Folding a nonbiological polymer into a compact multihelical structure

The only molecules that are currently known to fold into unique three-dimensional conformations and perform sophisticated functions are biological polymers - proteins and some RNA molecules. Our aim is to create a nonbiological sequence-specific polymer that folds in aqueous solution. Toward that end, we synthesized sequence-specific 30mer, 45mer, and 60mer peptoid oligomers (N-substituted glycine polymers) consisting of 15mer units we chained together by disulfide and oxime linkages to mimic the helical bundle structures commonly found in proteins. Because these 15mer sequences were previously shown to form defined helical structures that aggregate together at submillimolar concentrations, we expected that by covalently linking multiple 15mers together, they might fold as helical bundles. To probe whether they folded, we used fluorescence resonance energy transfer (FRET) reporter groups. We found that certain constructs fold up with a hydrophobic core and have cooperative folding transitions. Such molecules may ultimately provide a platform for designing specific functions resembling those of proteins.     

Helical peptoid mimics of magainin-2 amide

A series of peptoid oligomers were designed as helical, cationic, and facially amphipathic mimics of the magainin-2 amide antibacterial peptide. We used circular dichroism spectroscopy to determine the conformation of these peptoids in aqueous buffer and in the presence of bacterial membrane-mimetic lipid vesicles, composed of a 7:3 mol ratio of POPE:POPG. We found that certain peptoids, which displayed characteristically helical CD in buffer and lipid vesicles, exhibit selective (nonhemolytic) and potent antibacterial activity against both Gram-positive and Gram-negative bacteria. In contrast, peptoids that exhibit weak CD, reminiscent of that of a peptide random coil, were ineffective antibiotics. In a manner similar to the natural magainin peptides, we find a correlation between peptoid lipophilicity and hemolytic propensity. We observe that a minimum length of approximately 12 peptoid residues may be required for antibacterial activity. We also see evidence that a helix length between 24 and 34 A may provide optimal antibacterial efficacy. These results provide the first example of a water-soluble, structured, bioactive peptoid.     

Helical structure of single-crystalline ZnGa2O4 nanowires

Two unique helical zinc gallate (ZnGa2O4) nanostructures were synthesized by thermal evaporation using the zinc selenide (ZnSe) nanowires; helical ZnGa2O4 nanowire rolls either on a straight ZnSe nanowire support or without any support. They all consist of single-crystalline cubic ZnGa2O4 crystals without any dislocation over the entire helical structure and have four equivalent growth directions of 011 with the axial direction of [001]. We suggest that the lattice matching with the ZnSe nanowires would be an important factor in determining the growth direction of the helical ZnGa2O4 nanowires.     

Toward the synthesis of artificial proteins: the discovery of an amphiphilic helical peptoid assembly

While nature exploits folded biopolymers to achieve molecular recognition and catalysis, comparable abiological heteropolymer systems have been difficult to create. We synthesized and identified abiological peptoid heteroploymers capable of binding a dye. Using combinatorial synthesis, we constructed a library of 3400 amphiphilic 15-mer peptoids on an ultra-high-capacity beaded support. Individual macrobeads, each containing a single peptoid sequence, were arrayed into plates, cleaved, and screened in aqueous solution to locate dye binding heteropolymer assemblies. Resynthesis and characterization demonstrated the formation of defined helical assemblies as judged by size-exclusion chromatography, circular dichroism, and analytical ultracentrifugation. Inspired by nature's process of sequence variation and natural selection, we identified rare abiological sequence-specific heteropolymers that begin to mimic the structure and functional properties of their biological counterparts.     

Tuning peptoid secondary structure with pentafluoroaromatic functionality: a new design paradigm for the construction of discretely folded peptoid structures

