with a slight bend at the lesion site and no severe distortions of the sugar-phosphate backbone. The ϵdC adduct and its partner dC were displaced towards opposite grooves of the helix, resulting in a lesion-containing base-pair that was highly sheared but stabilized to some degree by the formation of a single hydrogen bond. Such a sheared base-pair alignment at the lesion site was previously observed for ϵdC·dG and ϵdC·T duplexes, and was also present in the crystal structures of duplexes containing dG·T and dG·U mismatches. These observations suggest the existence of a substrate structural motif that may be recognized by specific DNA glycosylases during the process of base excision repair.

The tetratricopeptide repeat: a structural motif mediating protein-protein interactions.

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s). Three-dimensional structural data have shown that a TPR motif contains two antiparallel alpha-helices such that tandem arrays of TPR motifs generate a right-handed helical structure with an amphipathic channel that might accommodate the complementary region of a target protein. Most TPR-containing proteins are associated with multiprotein complexes, and there is extensive evidence indicating that TPR motifs are important to the functioning of chaperone, cell-cycle, transcription, and protein transport complexes. The TPR motif may represent an ancient protein-protein interaction module that has been recruited by different proteins and adapted for specific functions. BioEssays 1999;21:932-939.

Synthesis and folding preferences of γ-amino acid oligopeptides: stereochemical control in the formation of a reverse turn and a helix

Abstract The stereoselective synthesis of α-cinnamyl γ-amino acids and the corresponding oligopeptides is described. Detailed 1D and 2D NMR studies in pyridine-d 5 show that the ( αR )-cinnamyl γ-amino acid tetrapeptide adopts a reverse turn structure, while the ( αS )-cinnamyl γ-amino acid tetrapeptide adopts a right-handed helical structure.

Self-assembly of disk-shaped molecules to coiled-coil aggregates with tunable helicity

A disk-shaped molecule with chiral tails is shown to form long fibers of molecular diameter and micrometer length by self-assembly in chloroform. The molecules are derived from crown ethers and contain a phthalocyanine ring. In the fibers, they have a clockwise, staggered orientation that leads to an overall right-handed helical structure. These structures, in turn, self-assemble to form coiled-coil aggregates with left-handed helicity. Addition of potassium ions to the fibers leaves their structure intact but blocks the transfer of the chirality from the tails to the cores, leading to loss of the helicity of the fibers. These tunable chiral materials have potential in optoelectronic applications and as components in sensor devices.

Solution structure of duplex DNA containing an extrahelical abasic site analog determined by NMR spectroscopy and molecular dynamics.

Translesional DNA synthesis past abasic sites proceeds with the preferential incorporation of dAMP opposite the lesion and, depending on the sequence context, one or two base deletions. High-resolution NMR spectroscopy and molecular dynamics simulations were used to determine the three-dimensional structure of a DNA heteroduplex containing a synthetic abasic site (tetrahydrofuran) residue positioned in a sequence that promotes one base deletions. Analysis of NMR spectra indicates that the stem region of the duplex adopts a right-handed helical structure and the glycosidic torsion angle is in anti orientation for all residues. NOE interactions establish Watson-Crick alignments for all canonical base pairs of the duplex. Measurement of distance interactions at the lesion site shows the abasic residue excluded from the helix. Restrained molecular dynamics simulations generated three-dimensional models in excellent agreement with the spectroscopic data. These structures show a regular duplex region and a slight bend at the lesion site. The tetrahydrofuran residue extrudes from the helix and is highly flexible. The model reported here, in conjunction with a previous study performed on abasic sites, explains the structural bias of one-base deletion mutations.

Solution structure of a DNA duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2'-deoxyguanosine.

Vinyl chloride reacts with cellular DNA producing 3,N4-etheno-2'-deoxycytidine (epsilonC) along with other exocyclic adducts. The solution structure of an oligodeoxynucleotide duplex containing an epsilonC.dG base pair was determined by high-resolution NMR spectroscopy and molecular dynamics simulations. NMR data indicated that the duplex adopts a right-handed helical structure having all residues in anti orientation around the glycosylic torsion angle. The epsilonC adduct has a sugar pucker in the C3'-endo/C4'-exo region while the rest of the residues are in the C2'-endo/C3'-exo range. NOE interactions established Watson-Crick alignments for canonical base pairs of the duplex. The imino proton of the lesion-containing base pair resonated as a sharp signal that was resistant to water exchange, suggesting hydrogen bonding. Restrained molecular dynamics simulations generated three-dimensional models in excellent agreement with the spectroscopic data. The refined structures are slightly bent at the lesion site without major perturbations of the sugar-phosphate backbone. The adduct is displaced and shifted toward the major groove of the helix while its partner on the complementary strand remains stacked. The epsilonC(anti).dG(anti) base pair alignment is sheared and stabilized by the formation of hydrogen bonds. The biological implications of structures of epsilonC-containing DNA duplexes are discussed.

