Promotion of sheet formation in alpha-peptide strands by a beta-peptide reverse turn

[structure: see text]We show that a tetrapeptide with a heterogeneous backbone, i.e., with two different classes of amino acid residues, adopts a hairpin conformation in which each type of residue plays a different structural role. The alpha-residues at the ends form hydrogen bonds characteristic of antiparallel beta-sheet secondary structure, while the central di-beta-peptide segment forms a reverse turn. The configuration of the turn residues is critical to sheet formation.     

Interstrand side chain--side chain interactions in a designed beta-hairpin: significance of both lateral and diagonal pairings

The contributions of interstrand side chain-side chain contacts to beta-sheet stability have been examined with an autonomously folding beta-hairpin model system. RYVEV(D)PGOKILQ-NH2 ((D)P = D-proline, O = ornithine) has previously been shown to adopt a beta-hairpin conformation in aqueous solution, with a two-residue loop at D-Pro-Gly. In the present study, side chains that display interstrand NOEs (Tyr-2, Lys-9, and Leu-11) are mutated to alanine or serine, and the conformational impact of the mutations is assessed. In the beta-hairpin conformation Tyr-2 and Leu-11 are directly across from one another (non-hydrogen bonded pair). This "lateral" juxtaposition of two hydrophobic side chains appears to contribute to beta-hairpin conformational stability, which is consistent with results from other beta-sheet model studies and with statistical analyses of interstrand residue contacts in protein crystal structures. Interaction between the side chains of Tyr-2 and Lys-9 also stabilizes the beta-hairpin conformation. Tyr-2/Lys-9 is a "diagonal" interstrand juxtaposition because these residues are not directly across from one another in terms of the hydrogen bonding registry between the strands. This diagonal interaction arises from the right-handed twist that is commonly observed among beta-sheets. Evidence of diagonal side chain-side chain contacts has been observed in other autonomously folding beta-sheet model systems, but we are not aware of other efforts to determine whether a diagonal interaction contributes to beta-sheet stability.     

Time-resolved EPR studies of main chain radicals from acrylic polymers. Effects of tacticity, solvent, and side group structure on chain stiffness

Main chain polymeric radicals from several acrylic polymers, produced by laser flash photolysis at 248 nm in liquid solution, have been studied using direct detection time-resolved electron paramagnetic resonance (TREPR) spectroscopy at 9.5 GHz. Highly isotactic poly(methyl methacrylate) (i-PMMA) shows a sharp, well-resolved spectrum at about 95 degrees C. Using synthetic methodology to disrupt the tacticity of i-PMMA, we observed different fast-motion hyperfine coupling constants for the main chain radicals. By raising the temperature of observation, we returned the coupling constants to the same value as those in the highly isotactic sample. This result is related qualitatively to the degree of stiffness of the polymer chains as a function of tacticity. The concept is tested further by comparison to two other acrylic polymers with bulky side chains: poly(fluorooctyl methacrylate) (PFOMA) and poly(adamantyl methacrylate) (PAMA), whose main chain radicals show significant line broadening even at 110 degrees C. Solvent effects on both spectral appearance (the alternating line-width effect) and kinetic decays (attributed to T1 relaxation) are also presented and discussed in terms of main chain conformational motion.     

Effect of molecular weight on microcrystalline structure formation in polymer with perylenediimide side chain

The effect of molecular weight on the molecular aggregation structure of polymers bearing a pendant perylenediimide (PDI) side chain, designated PAc12PDI, was investigated using synchrotron radiation X‐ray diffraction measurements. It was found that depending on molecular weight, either the main chain axis or the side chain axis behaves as the longitudinal axis in fiber samples and was aligned parallel to the fiber axis. A similar phenomenon is present in thin film samples, but was complicated by the additional influence of the interfacial free energy of the side chain group. Even in the case of the polymer with lower molecular weight, the face plane of PDI was found to show both parallel and perpendicular orientations to the substrate (i.e., flat‐on and edge‐on orientations). On the other hand, if the length of the main chain is sufficiently long with respect to the length of the side chain, the face plane of PDI was oriented perpendicular to the substrate, leading to an edge‐on orientation in the thin film. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 2275–2283     