Peptoids, or oligomers of N-substituted glycine, are an important class of non-native polymers whose close structural similarity to natural alpha-peptides and ease of synthesis offer significant advantages for the study of biomolecular interactions and the development of biomimetics. Peptoids that are N-substituted with alpha-chiral aromatic side chains have been shown to adopt either helical or "threaded loop" conformations, depending upon solvent and oligomer length. Elucidation of the factors that impact peptoid conformation is essential for the development of general rules for the design of peptoids with discrete and novel structures. Here, we report the first study of the effects of pentafluoroaromatic functionality on the conformational profiles of peptoids. This work was enabled by the synthesis of a new, alpha-chiral amine building block, (S)-1-(pentafluorophenyl)ethylamine (S-2), which was found to be highly compatible with peptoid synthesis (delivering (S)-N-(1-(pentafluorophenyl)ethyl)glycine oligomers). The incorporation of this fluorinated monomer unit allowed us to probe both the potential for pi-stacking interactions along the faces of peptoid helices and the role of side chain electrostatics in peptoid folding. A series of homo- and heteropeptoids derived from S-2 and non-fluorinated, alpha-chiral aromatic amide side chains were synthesized and characterized by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. Enhancement of pi-stacking by quadrupolar interactions did not appear to play a significant role in stabilizing the conformations of heteropeptoids with alternating fluorinated and non-fluorinated side chains. However, incorporation of (S)-N-(1-(pentafluorophenyl)ethyl)glycine monomers enforced helicity in peptoids that typically exhibit threaded loop conformations. Moreover, we found that the incorporation of a single (S)-N-(1-(pentafluorophenyl)ethyl)glycine monomer could be used to selectively promote looped or helical structure in this important peptoid class by tuning the electronics of nearby heteroatoms. The strategic installation of this monomer unit represents a new approach for the manipulation of canonical peptoid structure and the construction of novel peptoid architectures.     

Extraordinarily robust polyproline type I peptoid helices generated via the incorporation of α-chiral aromatic N-1-naphthylethyl side chains

Peptoids, or oligomers of N-substituted glycines, are a class of foldamers that have shown extraordinary functional potential since their inception nearly two decades ago. However, the generation of well-defined peptoid secondary structures remains a difficult task. This challenge is due, in part, to the lack of a thorough understanding of peptoid sequence-structure relationships and, consequently, an incomplete understanding of the peptoid folding process. We seek to delineate sequence-structure relationships through the systematic study of noncovalent interactions in peptoids and the design of novel amide side chains capable of such interactions. Herein, we report the synthesis and detailed structural analysis of a series of (S)-N-(1-naphthylethyl)glycine (Ns1npe) peptoid homo-oligomers by X-ray crystallography, NMR spectroscopy, and circular dichroism (CD) spectroscopy. Four of these peptoids were found to adopt well-defined structures in the solid state, with dihedral angles similar to those observed in polyproline type I (PPI) peptide helices and in peptoids with α-chiral side chains. The X-ray crystal structure of a representative Ns1npe tetramer revealed an all cis-amide helix, with approximately three residues per turn, and a helical pitch of approximately 6.0 ?. 2D-NMR analysis of the length-dependent Ns1npe series showed that these peptoids have very high overall backbone amide K(cis/trans) values in acetonitrile, indicative of conformationally homogeneous structures in solution. Additionally, CD spectroscopy studies of the Ns1npe homo-oligomers in acetonitrile and methanol revealed a striking length-dependent increase in ellipticity per amide. These Ns1npe helices represent the most robust peptoid helices to be reported, and the incorporation of (S)-N-(1-naphthylethyl)glycines provides a new approach for the generation of stable helical structure in this important class of foldamers.     

Low-temperature polymer-assisted synthesis of shape-tunable zinc oxide nanostructures dispersible in both aqueous and non-aqueous media

We report the shape-controlled synthesis of zinc oxide (ZnO) nanostructures by a poly(vinyl methyl ether) (PVME)-assisted alkaline hydrolysis of zinc acetate at low temperature (20 °C). In this method, ZnO nanostructures of various morphologies including dumbbells, lances and triangles have been successfully prepared via a simple variation of different reaction parameters such as polymer concentration, pH of the reaction mixture and precursor concentration. However, without PVME, ZnO of such structurally uniform morphologies were not formed; rather ZnO of a mixture of defined and undefined morphologies were obtained indicating PVME-assisted the growth of such regular shaped ZnO nanostructures. HRTEM analysis of lance- and triangle-shaped samples as well as SAED patterns of all kinds of samples (dumbbell, lance and triangle) revealed that the ZnO nanostrcutures are single crystalline in nature and might form through oriented growth. XRD analysis also revealed the formation of well crystalline ZnO with a hexagonal structure. FTIR spectroscopy and TGA analysis confirmed the adsorption of PVME on the surface of ZnO nanostructures. Being a solvent adaptable polymer, the adsorbed PVME makes these shaped ZnO nanostructures highly dispersible in both polar and non-polar organic solvents including water. The extent of dispersibility in different solvents was studied by spectroscopic and microscopic techniques. Such solvent adoptability of PVME-coated ZnO nanostructures increases its ease of applications in device fabrication as well as in biological systems.     

