Secondary Structure Of Poly Research Articles

Secondary Structures in Synthetic Poly(Amino Acids): Homo- and Copolymers of Poly(Aib), Poly(Glu), and Poly(Asp).

The secondary structure of poly(amino acids) is an excellent tool for controlling and understanding the functionality and properties of proteins. In this perspective article the secondary structures of the homopolymers of oligo- and poly-glutamic acid (Glu), aspartic acid (Asp), and α-aminoisobutyric acid (Aib) are discussed. Information on external and internal factors, such as the nature of side groups, interactions with solvents and interactions between chains is reviewed. A special focus is directed on the folding in hybrid-polymers consisting of oligo(amino acids) and synthetic polymers. Being part of the SFB TRR 102 "Polymers under multiple constraints: restricted and controlled molecular order and mobility" this overview is embedded into the cross section of protein fibrillation and supramolecular polymers. As polymer- and amino acid folding is an important step for the utilization and design of future biomolecules these principles guide to a deeper understanding of amyloid fibrillation.

DNA Sequence and Length Dictate the Assembly of Nucleic Acid Block Copolymers.

The self-assembly of block copolymers is often rationalized by structure and microphase separation; pathways that diverge from this parameter space may provide new mechanisms of polymer assembly. Here, we show that the sequence and length of single-stranded DNA directly influence the self-assembly of sequence-defined DNA block copolymers. While increasing the length of DNA led to predictable changes in self-assembly, changing only the sequence of DNA produced three distinct structures: spherical micelles (spherical nucleic acids, SNAs) from flexible poly(thymine) DNA, fibers from semirigid mixed-sequence DNA, and networked superstructures from rigid poly(adenine) DNA. The secondary structure of poly(adenine) DNA strands drives a temperature-dependent polymerization and assembly mechanism: copolymers stored in an SNA reservoir form fibers after thermal activation, which then aggregate upon cooling to form interwoven networks. DNA is often used as a programming code that aids in nanostructure addressability and function. Here, we show that the inherent physical and chemical properties of single-stranded DNA sequences also make them an ideal material to direct self-assembled morphologies and select for new methods of supramolecular polymerization.

Synthesis of polymethylacrylamide carrying R-phenylglycine pendant groups and effect of hydrogen bonds on main chain helicity

A series of chiral methacrylamide derivatives, RR-PEBM, RS-PEBM, and R-PMBM, were separately synthesized and radically polymerized to obtain the corresponding polymers (poly(RR-PEBM)s, poly(RS-PEBM)s, and poly(R-PMBM)s) in the present study. An interesting effect of the chiral carbon atom, which was away from the backbone, on the formations of the hydrogen bonds between the amide groups and chiroptical properties of polymers was observed. The chiroptical properties of the resulting polymers were investigated in detail by polarimetry, circular dichroism (CD), and UV–Vis spectroscopies. The specific optical rotation of poly(RS-PEBM) and poly(R-PMBM) showed a slight dependence on the solvent polarity, but in contrast, the polarity of the polymerization solvents clearly affected the values of the specific rotation of the poly(RR-PEBM)s. The polymers prepared in toluene displayed a larger optical rotation and stronger cotton effects than the one prepared in methanol. These results indicated that the hydrogen bonds formed between the amide groups in the polymers played an important role in both the polymerization process and the formation of the partial helical structure of the polymer. The secondary structure of poly(RR-PEBM) was relatively stable upon heating but unstable in THF by adding MeOH.

Functional Polystyrene Derivatives Influence the Miscibility and Helical Peptide Secondary Structures of Poly(γ-benzyl l-glutamate)

We synthesized polystyrene (PS) and poly(acetoxystyrene) (PAS) homopolymers through atom transfer radical polymerization (of styrene and 4-acetoxystryene monomers, respectively) and then prepared poly(vinylphenol) (PVPh) through acetoxyl hydrazinolysis of PAS with hydrazine monohydrate. To investigate the influences of these three functionalized polystyrene derivatives on the helical peptide secondary structures and miscibility behavior of polypeptide homopolymers, we blended PS, PAS, and PVPh with a low-molecular-weight poly(γ-benzyl l-glutamate) (PBLG) homopolymer and analyzed these blends using differential scanning calorimetry (DSC), Fourier transform infrared (FTIR) spectroscopy, solid state nuclear magnetic resonance (NMR) spectroscopy, and wide-angle X-ray diffraction (WAXD). Variations in the intermolecular interactions (e.g., π–π, dipole–dipole, hydrogen bonding) strongly affected the miscibility behavior and secondary structures of PBLG. The weak π–π interactions between PS and PBLG resulted in ...