Synthesis, structure and characterization of side chain cholesteric liquid crystalline polysiloxanes

A series of liquid crystalline homopolysiloxanes and copolysiloxanes were synthesized. The chemical structures of the monomers M₁-M₇ were confirmed by FTIR and ¹H NMR spectroscopy. The structure-property relationships of the monomers and polymers are discussed; their phase behaviour and optical properties were investigated by differential scanning calorimetry, thermogravimetric analysis, and polarizing optical microscopy. All the monomers, except M₂ and M₇ showed smectic and nematic phases; the copolymers P₈-P₁₅ displayed cholesteric phases. The homopolymers P₁-P₇ exhibited smectic phases. The selective reflection of cholesteric monomers and copolymers shifted to longer wavelengths with increasing length of the rigid mesogenic core, with decreasing length of the flexible spacer, or with increasing content of nematic units. Experimental results demonstrated that a flexible polymer backbone, a rigid mesogenic core and a long flexible spacer tended to produce a lower glass transition temperature, higher thermal stability, and wider mesophase temperature range.     

Synthesis of side chain liquid crystalline copolymers and characterization of their polar structure

A series of side chain liquid crystalline copolymers having different spacer lengths, copolymer compositions, and chromophore types were synthesized and characterized both in the bulk and at the gas‐water interface. Liquid crystalline properties were identified by differential scanning calorimetry (DSC), optical microscopy, and X‐ray diffraction (XRD). Copolymer with spacer lengths 4, 5, 10, and 11 showed smectic A (S_A) phases with a bâtonnet texture. The liquid crystalline (LC) phase stabilized as the spacer increased. Copolymers with different compositions were investigated both as monolayers and transferred films. The isotherms suggest nanodomain formation at the gas‐water interface in copolymers with high nitrobiphenyl (NBP) content. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 1057–1070, 1999     

Effect of solvent on aggregation structure and responsive properties of copolymeric gel with side chain crystals

The copolymeric gel films were prepared by a radical copolymerization of stearyl acrylate(SA), acrylic acid(AA) and N,N′-methylenebisacrylamide (MBAA) as a cross-linking agent. The copolymeric (molar ratio SA/AA/MBAA: 24.7/74.3/1.0) gel films with crystalline side chains were swollen in three different kinds of solvent and their aggregation structure and responsive properties have been investigated. In order to control the SA side chains-solvent interaction and to dissociate carboxyl groups in AA, solvents such as dimethyl sulfoxide (DMSO), (1-hexanol/DMSO) mixed solvents and water with different pH values were used. The responsive behaviors of the (SA/AA/MBAA) gel film swollen in different solvents were discussed on the basis of the weight swelling ratio. The X-ray diffraction study of the gel film revealed that the long period corresponding to a layer distance for the (SA/AA/MBAA) gel film swollen in DMSO increased with temperature or the swelling ratio, and the interchain distance of alkyl side chains remained constant with the variation of temperature up to the melting temperature of SA side chain crystals. The swelling ratio of the gel film in (1-hexanol/DMSO) mixed solvent exhibited an abrupt increase in the case of about 40wt% of 1-hexanol, because the SA side chain crystals of the gel film in the mixed solvents were dissolved due to an increase in SA-solvent interaction. On the other hand, the gel film in the water with different pH values showed a sharp increase in the swelling ratio above pH = 11, because the ionic repulsive force among the AA groups became greater than the aggregation one among alkyl side chains. These results indicate that the swelling ratio of the (SA/AA/MBAA) gel film can be controlled by temperature, pH and the magnitude of solubility parameter of swelling solvent.     