Helical peptoid mimics of lung surfactant protein C

Among the families of peptidomimetic foldamers under development as novel biomaterials and therapeutics, poly-N-substituted glycines (peptoids) with alpha-chiral side chains are of particular interest for their ability to adopt stable, helical secondary structure in organic and aqueous solution. Here, we show that a peptoid 22-mer with a biomimetic sequence of side chains and an amphipathic, helical secondary structure acts as an excellent mimic of surfactant protein C (SP-C), a small protein that plays an important role in surfactant replacement therapy for the treatment of neonatal respiratory distress syndrome. When integrated into a lipid film, the helical peptoid SP mimic captures the essential surface-active behaviors of the natural protein. This work provides an example of how an abiological oligomer that closely mimics both the hydrophobic/polar sequence patterning and the fold of a natural protein can also mimic its biophysical function.     

Solvent- and pH-induced self-assembly of cationic meta-linked poly(phenylene ethynylene): effects of helix formation on amplified fluorescence quenching and Förster resonance energy transfer

We reported here the synthesis and characterization of a novel water-soluble, meta-linked poly(phenylene ethynylene) (m-PPE-NEt(2)Me(+)) featuring quaternized side groups. We studied the solvent-induced self-assembly of m-PPE-NEt(2)Me(+) in MeOH/H(2)O solvent mixtures by using UV-vis absorption and fluorescence spectroscopies. The results showed that the polymer folded into a helical conformation and that the extent of helical folding increased with the volume % water in the solvent. This cationic polymer also exhibited unique pH-induced helix formation, which was attributed to the partial neutralization of quaternized side groups at high pH and the meta-links in the main chain of the polymer. Studies on the fluorescence quenching of m-PPE-NEt(2)Me(+) by anthraquinone-2,6-disulfonate (AQS) and Fe(CN)(6)(4-), two small-molecule anionic quenchers with different typical structures, revealed more efficient quenching of helical conformation by AQS than by Fe(CN)(6)(4-). We proposed that the two quenchers most likely interacted with the polymer helix in two different modes; that was, AQS featuring large planar aromatic ring could intercalate within adjacent π-stacked phenylene ethynylene units in the polymer helix, whereas Fe(CN)(6)(4-) mainly bound to the periphery of polymer helix through ion-pair formation. Finally, the results of FRET from the helical polymer to the fluorescein (C*)-labeled polyanions, ssDNA-C* (ssDNA: single-stranded DNA) and dsDNA-C* (dsDNA: double-stranded DNA) also suggested two different modes of interactions. As compared with the FRET to dsDNA-C*, the FRET to ssDNA-C* was slightly more efficient, which was believed to arise from the additional binding of ssDNA-C* with the polymer via intercalation of its exposed hydrophobic bases into the π stack of adjacent phenylene ethynylene units in the polymer helix.     

Synthesis of two mirror image 4-helix junctions derived from glycerol nucleic acid

Structural DNA nanotechnology relies on Watson-Crick base pairing rules to assemble DNA motifs into diverse arrangements of geometric shapes and patterns. While substantial effort has been devoted to expanding the programmability of natural DNA, considerably less attention has been given to the development of nucleic acid structures based on non-natural DNA polymers. Here we describe the use of glycerol nucleic acid (GNA), a simple polymer based on an acyclic repeating unit, as an alternative genetic material for assembling nucleic acid nanostructures independent of RNA or DNA recognition. We synthesized two 4-helix junctions based entirely on GNA self-pairing and showed that GNA provides easy access to highly stable nanostructures with left- and right-handed helical configurations.     