Synthesis and Secondary Structure of Poly(1-methylpropargyl-N-alkylcarbamate)s

A series of novel 1-methylpropargyl-N-alkylcarbamates, HC≡C-(R)-CH(CH3)OCONHCH2CO2CH2CH2CH3 [(R)-1], HC≡C-(S)-CH(CH3)OCONHCH2CO2CH2CH2CH3 [(S)-1], HC≡C-(S)-CH(CH3)OCONH-(R)-CH(CH3)CH2CH2CH2CH2CH3 [(S),(R)′-2], HC≡C-(S)-CH(CH3)OCONH-(R)-CH(CH3)CO2CH2CH2CH3 [(S),(R)′-3], HC≡CCH2OCONH-(R)-CH(CH3)CO2CH2CH2CH3 [(R)′-4], HC≡CCH2OCONH-(S)-CH(CH3)CO2CH2CH2CH3 [(S)′-4], and HC≡CCH2OCONHCH2CO2CH2CH2CH3 (5) were synthesized and polymerized using (nbd)Rh+[η6-C6H5B−(C6H5)3] (nbd = 2,5-norbornadiene) as a catalyst. Substituted cis-stereoregular polyacetylenes with moderate molecular weights were obtained in good yields. Poly[(R)-1], poly[(S)-1], poly[(S),(R)′-2], and poly[(S),(R)′-3] exhibited large optical rotations (|[α]D| = 344°−508°), clear CD signals (Δe = 4.8−7.0 M−1 cm−1) in CHCl3, and high viscosity indices (0.82−0.87), demonstrating the formation of helical structures with predominantly one-handed screw sense, which were stable up to 55 °C in the solvent. The solution state IR measurement confirmed the presenc...

Influence of Solvent on the Secondary Structure of Helical Poly(N-propargyl-(1R)-camphor-10-sulfamide)

The influence of solvent on the geometrical and secondary structure of poly(N-propargyl-(1R)-camphor-10-sulfamide) (poly(1)) was investigated. 1H NMR spectra of poly(1) measured in varied solvent and at varied temperature showed that solvent influenced the mobility of the polymer’s main chain. Poly(1) adopted stable helices or disordered states in different solvents. Poly(1) could take helical conformation in toluene. Further characterization showed that hydrogen bond could form between the neighboring sulfamide groups. In mixed solvent comprising toluene and methanol, poly(1) underwent aggregation rather than taking helix when the content of methanol exceeded 40 vol %. In another binary solvent comprising DMSO and chloroform, poly(1) changed gradually from helical to disordered conformation with increasing the content of DMSO.

Helical poly(phenylacetylene) derived fromL-tyrosine: A promising candidate for functional helical polymers carrying transformableN- andC-termini

A novel optically active phenylacetylene derivative, N-(tert-butoxycarbonyl)-4-ethynyl-L-phenylalanine methyl ester (1), was synthesized from L-tyrosine and polymerized with a rhodium catalyst. The corresponding polymer [poly(1)] with a moderate molecular weight was obtained in a high yield. The alkaline hydrolysis of poly(1) gave poly[N-(tert-butoxycarbonyl)-4-ethynyl-L-phenylalanine] [poly(2)] carrying free carboxy groups. Polarimetric, CD, and UV–vis spectroscopy analyses revealed that poly(1) took a predominantly one-handed helical structure in MeOH and toluene, and poly(2) took a helical structure in MeOH. The secondary structures of poly(1) and poly(2) could be tuned with heat and solvents. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 1691–1698, 2007

EFFECTS OF PHOSPHATE IONS ON THE POLYPEPTIDE - LIPOSOME MENBRANE INTERACTION

We find that positively charged polypeptide: poly-L-arginine (poly(Arg)) can translocate through the negatively charged liposome membranes in Tris-HCl buffer but cannot translocate in phosphate buffer. We also investigated the translocation ability of positively charged poly(Arg) through a mechanism involving poly(Arg) - lipid interactions in a model lipid membrane system under various buffer conditions. It was concluded that the secondary structure of poly(Arg) had the dominant effect on its transportability through the membrane.