Relationship between side chain structure and 14-helix stability of beta3-peptides in water

Folded polymers are used in Nature for virtually every vital process. Nonnatural folded polymers, or foldamers, have the potential for similar versatility, and the design and refinement of such molecules is of considerable current interest. Here we report a complete and systematic analysis of the relationship between side chain structure and the 14-helicity of a well-studied class of foldamers, beta(3)-peptides, in water. Our experimental results (1) verify the importance of macrodipole stabilization for maintaining 14-helix structure, (2) provide comprehensive evidence that beta(3)-amino acids branched at the first side chain carbon are 14-helix-stabilizing, (3) suggest a novel role for side chain hydrogen bonding as an additional stabilizing force in beta(3)-peptides containing beta(3)-homoserine or beta(3)-homothreonine, and (4) demonstrate that diverse functionality can be incorporated into a stable 14-helix. Gas- and solution-phase calculations and Monte Carlo simulations recapitulate the experimental trends only in the context of oligomers, yielding insight into the mechanisms behind 14-helix folding. The 14-helix propensities of beta(3)-amino acids differ starkly from the alpha-helix propensities of analogous alpha-amino acids. This contrast informs current models for alpha-helix folding, and suggests that 14-helix folding is governed by different biophysical forces than is alpha-helix folding. The ability to modulate 14-helix structure through side chain choice will assist rational design of 14-helical beta-peptide ligands for macromolecular targets.     

Synthesis, micro structure, and thermal stability of side chain liquid crystalline polysiloxane polymers with an oligo (ethylene oxide) unit in the side chain

A series of new alkene monomers [MS3BDBEn, n=1-3] containing 4-oligo (ethylene oxide) monomethyl ether 4-biphenyl ether carboxyl benzoate as terminal groups were synthesized. These polymers were prepared by grafting these monomers onto the poly (methylhydrosilox-ane) (PMHS) backbone. The transition temperatures, liquid crystalline textures, and thermal stability of the polysiloxane polymers have been determined by thermal data, by optical texture, and by X-ray diffraction patterns. Polymers PS3BDBEn showed smectic or smectic and nematic phases which were not analogous to their precursor nematic monomers. The terminal length of the polymers affects not only the mesophase transition temperatures but also the layer-spacing length (d₁) and the side-chain distance (d₂). The long- and short-range orders can remain to some extent above the isotropization temperature and below the melting point. The polymer PS3BDBE3 decomposed in air 20°C above the isotropization temperature and lost its short range orders as detected by the X-ray diffraction analysis.     

Liquid-crystalline structure of poly(L-lysine) containing azobenzene units in the side chain

The structure of poly(L -lysine) containing 44% azobenzene units in the side chain was studied by X-ray diffraction between room temperature and 150°C. The polymer exhibits a mesomorphic structure of the smectic A1 type. In this structure, stable at least until 150°C, each smectic layer of thickness d results from the superposition of two layers: one of thickness d_A contains the free lysine side chains, the other of thickness d_B contains the azobenzene modified lysine side chains and the polypeptide main chains, that in their planes are arranged as in the “antiparallel” β-structure classical for polypeptides.     

Hybrid peptides: expanding the beta turn in peptide hairpins by the insertion of beta-, gamma-, and delta-residues

The beta turn segment in designed peptide hairpins has been expanded by the insertion of beta-, gamma- and delta-amino acids at the i+2 position. The model octapeptides Boc-Leu-Phe-Val-DPro-Ac6c-Leu-Phe-Val-OMe (1), Boc-Leu-Phe-Val-DPro-beta3-Ac6c-Leu-Phe-Val-OMe (2), and Boc-Leu-Phe-Val-DPro-Gpn-Leu-Phe-Val-OMe (3) have been shown to adopt beta hairpin conformations in methanol by the observation of key diagnostic nuclear Overhauser effects. Boc-Leu-Val-Val-DPro-delta-Ava-Leu-Val-Val-OMe (4) adopts a beta hairpin conformation in crystals; this is stabilized by three cross-strand hydrogen bonds as demonstrated by X-ray diffraction. The canonical C10 turn in an alpha-alpha segment is expanded to C11, C12, and C13 turns in alpha-beta, alpha-gamma, and alpha-delta segments, respectively. The crystal structures of Piv-LPro-beta3-Ac6c-NHMe (5) and Boc-Ac6c-Gpn-Ac6c-OMe (6) reveal intramolecularly hydrogen-bonded C11 and C12 conformations, respectively. Computer modeling of octapeptide sequences that contain centrally positioned hybrid-turn segments, by using turn parameters derived from the structures of peptides 5 and 6, establishes the stereochemical acceptability of the beta hairpins in the cases of peptides 2 and 3. Accommodation of omega-amino acids into the turn segments is achieved by the adoption of gauche conformations around the backbone C--C bonds.     