Effect of Nα-Acyl Chain Length on the Membrane-Modifying Properties of Synthetic Analogs of the Lipopeptaibol Trichogin GA IV

Trichogin GA IV, an 11-residue lipopeptaibol blocked at the N-terminus by an n-octanoyl group and at the C-terminus by a 1,2-amino alcohol (l-leucinol), extracted from the fungus Trichoderma longibrachiatum, exhibits remarkable membrane-modifying properties. We have synthesized trichogin GA IV and several [l-Leu-OMe11] analogs carrying at the N-terminus an acyl chain of variable length (C2−C8, C10, C12, C14, C16, C18). A succinoylated head-to-head dimer was also prepared. A conformational analysis, carried out by FTIR absorption, CD, and NMR, showed that the right-handed helical structure of the natural lipopeptaibol is essentially preserved in all its analogs. Permeability measurements revealed that at least six carbon atoms in the Nα-blocking fatty acyl moiety are required for the onset of significant membrane-modifying properties. Also the head-to-head dimer is remarkably active. Possible models for the mechanism of membrane permeability of trichogin GA IV are discussed.

Isolation of intramitochondrial helical filaments appearing in outer compartment of mitochondria.

Packets of helical filaments have been observed in the outer compartment of occasional mitochondria in many cell types in a variety of animals. The composition and function of these intramitochondrial helical filaments (IMHF) are unknown. IMHF were induced in a hepatic mitochondria by administration of ethanol in the drinking water of rats. Hepatic mitochondria were isolated and ruptured by osmotic shock, releasing the IMHF. To purify these structures, the IMHF-containing supernatant was further fractionated by ammonium sulfate precipitation, a 50-60% solution of this reagent being the most effective in this regard. Isolated IMHF were examined by electron microscopy and were analyzed by SDS-PAGE. Isolated IMHF closely resembled their in situ counterparts: they had a right-handed helical structure with a 16 nm pitch. SDS-PAGE analysis revealed that they contained three polypeptides with molecular weight of 135, 98, and 53 kD, respectively. These observations will stand as a baseline for comparisons with IMHF that occur naturally or that are induced in other cell types by other kinds of experimental manipulation.

Effect of thymine tract length on the structure and stability of model telomeric sequences

DNA from the telomeres at the ends of eukaryotic chromosomes contains a stretch of simple tandemly repeated sequences in which clusters of G residues alternate with clusters of T/A sequences along one DNA strand. Model telomeric G-clusters form four-stranded structures in Na+ or K+, stabilized by Hoogsteen pairing between G bases. DNA containing a single copy of the G-cluster can self-associate to form tetramers, with a parallel-stranded, right-handed helical structure. Two copies of the 3'-terminal G strand form a folded-back hairpin that dimerizes to create an antiparallel quadruplex structure. We show here that the tetrameric structure is strongly influenced by the T residue flanking either side of the G-cluster. The parallel tetraplex formed by single copies of the sequences dTnG4 is most stable for n = 1 and least stable for n = 8, the longest tract we have studied. At least two thymine residues are required to allow formation of antiparallel folded-back hairpin dimers from two-copy oligomers of sequence d(TnG4)2 in Na+; additional T's destabilize this structure. In K+, the predominant structure formed is the four-stranded parallel tetramer in all cases. Kinetic analysis indicates that the quadruplex structure formed by Oxytricha telomeric DNA overhangs in the presence of Na+ arises by dimerization of two Hoogsteen base-paired hairpins, with a relatively low energy barrier.

Thermodynamics of G-tetraplex formation by telomeric DNAs.