Diffusion Coefficient and the Secondary Structure of Poly-l-glutamic Acid in Aqueous Solution

The diffusion coefficients (D) of poly-L-glutamic acid (PLG) at various pHs are investigated by the laser-induced transient-grating method with a new photoreactive probe molecule. The pH dependence of D is compared with that of the helical content of PLG measured by circular dichroism. It is found that the pH dependences of both quantities are very similar. Since the frictions of the translational diffusion of charged and protonated carboxyl groups are found to be similar each other, it is concluded that the conformation of the main polymer chain is the main factor in determining the diffusion process; in other words, the alpha-helix conformation makes the molecular diffusion faster. This result indicates that the conformational change of a protein can be detected by monitoring the diffusion coefficient.

Effect of Chiral Substituents on the Secondary Structure of Poly(N-alkynylamides)

Optically active N-alkynylamides (S)-HC⋮C(CH2)aNHCO(CH2)bCH(CH3)CH2CH3 (1: a = 1, b = 0; 2: a = 1, b = 1; 3: a = 1, b = 2; 4: a = 1, b = 3; 5: a = 2, b = 0; 6: a = 2, b = 1; 7: a = 3, b = 0), having several numbers of methylene spacers between the ethynyl group and chiral carbon or amide group, and (S)-HC⋮C(CH2)2OCOCH2CH(CH3)CH2CH3 (8) were polymerized with (nbd)Rh+[η6-C6H5B-(C6H5)3] to afford the corresponding polymers with moderate molecular weights (Mn = 11 000−21 000) in 67−99% yields. The 1H NMR spectra demonstrated that the resulting polymers had stereoregular structures (cis content = 79−100%). CD, UV−vis, and IR spectroscopic studies revealed that the position of the amide group and chiral center strongly affects the pitch and stability of helical structure of the polymers, and intramolecular hydrogen bonding is formed between the amide groups in CHCl3. By comparison with the results of CD measurements and molecular orbital calculation, the sign of Cotton effect and the relationship between...

The secondary structures of poly ( l-alanine) blocks in some diblock copolymers of poly( l-alanine)- b-poly(ethylene glycol) monomethyl ether in the solid state characterized by nuclear magnetic resonance and infrared spectrometry

The 13C cross-polarization/magic-angle spinning (CP/MAS) spectra of the solid-state nuclear magnetic resonance (NMR) and the infrared spectra of three diblock copolymers, poly ( l-alanine)- block-poly(ethylene glycol) monomethyl ether (PLA- b-MPEG), with various proportions of two blocks were studied in comparison with those of the homopolymer poly( l-alanine), PLA, and the blends of two blocks (PLA and MPEG). The secondary structures such as α-helix and β-sheet of poly ( l-alanine) (PLA) blocks in the block copolymers could be elucidated from the signals in the solid-state 13C CP/MAS NMR spectra and transmittance peaks in the Fourier-transformation infrared (FTIR) spectra. Dramatic differences in the secondary structures were observed for the diblock copolymers, homopolymer PLA and blend samples. It was found that with the increase of the fraction of PLA block in the block copolymers, the ratio of β-sheet to α-helical conformation of PLA block went up although the α-helical conformation was much more than β-sheet conformation in total. It contradicted the general prediction of the secondary structure of homopolypeptides or PLA/PEG blends, in which the β-sheet conformation content decreased with the decrease of the polymerization degree of PLA. The investigation in FTIR spectrometry resulted in the same conclusion.

Buildup of Exponentially Growing Multilayer Polypeptide Films with Internal Secondary Structure

The buildup and secondary structure of poly(l-glutamic acid)/poly(allylamine) (PGA/PAH) multilayer films were investigated by means of optical waveguide lightmode spectroscopy, quartz crystal microbalance, and Fourier transform infrared spectroscopy in attenuated total reflection mode. The thickness and the mass of these films grow exponentially with the number of deposited bilayers. Moreover, PGA undergoes a random/α-helix transition when interacting with PAH during the film buildup process. This structural transition leads to (PGA/PAH)i films with an α-helix content (contribution of the α-helices to the amide I band) that switches regularly between 30% and 40% during the film buildup, when the multilayer is alternatively brought into contact with the PAH and PGA solutions. The secondary structure of the film is thus entirely driven by the last deposited layer. The independence of the α-helix content with the number of deposited bilayers also strongly suggests that the film is structurally homogeneous over its whole thickness.