Sandwich layer structure of a novel polyimide with methylene spacing groups in biphenyl side chain

The aggregation structure of a novel polyimide (PI-6) with six methylene flexible spacing groups in biphenyl side chain was investigated using polarized optical microscope (POM), wide/small-angle X-ray diffraction (WAXD/SAXD) and molecular simulation approach. Depending on increasing temperature, the sandwich layer aggregation structure of PI-6 was developed from the thermo reversible gel. The backbones are lamellar stacking with 11.5 Å thickness. The side chains are randomly packed into the backbone lamellar intervals and the width of this layer for both backbone and side chain is about 23.1 Å which is consistent with the simulation data.     

Effects of the H-bond donor structure on the properties of supramolecular side chain liquid crystalline polymers based on poly(3-carboxypropylmethylsiloxane-co-dimethylsiloxane)s and stilbazoles

Supramolecular side chain liquid crystalline polymers (SCLCPs) based on poly(3-carboxypropylmethylsiloxane-co-dimethylsiloxane) (PSIX, X=100, 76, 60, 41 or 23, denoting the mole percentage of 3-carboxypropylmethylsiloxane unit in the polymer) and stilbazole derivatives have been obtained through intermolecular hydrogen bonding (H-bonding) interactions between the carboxylic acid and the pyridyl moieties. The formation of H-bonding and self-assembly results in the formation of new mesogenic units, in which H-bonds function as molecular connectors. FTIR shows the existence of H-bonding in the complexes. The polymeric complexes behave as single component liquid crystalline polymers and exhibit stable and enantiotropic mesophases. The liquid crystalline properties of the supramolecular SCLCPs were studied using differential scanning calorimetry, polarizing optical microscopy and X-ray diffraction, and were found to exhibit smectic A phases with focal-conic textures. The thermal stability of the SCLCP increases on increasing the carboxylic acid content in the polysiloxane and the concentration of the stilbazole derivative in the complex. However, the thermal stability decreases on increasing the chain length of the stilbazole derivative. The crystal phase was not formed even on cooling to the glass transition temperature of the polymeric complex.     

Effects of the H-bond donor structure on the properties of supramolecular side chain liquid crystalline polymers based on poly(3-carboxypropylmethylsiloxane-co-dimethylsiloxane)s and stilbazoles

Supramolecular side chain liquid crystalline polymers (SCLCPs) based on poly(3-carboxypropylmethylsiloxane-co-dimethylsiloxane) (PSIX, X=100, 76, 60, 41 or 23, denoting the mole percentage of 3-carboxypropylmethylsiloxane unit in the polymer) and stilbazole derivatives have been obtained through intermolecular hydrogen bonding (H-bonding) interactions between the carboxylic acid and the pyridyl moieties. The formation of H-bonding and self-assembly results in the formation of new mesogenic units, in which H-bonds function as molecular connectors. FTIR shows the existence of H-bonding in the complexes. The polymeric complexes behave as single component liquid crystalline polymers and exhibit stable and enantiotropic mesophases. The liquid crystalline properties of the supramolecular SCLCPs were studied using differential scanning calorimetry, polarizing optical microscopy and X-ray diffraction, and were found to exhibit smectic A phases with focal-conic textures. The thermal stability of the SCLCP increases on increasing the carboxylic acid content in the polysiloxane and the concentration of the stilbazole derivative in the complex. However, the thermal stability decreases on increasing the chain length of the stilbazole derivative. The crystal phase was not formed even on cooling to the glass transition temperature of the polymeric complex.     