Telomeres are structures at the ends of eukaryotic chromosomes, the DNA of which contains stretches of tandemly repeated sequences with G clusters along one strand. Model telomeric G-rich DNAs can form different tetraplex structures, stabilized by cyclic hydrogen bonding of four guanines in the presence of metal ions such as Na+ or K+. Oligonucleotides with a single copy of the Oxytricha sequence dT4G4 form a tetramer, with a parallel-stranded, right-handed helical structure. Additional copies favor folded-back structures that associate to form an antiparallel dimer. The parallel-stranded tetramer has all G's in the anti configuration, while the folded-back dimer has alternating syn and anti nucleotide conformations along each strand. Here we have constructed two G-tetraplex structures, containing identical G-tetrad base pairs, from oligonucleotides. One has the truncated telomeric sequence from Oxytricha, dG4T4G4, which forms an antiparallel G-quartet structure; the second is constrained to form a parallel G-strand arrangement by insertion of a 5'-p-5' linkage between two dT2G4 sequences. Each oligomer forms a defined G-tetraplex dimeric structure in the presence of Na+. The standard-state enthalpies, entropies, and free energy for formation of these tetraplexes have been determined. The parallel strand structure is thermodynamically more stable than the antiparallel one, primarily because of both greater enthalpy and entropy of formation. In addition, the two molecules differ in their interaction with sodium ions, reflecting a difference in ion binding and therefore in structure between the two forms.

Peptides from chiral Cα,α‐disubstituted glycines Synthesis and characterization, conformational energy computations and solution conformational analysis of Cα‐methyl, Cα‐isopropylglycine [(αMe)Val] derivatives and model peptides*

Conformational energy computations on Ac-L-(alpha Me)Val-NHMe indicate that turns and right-handed helical structures are particularly stable conformations for this chiral C alpha-methyl, C alpha-alkylglycyl residue. We have synthesized and characterized a variety of L-(alpha Me)Val derivatives and peptides (to the pentamer level). The results of the solution conformational analysis, performed using infrared absorption, 1H nuclear magnetic resonance, and circular dichroism, are in general agreement with those obtained from the theoretical investigation, in the sense that the L-(alpha Me)Val residue turns out to be a strong beta-turn and right-handed helix former. A comparison is also made with the conclusions extracted from published work on peptides rich in other C alpha-methyl, C alpha-alkylglycyl residues.

Scanning tunneling microscopy of collagen molecules

Calf skin collagen molecules adsorbed on a graphite substrate were directly imaged by scanning tunneling microscopy in air. The right-handed helical structures were observed and the average periodicity was quantitatively measured to be 31 Å, in good agreement with the value of about 28 Å estimated from biochemical studies. The intermolecular distance in a collagen bundle was 23 Å.

NMR studies of an oligonucleotide with an unusual structure induced by platinum anticancer drugs