Steric forces between brush layers of poly( l-glutamic acid) and their dependence on secondary structures as determined by FT-IR spectroscopy

Interactions between apposed poly( l-glutamic acid) monolayers in water were investigated by direct surface forces measurement. The average degree of polymerization was 21. The monolayers of anchored poly( l-glutamic acid) were prepared on mica surfaces by the Langmuir-Blodgett deposition of monolayers of an amphiphile containing the polypeptide as the hydrophilic head group. Various secondary structures of poly( l-glutamic acid) were formed in this monolayer at the air-water interface, through intra- and intermolecular hydrogen bonding, depending on the surface pressure and the pH value of the aqueous subphase, and transferred onto mica surfaces. Formation of the secondary structures was characterized by Fourier transform-infrared (FT-IR) spectroscopy prior to the forces measurement. Surface force profiles consisted of a long-range electrostatic and a short-range steric repulsion. Secondary structures of poly( l-glutamic acid), identified by FT-IR with respect to their composition and orientation, were found to determine the short-range steric repulsion. The obtained elastic compressibility moduli of the polypeptide monolayers were 5.6 ± 2.2 MPa for the β 2-structure rich layer, and 0.2 ± 0.1 MPa for the layer of ionized extended chains.

Unique property of cyanine dyes on charged poly( l-lysine)

Charged poly( l-lysine) forms a random coil in water (pH 7) and an α-helix in methanol. Cyanine (NK-2012) dyes combine with these charged poly( l-lysine)s to produce S-chiral and R-chiral dimers in water and methanol, respectively. The dimers on the α-helix show a circular dichroism strength (with a single Davydov splitting) 10 times greater than on the random coil (with several circular dichroism bands). These results indicate that the binding state of NK-2012 dyes is remarkably dependent on the secondary structure of poly( l-lysine) and the α-helix provides a single binding mode for the dyes.

Anesthetic–Protein Interaction: Effects of Volatile Anesthetics on the Secondary Structure of Poly(L-lysine)

Effects of volatile anesthetics (chloroform, halothane, and enflurane) on the secondary structure of poly(L-lysine) were analyzed by circular dichroism (CD). The relative proportions among α-helix, β-sheet, and random-coil conformations were calculated by the curve-fitting method on the CD data. Volatile anesthetics partially transformed α-helix to β-sheet but not to random-coil under the present experimental condition. When expressed by the anesthetic partial pressures in the gas phase in equilibrium with the solution, the values that partially transformed a to α to β conformation by 10% were 1.1 • 10−2, 4.7 • 10−2, and 7.9 • 10−2 atm for chloroform, halothane, and enflurane, respectively. The order of potency is in reasonable agreement with the order of the anesthetic potencies of the agents. The α-to-α transition was completely reversible when anesthetics were purged by nitrogen gas. Volatile anesthetics disrupted the hydrogen bonds of α-helix backbones and rearranged them to form the β-sheet conformation. The β-sheet conformation is stabilized mainly by the hydrophobic interaction among methylene side groups of poly(L-lysine). Volatile anesthetics promoted the transition by enhancing the hydrophobic interaction among side-chains and by rearranging the hydrogen bonds in the peptide backbone.

Molecular properties of poly(RGD) and its binding capacities to metastatic melanoma cells

We examined the binding capacity of anti-metastatic polypeptide containing repetitive Arg-Gly-Asp(RGD) sequence derived from cell binding site of fibronectin, poly(RGD), to the surface of tumor cells. Poly(RGD) competitively inhibited the binding of radiolabeled fibronectin to the cell surface more potently than oligo(RGD) or RGD tripeptide on a molar basis. Compared on a weight basis to oligo(RGD) or RGD peptide, poly(RGD) was more active than the oligo- and monomeric peptide at inhibiting tumor cell adhesion to immobilized fibronectin. The secondary structure of poly(RGD) was predicted to be a beta-turn from the data of CD spectra and its amino acid sequence. These findings suggest that poly(RGD)-mediated inhibition of cell adhesion is due to its potent binding capacity to fibronectin receptors on cell surface probably through its conformational properties.