Effects of the polyamide molecular structure on the performance of reverse osmosis membranes

Thin-film composite reverse osmosis membranes of polyamides were prepared by interfacial polymerization. Various benzenediamines and poly(aminostyrene) were interfacially reacted with various acyl chlorides to prepare a skin layer of composite membranes. Among the membranes prepared from the structural isomeric monomers of benzenediamines and acyl chlorides, i.e., the same chemical composition but different in the position of functional groups on the aromatic ring, the membrane with the best salt rejection was obtained when the reacting groups forming amide are located at the same position on the aromatic ring. Membranes prepared by interfacially reacting various diamines with trimesoyl chloride revealed that the salt rejection depends on the linear chain structure of polyamides and network formed by crosslinking. Membranes obtained by interfacial polymerization of poly(aminostyrene) with trimesoyl chloride showed higher water flux but lower salt rejection than those obtained by interfacial polymerization of various benzenediamines with trimesoyl chloride. Membranes obtained here showed the typical trade-off behavior between salt rejection and water flux. However, membranes prepared by interfacially reacting trimesoyl chloride with a mixture of poly(aminostyrene) and m-phenylenediamine or a mixture of poly(aminostyrene), m-phenylenediamine, and diaminobenzoic acid showed a performance advantage over usual membranes, i.e., a large positive deviation from the usual trade-off trend. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36 : 1821–1830, 1998     

Modeling the effects of structure and dynamics of the nitroxide side chain on the ESR spectra of spin-labeled proteins

In the companion paper (J. Phys. Chem. B 2006, 110, jp0629487), a study of the conformational dynamics of methanethiosulfonate spin probes linked at a surface-exposed alpha-helix has been presented. Here, on the basis of this analysis, X-band ESR spectra of these spin labels are simulated within the framework of the Stochastic Liouville equation (SLE) methodology. Slow reorientations of the whole protein are superimposed on fast chain motions, which have been identified with conformational jumps and fluctuations in the minima of the chain torsional potential. Fast chain motions are introduced in the SLE for the protein reorientations through partially averaged magnetic tensors and relaxation times calculated according to the motional narrowing theory. The 72R1 and 72R2 mutants of T4 lysozyme, which bear the spin label at a solvent-exposed helix site, have been taken as test systems. For the side chain of the R2 spin label, only a few noninterconverting conformers are possible, whose mobility is limited to torsional fluctuations, yielding almost identical spectra, typical of slightly mobile nitroxides. In the case of R1, more complex spectra result from the simultaneous presence of constrained and mobile chain conformers, with relative weights that can depend on the local environment. The model provides an explanation for the experimentally observed dependence of the spectral line shapes on temperature, solvent, and pattern of substituents in the pyrroline ring. The relatively simple methodology presented here allows the introduction of realistic features of the spin probe dynamics into the simulation of ESR spectra of spin-labeled proteins; moreover, it provides suggestions for a proper account of such dynamics in more sophisticated approaches.     

The structure of the antibiotic hedamycon. IV. Relative configurations in the diepoxide side chain

The relative configuraitons in the diepoxide side chain of the antibiotic hedamycin have been shown to be rel-(14R,16S,17R,18S).     

Peptoid oligomers with alpha-chiral, aromatic side chains: effects of chain length on secondary structure.

Oligomeric N-substituted glycines or "peptoids" with alpha-chiral, aromatic side chains can adopt stable helices in organic or aqueous solution, despite their lack of backbone chirality and their inability to form intrachain hydrogen bonds. Helical ordering appears to be stabilized by avoidance of steric clash as well as by electrostatic repulsion between backbone carbonyls and pi clouds of aromatic rings in the side chains. Interestingly, these peptoid helices exhibit intense circular dichroism (CD) spectra that closely resemble those of peptide alpha-helices. Here, we have utilized CD to systematically study the effects of oligomer length, concentration, and temperature on the chiral secondary structure of organosoluble peptoid homooligomers ranging from 3 to 20 (R)-N-(1-phenylethyl)glycine (Nrpe) monomers in length. We find that a striking evolution in CD spectral features occurs for Nrpe oligomers between 4 and 12 residues in length, which we attribute to a chain length-dependent population of alternate structured conformers having cis versus trans amide bonds. No significant changes are observed in CD spectra of oligomers between 13 and 20 monomers in length, suggesting a minimal chain length of about 13 residues for the formation of stable poly(Nrpe) helices. Moreover, no dependence of circular dichroism on concentration is observed for an Nrpe hexamer, providing evidence that these helices remain monomeric in solution. In light of these new data, we discuss chain length-related factors that stabilize organosoluble peptoid helices of this class, which are important for the design of helical, biomimetic peptoids sharing this structural motif.