Site selection in tandem arrays of metal-binding domains

The metal binding properties of peptides corresponding to metal-binding sites spanning regions that normally function as linkers in tandem arrays of metal-binding domain-containing proteins were examined. For a peptide with two His residues from one TFIIIA-like zinc finger domain, a canonical TFIIIA-like linker, and two Cys residues from an adjacent zinc domain, the dissociation constant for the 1:1 peptide to cobalt(II) was found to be 15 +/- 10 microM, compared with 60 nM for the corresponding zinc finger domains themselves. Peptides overlapping two sets of metal-binding domains from human TRAF (tumor necrosis factor receptor-associated factor) proteins were examined. In one case, the affinity of the presumed metal-binding domain and that for the linker region were comparable, while in the second case, the affinity of the linker peptide was higher than that for the corresponding presumed metal-binding domain peptide. These studies revealed that cobalt(II) affinities in the micromolar range can occur even for peptides that do not correspond to natural zinc-binding domains and that the degree of distinction between authentic metal-binding domains and the corresponding linker-spanning peptides may be modest, at least for single domain peptide models.     

Tetrakis(2-quinolinylmethyl)ethylenediamine (TQEN) as a new fluorescent sensor for zinc

A new fluorescent sensor for zinc that binds 1 equivalent of zinc ion, N,N,N',N'-tetrakis(2-quinolylmethyl)ethylenediamine (TQEN), has been prepared and characterized. Zinc-bound TQEN exhibits fluorescence around 383 nm upon excitation at 317 nm, while free TQEN emits very weak fluorescence. UV-Vis and 1H NMR spectral changes also detected the binding of TQEN with zinc ion. The crystal structure of zinc complex with TQEN was determined by X-ray crystallography and compared with that of the TPEN-Zn complex (TPEN =N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine). The binding affinity of TQEN with zinc ion is very high (Kd < 1 microM in aqueous dmf solution). Competition experiments reveal that the zinc-binding affinity of TQEN is lower than the parent, strong metal ion chelator TPEN, and comparable to EGTA (EGTA = ethylene glycol-bis(2-aminomethyl)-N,N,N',N'-tetraacetic acid).     

Multiple time scale dynamics of distance fluctuations in a semiflexible polymer: a one-dimensional generalized Langevin equation treatment

Time-dependent fluctuations in the distance x(t) between two segments along a polymer are one measure of its overall conformational dynamics. The dynamics of x(t), modeled as the coordinate of a particle moving in a one-dimensional potential well in thermal contact with a reservoir, is treated with a generalized Langevin equation whose memory kernel K(t) can be calculated from the time-correlation function of distance fluctuations C(t) identical with x(0)x(t). We compute C(t) for a semiflexible continuum model of the polymer and use it to determine K(t) via the GLE. The calculations demonstrate that C(t) is well approximated by a Mittag-Leffler function and K(t) by a power-law decay on time scales of several decades. Both functions depend on a number of parameters characterizing the polymer, including chain length, degree of stiffness, and the number of intervening residues between the two segments. The calculations are compared with the recent observation of a nonexponential C(t) and a power law K(t) in the conformational dynamics within single molecule proteins [Min et al., Phys. Rev. Lett. 94, 198302 (2005)].     

Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains

Substantial progress has been made in the synthesis and characterization of various oligomeric molecules capable of autonomous folding to well-defined, repetitive secondary structures. It is now possible to investigate sequence-structure relationships and the driving forces for folding in these systems. Here, we present detailed analysis by X-ray crystallography, NMR, and circular dichroism (CD) of the helical structures formed by N-substituted glycine (or "peptoid") oligomers with alpha-chiral, aliphatic side chains. The X-ray crystal structure of a N-(1-cyclohexylethyl)glycine pentamer, the first reported for any peptoid, shows a helix with cis-amide bonds, approximately 3 residues per turn, and a pitch of approximately 6.7 A. The backbone dihedral angles of this pentamer are similar to those of a polyproline type I peptide helix, in agreement with prior modeling predictions. This crystal structure likely represents the major solution conformers, since the CD spectra of analogous peptoid hexamers, dodecamers, and pentadecamers, composed entirely of either (S)-N-(1-cyclohexylethyl)glycine or (S)-N-(sec-butyl)glycine monomers, also have features similar to those of the polyproline type I helix. Furthermore, this crystal structure is similar to a solution NMR structure previously described for a peptoid pentamer comprised of chiral, aromatic side chains, which suggests that peptoids containing either aromatic or aliphatic alpha-chiral side chains adopt fundamentally similar helical structures in solution, despite distinct CD spectra. The elucidation of detailed structural information for peptoid helices with alpha-chiral aliphatic side chains will facilitate the mimicry of biomolecules, such as transmembrane protein domains, in a distinctly stable form.     