Pressure‐induced reversible changes in secondary structure of poly(L‐lysine): An ir spectroscopic study

AbstractThe effect of elevated hydrostatic pressure on the secondary structure of poly(L‐lysine) was studied using Fourier transform ir spectroscopy. According to changes observed in the amide I band, both the β‐sheet and the unordered polypeptide undergo a reversible, pressure‐induced conformational change to α‐helix. The conversion occurs at a much higher pressure from the unordered conformer (∼ 9 kbar) than from the β‐sheets (∼ 2 kbar). The structural changes were found to be slower at pH > 11, especially at the highest concentration investigated (10 wt%), reflecting the fact that extensive hydrogen‐bond networks have to reorganize. This study shows that alterations of polypeptidic conformations induced by elevated hydrostatic pressure are reversible, but that an apparent irreversibility can result from kinetic factors in the case of conformational changes involving extensive rearrangements. The present results also show that the strength of the hydrogen bonds between the backbone amide groups is not the only factor that determines the closest packing of the polypeptide molecules.

Right-handed and left-handed helices of poly(dA-dC) X (dG-dT).

The secondary structures of poly(dA-dC) X (dG-dT) were studied using CD and IR spectroscopies. We give spectroscopic evidence of secondary structure transitions of poly(dA-dC) X (dG-dT) from a B to a Z-like helix, induced by transition metal ions (Ni2+) in presence of high concentrations of Cs+ and Na+. In the presence of Na+, the B in equilibrium Z transition occurs at any temperature, whereas premelting conditions are required in presence of Cs+. For these two alkali ions the Z-like form is only induced by Ni2+ ions through their specific interactions at N7 of purines, under conditions of low water activity due to the high alkali salt concentration. We also show that the CD spectrum obtained in presence of Cs+ ions and characterized by a negative band at 275 nm, cannot be interpreted in terms of Z-like left-handed helix but reflects a modified B right-handed helix.

A polycationic amine that induces unique conformational changes in poly(dA-dT) in low salt.

Circular dichroism was used to examine alterations in the secondary structure of poly(dA-dT) X poly(dA-dT) upon binding polymer X, a polycationic CD probe for aspects of DNA structure. Stable complex formation is evidenced by increasing Tm and the appearance of large extrinsic bands in the greater than 300 nm, region which increase proportionally with r (ratio of polymer charge to DNa phosphate), in the range 0.0 to 0.32. At relatively low values of r (less than .32), CD spectra of the poly(dA-dT) X poly(dA-dT)-polymer X complex show a gradual non-cooperative inversion in the long wavelength portion (275 nm) of the intrinsic band in low salt solutions suggesting structural and conformational flexibility in poly(dA-dT) X poly(dA-dT) and further implicating polymer X as a potential probe for variations in DNA secondary structure. The dinucleotide repeat configuration of poly(dA-dT) X poly(dA-dT) is presumed to play a role in the observed intrinsic CD changes. NMR data support an "alternating B" conformation for the complex.

Interaction of Z form poly(dG-dC).poly(dG-dC) with divalent metal ions: localization of the binding sites by I.R. spectroscopy.

The secondary structures of poly(dG-dC).poly(dG-dC) in the presence of alcaline , alcaline earth and first row transition metal ions (Na+, Mg2+, Co2+, Ni2+) are investigated by infrared spectroscopy. The conformational transitions are studied as a function of the hydration of the polynucleotide and counter-ion nature and content. The use of selectively deuterated poly(dG-dC).poly(dG-dC) on the 8-carbon of guanines allows to show that a direct interaction occurs between the N7 site of guanines and the transition metal ions Co2+ and Ni2+. In the case of Mg2+, for high ion/nucleotide ratios, the interaction occurs essentially at the level of the phosphate groups. This interaction leads to a modification of the left-handed conformation. Based on the IR spectroscopy results, an explanation is proposed for the different efficiencies of these various ions to induce the B----Z transition.