The 31P NMR spectra of Pt( en){ d( T 1 A 2 T 3 G 4 G5 G 6 T 7 A 8 C 9 C 10 C 11 A 12 T 13 A 14)} (14-me r) and Pt( en){ d( A 2 T 3 G 4 G 5 G 6 T 7 A 8 C 9 C 10 C 11 A 12 T 13)} (12-mer) (en = ethylenediamine) each contai far downfield ( ca. −2.9 and −2.6 ppm from trimethylphosphate standard), two signals slightly downfield, and at least one signal slightly upfield of the normal range ( ca. −4.0 to −4.4 ppm). This pattern suggested a distorted structure. The unusual 31P signals of the 12-mer were assigned by analogy to signals of the 14-mer previously assigned by 17O-labeling methods. A combination of heteronuclear multiple-quantum coherence, one-dimensional and two-dimensional nuclear Overhauser effect (1D- and 2D-NOE) and homonuclear shift correlation spectroscopy (COSY) experiments assigned all aromatic 1H signals of the 12-mer except H8 of G 5 or G 6. One of these H8 signals is missing from the spectrum and the nucleotide is labeled G m. The other H8 is the most downfield signal and has a strong NOE to its H1'. Since this strong NOE indicates that this nucleoside exists in a syn conformation, it is labeled G s. A strong NOE was observed between the G s and A 8 H8 signals. Several lines of evidence suggested a hairpin-like structure with a loop region (G 6T 7A 8C 9) and a stem region involving A 2T 3G 4G 5 and C 10C 11A 12T 13. The 31P signals for the stem region are within or slightly outside the normal range, 3 J H3'-Pvalues (3–6 Hz), measured by a 2D- J experiment, of stem nucleotides were characteristic for a DNA duplex. Imino signals for base pairs A 2T 13,T 3A 12, G 4C 11, and probably G 5C 10, and the observation of internucleotide NOE connectivities for these nucleotides (e.g. between an H8 signal and the H1' signal of the 5' nucleotide) suggested a right-handed helical structure. For the loop region, a distorted sugar-phosphate backbone is indicated by far downfield positions of the G 5pG 6 and A 8pC 9 31P signals, the if 3J H3′−P values for C 9p (8.0 Hz) and A 8p (6.8 Hz), and the absence of H3'-P coupling for G 5p. In the loop region, no imino signals or internucleotide NOEs characteristic of a right-handed duplex were observed. However, A 8H8, C 9H6, and C 10H6 each exhibited unusual internucleotide NOEs to the H4' signal of the 5' residue. NOE crosspeaks between T 7 1H signals and signals attributed to sugars of the G s and G m suggested that the T 7 moiety is located within the space encircled by the loop. The few NOE crosspeaks, pH dependence, and Cu 2+ broadening of C 9 1H signals indicate an isolated location accessible to solvent. Selective reverse chemical shift correlation, 1D- and 2D-NOE, and COSY experiments for the 14-mer produced results very similar to those described above for the 12-mer. We evaluated the following four models for the structure of the loop region of the 12-mer and the 14-mer: (1) Model I, in which Pt is bound to G 5G 6; (2) Model II, in which Pt is bound to three bases, G 5, G 6, and A 8; (3) a variation of Model II (Model IIC), in which one of the G bases forms a Pt—C8 bond; and (4) Model III, in which Pt is bound to A 8 and either G 5 or G 6. Model I does not explain the NOE between the A 8 and G s H8 signals nor the missing H8 signal. Two sets of results provide evidence against Model II and Model IIC. First, the 195Pt NMR spectra of the 12-mer and 14-mer have signals (−2645 and −2640 ppm respectively) similar to the reported shift for (Pt(en)(Guo) 2-N7,N7) 2+. Second, the presence of all fifteen signals in the 9–7 ppm region for 12-mer after Pt removal by KCN in D 2O suggested that Pt does not bind at C8. Model III provides the best explanation for our results. A pH dependence study of the 12-mer tentatively assigned G s as G 5. In summary, we believe that Model III, in which Pt binds G 5, is most reasonable and that a bend may occur at the intersection of the loop and stem regions.

Enhanced recA Protein Binding to Z DNA Represents a Kinetic Perturbation of a General Duplex DNA Binding Pathway

recA protein binding to duplex DNA is enhanced when a B form DNA substrate is replaced with a left-handed Z form helix. This represents a kinetic rather than an equilibrium effect. Binding to Z DNA is much faster than binding to B DNA. In other respects, binding to the two DNA forms is quite similar. recA protein binds to B or Z DNA with a stoichiometry of 1 monomer/4 base pairs. The final protein filament exhibits a right-handed helical structure when either B or Z form DNAs are bound. There are only two evident differences: the kcat for ATP hydrolysis is reduced 3-4-fold when Z DNA is bound, and recA binding at equilibrium is less stable on Z DNA than on B DNA. At steady state, the binding favors B DNA in competition experiments. The results indicate that Z DNA binding by recA protein follows the same pathway as for recA binding to B DNA, but that the nucleation step is faster on the Z form helix.

Thermotropic Cellulose Derivatives with Flexible Substituents. I. Preparation of Tri-o-(β-methoxyethoxy)ethyl Cellulose and its Cholesteric Mesophase Properties

Abstract Tri-o-(β-methoxyethoxy)ethyl cellulose was prepared by reacting the regenerated cellulose with 2-(2-methoxyethoxy)ethyl iodide and characterized as a fully substituted derivative. The resultant derivative forms a thermotropic liquid crystal in the wide temperature range from room temperature to the isotropization temperature of 180°C, showing that the (methoxyethoxy)ethyl side-chain substituent is long and flexible enough to inhibit crystallization of the extended cellulose chains and facilitate formation of liquid crystals. This is the first example of a thermotropic liquid crystalline cellulose derivative with a homogeneous side chain. This type of liquid crystal is cholesteric with a right-handed helical structure. The cholesteric pitch increases with increasing temperature, with the magnitudes comparable to the wavelength of visible light in the temperature range below 120°C.