Spectroscopic investigation on chirality transfer in additive-driven self-assembly of block polymers

Chiral supramolecules prepared by the additive-driven self-assembly of block copolymers provide a facile method to construct helical nanostructures. In this study, we investigated the chiral transfer from chiral tartaric acid to poly(styrene)-b-poly(ethylene oxide) using small-angle X-ray scattering, transmission electron microscopy, circular dichroism, and vibrational circular dichroism. The results showed that the chirality was transferred to both the segments of block copolymer irrespective of the interaction with the chiral additives and formation of helical phase structure. However, the chirality transfer was carried out using different methods: for poly(ethylene oxide) segments, the chirality transfer was carried out via direct hydrogen bond formation; for polystyrene segments, the chirality transfer was carried out via the cooperative motion of block copolymers during the thermal annealing.     

Meta-linked poly(phenylene ethynylene) conjugated polyelectrolyte featuring a chiral side group: helical folding and guest binding

A water soluble, meta-linked poly(phenylene ethynylene) featuring chiral and optically active side groups based on L-alanine (mPPE-Ala) has been studied by using absorption, fluorescence, and circular dichroism spectroscopy. Studies of mPPE-Ala in methanol/water solvent mixtures show that the polymer folds into a helical conformation, and the extent of helical folding increases with the volume % water in the solvent. The presence of the helical conformation is signaled by the appearance of a broad, excimer-like visible fluorescence band, combined with a strong bisignate circular dichroism signal in the region of the pi,pi absorption of the polymer backbone. The circular dichroism signal exhibits negative chirality, suggesting that the left-handed (M-form) of the helix is in enantiomeric excess. Binding of the metallointercalator [Ru(bpy)2(dppz)]2+ (where bpy = 2,2-bipyridine and dppz = dipyrido[3,2-a:2',3'-c]phenazine) with the helical polymer is accompanied by the appearance of the orange-red photoluminescence from the metal complex. This effect is directly analogous to that observed when [Ru(bpy)2(dppz)]2+ binds to DNA via intercalation, suggesting that the metal complex binds to mPPE-Ala by intercalating between the pi-stacked phenylene ethynylene residues. Cationic cyanine dyes also bind to the periphery of the helical polymer in a manner that is interpreted as "groove binding". A circular dichroism signal is observed that is believed to arise from exciton coupling within the chiral cyanine dye chromophore aggregate that is formed as the dye molecules are oriented by the helical mPPE-Ala "template".     

Metal phthalocyanine nanoribbons and nanowires

Nanoribbons and nanowires of different metal phthalocyanines (copper, nickel, iron, cobalt, and zinc), as well as copper hexadecafluorophthalocyanine (F(16)CuPc), have been grown by organic vapor-phase deposition. Their properties, as a function of substrate type, source-to-substrate distance, and substrate temperature, were studied by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, and absorption measurements. The size and morphology of the nanostructures were found to be mainly determined by the substrate temperature. The crystal structure was dependent on the substrate temperature as well. At substrate temperatures below 200 degrees C, in addition to straight nanoribbons, twisted nanoribbons were found for all investigated materials except F(16)CuPc, which formed helical nanoribbons upon exposure to an electron beam. The formation of different nanostructures (nanoribbons, twisted nanoribbons, and helical nanoribbons) is discussed.     

Conformational rearrangements by water-soluble peptoid foldamers

Peptoids are a family of N-substituted glycine oligomers that are capable of forming stable helical structures. We seek peptoid monomers that can establish a strong folding propensity in aqueous conditions. Here we utilize L-phenylalanine tert-butyl ester as a readily available reagent for the synthesis of (S)-N-(1-carboxy-2-phenylethyl)glycine oligomers. The products form stable secondary structures in aqueous solution in which the conformation is dramatically responsive to variations in pH and solvent composition.